initial commit

.gitattributes

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+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
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.gitignore

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+.eggs/
+dist/
+*.pyc
+__pycache__/
+*.py[cod]
+*$py.class
+__tmp/*
+*.pyi
+.mypycache
+.ruff_cache
+node_modules
+**/backend/**/templates/
+**/cached_examples/*

LICENSE.md

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+# License
+
+MIT License
+
+Copyright (c) Meta, Inc. and its affiliates.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+---
+title: FAIR Chem UMA Educational Demo
+emoji: 😻
+colorFrom: gray
+colorTo: gray
+sdk: gradio
+sdk_version: 5.23.3
+app_file: app.py
+hf_oauth: true
+hf_oauth_scopes:
+  - read-repos
+---
+
+This repo houses the FAIR chemistry UMA educational demo. The UMA models are available under a FAIR Chemistry license at https://huggingface.co/facebook/UMA .
+
+1. Try examples to see how UMA works across molecules and materials
+2. Explore how the UMA tasks should be applied to different structures
+3. Try the UMA model with your own structures!
+
+This repo also uses a fork of the excellent `gradio_molecule3d` package (https://huggingface.co/spaces/simonduerr/gradio_molecule3d/tree/main) in the `gradio_molecule3d` subdirectory for visualization of structures in 3dmol.js via gradio components. There are a number of small changes needed for the demo here, primarily:
+* Add support for PBC visualization
+* Add support for conversion of formats unsupported by 3dmol.js via ASE
+* Remove UI elements that are unnecessary for this demo
+* Add multi-model PDBs as frames to enable visualization of trajectories. 

app.py

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+"""
+Copyright (c) Meta Platforms, Inc. and affiliates.
+
+This source code is licensed under the MIT license found in the
+LICENSE file in the root directory of this source tree.
+"""
+
+import os
+import subprocess
+import sys
+from pathlib import Path
+
+import gradio as gr
+
+from simulation_scripts import run_md_simulation, run_relaxation_simulation
+
+DEFAULT_MOLECULAR_REPRESENTATIONS = [
+    {
+        "model": 0,
+        "chain": "",
+        "resname": "",
+        "style": "sphere",
+        "color": "Jmol",
+        "around": 0,
+        "byres": False,
+        "scale": 0.3,
+    },
+    {
+        "model": 0,
+        "chain": "",
+        "resname": "",
+        "style": "stick",
+        "color": "Jmol",
+        "around": 0,
+        "byres": False,
+        "scale": 0.2,
+    },
+]
+DEFAULT_MOLECULAR_SETTINGS = {
+    "backgroundColor": "white",
+    "orthographic": False,
+    "disableFog": False,
+}
+
+
+def main():
+
+    input_structure = gr.File(
+        label="ASE-compatible structure",
+        file_types=[".cif", ".pdb", ".xyz", ".traj", "INCAR", "POSCAR"],
+        height=150,
+    )
+    output_traj = gr.File(
+        label="Simulation Trajectory (ASE traj file)",
+        interactive=False,
+        height=150,
+    )
+    input_visualization = Molecule3D(
+        label="Input Visualization",
+        reps=DEFAULT_MOLECULAR_REPRESENTATIONS,
+        config=DEFAULT_MOLECULAR_SETTINGS,
+        render=False,
+        inputs=[input_structure],
+        value=lambda x: x,
+        interactive=False,
+    )
+    md_steps = gr.Slider(minimum=1, maximum=500, value=100, label="MD Steps")
+    prerelax_steps = gr.Slider(
+        minimum=0, maximum=100, value=20, label="Pre-Relaxation Steps"
+    )
+    temperature_k = gr.Slider(
+        minimum=0.0,
+        maximum=1500.0,  # Adjusted max value for temperature
+        value=300.0,
+        label="Temp [K]",
+    )
+    md_timestep = gr.Slider(minimum=0.1, maximum=5.0, value=1.0, label="Timestep [fs]")
+    md_ensemble = gr.Radio(
+        label="Thermodynamic Ensemble", choices=["NVE", "NVT"], value="NVE"
+    )
+    optimization_steps = gr.Slider(
+        minimum=1, maximum=500, value=300, step=1, label="Max Steps"
+    )
+    fmax = gr.Slider(value=0.05, minimum=0.001, maximum=0.5, label="Opt. Fmax [eV/Å]")
+
+    task_name = gr.Radio(
+        value="OMol", choices=["OMol", "OMC", "OMat", "OC20", "ODAC"], label="Task Name"
+    )
+
+    gr.Markdown("OMol-specific settings for total charge and spin multiplicity")
+    total_charge = gr.Slider(
+        value=0, label="Total Charge", minimum=-10, maximum=10, step=1
+    )
+    spin_multiplicity = gr.Slider(
+        value=1, maximum=11, minimum=1, step=1, label="Spin Multiplicity "
+    )
+    relax_unit_cell = gr.Checkbox(value=False, label="Relax Unit Cell")
+
+    md_button = gr.Button("Run MD Simulation")
+    optimization_button = gr.Button("Run Optimization")
+
+    output_structure = Molecule3D(
+        label="Simulation Visualization",
+        reps=DEFAULT_MOLECULAR_REPRESENTATIONS,
+        config=DEFAULT_MOLECULAR_SETTINGS,
+        render=False,
+        elem_classes="structures",
+        height=500,
+        inputs=[output_traj],
+        value=lambda x: x,
+        interactive=False,
+    )
+
+    explanation = gr.Markdown()
+    explanation_buffer = gr.Markdown()
+
+    output_text = gr.Code(lines=20, max_lines=30, label="Log", interactive=False)
+
+    reproduction_script = gr.Code(
+        interactive=False,
+        max_lines=30,
+        language="python",
+        label="ASE Reproduction Script",
+    )
+
+    with gr.Blocks(theme=gr.themes.Ocean()) as demo:
+        with gr.Row():
+            with gr.Column(scale=2):
+
+                with gr.Column(variant="panel"):
+                    gr.Markdown(
+                        "# Meta's Universal Model for Atoms (UMA) Educational Demo"
+                    )
+
+                    with gr.Tab("1. Your first UMA simulation"):
+
+                        with gr.Row():
+                            gr.Examples(
+                                examples=[
+                                    [
+                                        str(
+                                            Path(__file__).parent
+                                            / "./examples/metal_cplx.pdb"
+                                        ),
+                                        100,
+                                        20,
+                                        1.0,
+                                        300.0,
+                                        "NVE",
+                                        "OMol",
+                                        1,
+                                        6,
+                                        "Congratulations, you just ran your first UMA simulation! This is a molecular dynamics simulation of a transition metal complex that shows the atoms vibrating from thermal motion. Now try running some of the examples in the next tab to more thoroughly explore how UMA can be applied to different domains and types of structures.",
+                                    ],
+                                    [
+                                        str(
+                                            Path(__file__).parent
+                                            / "./examples/inorganic_crystal.cif"
+                                        ),
+                                        200,
+                                        20,
+                                        1.0,
+                                        300.0,
+                                        "NVE",
+                                        "OMat",
+                                        0,
+                                        1,
+                                        "Congratulations, you just ran your first UMA simulation! This is a molecular dynamics simulation of a transition metal complex that shows the atoms vibrating from thermal motion. Now try running some of the examples in the next tab to more thoroughly explore how UMA can be applied to different domains and types of structures.",
+                                    ],
+                                ],
+                                example_labels=[
+                                    "A transition metal complex",
+                                    "An inorganic crystal",
+                                ],
+                                inputs=[
+                                    input_structure,
+                                    md_steps,
+                                    prerelax_steps,
+                                    md_timestep,
+                                    temperature_k,
+                                    md_ensemble,
+                                    task_name,
+                                    total_charge,
+                                    spin_multiplicity,
+                                    explanation_buffer,
+                                ],
+                                outputs=[
+                                    output_traj,
+                                    output_text,
+                                    reproduction_script,
+                                    explanation,
+                                ],
+                                fn=run_md_simulation,
+                                run_on_click=True,
+                                cache_examples=True,
+                                label="Molecular Dynamics Examples",
+                            )
+
+                        gr.Markdown(
+                            """
+                            Start by clicking one of the above examples to see how the demo works and what the inputs and outputs will look like. 
+                            * Every example is a specific molecular structure or material that can be simulated using the UMA model. 
+                            * Each simulation you see would take days or weeks using a traditional quantum chemistry simulation, but UMA can do it in seconds or minutes! 
+                            * Examples in the demo are cached ahead of time so they should load right away, but if you run a custom simulation you'll see a progress bar while the simulation runs.
+                            
+                            When you've run your first simulation, click on the next tab above to explore the UMA model in more detail and see how it works across many different domains/examples!
+                            """
+                        )
+
+                    with gr.Tab("2. Explore UMA's capabilities"):
+                        gr.Markdown(
+                            """
+    These next examples are designed to show how the UMA model can be applied to different domains and types of structures, and how different model inputs can impact the results!
+    * As you try each one, look at how the inputs change below, and the simulation outputs change on the right
+    * Each UMA task corresponds to a different domain of chemistry, and a different Density Functional Theory (DFT) code and level of theory that was used for the training data.
+    * Feel free to try changing some of the settings below and re-run the simulations to see how the results can vary!
+    """
+                        )
+                        gr.Examples(
+                            examples=[
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/metal_cplx.pdb"
+                                    ),
+                                    100,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "OMol",
+                                    1,
+                                    6,
+                                    "This metal complex showcases the UMA's ability to handle complicated transition metal complexes with ligands, spin, and charge.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/organic_molecular_crystal.cif"
+                                    ),
+                                    200,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "OMC",
+                                    0,
+                                    1,
+                                    "This organic crystal showcases the UMA's ability to handle organic molecular crystals using the OMC task, using a random packing of a molecule from OE62. You could also try using the OMol or OMat tasks and see how the simulations differ!",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/inorganic_crystal.cif"
+                                    ),
+                                    200,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "OMat",
+                                    0,
+                                    1,
+                                    "This inorganic crystal from the Materials Project showcases the UMA's ability to handle inorganic materials using the OMat task. You should be careful with the output energies since the analysis might require careful application of the Materials Project GGA/GGA+U correction schemes.",
+                                ],
+                                [
+                                    str(Path(__file__).parent / "./examples/HEA.cif"),
+                                    200,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "OMat",
+                                    0,
+                                    1,
+                                    "High-entropy alloys are materials with 4 or more elements, and this example shows the OMat model can also be applied to HEAs. This particular HEA is equimolar Cr/Fe/Ni/Sn, but could exist in other lattice configurations. ",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/catalyst.traj"
+                                    ),
+                                    200,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "OC20",
+                                    0,
+                                    1,
+                                    "This example shows the OC20 model can be applied to small molecules on a catalyst surface, and that OC20 has recently been extended with datasets for multi-adsorbate interactions. Notice some of the adsorbates wrap around the periodic boundary conditions. Some of the adsorbates are weakly bound and desorbing from the surface based on this starting configuration.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/gold_nanoparticle_crystal.cif"
+                                    ),
+                                    200,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "OMat",
+                                    0,
+                                    1,
+                                    "This example is an experimentally solved crystal structure for a thiolate protected gold nanocluster from an[open-access academic paper](https://pubs.rsc.org/en/content/articlelanding/2016/sc/c5sc02134k) and [available in the COD](https://www.crystallography.net/cod/1540567.html). This is a fun example because it combines small molecules, inorganic materials, and surface chemistry, so it's not so clear which task to use. Try the OMat, OMol, and OC20 tasks to see how the results differ! Further, the experimental paper reported different crystal structures based on the charge and spin multiplicity, so try changing the charge and spin multiplicity to see how the results differ.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/ethylene_carbonate.xyz"
+                                    ),
+                                    500,
+                                    20,
+                                    1.0,
+                                    1000.0,
+                                    "NVE",
+                                    "OMol",
+                                    0,
+                                    1,
+                                    "Ethylene carbonate is a common electrolyte in batteries, and an important precursor to the solid/electrolyte interface (SEI) formation. This example is the neutral version of ethylene carbonate and it is quite stable even at high temperatures! Try the radical anion version of ethylene carbonate in the next example.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/ethylene_carbonate.xyz"
+                                    ),
+                                    500,
+                                    20,
+                                    1.0,
+                                    1000.0,
+                                    "NVE",
+                                    "OMol",
+                                    -1,
+                                    2,
+                                    "With charge of -1 and spin multiplicity of 2, this radical anion version of ethylene carbonate is much less stable than the neutral version and can undergo spontaneous ring-opening at high temperatures, which initiates the formation of a battery's solid/electrolyte interface (SEI). If the simulation doesn't show a ring opening reaction, try clicking the molecular dynamic buttons again to see another short simulation. Only OMol currently supports arbitrary charge/spin multiplicity.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent / "./examples/protein.pdb"
+                                    ),
+                                    200,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "OMol",
+                                    0,
+                                    1,
+                                    "This is a solvated structure of a small protein fragment using the OMol task. Very little is likely happen in a very short MD simulations. Try increasing the number of MD steps to see how the protein moves. You can also try using the OMat task, but be careful with the results since the OMat task is not trained on solvated systems.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/MOF_CO2.traj"
+                                    ),
+                                    200,
+                                    20,
+                                    1.0,
+                                    300.0,
+                                    "NVE",
+                                    "ODAC",
+                                    0,
+                                    1,
+                                    "This is a metal organic framework (MOF) structure using the ODac task. You might study structures like if designing MOFs for direct air capture calculations. Look carefully for the red/gray CO2 molecule in the pores of the MOF! You can also try the OMol and OMat tasks to see if the results differ.",
+                                ],
+                            ],
+                            example_labels=[
+                                "Simulate a  transition metal complex",
+                                "Simulate an organic molecular crystal",
+                                "Simulate an inorganic crystal",
+                                "Simulate a high-entropy alloy",
+                                "Simulate a catalyst surface/adsorbate",
+                                "Simulate a ligated gold nanoparticle crystal",
+                                "Simulate a neutral ethylene carbonate",
+                                "Simulate a radical anion ethylene carbonate",
+                                "Simulate a solvated protein",
+                                "Simulate CO2 in a metal organic framework",
+                            ],
+                            inputs=[
+                                input_structure,
+                                md_steps,
+                                prerelax_steps,
+                                md_timestep,
+                                temperature_k,
+                                md_ensemble,
+                                task_name,
+                                total_charge,
+                                spin_multiplicity,
+                                explanation_buffer,
+                            ],
+                            outputs=[
+                                output_traj,
+                                output_text,
+                                reproduction_script,
+                                explanation,
+                            ],
+                            fn=run_md_simulation,
+                            run_on_click=True,
+                            cache_examples=True,
+                            label="Molecular Dynamics Examples",
+                        )
+
+                        gr.Examples(
+                            examples=[
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/bis(EDA)Cu.xyz"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "OMol",
+                                    1,
+                                    1,
+                                    False,
+                                    "This is a super fun example of a transition metal complex that changes its geometry based on the assumed charge/spin multiplicity and actually has different local minima. It highlights the ability of the OMol task to handle these additional inputs. In this first example it forms a tetragonal geometry - try clicking on the next example (with charge=+2 and spin multiplicity 2) to see the other local minima!",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/bis(EDA)Cu.xyz"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "OMol",
+                                    2,
+                                    2,
+                                    False,
+                                    "This is a super fun example of a transition metal complex that changes its geometry based on the assumed charge/spin multiplicity and actually has different local minima. In contrast to the previous example (charge=+1 and spin multiplicity 1), this one forms a square planar geometry.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/metal_cplx.pdb"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "OMol",
+                                    1,
+                                    6,
+                                    False,
+                                    "This metal complex showcases the UMA's ability to handle complicated transition metal complexes with ligands, spin, and charge.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/organic_molecular_crystal.cif"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "OMC",
+                                    0,
+                                    1,
+                                    True,
+                                    "This organic crystal showcases the UMA's ability to handle organic molecular crystals using the OMC task, using a random packing of a molecule from OE62. You could also try using the OMol or OMat tasks and see how the simulations differ!",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/inorganic_crystal.cif"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "OMat",
+                                    0,
+                                    1,
+                                    True,
+                                    "This inorganic crystal from the Materials Project showcases the UMA's ability to handle inorganic materials using the OMat task. You should be careful with the output energies since the analysis might require careful application of the Materials Project GGA/GGA+U correction schemes.",
+                                ],
+                                [
+                                    str(Path(__file__).parent / "./examples/HEA.cif"),
+                                    300,
+                                    0.05,
+                                    "OMat",
+                                    0,
+                                    1,
+                                    True,
+                                    "High-entropy alloys are materials with 4 or more elements, and this example shows the OMat model can also be applied to HEAs. This particular HEA is equimolar Cr/Fe/Ni/Sn, but could exist in other lattice configurations. ",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/catalyst.traj"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "OC20",
+                                    0,
+                                    1,
+                                    False,
+                                    "This example shows the OC20 model can be applied to small molecules on a catalyst surface, and that OC20 has recently been extended with datasets for multi-adsorbate interactions. Notice some of the adsorbates wrap around the periodic boundary conditions. Some of the adsorbates are weakly bound and desorbing from the surface based on this starting configuration.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent / "./examples/protein.pdb"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "OMol",
+                                    0,
+                                    1,
+                                    True,
+                                    "This is a solvated structure of a small protein fragment using the OMol task. Very little is likely happen in a very short MD simulations. Try increasing the number of MD steps to see how the protein moves. You can also try using the OMat task, but be careful with the results since the OMat task is not trained on solvated systems.",
+                                ],
+                                [
+                                    str(
+                                        Path(__file__).parent
+                                        / "./examples/MOF_CO2_2H2O.traj"
+                                    ),
+                                    300,
+                                    0.05,
+                                    "ODAC",
+                                    0,
+                                    1,
+                                    False,
+                                    "This is a metal organic framework (MOF) structure using the ODac task. You might study structures like if designing MOFs for direct air capture (DAC) calculations. Look carefully for the co-adsorption between CO2 and two water molecules in the pore, which you might study if you were interested in the effect of humidity on DAC performance! You can also try the OMol and OMat tasks to see if the results differ.",
+                                ],
+                            ],
+                            example_labels=[
+                                "Relax bis(EDA)Cu TM complex with charge=1, spin=1",
+                                "Relax bis(EDA)Cu TM complex with charge=2, spin=2",
+                                "Relax a  transition metal complex w ligands",
+                                "Relax an organic molecular crystal",
+                                "Relax an inorganic crystal",
+                                "Relax a high-entropy alloy",
+                                "Relax a catalyst surface/adsorbate",
+                                "Relax a solvated protein",
+                                "Relax co-adsorbed H2O/CO2 in a metal organic framework",
+                            ],
+                            inputs=[
+                                input_structure,
+                                optimization_steps,
+                                fmax,
+                                task_name,
+                                total_charge,
+                                spin_multiplicity,
+                                relax_unit_cell,
+                                explanation_buffer,
+                            ],
+                            outputs=[
+                                output_traj,
+                                output_text,
+                                reproduction_script,
+                                explanation,
+                            ],
+                            fn=run_relaxation_simulation,
+                            run_on_click=True,
+                            cache_examples=True,
+                            label="Relaxation Examples",
+                        )
+
+                        gr.Markdown(
+                            "Once you understand how the UMA model can be applied to different types of molecules and materials, the final tab above will help you try it out with your own structures! "
+                        )
+
+                    with gr.Tab("3. Try UMA with your own structures!"):
+                        gr.Markdown(
+                            """
+                            As the final step of the demo, try running your own structure through the UMA model!
+
+                            To use a custom input structure with this demo:
+                            1. [Request gated model access.](https://huggingface.co/facebook/UMA) Requests for model access are typically processed within a matter of minutes.
+                            2. Login to Hugging Face using the "Sign in with Hugging Face button" in the .                       
+                            3. Then upload a structure file below and click run!
+
+                            * Note that uploaded structure will be stored by this demo to analyze model usage and identify domains where model accuracy can be improved.
+                            * If you get a redirect error when logging in, please try visiting the direct demo url (https://facebook-fairchem-uma-demo.hf.space/) and try again
+                            * Your structure should be in a format supported by ASE 3.25, including .xyz, .cif, .pdb, ASE .traj, INCAR, or POSCAR.
+                            * Your structure should either have periodic boundary conditions (PBC) all True, or all False. Support for mixed PBC may be added in the future. 
+                            """
+                        )
+
+                with gr.Column(variant="panel"):
+                    gr.Markdown(
+                        "## Learn more about the Universal Model for Atoms (UMA)"
+                    )
+                    with gr.Accordion(
+                        "What is the Universal Model for Atoms?", open=False
+                    ):
+                        gr.Markdown(
+                            """
+    * UMA models predict motion and behavior at the atomic scale, ultimately reducing the development cycle in molecular and materials discovery and unlocking new possibilities for innovation and impact.  
+    * UMA models are based on Density Functional Theory (DFT) training datasets. DFT simulations are a commonly used quantum chemistry method to simulate and understand behavior at the atomic scale.
+    * UMA models are large mixture-of-linear-experts graph networks models trained on billions of atoms across five open-science simulation datasets released by the FAIR Chemistry team over the past 5 years. This demo uses the small UMA model with 146M total parameters, 32 experts, and 6M active parameters at any time to predict across all of these domains.  
+
+    Read the UMA paper for details or download the UMA model and FAIR Chemistry repository to use this yourself!
+    """
+                        )
+                    with gr.Accordion(
+                        "Should I trust the UMA simulations?", open=False
+                    ):
+                        gr.Markdown(
+                            """
+    * The UMA model paper contains rigorous accuracy benchmarks on a number of validation sets across chemistry and materials science. As of model release the UMA model was at or near the state-of-the-art for generalization machine learning potentials.  Read the UMA paper for details.
+    * Rigorously predicting when AI/ML models will extrapolate (or not) to new domains is an ongoing research area. The best approach is to find or build benchmarks that are similar to the questions you are studying, or be prepared to run some DFT simulations on predictions to validate results on a sample of structures that are relevant to your research problem. 
+    """
+                        )
+                    with gr.Accordion("Why does this matter?", open=False):
+                        gr.Markdown(
+                            """
+    * Many important technological challenges, including developing new molecules to accelerate industrial progress and discovering new materials for energy storage and climate change mitigation, require scientists and engineers to design at the atomic scale.
+    * Traditional experimental discovery and design processes are extremely time consuming and often take decades from ideation to scaled manufacturing. 
+    * Meta's Fundamental AI Research Lab (FAIR) is drastically accelerating this process by developing accurate and generalizable machine learning models, building on work by academic, industrial, and national lab collaborators. 
+    """
+                        )
+                    with gr.Accordion(
+                        "Open source packages used in this demo", open=False
+                    ):
+                        gr.Markdown(
+                            """
+    * The model code is available on github at [FAIR chemistry repo](https://github.com/facebookresearch/fairchem)
+    * This demo builds on a number of great open source packages like [gradio_molecule3d](https://huggingface.co/spaces/simonduerr/gradio_molecule3d), [3dmol.js](https://3dmol.csb.pitt.edu/), [ASE](https://wiki.fysik.dtu.dk/ase/), and many others!
+    """
+                        )
+
+                gr.Markdown("## Simulation inputs")
+
+                with gr.Column(variant="panel"):
+                    gr.Markdown("### 1. Example structure (or upload your own!)")
+                    with gr.Row():
+                        with gr.Column():
+
+                            input_structure.render()
+
+                            gr.LoginButton(size="large")
+
+                            gr.Markdown(
+                                """
+                            To use your own structures, you need access to the [gated UMA model repository](https://huggingface.co/facebook/UMA) and you need to login with the button above. 
+                            * See the final tab above '3. Try UMA with your own structures!' for more details and debugging steps!
+                            * Note that uploaded structure will be stored by this demo to analyze model usage and identify domains where model accuracy can be improved.
+                            * If you get a redirect error when logging in, please try visiting the direct demo url (https://facebook-fairchem-uma-demo.hf.space/) and try again
+                            
+                            """
+                            )
+                        with gr.Column(scale=3):
+                            input_visualization.render()
+
+                with gr.Column(variant="panel"):
+                    gr.Markdown("### 2. Choose the UMA Model Task")
+                    with gr.Row():
+                        with gr.Column():
+                            task_name.render()
+
+                            with gr.Row():
+                                total_charge.render()
+                                spin_multiplicity.render()
+
+                        with gr.Column(scale=2):
+                            with gr.Tabs() as task_name_tabs:
+                                with gr.TabItem("OMol", id=0):
+                                    gr.Markdown(
+                                        """
+
+                                        OMol25 comprises over 100 million calculations covering small molecules, biomolecules, metal complexes, and electrolytes.
+
+                                        **Relevant applications:** Biology, organic chemistry, protein folding, small-molecule pharmaceuticals, organic liquid properties, homogeneous catalysis
+
+                                        **Level of theory:** wB97M-V/def2-TZVPD as implemented in ORCA6, including many-body dispersion. All solvation should be explicit. 
+
+                                        **Additional inputs:** total charge and spin multiplicity. If you don't know what these are, you should be very careful if modeling charged or open-shell systems. This can be used to study radical chemistry or understand the impact of magnetic states on the structure of a molecule.
+
+                                        **Caveats:** All training data is aperiodic, so any periodic systems should be treated with some caution. Probably won't work well for inorganic materials. 
+                                        """
+                                    )
+                                with gr.TabItem("OMC", id=1):
+                                    gr.Markdown(
+                                        """
+
+                                        OMC25 comprises ~25 million calculations of organic molecular crystals from random packing of OE62 structures into various 3D unit cells. 
+
+                                        **Relevant applications:** Pharmaceutical packaging, bio-inspired materials, organic electronics, organic LEDs
+
+                                        **Level of theory:** PBE+D3 as implemented in VASP.
+
+                                        **Additional inputs:** UMA has not seen varying charge or spin multiplicity for the OMC task, and expects total_charge=0 and spin multiplicity=0 as model inputs. 
+
+                                        """
+                                    )
+
+                                with gr.TabItem("OMat", id=2):
+                                    gr.Markdown(
+                                        """
+
+                                        OMat24 comprises >100 million calculations or inorganic materials collected from many open databases like Materials Project and Alexandria, and randomly sampled far from equilibria. 
+
+                                        **Relevant applications:** Inorganic materials discovery, solar photovoltaics, advanced alloys, superconductors, electronic materials, optical materials
+
+                                        **Level of theory:** PBE/PBE+U as implemented in VASP using Materials Project suggested settings, except with VASP6 pseudopotentials. No dispersion.
+
+                                        **Additional inputs:** UMA has not seen varying charge or spin multiplicity for the OMat task, and expects total_charge=0 and spin multiplicity=0 as model inputs. 
+
+                                        **Caveats:** Spin polarization effects are included, but you can't select the magnetic state. Further, OMat24 did not fully sample possible spin states in the training data.
+                                        """
+                                    )
+
+                                with gr.TabItem("OC20", id=3):
+                                    gr.Markdown(
+                                        """
+
+                                        OC20 comprises >100 million calculations of small molecules adsorbed on catalyst surfaces formed from materials in the Materials Project. 
+
+                                        **Relevant applications:** Renewable energy, catalysis, fuel cells, energy conversion, sustainable fertilizer production, chemical refining, plastics synthesis/upcycling
+
+                                        **Level of theory:** RPBE as implemented in VASP, with VASP5.4 pseudopotentials. No dispersion.
+
+                                        **Additional inputs:** UMA has not seen varying charge or spin multiplicity for the OC20 task, and expects total_charge=0 and spin multiplicity=0 as model inputs.  
+
+                                        **Caveats:** No oxides or explicit solvents are included in OC20. The model works surprisingly well for transition state searches given the nature of the training data, but you should be careful. RPBE works well for small molecules, but dispersion will be important for larger molecules on surfaces. 
+                                        """
+                                    )
+
+                                with gr.TabItem("ODAC", id=4):
+                                    gr.Markdown(
+                                        """
+
+                                        ODAC23 comprises >10 million calculations of CO2/H2O molecules adsorbed in Metal Organic Frameworks sampled from various open databases like CoreMOF.
+
+                                        **Relevant applications:** Direct air capture, carbon capture and storage, CO2 conversion, catalysis
+
+                                        **Level of theory:** PBE+D3 as implemented in VASP, with VASP5.4 pseudopotentials. 
+
+                                        **Additional inputs:** UMA has not seen varying charge or spin multiplicity for the ODAC task, and expects total_charge=0 and spin multiplicity=0 as model inputs.  
+
+                                        **Caveats:** The ODAC23 dataset only contains CO2/H2O water absorption, so anything more than might be inaccurate (e.g. hydrocarbons in MOFs). Further, there is a limited number of bare-MOF structures in the training data, so you should be careful if you are using a new MOF structure.
+                                        """
+                                    )
+
+                with gr.Column(variant="panel"):
+                    gr.Markdown("### 3. Run Your Simulation")
+                    with gr.Row():
+                        with gr.Column():
+                            gr.Markdown("### Molecular Dynamics")
+                            prerelax_steps.render()
+                            md_steps.render()
+                            temperature_k.render()
+                            md_timestep.render()
+                            md_ensemble.render()
+                            md_button.render()
+
+                        with gr.Column():
+                            gr.Markdown("### Relaxation")
+                            optimization_steps.render()
+                            fmax.render()
+                            relax_unit_cell.render()
+                            optimization_button.render()
+
+            with gr.Column(variant="panel", elem_id="results", min_width=500):
+                gr.Markdown("## UMA Simulation Results")
+                with gr.Tab("Visualization"):
+                    output_structure.render()
+                    with gr.Accordion(
+                        "What should I look for in this simulation?", open=True
+                    ):
+                        explanation.render()
+                    with gr.Accordion("Model Disclaimers", open=False):
+                        gr.Markdown(
+                            """
+    * While UMA represents a step forward in terms of having a single model that works across chemistry and materials science, we know the model has limitations and weaknesses and there will be cases where the model fails to produce an accurate simulation.
+    * Ab-initio calculations are not perfect. You should always consider the limitations of the level of theory, the code, and the pseudopotentials. 
+    """
+                        )
+                    with gr.Accordion(
+                        "How long should I wait for this simulation?", open=False
+                    ):
+                        gr.Markdown(
+                            """
+* Every calculation uses a pool of GPUs to process simulations for all current users. You can achieve much higher performance with a dedicated GPU and MD-mode enabled. 
+* Most simulation should finish within a few minutes. Example results are cached, and if you are running a custom simulation you can follow the progress bar
+* if you don't see progress or the simulation takes more than ~5min, probably there was an error and please try submitting again. 
+* If you notice any issues please submit them as issues on the [FAIR Chemistry GitHub](https://github.com/facebookresearch/fairchem).
+"""
+                        )
+
+                    output_traj.render()
+                with gr.Tab("Log"):
+                    output_text.render()
+                with gr.Tab("Script"):
+                    reproduction_script.render()
+
+        md_button.click(
+            run_md_simulation,
+            inputs=[
+                input_structure,
+                md_steps,
+                prerelax_steps,
+                md_timestep,
+                temperature_k,
+                md_ensemble,
+                task_name,
+                total_charge,
+                spin_multiplicity,
+            ],
+            outputs=[output_traj, output_text, reproduction_script, explanation],
+            scroll_to_output=True,
+            concurrency_limit=10,
+            concurrency_id="simulation_queue",
+        )
+        optimization_button.click(
+            run_relaxation_simulation,
+            inputs=[
+                input_structure,
+                optimization_steps,
+                fmax,
+                task_name,
+                total_charge,
+                spin_multiplicity,
+                relax_unit_cell,
+            ],
+            outputs=[output_traj, output_text, reproduction_script, explanation],
+            scroll_to_output=True,
+            concurrency_id="simulation_queue",
+        )
+
+        # Change the tab based on the current task name
+        task_name.input(
+            lambda x: gr.Tabs(
+                selected={"OMol": 0, "OMC": 1, "OMat": 2, "OC20": 3, "ODAC": 4}[x]
+            ),
+            [task_name],
+            task_name_tabs,
+        )
+
+        # Only show charge/spin inputs for OMol task
+        task_name.input(
+            lambda x: (
+                gr.Number(visible=True) if x == "OMol" else gr.Number(visible=False)
+            ),
+            [task_name],
+            total_charge,
+        )
+        task_name.input(
+            lambda x: (
+                gr.Number(visible=True) if x == "OMol" else gr.Number(visible=False)
+            ),
+            [task_name],
+            spin_multiplicity,
+        )
+
+    demo.launch()
+
+
+if __name__ == "__main__":
+
+    # On load, build and install the gradio_molecul3d fork
+    subprocess.call(
+        ["gradio", "cc", "install"], cwd=Path(__file__).parent / "gradio_molecule3d/"
+    )
+    subprocess.call(
+        ["gradio", "cc", "build"], cwd=Path(__file__).parent / "gradio_molecule3d/"
+    )
+    subprocess.call(
+        [
+            sys.executable,
+            "-m",
+            "pip",
+            "install",
+            Path(__file__).parent
+            / "gradio_molecule3d/"
+            / "dist/gradio_molecule3d-0.0.7-py3-none-any.whl",
+        ],
+        cwd=Path(__file__).parent.parent,
+    )
+
+    os.makedirs("/data/custom_inputs", exist_ok=True)
+
+    # Load gradio_molecule3d only once it's built and installed
+    from gradio_molecule3d import Molecule3D
+
+    main()

examples/HEA.cif

@@ -0,0 +1,89 @@
+data_image0
+_chemical_formula_structural       Cr16Fe16Ni16Sn16
+_chemical_formula_sum              "Cr16 Fe16 Ni16 Sn16"
+_cell_length_a       6.28036836238552
+_cell_length_b       9.729504828593834
+_cell_length_c       16.851996690897195
+_cell_angle_alpha    95.52183275573677
+_cell_angle_beta     98.573104985915
+_cell_angle_gamma    97.41755573965753
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Cr  Cr1       1.0  0.0  0.0  0.0  1.0000
+  Cr  Cr2       1.0  0.37500000000000006  0.25  0.3125  1.0000
+  Cr  Cr3       1.0  0.06250000000000003  0.375  0.71875  1.0000
+  Cr  Cr4       1.0  0.25  0.5  0.875  1.0000
+  Cr  Cr5       1.0  0.5625  0.37499999999999994  0.96875  1.0000
+  Cr  Cr6       1.0  0.12499999999999997  0.7499999999999999  0.4375  1.0000
+  Cr  Cr7       1.0  0.6875000000000001  0.12499999999999986  0.9062500000000001  1.0000
+  Cr  Cr8       1.0  0.37500000000000006  0.75  0.31250000000000006  1.0000
+  Cr  Cr9       1.0  0.7500000000000001  0.0  0.625  1.0000
+  Cr  Cr10      1.0  0.3125  0.375  0.09375000000000003  1.0000
+  Cr  Cr11      1.0  0.6875000000000001  0.625  0.40625  1.0000
+  Cr  Cr12      1.0  0.8749999999999999  0.7499999999999998  0.5625  1.0000
+  Cr  Cr13      1.0  0.625  0.24999999999999992  0.1875  1.0000
+  Cr  Cr14      1.0  0.125  0.25  0.4375  1.0000
+  Cr  Cr15      1.0  0.3125  0.375  0.59375  1.0000
+  Cr  Cr16      1.0  0.43750000000000006  0.125  0.53125  1.0000
+  Fe  Fe1       1.0  0.18750000000000003  0.125  0.15625  1.0000
+  Fe  Fe2       1.0  0.5625000000000001  0.375  0.46875000000000006  1.0000
+  Fe  Fe3       1.0  0.7500000000000001  0.5  0.625  1.0000
+  Fe  Fe4       1.0  0.9375000000000001  0.625  0.7812500000000001  1.0000
+  Fe  Fe5       1.0  0.12499999999999997  0.7499999999999998  0.9375000000000001  1.0000
+  Fe  Fe6       1.0  0.6875000000000001  0.12499999999999996  0.40625  1.0000
+  Fe  Fe7       1.0  0.7499999999999999  0.49999999999999994  0.12499999999999997  1.0000
+  Fe  Fe8       1.0  0.3125  0.8749999999999999  0.59375  1.0000
+  Fe  Fe9       1.0  0.8750000000000001  0.25  0.0625  1.0000
+  Fe  Fe10      1.0  0.8125000000000001  0.8750000000000001  0.84375  1.0000
+  Fe  Fe11      1.0  0.18750000000000003  0.625  0.15624999999999997  1.0000
+  Fe  Fe12      1.0  0.1250000000000001  0.25  0.9375000000000001  1.0000
+  Fe  Fe13      1.0  0.5  0.5  0.25  1.0000
+  Fe  Fe14      1.0  0.8125  0.375  0.34375000000000006  1.0000
+  Fe  Fe15      1.0  0.7500000000000001  0.0  0.125  1.0000
+  Fe  Fe16      1.0  0.8750000000000001  0.7499999999999999  0.06250000000000001  1.0000
+  Ni  Ni1       1.0  0.3125000000000001  0.8750000000000001  0.09375  1.0000
+  Ni  Ni2       1.0  0.5  0.0  0.25  1.0000
+  Ni  Ni3       1.0  0.43750000000000006  0.625  0.031249999999999976  1.0000
+  Ni  Ni4       1.0  0.625  0.75  0.18750000000000006  1.0000
+  Ni  Ni5       1.0  0.18750000000000003  0.12499999999999996  0.65625  1.0000
+  Ni  Ni6       1.0  0.25  0.5  0.375  1.0000
+  Ni  Ni7       1.0  0.625  0.7499999999999998  0.6875000000000001  1.0000
+  Ni  Ni8       1.0  0.0  0.5  0.0  1.0000
+  Ni  Ni9       1.0  0.9375000000000001  0.12499999999999996  0.78125  1.0000
+  Ni  Ni10      1.0  0.43750000000000006  0.125  0.03125  1.0000
+  Ni  Ni11      1.0  0.18750000000000003  0.625  0.65625  1.0000
+  Ni  Ni12      1.0  0.49999999999999994  0.49999999999999994  0.75  1.0000
+  Ni  Ni13      1.0  0.6875000000000002  0.6250000000000001  0.9062500000000001  1.0000
+  Ni  Ni14      1.0  0.06249999999999995  0.8749999999999999  0.21875  1.0000
+  Ni  Ni15      1.0  0.625  0.24999999999999992  0.6875000000000001  1.0000
+  Ni  Ni16      1.0  0.8125  0.37499999999999994  0.84375  1.0000
+  Sn  Sn1       1.0  0.8750000000000001  0.25000000000000006  0.5625000000000001  1.0000
+  Sn  Sn2       1.0  0.8125  0.8749999999999999  0.34375  1.0000
+  Sn  Sn3       1.0  0.0  0.0  0.5  1.0000
+  Sn  Sn4       1.0  0.37500000000000006  0.25  0.8125  1.0000
+  Sn  Sn5       1.0  0.9375000000000001  0.625  0.28124999999999994  1.0000
+  Sn  Sn6       1.0  0.5  0.0  0.7500000000000001  1.0000
+  Sn  Sn7       1.0  0.062499999999999986  0.37499999999999994  0.21875  1.0000
+  Sn  Sn8       1.0  0.43749999999999994  0.6249999999999999  0.53125  1.0000
+  Sn  Sn9       1.0  0.5625000000000002  0.8750000000000001  0.46875000000000006  1.0000
+  Sn  Sn10      1.0  0.06250000000000003  0.8750000000000001  0.71875  1.0000
+  Sn  Sn11      1.0  0.25  0.9999999999999999  0.8750000000000001  1.0000
+  Sn  Sn12      1.0  0.0  0.5  0.5  1.0000
+  Sn  Sn13      1.0  0.3750000000000001  0.7499999999999999  0.8125000000000001  1.0000
+  Sn  Sn14      1.0  0.5625  0.8749999999999999  0.96875  1.0000
+  Sn  Sn15      1.0  0.9375000000000001  0.12499999999999999  0.28125000000000006  1.0000
+  Sn  Sn16      1.0  0.25  0.0  0.37500000000000006  1.0000

examples/bis(EDA)Cu.xyz

@@ -0,0 +1,27 @@
+25
+
+Cu    -0.2209807697981   0.1562206673100  -0.2702543144077
+N      1.3137548957875   0.5160811070801  -0.0621790201316
+N     -1.1697941926852   1.4084676437792  -0.0263661851676
+N     -0.7320211993524  -0.9279028046343   0.7746834539678
+N     -0.2960297954951  -0.3714737952478  -1.7682696819292
+H      1.7700594700635   0.1119337839006   0.7526330653817
+C      2.0438061361622   0.0308270007188  -1.2618458080557
+H     -1.0108892443997   0.0422201550814  -2.3628208275489
+C      1.0207299436500  -0.0899056474093  -2.3958258294877
+C    -2.2538881983659   0.9615829458907   0.8858629213719
+H    -0.7134131668629   2.1820906425597   0.4512217736737
+C    -1.7253926400061  -0.2555826059551   1.6515646734439
+H    -1.2262564948403  -1.7086072518402   0.3492806868790
+H    -3.1395531268796   0.6889984401720   0.3030099080986
+H    -2.5740755889657   1.7602483067208   1.5638712990201
+H    -1.2429302450851   0.0606801517349   2.5817426367378
+H    -2.5346090735134  -0.9320481538840   1.9474572953618
+H     2.4943754630577  -0.9442944371524  -1.0510333860111
+H     2.8734708369333   0.6931121163594  -1.5322893849642
+H     0.9687160022358   0.8454661710213  -2.9622572009160
+H     1.3042473510312  -0.8635089531977  -3.1178965470356
+H    -0.4235273777421  -1.3779232965060  -1.8421840816046
+H     1.4990253393107   1.5151243421802  -0.0145688038723
+H    -0.0275971835230  -1.3439425457617   1.3799526346530
+H    -1.6118216269878   1.8130129511840  -0.8489698824425

examples/ethylene_carbonate.xyz

@@ -0,0 +1,12 @@
+10
+ethylene carbonate
+O         -0.12334       -1.10922        0.16737
+C          0.64058        0.00703        0.00189
+C         -1.46757       -0.74526       -0.08091
+C         -1.47502        0.74033        0.08533
+O         -0.13418        1.11813       -0.16228
+O          1.86114        0.01331        0.00048
+H         -2.13521       -1.24337        0.62850
+H         -1.74077       -1.05266       -1.09551
+H         -1.75177        1.04514        1.09984
+H         -2.14685        1.23129       -0.62434

examples/gold_nanoparticle_crystal.cif

@@ -0,0 +1,1944 @@
+#------------------------------------------------------------------------------
+#$Date: 2016-03-05 10:55:21 +0200 (Sat, 05 Mar 2016) $
+#$Revision: 177732 $
+#$URL: file:///home/coder/svn-repositories/cod/cif/1/54/05/1540567.cif $
+#------------------------------------------------------------------------------
+#
+# This file is available in the Crystallography Open Database (COD),
+# http://www.crystallography.net/
+#
+# All data on this site have been placed in the public domain by the
+# contributors.
+#
+data_1540567
+loop_
+_publ_author_name
+'Tofanelli, Marcus A.'
+'Salorinne, Kirsi'
+'Ni, Thomas W.'
+'Malola, Sami'
+'Newell, Brian'
+'Phillips, Billy'
+'H\"akkinen, Hannu'
+'Ackerson, Christopher J.'
+_publ_section_title
+;
+ Jahn--Teller effects in Au25(SR)18
+;
+_journal_issue                   3
+_journal_name_full               'Chem. Sci.'
+_journal_page_first              1882
+_journal_paper_doi               10.1039/C5SC02134K
+_journal_volume                  7
+_journal_year                    2016
+_chemical_formula_moiety         'C144 H144 Au25 S18'
+_chemical_formula_sum            'C148 H170 Au25 O2 S36'
+_chemical_formula_weight         8059.15
+_chemical_name_systematic        'Au25(PET)18 in the neutral charge state'
+_space_group_crystal_system      triclinic
+_space_group_IT_number           2
+_space_group_name_Hall           '-P 1'
+_space_group_name_H-M_alt        'P -1'
+_symmetry_space_group_name_Hall  '-P 1'
+_symmetry_space_group_name_H-M   'P -1'
+_atom_sites_solution_hydrogens   geom
+_audit_creation_method           SHELXL-2013
+_audit_update_record
+;
+2015-03-19 deposited with the CCDC.
+2015-11-24 downloaded from the CCDC.
+;
+_cell_angle_alpha                65.00(3)
+_cell_angle_beta                 64.00(3)
+_cell_angle_gamma                81.00(3)
+_cell_formula_units_Z            1
+_cell_length_a                   16.174(3)
+_cell_length_b                   17.746(4)
+_cell_length_c                   17.830(4)
+_cell_measurement_temperature    293(2)
+_cell_volume                     4166(2)
+_computing_structure_refinement  'SHELXL-2013 (Sheldrick, 2013)'
+_diffrn_ambient_temperature      293(2)
+_diffrn_measured_fraction_theta_full 0.999
+_diffrn_measured_fraction_theta_max 1.000
+_diffrn_radiation_type           MoK\a
+_diffrn_radiation_wavelength     0.71073
+_diffrn_reflns_av_R_equivalents  0.1424
+_diffrn_reflns_av_unetI/netI     0.0723
+_diffrn_reflns_laue_measured_fraction_full 0.999
+_diffrn_reflns_laue_measured_fraction_max 1.000
+_diffrn_reflns_limit_h_max       22
+_diffrn_reflns_limit_h_min       -22
+_diffrn_reflns_limit_k_max       24
+_diffrn_reflns_limit_k_min       -24
+_diffrn_reflns_limit_l_max       24
+_diffrn_reflns_limit_l_min       -24
+_diffrn_reflns_number            202701
+_diffrn_reflns_point_group_measured_fraction_full 0.999
+_diffrn_reflns_point_group_measured_fraction_max 1.000
+_diffrn_reflns_theta_full        25.242
+_diffrn_reflns_theta_max         29.130
+_diffrn_reflns_theta_min         1.506
+_exptl_absorpt_coefficient_mu    22.409
+_exptl_crystal_colour            Black
+_exptl_crystal_density_diffrn    3.212
+_exptl_crystal_F_000             3625
+_refine_diff_density_max         2.625
+_refine_diff_density_min         -2.947
+_refine_diff_density_rms         0.583
+_refine_ls_extinction_method     none
+_refine_ls_goodness_of_fit_ref   1.031
+_refine_ls_hydrogen_treatment    constr
+_refine_ls_matrix_type           full
+_refine_ls_number_parameters     897
+_refine_ls_number_reflns         22436
+_refine_ls_number_restraints     27
+_refine_ls_restrained_S_all      1.030
+_refine_ls_R_factor_all          0.0891
+_refine_ls_R_factor_gt           0.0387
+_refine_ls_shift/su_max          0.096
+_refine_ls_shift/su_mean         0.001
+_refine_ls_structure_factor_coef Fsqd
+_refine_ls_weighting_details
+'w=1/[\s^2^(Fo^2^)+(0.0517P)^2^+4.0385P] where P=(Fo^2^+2Fc^2^)/3'
+_refine_ls_weighting_scheme      calc
+_refine_ls_wR_factor_gt          0.0826
+_refine_ls_wR_factor_ref         0.1095
+_reflns_Friedel_coverage         0.000
+_reflns_number_gt                14888
+_reflns_number_total             22436
+_reflns_threshold_expression     'I > 2\s(I)'
+_cod_data_source_file            c5sc02134k2.cif
+_cod_data_source_block           ca05_trunc_r3
+_cod_depositor_comments
+'Adding full bibliography for 1540567--1540568.cif.'
+_cod_database_code               1540567
+_shelx_space_group_comment
+;
+The symmetry employed for this shelxl refinement is uniquely defined
+by the following loop, which should always be used as a source of
+symmetry information in preference to the above space-group names.
+They are only intended as comments.
+;
+_shelxl_version_number           2013-4
+_shelx_res_file
+;
+TITL ca05_trunc in P-1
+CELL 0.71073  16.1735  17.7462  17.8295  65.000  64.000  81.000
+ZERR    1.00   0.0032   0.0035   0.0036   0.030   0.030   0.030
+LATT 1
+SFAC C  H  O  S  Au
+UNIT 148  170  2  36  25
+L.S. 20
+BOND $H
+ACTA
+WPDB 2
+FMAP 2
+PLAN 20
+WGHT    0.051700    4.038500
+FVAR       0.09933
+MOLE 1
+
+FLAT C3_2001 C4_2001 C5_2001 C6_2001 C7_2001 C8_2001
+FLAT C3_2002 C4_2002 C5_2002 C6_2002 C7_2002 C8_2002
+FLAT 0.01 C3_2004 C4_2004 C5_2004 C6_2004 C7_2004 C8_2004
+FLAT C3_2003 C4_2003 C5_2003 C6_2003 C7_2003 C8_2003
+FLAT C3_2006 C4_2006 C5_2006 C6_2006 C7_2006 C8_2006
+FLAT 0.01 C3_2005 C4_2005 C5_2005 C6_2005 C7_2005 C8_2005
+FLAT C3_2007 C4_2007 C5_2007 C6_2007 C7_2007 C8_2007
+FLAT C3_2008 C4_2008 C5_2008 C6_2008 C7_2008 C8_2008
+FLAT C3_2009 C4_2009 C5_2009 C6_2009 C7_2009 C8_2009
+
+AU1   5    0.500000    1.000000    0.500000    10.50000    0.01234    0.00967 =
+         0.02021   -0.00584   -0.00247   -0.00132
+AU2   5    0.396355    0.851887    0.617958    11.00000    0.01516    0.01120 =
+         0.02514   -0.00534   -0.00459   -0.00192
+AU3   5    0.420886    0.967878    0.684774    11.00000    0.02008    0.01277 =
+         0.02147   -0.00665   -0.00453   -0.00044
+AU4   5    0.447349    1.130230    0.556841    11.00000    0.01981    0.01100 =
+         0.02343   -0.00752   -0.00432    0.00022
+AU5   5    0.204672    0.861555    0.592108    11.00000    0.01815    0.01637 =
+         0.03260   -0.00846   -0.01056   -0.00112
+AU6   5    0.778061    0.927380    0.557546    11.00000    0.01913    0.01761 =
+         0.04043   -0.01239   -0.01518    0.00265
+AU7   5    0.567938    0.869009    0.610514    11.00000    0.01708    0.01288 =
+         0.02907   -0.00627   -0.00880    0.00120
+AU8   5    0.259202    1.082522    0.728702    11.00000    0.02221    0.01853 =
+         0.03178   -0.01465   -0.00051   -0.00338
+AU9   5    0.611560    1.044282    0.560689    11.00000    0.01737    0.01695 =
+         0.02895   -0.01097   -0.00794    0.00042
+AU10  5    0.310848    1.006642    0.581143    11.00000    0.01506    0.01754 =
+         0.02551   -0.00949   -0.00397    0.00201
+AU11  5    0.473871    1.099086    0.728856    11.00000    0.02993    0.01807 =
+         0.02641   -0.01029   -0.00944    0.00016
+AU12  5    0.425883    0.772844    0.802394    11.00000    0.02546    0.01508 =
+         0.02907   -0.00556   -0.01001    0.00070
+AU13  5    0.510210    0.698719    0.627751    11.00000    0.02315    0.01130 =
+         0.03110   -0.00649   -0.01302    0.00043
+S14   4    0.276225    0.755973    0.670154    11.00000    0.01876    0.01461 =
+         0.03054   -0.00769   -0.00829   -0.00287
+S15   4    0.630390    1.085767    0.663162    11.00000    0.03237    0.02595 =
+         0.03429   -0.01238   -0.01822    0.00210
+S16   4    0.442688    0.649863    0.784142    11.00000    0.02578    0.01315 =
+         0.03387   -0.00300   -0.01422   -0.00080
+S20   4    0.121487    0.959024    0.521413    11.00000    0.02021    0.01767 =
+         0.04519   -0.01155   -0.01569    0.00201
+S21   4    0.410520    0.887810    0.835181    11.00000    0.04204    0.01769 =
+         0.02492   -0.00491   -0.00913   -0.00174
+S24   4    0.320146    1.109068    0.810828    11.00000    0.03377    0.01502 =
+         0.02836   -0.01124   -0.00374   -0.00331
+S25   4    0.183001    1.073993    0.650035    11.00000    0.01779    0.04766 =
+         0.05824   -0.03797   -0.00846    0.00800
+S26   4    0.695586    0.801892    0.639070    11.00000    0.02021    0.02048 =
+         0.03912   -0.01008   -0.01459    0.00153
+S28   4    0.413373    1.271354    0.525290    11.00000    0.01913    0.01486 =
+         0.03610   -0.01230   -0.01075    0.00164
+RESI 2001 PET
+C1    1    0.300085    1.220505    0.784447    11.00000    0.02417    0.02188 =
+         0.04554   -0.01952    0.00423   -0.00264
+AFIX  23
+H1A   2    0.314411    1.249724    0.720086    11.00000   -1.20000
+H1B   2    0.235555    1.227793    0.818181    11.00000   -1.20000
+AFIX   0
+C2    1    0.359157    1.258457    0.808668    11.00000    0.03815    0.02319 =
+         0.04786   -0.02309   -0.00405   -0.01158
+AFIX  23
+H2A   2    0.341410    1.232228    0.873821    11.00000   -1.20000
+H2B   2    0.423338    1.247332    0.778676    11.00000   -1.20000
+AFIX   0
+C3    1    0.348322    1.350577    0.780452    11.00000    0.02943    0.02621 =
+         0.03952   -0.01772   -0.01037   -0.00093
+C4    1    0.423542    1.404830    0.727687    11.00000    0.03111    0.03852 =
+         0.02227   -0.01706   -0.00256   -0.00985
+AFIX  43
+H4    2    0.482017    1.384574    0.705723    11.00000   -1.20000
+AFIX   0
+C5    1    0.413187    1.490062    0.706659    11.00000    0.04394    0.01788 =
+         0.03745   -0.00506   -0.00770   -0.01142
+AFIX  43
+H5    2    0.464243    1.526577    0.671038    11.00000   -1.20000
+AFIX   0
+C6    1    0.326479    1.518967    0.739424    11.00000    0.05839    0.01857 =
+         0.08439   -0.02772   -0.03985    0.00968
+AFIX  43
+H6    2    0.319062    1.575829    0.724037    11.00000   -1.20000
+AFIX   0
+C7    1    0.250324    1.465981    0.794414    11.00000    0.05004    0.05202 =
+         0.17420   -0.07624   -0.05566    0.02082
+AFIX  43
+H7    2    0.192329    1.486578    0.817618    11.00000   -1.20000
+AFIX   0
+C8    1    0.260857    1.381056    0.815071    11.00000    0.02938    0.04691 =
+         0.14521   -0.06154   -0.01385    0.00110
+AFIX  43
+H8    2    0.209697    1.344685    0.851879    11.00000   -1.20000
+AFIX   0
+
+RESI 2002 PET
+C1    1    0.648882    0.986777    0.748784    11.00000    0.04532    0.04584 =
+         0.06188   -0.01509   -0.02590   -0.00431
+AFIX  23
+H1A   2    0.610899    0.942233    0.760847    11.00000   -1.20000
+H1B   2    0.712797    0.972027    0.725309    11.00000   -1.20000
+AFIX   0
+C2    1    0.622457    0.998326    0.841220    11.00000    0.07522
+AFIX  23
+H2A   2    0.556130    1.001761    0.869899    11.00000   -1.20000
+H2B   2    0.639788    0.948986    0.882188    11.00000   -1.20000
+AFIX   0
+C3    1    0.663817    1.069289    0.831110    11.00000    0.14378    0.10251 =
+         0.08349   -0.05342   -0.07883    0.05527
+C4    1    0.759866    1.078144    0.792815    11.00000    0.12089    0.20486 =
+         0.25598   -0.19795   -0.10694    0.06019
+AFIX  43
+H4    2    0.794718    1.036558    0.775698    11.00000   -1.20000
+AFIX   0
+C5    1    0.808034    1.149427    0.778418    11.00000    0.10367    0.28018 =
+         0.39079   -0.31196   -0.06789    0.03629
+AFIX  43
+H5    2    0.872027    1.152209    0.753041    11.00000   -1.20000
+AFIX   0
+C6    1    0.759470    1.211829    0.802064    11.00000    0.15834    0.15707 =
+         0.16649   -0.12731   -0.03836    0.00483
+AFIX  43
+H6    2    0.788163    1.259206    0.791164    11.00000   -1.20000
+AFIX   0
+C7    1    0.661505    1.199898    0.844741    11.00000    0.13477    0.10881 =
+         0.10983   -0.08168   -0.04888    0.05062
+AFIX  43
+H7    2    0.625836    1.238376    0.867208    11.00000   -1.20000
+AFIX   0
+C8    1    0.617570    1.133494    0.854001    11.00000    0.11890    0.06357 =
+         0.05997    0.00129   -0.05038   -0.03986
+AFIX  43
+H8    2    0.553672    1.132332    0.876820    11.00000   -1.20000
+AFIX   0
+
+RESI 2003 PET
+C1    1    0.480446    1.318789    0.556058    11.00000    0.02616    0.02281 =
+         0.02993   -0.01276   -0.00476   -0.00744
+AFIX  23
+H1A   2    0.465686    1.377055    0.540179    11.00000   -1.20000
+H1B   2    0.459456    1.292855    0.621660    11.00000   -1.20000
+AFIX   0
+C2    1    0.583843    1.313932    0.513993    11.00000    0.02508    0.01910 =
+         0.02704   -0.00825   -0.00965   -0.00296
+AFIX  23
+H2A   2    0.606735    1.337012    0.448219    11.00000   -1.20000
+H2B   2    0.601112    1.256311    0.534194    11.00000   -1.20000
+AFIX   0
+C3    1    0.625834    1.362722    0.542357    11.00000    0.01293    0.04393 =
+         0.04357   -0.02682    0.00017   -0.00690
+C4    1    0.634428    1.448230    0.497119    11.00000    0.03389    0.03538 =
+         0.06679   -0.03662   -0.01048   -0.00362
+AFIX  43
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+AFIX   0
+C5    1    0.672662    1.496351    0.518410    11.00000    0.03508    0.05792 =
+         0.09776   -0.05616   -0.02591    0.00562
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+AFIX   0
+C6    1    0.701802    1.458515    0.586915    11.00000    0.04225    0.09194 =
+         0.09617   -0.08141   -0.01776    0.01395
+AFIX  43
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+AFIX   0
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+         0.06846   -0.05121   -0.03568    0.01683
+AFIX  43
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+C8    1    0.655532    1.325773    0.609839    11.00000    0.03075    0.06100 =
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+AFIX  43
+H8    2    0.650253    1.268217    0.640887    11.00000   -1.20000
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+
+RESI 2004 PET
+C1    1    0.297363    0.881791    0.927094    11.00000    0.06783    0.02252 =
+         0.02556   -0.00787   -0.00930    0.00194
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+H1A   2    0.299008    0.841373    0.983756    11.00000   -1.20000
+H1B   2    0.286004    0.935393    0.931521    11.00000   -1.20000
+AFIX   0
+C2    1    0.222470    0.859989    0.918747    11.00000    0.05965    0.03806 =
+         0.08290   -0.03016   -0.03256    0.00201
+AFIX  23
+H2A   2    0.232164    0.806365    0.914419    11.00000   -1.20000
+H2B   2    0.217685    0.901010    0.863833    11.00000   -1.20000
+AFIX   0
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+         0.06598   -0.00833   -0.00660   -0.00506
+C4    1    0.120725    0.793897    1.089687    11.00000    0.13937    0.05043 =
+         0.09476   -0.03123    0.00424    0.02904
+AFIX  43
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+AFIX  43
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+AFIX   0
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+AFIX  43
+H7    2   -0.062789    0.924773    1.081984    11.00000   -1.20000
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+         0.10544   -0.05519    0.01552    0.06871
+AFIX  43
+H8    2    0.065584    0.943795    0.950554    11.00000   -1.20000
+AFIX   0
+
+RESI 2005 PET
+C1    1    0.207333    0.732635    0.790931    11.00000    0.01214    0.02961 =
+         0.03163   -0.01200   -0.00661   -0.00122
+AFIX  23
+H1A   2    0.240991    0.697206    0.825965    11.00000   -1.20000
+H1B   2    0.194813    0.783766    0.800761    11.00000   -1.20000
+AFIX   0
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+         0.04882    0.00759   -0.01450   -0.01008
+AFIX  23
+H2A   2    0.079602    0.726772    0.793036    11.00000   -1.20000
+H2B   2    0.129347    0.641676    0.805019    11.00000   -1.20000
+AFIX   0
+C3    1    0.065494    0.659037    0.924724    11.00000    0.01992    0.05456 =
+         0.04525    0.00375   -0.00542   -0.01376
+C4    1    0.018168    0.715267    0.964434    11.00000    0.11229    0.12524 =
+         0.10794    0.02811    0.08907    0.08062
+AFIX  43
+H4    2    0.014353    0.770036    0.926813    11.00000   -1.20000
+AFIX   0
+C5    1   -0.023373    0.691828    1.058443    11.00000    0.08178    0.07673 =
+         0.08907   -0.05321   -0.00141    0.00629
+AFIX  43
+H5    2   -0.054501    0.729384    1.084486    11.00000   -1.20000
+AFIX   0
+C6    1   -0.015387    0.607117    1.112236    11.00000    0.06002    0.07271 =
+         0.03827   -0.00634   -0.00235   -0.00793
+AFIX  43
+H6    2   -0.042315    0.588126    1.175339    11.00000   -1.20000
+AFIX   0
+C7    1    0.031275    0.553509    1.072325    11.00000    0.07768    0.04023 =
+         0.03785   -0.00415   -0.02700   -0.00194
+AFIX  43
+H7    2    0.036830    0.498230    1.107427    11.00000   -1.20000
+AFIX   0
+C8    1    0.068271    0.581835    0.982950    11.00000    0.10778    0.02755 =
+         0.04233   -0.01457   -0.03562   -0.00026
+AFIX  43
+H8    2    0.099779    0.543865    0.957663    11.00000   -1.20000
+AFIX   0
+
+RESI 2006 PET
+C1    1    0.536807    0.601931    0.816565    11.00000    0.04287    0.01736 =
+         0.04446   -0.00635   -0.02743    0.00411
+AFIX  23
+H1A   2    0.586151    0.643131    0.787730    11.00000   -1.20000
+H1B   2    0.515240    0.582558    0.881942    11.00000   -1.20000
+AFIX   0
+C2    1    0.573348    0.529518    0.788807    11.00000    0.03083    0.02567 =
+         0.03255   -0.01590   -0.01082    0.00834
+AFIX  23
+H2A   2    0.597465    0.549348    0.723146    11.00000   -1.20000
+H2B   2    0.523386    0.489508    0.815406    11.00000   -1.20000
+AFIX   0
+C3    1    0.649249    0.486855    0.819731    11.00000    0.03373    0.02397 =
+         0.05079   -0.01176   -0.02743    0.00975
+C4    1    0.629952    0.424743    0.903478    11.00000    0.05619    0.04127 =
+         0.05749    0.01284   -0.04010   -0.01274
+AFIX  43
+H4    2    0.568700    0.409023    0.943155    11.00000   -1.20000
+AFIX   0
+C5    1    0.697533    0.384104    0.931976    11.00000    0.11321    0.05556 =
+         0.14314   -0.00678   -0.10362    0.00088
+AFIX  43
+H5    2    0.682940    0.341509    0.989388    11.00000   -1.20000
+AFIX   0
+C6    1    0.784896    0.408514    0.873606    11.00000    0.08806    0.05049 =
+         0.18910   -0.05017   -0.11182    0.03585
+AFIX  43
+H6    2    0.831423    0.382490    0.891889    11.00000   -1.20000
+AFIX   0
+C7    1    0.809141    0.470798    0.787179    11.00000    0.03072    0.09420 =
+         0.12059   -0.07333   -0.02497    0.00594
+AFIX  43
+H7    2    0.870532    0.485964    0.747627    11.00000   -1.20000
+AFIX   0
+C8    1    0.738474    0.510034    0.761400    11.00000    0.03382    0.05307 =
+         0.06136   -0.03648   -0.02010    0.00896
+AFIX  43
+H8    2    0.752559    0.552339    0.703893    11.00000   -1.20000
+AFIX   0
+
+RESI 2007 PET
+C1    1    0.088911    0.975975    0.746423    11.00000    0.02862    0.17345 =
+         0.11110   -0.12038   -0.03312    0.04780
+AFIX  23
+H1A   2    0.104887    0.925792    0.734737    11.00000   -1.20000
+H1B   2    0.078952    0.964096    0.808155    11.00000   -1.20000
+AFIX   0
+C2    1    0.018982    1.013857    0.726968    11.00000    0.25665    0.06204 =
+         0.12147   -0.05046   -0.13580    0.07981
+AFIX  23
+H2A   2    0.027498    1.024501    0.665962    11.00000   -1.20000
+H2B   2    0.002533    1.064167    0.738370    11.00000   -1.20000
+AFIX   0
+C3    1   -0.054711    0.929740    0.810232    11.00000    0.18561    0.18059 =
+         0.06220   -0.05667    0.06530   -0.17028
+C4    1   -0.111914    0.924673    0.896127    11.00000    0.16659    0.21513 =
+         0.05871   -0.09134    0.07407   -0.15720
+AFIX  43
+H4    2   -0.099530    0.959828    0.916860    11.00000   -1.20000
+AFIX   0
+C5    1   -0.182929    0.872932    0.950276    11.00000    0.07497    0.09238 =
+         0.01893   -0.02206    0.01058   -0.03393
+AFIX  43
+H5    2   -0.219317    0.870986    1.008473    11.00000   -1.20000
+AFIX   0
+C6    1   -0.202940    0.822727    0.921374    11.00000    0.02961    0.07588 =
+         0.07308   -0.04477   -0.00742   -0.00448
+AFIX  43
+H6    2   -0.254953    0.787404    0.958553    11.00000   -1.20000
+AFIX   0
+C7    1   -0.148034    0.823254    0.838749    11.00000    0.03512    0.07653 =
+         0.08517   -0.05636   -0.01251   -0.00062
+AFIX  43
+H7    2   -0.160918    0.786755    0.819845    11.00000   -1.20000
+AFIX   0
+C8    1   -0.073838    0.876727    0.782635    11.00000    0.07489    0.05786 =
+         0.04665   -0.02747   -0.00467   -0.02214
+AFIX  43
+H8    2   -0.036194    0.877001    0.725370    11.00000   -1.20000
+AFIX   0
+
+RESI 2008 PET
+C1    1    0.119661    0.926676    0.437001    11.00000    0.02547
+AFIX  23
+H1A   2    0.110827    0.974959    0.388761    11.00000   -1.20000
+H1B   2    0.178620    0.904096    0.410212    11.00000   -1.20000
+AFIX   0
+C2    1    0.044217    0.862155    0.478266    11.00000    0.02484    0.02406 =
+         0.06048   -0.02065   -0.02543    0.00485
+AFIX  23
+H2A   2   -0.014049    0.884912    0.506446    11.00000   -1.20000
+H2B   2    0.041944    0.852662    0.429459    11.00000   -1.20000
+AFIX   0
+C3    1    0.052885    0.779458    0.547983    11.00000    0.02006    0.03078 =
+         0.05076   -0.01895   -0.01596    0.00125
+C4    1    0.126390    0.729675    0.523210    11.00000    0.03430    0.02516 =
+         0.04413   -0.01151   -0.01415   -0.00002
+AFIX  43
+H4    2    0.172436    0.748710    0.464303    11.00000   -1.20000
+AFIX   0
+C5    1    0.130878    0.651229    0.586845    11.00000    0.02581    0.02395 =
+         0.06667   -0.01529   -0.01730    0.00241
+AFIX  43
+H5    2    0.180384    0.618188    0.570191    11.00000   -1.20000
+AFIX   0
+C6    1    0.063469    0.622122    0.673495    11.00000    0.03435    0.02928 =
+         0.05562   -0.00399   -0.02132   -0.00515
+AFIX  43
+H6    2    0.065704    0.569154    0.715581    11.00000   -1.20000
+AFIX   0
+C7    1   -0.007745    0.673083    0.696925    11.00000    0.03668    0.05802 =
+         0.04245   -0.01549   -0.00903   -0.01065
+AFIX  43
+H7    2   -0.053303    0.654319    0.756087    11.00000   -1.20000
+AFIX   0
+C8    1   -0.013545    0.750738    0.635621    11.00000    0.02328    0.04428 =
+         0.03840   -0.02389   -0.00741   -0.00230
+AFIX  43
+H8    2   -0.062447    0.783909    0.653414    11.00000   -1.20000
+AFIX   0
+
+RESI 2009 PET
+C1    1    0.741225    0.747563    0.561351    11.00000    0.02116    0.01894 =
+         0.03330   -0.00681   -0.00824   -0.00392
+AFIX  23
+H1A   2    0.707723    0.694863    0.590085    11.00000   -1.20000
+H1B   2    0.732571    0.780939    0.506160    11.00000   -1.20000
+AFIX   0
+C2    1    0.841588    0.732456    0.537957    11.00000    0.01972    0.03267 =
+         0.04808   -0.02013   -0.01335    0.00053
+AFIX  23
+H2A   2    0.850051    0.702682    0.593782    11.00000   -1.20000
+H2B   2    0.874940    0.785590    0.506254    11.00000   -1.20000
+AFIX   0
+C3    1    0.881834    0.683225    0.479268    11.00000    0.01622    0.02619 =
+         0.06294   -0.02885   -0.00763   -0.00030
+C4    1    0.963055    0.646489    0.472814    11.00000    0.04812    0.10185 =
+         0.14000   -0.09731   -0.04922    0.03822
+AFIX  43
+H4    2    0.992698    0.652379    0.504564    11.00000   -1.20000
+AFIX   0
+C5    1    1.003076    0.600754    0.420799    11.00000    0.06054    0.18286 =
+         0.21817   -0.15591   -0.06877    0.06612
+AFIX  43
+H5    2    1.060099    0.577879    0.415842    11.00000   -1.20000
+AFIX   0
+C6    1    0.958653    0.588821    0.376004    11.00000    0.04601    0.13234 =
+         0.18330   -0.13515   -0.03113    0.03506
+AFIX  43
+H6    2    0.983133    0.553765    0.345270    11.00000   -1.20000
+AFIX   0
+C7    1    0.880226    0.627393    0.376308    11.00000    0.03928    0.06855 =
+         0.07728   -0.04634   -0.00788   -0.00332
+AFIX  43
+H7    2    0.852684    0.622544    0.342350    11.00000   -1.20000
+AFIX   0
+C8    1    0.840501    0.674946    0.428347    11.00000    0.03573    0.04429 =
+         0.06772   -0.03415   -0.01782    0.00626
+AFIX  43
+H8    2    0.785926    0.701453    0.429214    11.00000   -1.20000
+AFIX   0
+
+RESI 2010 Tol
+C9    1    0.550830    0.750447    0.970782    11.00000    0.03373    0.09421 =
+         0.03484   -0.00115   -0.01177    0.00994
+AFIX  43
+H9    2    0.505962    0.790169    0.974328    11.00000   -1.20000
+AFIX   0
+C10   1    0.608251    0.745408    0.889406    11.00000    0.05646    0.06493 =
+         0.05465   -0.00439   -0.03762   -0.00551
+AFIX  43
+H10   2    0.601092    0.781573    0.836929    11.00000   -1.20000
+AFIX   0
+C11   1    0.676767    0.687677    0.883442    11.00000    0.04308    0.06231 =
+         0.02372   -0.00911   -0.01362   -0.01401
+AFIX  43
+H11   2    0.716748    0.686675    0.827280    11.00000   -1.20000
+AFIX   0
+C12   1    0.684902    0.631946    0.961511    11.00000    0.04753    0.03699 =
+         0.04899   -0.01926   -0.01786    0.00318
+AFIX  43
+H12   2    0.729675    0.592113    0.958404    11.00000   -1.20000
+AFIX   0
+C13   1    0.764166    0.570533    0.957088    11.00000    0.14451    0.07218 =
+         0.08060   -0.05069   -0.04360    0.05040
+AFIX  33
+H13A  2    0.798576    0.575448    0.895498    11.00000   -1.50000
+H13B  2    0.739202    0.514738    0.995401    11.00000   -1.50000
+H13C  2    0.803999    0.583231    0.977614    11.00000   -1.50000
+AFIX   0
+C14   1    0.627656    0.634834    1.043389    11.00000    0.04359    0.04627 =
+         0.02319    0.00134   -0.00588    0.00627
+AFIX  43
+H14   2    0.632949    0.596797    1.096199    11.00000   -1.20000
+AFIX   0
+C15   1    0.562386    0.693858    1.047650    11.00000    0.05258    0.07618 =
+         0.03783   -0.00710   -0.01071    0.01145
+AFIX  43
+H15   2    0.524630    0.696144    1.103707    11.00000   -1.20000
+
+AFIX   0
+HKLF 4
+
+REM  ca05_trunc in P-1
+REM R1 =  0.0387 for   14888 Fo > 4sig(Fo)  and  0.0891 for all   22436 data
+REM    897 parameters refined using     27 restraints
+
+END
+
+WGHT      0.0483      0.0000
+
+REM Highest difference peak  2.625,  deepest hole -2.947,  1-sigma level  0.583
+Q1    1   0.5570  1.1478  0.9079  11.00000  0.05    2.62
+Q2    1  -0.0717  0.9465  0.8020  11.00000  0.05    2.35
+Q3    1   0.4768  1.1258  0.9414  11.00000  0.05    2.29
+Q4    1   0.5205  1.0150  0.9011  11.00000  0.05    2.25
+Q5    1   0.2192  0.9286  0.4472  11.00000  0.05    2.12
+Q6    1   0.6393  1.0328  0.7284  11.00000  0.05    2.12
+Q7    1   0.4434  1.0521  0.9572  11.00000  0.05    2.10
+Q8    1   0.6405  0.9484  0.7500  11.00000  0.05    2.08
+Q9    1   0.6992  1.0026  0.7353  11.00000  0.05    2.06
+Q10   1   0.5639  0.9137  0.9771  11.00000  0.05    2.04
+Q11   1   0.6395  1.0823  0.5582  11.00000  0.05    2.04
+Q12   1   0.6820  0.9831  0.8123  11.00000  0.05    2.01
+Q13   1   0.6994  0.8774  0.8839  11.00000  0.05    2.01
+Q14   1   0.1616  0.9292  0.3949  11.00000  0.05    1.99
+Q15   1   0.5132  0.9007  0.9593  11.00000  0.05    1.92
+Q16   1   0.7975  0.9157  0.5158  11.00000  0.05    1.91
+Q17   1   0.5783  0.8581  0.9558  11.00000  0.05    1.90
+Q18   1   0.6804  1.0623  0.8475  11.00000  0.05    1.90
+Q19   1   0.7036  1.2139  0.5919  11.00000  0.05    1.88
+Q20   1  -0.0764  0.9319  0.5352  11.00000  0.05    1.88
+;
+_shelx_res_checksum              81280
+loop_
+_space_group_symop_operation_xyz
+'x, y, z'
+'-x, -y, -z'
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_U_iso_or_equiv
+_atom_site_adp_type
+_atom_site_occupancy
+_atom_site_site_symmetry_order
+_atom_site_calc_flag
+_atom_site_refinement_flags_posn
+_atom_site_refinement_flags_adp
+_atom_site_refinement_flags_occupancy
+Au1 Au 0.5000 1.0000 0.5000 0.01559(12) Uani 1 2 d S . P
+Au2 Au 0.39635(3) 0.85189(2) 0.61796(3) 0.01907(9) Uani 1 1 d . . .
+Au3 Au 0.42089(3) 0.96788(2) 0.68477(3) 0.01966(9) Uani 1 1 d . . .
+Au4 Au 0.44735(3) 1.13023(2) 0.55684(3) 0.01964(9) Uani 1 1 d . . .
+Au5 Au 0.20467(3) 0.86156(3) 0.59211(3) 0.02264(10) Uani 1 1 d . . .
+Au6 Au 0.77806(3) 0.92738(3) 0.55755(3) 0.02457(10) Uani 1 1 d . . .
+Au7 Au 0.56794(3) 0.86901(2) 0.61051(3) 0.02087(10) Uani 1 1 d . . .
+Au8 Au 0.25920(3) 1.08252(3) 0.72870(3) 0.02614(11) Uani 1 1 d . . .
+Au9 Au 0.61156(3) 1.04428(3) 0.56069(3) 0.02105(10) Uani 1 1 d . . .
+Au10 Au 0.31085(3) 1.00664(3) 0.58114(3) 0.02098(9) Uani 1 1 d . . .
+Au11 Au 0.47387(3) 1.09909(3) 0.72886(3) 0.02508(10) Uani 1 1 d . . .
+Au12 Au 0.42588(3) 0.77284(3) 0.80239(3) 0.02495(10) Uani 1 1 d . . .
+Au13 Au 0.51021(3) 0.69872(2) 0.62775(3) 0.02188(10) Uani 1 1 d . . .
+S14 S 0.27622(18) 0.75597(16) 0.6702(2) 0.0221(6) Uani 1 1 d . . .
+S15 S 0.6304(2) 1.08577(19) 0.6632(2) 0.0291(7) Uani 1 1 d . . .
+S16 S 0.4427(2) 0.64986(17) 0.7841(2) 0.0258(6) Uani 1 1 d . . .
+S20 S 0.12149(19) 0.95902(17) 0.5214(2) 0.0274(7) Uani 1 1 d . . .
+S21 S 0.4105(2) 0.88781(18) 0.8352(2) 0.0311(7) Uani 1 1 d . . .
+S24 S 0.3201(2) 1.10907(17) 0.8108(2) 0.0278(7) Uani 1 1 d . . .
+S25 S 0.1830(2) 1.0740(2) 0.6500(3) 0.0386(8) Uani 1 1 d . . .
+S26 S 0.69559(19) 0.80189(18) 0.6391(2) 0.0265(6) Uani 1 1 d . . .
+S28 S 0.41337(18) 1.27135(16) 0.5253(2) 0.0230(6) Uani 1 1 d . . .
+C1_2001 C 0.3001(8) 1.2205(7) 0.7844(10) 0.035(3) Uani 1 1 d . . .
+H1A_2001 H 0.3144 1.2497 0.7201 0.042 Uiso 1 1 calc R U .
+H1B_2001 H 0.2356 1.2278 0.8182 0.042 Uiso 1 1 calc R U .
+C2_2001 C 0.3592(9) 1.2585(7) 0.8087(10) 0.037(3) Uani 1 1 d . . .
+H2A_2001 H 0.3414 1.2322 0.8738 0.044 Uiso 1 1 calc R U .
+H2B_2001 H 0.4233 1.2473 0.7787 0.044 Uiso 1 1 calc R U .
+C3_2001 C 0.3483(8) 1.3506(7) 0.7805(8) 0.031(3) Uani 1 1 d . . .
+C4_2001 C 0.4235(8) 1.4048(8) 0.7277(7) 0.031(3) Uani 1 1 d . . .
+H4_2001 H 0.4820 1.3846 0.7057 0.037 Uiso 1 1 calc R U .
+C5_2001 C 0.4132(9) 1.4901(7) 0.7067(9) 0.037(3) Uani 1 1 d . . .
+H5_2001 H 0.4642 1.5266 0.6710 0.045 Uiso 1 1 calc R U .
+C6_2001 C 0.3265(10) 1.5190(8) 0.7394(11) 0.048(4) Uani 1 1 d . . .
+H6_2001 H 0.3191 1.5758 0.7240 0.058 Uiso 1 1 calc R U .
+C7_2001 C 0.2503(12) 1.4660(10) 0.7944(16) 0.079(7) Uani 1 1 d . . .
+H7_2001 H 0.1923 1.4866 0.8176 0.095 Uiso 1 1 calc R U .
+C8_2001 C 0.2609(10) 1.3811(10) 0.8151(14) 0.074(7) Uani 1 1 d . . .
+H8_2001 H 0.2097 1.3447 0.8519 0.089 Uiso 1 1 calc R U .
+C1_2002 C 0.6489(10) 0.9868(9) 0.7488(11) 0.051(4) Uani 1 1 d . . .
+H1A_2002 H 0.6109 0.9422 0.7608 0.061 Uiso 1 1 calc R U .
+H1B_2002 H 0.7128 0.9720 0.7253 0.061 Uiso 1 1 calc R U .
+C2_2002 C 0.6225(14) 0.9983(13) 0.8412(14) 0.075(6) Uiso 1 1 d . . .
+H2A_2002 H 0.5561 1.0018 0.8699 0.090 Uiso 1 1 calc R U .
+H2B_2002 H 0.6398 0.9490 0.8822 0.090 Uiso 1 1 calc R U .
+C3_2002 C 0.664(2) 1.0693(16) 0.8311(15) 0.098(8) Uani 1 1 d . . .
+C4_2002 C 0.760(2) 1.0781(17) 0.7928(18) 0.150(14) Uani 1 1 d . . .
+H4_2002 H 0.7947 1.0366 0.7757 0.180 Uiso 1 1 calc R U .
+C5_2002 C 0.808(2) 1.1494(18) 0.778(2) 0.21(2) Uani 1 1 d . . .
+H5_2002 H 0.8720 1.1522 0.7530 0.250 Uiso 1 1 calc R U .
+C6_2002 C 0.759(2) 1.2118(19) 0.802(2) 0.148(13) Uani 1 1 d . . .
+H6_2002 H 0.7882 1.2592 0.7912 0.178 Uiso 1 1 calc R U .
+C7_2002 C 0.662(2) 1.1999(16) 0.8447(17) 0.110(9) Uani 1 1 d . . .
+H7_2002 H 0.6258 1.2384 0.8672 0.132 Uiso 1 1 calc R U .
+C8_2002 C 0.6176(17) 1.1335(12) 0.8540(13) 0.080(7) Uani 1 1 d . . .
+H8_2002 H 0.5537 1.1323 0.8768 0.096 Uiso 1 1 calc R U .
+C1_2003 C 0.4804(7) 1.3188(7) 0.5561(8) 0.027(3) Uani 1 1 d . . .
+H1A_2003 H 0.4657 1.3771 0.5402 0.033 Uiso 1 1 calc R U .
+H1B_2003 H 0.4595 1.2929 0.6217 0.033 Uiso 1 1 calc R U .
+C2_2003 C 0.5838(7) 1.3139(7) 0.5140(8) 0.024(2) Uani 1 1 d . . .
+H2A_2003 H 0.6067 1.3370 0.4482 0.029 Uiso 1 1 calc R U .
+H2B_2003 H 0.6011 1.2563 0.5342 0.029 Uiso 1 1 calc R U .
+C3_2003 C 0.6258(7) 1.3627(8) 0.5424(9) 0.034(3) Uani 1 1 d . . .
+C4_2003 C 0.6344(8) 1.4482(8) 0.4971(10) 0.043(4) Uani 1 1 d . . .
+H4_2003 H 0.6139 1.4740 0.4512 0.051 Uiso 1 1 calc R U .
+C5_2003 C 0.6727(9) 1.4964(10) 0.5184(13) 0.055(5) Uani 1 1 d . . .
+H5_2003 H 0.6786 1.5538 0.4866 0.066 Uiso 1 1 calc R U .
+C6_2003 C 0.7018(11) 1.4585(13) 0.5869(14) 0.066(6) Uani 1 1 d . . .
+H6_2003 H 0.7270 1.4906 0.6022 0.079 Uiso 1 1 calc R U .
+C7_2003 C 0.6941(11) 1.3737(12) 0.6332(12) 0.058(5) Uani 1 1 d . . .
+H7_2003 H 0.7142 1.3481 0.6794 0.069 Uiso 1 1 calc R U .
+C8_2003 C 0.6555(9) 1.3258(10) 0.6098(10) 0.041(4) Uani 1 1 d . . .
+H8_2003 H 0.6503 1.2682 0.6409 0.050 Uiso 1 1 calc R U .
+C1_2004 C 0.2974(10) 0.8818(8) 0.9271(9) 0.043(4) Uani 1 1 d . . .
+H1A_2004 H 0.2990 0.8414 0.9838 0.052 Uiso 1 1 calc R U .
+H1B_2004 H 0.2860 0.9354 0.9315 0.052 Uiso 1 1 calc R U .
+C2_2004 C 0.2225(11) 0.8600(10) 0.9187(13) 0.057(4) Uani 1 1 d . . .
+H2A_2004 H 0.2322 0.8064 0.9144 0.068 Uiso 1 1 calc R U .
+H2B_2004 H 0.2177 0.9010 0.8638 0.068 Uiso 1 1 calc R U .
+C3_2004 C 0.1307(11) 0.8558(10) 1.0046(12) 0.064(5) Uani 1 1 d . . .
+C4_2004 C 0.1207(15) 0.7939(11) 1.0897(15) 0.118(10) Uani 1 1 d . . .
+H4_2004 H 0.1685 0.7580 1.0942 0.142 Uiso 1 1 calc R U .
+C5_2004 C 0.0380(17) 0.7850(15) 1.170(2) 0.27(3) Uani 1 1 d . . .
+H5_2004 H 0.0324 0.7438 1.2259 0.323 Uiso 1 1 calc R U .
+C6_2004 C -0.0291(14) 0.8350(13) 1.1638(18) 0.096(8) Uani 1 1 d . . .
+H6_2004 H -0.0840 0.8308 1.2142 0.115 Uiso 1 1 calc R U .
+C7_2004 C -0.0153(15) 0.8886(17) 1.0864(19) 0.132(12) Uani 1 1 d . . .
+H7_2004 H -0.0628 0.9248 1.0820 0.158 Uiso 1 1 calc R U .
+C8_2004 C 0.0636(15) 0.9013(15) 1.0047(18) 0.151(14) Uani 1 1 d . . .
+H8_2004 H 0.0656 0.9438 0.9506 0.181 Uiso 1 1 calc R U .
+C1_2005 C 0.2073(7) 0.7326(7) 0.7909(8) 0.025(3) Uani 1 1 d . . .
+H1A_2005 H 0.2410 0.6972 0.8260 0.030 Uiso 1 1 calc R U .
+H1B_2005 H 0.1948 0.7838 0.8008 0.030 Uiso 1 1 calc R U .
+C2_2005 C 0.1169(9) 0.6887(9) 0.8222(10) 0.047(4) Uani 1 1 d . . .
+H2A_2005 H 0.0796 0.7268 0.7930 0.056 Uiso 1 1 calc R U .
+H2B_2005 H 0.1293 0.6417 0.8050 0.056 Uiso 1 1 calc R U .
+C3_2005 C 0.0655(8) 0.6590(10) 0.9247(10) 0.050(4) Uani 1 1 d . . .
+C4_2005 C 0.0182(9) 0.7153(14) 0.9644(15) 0.21(2) Uani 1 1 d . . .
+H4_2005 H 0.0144 0.7700 0.9268 0.248 Uiso 1 1 calc R U .
+C5_2005 C -0.0234(11) 0.6918(13) 1.0584(15) 0.089(7) Uani 1 1 d . . .
+H5_2005 H -0.0545 0.7294 1.0845 0.107 Uiso 1 1 calc R U .
+C6_2005 C -0.0154(10) 0.6071(12) 1.1122(12) 0.069(5) Uani 1 1 d . . .
+H6_2005 H -0.0423 0.5881 1.1753 0.083 Uiso 1 1 calc R U .
+C7_2005 C 0.0313(10) 0.5535(10) 1.0723(11) 0.055(4) Uani 1 1 d . . .
+H7_2005 H 0.0368 0.4982 1.1074 0.065 Uiso 1 1 calc R U .
+C8_2005 C 0.0683(10) 0.5818(9) 0.9830(11) 0.057(5) Uani 1 1 d . . .
+H8_2005 H 0.0998 0.5439 0.9577 0.068 Uiso 1 1 calc R U .
+C1_2006 C 0.5368(9) 0.6019(7) 0.8166(10) 0.034(3) Uani 1 1 d . . .
+H1A_2006 H 0.5862 0.6431 0.7877 0.041 Uiso 1 1 calc R U .
+H1B_2006 H 0.5152 0.5826 0.8819 0.041 Uiso 1 1 calc R U .
+C2_2006 C 0.5733(8) 0.5295(7) 0.7888(9) 0.030(3) Uani 1 1 d . . .
+H2A_2006 H 0.5975 0.5493 0.7231 0.036 Uiso 1 1 calc R U .
+H2B_2006 H 0.5234 0.4895 0.8154 0.036 Uiso 1 1 calc R U .
+C3_2006 C 0.6492(9) 0.4869(7) 0.8197(10) 0.035(3) Uani 1 1 d . . .
+C4_2006 C 0.6300(11) 0.4247(8) 0.9035(11) 0.056(5) Uani 1 1 d . . .
+H4_2006 H 0.5687 0.4090 0.9432 0.067 Uiso 1 1 calc R U .
+C5_2006 C 0.6975(16) 0.3841(12) 0.9320(17) 0.096(8) Uani 1 1 d . . .
+H5_2006 H 0.6829 0.3415 0.9894 0.115 Uiso 1 1 calc R U .
+C6_2006 C 0.7849(15) 0.4085(12) 0.874(2) 0.091(8) Uani 1 1 d . . .
+H6_2006 H 0.8314 0.3825 0.8919 0.109 Uiso 1 1 calc R U .
+C7_2006 C 0.8091(11) 0.4708(13) 0.7872(16) 0.073(6) Uani 1 1 d . . .
+H7_2006 H 0.8705 0.4860 0.7476 0.088 Uiso 1 1 calc R U .
+C8_2006 C 0.7385(9) 0.5100(10) 0.7614(11) 0.045(4) Uani 1 1 d . . .
+H8_2006 H 0.7526 0.5523 0.7039 0.054 Uiso 1 1 calc R U .
+C1_2007 C 0.0889(10) 0.9760(15) 0.7464(15) 0.084(8) Uani 1 1 d . . .
+H1A_2007 H 0.1049 0.9258 0.7347 0.101 Uiso 1 1 calc R U .
+H1B_2007 H 0.0790 0.9641 0.8082 0.101 Uiso 1 1 calc R U .
+C2_2007 C 0.019(2) 1.0139(13) 0.7270(18) 0.128(12) Uani 1 1 d . . .
+H2A_2007 H 0.0275 1.0245 0.6660 0.154 Uiso 1 1 calc R U .
+H2B_2007 H 0.0025 1.0642 0.7384 0.154 Uiso 1 1 calc R U .
+C3_2007 C -0.0547(17) 0.9297(15) 0.8102(14) 0.163(16) Uani 1 1 d . . .
+C4_2007 C -0.1119(14) 0.9247(13) 0.8961(12) 0.160(16) Uani 1 1 d . . .
+H4_2007 H -0.0995 0.9598 0.9169 0.192 Uiso 1 1 calc R U .
+C5_2007 C -0.1829(12) 0.8729(11) 0.9503(10) 0.069(6) Uani 1 1 d . . .
+H5_2007 H -0.2193 0.8710 1.0085 0.083 Uiso 1 1 calc R U .
+C6_2007 C -0.2029(10) 0.8227(11) 0.9214(12) 0.059(5) Uani 1 1 d . . .
+H6_2007 H -0.2550 0.7874 0.9586 0.070 Uiso 1 1 calc R U .
+C7_2007 C -0.1480(10) 0.8233(11) 0.8387(13) 0.061(5) Uani 1 1 d . . .
+H7_2007 H -0.1609 0.7868 0.8198 0.073 Uiso 1 1 calc R U .
+C8_2007 C -0.0738(12) 0.8767(10) 0.7826(12) 0.062(5) Uani 1 1 d . . .
+H8_2007 H -0.0362 0.8770 0.7254 0.075 Uiso 1 1 calc R U .
+C1_2008 C 0.1197(8) 0.9267(7) 0.4370(8) 0.025(2) Uiso 1 1 d . . .
+H1A_2008 H 0.1108 0.9750 0.3888 0.031 Uiso 1 1 calc R U .
+H1B_2008 H 0.1786 0.9041 0.4102 0.031 Uiso 1 1 calc R U .
+C2_2008 C 0.0442(8) 0.8622(7) 0.4783(10) 0.033(3) Uani 1 1 d . . .
+H2A_2008 H -0.0140 0.8849 0.5064 0.039 Uiso 1 1 calc R U .
+H2B_2008 H 0.0419 0.8527 0.4295 0.039 Uiso 1 1 calc R U .
+C3_2008 C 0.0529(8) 0.7795(8) 0.5480(10) 0.032(3) Uani 1 1 d . . .
+C4_2008 C 0.1264(9) 0.7297(7) 0.5232(10) 0.036(3) Uani 1 1 d . . .
+H4_2008 H 0.1724 0.7487 0.4643 0.043 Uiso 1 1 calc R U .
+C5_2008 C 0.1309(8) 0.6512(8) 0.5868(10) 0.041(4) Uani 1 1 d . . .
+H5_2008 H 0.1804 0.6182 0.5702 0.049 Uiso 1 1 calc R U .
+C6_2008 C 0.0635(9) 0.6221(8) 0.6735(11) 0.043(4) Uani 1 1 d . . .
+H6_2008 H 0.0657 0.5692 0.7156 0.051 Uiso 1 1 calc R U .
+C7_2008 C -0.0077(10) 0.6731(10) 0.6969(11) 0.049(4) Uani 1 1 d . . .
+H7_2008 H -0.0533 0.6543 0.7561 0.059 Uiso 1 1 calc R U .
+C8_2008 C -0.0135(8) 0.7507(8) 0.6356(9) 0.034(3) Uani 1 1 d . . .
+H8_2008 H -0.0624 0.7839 0.6534 0.041 Uiso 1 1 calc R U .
+C1_2009 C 0.7412(7) 0.7476(7) 0.5614(9) 0.026(3) Uani 1 1 d . . .
+H1A_2009 H 0.7077 0.6949 0.5901 0.032 Uiso 1 1 calc R U .
+H1B_2009 H 0.7326 0.7809 0.5062 0.032 Uiso 1 1 calc R U .
+C2_2009 C 0.8416(8) 0.7325(8) 0.5380(10) 0.032(3) Uani 1 1 d . . .
+H2A_2009 H 0.8501 0.7027 0.5938 0.039 Uiso 1 1 calc R U .
+H2B_2009 H 0.8749 0.7856 0.5063 0.039 Uiso 1 1 calc R U .
+C3_2009 C 0.8818(8) 0.6832(7) 0.4793(10) 0.034(3) Uani 1 1 d . . .
+C4_2009 C 0.9631(11) 0.6465(10) 0.4728(13) 0.079(7) Uani 1 1 d . . .
+H4_2009 H 0.9927 0.6524 0.5046 0.094 Uiso 1 1 calc R U .
+C5_2009 C 1.0031(13) 0.6008(14) 0.4208(17) 0.129(12) Uani 1 1 d . . .
+H5_2009 H 1.0601 0.5779 0.4158 0.155 Uiso 1 1 calc R U .
+C6_2009 C 0.9587(12) 0.5888(14) 0.3760(17) 0.104(9) Uani 1 1 d . . .
+H6_2009 H 0.9831 0.5538 0.3453 0.125 Uiso 1 1 calc R U .
+C7_2009 C 0.8802(10) 0.6274(11) 0.3763(13) 0.061(5) Uani 1 1 d . . .
+H7_2009 H 0.8527 0.6225 0.3424 0.073 Uiso 1 1 calc R U .
+C8_2009 C 0.8405(10) 0.6749(9) 0.4283(11) 0.047(4) Uani 1 1 d . . .
+H8_2009 H 0.7859 0.7015 0.4292 0.056 Uiso 1 1 calc R U .
+C9_2010 C 0.5508(10) 0.7504(12) 0.9708(11) 0.066(5) Uani 1 1 d . . .
+H9_2010 H 0.5060 0.7902 0.9743 0.079 Uiso 1 1 calc R U .
+C10_2010 C 0.6083(11) 0.7454(11) 0.8894(12) 0.059(5) Uani 1 1 d . . .
+H10_2010 H 0.6011 0.7816 0.8369 0.071 Uiso 1 1 calc R U .
+C11_2010 C 0.6768(10) 0.6877(10) 0.8834(10) 0.044(4) Uani 1 1 d . . .
+H11_2010 H 0.7167 0.6867 0.8273 0.053 Uiso 1 1 calc R U .
+C12_2010 C 0.6849(10) 0.6319(9) 0.9615(11) 0.045(4) Uani 1 1 d . . .
+H12_2010 H 0.7297 0.5921 0.9584 0.054 Uiso 1 1 calc R U .
+C13_2010 C 0.7642(16) 0.5705(13) 0.9571(15) 0.099(8) Uani 1 1 d . . .
+H13A_2010 H 0.7986 0.5754 0.8955 0.148 Uiso 1 1 calc R U .
+H13B_2010 H 0.7392 0.5147 0.9954 0.148 Uiso 1 1 calc R U .
+H13C_2010 H 0.8040 0.5832 0.9776 0.148 Uiso 1 1 calc R U .
+C14_2010 C 0.6277(10) 0.6348(9) 1.0434(10) 0.047(4) Uani 1 1 d . . .
+H14_2010 H 0.6329 0.5968 1.0962 0.057 Uiso 1 1 calc R U .
+C15_2010 C 0.5624(11) 0.6939(11) 1.0476(12) 0.066(5) Uani 1 1 d . . .
+H15_2010 H 0.5246 0.6961 1.1037 0.079 Uiso 1 1 calc R U .
+loop_
+_atom_site_aniso_label
+_atom_site_aniso_U_11
+_atom_site_aniso_U_22
+_atom_site_aniso_U_33
+_atom_site_aniso_U_23
+_atom_site_aniso_U_13
+_atom_site_aniso_U_12
+Au1 0.0123(2) 0.0097(2) 0.0202(3) -0.0058(2) -0.0025(2) -0.00132(19)
+Au2 0.01516(19) 0.01120(18) 0.0251(2) -0.00534(17) -0.00459(17) -0.00192(14)
+Au3 0.0201(2) 0.01277(18) 0.0215(2) -0.00665(17) -0.00453(17) -0.00044(15)
+Au4 0.0198(2) 0.01100(18) 0.0234(2) -0.00752(17) -0.00432(17) 0.00022(15)
+Au5 0.0181(2) 0.0164(2) 0.0326(3) -0.00846(19) -0.01056(19) -0.00112(16)
+Au6 0.0191(2) 0.0176(2) 0.0404(3) -0.0124(2) -0.0152(2) 0.00265(16)
+Au7 0.01708(19) 0.01288(19) 0.0291(2) -0.00627(17) -0.00880(18) 0.00120(15)
+Au8 0.0222(2) 0.0185(2) 0.0318(3) -0.0147(2) -0.00051(19) -0.00338(17)
+Au9 0.01737(19) 0.0170(2) 0.0290(2) -0.01097(18) -0.00794(18) 0.00042(16)
+Au10 0.01506(19) 0.0175(2) 0.0255(2) -0.00949(18) -0.00397(17) 0.00201(15)
+Au11 0.0299(2) 0.0181(2) 0.0264(2) -0.01029(19) -0.0094(2) 0.00016(17)
+Au12 0.0255(2) 0.0151(2) 0.0291(3) -0.00556(18) -0.0100(2) 0.00070(17)
+Au13 0.0232(2) 0.01130(18) 0.0311(3) -0.00649(18) -0.01302(19) 0.00043(16)
+S14 0.0188(13) 0.0146(12) 0.0305(16) -0.0077(12) -0.0083(12) -0.0029(10)
+S15 0.0324(16) 0.0260(15) 0.0343(18) -0.0124(14) -0.0182(14) 0.0021(12)
+S16 0.0258(14) 0.0132(12) 0.0339(17) -0.0030(12) -0.0142(13) -0.0008(11)
+S20 0.0202(13) 0.0177(13) 0.0452(19) -0.0116(13) -0.0157(14) 0.0020(11)
+S21 0.0420(18) 0.0177(14) 0.0249(16) -0.0049(12) -0.0091(14) -0.0017(13)
+S24 0.0338(16) 0.0150(13) 0.0284(17) -0.0112(12) -0.0037(13) -0.0033(12)
+S25 0.0178(14) 0.048(2) 0.058(2) -0.0380(19) -0.0085(15) 0.0080(13)
+S26 0.0202(14) 0.0205(14) 0.0391(18) -0.0101(13) -0.0146(13) 0.0015(11)
+S28 0.0191(13) 0.0149(12) 0.0361(17) -0.0123(12) -0.0107(12) 0.0016(10)
+C1_2001 0.024(6) 0.022(6) 0.046(8) -0.020(6) 0.004(6) -0.003(5)
+C2_2001 0.038(7) 0.023(6) 0.048(9) -0.023(6) -0.004(6) -0.012(5)
+C3_2001 0.029(6) 0.026(6) 0.040(8) -0.018(6) -0.010(6) -0.001(5)
+C4_2001 0.031(6) 0.039(7) 0.022(7) -0.017(6) -0.003(5) -0.010(5)
+C5_2001 0.044(8) 0.018(6) 0.037(8) -0.005(6) -0.008(6) -0.011(5)
+C6_2001 0.058(9) 0.019(6) 0.084(12) -0.028(8) -0.040(9) 0.010(6)
+C7_2001 0.050(10) 0.052(10) 0.17(2) -0.076(14) -0.056(13) 0.021(8)
+C8_2001 0.029(8) 0.047(10) 0.145(19) -0.062(12) -0.014(10) 0.001(7)
+C1_2002 0.045(9) 0.046(9) 0.062(11) -0.015(8) -0.026(8) -0.004(7)
+C3_2002 0.14(2) 0.103(19) 0.083(17) -0.053(15) -0.079(17) 0.055(17)
+C4_2002 0.12(2) 0.20(3) 0.26(4) -0.20(3) -0.11(3) 0.06(2)
+C5_2002 0.10(2) 0.28(4) 0.39(6) -0.31(5) -0.07(3) 0.04(2)
+C6_2002 0.16(3) 0.16(3) 0.17(3) -0.13(3) -0.04(3) 0.00(2)
+C7_2002 0.13(2) 0.11(2) 0.11(2) -0.082(18) -0.049(19) 0.051(18)
+C8_2002 0.119(18) 0.064(13) 0.060(13) 0.001(10) -0.050(13) -0.040(12)
+C1_2003 0.026(6) 0.023(6) 0.030(7) -0.013(5) -0.005(5) -0.007(5)
+C2_2003 0.025(6) 0.019(5) 0.027(6) -0.008(5) -0.010(5) -0.003(4)
+C3_2003 0.013(5) 0.044(8) 0.044(8) -0.027(7) 0.000(5) -0.007(5)
+C4_2003 0.034(7) 0.035(7) 0.067(10) -0.037(8) -0.010(7) -0.004(6)
+C5_2003 0.035(8) 0.058(10) 0.098(14) -0.056(11) -0.026(9) 0.006(7)
+C6_2003 0.042(9) 0.092(15) 0.096(15) -0.081(13) -0.018(10) 0.014(9)
+C7_2003 0.051(10) 0.084(13) 0.068(12) -0.051(11) -0.036(9) 0.017(9)
+C8_2003 0.031(7) 0.061(10) 0.052(9) -0.039(8) -0.021(7) 0.011(7)
+C1_2004 0.068(10) 0.023(6) 0.026(7) -0.008(6) -0.009(7) 0.002(6)
+C2_2004 0.060(10) 0.038(9) 0.083(13) -0.030(9) -0.033(10) 0.002(7)
+C3_2004 0.049(10) 0.042(9) 0.066(13) -0.008(9) -0.007(9) -0.005(8)
+C4_2004 0.14(2) 0.050(12) 0.095(19) -0.031(13) 0.004(16) 0.029(13)
+C5_2004 0.12(2) 0.068(18) 0.29(5) -0.01(2) 0.14(3) -0.013(17)
+C6_2004 0.065(13) 0.057(13) 0.12(2) -0.039(14) 0.009(14) -0.001(11)
+C7_2004 0.11(2) 0.13(2) 0.10(2) -0.07(2) 0.027(17) 0.030(18)
+C8_2004 0.15(2) 0.10(2) 0.11(2) -0.055(18) 0.016(18) 0.069(19)
+C1_2005 0.012(5) 0.030(6) 0.032(7) -0.012(5) -0.007(5) -0.001(4)
+C2_2005 0.026(7) 0.040(8) 0.049(9) 0.008(7) -0.014(7) -0.010(6)
+C3_2005 0.020(6) 0.055(9) 0.045(9) 0.004(8) -0.005(6) -0.014(6)
+C4_2005 0.112(19) 0.13(2) 0.11(2) 0.028(17) 0.089(17) 0.081(17)
+C5_2005 0.082(14) 0.077(15) 0.089(17) -0.053(14) -0.001(12) 0.006(12)
+C6_2005 0.060(11) 0.073(13) 0.038(10) -0.006(9) -0.002(9) -0.008(10)
+C7_2005 0.078(12) 0.040(9) 0.038(9) -0.004(7) -0.027(9) -0.002(8)
+C8_2005 0.108(14) 0.028(7) 0.042(10) -0.015(7) -0.036(10) 0.000(8)
+C1_2006 0.043(7) 0.017(6) 0.044(8) -0.006(6) -0.027(7) 0.004(5)
+C2_2006 0.031(6) 0.026(6) 0.033(7) -0.016(6) -0.011(6) 0.008(5)
+C3_2006 0.034(7) 0.024(6) 0.051(9) -0.012(6) -0.027(7) 0.010(5)
+C4_2006 0.056(10) 0.041(9) 0.057(11) 0.013(8) -0.040(9) -0.013(7)
+C5_2006 0.113(18) 0.056(12) 0.14(2) -0.007(13) -0.104(19) 0.001(12)
+C6_2006 0.088(15) 0.050(12) 0.19(3) -0.050(15) -0.112(19) 0.036(11)
+C7_2006 0.031(8) 0.094(16) 0.121(19) -0.073(15) -0.025(10) 0.006(9)
+C8_2006 0.034(7) 0.053(9) 0.061(11) -0.036(8) -0.020(7) 0.009(7)
+C1_2007 0.029(8) 0.17(2) 0.111(17) -0.120(18) -0.033(10) 0.048(11)
+C2_2007 0.26(4) 0.062(14) 0.12(2) -0.050(15) -0.14(3) 0.080(19)
+C3_2007 0.19(3) 0.18(3) 0.062(15) -0.057(17) 0.065(16) -0.17(2)
+C4_2007 0.17(2) 0.22(3) 0.059(14) -0.091(18) 0.074(15) -0.16(2)
+C5_2007 0.075(12) 0.092(14) 0.019(8) -0.022(9) 0.011(8) -0.034(11)
+C6_2007 0.030(8) 0.076(12) 0.073(13) -0.045(11) -0.007(8) -0.004(8)
+C7_2007 0.035(8) 0.077(12) 0.085(14) -0.056(11) -0.013(9) -0.001(8)
+C8_2007 0.075(12) 0.058(11) 0.047(10) -0.027(9) -0.005(9) -0.022(9)
+C2_2008 0.025(6) 0.024(6) 0.060(9) -0.021(6) -0.025(6) 0.005(5)
+C3_2008 0.020(6) 0.031(7) 0.051(9) -0.019(6) -0.016(6) 0.001(5)
+C4_2008 0.034(7) 0.025(6) 0.044(8) -0.012(6) -0.014(6) 0.000(5)
+C5_2008 0.026(6) 0.024(6) 0.067(11) -0.015(7) -0.017(7) 0.002(5)
+C6_2008 0.034(7) 0.029(7) 0.056(10) -0.004(7) -0.021(7) -0.005(6)
+C7_2008 0.037(8) 0.058(10) 0.042(9) -0.015(8) -0.009(7) -0.011(7)
+C8_2008 0.023(6) 0.044(8) 0.038(8) -0.024(7) -0.007(6) -0.002(6)
+C1_2009 0.021(6) 0.019(6) 0.033(7) -0.007(5) -0.008(5) -0.004(4)
+C2_2009 0.020(6) 0.033(7) 0.048(8) -0.020(6) -0.013(6) 0.001(5)
+C3_2009 0.016(5) 0.026(6) 0.063(10) -0.029(7) -0.008(6) 0.000(5)
+C4_2009 0.048(10) 0.102(15) 0.14(2) -0.097(16) -0.049(12) 0.038(10)
+C5_2009 0.061(14) 0.18(3) 0.22(3) -0.16(3) -0.069(19) 0.066(17)
+C6_2009 0.046(11) 0.13(2) 0.18(3) -0.14(2) -0.031(14) 0.035(12)
+C7_2009 0.039(9) 0.069(11) 0.077(13) -0.046(11) -0.008(9) -0.003(8)
+C8_2009 0.036(8) 0.044(9) 0.068(11) -0.034(8) -0.018(8) 0.006(6)
+C9_2010 0.034(8) 0.094(14) 0.035(9) -0.001(9) -0.012(7) 0.010(9)
+C10_2010 0.056(10) 0.065(11) 0.055(11) -0.004(9) -0.038(9) -0.006(9)
+C11_2010 0.043(8) 0.062(10) 0.024(7) -0.009(7) -0.014(6) -0.014(7)
+C12_2010 0.048(8) 0.037(8) 0.049(10) -0.019(7) -0.018(8) 0.003(7)
+C13_2010 0.14(2) 0.072(14) 0.081(16) -0.051(13) -0.044(15) 0.050(14)
+C14_2010 0.044(8) 0.046(9) 0.023(7) 0.001(6) -0.006(6) 0.006(7)
+C15_2010 0.053(10) 0.076(13) 0.038(10) -0.007(9) -0.011(8) 0.011(9)
+loop_
+_atom_type_symbol
+_atom_type_description
+_atom_type_scat_dispersion_real
+_atom_type_scat_dispersion_imag
+_atom_type_scat_source
+C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+S S 0.1246 0.1234 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+Au Au -2.0133 8.8022 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+loop_
+_geom_angle_atom_site_label_1
+_geom_angle_atom_site_label_2
+_geom_angle_atom_site_label_3
+_geom_angle
+_geom_angle_site_symmetry_1
+_geom_angle_site_symmetry_3
+Au10 Au1 Au10 180.0 . 2_676
+Au10 Au1 Au4 68.67(3) . .
+Au10 Au1 Au4 111.33(3) 2_676 .
+Au10 Au1 Au4 111.34(3) . 2_676
+Au10 Au1 Au4 68.67(3) 2_676 2_676
+Au4 Au1 Au4 180.0 . 2_676
+Au10 Au1 Au7 67.61(4) . 2_676
+Au10 Au1 Au7 112.39(4) 2_676 2_676
+Au4 Au1 Au7 67.73(2) . 2_676
+Au4 Au1 Au7 112.27(2) 2_676 2_676
+Au10 Au1 Au7 112.39(4) . .
+Au10 Au1 Au7 67.61(4) 2_676 .
+Au4 Au1 Au7 112.27(2) . .
+Au4 Au1 Au7 67.73(2) 2_676 .
+Au7 Au1 Au7 180.0 2_676 .
+Au10 Au1 Au2 118.79(4) . 2_676
+Au10 Au1 Au2 61.21(4) 2_676 2_676
+Au4 Au1 Au2 64.13(3) . 2_676
+Au4 Au1 Au2 115.87(3) 2_676 2_676
+Au7 Au1 Au2 59.91(3) 2_676 2_676
+Au7 Au1 Au2 120.09(3) . 2_676
+Au10 Au1 Au2 61.21(4) . .
+Au10 Au1 Au2 118.79(4) 2_676 .
+Au4 Au1 Au2 115.88(3) . .
+Au4 Au1 Au2 64.12(3) 2_676 .
+Au7 Au1 Au2 120.09(3) 2_676 .
+Au7 Au1 Au2 59.91(3) . .
+Au2 Au1 Au2 180.0 2_676 .
+Au10 Au1 Au3 63.35(3) . .
+Au10 Au1 Au3 116.65(3) 2_676 .
+Au4 Au1 Au3 59.71(3) . .
+Au4 Au1 Au3 120.29(3) 2_676 .
+Au7 Au1 Au3 117.28(3) 2_676 .
+Au7 Au1 Au3 62.72(3) . .
+Au2 Au1 Au3 116.66(3) 2_676 .
+Au2 Au1 Au3 63.34(3) . .
+Au10 Au1 Au3 116.65(3) . 2_676
+Au10 Au1 Au3 63.35(4) 2_676 2_676
+Au4 Au1 Au3 120.29(3) . 2_676
+Au4 Au1 Au3 59.70(3) 2_676 2_676
+Au7 Au1 Au3 62.72(3) 2_676 2_676
+Au7 Au1 Au3 117.28(3) . 2_676
+Au2 Au1 Au3 63.35(4) 2_676 2_676
+Au2 Au1 Au3 116.65(4) . 2_676
+Au3 Au1 Au3 179.999(18) . 2_676
+Au10 Au1 Au9 59.20(2) . 2_676
+Au10 Au1 Au9 120.81(2) 2_676 2_676
+Au4 Au1 Au9 118.41(2) . 2_676
+Au4 Au1 Au9 61.59(2) 2_676 2_676
+Au7 Au1 Au9 63.92(2) 2_676 2_676
+Au7 Au1 Au9 116.08(2) . 2_676
+Au2 Au1 Au9 115.69(3) 2_676 2_676
+Au2 Au1 Au9 64.31(3) . 2_676
+Au3 Au1 Au9 115.07(3) . 2_676
+Au3 Au1 Au9 64.92(3) 2_676 2_676
+Au10 Au1 Au9 120.80(2) . .
+Au10 Au1 Au9 59.19(2) 2_676 .
+Au4 Au1 Au9 61.59(2) . .
+Au4 Au1 Au9 118.41(2) 2_676 .
+Au7 Au1 Au9 116.09(2) 2_676 .
+Au7 Au1 Au9 63.92(2) . .
+Au2 Au1 Au9 64.31(3) 2_676 .
+Au2 Au1 Au9 115.69(3) . .
+Au3 Au1 Au9 64.93(3) . .
+Au3 Au1 Au9 115.08(3) 2_676 .
+Au9 Au1 Au9 180.0 2_676 .
+S14 Au2 Au7 144.92(7) . .
+S14 Au2 Au1 153.26(8) . .
+Au7 Au2 Au1 59.93(3) . .
+S14 Au2 Au10 103.07(7) . .
+Au7 Au2 Au10 110.50(3) . .
+Au1 Au2 Au10 58.95(3) . .
+S14 Au2 Au3 133.63(7) . .
+Au7 Au2 Au3 60.96(3) . .
+Au1 Au2 Au3 58.34(2) . .
+Au10 Au2 Au3 60.85(2) . .
+S14 Au2 Au4 115.94(8) . 2_676
+Au7 Au2 Au4 65.30(3) . 2_676
+Au1 Au2 Au4 57.77(4) . 2_676
+Au10 Au2 Au4 104.63(4) . 2_676
+Au3 Au2 Au4 110.31(3) . 2_676
+S14 Au2 Au9 95.68(8) . 2_676
+Au7 Au2 Au9 110.94(4) . 2_676
+Au1 Au2 Au9 58.31(3) . 2_676
+Au10 Au2 Au9 56.57(3) . 2_676
+Au3 Au2 Au9 106.28(3) . 2_676
+Au4 Au2 Au9 57.69(3) 2_676 2_676
+S14 Au2 Au13 82.36(7) . .
+Au7 Au2 Au13 65.73(3) . .
+Au1 Au2 Au13 113.39(3) . .
+Au10 Au2 Au13 171.15(2) . .
+Au3 Au2 Au13 120.29(2) . .
+Au4 Au2 Au13 66.56(4) 2_676 .
+Au9 Au2 Au13 116.39(3) 2_676 .
+S14 Au2 Au12 95.30(8) . .
+Au7 Au2 Au12 60.76(4) . .
+Au1 Au2 Au12 110.30(3) . .
+Au10 Au2 Au12 116.85(3) . .
+Au3 Au2 Au12 62.97(3) . .
+Au4 Au2 Au12 120.04(3) 2_676 .
+Au9 Au2 Au12 168.352(18) 2_676 .
+Au13 Au2 Au12 69.01(3) . .
+S14 Au2 Au5 44.36(7) . .
+Au7 Au2 Au5 169.67(2) . .
+Au1 Au2 Au5 110.07(3) . .
+Au10 Au2 Au5 62.62(3) . .
+Au3 Au2 Au5 117.32(3) . .
+Au4 Au2 Au5 107.92(3) 2_676 .
+Au9 Au2 Au5 59.08(4) 2_676 .
+Au13 Au2 Au5 119.83(3) . .
+Au12 Au2 Au5 128.62(3) . .
+S21 Au3 Au4 141.17(8) . .
+S21 Au3 Au1 150.50(8) . .
+Au4 Au3 Au1 59.95(3) . .
+S21 Au3 Au7 91.98(8) . .
+Au4 Au3 Au7 109.00(4) . .
+Au1 Au3 Au7 58.52(3) . .
+S21 Au3 Au10 139.98(8) . .
+Au4 Au3 Au10 66.62(3) . .
+Au1 Au3 Au10 57.89(2) . .
+Au7 Au3 Au10 104.82(3) . .
+S21 Au3 Au2 107.14(8) . .
+Au4 Au3 Au2 111.69(3) . .
+Au1 Au3 Au2 58.32(3) . .
+Au7 Au3 Au2 57.01(2) . .
+Au10 Au3 Au2 57.85(2) . .
+S21 Au3 Au9 109.92(9) . .
+Au4 Au3 Au9 59.25(4) . .
+Au1 Au3 Au9 57.99(3) . .
+Au7 Au3 Au9 60.18(3) . .
+Au10 Au3 Au9 109.96(3) . .
+Au2 Au3 Au9 106.11(3) . .
+S21 Au3 Au8 98.77(8) . .
+Au4 Au3 Au8 64.51(4) . .
+Au1 Au3 Au8 110.62(4) . .
+Au7 Au3 Au8 168.52(2) . .
+Au10 Au3 Au8 64.18(3) . .
+Au2 Au3 Au8 115.27(3) . .
+Au9 Au3 Au8 118.89(3) . .
+S21 Au3 Au11 78.10(8) . .
+Au4 Au3 Au11 63.40(2) . .
+Au1 Au3 Au11 113.81(4) . .
+Au7 Au3 Au11 116.72(3) . .
+Au10 Au3 Au11 122.48(3) . .
+Au2 Au3 Au11 171.35(2) . .
+Au9 Au3 Au11 65.35(3) . .
+Au8 Au3 Au11 69.87(2) . .
+S21 Au3 Au12 45.63(8) . .
+Au4 Au3 Au12 168.63(2) . .
+Au1 Au3 Au12 110.14(4) . .
+Au7 Au3 Au12 59.64(4) . .
+Au10 Au3 Au12 114.09(3) . .
+Au2 Au3 Au12 62.79(2) . .
+Au9 Au3 Au12 111.53(4) . .
+Au8 Au3 Au12 126.56(4) . .
+Au11 Au3 Au12 120.59(3) . .
+S28 Au4 Au3 148.05(8) . .
+S28 Au4 Au1 149.75(8) . .
+Au3 Au4 Au1 60.34(2) . .
+S28 Au4 Au9 130.59(7) . .
+Au3 Au4 Au9 64.51(4) . .
+Au1 Au4 Au9 59.87(2) . .
+S28 Au4 Au2 99.32(9) . 2_676
+Au3 Au4 Au2 111.94(4) . 2_676
+Au1 Au4 Au2 58.10(3) . 2_676
+Au9 Au4 Au2 61.65(3) . 2_676
+S28 Au4 Au11 94.71(8) . .
+Au3 Au4 Au11 63.36(3) . .
+Au1 Au4 Au11 114.09(3) . .
+Au9 Au4 Au11 67.02(3) . .
+Au2 Au4 Au11 122.47(3) 2_676 .
+S28 Au4 Au7 94.97(8) . 2_676
+Au3 Au4 Au7 108.16(3) . 2_676
+Au1 Au4 Au7 56.19(3) . 2_676
+Au9 Au4 Au7 105.56(3) . 2_676
+Au2 Au4 Au7 54.65(2) 2_676 2_676
+Au11 Au4 Au7 170.263(18) . 2_676
+S28 Au4 Au10 120.96(7) . .
+Au3 Au4 Au10 58.90(3) . .
+Au1 Au4 Au10 55.44(2) . .
+Au9 Au4 Au10 108.12(2) . .
+Au2 Au4 Au10 103.56(4) 2_676 .
+Au11 Au4 Au10 115.77(4) . .
+Au7 Au4 Au10 59.43(4) 2_676 .
+S28 Au4 Au8 88.71(8) . .
+Au3 Au4 Au8 62.56(4) . .
+Au1 Au4 Au8 109.41(4) . .
+Au9 Au4 Au8 121.86(3) . .
+Au2 Au4 Au8 164.78(2) 2_676 .
+Au11 Au4 Au8 69.18(3) . .
+Au7 Au4 Au8 112.08(3) 2_676 .
+Au10 Au4 Au8 61.26(3) . .
+S28 Au4 Au13 44.50(8) . 2_676
+Au3 Au4 Au13 166.48(2) . 2_676
+Au1 Au4 Au13 106.33(3) . 2_676
+Au9 Au4 Au13 112.15(4) . 2_676
+Au2 Au4 Au13 57.73(4) 2_676 2_676
+Au11 Au4 Au13 128.66(3) . 2_676
+Au7 Au4 Au13 59.24(2) 2_676 2_676
+Au10 Au4 Au13 112.77(4) . 2_676
+Au8 Au4 Au13 124.81(4) . 2_676
+S20 Au5 S14 174.77(10) . .
+S20 Au5 Au9 91.11(8) . 2_676
+S14 Au5 Au9 93.84(8) . 2_676
+S20 Au5 Au10 90.28(7) . .
+S14 Au5 Au10 94.10(7) . .
+Au9 Au5 Au10 51.68(3) 2_676 .
+S20 Au5 Au2 138.97(7) . .
+S14 Au5 Au2 46.12(7) . .
+Au9 Au5 Au2 55.36(3) 2_676 .
+Au10 Au5 Au2 51.43(2) . .
+S20 Au6 S26 171.56(10) 2_676 .
+S20 Au6 Au10 92.62(9) 2_676 2_676
+S26 Au6 Au10 93.59(8) . 2_676
+S20 Au6 Au9 90.62(7) 2_676 .
+S26 Au6 Au9 97.70(8) . .
+Au10 Au6 Au9 52.36(3) 2_676 .
+S20 Au6 Au7 142.86(8) 2_676 .
+S26 Au6 Au7 45.48(8) . .
+Au10 Au6 Au7 57.20(3) 2_676 .
+Au9 Au6 Au7 54.64(2) . .
+S26 Au7 Au2 147.14(7) . .
+S26 Au7 Au1 148.92(8) . .
+Au2 Au7 Au1 60.16(4) . .
+S26 Au7 Au3 136.21(8) . .
+Au2 Au7 Au3 62.03(2) . .
+Au1 Au7 Au3 58.76(3) . .
+S26 Au7 Au9 101.19(7) . .
+Au2 Au7 Au9 111.35(4) . .
+Au1 Au7 Au9 58.62(2) . .
+Au3 Au7 Au9 61.75(3) . .
+S26 Au7 Au12 94.76(8) . .
+Au2 Au7 Au12 66.57(3) . .
+Au1 Au7 Au12 115.20(3) . .
+Au3 Au7 Au12 65.33(3) . .
+Au9 Au7 Au12 117.62(4) . .
+S26 Au7 Au10 93.41(8) . 2_676
+Au2 Au7 Au10 108.96(4) . 2_676
+Au1 Au7 Au10 55.90(3) . 2_676
+Au3 Au7 Au10 104.25(4) . 2_676
+Au9 Au7 Au10 54.17(3) . 2_676
+Au12 Au7 Au10 169.57(2) . 2_676
+S26 Au7 Au4 116.36(8) . 2_676
+Au2 Au7 Au4 60.06(3) . 2_676
+Au1 Au7 Au4 56.08(2) . 2_676
+Au3 Au7 Au4 107.20(3) . 2_676
+Au9 Au7 Au4 104.89(4) . 2_676
+Au12 Au7 Au4 120.55(3) . 2_676
+Au10 Au7 Au4 60.72(2) 2_676 2_676
+S26 Au7 Au13 87.76(7) . .
+Au2 Au7 Au13 60.84(3) . .
+Au1 Au7 Au13 109.66(3) . .
+Au3 Au7 Au13 116.90(3) . .
+Au9 Au7 Au13 167.73(2) . .
+Au12 Au7 Au13 69.36(4) . .
+Au10 Au7 Au13 117.48(4) 2_676 .
+Au4 Au7 Au13 63.28(3) 2_676 .
+S26 Au7 Au6 44.26(7) . .
+Au2 Au7 Au6 166.69(2) . .
+Au1 Au7 Au6 106.92(4) . .
+Au3 Au7 Au6 115.51(3) . .
+Au9 Au7 Au6 59.48(3) . .
+Au12 Au7 Au6 125.46(3) . .
+Au10 Au7 Au6 58.15(3) 2_676 .
+Au4 Au7 Au6 111.13(4) 2_676 .
+Au13 Au7 Au6 126.17(3) . .
+S25 Au8 S24 170.50(11) . .
+S25 Au8 Au3 101.56(8) . .
+S24 Au8 Au3 87.77(8) . .
+S25 Au8 Au4 92.69(9) . .
+S24 Au8 Au4 91.51(8) . .
+Au3 Au8 Au4 52.94(3) . .
+S25 Au8 Au10 47.06(8) . .
+S24 Au8 Au10 141.63(8) . .
+Au3 Au8 Au10 55.37(3) . .
+Au4 Au8 Au10 59.22(3) . .
+S15 Au9 Au10 149.01(8) . 2_676
+S15 Au9 Au1 151.43(8) . .
+Au10 Au9 Au1 59.43(2) 2_676 .
+S15 Au9 Au4 98.65(8) . .
+Au10 Au9 Au4 108.96(3) 2_676 .
+Au1 Au9 Au4 58.536(19) . .
+S15 Au9 Au7 121.51(8) . .
+Au10 Au9 Au7 65.16(4) 2_676 .
+Au1 Au9 Au7 57.46(3) . .
+Au4 Au9 Au7 104.76(3) . .
+S15 Au9 Au2 129.63(8) . 2_676
+Au10 Au9 Au2 58.84(3) 2_676 2_676
+Au1 Au9 Au2 57.38(3) . 2_676
+Au4 Au9 Au2 60.66(4) . 2_676
+Au7 Au9 Au2 108.49(4) . 2_676
+S15 Au9 Au3 96.81(8) . .
+Au10 Au9 Au3 110.00(3) 2_676 .
+Au1 Au9 Au3 57.09(2) . .
+Au4 Au9 Au3 56.24(3) . .
+Au7 Au9 Au3 58.07(4) . .
+Au2 Au9 Au3 104.76(4) 2_676 .
+S15 Au9 Au5 89.70(8) . 2_676
+Au10 Au9 Au5 66.01(3) 2_676 2_676
+Au1 Au9 Au5 114.89(3) . 2_676
+Au4 Au9 Au5 115.77(3) . 2_676
+Au7 Au9 Au5 123.95(4) . 2_676
+Au2 Au9 Au5 65.56(3) 2_676 2_676
+Au3 Au9 Au5 170.31(2) . 2_676
+S15 Au9 Au6 90.52(8) . .
+Au10 Au9 Au6 63.58(3) 2_676 .
+Au1 Au9 Au6 111.18(2) . .
+Au4 Au9 Au6 169.57(2) . .
+Au7 Au9 Au6 65.88(3) . .
+Au2 Au9 Au6 116.65(4) 2_676 .
+Au3 Au9 Au6 117.96(3) . .
+Au5 Au9 Au6 68.95(3) 2_676 .
+S15 Au9 Au11 44.30(8) . .
+Au10 Au9 Au11 166.68(2) 2_676 .
+Au1 Au9 Au11 107.26(3) . .
+Au4 Au9 Au11 59.80(3) . .
+Au7 Au9 Au11 109.08(4) . .
+Au2 Au9 Au11 115.15(3) 2_676 .
+Au3 Au9 Au11 58.53(3) . .
+Au5 Au9 Au11 124.07(3) 2_676 .
+Au6 Au9 Au11 126.41(3) . .
+S25 Au10 Au9 141.51(10) . 2_676
+S25 Au10 Au1 148.02(8) . .
+Au9 Au10 Au1 61.38(3) 2_676 .
+S25 Au10 Au2 141.13(10) . .
+Au9 Au10 Au2 64.59(3) 2_676 .
+Au1 Au10 Au2 59.84(4) . .
+S25 Au10 Au3 105.50(10) . .
+Au9 Au10 Au3 112.98(3) 2_676 .
+Au1 Au10 Au3 58.76(2) . .
+Au2 Au10 Au3 61.31(3) . .
+S25 Au10 Au7 109.38(10) . 2_676
+Au9 Au10 Au7 60.66(3) 2_676 2_676
+Au1 Au10 Au7 56.48(4) . 2_676
+Au2 Au10 Au7 109.38(4) . 2_676
+Au3 Au10 Au7 104.86(3) . 2_676
+S25 Au10 Au6 77.99(10) . 2_676
+Au9 Au10 Au6 64.06(3) 2_676 2_676
+Au1 Au10 Au6 113.08(3) . 2_676
+Au2 Au10 Au6 122.12(3) . 2_676
+Au3 Au10 Au6 169.41(2) . 2_676
+Au7 Au10 Au6 64.65(3) 2_676 2_676
+S25 Au10 Au4 92.13(8) . .
+Au9 Au10 Au4 109.45(4) 2_676 .
+Au1 Au10 Au4 55.90(3) . .
+Au2 Au10 Au4 104.76(3) . .
+Au3 Au10 Au4 54.48(3) . .
+Au7 Au10 Au4 59.85(3) 2_676 .
+Au6 Au10 Au4 115.93(3) 2_676 .
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+Au9 Au10 Au8 168.87(2) 2_676 .
+Au1 Au10 Au8 108.27(3) . .
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+Au7 Au10 Au8 110.95(3) 2_676 .
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+Au4 Au10 Au8 59.52(3) . .
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+Au9 Au10 Au5 62.31(3) 2_676 .
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+Au2 Au10 Au5 65.95(2) . .
+Au3 Au10 Au5 120.66(3) . .
+Au7 Au10 Au5 116.82(3) 2_676 .
+Au6 Au10 Au5 67.87(3) 2_676 .
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+Au8 Au10 Au5 128.42(3) . .
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+S24 Au11 Au3 87.88(8) . .
+S15 Au11 Au3 96.39(8) . .
+S24 Au11 Au4 92.96(9) . .
+S15 Au11 Au4 94.36(9) . .
+Au3 Au11 Au4 53.25(3) . .
+S24 Au11 Au9 140.11(8) . .
+S15 Au11 Au9 46.34(8) . .
+Au3 Au11 Au9 56.12(3) . .
+Au4 Au11 Au9 53.19(2) . .
+S16 Au12 S21 173.84(12) . .
+S16 Au12 Au7 94.20(9) . .
+S21 Au12 Au7 89.91(9) . .
+S16 Au12 Au2 85.19(8) . .
+S21 Au12 Au2 100.96(9) . .
+Au7 Au12 Au2 52.67(2) . .
+S16 Au12 Au3 138.18(8) . .
+S21 Au12 Au3 47.90(8) . .
+Au7 Au12 Au3 55.03(4) . .
+Au2 Au12 Au3 54.24(3) . .
+S28 Au13 S16 171.64(10) 2_676 .
+S28 Au13 Au2 98.69(8) 2_676 .
+S16 Au13 Au2 89.57(8) . .
+S28 Au13 Au7 94.57(8) 2_676 .
+S16 Au13 Au7 91.40(8) . .
+Au2 Au13 Au7 53.429(19) . .
+S28 Au13 Au4 45.89(7) 2_676 2_676
+S16 Au13 Au4 142.31(7) . 2_676
+Au2 Au13 Au4 55.71(3) . 2_676
+Au7 Au13 Au4 57.49(3) . 2_676
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+C1_2005 S14 Au2 107.4(4) . .
+Au5 S14 Au2 89.52(10) . .
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+Au11 S15 Au9 89.36(11) . .
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+Au12 S21 Au3 86.47(11) . .
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+Au8 S25 Au10 86.96(11) . .
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+C1_2009 S26 Au7 102.2(4) . .
+Au6 S26 Au7 90.26(11) . .
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+loop_
+_geom_bond_atom_site_label_1
+_geom_bond_atom_site_label_2
+_geom_bond_distance
+_geom_bond_site_symmetry_2
+Au1 Au10 2.7599(10) .
+Au1 Au10 2.7599(10) 2_676
+Au1 Au4 2.7750(8) .
+Au1 Au4 2.7751(8) 2_676
+Au1 Au7 2.7787(11) 2_676
+Au1 Au7 2.7787(12) .
+Au1 Au2 2.7851(15) 2_676
+Au1 Au2 2.7851(15) .
+Au1 Au3 2.7858(11) .
+Au1 Au3 2.7858(11) 2_676
+Au1 Au9 2.8138(7) 2_676
+Au1 Au9 2.8139(7) .
+Au2 S14 2.377(3) .
+Au2 Au7 2.7781(8) .
+Au2 Au10 2.8230(11) .
+Au2 Au3 2.9251(8) .
+Au2 Au4 2.9516(15) 2_676
+Au2 Au9 2.9799(12) 2_676
+Au2 Au13 3.0207(11) .
+Au2 Au12 3.2059(11) .
+Au2 Au5 3.2973(9) .
+Au3 S21 2.387(3) .
+Au3 Au4 2.7681(13) .
+Au3 Au7 2.8957(12) .
+Au3 Au10 2.9121(10) .
+Au3 Au9 3.0057(16) .
+Au3 Au8 3.0786(12) .
+Au3 Au11 3.0879(9) .
+Au3 Au12 3.2109(13) .
+Au4 S28 2.354(3) .
+Au4 Au9 2.8616(11) .
+Au4 Au2 2.9516(15) 2_676
+Au4 Au11 3.0890(10) .
+Au4 Au7 3.0946(9) 2_676
+Au4 Au10 3.1217(11) .
+Au4 Au8 3.1312(17) .
+Au4 Au13 3.2778(17) 2_676
+Au5 S20 2.304(3) .
+Au5 S14 2.306(3) .
+Au5 Au9 3.1073(18) 2_676
+Au5 Au10 3.2062(10) .
+Au6 S20 2.303(3) 2_676
+Au6 S26 2.312(3) .
+Au6 Au10 3.1139(11) 2_676
+Au6 Au9 3.1268(11) .
+Au6 Au7 3.3128(11) .
+Au7 S26 2.362(3) .
+Au7 Au9 2.9603(10) .
+Au7 Au12 3.0489(18) .
+Au7 Au10 3.0816(19) 2_676
+Au7 Au4 3.0946(9) 2_676
+Au7 Au13 3.1536(9) .
+Au8 S25 2.294(4) .
+Au8 S24 2.309(3) .
+Au8 Au10 3.1857(11) .
+Au9 S15 2.381(3) .
+Au9 Au10 2.7533(10) 2_676
+Au9 Au2 2.9799(13) 2_676
+Au9 Au5 3.1073(18) 2_676
+Au9 Au11 3.2906(14) .
+Au10 S25 2.335(3) .
+Au10 Au9 2.7533(10) 2_676
+Au10 Au7 3.0816(19) 2_676
+Au10 Au6 3.1140(11) 2_676
+Au11 S24 2.290(3) .
+Au11 S15 2.299(3) .
+Au12 S16 2.298(3) .
+Au12 S21 2.300(3) .
+Au13 S28 2.298(3) 2_676
+Au13 S16 2.303(3) .
+Au13 Au4 3.2779(17) 2_676
+S14 C1_2005 1.827(12) .
+S15 C1_2002 1.864(16) .
+S16 C1_2006 1.824(12) .
+S20 C1_2008 1.836(12) .
+S20 Au6 2.303(3) 2_676
+S21 C1_2004 1.825(14) .
+S24 C1_2001 1.840(12) .
+S25 C1_2007 2.07(2) .
+S26 C1_2009 1.845(12) .
+S28 C1_2003 1.840(11) .
+S28 Au13 2.298(3) 2_676
+C1_2001 C2_2001 1.537(17) .
+C1_2001 H1A_2001 0.9700 .
+C1_2001 H1B_2001 0.9700 .
+C2_2001 C3_2001 1.500(16) .
+C2_2001 H2A_2001 0.9700 .
+C2_2001 H2B_2001 0.9700 .
+C3_2001 C4_2001 1.375(16) .
+C3_2001 C8_2001 1.397(18) .
+C4_2001 C5_2001 1.397(17) .
+C4_2001 H4_2001 0.9300 .
+C5_2001 C6_2001 1.371(19) .
+C5_2001 H5_2001 0.9300 .
+C6_2001 C7_2001 1.37(2) .
+C6_2001 H6_2001 0.9300 .
+C7_2001 C8_2001 1.39(2) .
+C7_2001 H7_2001 0.9300 .
+C8_2001 H8_2001 0.9300 .
+C1_2002 C2_2002 1.61(2) .
+C1_2002 H1A_2002 0.9700 .
+C1_2002 H1B_2002 0.9700 .
+C2_2002 C3_2002 1.43(3) .
+C2_2002 H2A_2002 0.9700 .
+C2_2002 H2B_2002 0.9700 .
+C3_2002 C8_2002 1.37(3) .
+C3_2002 C4_2002 1.40(3) .
+C4_2002 C5_2002 1.46(3) .
+C4_2002 H4_2002 0.9300 .
+C5_2002 C6_2002 1.36(3) .
+C5_2002 H5_2002 0.9300 .
+C6_2002 C7_2002 1.43(4) .
+C6_2002 H6_2002 0.9300 .
+C7_2002 C8_2002 1.38(3) .
+C7_2002 H7_2002 0.9300 .
+C8_2002 H8_2002 0.9300 .
+C1_2003 C2_2003 1.509(15) .
+C1_2003 H1A_2003 0.9700 .
+C1_2003 H1B_2003 0.9700 .
+C2_2003 C3_2003 1.524(16) .
+C2_2003 H2A_2003 0.9700 .
+C2_2003 H2B_2003 0.9700 .
+C3_2003 C8_2003 1.36(2) .
+C3_2003 C4_2003 1.380(19) .
+C4_2003 C5_2003 1.379(18) .
+C4_2003 H4_2003 0.9300 .
+C5_2003 C6_2003 1.37(3) .
+C5_2003 H5_2003 0.9300 .
+C6_2003 C7_2003 1.37(2) .
+C6_2003 H6_2003 0.9300 .
+C7_2003 C8_2003 1.41(2) .
+C7_2003 H7_2003 0.9300 .
+C8_2003 H8_2003 0.9300 .
+C1_2004 C2_2004 1.41(2) .
+C1_2004 H1A_2004 0.9700 .
+C1_2004 H1B_2004 0.9700 .
+C2_2004 C3_2004 1.58(2) .
+C2_2004 H2A_2004 0.9700 .
+C2_2004 H2B_2004 0.9700 .
+C3_2004 C8_2004 1.25(3) .
+C3_2004 C4_2004 1.40(3) .
+C4_2004 C5_2004 1.43(3) .
+C4_2004 H4_2004 0.9300 .
+C5_2004 C6_2004 1.30(3) .
+C5_2004 H5_2004 0.9300 .
+C6_2004 C7_2004 1.24(3) .
+C6_2004 H6_2004 0.9300 .
+C7_2004 C8_2004 1.41(3) .
+C7_2004 H7_2004 0.9300 .
+C8_2004 H8_2004 0.9300 .
+C1_2005 C2_2005 1.527(16) .
+C1_2005 H1A_2005 0.9700 .
+C1_2005 H1B_2005 0.9700 .
+C2_2005 C3_2005 1.52(2) .
+C2_2005 H2A_2005 0.9700 .
+C2_2005 H2B_2005 0.9700 .
+C3_2005 C8_2005 1.33(2) .
+C3_2005 C4_2005 1.40(3) .
+C4_2005 C5_2005 1.39(3) .
+C4_2005 H4_2005 0.9300 .
+C5_2005 C6_2005 1.42(3) .
+C5_2005 H5_2005 0.9300 .
+C6_2005 C7_2005 1.36(2) .
+C6_2005 H6_2005 0.9300 .
+C7_2005 C8_2005 1.32(2) .
+C7_2005 H7_2005 0.9300 .
+C8_2005 H8_2005 0.9300 .
+C1_2006 C2_2006 1.513(16) .
+C1_2006 H1A_2006 0.9700 .
+C1_2006 H1B_2006 0.9700 .
+C2_2006 C3_2006 1.528(17) .
+C2_2006 H2A_2006 0.9700 .
+C2_2006 H2B_2006 0.9700 .
+C3_2006 C4_2006 1.360(19) .
+C3_2006 C8_2006 1.357(19) .
+C4_2006 C5_2006 1.38(2) .
+C4_2006 H4_2006 0.9300 .
+C5_2006 C6_2006 1.34(3) .
+C5_2006 H5_2006 0.9300 .
+C6_2006 C7_2006 1.38(3) .
+C6_2006 H6_2006 0.9300 .
+C7_2006 C8_2006 1.39(2) .
+C7_2006 H7_2006 0.9300 .
+C8_2006 H8_2006 0.9300 .
+C1_2007 C2_2007 1.33(3) .
+C1_2007 H1A_2007 0.9700 .
+C1_2007 H1B_2007 0.9700 .
+C2_2007 C3_2007 1.73(3) .
+C2_2007 H2A_2007 0.9700 .
+C2_2007 H2B_2007 0.9700 .
+C3_2007 C8_2007 1.36(3) .
+C3_2007 C4_2007 1.37(3) .
+C4_2007 C5_2007 1.30(2) .
+C4_2007 H4_2007 0.9300 .
+C5_2007 C6_2007 1.34(2) .
+C5_2007 H5_2007 0.9300 .
+C6_2007 C7_2007 1.34(2) .
+C6_2007 H6_2007 0.9300 .
+C7_2007 C8_2007 1.36(2) .
+C7_2007 H7_2007 0.9300 .
+C8_2007 H8_2007 0.9300 .
+C1_2008 C2_2008 1.510(15) .
+C1_2008 H1A_2008 0.9700 .
+C1_2008 H1B_2008 0.9700 .
+C2_2008 C3_2008 1.505(18) .
+C2_2008 H2A_2008 0.9700 .
+C2_2008 H2B_2008 0.9700 .
+C3_2008 C8_2008 1.372(18) .
+C3_2008 C4_2008 1.389(17) .
+C4_2008 C5_2008 1.391(18) .
+C4_2008 H4_2008 0.9300 .
+C5_2008 C6_2008 1.37(2) .
+C5_2008 H5_2008 0.9300 .
+C6_2008 C7_2008 1.37(2) .
+C6_2008 H6_2008 0.9300 .
+C7_2008 C8_2008 1.37(2) .
+C7_2008 H7_2008 0.9300 .
+C8_2008 H8_2008 0.9300 .
+C1_2009 C2_2009 1.498(15) .
+C1_2009 H1A_2009 0.9700 .
+C1_2009 H1B_2009 0.9700 .
+C2_2009 C3_2009 1.510(17) .
+C2_2009 H2A_2009 0.9700 .
+C2_2009 H2B_2009 0.9700 .
+C3_2009 C4_2009 1.352(19) .
+C3_2009 C8_2009 1.40(2) .
+C4_2009 C5_2009 1.37(3) .
+C4_2009 H4_2009 0.9300 .
+C5_2009 C6_2009 1.38(3) .
+C5_2009 H5_2009 0.9300 .
+C6_2009 C7_2009 1.34(2) .
+C6_2009 H6_2009 0.9300 .
+C7_2009 C8_2009 1.40(2) .
+C7_2009 H7_2009 0.9300 .
+C8_2009 H8_2009 0.9300 .
+C9_2010 C10_2010 1.37(2) .
+C9_2010 C15_2010 1.39(2) .
+C9_2010 H9_2010 0.9300 .
+C10_2010 C11_2010 1.39(2) .
+C10_2010 H10_2010 0.9300 .
+C11_2010 C12_2010 1.37(2) .
+C11_2010 H11_2010 0.9300 .
+C12_2010 C14_2010 1.36(2) .
+C12_2010 C13_2010 1.54(2) .
+C12_2010 H12_2010 0.9300 .
+C13_2010 H13A_2010 0.9600 .
+C13_2010 H13B_2010 0.9600 .
+C13_2010 H13C_2010 0.9600 .
+C14_2010 C15_2010 1.37(2) .
+C14_2010 H14_2010 0.9300 .
+C15_2010 H15_2010 0.9300 .

examples/inorganic_crystal.cif

@@ -0,0 +1,75 @@
+# generated using pymatgen
+data_LiMn2O4
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   5.70118782
+_cell_length_b   8.06767022
+_cell_length_c   9.87795035
+_cell_angle_alpha   114.09949373
+_cell_angle_beta   106.76964054
+_cell_angle_gamma   90.00002135
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   LiMn2O4
+_chemical_formula_sum   'Li6 Mn12 O24'
+_cell_volume   393.47630577
+_cell_formula_units_Z   6
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_type_symbol
+ _atom_type_oxidation_number
+  Li+  1.0
+  Mn3+  3.0
+  Mn4+  4.0
+  O2-  -2.0
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Li+  Li0  1  0.91714273  0.04131819  0.83347123  1
+  Li+  Li1  1  0.58335526  0.70911487  0.16676469  1
+  Li+  Li2  1  0.08323822  0.95802295  0.16684024  1
+  Li+  Li3  1  0.75056154  0.62548778  0.49989611  1
+  Li+  Li4  1  0.41715766  0.29060308  0.83357001  1
+  Li+  Li5  1  0.25003958  0.37445342  0.50018293  1
+  Mn3+  Mn6  1  0.83358214  0.33306641  0.16680334  1
+  Mn3+  Mn7  1  0.66809993  0.66615172  0.83358383  1
+  Mn3+  Mn8  1  0.16797705  0.66624466  0.83358751  1
+  Mn3+  Mn9  1  0.00039185  0.99958913  0.50013453  1
+  Mn3+  Mn10  1  0.33359680  0.33299799  0.16683103  1
+  Mn3+  Mn11  1  0.50029665  0.99960030  0.50012492  1
+  Mn4+  Mn12  1  0.50070403  0.99972330  0.00020421  1
+  Mn4+  Mn13  1  0.16707531  0.66622817  0.33349613  1
+  Mn4+  Mn14  1  0.00077602  0.49968002  0.00022251  1
+  Mn4+  Mn15  1  0.83417104  0.33282978  0.66685445  1
+  Mn4+  Mn16  1  0.33430183  0.83272152  0.66698147  1
+  Mn4+  Mn17  1  0.66698763  0.16655350  0.33349705  1
+  O2-  O18  1  0.82542226  0.08711994  0.65018107  1
+  O2-  O19  1  0.14258653  0.42877551  0.83357077  1
+  O2-  O20  1  0.50865415  0.24534957  0.01687179  1
+  O2-  O21  1  0.49291906  0.75395612  0.98347559  1
+  O2-  O22  1  0.97542250  0.23692762  0.50009031  1
+  O2-  O23  1  0.35872214  0.09551602  0.16675809  1
+  O2-  O24  1  0.47548904  0.76218014  0.50013846  1
+  O2-  O25  1  0.00871754  0.27056033  0.01682709  1
+  O2-  O26  1  0.30894205  0.57045269  0.16695366  1
+  O2-  O27  1  0.67541170  0.93741069  0.35024778  1
+  O2-  O28  1  0.15852979  0.42048160  0.31679160  1
+  O2-  O29  1  0.32540385  0.06180908  0.65010675  1
+  O2-  O30  1  0.65862057  0.39554984  0.31685382  1
+  O2-  O31  1  0.64264563  0.90368470  0.83363130  1
+  O2-  O32  1  0.99298078  0.72871349  0.98362566  1
+  O2-  O33  1  0.34299453  0.60372501  0.68359964  1
+  O2-  O34  1  0.02584613  0.76221785  0.50030835  1
+  O2-  O35  1  0.17534743  0.91197518  0.35010492  1
+  O2-  O36  1  0.69255997  0.42879261  0.83354118  1
+  O2-  O37  1  0.19251743  0.90360317  0.83355327  1
+  O2-  O38  1  0.85869384  0.57047595  0.16677477  1
+  O2-  O39  1  0.80876520  0.09575025  0.16693826  1
+  O2-  O40  1  0.84299557  0.57868936  0.68355179  1
+  O2-  O41  1  0.52556405  0.23711750  0.50026589  1

examples/metal_cplx.pdb

@@ -0,0 +1,243 @@
+TITLE     7043848_molecule_0_1_6
+REMARK   4      COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
+REMARK 888
+REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
+HETATM    1 Fe1  UNK     0       4.781  17.798   5.309  1.00  1.98          Fe3+
+ANISOU    1 Fe1  UNK     0      246    268    262      0    132      0
+HETATM    2  N2  UNK     0       4.953  17.762   3.418  1.00  2.65           N1-
+ANISOU    2  N2  UNK     0      390    350    260     10    130     40
+HETATM    3  N1  UNK     0       3.512  16.312   4.982  1.00  2.46           N  
+ANISOU    3  N1  UNK     0      250    260    440      0    170     40
+HETATM    4  N4  UNK     0       6.171  19.186   5.425  1.00  3.51           N  
+ANISOU    4  N4  UNK     0      470    450    510    -30    310    -90
+HETATM    5  C7  UNK     0       5.365  18.820   2.668  1.00  2.42           C  
+ANISOU    5  C7  UNK     0      270    390    260     20    120    -10
+HETATM    6  C12 UNK     0       6.032  19.891   3.329  1.00  3.08           C  
+ANISOU    6  C12 UNK     0      320    510    390     90    210      0
+HETATM    7  N3  UNK     0       6.513  19.986   4.632  1.00  4.46           N  
+ANISOU    7  N3  UNK     0      520    720    400    260    150     60
+HETATM    8  C13 UNK     0       6.910  19.549   6.760  1.00  3.30           C  
+ANISOU    8  C13 UNK     0      420    630    300    210    250    100
+HETATM    9  C1  UNK     0       2.707  15.711   5.860  1.00  3.34           C  
+ANISOU    9  C1  UNK     0      460    200    760     70    410     50
+HETATM   10  C14 UNK     0       7.673  18.569   7.310  1.00  2.79           C  
+ANISOU   10  C14 UNK     0      280    500    340   -100    190   -100
+HETATM   11  O1  UNK     0       4.772  16.216   1.692  1.00  6.63           O  
+ANISOU   11  O1  UNK     0     1480    550    280   -220    190    -90
+HETATM   12  C5  UNK     0       3.640  15.794   3.749  1.00  3.19           C  
+ANISOU   12  C5  UNK     0      370    360    330      0     10      0
+HETATM   13  C15 UNK     0       8.274  18.767   8.525  1.00  2.91           C  
+ANISOU   13  C15 UNK     0      240    550    300     50    110    110
+HETATM   14  C8  UNK     0       5.128  18.979   1.304  1.00  3.02           C  
+ANISOU   14  C8  UNK     0      340    490    300     30    120     50
+HETATM   15  C16 UNK     0       8.083  19.993   9.175  1.00  4.18           C  
+ANISOU   15  C16 UNK     0      340    970    280   -230    120   -250
+HETATM   16  C9  UNK     0       5.471  20.152   0.664  1.00  3.81           C  
+ANISOU   16  C9  UNK     0      540    610    340     40    220     50
+HETATM   17  C11 UNK     0       6.403  21.059   2.630  1.00  3.99           C  
+ANISOU   17  C11 UNK     0      460    520    620    -80    310    -30
+HETATM   18  C6  UNK     0       4.513  16.587   2.809  1.00  3.83           C  
+ANISOU   18  C6  UNK     0      580    370    370    -40     80    -30
+HETATM   19  C10 UNK     0       6.098  21.183   1.318  1.00  4.23           C  
+ANISOU   19  C10 UNK     0      690    550    590     30    480    100
+HETATM   20  C17 UNK     0       7.314  20.974   8.581  1.00  4.90           C  
+ANISOU   20  C17 UNK     0      700    440   1020   -100    660   -210
+HETATM   21  C2  UNK     0       1.947  14.568   5.459  1.00  4.66           C  
+ANISOU   21  C2  UNK     0      520    340   1120     60    540    140
+HETATM   22  C18 UNK     0       6.742  20.747   7.360  1.00  4.05           C  
+ANISOU   22  C18 UNK     0      510    600    470    130    250    170
+HETATM   23  C4  UNK     0       2.978  14.690   3.315  1.00  4.66           C  
+ANISOU   23  C4  UNK     0      580    340    630    -50     60    -50
+HETATM   24  C3  UNK     0       2.096  14.097   4.189  1.00  4.97           C  
+ANISOU   24  C3  UNK     0      350    330   1070    -80    180    -60
+HETATM   25  N2  UNK     0       4.609  17.762   7.200  1.00  2.65           N1-
+ANISOU   25  N2  UNK     0      390    350    260     10    130     40
+HETATM   26  N1  UNK     0       6.050  16.312   5.636  1.00  2.46           N  
+ANISOU   26  N1  UNK     0      250    260    440      0    170     40
+HETATM   27  N4  UNK     0       3.391  19.186   5.194  1.00  3.51           N  
+ANISOU   27  N4  UNK     0      470    450    510    -30    310    -90
+HETATM   28  C7  UNK     0       4.197  18.820   7.950  1.00  2.42           C  
+ANISOU   28  C7  UNK     0      270    390    260     20    120    -10
+HETATM   29  C12 UNK     0       3.530  19.891   7.290  1.00  3.08           C  
+ANISOU   29  C12 UNK     0      320    510    390     90    210      0
+HETATM   30  N3  UNK     0       3.049  19.986   5.987  1.00  4.46           N  
+ANISOU   30  N3  UNK     0      520    720    400    260    150     60
+HETATM   31  C13 UNK     0       2.652  19.549   3.859  1.00  3.30           C  
+ANISOU   31  C13 UNK     0      420    630    300    210    250    100
+HETATM   32  C1  UNK     0       6.855  15.711   4.758  1.00  3.34           C  
+ANISOU   32  C1  UNK     0      460    200    760     70    410     50
+HETATM   33  C14 UNK     0       1.889  18.569   3.309  1.00  2.79           C  
+ANISOU   33  C14 UNK     0      280    500    340   -100    190   -100
+HETATM   34  O1  UNK     0       4.790  16.216   8.927  1.00  6.63           O  
+ANISOU   34  O1  UNK     0     1480    550    280   -220    190    -90
+HETATM   35  C5  UNK     0       5.922  15.794   6.869  1.00  3.19           C  
+ANISOU   35  C5  UNK     0      370    360    330      0     10      0
+HETATM   36  C15 UNK     0       1.288  18.767   2.094  1.00  2.91           C  
+ANISOU   36  C15 UNK     0      240    550    300     50    110    110
+HETATM   37  C8  UNK     0       4.434  18.979   9.315  1.00  3.02           C  
+ANISOU   37  C8  UNK     0      340    490    300     30    120     50
+HETATM   38  C16 UNK     0       1.479  19.993   1.443  1.00  4.18           C  
+ANISOU   38  C16 UNK     0      340    970    280   -230    120   -250
+HETATM   39  C9  UNK     0       4.091  20.152   9.955  1.00  3.81           C  
+ANISOU   39  C9  UNK     0      540    610    340     40    220     50
+HETATM   40  C11 UNK     0       3.159  21.059   7.988  1.00  3.99           C  
+ANISOU   40  C11 UNK     0      460    520    620    -80    310    -30
+HETATM   41  C6  UNK     0       5.049  16.587   7.810  1.00  3.83           C  
+ANISOU   41  C6  UNK     0      580    370    370    -40     80    -30
+HETATM   42  C10 UNK     0       3.464  21.183   9.301  1.00  4.23           C  
+ANISOU   42  C10 UNK     0      690    550    590     30    480    100
+HETATM   43  C17 UNK     0       2.248  20.974   2.038  1.00  4.90           C  
+ANISOU   43  C17 UNK     0      700    440   1020   -100    660   -210
+HETATM   44  C2  UNK     0       7.615  14.568   5.160  1.00  4.66           C  
+ANISOU   44  C2  UNK     0      520    340   1120     60    540    140
+HETATM   45  C18 UNK     0       2.820  20.747   3.259  1.00  4.05           C  
+ANISOU   45  C18 UNK     0      510    600    470    130    250    170
+HETATM   46  C4  UNK     0       6.584  14.690   7.303  1.00  4.66           C  
+ANISOU   46  C4  UNK     0      580    340    630    -50     60    -50
+HETATM   47  C3  UNK     0       7.466  14.097   6.430  1.00  4.97           C  
+ANISOU   47  C3  UNK     0      350    330   1070    -80    180    -60
+HETATM   48  H1  UNK     0       2.640  16.034   6.729  1.00  4.03           H  
+HETATM   49  H14 UNK     0       7.789  17.763   6.859  1.00  3.32           H  
+HETATM   50  H15 UNK     0       8.795  18.100   8.910  1.00  3.47           H  
+HETATM   51  H8  UNK     0       4.734  18.289   0.821  1.00  3.63           H  
+HETATM   52  H16 UNK     0       8.474  20.147  10.006  1.00  5.05           H  
+HETATM   53  H9  UNK     0       5.272  20.247  -0.240  1.00  4.58           H  
+HETATM   54  H11 UNK     0       6.856  21.741   3.071  1.00  4.82           H  
+HETATM   55  H10 UNK     0       6.313  21.965   0.861  1.00  5.05           H  
+HETATM   56  H17 UNK     0       7.184  21.788   9.011  1.00  5.84           H  
+HETATM   57  H2  UNK     0       1.361  14.154   6.052  1.00  5.61           H  
+HETATM   58  H18 UNK     0       6.242  21.411   6.945  1.00  4.90           H  
+HETATM   59  H4  UNK     0       3.116  14.347   2.461  1.00  5.61           H  
+HETATM   60  H3  UNK     0       1.595  13.366   3.909  1.00  5.92           H  
+HETATM   61  H1  UNK     0       6.922  16.034   3.889  1.00  4.03           H  
+HETATM   62  H14 UNK     0       1.773  17.763   3.759  1.00  3.32           H  
+HETATM   63  H15 UNK     0       0.767  18.100   1.708  1.00  3.47           H  
+HETATM   64  H8  UNK     0       4.828  18.289   9.798  1.00  3.63           H  
+HETATM   65  H16 UNK     0       1.088  20.147   0.613  1.00  5.05           H  
+HETATM   66  H9  UNK     0       4.290  20.247  10.859  1.00  4.58           H  
+HETATM   67  H11 UNK     0       2.706  21.741   7.548  1.00  4.82           H  
+HETATM   68  H10 UNK     0       3.249  21.965   9.758  1.00  5.05           H  
+HETATM   69  H17 UNK     0       2.378  21.788   1.608  1.00  5.84           H  
+HETATM   70  H2  UNK     0       8.201  14.154   4.567  1.00  5.61           H  
+HETATM   71  H18 UNK     0       3.320  21.411   3.673  1.00  4.90           H  
+HETATM   72  H4  UNK     0       6.446  14.347   8.157  1.00  5.61           H  
+HETATM   73  H3  UNK     0       7.967  13.366   6.709  1.00  5.92           H  
+CONECT    1    2   25    4   27
+CONECT    1   26    3
+CONECT    2    1    5   18
+CONECT    3    1    9   12
+CONECT    3   12
+CONECT    4    1    7    8
+CONECT    4    7
+CONECT    5    2   14    6
+CONECT    5   14
+CONECT    6    5    7   17
+CONECT    6   17
+CONECT    7    4    6
+CONECT    7    4
+CONECT    8    4   22   10
+CONECT    8   22
+CONECT    9    3   48   21
+CONECT    9   21
+CONECT   48    9
+CONECT   10    8   49   13
+CONECT   10   13
+CONECT   49   10
+CONECT   11   18
+CONECT   11   18
+CONECT   12    3   23   18
+CONECT   12    3
+CONECT   13   10   50   15
+CONECT   13   10
+CONECT   50   13
+CONECT   14    5   51   16
+CONECT   14    5
+CONECT   51   14
+CONECT   15   13   52   20
+CONECT   15   20
+CONECT   52   15
+CONECT   16   14   53   19
+CONECT   16   19
+CONECT   53   16
+CONECT   17    6   54   19
+CONECT   17    6
+CONECT   54   17
+CONECT   18    2   11   12
+CONECT   18   11
+CONECT   19   16   17   55
+CONECT   19   16
+CONECT   55   19
+CONECT   20   15   56   22
+CONECT   20   15
+CONECT   56   20
+CONECT   21    9   57   24
+CONECT   21    9
+CONECT   57   21
+CONECT   22    8   20   58
+CONECT   22    8
+CONECT   58   22
+CONECT   23   12   59   24
+CONECT   23   24
+CONECT   59   23
+CONECT   24   21   23   60
+CONECT   24   23
+CONECT   60   24
+CONECT   25    1   28   41
+CONECT   26    1   32   35
+CONECT   26   35
+CONECT   27    1   30   31
+CONECT   27   30
+CONECT   28   25   37   29
+CONECT   28   37
+CONECT   29   28   30   40
+CONECT   29   40
+CONECT   30   27   29
+CONECT   30   27
+CONECT   31   27   45   33
+CONECT   31   45
+CONECT   32   26   61   44
+CONECT   32   44
+CONECT   61   32
+CONECT   33   31   62   36
+CONECT   33   36
+CONECT   62   33
+CONECT   34   41
+CONECT   34   41
+CONECT   35   26   46   41
+CONECT   35   26
+CONECT   36   33   63   38
+CONECT   36   33
+CONECT   63   36
+CONECT   37   28   64   39
+CONECT   37   28
+CONECT   64   37
+CONECT   38   36   65   43
+CONECT   38   43
+CONECT   65   38
+CONECT   39   37   66   42
+CONECT   39   42
+CONECT   66   39
+CONECT   40   29   67   42
+CONECT   40   29
+CONECT   67   40
+CONECT   41   25   34   35
+CONECT   41   34
+CONECT   42   39   40   68
+CONECT   42   39
+CONECT   68   42
+CONECT   43   38   69   45
+CONECT   43   38
+CONECT   69   43
+CONECT   44   32   70   47
+CONECT   44   32
+CONECT   70   44
+CONECT   45   31   43   71
+CONECT   45   31
+CONECT   71   45
+CONECT   46   35   72   47
+CONECT   46   47
+CONECT   72   46
+CONECT   47   44   46   73
+CONECT   47   46
+CONECT   73   47
+END   

examples/organic_molecular_crystal.cif

@@ -0,0 +1,257 @@
+data_image0
+_chemical_formula_structural       SO2NC2H2C3HCHCHCH2C2HBrC2HCOHSO2NC2H2C3HCHCHCH2C2HBrC2HCOHSO2NC2H2C3HCHCHCH2C2HBrC2HCOHSO2NC2H2C3HCHCHCH2C2HBrC2HCOHSO2NC2H2C3HCHCHCH2C2HBrC2HCOHSO2NC2H2C3HCHCHCH2C2HBrC2HCOHSO2NC2H2C3HCHCHCH2C2HBrC2HCOHSO2NC2H2C3HCHCHCH2C2HBrC2HCOH
+_chemical_formula_sum              "S8 O24 N8 C104 H80 Br8"
+_cell_length_a       13.423146423109205
+_cell_length_b       13.423146423109205
+_cell_length_c       13.6638898495986
+_cell_angle_alpha    90.0
+_cell_angle_beta     90.0
+_cell_angle_gamma    90.0
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  S   S1        1.0  0.9275461529470431  0.8155896023122877  0.2941211283258369  1.0000
+  O   O1        1.0  0.9372220992434028  0.9265573250362035  0.2881057270882305  1.0000
+  O   O2        1.0  0.7938257294941448  0.613458320160412  0.3325817036686815  1.0000
+  N   N1        1.0  0.7094294676765264  0.6315815144358788  0.3643853618085062  1.0000
+  C   C1        1.0  0.04722194744393815  0.7664571194860146  0.3324408693324965  1.0000
+  C   C2        1.0  0.8637010100550786  0.7901090817201828  0.41480828284433924  1.0000
+  H   H1        1.0  0.8828132168696473  0.713926921711797  0.4356050026060773  1.0000
+  H   H2        1.0  0.8990216567280933  0.8438518355897033  0.4644104859507723  1.0000
+  C   C3        1.0  0.7547742291758802  0.8091132478236331  0.40549736222237937  1.0000
+  C   C4        1.0  0.6823975071369104  0.7367685032901754  0.38218155259699743  1.0000
+  C   C5        1.0  0.5812093405094393  0.7596978068934275  0.37558287238095706  1.0000
+  H   H3        1.0  0.5289766916653209  0.7000637700023311  0.35916711510461696  1.0000
+  C   C6        1.0  0.5496372088965512  0.8573060172331419  0.3891811661042275  1.0000
+  H   H4        1.0  0.4709107389129744  0.8756720552830178  0.3825211764085389  1.0000
+  C   C7        1.0  0.6195186980453679  0.9309846509461215  0.4114651541949892  1.0000
+  H   H5        1.0  0.5957249701097564  0.007785244103282407  0.4223759572337825  1.0000
+  C   C8        1.0  0.7199004905916212  0.9066603112226315  0.4202079011847202  1.0000
+  H   H6        1.0  0.7741686341527089  0.9642133552690426  0.4380555929366669  1.0000
+  H   H7        1.0  0.10728745316766286  0.9129321031479888  0.35471103015530164  1.0000
+  C   C9        1.0  0.15729100969569187  0.6271254223041515  0.3583665559774094  1.0000
+  C   C10       1.0  0.0639946379748706  0.66374801042789  0.33171135136525254  1.0000
+  H   H8        1.0  0.004899415930414541  0.6122306354425116  0.31063325530424696  1.0000
+  Br  Br1       1.0  0.3599752297084762  0.6443068017173645  0.42009103215509896  1.0000
+  C   C11       1.0  0.12256687007673928  0.8331621497102379  0.3571832339149155  1.0000
+  C   C12       1.0  0.21619123110409633  0.7968984767016225  0.38363901688186314  1.0000
+  H   H9        1.0  0.276002226249074  0.8478692462897375  0.40328266801719487  1.0000
+  C   C13       1.0  0.23232330779138866  0.694247403522436  0.3842252287422828  1.0000
+  O   O3        1.0  0.645815613938436  0.5678074831662694  0.38140471043720314  1.0000
+  H   H10       1.0  0.17175608640296902  0.5473527460604474  0.3585904002479444  1.0000
+  S   S2        1.0  0.8155896023122877  0.07245384705295688  0.7058790442100105  1.0000
+  O   O4        1.0  0.9265573250362035  0.06277790075659728  0.7118944454476168  1.0000
+  O   O5        1.0  0.613458320160412  0.20617427050585538  0.6674184688671658  1.0000
+  N   N2        1.0  0.6315815144358788  0.29057053232347374  0.6356148107273412  1.0000
+  C   C14       1.0  0.7664571194860146  0.9527780525560618  0.6675593032033508  1.0000
+  C   C15       1.0  0.7901090817201828  0.1362989899449214  0.5851918896915079  1.0000
+  H   H11       1.0  0.713926921711797  0.11718678313035269  0.56439516992977  1.0000
+  H   H12       1.0  0.8438518355897033  0.1009783432719068  0.5355896865850751  1.0000
+  C   C16       1.0  0.8091132478236331  0.2452257708241198  0.5945028103134679  1.0000
+  C   C17       1.0  0.7367685032901754  0.31760249286308967  0.6178186199388498  1.0000
+  C   C18       1.0  0.7596978068934275  0.4187906594905607  0.6244173001548903  1.0000
+  H   H13       1.0  0.7000637700023311  0.47102330833467915  0.6408330574312303  1.0000
+  C   C19       1.0  0.8573060172331419  0.45036279110344885  0.6108190064316199  1.0000
+  H   H14       1.0  0.8756720552830178  0.5290892610870257  0.6174789961273085  1.0000
+  C   C20       1.0  0.9309846509461215  0.38048130195463215  0.5885350183408582  1.0000
+  H   H15       1.0  0.007785244103282407  0.40427502989024366  0.5776242153020649  1.0000
+  C   C21       1.0  0.9066603112226315  0.2800995094083789  0.5797922713511272  1.0000
+  H   H16       1.0  0.9642133552690426  0.22583136584729124  0.5619445795991804  1.0000
+  H   H17       1.0  0.9129321031479888  0.8927125468323371  0.6452891423805457  1.0000
+  C   C22       1.0  0.6271254223041515  0.8427089903043081  0.6416336165584379  1.0000
+  C   C23       1.0  0.66374801042789  0.9360053620251294  0.6682888211705948  1.0000
+  H   H18       1.0  0.6122306354425116  0.9951005840695855  0.6893669172316004  1.0000
+  Br  Br2       1.0  0.6443068017173645  0.6400247702915238  0.5799091403807484  1.0000
+  C   C24       1.0  0.8331621497102379  0.877433129923261  0.6428169386209319  1.0000
+  C   C25       1.0  0.7968984767016225  0.7838087688959037  0.6163611556539842  1.0000
+  H   H19       1.0  0.8478692462897375  0.723997773750926  0.5967175045186525  1.0000
+  C   C26       1.0  0.694247403522436  0.7676766922086116  0.6157749437935646  1.0000
+  O   O6        1.0  0.5678074831662694  0.35418438606156416  0.6185954620986442  1.0000
+  H   H20       1.0  0.5473527460604474  0.828243913597031  0.6414097722879029  1.0000
+  S   S3        1.0  0.07245384705295688  0.18441039768771228  0.2941211283258369  1.0000
+  O   O7        1.0  0.06277790075659728  0.07344267496379653  0.2881057270882305  1.0000
+  O   O8        1.0  0.20617427050585538  0.386541679839588  0.3325817036686815  1.0000
+  N   N3        1.0  0.29057053232347374  0.36841848556412116  0.3643853618085062  1.0000
+  C   C27       1.0  0.9527780525560618  0.23354288051398545  0.3324408693324965  1.0000
+  C   C28       1.0  0.1362989899449214  0.2098909182798172  0.41480828284433924  1.0000
+  H   H21       1.0  0.11718678313035269  0.28607307828820305  0.4356050026060773  1.0000
+  H   H22       1.0  0.1009783432719068  0.15614816441029666  0.4644104859507723  1.0000
+  C   C29       1.0  0.2452257708241198  0.1908867521763669  0.40549736222237937  1.0000
+  C   C30       1.0  0.31760249286308967  0.2632314967098247  0.38218155259699743  1.0000
+  C   C31       1.0  0.4187906594905607  0.24030219310657253  0.37558287238095706  1.0000
+  H   H23       1.0  0.47102330833467915  0.29993622999766906  0.35916711510461696  1.0000
+  C   C32       1.0  0.45036279110344885  0.14269398276685819  0.3891811661042275  1.0000
+  H   H24       1.0  0.5290892610870257  0.12432794471698216  0.3825211764085389  1.0000
+  C   C33       1.0  0.38048130195463215  0.06901534905387852  0.4114651541949892  1.0000
+  H   H25       1.0  0.40427502989024366  0.9922147558967178  0.4223759572337825  1.0000
+  C   C34       1.0  0.2800995094083789  0.09333968877736865  0.4202079011847202  1.0000
+  H   H26       1.0  0.22583136584729124  0.0357866447309575  0.4380555929366669  1.0000
+  H   H27       1.0  0.8927125468323371  0.08706789685201123  0.35471103015530164  1.0000
+  C   C35       1.0  0.8427089903043081  0.3728745776958487  0.3583665559774094  1.0000
+  C   C36       1.0  0.9360053620251294  0.33625198957211  0.33171135136525254  1.0000
+  H   H28       1.0  0.9951005840695855  0.3877693645574885  0.31063325530424696  1.0000
+  Br  Br3       1.0  0.6400247702915238  0.3556931982826356  0.42009103215509896  1.0000
+  C   C37       1.0  0.877433129923261  0.16683785028976206  0.3571832339149155  1.0000
+  C   C38       1.0  0.7838087688959037  0.2031015232983776  0.38363901688186314  1.0000
+  H   H29       1.0  0.723997773750926  0.15213075371026252  0.40328266801719487  1.0000
+  C   C39       1.0  0.7676766922086116  0.3057525964775641  0.3842252287422828  1.0000
+  O   O9        1.0  0.35418438606156416  0.4321925168337306  0.38140471043720314  1.0000
+  H   H30       1.0  0.828243913597031  0.4526472539395527  0.3585904002479444  1.0000
+  S   S4        1.0  0.18441039768771228  0.9275461529470431  0.7058790442100105  1.0000
+  O   O10       1.0  0.07344267496379653  0.9372220992434028  0.7118944454476168  1.0000
+  O   O11       1.0  0.386541679839588  0.7938257294941448  0.6674184688671658  1.0000
+  N   N4        1.0  0.36841848556412116  0.7094294676765264  0.6356148107273412  1.0000
+  C   C40       1.0  0.23354288051398545  0.04722194744393815  0.6675593032033508  1.0000
+  C   C41       1.0  0.2098909182798172  0.8637010100550786  0.5851918896915079  1.0000
+  H   H31       1.0  0.28607307828820305  0.8828132168696473  0.56439516992977  1.0000
+  H   H32       1.0  0.15614816441029666  0.8990216567280933  0.5355896865850751  1.0000
+  C   C42       1.0  0.1908867521763669  0.7547742291758802  0.5945028103134679  1.0000
+  C   C43       1.0  0.2632314967098247  0.6823975071369104  0.6178186199388498  1.0000
+  C   C44       1.0  0.24030219310657253  0.5812093405094393  0.6244173001548903  1.0000
+  H   H33       1.0  0.29993622999766906  0.5289766916653209  0.6408330574312303  1.0000
+  C   C45       1.0  0.14269398276685819  0.5496372088965512  0.6108190064316199  1.0000
+  H   H34       1.0  0.12432794471698216  0.4709107389129744  0.6174789961273085  1.0000
+  C   C46       1.0  0.06901534905387852  0.6195186980453679  0.5885350183408582  1.0000
+  H   H35       1.0  0.9922147558967178  0.5957249701097564  0.5776242153020649  1.0000
+  C   C47       1.0  0.09333968877736865  0.7199004905916212  0.5797922713511272  1.0000
+  H   H36       1.0  0.0357866447309575  0.7741686341527089  0.5619445795991804  1.0000
+  H   H37       1.0  0.08706789685201123  0.10728745316766286  0.6452891423805457  1.0000
+  C   C48       1.0  0.3728745776958487  0.15729100969569187  0.6416336165584379  1.0000
+  C   C49       1.0  0.33625198957211  0.0639946379748706  0.6682888211705948  1.0000
+  H   H38       1.0  0.3877693645574885  0.004899415930414541  0.6893669172316004  1.0000
+  Br  Br4       1.0  0.3556931982826356  0.3599752297084762  0.5799091403807484  1.0000
+  C   C50       1.0  0.16683785028976206  0.12256687007673928  0.6428169386209319  1.0000
+  C   C51       1.0  0.2031015232983776  0.21619123110409633  0.6163611556539842  1.0000
+  H   H39       1.0  0.15213075371026252  0.276002226249074  0.5967175045186525  1.0000
+  C   C52       1.0  0.3057525964775641  0.23232330779138866  0.6157749437935646  1.0000
+  O   O12       1.0  0.4321925168337306  0.645815613938436  0.6185954620986442  1.0000
+  H   H40       1.0  0.4526472539395527  0.17175608640296902  0.6414097722879029  1.0000
+  S   S5        1.0  0.427546152947043  0.6844103976877124  0.2058790442100104  1.0000
+  O   O13       1.0  0.43722209924340266  0.5734426749637965  0.21189444544761685  1.0000
+  O   O14       1.0  0.29382572949414465  0.886541679839588  0.1674184688671658  1.0000
+  N   N5        1.0  0.2094294676765263  0.8684184855641212  0.1356148107273411  1.0000
+  C   C53       1.0  0.5472219474439382  0.7335428805139854  0.16755930320335088  1.0000
+  C   C54       1.0  0.3637010100550786  0.7098909182798173  0.08519188969150808  1.0000
+  H   H41       1.0  0.38281321686964725  0.786073078288203  0.06439516992977005  1.0000
+  H   H42       1.0  0.39902165672809314  0.6561481644102967  0.03558968658507505  1.0000
+  C   C55       1.0  0.25477422917588033  0.6908867521763669  0.09450281031346801  1.0000
+  C   C56       1.0  0.1823975071369104  0.7632314967098247  0.11781861993884989  1.0000
+  C   C57       1.0  0.08120934050943918  0.7403021931065726  0.12441730015489026  1.0000
+  H   H43       1.0  0.02897669166532091  0.799936229997669  0.14083305743123042  1.0000
+  C   C58       1.0  0.04963720889655133  0.6426939827668582  0.1108190064316199  1.0000
+  H   H44       1.0  0.9709107389129743  0.6243279447169823  0.1174789961273085  1.0000
+  C   C59       1.0  0.11951869804536797  0.5690153490538785  0.0885350183408582  1.0000
+  H   H45       1.0  0.09572497010975622  0.4922147558967178  0.07762421530206486  1.0000
+  C   C60       1.0  0.2199004905916211  0.5933396887773688  0.07979227135112721  1.0000
+  H   H46       1.0  0.27416863415270876  0.5357866447309575  0.061944579599180476  1.0000
+  H   H47       1.0  0.6072874531676629  0.5870678968520112  0.1452891423805457  1.0000
+  C   C61       1.0  0.6572910096956919  0.8728745776958486  0.14163361655843795  1.0000
+  C   C62       1.0  0.5639946379748706  0.83625198957211  0.16828882117059485  1.0000
+  H   H48       1.0  0.5048994159304145  0.8877693645574886  0.18936691723160043  1.0000
+  Br  Br5       1.0  0.8599752297084763  0.8556931982826356  0.07990914038074841  1.0000
+  C   C63       1.0  0.6225668700767392  0.6668378502897622  0.14281693862093187  1.0000
+  C   C64       1.0  0.7161912311040964  0.7031015232983776  0.11636115565398424  1.0000
+  H   H49       1.0  0.776002226249074  0.6521307537102625  0.09671750451865246  1.0000
+  C   C65       1.0  0.7323233077913884  0.8057525964775641  0.11577494379356457  1.0000
+  O   O15       1.0  0.1458156139384359  0.9321925168337307  0.11859546209864419  1.0000
+  H   H50       1.0  0.671756086402969  0.9526472539395526  0.1414097722879029  1.0000
+  S   S6        1.0  0.3155896023122877  0.427546152947043  0.7941211283258368  1.0000
+  O   O16       1.0  0.4265573250362036  0.43722209924340266  0.7881057270882305  1.0000
+  O   O17       1.0  0.11345832016041202  0.29382572949414465  0.8325817036686816  1.0000
+  N   N6        1.0  0.13158151443587895  0.2094294676765263  0.8643853618085062  1.0000
+  C   C66       1.0  0.2664571194860146  0.5472219474439382  0.8324408693324965  1.0000
+  C   C67       1.0  0.29010908172018285  0.3637010100550786  0.9148082828443393  1.0000
+  H   H51       1.0  0.21392692171179695  0.38281321686964725  0.9356050026060773  1.0000
+  H   H52       1.0  0.34385183558970334  0.39902165672809314  0.9644104859507722  1.0000
+  C   C68       1.0  0.30911324782363314  0.25477422917588033  0.9054973622223793  1.0000
+  C   C69       1.0  0.2367685032901754  0.1823975071369104  0.8821815525969975  1.0000
+  C   C70       1.0  0.25969780689342753  0.08120934050943918  0.875582872380957  1.0000
+  H   H53       1.0  0.2000637700023309  0.02897669166532091  0.859167115104617  1.0000
+  C   C71       1.0  0.3573060172331419  0.04963720889655133  0.8891811661042275  1.0000
+  H   H54       1.0  0.37567205528301795  0.9709107389129743  0.8825211764085389  1.0000
+  C   C72       1.0  0.4309846509461215  0.11951869804536797  0.9114651541949892  1.0000
+  H   H55       1.0  0.5077852441032822  0.09572497010975622  0.9223759572337825  1.0000
+  C   C73       1.0  0.4066603112226313  0.2199004905916211  0.9202079011847202  1.0000
+  H   H56       1.0  0.4642133552690426  0.27416863415270876  0.9380555929366668  1.0000
+  H   H57       1.0  0.41293210314798895  0.6072874531676629  0.8547110301553016  1.0000
+  C   C74       1.0  0.12712542230415136  0.6572910096956919  0.8583665559774093  1.0000
+  C   C75       1.0  0.1637480104278901  0.5639946379748706  0.8317113513652525  1.0000
+  H   H58       1.0  0.11223063544251156  0.5048994159304145  0.8106332553042469  1.0000
+  Br  Br6       1.0  0.14430680171736432  0.8599752297084763  0.9200910321550989  1.0000
+  C   C76       1.0  0.33316214971023794  0.6225668700767392  0.8571832339149155  1.0000
+  C   C77       1.0  0.2968984767016223  0.7161912311040964  0.8836390168818631  1.0000
+  H   H59       1.0  0.3478692462897375  0.776002226249074  0.9032826680171948  1.0000
+  C   C78       1.0  0.194247403522436  0.7323233077913884  0.8842252287422828  1.0000
+  O   O18       1.0  0.06780748316626939  0.1458156139384359  0.8814047104372031  1.0000
+  H   H60       1.0  0.04735274606044726  0.671756086402969  0.8585904002479444  1.0000
+  S   S7        1.0  0.5724538470529569  0.3155896023122877  0.2058790442100104  1.0000
+  O   O19       1.0  0.5627779007565973  0.4265573250362036  0.21189444544761685  1.0000
+  O   O20       1.0  0.7061742705058554  0.11345832016041202  0.1674184688671658  1.0000
+  N   N7        1.0  0.7905705323234737  0.13158151443587895  0.1356148107273411  1.0000
+  C   C79       1.0  0.45277805255606185  0.2664571194860146  0.16755930320335088  1.0000
+  C   C80       1.0  0.6362989899449214  0.29010908172018285  0.08519188969150808  1.0000
+  H   H61       1.0  0.6171867831303527  0.21392692171179695  0.06439516992977005  1.0000
+  H   H62       1.0  0.6009783432719068  0.34385183558970334  0.03558968658507505  1.0000
+  C   C81       1.0  0.7452257708241198  0.30911324782363314  0.09450281031346801  1.0000
+  C   C82       1.0  0.8176024928630897  0.2367685032901754  0.11781861993884989  1.0000
+  C   C83       1.0  0.9187906594905607  0.25969780689342753  0.12441730015489026  1.0000
+  H   H63       1.0  0.9710233083346791  0.2000637700023309  0.14083305743123042  1.0000
+  C   C84       1.0  0.9503627911034489  0.3573060172331419  0.1108190064316199  1.0000
+  H   H64       1.0  0.029089261087025697  0.37567205528301795  0.1174789961273085  1.0000
+  C   C85       1.0  0.8804813019546321  0.4309846509461215  0.0885350183408582  1.0000
+  H   H65       1.0  0.9042750298902437  0.5077852441032822  0.07762421530206486  1.0000
+  C   C86       1.0  0.7800995094083789  0.4066603112226313  0.07979227135112721  1.0000
+  H   H66       1.0  0.7258313658472912  0.4642133552690426  0.061944579599180476  1.0000
+  H   H67       1.0  0.39271254683233714  0.41293210314798895  0.1452891423805457  1.0000
+  C   C87       1.0  0.3427089903043081  0.12712542230415136  0.14163361655843795  1.0000
+  C   C88       1.0  0.43600536202512946  0.1637480104278901  0.16828882117059485  1.0000
+  H   H68       1.0  0.49510058406958546  0.11223063544251156  0.18936691723160043  1.0000
+  Br  Br7       1.0  0.14002477029152383  0.14430680171736432  0.07990914038074841  1.0000
+  C   C89       1.0  0.377433129923261  0.33316214971023794  0.14281693862093187  1.0000
+  C   C90       1.0  0.2838087688959037  0.2968984767016223  0.11636115565398424  1.0000
+  H   H69       1.0  0.22399777375092603  0.3478692462897375  0.09671750451865246  1.0000
+  C   C91       1.0  0.26767669220861157  0.194247403522436  0.11577494379356457  1.0000
+  O   O21       1.0  0.8541843860615641  0.06780748316626939  0.11859546209864419  1.0000
+  H   H70       1.0  0.32824391359703103  0.04735274606044726  0.1414097722879029  1.0000
+  S   S8        1.0  0.6844103976877124  0.5724538470529569  0.7941211283258368  1.0000
+  O   O22       1.0  0.5734426749637965  0.5627779007565973  0.7881057270882305  1.0000
+  O   O23       1.0  0.886541679839588  0.7061742705058554  0.8325817036686816  1.0000
+  N   N8        1.0  0.8684184855641212  0.7905705323234737  0.8643853618085062  1.0000
+  C   C92       1.0  0.7335428805139854  0.45277805255606185  0.8324408693324965  1.0000
+  C   C93       1.0  0.7098909182798173  0.6362989899449214  0.9148082828443393  1.0000
+  H   H71       1.0  0.786073078288203  0.6171867831303527  0.9356050026060773  1.0000
+  H   H72       1.0  0.6561481644102967  0.6009783432719068  0.9644104859507722  1.0000
+  C   C94       1.0  0.6908867521763669  0.7452257708241198  0.9054973622223793  1.0000
+  C   C95       1.0  0.7632314967098247  0.8176024928630897  0.8821815525969975  1.0000
+  C   C96       1.0  0.7403021931065726  0.9187906594905607  0.875582872380957  1.0000
+  H   H73       1.0  0.799936229997669  0.9710233083346791  0.859167115104617  1.0000
+  C   C97       1.0  0.6426939827668582  0.9503627911034489  0.8891811661042275  1.0000
+  H   H74       1.0  0.6243279447169823  0.029089261087025697  0.8825211764085389  1.0000
+  C   C98       1.0  0.5690153490538785  0.8804813019546321  0.9114651541949892  1.0000
+  H   H75       1.0  0.4922147558967178  0.9042750298902437  0.9223759572337825  1.0000
+  C   C99       1.0  0.5933396887773688  0.7800995094083789  0.9202079011847202  1.0000
+  H   H76       1.0  0.5357866447309575  0.7258313658472912  0.9380555929366668  1.0000
+  H   H77       1.0  0.5870678968520112  0.39271254683233714  0.8547110301553016  1.0000
+  C   C100      1.0  0.8728745776958486  0.3427089903043081  0.8583665559774093  1.0000
+  C   C101      1.0  0.83625198957211  0.43600536202512946  0.8317113513652525  1.0000
+  H   H78       1.0  0.8877693645574886  0.49510058406958546  0.8106332553042469  1.0000
+  Br  Br8       1.0  0.8556931982826356  0.14002477029152383  0.9200910321550989  1.0000
+  C   C102      1.0  0.6668378502897622  0.377433129923261  0.8571832339149155  1.0000
+  C   C103      1.0  0.7031015232983776  0.2838087688959037  0.8836390168818631  1.0000
+  H   H79       1.0  0.6521307537102625  0.22399777375092603  0.9032826680171948  1.0000
+  C   C104      1.0  0.8057525964775641  0.26767669220861157  0.8842252287422828  1.0000
+  O   O24       1.0  0.9321925168337307  0.8541843860615641  0.8814047104372031  1.0000
+  H   H80       1.0  0.9526472539395526  0.32824391359703103  0.8585904002479444  1.0000

examples/protein.pdb

@@ -0,0 +1,755 @@
+CRYST1   27.285   19.353   21.501  90.00  90.00  90.00 P 1
+MODEL     1
+ATOM      1    N ILE     1       4.769   7.706  15.234  1.00  1.36           N  
+ATOM      2   CA ILE     1       5.318   7.181  13.957  1.00  0.28           C  
+ATOM      3    C ILE     1       6.145   8.241  13.237  1.00  0.30           C  
+ATOM      4    O ILE     1       5.612   9.248  12.771  1.00  0.55           O  
+ATOM      5   CB ILE     1       4.190   6.704  13.019  1.00  1.48           C  
+ATOM      6  CG1 ILE     1       3.351   5.624  13.706  1.00  1.64           C  
+ATOM      7  CG2 ILE     1       4.770   6.184  11.711  1.00  2.51           C  
+ATOM      8  CD1 ILE     1       2.117   5.224  12.922  1.00  2.53           C  
+ATOM      9   H1 ILE     1       4.128   8.502  15.046  1.00  1.90           H  
+ATOM     10   H2 ILE     1       5.541   8.033  15.848  1.00  1.95           H  
+ATOM     11   H3 ILE     1       4.242   6.959  15.730  1.00  1.91           H  
+ATOM     12   HA ILE     1       5.954   6.336  14.182  1.00  1.02           H  
+ATOM     13   HB ILE     1       3.559   7.550  12.792  1.00  2.12           H  
+ATOM     14 HG12 ILE     1       3.955   4.739  13.841  1.00  1.76           H  
+ATOM     15 HG13 ILE     1       3.030   5.986  14.671  1.00  1.90           H  
+ATOM     16 HG21 ILE     1       3.968   5.865  11.062  1.00  3.01           H  
+ATOM     17 HG22 ILE     1       5.423   5.348  11.913  1.00  2.95           H  
+ATOM     18 HG23 ILE     1       5.332   6.970  11.228  1.00  2.97           H  
+ATOM     19 HD11 ILE     1       2.412   4.823  11.966  1.00  2.80           H  
+ATOM     20 HD12 ILE     1       1.491   6.092  12.771  1.00  3.03           H  
+ATOM     21 HD13 ILE     1       1.567   4.476  13.474  1.00  3.02           H  
+ATOM     22    N LYS     2       7.451   8.007  13.152  1.00  0.08           N  
+ATOM     23   CA LYS     2       8.350   8.942  12.484  1.00  0.07           C  
+ATOM     24    C LYS     2       8.153   8.903  10.970  1.00  0.08           C  
+ATOM     25    O LYS     2       8.090   7.830  10.369  1.00  0.09           O  
+ATOM     26   CB LYS     2       9.812   8.619  12.813  1.00  0.08           C  
+ATOM     27   CG LYS     2      10.200   8.880  14.260  1.00  0.11           C  
+ATOM     28   CD LYS     2      11.632   8.440  14.552  1.00  0.12           C  
+ATOM     29   CE LYS     2      11.713   6.946  14.820  1.00  0.62           C  
+ATOM     30   NZ LYS     2      11.445   6.137  13.600  1.00  1.15           N  
+ATOM     31    H LYS     2       7.818   7.190  13.548  1.00  0.19           H  
+ATOM     32   HA LYS     2       8.121   9.935  12.839  1.00  0.09           H  
+ATOM     33  HB2 LYS     2       9.996   7.577  12.597  1.00  0.10           H  
+ATOM     34  HB3 LYS     2      10.448   9.221  12.180  1.00  0.10           H  
+ATOM     35  HG2 LYS     2      10.113   9.939  14.459  1.00  0.13           H  
+ATOM     36  HG3 LYS     2       9.528   8.334  14.905  1.00  0.12           H  
+ATOM     37  HD2 LYS     2      12.262   8.678  13.700  1.00  0.56           H  
+ATOM     38  HD3 LYS     2      11.990   8.972  15.421  1.00  0.49           H  
+ATOM     39  HE2 LYS     2      12.703   6.714  15.183  1.00  1.15           H  
+ATOM     40  HE3 LYS     2      10.987   6.690  15.578  1.00  1.06           H  
+ATOM     41  HZ1 LYS     2      12.140   6.362  12.860  1.00  1.67           H  
+ATOM     42  HZ2 LYS     2      10.492   6.339  13.240  1.00  1.71           H  
+ATOM     43  HZ3 LYS     2      11.510   5.123  13.823  1.00  1.58           H  
+ATOM     44    N LYS     3       8.050  10.080  10.364  1.00  0.08           N  
+ATOM     45   CA LYS     3       7.886  10.189   8.922  1.00  0.09           C  
+ATOM     46    C LYS     3       9.237  10.505   8.308  1.00  0.06           C  
+ATOM     47    O LYS     3       9.838   9.674   7.627  1.00  0.07           O  
+ATOM     48   CB LYS     3       6.873  11.280   8.573  1.00  0.12           C  
+ATOM     49   CG LYS     3       5.495  11.049   9.176  1.00  0.17           C  
+ATOM     50   CD LYS     3       4.537  12.181   8.840  1.00  0.70           C  
+ATOM     51   CE LYS     3       4.204  12.213   7.356  1.00  1.36           C  
+ATOM     52   NZ LYS     3       3.564  10.947   6.902  1.00  2.00           N  
+ATOM     53    H LYS     3       8.100  10.899  10.897  1.00  0.09           H  
+ATOM     54   HA LYS     3       7.537   9.237   8.547  1.00  0.11           H  
+ATOM     55  HB2 LYS     3       7.244  12.228   8.933  1.00  0.12           H  
+ATOM     56  HB3 LYS     3       6.768  11.329   7.499  1.00  0.13           H  
+ATOM     57  HG2 LYS     3       5.093  10.124   8.787  1.00  0.62           H  
+ATOM     58  HG3 LYS     3       5.592  10.978  10.250  1.00  0.55           H  
+ATOM     59  HD2 LYS     3       3.623  12.043   9.398  1.00  1.30           H  
+ATOM     60  HD3 LYS     3       4.993  13.120   9.118  1.00  1.35           H  
+ATOM     61  HE2 LYS     3       3.530  13.035   7.168  1.00  1.96           H  
+ATOM     62  HE3 LYS     3       5.118  12.363   6.799  1.00  1.95           H  
+ATOM     63  HZ1 LYS     3       2.678  10.785   7.424  1.00  2.29           H  
+ATOM     64  HZ2 LYS     3       4.203  10.144   7.070  1.00  2.50           H  
+ATOM     65  HZ3 LYS     3       3.350  11.000   5.886  1.00  2.53           H  
+ATOM     66    N ILE     4       9.708  11.720   8.555  1.00  0.05           N  
+ATOM     67   CA ILE     4      11.010  12.144   8.083  1.00  0.05           C  
+ATOM     68    C ILE     4      12.047  11.833   9.147  1.00  0.05           C  
+ATOM     69    O ILE     4      13.197  11.517   8.848  1.00  0.09           O  
+ATOM     70   CB ILE     4      11.030  13.652   7.757  1.00  0.09           C  
+ATOM     71  CG1 ILE     4      10.008  13.981   6.663  1.00  0.13           C  
+ATOM     72  CG2 ILE     4      12.427  14.093   7.340  1.00  0.11           C  
+ATOM     73  CD1 ILE     4      10.257  13.267   5.350  1.00  0.56           C  
+ATOM     74    H ILE     4       9.163  12.351   9.072  1.00  0.07           H  
+ATOM     75   HA ILE     4      11.245  11.586   7.191  1.00  0.05           H  
+ATOM     76   HB ILE     4      10.765  14.185   8.656  1.00  0.11           H  
+ATOM     77 HG12 ILE     4       9.023  13.704   7.007  1.00  0.46           H  
+ATOM     78 HG13 ILE     4      10.029  15.045   6.472  1.00  0.43           H  
+ATOM     79 HG21 ILE     4      12.728  13.551   6.456  1.00  0.97           H  
+ATOM     80 HG22 ILE     4      13.123  13.890   8.141  1.00  1.02           H  
+ATOM     81 HG23 ILE     4      12.422  15.152   7.128  1.00  1.01           H  
+ATOM     82 HD11 ILE     4      11.232  13.537   4.974  1.00  1.20           H  
+ATOM     83 HD12 ILE     4       9.502  13.555   4.635  1.00  1.04           H  
+ATOM     84 HD13 ILE     4      10.215  12.200   5.508  1.00  1.09           H  
+ATOM     85    N LEU     5      11.613  11.920  10.403  1.00  0.05           N  
+ATOM     86   CA LEU     5      12.471  11.633  11.540  1.00  0.07           C  
+ATOM     87    C LEU     5      12.819  10.151  11.573  1.00  0.06           C  
+ATOM     88    O LEU     5      13.675   9.721  12.340  1.00  0.08           O  
+ATOM     89   CB LEU     5      11.776  12.042  12.842  1.00  0.09           C  
+ATOM     90   CG LEU     5      11.696  13.548  13.103  1.00  0.26           C  
+ATOM     91  CD1 LEU     5      10.978  14.260  11.970  1.00  1.43           C  
+ATOM     92  CD2 LEU     5      10.989  13.814  14.421  1.00  1.25           C  
+ATOM     93    H LEU     5      10.684  12.189  10.567  1.00  0.06           H  
+ATOM     94   HA LEU     5      13.378  12.205  11.427  1.00  0.08           H  
+ATOM     95  HB2 LEU     5      10.771  11.647  12.826  1.00  0.16           H  
+ATOM     96  HB3 LEU     5      12.307  11.588  13.661  1.00  0.14           H  
+ATOM     97   HG LEU     5      12.696  13.951  13.173  1.00  1.14           H  
+ATOM     98 HD11 LEU     5      11.554  14.161  11.063  1.00  2.10           H  
+ATOM     99 HD12 LEU     5      10.864  15.304  12.213  1.00  1.95           H  
+ATOM    100 HD13 LEU     5      10.004  13.815  11.827  1.00  1.99           H  
+ATOM    101 HD21 LEU     5      10.000  13.383  14.388  1.00  1.86           H  
+ATOM    102 HD22 LEU     5      10.914  14.878  14.581  1.00  1.80           H  
+ATOM    103 HD23 LEU     5      11.550  13.366  15.227  1.00  1.89           H  
+ATOM    104    N SER     6      12.132   9.374  10.736  1.00  0.05           N  
+ATOM    105   CA SER     6      12.359   7.934  10.651  1.00  0.06           C  
+ATOM    106    C SER     6      13.630   7.656   9.866  1.00  0.07           C  
+ATOM    107    O SER     6      14.596   7.112  10.402  1.00  0.09           O  
+ATOM    108   CB SER     6      11.170   7.241   9.985  1.00  0.07           C  
+ATOM    109   OG SER     6      11.405   5.850   9.840  1.00  0.10           O  
+ATOM    110    H SER     6      11.463   9.785  10.152  1.00  0.04           H  
+ATOM    111   HA SER     6      12.476   7.555  11.655  1.00  0.07           H  
+ATOM    112  HB2 SER     6      10.290   7.381  10.595  1.00  0.10           H  
+ATOM    113  HB3 SER     6      11.003   7.671   9.008  1.00  0.09           H  
+ATOM    114   HG SER     6      12.184   5.713   9.297  1.00  0.91           H  
+ATOM    115    N LYS     7      13.621   8.024   8.587  1.00  0.08           N  
+ATOM    116   CA LYS     7      14.791   7.845   7.742  1.00  0.10           C  
+ATOM    117    C LYS     7      15.961   8.580   8.376  1.00  0.10           C  
+ATOM    118    O LYS     7      17.125   8.244   8.160  1.00  0.12           O  
+ATOM    119   CB LYS     7      14.527   8.378   6.333  1.00  0.13           C  
+ATOM    120   CG LYS     7      14.215   9.869   6.295  1.00  0.15           C  
+ATOM    121   CD LYS     7      13.850  10.335   4.893  1.00  0.21           C  
+ATOM    122   CE LYS     7      15.026  10.223   3.936  1.00  1.35           C  
+ATOM    123   NZ LYS     7      14.702  10.781   2.594  1.00  2.09           N  
+ATOM    124    H LYS     7      12.811   8.426   8.207  1.00  0.08           H  
+ATOM    125   HA LYS     7      15.016   6.789   7.693  1.00  0.11           H  
+ATOM    126  HB2 LYS     7      15.401   8.201   5.722  1.00  0.17           H  
+ATOM    127  HB3 LYS     7      13.688   7.847   5.908  1.00  0.14           H  
+ATOM    128  HG2 LYS     7      13.385  10.068   6.956  1.00  0.19           H  
+ATOM    129  HG3 LYS     7      15.085  10.415   6.630  1.00  0.18           H  
+ATOM    130  HD2 LYS     7      13.039   9.726   4.523  1.00  1.10           H  
+ATOM    131  HD3 LYS     7      13.534  11.366   4.941  1.00  1.04           H  
+ATOM    132  HE2 LYS     7      15.864  10.764   4.349  1.00  2.08           H  
+ATOM    133  HE3 LYS     7      15.290   9.180   3.830  1.00  1.93           H  
+ATOM    134  HZ1 LYS     7      14.450  11.787   2.676  1.00  2.64           H  
+ATOM    135  HZ2 LYS     7      13.901  10.267   2.177  1.00  2.54           H  
+ATOM    136  HZ3 LYS     7      15.524  10.690   1.962  1.00  2.44           H  
+ATOM    137    N ILE     8      15.617   9.590   9.168  1.00  0.09           N  
+ATOM    138   CA ILE     8      16.598  10.397   9.879  1.00  0.10           C  
+ATOM    139    C ILE     8      17.063   9.692  11.155  1.00  0.08           C  
+ATOM    140    O ILE     8      18.226   9.794  11.540  1.00  0.08           O  
+ATOM    141   CB ILE     8      16.005  11.774  10.239  1.00  0.11           C  
+ATOM    142  CG1 ILE     8      15.951  12.676   8.999  1.00  0.13           C  
+ATOM    143  CG2 ILE     8      16.806  12.434  11.350  1.00  0.11           C  
+ATOM    144  CD1 ILE     8      17.311  12.986   8.404  1.00  0.16           C  
+ATOM    145    H ILE     8      14.662   9.806   9.272  1.00  0.09           H  
+ATOM    146   HA ILE     8      17.447  10.549   9.230  1.00  0.12           H  
+ATOM    147   HB ILE     8      14.996  11.615  10.601  1.00  0.10           H  
+ATOM    148 HG12 ILE     8      15.361  12.192   8.236  1.00  0.13           H  
+ATOM    149 HG13 ILE     8      15.484  13.614   9.265  1.00  0.14           H  
+ATOM    150 HG21 ILE     8      17.853  12.431  11.087  1.00  1.00           H  
+ATOM    151 HG22 ILE     8      16.663  11.884  12.269  1.00  1.01           H  
+ATOM    152 HG23 ILE     8      16.469  13.451  11.483  1.00  1.03           H  
+ATOM    153 HD11 ILE     8      17.919  13.491   9.140  1.00  1.01           H  
+ATOM    154 HD12 ILE     8      17.188  13.620   7.539  1.00  0.97           H  
+ATOM    155 HD13 ILE     8      17.793  12.066   8.110  1.00  1.05           H  
+ATOM    156    N LYS     9      16.140   8.987  11.805  1.00  0.08           N  
+ATOM    157   CA LYS     9      16.444   8.262  13.038  1.00  0.07           C  
+ATOM    158    C LYS     9      17.712   7.426  12.887  1.00  0.04           C  
+ATOM    159    O LYS     9      18.456   7.228  13.847  1.00  0.07           O  
+ATOM    160   CB LYS     9      15.275   7.354  13.421  1.00  0.11           C  
+ATOM    161   CG LYS     9      15.356   6.829  14.845  1.00  0.17           C  
+ATOM    162   CD LYS     9      14.879   5.387  14.939  1.00  0.31           C  
+ATOM    163   CE LYS     9      14.924   4.879  16.371  1.00  0.95           C  
+ATOM    164   NZ LYS     9      14.480   3.462  16.473  1.00  1.63           N  
+ATOM    165    H LYS     9      15.225   8.961  11.454  1.00  0.08           H  
+ATOM    166   HA LYS     9      16.595   8.987  13.820  1.00  0.10           H  
+ATOM    167  HB2 LYS     9      14.355   7.907  13.317  1.00  0.12           H  
+ATOM    168  HB3 LYS     9      15.253   6.509  12.749  1.00  0.12           H  
+ATOM    169  HG2 LYS     9      16.379   6.881  15.183  1.00  0.23           H  
+ATOM    170  HG3 LYS     9      14.732   7.445  15.478  1.00  0.20           H  
+ATOM    171  HD2 LYS     9      13.865   5.327  14.579  1.00  0.68           H  
+ATOM    172  HD3 LYS     9      15.520   4.767  14.328  1.00  0.74           H  
+ATOM    173  HE2 LYS     9      15.938   4.956  16.737  1.00  1.50           H  
+ATOM    174  HE3 LYS     9      14.277   5.495  16.977  1.00  1.67           H  
+ATOM    175  HZ1 LYS     9      15.096   2.852  15.898  1.00  1.93           H  
+ATOM    176  HZ2 LYS     9      13.502   3.368  16.130  1.00  2.14           H  
+ATOM    177  HZ3 LYS     9      14.520   3.144  17.462  1.00  2.25           H  
+ATOM    178    N LYS    10      17.947   6.937  11.674  1.00  0.06           N  
+ATOM    179   CA LYS    10      19.117   6.113  11.393  1.00  0.10           C  
+ATOM    180    C LYS    10      20.300   6.962  10.940  1.00  0.11           C  
+ATOM    181    O LYS    10      21.456   6.554  11.070  1.00  0.16           O  
+ATOM    182   CB LYS    10      18.785   5.066  10.327  1.00  0.15           C  
+ATOM    183   CG LYS    10      17.736   4.060  10.772  1.00  0.20           C  
+ATOM    184   CD LYS    10      17.405   3.065   9.670  1.00  0.28           C  
+ATOM    185   CE LYS    10      16.672   3.732   8.517  1.00  1.21           C  
+ATOM    186   NZ LYS    10      15.384   4.335   8.953  1.00  2.02           N  
+ATOM    187    H LYS    10      17.321   7.144  10.948  1.00  0.07           H  
+ATOM    188   HA LYS    10      19.387   5.605  12.306  1.00  0.10           H  
+ATOM    189  HB2 LYS    10      18.418   5.571   9.445  1.00  0.15           H  
+ATOM    190  HB3 LYS    10      19.685   4.527  10.074  1.00  0.20           H  
+ATOM    191  HG2 LYS    10      18.109   3.521  11.630  1.00  0.23           H  
+ATOM    192  HG3 LYS    10      16.835   4.593  11.045  1.00  0.19           H  
+ATOM    193  HD2 LYS    10      18.325   2.637   9.299  1.00  1.06           H  
+ATOM    194  HD3 LYS    10      16.782   2.284  10.078  1.00  0.95           H  
+ATOM    195  HE2 LYS    10      17.301   4.508   8.107  1.00  1.88           H  
+ATOM    196  HE3 LYS    10      16.476   2.990   7.755  1.00  1.79           H  
+ATOM    197  HZ1 LYS    10      15.551   5.263   9.390  1.00  2.60           H  
+ATOM    198  HZ2 LYS    10      14.914   3.716   9.646  1.00  2.39           H  
+ATOM    199  HZ3 LYS    10      14.752   4.458   8.135  1.00  2.43           H  
+ATOM    200    N LEU    11      20.008   8.143  10.406  1.00  0.08           N  
+ATOM    201   CA LEU    11      21.050   9.046   9.927  1.00  0.12           C  
+ATOM    202    C LEU    11      21.619   9.898  11.060  1.00  0.13           C  
+ATOM    203    O LEU    11      22.776   9.733  11.447  1.00  0.17           O  
+ATOM    204   CB LEU    11      20.502   9.947   8.817  1.00  0.13           C  
+ATOM    205   CG LEU    11      20.046   9.216   7.552  1.00  0.13           C  
+ATOM    206  CD1 LEU    11      19.395  10.190   6.582  1.00  0.16           C  
+ATOM    207  CD2 LEU    11      21.221   8.509   6.890  1.00  0.18           C  
+ATOM    208    H LEU    11      19.069   8.414  10.329  1.00  0.08           H  
+ATOM    209   HA LEU    11      21.846   8.439   9.520  1.00  0.16           H  
+ATOM    210  HB2 LEU    11      19.662  10.498   9.211  1.00  0.14           H  
+ATOM    211  HB3 LEU    11      21.274  10.649   8.540  1.00  0.15           H  
+ATOM    212   HG LEU    11      19.313   8.470   7.820  1.00  0.14           H  
+ATOM    213 HD11 LEU    11      19.053   9.653   5.709  1.00  1.00           H  
+ATOM    214 HD12 LEU    11      20.116  10.937   6.283  1.00  1.01           H  
+ATOM    215 HD13 LEU    11      18.556  10.669   7.062  1.00  1.06           H  
+ATOM    216 HD21 LEU    11      21.974   9.236   6.625  1.00  0.98           H  
+ATOM    217 HD22 LEU    11      20.879   8.002   6.000  1.00  0.96           H  
+ATOM    218 HD23 LEU    11      21.642   7.789   7.577  1.00  1.08           H  
+ATOM    219    N LEU    12      20.805  10.810  11.590  1.00  0.12           N  
+ATOM    220   CA LEU    12      21.249  11.684  12.674  1.00  0.16           C  
+ATOM    221    C LEU    12      20.242  11.722  13.822  1.00  0.18           C  
+ATOM    222    O LEU    12      20.523  11.228  14.914  1.00  0.26           O  
+ATOM    223   CB LEU    12      21.502  13.103  12.153  1.00  0.24           C  
+ATOM    224   CG LEU    12      20.502  13.609  11.110  1.00  0.19           C  
+ATOM    225  CD1 LEU    12      20.252  15.097  11.289  1.00  0.30           C  
+ATOM    226  CD2 LEU    12      21.010  13.319   9.706  1.00  0.24           C  
+ATOM    227    H LEU    12      19.891  10.895  11.245  1.00  0.10           H  
+ATOM    228   HA LEU    12      22.179  11.285  13.050  1.00  0.23           H  
+ATOM    229  HB2 LEU    12      21.484  13.779  12.997  1.00  0.40           H  
+ATOM    230  HB3 LEU    12      22.488  13.132  11.716  1.00  0.36           H  
+ATOM    231   HG LEU    12      19.562  13.093  11.242  1.00  0.24           H  
+ATOM    232 HD11 LEU    12      21.179  15.637  11.161  1.00  0.93           H  
+ATOM    233 HD12 LEU    12      19.863  15.282  12.280  1.00  1.07           H  
+ATOM    234 HD13 LEU    12      19.536  15.433  10.554  1.00  1.11           H  
+ATOM    235 HD21 LEU    12      21.899  13.901   9.516  1.00  0.98           H  
+ATOM    236 HD22 LEU    12      20.248  13.580   8.986  1.00  1.04           H  
+ATOM    237 HD23 LEU    12      21.242  12.268   9.618  1.00  1.08           H  
+ATOM    238    N LYS    13      19.073  12.313  13.571  1.00  0.24           N  
+ATOM    239   CA LYS    13      18.029  12.423  14.590  1.00  0.34           C  
+ATOM    240    C LYS    13      18.520  13.234  15.786  1.00  0.74           C  
+ATOM    241    O LYS    13      18.299  14.463  15.796  1.00  1.46           O  
+ATOM    242   CB LYS    13      17.570  11.035  15.046  1.00  0.26           C  
+ATOM    243   CG LYS    13      16.554  11.065  16.180  1.00  0.26           C  
+ATOM    244   CD LYS    13      15.205  11.595  15.720  1.00  0.77           C  
+ATOM    245   CE LYS    13      14.250  10.465  15.359  1.00  0.29           C  
+ATOM    246   NZ LYS    13      14.086   9.500  16.480  1.00  1.13           N  
+ATOM    247  OXT LYS    13      19.125  12.635  16.701  1.00  1.39           O  
+ATOM    248    H LYS    13      18.908  12.681  12.681  1.00  0.26           H  
+ATOM    249   HA LYS    13      17.191  12.939  14.144  1.00  0.60           H  
+ATOM    250  HB2 LYS    13      17.122  10.526  14.207  1.00  0.52           H  
+ATOM    251  HB3 LYS    13      18.431  10.473  15.378  1.00  0.49           H  
+ATOM    252  HG2 LYS    13      16.424  10.062  16.559  1.00  0.74           H  
+ATOM    253  HG3 LYS    13      16.931  11.701  16.968  1.00  0.63           H  
+ATOM    254  HD2 LYS    13      14.770  12.181  16.515  1.00  1.56           H  
+ATOM    255  HD3 LYS    13      15.353  12.218  14.850  1.00  1.50           H  
+ATOM    256  HE2 LYS    13      13.286  10.892  15.122  1.00  0.93           H  
+ATOM    257  HE3 LYS    13      14.632   9.942  14.496  1.00  0.64           H  
+ATOM    258  HZ1 LYS    13      13.705   9.986  17.318  1.00  1.65           H  
+ATOM    259  HZ2 LYS    13      15.003   9.077  16.727  1.00  1.80           H  
+ATOM    260  HZ3 LYS    13      13.431   8.740  16.206  1.00  1.60           H  
+ATOM    261   CL CL      1       9.897   9.251   3.567  1.00  0.00          CL  
+ATOM    262    O SPC     1       6.261   1.831  15.733  1.00  0.00           O  
+ATOM    263   H1 SPC     1       6.919   1.134  15.447  1.00  0.00           H  
+ATOM    264   H2 SPC     1       6.561   2.727  15.405  1.00  0.00           H  
+ATOM    265   CL CL      2       7.297   8.301  18.972  1.00  0.00          CL  
+ATOM    266    O SPC     2       5.298  13.416  16.279  1.00  0.00           O  
+ATOM    267   H1 SPC     2       4.303  13.510  16.233  1.00  0.00           H  
+ATOM    268   H2 SPC     2       5.652  13.988  17.019  1.00  0.00           H  
+ATOM    269   CL CL      3      26.559   3.463   7.601  1.00  0.00          CL  
+ATOM    270    O SPC     3      16.856   1.187   2.515  1.00  0.00           O  
+ATOM    271   H1 SPC     3      15.863   1.216   2.634  1.00  0.00           H  
+ATOM    272   H2 SPC     3      17.123   0.287   2.170  1.00  0.00           H  
+ATOM    273   CL CL      4      23.395  17.562  10.867  1.00  0.00          CL  
+ATOM    274    O SPC     4      18.956  17.830   1.634  1.00  0.00           O  
+ATOM    275   H1 SPC     4      19.856  17.797   1.200  1.00  0.00           H  
+ATOM    276   H2 SPC     4      19.055  17.682   2.618  1.00  0.00           H  
+ATOM    277   CL CL      5      21.358  18.733   6.168  1.00  0.00          CL  
+ATOM    278    O SPC     5      10.657   0.664  14.626  1.00  0.00           O  
+ATOM    279   H1 SPC     5      10.920  -0.198  14.193  1.00  0.00           H  
+ATOM    280   H2 SPC     5      11.426   1.018  15.158  1.00  0.00           H  
+ATOM    281   CL CL      6       6.667   5.421   2.438  1.00  0.00          CL  
+ATOM    282    O SPC     6      12.517  17.139  20.263  1.00  0.00           O  
+ATOM    283   H1 SPC     6      12.551  16.600  19.421  1.00  0.00           H  
+ATOM    284   H2 SPC     6      12.134  18.042  20.065  1.00  0.00           H  
+ATOM    285    O SPC     7      19.141  10.625   1.841  1.00  0.00           O  
+ATOM    286   H1 SPC     7      19.462  10.641   2.788  1.00  0.00           H  
+ATOM    287   H2 SPC     7      19.510  11.414   1.350  1.00  0.00           H  
+ATOM    288    O SPC     8      19.223  14.264   2.661  1.00  0.00           O  
+ATOM    289   H1 SPC     8      19.942  14.112   1.984  1.00  0.00           H  
+ATOM    290   H2 SPC     8      18.352  13.925   2.304  1.00  0.00           H  
+ATOM    291    O SPC     9      13.406  17.838   5.743  1.00  0.00           O  
+ATOM    292   H1 SPC     9      13.573  17.071   6.363  1.00  0.00           H  
+ATOM    293   H2 SPC     9      12.463  17.800   5.413  1.00  0.00           H  
+ATOM    294    O SPC    10      21.294   4.393  14.866  1.00  0.00           O  
+ATOM    295   H1 SPC    10      21.576   3.433  14.878  1.00  0.00           H  
+ATOM    296   H2 SPC    10      21.379   4.752  13.936  1.00  0.00           H  
+ATOM    297    O SPC    11       5.918  15.436  18.750  1.00  0.00           O  
+ATOM    298   H1 SPC    11       5.520  16.336  18.930  1.00  0.00           H  
+ATOM    299   H2 SPC    11       5.291  14.725  19.067  1.00  0.00           H  
+ATOM    300    O SPC    12      20.585   6.909  18.582  1.00  0.00           O  
+ATOM    301   H1 SPC    12      20.293   6.188  19.210  1.00  0.00           H  
+ATOM    302   H2 SPC    12      20.234   6.716  17.666  1.00  0.00           H  
+ATOM    303    O SPC    13      12.344   7.267  18.653  1.00  0.00           O  
+ATOM    304   H1 SPC    13      11.490   7.357  18.140  1.00  0.00           H  
+ATOM    305   H2 SPC    13      12.474   6.312  18.921  1.00  0.00           H  
+ATOM    306    O SPC    14      17.718  16.195   6.438  1.00  0.00           O  
+ATOM    307   H1 SPC    14      17.305  17.003   6.858  1.00  0.00           H  
+ATOM    308   H2 SPC    14      18.294  15.728   7.110  1.00  0.00           H  
+ATOM    309    O SPC    15       9.912  14.515  19.459  1.00  0.00           O  
+ATOM    310   H1 SPC    15       9.733  14.289  18.502  1.00  0.00           H  
+ATOM    311   H2 SPC    15      10.550  15.284  19.507  1.00  0.00           H  
+ATOM    312    O SPC    16      11.920  11.940  19.925  1.00  0.00           O  
+ATOM    313   H1 SPC    16      11.855  12.599  20.675  1.00  0.00           H  
+ATOM    314   H2 SPC    16      11.004  11.626  19.677  1.00  0.00           H  
+ATOM    315    O SPC    17      20.400   3.866   3.797  1.00  0.00           O  
+ATOM    316   H1 SPC    17      20.658   4.772   3.463  1.00  0.00           H  
+ATOM    317   H2 SPC    17      19.636   3.516   3.256  1.00  0.00           H  
+ATOM    318    O SPC    18       5.982  15.132  12.363  1.00  0.00           O  
+ATOM    319   H1 SPC    18       5.536  14.306  12.019  1.00  0.00           H  
+ATOM    320   H2 SPC    18       5.857  15.876  11.707  1.00  0.00           H  
+ATOM    321    O SPC    19      11.014   3.970  20.071  1.00  0.00           O  
+ATOM    322   H1 SPC    19      11.995   4.059  19.901  1.00  0.00           H  
+ATOM    323   H2 SPC    19      10.838   3.125  20.576  1.00  0.00           H  
+ATOM    324    O SPC    20       4.258  13.880   3.901  1.00  0.00           O  
+ATOM    325   H1 SPC    20       3.792  13.612   4.744  1.00  0.00           H  
+ATOM    326   H2 SPC    20       5.219  14.073   4.097  1.00  0.00           H  
+ATOM    327    O SPC    21      14.164   1.782   2.849  1.00  0.00           O  
+ATOM    328   H1 SPC    21      14.182   2.690   2.429  1.00  0.00           H  
+ATOM    329   H2 SPC    21      13.232   1.567   3.140  1.00  0.00           H  
+ATOM    330    O SPC    22       7.985   3.467   7.556  1.00  0.00           O  
+ATOM    331   H1 SPC    22       7.309   4.176   7.754  1.00  0.00           H  
+ATOM    332   H2 SPC    22       7.836   2.686   8.163  1.00  0.00           H  
+ATOM    333    O SPC    23      16.618  17.897  11.065  1.00  0.00           O  
+ATOM    334   H1 SPC    23      17.509  18.275  11.316  1.00  0.00           H  
+ATOM    335   H2 SPC    23      16.063  18.608  10.634  1.00  0.00           H  
+ATOM    336    O SPC    24      11.707   1.635   4.132  1.00  0.00           O  
+ATOM    337   H1 SPC    24      11.422   1.100   4.927  1.00  0.00           H  
+ATOM    338   H2 SPC    24      12.027   2.534   4.432  1.00  0.00           H  
+ATOM    339    O SPC    25      10.599   2.726   7.183  1.00  0.00           O  
+ATOM    340   H1 SPC    25       9.633   2.922   7.352  1.00  0.00           H  
+ATOM    341   H2 SPC    25      10.837   1.844   7.589  1.00  0.00           H  
+ATOM    342    O SPC    26       7.809  10.947  16.146  1.00  0.00           O  
+ATOM    343   H1 SPC    26       8.603  11.000  16.752  1.00  0.00           H  
+ATOM    344   H2 SPC    26       7.188  10.234  16.472  1.00  0.00           H  
+ATOM    345    O SPC    27      19.669  18.552  11.161  1.00  0.00           O  
+ATOM    346   H1 SPC    27      19.731  18.823  10.200  1.00  0.00           H  
+ATOM    347   H2 SPC    27      20.224  17.734  11.314  1.00  0.00           H  
+ATOM    348    O SPC    28       4.856  18.276   3.656  1.00  0.00           O  
+ATOM    349   H1 SPC    28       5.410  18.559   4.438  1.00  0.00           H  
+ATOM    350   H2 SPC    28       4.204  17.575   3.945  1.00  0.00           H  
+ATOM    351    O SPC    29      21.625   1.298  18.698  1.00  0.00           O  
+ATOM    352   H1 SPC    29      22.155   2.125  18.510  1.00  0.00           H  
+ATOM    353   H2 SPC    29      21.384   1.270  19.668  1.00  0.00           H  
+ATOM    354    O SPC    30      16.688  18.172   7.860  1.00  0.00           O  
+ATOM    355   H1 SPC    30      16.240  18.965   7.448  1.00  0.00           H  
+ATOM    356   H2 SPC    30      17.356  18.480   8.537  1.00  0.00           H  
+ATOM    357    O SPC    31       8.823  17.984   4.545  1.00  0.00           O  
+ATOM    358   H1 SPC    31       9.592  17.404   4.276  1.00  0.00           H  
+ATOM    359   H2 SPC    31       8.400  18.376   3.728  1.00  0.00           H  
+ATOM    360    O SPC    32       4.721   3.752  18.667  1.00  0.00           O  
+ATOM    361   H1 SPC    32       5.555   4.251  18.430  1.00  0.00           H  
+ATOM    362   H2 SPC    32       4.061   4.381  19.077  1.00  0.00           H  
+ATOM    363    O SPC    33      14.212   4.749   2.506  1.00  0.00           O  
+ATOM    364   H1 SPC    33      14.108   4.871   3.493  1.00  0.00           H  
+ATOM    365   H2 SPC    33      14.965   5.318   2.177  1.00  0.00           H  
+ATOM    366    O SPC    34       9.087   4.361   4.883  1.00  0.00           O  
+ATOM    367   H1 SPC    34       9.043   3.762   4.084  1.00  0.00           H  
+ATOM    368   H2 SPC    34       9.715   3.973   5.557  1.00  0.00           H  
+ATOM    369    O SPC    35      22.138  17.630  16.643  1.00  0.00           O  
+ATOM    370   H1 SPC    35      23.135  17.693  16.598  1.00  0.00           H  
+ATOM    371   H2 SPC    35      21.813  18.074  17.478  1.00  0.00           H  
+ATOM    372    O SPC    36       6.593   1.462  18.547  1.00  0.00           O  
+ATOM    373   H1 SPC    36       6.607   1.684  17.572  1.00  0.00           H  
+ATOM    374   H2 SPC    36       5.915   2.033  19.009  1.00  0.00           H  
+ATOM    375    O SPC    37      19.103  16.688   4.060  1.00  0.00           O  
+ATOM    376   H1 SPC    37      18.866  15.885   3.513  1.00  0.00           H  
+ATOM    377   H2 SPC    37      18.602  16.663   4.925  1.00  0.00           H  
+ATOM    378    O SPC    38       6.487   1.180  12.550  1.00  0.00           O  
+ATOM    379   H1 SPC    38       6.846   0.976  13.460  1.00  0.00           H  
+ATOM    380   H2 SPC    38       6.402   2.171  12.440  1.00  0.00           H  
+ATOM    381    O SPC    39       7.987  18.699  14.735  1.00  0.00           O  
+ATOM    382   H1 SPC    39       8.933  19.008  14.834  1.00  0.00           H  
+ATOM    383   H2 SPC    39       7.977  17.762  14.385  1.00  0.00           H  
+ATOM    384    O SPC    40       9.451   3.332  15.442  1.00  0.00           O  
+ATOM    385   H1 SPC    40       9.442   2.387  15.117  1.00  0.00           H  
+ATOM    386   H2 SPC    40       9.388   3.954  14.661  1.00  0.00           H  
+ATOM    387    O SPC    41      14.629  17.007  17.563  1.00  0.00           O  
+ATOM    388   H1 SPC    41      15.022  16.841  18.467  1.00  0.00           H  
+ATOM    389   H2 SPC    41      15.255  16.667  16.860  1.00  0.00           H  
+ATOM    390    O SPC    42      18.095  18.198  17.459  1.00  0.00           O  
+ATOM    391   H1 SPC    42      17.283  18.734  17.689  1.00  0.00           H  
+ATOM    392   H2 SPC    42      18.620  18.016  18.291  1.00  0.00           H  
+ATOM    393    O SPC    43       7.751  12.684   2.074  1.00  0.00           O  
+ATOM    394   H1 SPC    43       8.272  13.385   1.587  1.00  0.00           H  
+ATOM    395   H2 SPC    43       6.906  12.491   1.576  1.00  0.00           H  
+ATOM    396    O SPC    44       6.761  14.926   4.575  1.00  0.00           O  
+ATOM    397   H1 SPC    44       7.479  14.385   5.013  1.00  0.00           H  
+ATOM    398   H2 SPC    44       7.103  15.298   3.712  1.00  0.00           H  
+ATOM    399    O SPC    45      21.072   2.084  12.096  1.00  0.00           O  
+ATOM    400   H1 SPC    45      20.445   1.317  11.959  1.00  0.00           H  
+ATOM    401   H2 SPC    45      21.539   1.979  12.974  1.00  0.00           H  
+ATOM    402    O SPC    46       9.511   4.678  17.663  1.00  0.00           O  
+ATOM    403   H1 SPC    46       9.351   4.034  16.915  1.00  0.00           H  
+ATOM    404   H2 SPC    46       9.858   4.184  18.460  1.00  0.00           H  
+ATOM    405    O SPC    47      19.135   9.231  18.266  1.00  0.00           O  
+ATOM    406   H1 SPC    47      19.818   8.510  18.383  1.00  0.00           H  
+ATOM    407   H2 SPC    47      19.085   9.783  19.098  1.00  0.00           H  
+ATOM    408    O SPC    48       6.482   5.844   8.313  1.00  0.00           O  
+ATOM    409   H1 SPC    48       6.638   5.763   9.297  1.00  0.00           H  
+ATOM    410   H2 SPC    48       5.544   5.572   8.100  1.00  0.00           H  
+ATOM    411    O SPC    49       5.359  17.384   8.062  1.00  0.00           O  
+ATOM    412   H1 SPC    49       5.184  17.496   9.040  1.00  0.00           H  
+ATOM    413   H2 SPC    49       5.918  18.145   7.734  1.00  0.00           H  
+ATOM    414    O SPC    50      13.657   4.551   5.299  1.00  0.00           O  
+ATOM    415   H1 SPC    50      14.115   4.420   6.178  1.00  0.00           H  
+ATOM    416   H2 SPC    50      13.042   5.338   5.357  1.00  0.00           H  
+ATOM    417    O SPC    51      16.589   6.095   2.292  1.00  0.00           O  
+ATOM    418   H1 SPC    51      16.819   6.762   2.999  1.00  0.00           H  
+ATOM    419   H2 SPC    51      17.197   5.304   2.368  1.00  0.00           H  
+ATOM    420    O SPC    52       9.029   0.856  11.098  1.00  0.00           O  
+ATOM    421   H1 SPC    52       9.717   0.588  11.772  1.00  0.00           H  
+ATOM    422   H2 SPC    52       8.116   0.681  11.466  1.00  0.00           H  
+ATOM    423    O SPC    53      11.303   0.988  19.585  1.00  0.00           O  
+ATOM    424   H1 SPC    53      10.559   0.668  18.998  1.00  0.00           H  
+ATOM    425   H2 SPC    53      10.933   1.255  20.475  1.00  0.00           H  
+ATOM    426    O SPC    54      22.625   4.355   7.686  1.00  0.00           O  
+ATOM    427   H1 SPC    54      22.459   3.600   7.052  1.00  0.00           H  
+ATOM    428   H2 SPC    54      22.613   4.011   8.625  1.00  0.00           H  
+ATOM    429    O SPC    55      14.411  16.629   3.546  1.00  0.00           O  
+ATOM    430   H1 SPC    55      14.129  17.141   4.357  1.00  0.00           H  
+ATOM    431   H2 SPC    55      13.960  17.009   2.738  1.00  0.00           H  
+ATOM    432    O SPC    56      12.497  15.449  17.708  1.00  0.00           O  
+ATOM    433   H1 SPC    56      13.385  15.901  17.618  1.00  0.00           H  
+ATOM    434   H2 SPC    56      12.620  14.458  17.649  1.00  0.00           H  
+ATOM    435    O SPC    57      10.650  18.495   6.345  1.00  0.00           O  
+ATOM    436   H1 SPC    57      10.490  18.642   7.321  1.00  0.00           H  
+ATOM    437   H2 SPC    57       9.863  18.026   5.945  1.00  0.00           H  
+ATOM    438    O SPC    58       9.230  18.485  18.121  1.00  0.00           O  
+ATOM    439   H1 SPC    58       8.475  19.011  17.729  1.00  0.00           H  
+ATOM    440   H2 SPC    58       9.326  17.621  17.627  1.00  0.00           H  
+ATOM    441    O SPC    59       5.443  11.472  19.165  1.00  0.00           O  
+ATOM    442   H1 SPC    59       5.348  10.913  18.342  1.00  0.00           H  
+ATOM    443   H2 SPC    59       5.660  10.884  19.944  1.00  0.00           H  
+ATOM    444    O SPC    60       5.856   9.963   2.730  1.00  0.00           O  
+ATOM    445   H1 SPC    60       5.040   9.579   3.160  1.00  0.00           H  
+ATOM    446   H2 SPC    60       6.658   9.754   3.290  1.00  0.00           H  
+ATOM    447    O SPC    61       4.298  13.641  19.867  1.00  0.00           O  
+ATOM    448   H1 SPC    61       4.782  12.820  19.565  1.00  0.00           H  
+ATOM    449   H2 SPC    61       4.093  13.567  20.843  1.00  0.00           H  
+ATOM    450    O SPC    62      22.334   1.767  14.655  1.00  0.00           O  
+ATOM    451   H1 SPC    62      21.720   1.051  14.988  1.00  0.00           H  
+ATOM    452   H2 SPC    62      23.132   1.828  15.255  1.00  0.00           H  
+ATOM    453    O SPC    63       4.784  17.732  19.659  1.00  0.00           O  
+ATOM    454   H1 SPC    63       4.767  17.787  20.657  1.00  0.00           H  
+ATOM    455   H2 SPC    63       4.976  18.637  19.278  1.00  0.00           H  
+ATOM    456    O SPC    64      11.068  16.275   3.866  1.00  0.00           O  
+ATOM    457   H1 SPC    64      11.664  16.630   3.146  1.00  0.00           H  
+ATOM    458   H2 SPC    64      11.200  15.288   3.953  1.00  0.00           H  
+ATOM    459    O SPC    65      20.355   4.147  17.856  1.00  0.00           O  
+ATOM    460   H1 SPC    65      20.727   3.808  16.991  1.00  0.00           H  
+ATOM    461   H2 SPC    65      19.392   3.888  17.928  1.00  0.00           H  
+ATOM    462    O SPC    66       4.815  17.547  10.820  1.00  0.00           O  
+ATOM    463   H1 SPC    66       4.152  16.921  11.231  1.00  0.00           H  
+ATOM    464   H2 SPC    66       4.746  18.442  11.259  1.00  0.00           H  
+ATOM    465    O SPC    67      22.062   9.053   3.444  1.00  0.00           O  
+ATOM    466   H1 SPC    67      21.873   8.526   2.616  1.00  0.00           H  
+ATOM    467   H2 SPC    67      21.212   9.454   3.785  1.00  0.00           H  
+ATOM    468    O SPC    68       6.834   0.527   6.251  1.00  0.00           O  
+ATOM    469   H1 SPC    68       7.614   0.241   5.695  1.00  0.00           H  
+ATOM    470   H2 SPC    68       6.765   1.524   6.241  1.00  0.00           H  
+ATOM    471    O SPC    69      12.762  17.941  10.027  1.00  0.00           O  
+ATOM    472   H1 SPC    69      13.754  18.035  10.105  1.00  0.00           H  
+ATOM    473   H2 SPC    69      12.477  17.071  10.430  1.00  0.00           H  
+ATOM    474    O SPC    70      16.766  13.324  20.246  1.00  0.00           O  
+ATOM    475   H1 SPC    70      16.271  12.562  20.663  1.00  0.00           H  
+ATOM    476   H2 SPC    70      16.680  13.274  19.251  1.00  0.00           H  
+ATOM    477    O SPC    71       7.652  16.077   2.148  1.00  0.00           O  
+ATOM    478   H1 SPC    71       7.170  15.894   1.291  1.00  0.00           H  
+ATOM    479   H2 SPC    71       8.576  15.696   2.098  1.00  0.00           H  
+ATOM    480    O SPC    72      16.286  15.930  19.543  1.00  0.00           O  
+ATOM    481   H1 SPC    72      16.200  15.181  20.200  1.00  0.00           H  
+ATOM    482   H2 SPC    72      17.041  16.527  19.814  1.00  0.00           H  
+ATOM    483    O SPC    73      13.664   1.172  12.470  1.00  0.00           O  
+ATOM    484   H1 SPC    73      14.046   0.867  11.598  1.00  0.00           H  
+ATOM    485   H2 SPC    73      13.463   2.150  12.423  1.00  0.00           H  
+ATOM    486    O SPC    74       6.873   1.924   9.405  1.00  0.00           O  
+ATOM    487   H1 SPC    74       7.192   1.611  10.300  1.00  0.00           H  
+ATOM    488   H2 SPC    74       5.956   2.313   9.495  1.00  0.00           H  
+ATOM    489    O SPC    75       8.784   6.377   6.759  1.00  0.00           O  
+ATOM    490   H1 SPC    75       7.952   6.473   7.305  1.00  0.00           H  
+ATOM    491   H2 SPC    75       8.718   5.556   6.192  1.00  0.00           H  
+ATOM    492    O SPC    76      17.750   3.671   2.186  1.00  0.00           O  
+ATOM    493   H1 SPC    76      17.577   2.712   2.411  1.00  0.00           H  
+ATOM    494   H2 SPC    76      17.853   3.768   1.196  1.00  0.00           H  
+ATOM    495    O SPC    77      15.646  14.881   5.366  1.00  0.00           O  
+ATOM    496   H1 SPC    77      16.376  15.291   5.913  1.00  0.00           H  
+ATOM    497   H2 SPC    77      15.259  15.572   4.756  1.00  0.00           H  
+ATOM    498    O SPC    78       7.903  16.016  13.873  1.00  0.00           O  
+ATOM    499   H1 SPC    78       7.006  15.938  13.438  1.00  0.00           H  
+ATOM    500   H2 SPC    78       7.864  15.618  14.790  1.00  0.00           H  
+ATOM    501    O SPC    79      13.572  16.924  13.138  1.00  0.00           O  
+ATOM    502   H1 SPC    79      13.432  17.856  12.803  1.00  0.00           H  
+ATOM    503   H2 SPC    79      12.685  16.485  13.282  1.00  0.00           H  
+ATOM    504    O SPC    80      16.856   1.187  21.136  1.00  0.00           O  
+ATOM    505   H1 SPC    80      15.863   1.216  21.255  1.00  0.00           H  
+ATOM    506   H2 SPC    80      17.123   0.287  20.791  1.00  0.00           H  
+ATOM    507    O SPC    81      18.956  17.830  20.255  1.00  0.00           O  
+ATOM    508   H1 SPC    81      19.856  17.797  19.821  1.00  0.00           H  
+ATOM    509   H2 SPC    81      19.055  17.682  21.239  1.00  0.00           H  
+ATOM    510    O SPC    82      12.517  17.139   1.642  1.00  0.00           O  
+ATOM    511   H1 SPC    82      12.551  16.600   0.800  1.00  0.00           H  
+ATOM    512   H2 SPC    82      12.134  18.042   1.445  1.00  0.00           H  
+ATOM    513    O SPC    83      19.141  10.625  20.461  1.00  0.00           O  
+ATOM    514   H1 SPC    83      19.462  10.641  21.408  1.00  0.00           H  
+ATOM    515   H2 SPC    83      19.510  11.414  19.971  1.00  0.00           H  
+ATOM    516    O SPC    84       9.912  14.515   0.839  1.00  0.00           O  
+ATOM    517   H1 SPC    84       9.733  14.289  -0.119  1.00  0.00           H  
+ATOM    518   H2 SPC    84      10.550  15.284   0.886  1.00  0.00           H  
+ATOM    519    O SPC    85      11.014   3.970   1.451  1.00  0.00           O  
+ATOM    520   H1 SPC    85      11.995   4.059   1.280  1.00  0.00           H  
+ATOM    521   H2 SPC    85      10.838   3.125   1.956  1.00  0.00           H  
+ATOM    522    O SPC    86       7.751  12.684  20.695  1.00  0.00           O  
+ATOM    523   H1 SPC    86       8.272  13.385  20.207  1.00  0.00           H  
+ATOM    524   H2 SPC    86       6.906  12.491  20.197  1.00  0.00           H  
+ATOM    525    O SPC    87      16.589   6.095  20.912  1.00  0.00           O  
+ATOM    526   H1 SPC    87      16.819   6.762  21.620  1.00  0.00           H  
+ATOM    527   H2 SPC    87      17.197   5.304  20.989  1.00  0.00           H  
+ATOM    528    O SPC    88      11.303   0.988   0.965  1.00  0.00           O  
+ATOM    529   H1 SPC    88      10.559   0.668   0.377  1.00  0.00           H  
+ATOM    530   H2 SPC    88      10.933   1.255   1.854  1.00  0.00           H  
+ATOM    531    O SPC    89       4.298  13.641   1.247  1.00  0.00           O  
+ATOM    532   H1 SPC    89       4.782  12.820   0.945  1.00  0.00           H  
+ATOM    533   H2 SPC    89       4.093  13.567   2.223  1.00  0.00           H  
+ATOM    534    O SPC    90       4.784  17.732   1.038  1.00  0.00           O  
+ATOM    535   H1 SPC    90       4.767  17.787   2.036  1.00  0.00           H  
+ATOM    536   H2 SPC    90       4.976  18.637   0.658  1.00  0.00           H  
+ATOM    537    O SPC    91      16.766  13.324   1.625  1.00  0.00           O  
+ATOM    538   H1 SPC    91      16.271  12.562   2.042  1.00  0.00           H  
+ATOM    539   H2 SPC    91      16.680  13.274   0.630  1.00  0.00           H  
+ATOM    540    O SPC    92       7.652  16.077  20.768  1.00  0.00           O  
+ATOM    541   H1 SPC    92       7.170  15.894  19.911  1.00  0.00           H  
+ATOM    542   H2 SPC    92       8.576  15.696  20.719  1.00  0.00           H  
+ATOM    543    O SPC    93      16.286  15.930   0.922  1.00  0.00           O  
+ATOM    544   H1 SPC    93      16.200  15.181   1.579  1.00  0.00           H  
+ATOM    545   H2 SPC    93      17.041  16.527   1.193  1.00  0.00           H  
+ATOM    546    O SPC    94      17.750   3.671  20.807  1.00  0.00           O  
+ATOM    547   H1 SPC    94      17.577   2.712  21.032  1.00  0.00           H  
+ATOM    548   H2 SPC    94      17.853   3.768  19.817  1.00  0.00           H  
+ATOM    549    O SPC    95      24.882   1.831  15.733  1.00  0.00           O  
+ATOM    550   H1 SPC    95      25.540   1.134  15.447  1.00  0.00           H  
+ATOM    551   H2 SPC    95      25.182   2.727  15.405  1.00  0.00           H  
+ATOM    552    O SPC    96       1.798  12.257  13.339  1.00  0.00           O  
+ATOM    553   H1 SPC    96       2.693  11.812  13.387  1.00  0.00           H  
+ATOM    554   H2 SPC    96       1.099  11.577  13.117  1.00  0.00           H  
+ATOM    555    O SPC    97      23.919  13.416  16.279  1.00  0.00           O  
+ATOM    556   H1 SPC    97      22.924  13.510  16.233  1.00  0.00           H  
+ATOM    557   H2 SPC    97      24.273  13.988  17.019  1.00  0.00           H  
+ATOM    558    O SPC    98       1.285  12.800   5.118  1.00  0.00           O  
+ATOM    559   H1 SPC    98       0.812  13.133   5.933  1.00  0.00           H  
+ATOM    560   H2 SPC    98       1.074  13.395   4.343  1.00  0.00           H  
+ATOM    561    O SPC    99      23.846  12.106   7.927  1.00  0.00           O  
+ATOM    562   H1 SPC    99      23.104  11.507   7.628  1.00  0.00           H  
+ATOM    563   H2 SPC    99      23.575  13.061   7.800  1.00  0.00           H  
+ATOM    564    O SPC   100       0.520  10.625   1.841  1.00  0.00           O  
+ATOM    565   H1 SPC   100       0.842  10.641   2.788  1.00  0.00           H  
+ATOM    566   H2 SPC   100       0.889  11.414   1.350  1.00  0.00           H  
+ATOM    567    O SPC   101       0.602  14.264   2.661  1.00  0.00           O  
+ATOM    568   H1 SPC   101       1.322  14.112   1.984  1.00  0.00           H  
+ATOM    569   H2 SPC   101      -0.269  13.925   2.304  1.00  0.00           H  
+ATOM    570    O SPC   102      26.321   8.416   4.919  1.00  0.00           O  
+ATOM    571   H1 SPC   102      25.775   8.888   5.611  1.00  0.00           H  
+ATOM    572   H2 SPC   102      26.424   7.455   5.175  1.00  0.00           H  
+ATOM    573    O SPC   103      24.539  15.436  18.750  1.00  0.00           O  
+ATOM    574   H1 SPC   103      24.141  16.336  18.930  1.00  0.00           H  
+ATOM    575   H2 SPC   103      23.911  14.725  19.067  1.00  0.00           H  
+ATOM    576    O SPC   104       1.965   6.909  18.582  1.00  0.00           O  
+ATOM    577   H1 SPC   104       1.673   6.188  19.210  1.00  0.00           H  
+ATOM    578   H2 SPC   104       1.614   6.716  17.666  1.00  0.00           H  
+ATOM    579    O SPC   105      26.115   9.341   9.983  1.00  0.00           O  
+ATOM    580   H1 SPC   105      26.904   8.833   9.641  1.00  0.00           H  
+ATOM    581   H2 SPC   105      26.403   9.944  10.728  1.00  0.00           H  
+ATOM    582    O SPC   106       2.876  18.601   9.014  1.00  0.00           O  
+ATOM    583   H1 SPC   106       3.273  17.956   9.667  1.00  0.00           H  
+ATOM    584   H2 SPC   106       3.358  18.530   8.141  1.00  0.00           H  
+ATOM    585    O SPC   107       1.245  10.221   4.500  1.00  0.00           O  
+ATOM    586   H1 SPC   107       0.662   9.700   5.123  1.00  0.00           H  
+ATOM    587   H2 SPC   107       1.118  11.200   4.666  1.00  0.00           H  
+ATOM    588    O SPC   108       3.411   2.574   5.422  1.00  0.00           O  
+ATOM    589   H1 SPC   108       2.956   3.365   5.014  1.00  0.00           H  
+ATOM    590   H2 SPC   108       4.367   2.800   5.611  1.00  0.00           H  
+ATOM    591    O SPC   109       1.780   3.866   3.797  1.00  0.00           O  
+ATOM    592   H1 SPC   109       2.038   4.772   3.463  1.00  0.00           H  
+ATOM    593   H2 SPC   109       1.015   3.516   3.256  1.00  0.00           H  
+ATOM    594    O SPC   110       2.715  18.729   6.229  1.00  0.00           O  
+ATOM    595   H1 SPC   110       2.720  17.982   5.564  1.00  0.00           H  
+ATOM    596   H2 SPC   110       3.101  19.551   5.809  1.00  0.00           H  
+ATOM    597    O SPC   111      22.878  13.880   3.901  1.00  0.00           O  
+ATOM    598   H1 SPC   111      22.413  13.612   4.744  1.00  0.00           H  
+ATOM    599   H2 SPC   111      23.839  14.073   4.097  1.00  0.00           H  
+ATOM    600    O SPC   112       3.617   5.961   5.521  1.00  0.00           O  
+ATOM    601   H1 SPC   112       4.024   5.242   6.085  1.00  0.00           H  
+ATOM    602   H2 SPC   112       3.974   6.850   5.806  1.00  0.00           H  
+ATOM    603    O SPC   113      24.422   7.751  13.389  1.00  0.00           O  
+ATOM    604   H1 SPC   113      24.196   7.067  12.695  1.00  0.00           H  
+ATOM    605   H2 SPC   113      23.723   8.466  13.391  1.00  0.00           H  
+ATOM    606    O SPC   114      26.430  10.947  16.146  1.00  0.00           O  
+ATOM    607   H1 SPC   114      27.224  11.000  16.752  1.00  0.00           H  
+ATOM    608   H2 SPC   114      25.809  10.234  16.472  1.00  0.00           H  
+ATOM    609    O SPC   115       1.049  18.552  11.161  1.00  0.00           O  
+ATOM    610   H1 SPC   115       1.110  18.823  10.200  1.00  0.00           H  
+ATOM    611   H2 SPC   115       1.603  17.734  11.314  1.00  0.00           H  
+ATOM    612    O SPC   116       3.005   1.298  18.698  1.00  0.00           O  
+ATOM    613   H1 SPC   116       3.534   2.125  18.510  1.00  0.00           H  
+ATOM    614   H2 SPC   116       2.763   1.270  19.668  1.00  0.00           H  
+ATOM    615    O SPC   117      26.598  10.908  12.079  1.00  0.00           O  
+ATOM    616   H1 SPC   117      25.918  11.051  12.798  1.00  0.00           H  
+ATOM    617   H2 SPC   117      27.516  10.953  12.474  1.00  0.00           H  
+ATOM    618    O SPC   118      23.342   3.752  18.667  1.00  0.00           O  
+ATOM    619   H1 SPC   118      24.175   4.251  18.430  1.00  0.00           H  
+ATOM    620   H2 SPC   118      22.682   4.381  19.077  1.00  0.00           H  
+ATOM    621    O SPC   119       3.517  17.630  16.643  1.00  0.00           O  
+ATOM    622   H1 SPC   119       4.514  17.693  16.598  1.00  0.00           H  
+ATOM    623   H2 SPC   119       3.192  18.074  17.478  1.00  0.00           H  
+ATOM    624    O SPC   120      25.214   1.462  18.547  1.00  0.00           O  
+ATOM    625   H1 SPC   120      25.228   1.684  17.572  1.00  0.00           H  
+ATOM    626   H2 SPC   120      24.535   2.033  19.009  1.00  0.00           H  
+ATOM    627    O SPC   121       0.544  13.127   7.849  1.00  0.00           O  
+ATOM    628   H1 SPC   121      -0.134  12.468   8.174  1.00  0.00           H  
+ATOM    629   H2 SPC   121       0.538  13.932   8.443  1.00  0.00           H  
+ATOM    630    O SPC   122       0.483  16.688   4.060  1.00  0.00           O  
+ATOM    631   H1 SPC   122       0.246  15.885   3.513  1.00  0.00           H  
+ATOM    632   H2 SPC   122      -0.018  16.663   4.925  1.00  0.00           H  
+ATOM    633    O SPC   123       2.700   7.033   8.371  1.00  0.00           O  
+ATOM    634   H1 SPC   123       3.508   7.041   8.961  1.00  0.00           H  
+ATOM    635   H2 SPC   123       2.819   6.348   7.652  1.00  0.00           H  
+ATOM    636    O SPC   124      25.601   5.623  10.942  1.00  0.00           O  
+ATOM    637   H1 SPC   124      26.518   5.406  10.607  1.00  0.00           H  
+ATOM    638   H2 SPC   124      25.335   4.958  11.640  1.00  0.00           H  
+ATOM    639    O SPC   125       2.679   1.302   2.905  1.00  0.00           O  
+ATOM    640   H1 SPC   125       3.629   1.006   3.005  1.00  0.00           H  
+ATOM    641   H2 SPC   125       2.476   2.007   3.584  1.00  0.00           H  
+ATOM    642    O SPC   126       2.840  16.317  12.099  1.00  0.00           O  
+ATOM    643   H1 SPC   126       3.113  15.972  12.997  1.00  0.00           H  
+ATOM    644   H2 SPC   126       2.173  15.693  11.691  1.00  0.00           H  
+ATOM    645    O SPC   127       1.342   6.630   4.320  1.00  0.00           O  
+ATOM    646   H1 SPC   127       0.648   6.245   4.929  1.00  0.00           H  
+ATOM    647   H2 SPC   127       2.225   6.647   4.789  1.00  0.00           H  
+ATOM    648    O SPC   128      25.243   5.398   2.478  1.00  0.00           O  
+ATOM    649   H1 SPC   128      26.163   5.688   2.741  1.00  0.00           H  
+ATOM    650   H2 SPC   128      25.119   5.533   1.495  1.00  0.00           H  
+ATOM    651    O SPC   129       4.116   2.589   9.891  1.00  0.00           O  
+ATOM    652   H1 SPC   129       3.309   2.104   9.553  1.00  0.00           H  
+ATOM    653   H2 SPC   129       3.897   3.033  10.760  1.00  0.00           H  
+ATOM    654    O SPC   130      26.607  18.699  14.735  1.00  0.00           O  
+ATOM    655   H1 SPC   130      27.554  19.008  14.834  1.00  0.00           H  
+ATOM    656   H2 SPC   130      26.597  17.762  14.385  1.00  0.00           H  
+ATOM    657    O SPC   131      26.372  12.684   2.074  1.00  0.00           O  
+ATOM    658   H1 SPC   131      26.893  13.385   1.587  1.00  0.00           H  
+ATOM    659   H2 SPC   131      25.527  12.491   1.576  1.00  0.00           H  
+ATOM    660    O SPC   132      23.812  14.967   7.121  1.00  0.00           O  
+ATOM    661   H1 SPC   132      24.197  15.006   6.198  1.00  0.00           H  
+ATOM    662   H2 SPC   132      23.813  15.884   7.521  1.00  0.00           H  
+ATOM    663    O SPC   133       2.108  12.809  18.973  1.00  0.00           O  
+ATOM    664   H1 SPC   133       1.942  13.016  18.009  1.00  0.00           H  
+ATOM    665   H2 SPC   133       3.015  13.141  19.234  1.00  0.00           H  
+ATOM    666    O SPC   134       0.682  14.342  11.973  1.00  0.00           O  
+ATOM    667   H1 SPC   134       1.014  13.536  12.464  1.00  0.00           H  
+ATOM    668   H2 SPC   134      -0.119  14.094  11.429  1.00  0.00           H  
+ATOM    669    O SPC   135      25.381  14.926   4.575  1.00  0.00           O  
+ATOM    670   H1 SPC   135      26.099  14.385   5.013  1.00  0.00           H  
+ATOM    671   H2 SPC   135      25.723  15.298   3.712  1.00  0.00           H  
+ATOM    672    O SPC   136      23.022   6.220  16.426  1.00  0.00           O  
+ATOM    673   H1 SPC   136      22.991   6.151  17.423  1.00  0.00           H  
+ATOM    674   H2 SPC   136      22.351   5.595  16.027  1.00  0.00           H  
+ATOM    675    O SPC   137      25.409   5.467  18.293  1.00  0.00           O  
+ATOM    676   H1 SPC   137      25.493   6.419  18.589  1.00  0.00           H  
+ATOM    677   H2 SPC   137      26.320   5.062  18.213  1.00  0.00           H  
+ATOM    678    O SPC   138       0.514   9.231  18.266  1.00  0.00           O  
+ATOM    679   H1 SPC   138       1.197   8.510  18.383  1.00  0.00           H  
+ATOM    680   H2 SPC   138       0.465   9.783  19.098  1.00  0.00           H  
+ATOM    681    O SPC   139       2.630  13.525  16.202  1.00  0.00           O  
+ATOM    682   H1 SPC   139       2.685  14.435  15.789  1.00  0.00           H  
+ATOM    683   H2 SPC   139       1.786  13.077  15.909  1.00  0.00           H  
+ATOM    684    O SPC   140       4.004   4.355   7.686  1.00  0.00           O  
+ATOM    685   H1 SPC   140       3.838   3.600   7.052  1.00  0.00           H  
+ATOM    686   H2 SPC   140       3.992   4.011   8.625  1.00  0.00           H  
+ATOM    687    O SPC   141      24.064  11.472  19.165  1.00  0.00           O  
+ATOM    688   H1 SPC   141      23.969  10.913  18.342  1.00  0.00           H  
+ATOM    689   H2 SPC   141      24.281  10.884  19.944  1.00  0.00           H  
+ATOM    690    O SPC   142      24.477   9.963   2.730  1.00  0.00           O  
+ATOM    691   H1 SPC   142      23.660   9.579   3.160  1.00  0.00           H  
+ATOM    692   H2 SPC   142      25.279   9.754   3.290  1.00  0.00           H  
+ATOM    693    O SPC   143      22.918  13.641  19.867  1.00  0.00           O  
+ATOM    694   H1 SPC   143      23.403  12.820  19.565  1.00  0.00           H  
+ATOM    695   H2 SPC   143      22.713  13.567  20.843  1.00  0.00           H  
+ATOM    696    O SPC   144       3.714   1.767  14.655  1.00  0.00           O  
+ATOM    697   H1 SPC   144       3.100   1.051  14.988  1.00  0.00           H  
+ATOM    698   H2 SPC   144       4.511   1.828  15.255  1.00  0.00           H  
+ATOM    699    O SPC   145      23.405  17.732  19.659  1.00  0.00           O  
+ATOM    700   H1 SPC   145      23.388  17.787  20.657  1.00  0.00           H  
+ATOM    701   H2 SPC   145      23.597  18.637  19.278  1.00  0.00           H  
+ATOM    702    O SPC   146       1.734   4.147  17.856  1.00  0.00           O  
+ATOM    703   H1 SPC   146       2.106   3.808  16.991  1.00  0.00           H  
+ATOM    704   H2 SPC   146       0.771   3.888  17.928  1.00  0.00           H  
+ATOM    705    O SPC   147      24.668   8.740  16.368  1.00  0.00           O  
+ATOM    706   H1 SPC   147      25.324   8.515  15.648  1.00  0.00           H  
+ATOM    707   H2 SPC   147      23.958   8.037  16.404  1.00  0.00           H  
+ATOM    708    O SPC   148       3.441   9.053   3.444  1.00  0.00           O  
+ATOM    709   H1 SPC   148       3.253   8.526   2.616  1.00  0.00           H  
+ATOM    710   H2 SPC   148       2.591   9.454   3.785  1.00  0.00           H  
+ATOM    711    O SPC   149      25.807  10.518   6.606  1.00  0.00           O  
+ATOM    712   H1 SPC   149      26.168  10.094   7.436  1.00  0.00           H  
+ATOM    713   H2 SPC   149      25.034  11.107   6.841  1.00  0.00           H  
+ATOM    714    O SPC   150      25.024   4.455  15.245  1.00  0.00           O  
+ATOM    715   H1 SPC   150      25.904   4.839  14.964  1.00  0.00           H  
+ATOM    716   H2 SPC   150      24.564   5.093  15.863  1.00  0.00           H  
+ATOM    717    O SPC   151      26.273  16.077   2.148  1.00  0.00           O  
+ATOM    718   H1 SPC   151      25.791  15.894   1.291  1.00  0.00           H  
+ATOM    719   H2 SPC   151      27.197  15.696   2.098  1.00  0.00           H  
+ATOM    720    O SPC   152       3.137  16.467   4.329  1.00  0.00           O  
+ATOM    721   H1 SPC   152       3.688  15.693   4.017  1.00  0.00           H  
+ATOM    722   H2 SPC   152       2.169  16.274   4.167  1.00  0.00           H  
+ATOM    723    O SPC   153      24.168   3.773  12.681  1.00  0.00           O  
+ATOM    724   H1 SPC   153      23.305   4.108  12.302  1.00  0.00           H  
+ATOM    725   H2 SPC   153      24.345   4.225  13.555  1.00  0.00           H  
+ATOM    726    O SPC   154       2.208  16.036  14.973  1.00  0.00           O  
+ATOM    727   H1 SPC   154       2.785  16.650  15.511  1.00  0.00           H  
+ATOM    728   H2 SPC   154       1.442  16.551  14.588  1.00  0.00           H  
+ATOM    729    O SPC   155      26.523  16.016  13.873  1.00  0.00           O  
+ATOM    730   H1 SPC   155      25.627  15.938  13.438  1.00  0.00           H  
+ATOM    731   H2 SPC   155      26.485  15.618  14.790  1.00  0.00           H  
+ATOM    732    O SPC   156      24.982  11.785  14.019  1.00  0.00           O  
+ATOM    733   H1 SPC   156      25.590  11.349  14.684  1.00  0.00           H  
+ATOM    734   H2 SPC   156      24.517  12.558  14.450  1.00  0.00           H  
+ATOM    735    O SPC   157       0.520  10.625  20.461  1.00  0.00           O  
+ATOM    736   H1 SPC   157       0.842  10.641  21.408  1.00  0.00           H  
+ATOM    737   H2 SPC   157       0.889  11.414  19.971  1.00  0.00           H  
+ATOM    738    O SPC   158      25.243   5.398  21.099  1.00  0.00           O  
+ATOM    739   H1 SPC   158      26.163   5.688  21.362  1.00  0.00           H  
+ATOM    740   H2 SPC   158      25.119   5.533  20.116  1.00  0.00           H  
+ATOM    741    O SPC   159      26.372  12.684  20.695  1.00  0.00           O  
+ATOM    742   H1 SPC   159      26.893  13.385  20.207  1.00  0.00           H  
+ATOM    743   H2 SPC   159      25.527  12.491  20.197  1.00  0.00           H  
+ATOM    744    O SPC   160      22.918  13.641   1.247  1.00  0.00           O  
+ATOM    745   H1 SPC   160      23.403  12.820   0.945  1.00  0.00           H  
+ATOM    746   H2 SPC   160      22.713  13.567   2.223  1.00  0.00           H  
+ATOM    747    O SPC   161      23.405  17.732   1.038  1.00  0.00           O  
+ATOM    748   H1 SPC   161      23.388  17.787   2.036  1.00  0.00           H  
+ATOM    749   H2 SPC   161      23.597  18.637   0.658  1.00  0.00           H  
+ATOM    750    O SPC   162      26.273  16.077  20.768  1.00  0.00           O  
+ATOM    751   H1 SPC   162      25.791  15.894  19.911  1.00  0.00           H  
+ATOM    752   H2 SPC   162      27.197  15.696  20.719  1.00  0.00           H  
+ENDMDL

gradio_molecule3d/LICENSE

@@ -0,0 +1,7 @@
+Copyright 2023 Simon Dürr
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

gradio_molecule3d/README.md

@@ -0,0 +1,438 @@
+---
+tags: [gradio-custom-component, File]
+title: gradio_molecule3d
+short_description: A gradio custom component
+colorFrom: blue
+colorTo: yellow
+sdk: gradio
+pinned: false
+app_file: space.py
+---
+
+# `gradio_molecule3d`
+<a href="https://pypi.org/project/gradio_molecule3d/" target="_blank"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/gradio_molecule3d"></a>  
+
+Python library for easily interacting with trained machine learning models
+
+## Installation
+
+```bash
+pip install gradio_molecule3d
+```
+
+## Usage
+
+```python
+
+import gradio as gr
+from gradio_molecule3d import Molecule3D
+
+
+example = Molecule3D().example_value()
+
+
+reps =    [
+    {
+      "model": 0,
+      "chain": "",
+      "resname": "",
+      "style": "cartoon",
+      "color": "hydrophobicity",
+      # "residue_range": "",
+      "around": 0,
+      "byres": False,
+      # "visible": False,
+      # "opacity": 0.5
+    }
+  ]
+
+
+
+def predict(x):
+    print("predict function", x)
+    print(x.name)
+    return x
+
+# def update_color(mol, color):
+#     reps[0]['color'] = color
+#     print(reps)
+#     return Molecule3D(mol, reps=reps)
+
+with gr.Blocks() as demo:
+    gr.Markdown("# Molecule3D")
+    # color_choices = ['redCarbon', 'greenCarbon', 'orangeCarbon', 'blackCarbon', 'blueCarbon', 'grayCarbon', 'cyanCarbon']
+
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    # cdr_color = gr.Dropdown(choices=color_choices, label="CDR color", value='redCarbon')
+    out = Molecule3D(label="Output", reps=reps)
+    # cdr_color.change(update_color, inputs=[inp,cdr_color], outputs=out)
+    btn = gr.Button("Predict")
+    gr.Markdown(""" 
+    You can configure the default rendering of the molecule by adding a list of representations
+    <pre>
+        reps =    [
+        {
+          "model": 0,
+          "style": "cartoon",
+          "color": "whiteCarbon",
+          "residue_range": "",
+          "around": 0,
+          "opacity":1
+          
+        },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red"
+        }
+      ]
+    </pre>
+    """)
+    btn.click(predict, inputs=inp, outputs=out)
+
+
+if __name__ == "__main__":
+    demo.launch()
+
+```
+
+## `Molecule3D`
+
+### Initialization
+
+<table>
+<thead>
+<tr>
+<th align="left">name</th>
+<th align="left" style="width: 25%;">type</th>
+<th align="left">default</th>
+<th align="left">description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td align="left"><code>value</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | list[str] | Callable | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.</td>
+</tr>
+
+<tr>
+<td align="left"><code>reps</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Any | None
+```
+
+</td>
+<td align="left"><code>[]</code></td>
+<td align="left">None</td>
+</tr>
+
+<tr>
+<td align="left"><code>config</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Any | None
+```
+
+</td>
+<td align="left"><code>{
+    "backgroundColor": "white",
+    "orthographic": False,
+    "disableFog": False,
+    "unitCell": True,
+}</code></td>
+<td align="left">dictionary of config options</td>
+</tr>
+
+<tr>
+<td align="left"><code>confidenceLabel</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>"pLDDT"</code></td>
+<td align="left">label for confidence values stored in the bfactor column of a pdb file</td>
+</tr>
+
+<tr>
+<td align="left"><code>file_count</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Literal["single", "multiple", "directory"]
+```
+
+</td>
+<td align="left"><code>"single"</code></td>
+<td align="left">if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".</td>
+</tr>
+
+<tr>
+<td align="left"><code>file_types</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+list[str] | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">List of file extensions or types of files to be uploaded (e.g. ['image', '.json', '.mp4']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.</td>
+</tr>
+
+<tr>
+<td align="left"><code>type</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Literal["filepath", "binary"]
+```
+
+</td>
+<td align="left"><code>"filepath"</code></td>
+<td align="left">Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.</td>
+</tr>
+
+<tr>
+<td align="left"><code>label</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.</td>
+</tr>
+
+<tr>
+<td align="left"><code>every</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Timer | float | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.</td>
+</tr>
+
+<tr>
+<td align="left"><code>inputs</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+Component | Sequence[Component] | set[Component] | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.</td>
+</tr>
+
+<tr>
+<td align="left"><code>show_label</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if True, will display label.</td>
+</tr>
+
+<tr>
+<td align="left"><code>container</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If True, will place the component in a container - providing some extra padding around the border.</td>
+</tr>
+
+<tr>
+<td align="left"><code>scale</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.</td>
+</tr>
+
+<tr>
+<td align="left"><code>min_width</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int
+```
+
+</td>
+<td align="left"><code>160</code></td>
+<td align="left">minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.</td>
+</tr>
+
+<tr>
+<td align="left"><code>height</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | float | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.</td>
+</tr>
+
+<tr>
+<td align="left"><code>interactive</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.</td>
+</tr>
+
+<tr>
+<td align="left"><code>visible</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If False, component will be hidden.</td>
+</tr>
+
+<tr>
+<td align="left"><code>elem_id</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.</td>
+</tr>
+
+<tr>
+<td align="left"><code>elem_classes</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+list[str] | str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.</td>
+</tr>
+
+<tr>
+<td align="left"><code>render</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.</td>
+</tr>
+
+<tr>
+<td align="left"><code>key</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+int | str | None
+```
+
+</td>
+<td align="left"><code>None</code></td>
+<td align="left">if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.</td>
+</tr>
+
+<tr>
+<td align="left"><code>showviewer</code></td>
+<td align="left" style="width: 25%;">
+
+```python
+bool
+```
+
+</td>
+<td align="left"><code>True</code></td>
+<td align="left">If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.</td>
+</tr>
+</tbody></table>
+
+
+### Events
+
+| name | description |
+|:-----|:------------|
+| `change` | Triggered when the value of the Molecule3D changes either because of user input (e.g. a user types in a textbox) OR because of a function update (e.g. an image receives a value from the output of an event trigger). See `.input()` for a listener that is only triggered by user input. |
+| `select` | Event listener for when the user selects or deselects the Molecule3D. Uses event data gradio.SelectData to carry `value` referring to the label of the Molecule3D, and `selected` to refer to state of the Molecule3D. See EventData documentation on how to use this event data |
+| `clear` | This listener is triggered when the user clears the Molecule3D using the clear button for the component. |
+| `upload` | This listener is triggered when the user uploads a file into the Molecule3D. |
+| `delete` | This listener is triggered when the user deletes and item from the Molecule3D. Uses event data gradio.DeletedFileData to carry `value` referring to the file that was deleted as an instance of FileData. See EventData documentation on how to use this event data |
+
+
+
+### User function
+
+The impact on the users predict function varies depending on whether the component is used as an input or output for an event (or both).
+
+- When used as an Input, the component only impacts the input signature of the user function.
+- When used as an output, the component only impacts the return signature of the user function.
+
+The code snippet below is accurate in cases where the component is used as both an input and an output.
+
+- **As output:** Is passed, passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.
+- **As input:** Should return, expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.
+
+ ```python
+ def predict(
+     value: bytes | str | list[bytes] | list[str] | None
+ ) -> str | list[str] | None:
+     return value
+ ```
+ 

gradio_molecule3d/backend/gradio_molecule3d/__init__.py

@@ -0,0 +1,4 @@
+
+from .molecule3d import Molecule3D
+
+__all__ = ['Molecule3D']

gradio_molecule3d/backend/gradio_molecule3d/molecule3d.py

@@ -0,0 +1,352 @@
+"""gr.File() component"""
+
+from __future__ import annotations
+
+import tempfile
+import warnings
+from pathlib import Path
+from typing import TYPE_CHECKING, Any, Callable, Literal, Sequence
+
+import gradio_client.utils as client_utils
+from gradio_client import handle_file
+from gradio_client.documentation import document
+
+from gradio import processing_utils
+from gradio.components.base import Component
+from gradio.data_classes import FileData, ListFiles
+from gradio.events import Events
+from gradio.utils import NamedString
+import ase.io
+import numpy as np
+
+if TYPE_CHECKING:
+    from gradio.components import Timer
+
+
+def write_proteindatabank(fileobj, images, write_arrays=True):
+    """Write images to PDB-file.
+    From ASE, but edited to not use the upper-case element symbols.
+    """
+    rot_t = None
+    if hasattr(images, 'get_positions'):
+        images = [images]
+
+    #     1234567 123 6789012345678901   89   67   456789012345678901234567 890
+    format = ('ATOM  %5d %4s %4s %4d    %8.3f%8.3f%8.3f%6.2f%6.2f'
+              '          %2s  \n')
+
+    # RasMol complains if the atom index exceeds 100000. There might
+    # be a limit of 5 digit numbers in this field.
+    MAXNUM = 100000
+
+    symbols = images[0].get_chemical_symbols()
+    natoms = len(symbols)
+
+    for n, atoms in enumerate(images):
+        if atoms.get_pbc().any():
+            currentcell = atoms.get_cell()
+            cellpar = currentcell.cellpar()
+            _, rot_t = currentcell.standard_form()
+            # ignoring Z-value, using P1 since we have all atoms defined
+            # explicitly
+            cellformat = 'CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1\n'
+            fileobj.write(cellformat % (cellpar[0], cellpar[1], cellpar[2],
+                                        cellpar[3], cellpar[4], cellpar[5]))
+        fileobj.write('MODEL     ' + str(n + 1) + '\n')
+        p = atoms.get_positions()
+        if rot_t is not None:
+            p = p.dot(rot_t.T)
+        occupancy = np.ones(len(atoms))
+        bfactor = np.zeros(len(atoms))
+        residuenames = ['MOL '] * len(atoms)
+        residuenumbers = np.ones(len(atoms))
+        names = atoms.get_chemical_symbols()
+        if write_arrays:
+            if 'occupancy' in atoms.arrays:
+                occupancy = atoms.get_array('occupancy')
+            if 'bfactor' in atoms.arrays:
+                bfactor = atoms.get_array('bfactor')
+            if 'residuenames' in atoms.arrays:
+                residuenames = atoms.get_array('residuenames')
+            if 'residuenumbers' in atoms.arrays:
+                residuenumbers = atoms.get_array('residuenumbers')
+            if 'atomtypes' in atoms.arrays:
+                names = atoms.get_array('atomtypes')
+        for a in range(natoms):
+            x, y, z = p[a]
+            occ = occupancy[a]
+            bf = bfactor[a]
+            resname = residuenames[a].ljust(4)
+            resseq = residuenumbers[a]
+            name = names[a]
+            fileobj.write(format % ((a + 1) % MAXNUM, name, resname, resseq,
+                                    x, y, z, occ, bf, symbols[a]))
+        fileobj.write('ENDMDL\n')
+
+def find_minimum_repeats(atoms, min_length):
+    """
+    Find the minimum number of repeats in each unit cell direction
+    to meet at least `min_length` angstroms.
+
+    Parameters:
+        atoms (ase.Atoms): The ASE Atoms object.
+        min_length (float): The minimum length required in each direction.
+
+    Returns:
+        tuple: A tuple of integers representing the number of repeats
+               in the x, y, and z directions.
+    """
+    cell_lengths = atoms.get_cell().lengths()  # Get the lengths of the unit cell
+    repeats = [max(1, int(np.ceil(min_length / length))) for length in cell_lengths]
+    return tuple(repeats)
+
+def convert_file_to_pdb(file_path: str | Path, gradio_cache: str | Path) -> str:
+    # Read the file using ASE, and convert even if it's pdb to make sure all elements go lower case
+    structures = ase.io.read(file_path, ':')
+
+    if all(structures[0].pbc):
+        # find the minimum number of repeats in each unit cell direction to meet at least 20 angstroms
+        repeats = find_minimum_repeats(structures[0], min_length=15.0)
+
+    structures = [s.repeat(repeats) if all(s.pbc) else s for s in structures]
+
+    # Create a temporary PDB file
+    with tempfile.NamedTemporaryFile(
+        delete=False, dir=gradio_cache, suffix=".pdb", mode='w',
+    ) as temp_pdb_file:
+        write_proteindatabank(temp_pdb_file, structures)
+    file_name = temp_pdb_file.name
+    return file_name
+   
+
+class Molecule3D(Component):
+    """
+    Creates a file component that allows uploading one or more generic files (when used as an input) or displaying generic files or URLs for download (as output).
+
+    Demo: zip_files, zip_to_json
+    """
+
+    EVENTS = [Events.change, Events.select, Events.clear, Events.upload, Events.delete]
+
+    def __init__(
+        self,
+        value: str | list[str] | Callable | None = None,
+        reps: Any | None = [],
+        config: Any | None = {
+    "backgroundColor": "white",
+    "orthographic": False,
+    "disableFog": False,
+  },
+        confidenceLabel: str | None = "pLDDT",
+        *,
+        file_count: Literal["single", "multiple", "directory"] = "single",
+        file_types: list[str] | None = None,
+        type: Literal["filepath", "binary"] = "filepath",
+        label: str | None = None,
+        every: Timer | float | None = None,
+        inputs: Component | Sequence[Component] | set[Component] | None = None,
+        show_label: bool | None = None,
+        container: bool = True,
+        scale: int | None = None,
+        min_width: int = 160,
+        height: int | float | None = None,
+        interactive: bool | None = None,
+        visible: bool = True,
+        elem_id: str | None = None,
+        elem_classes: list[str] | str | None = None,
+        render: bool = True,
+        key: int | str | None = None,
+        showviewer: bool = True      
+    ):
+        """
+        Parameters:
+            value: Default file(s) to display, given as a str file path or URL, or a list of str file paths / URLs. If callable, the function will be called whenever the app loads to set the initial value of the component.
+            file_count: if single, allows user to upload one file. If "multiple", user uploads multiple files. If "directory", user uploads all files in selected directory. Return type will be list for each file in case of "multiple" or "directory".
+            file_types: List of file extensions or types of files to be uploaded (e.g. ['image', '.json', '.mp4']). "file" allows any file to be uploaded, "image" allows only image files to be uploaded, "audio" allows only audio files to be uploaded, "video" allows only video files to be uploaded, "text" allows only text files to be uploaded.
+            representations: list of representation objects
+            config: dictionary of config options
+            confidenceLabel: label for confidence values stored in the bfactor column of a pdb file
+            type: Type of value to be returned by component. "file" returns a temporary file object with the same base name as the uploaded file, whose full path can be retrieved by file_obj.name, "binary" returns an bytes object.
+            label: The label for this component. Appears above the component and is also used as the header if there are a table of examples for this component. If None and used in a `gr.Interface`, the label will be the name of the parameter this component is assigned to.
+            every: Continously calls `value` to recalculate it if `value` is a function (has no effect otherwise). Can provide a Timer whose tick resets `value`, or a float that provides the regular interval for the reset Timer.
+            inputs: Components that are used as inputs to calculate `value` if `value` is a function (has no effect otherwise). `value` is recalculated any time the inputs change.
+            show_label: if True, will display label.
+            container: If True, will place the component in a container - providing some extra padding around the border.
+            scale: relative size compared to adjacent Components. For example if Components A and B are in a Row, and A has scale=2, and B has scale=1, A will be twice as wide as B. Should be an integer. scale applies in Rows, and to top-level Components in Blocks where fill_height=True.
+            min_width: minimum pixel width, will wrap if not sufficient screen space to satisfy this value. If a certain scale value results in this Component being narrower than min_width, the min_width parameter will be respected first.
+            height: The maximum height of the file component, specified in pixels if a number is passed, or in CSS units if a string is passed. If more files are uploaded than can fit in the height, a scrollbar will appear.
+            interactive: if True, will allow users to upload a file; if False, can only be used to display files. If not provided, this is inferred based on whether the component is used as an input or output.
+            visible: If False, component will be hidden.
+            elem_id: An optional string that is assigned as the id of this component in the HTML DOM. Can be used for targeting CSS styles.
+            elem_classes: An optional list of strings that are assigned as the classes of this component in the HTML DOM. Can be used for targeting CSS styles.
+            render: If False, component will not render be rendered in the Blocks context. Should be used if the intention is to assign event listeners now but render the component later.
+            key: if assigned, will be used to assume identity across a re-render. Components that have the same key across a re-render will have their value preserved.
+            showviewer: If True, will display the 3Dmol.js viewer. If False, will not display the 3Dmol.js viewer.
+        """
+        file_count_valid_types = ["single", "multiple", "directory"]
+        self.file_count = file_count
+
+        if self.file_count not in file_count_valid_types:
+            raise ValueError(
+                f"Parameter file_count must be one of them: {file_count_valid_types}"
+            )
+        elif self.file_count in ["multiple", "directory"]:
+            self.data_model = ListFiles
+        else:
+            self.data_model = FileData
+        self.file_types = file_types
+        if file_types is not None and not isinstance(file_types, list):
+            raise ValueError(
+                f"Parameter file_types must be a list. Received {file_types.__class__.__name__}"
+            )
+        valid_types = [
+            "filepath",
+            "binary",
+        ]
+        if type not in valid_types:
+            raise ValueError(
+                f"Invalid value for parameter `type`: {type}. Please choose from one of: {valid_types}"
+            )
+        if file_count == "directory" and file_types is not None:
+            warnings.warn(
+                "The `file_types` parameter is ignored when `file_count` is 'directory'."
+            )
+        super().__init__(
+            label=label,
+            every=every,
+            inputs=inputs,
+            show_label=show_label,
+            container=container,
+            scale=scale,
+            min_width=min_width,
+            interactive=interactive,
+            visible=visible,
+            elem_id=elem_id,
+            elem_classes=elem_classes,
+            render=render,
+            key=key,
+            value=value,
+        )
+        self.type = type
+        self.height = height
+        self.reps = reps
+        self.config = config
+        self.confidenceLabel = confidenceLabel
+        self.showviewer = showviewer
+
+    def _process_single_file(self, f: FileData) -> NamedString | bytes:
+        file_name = f.path
+        
+        file_name = convert_file_to_pdb(file_name, self.GRADIO_CACHE)
+
+        if self.type == "filepath":
+            return NamedString(file_name)
+        elif self.type == "binary":
+            with open(file_name, "rb") as file_data:
+                return file_data.read()
+        else:
+            raise ValueError(
+                "Unknown type: "
+                + str(type)
+                + ". Please choose from: 'filepath', 'binary'."
+            )
+
+    def preprocess(
+        self, payload: ListFiles | FileData | None
+    ) -> bytes | str | list[bytes] | list[str] | None:
+        """
+        Parameters:
+            payload: molecule3d information as a FileData object, or a list of FileData objects.
+        Returns:
+            Passes the file as a `str` or `bytes` object, or a list of `str` or list of `bytes` objects, depending on `type` and `file_count`.
+        """
+        if payload is None:
+            return None
+
+        if self.file_count == "single":
+            if isinstance(payload, ListFiles):
+                return self._process_single_file(payload[0])
+            return self._process_single_file(payload)
+        if isinstance(payload, ListFiles):
+            return [self._process_single_file(f) for f in payload]  # type: ignore
+        return [self._process_single_file(payload)]  # type: ignore
+
+    def _download_files(self, value: str | list[str]) -> str | list[str]:
+        downloaded_files = []
+        if isinstance(value, list):
+            for file in value:
+                if client_utils.is_http_url_like(file):
+                    downloaded_file = processing_utils.save_url_to_cache(
+                        file, self.GRADIO_CACHE
+                    )
+                    downloaded_files.append(downloaded_file)
+                else:
+                    downloaded_files.append(file)
+            return downloaded_files
+        if client_utils.is_http_url_like(value):
+            downloaded_file = processing_utils.save_url_to_cache(
+                value, self.GRADIO_CACHE
+            )
+            return downloaded_file
+        else:
+            return value
+
+    def postprocess(self, value: str | list[str] | None) -> ListFiles | FileData | None:
+        """
+        Parameters:
+            value: Expects a `str` filepath or URL, or a `list[str]` of filepaths/URLs.
+        Returns:
+            molecule3d information as a FileData object, or a list of FileData objects.
+        """
+        if value is None:
+            return None
+        value = self._download_files(value)
+
+        
+        if isinstance(value, list):
+            value = [convert_file_to_pdb(str(path), self.GRADIO_CACHE) for path in value]
+            return ListFiles(
+                root=[
+                    FileData(
+                        path=file,
+                        orig_name=Path(file).name,
+                        size=Path(file).stat().st_size,
+                    )
+                    for file in value
+                ]
+            )
+        else:
+            value = convert_file_to_pdb(str(value), self.GRADIO_CACHE)
+            return FileData(
+                path=value,
+                orig_name=Path(value).name,
+                size=Path(value).stat().st_size,
+            )
+
+    def process_example(self, value: str | list | None) -> str:
+        if value is None:
+            return ""
+        elif isinstance(value, list):
+            return ", ".join([Path(file).name for file in value])
+        else:
+            return Path(value).name
+
+    def example_payload(self) -> Any:
+        if self.file_count == "single":
+            return handle_file(
+                "https://files.rcsb.org/view/1PGA.pdb"
+            )
+        else:
+            return [
+                handle_file(
+                    "https://files.rcsb.org/view/1PGA.pdb"
+                )
+            ]
+
+    def example_value(self) -> Any:
+        if self.file_count == "single":
+            return "https://files.rcsb.org/view/1PGA.pdb"
+        else:
+            return [
+                "https://files.rcsb.org/view/1PGA.pdb"
+            ]

gradio_molecule3d/demo/app.py

@@ -0,0 +1,72 @@
+
+import gradio as gr
+from gradio_molecule3d import Molecule3D
+
+
+example = Molecule3D().example_value()
+
+
+reps =    [
+    {
+      "model": 0,
+      "chain": "",
+      "resname": "",
+      "style": "cartoon",
+      "color": "hydrophobicity",
+      # "residue_range": "",
+      "around": 0,
+      "byres": False,
+      # "visible": False,
+      # "opacity": 0.5
+    }
+  ]
+
+
+
+def predict(x):
+    print("predict function", x)
+    print(x.name)
+    return x
+
+# def update_color(mol, color):
+#     reps[0]['color'] = color
+#     print(reps)
+#     return Molecule3D(mol, reps=reps)
+
+with gr.Blocks() as demo:
+    gr.Markdown("# Molecule3D")
+    # color_choices = ['redCarbon', 'greenCarbon', 'orangeCarbon', 'blackCarbon', 'blueCarbon', 'grayCarbon', 'cyanCarbon']
+
+    inp = Molecule3D(label="Molecule3D", reps=reps)
+    # cdr_color = gr.Dropdown(choices=color_choices, label="CDR color", value='redCarbon')
+    out = Molecule3D(label="Output", reps=reps)
+    # cdr_color.change(update_color, inputs=[inp,cdr_color], outputs=out)
+    btn = gr.Button("Predict")
+    gr.Markdown(""" 
+    You can configure the default rendering of the molecule by adding a list of representations
+    <pre>
+        reps =    [
+        {
+          "model": 0,
+          "style": "cartoon",
+          "color": "whiteCarbon",
+          "residue_range": "",
+          "around": 0,
+          "opacity":1
+          
+        },
+        {
+          "model": 0,
+          "chain": "A",
+          "resname": "HIS",
+          "style": "stick",
+          "color": "red"
+        }
+      ]
+    </pre>
+    """)
+    btn.click(predict, inputs=inp, outputs=out)
+
+
+if __name__ == "__main__":
+    demo.launch()

gradio_molecule3d/demo/css.css

@@ -0,0 +1,157 @@
+html {
+	font-family: Inter;
+	font-size: 16px;
+	font-weight: 400;
+	line-height: 1.5;
+	-webkit-text-size-adjust: 100%;
+	background: #fff;
+	color: #323232;
+	-webkit-font-smoothing: antialiased;
+	-moz-osx-font-smoothing: grayscale;
+	text-rendering: optimizeLegibility;
+}
+
+:root {
+	--space: 1;
+	--vspace: calc(var(--space) * 1rem);
+	--vspace-0: calc(3 * var(--space) * 1rem);
+	--vspace-1: calc(2 * var(--space) * 1rem);
+	--vspace-2: calc(1.5 * var(--space) * 1rem);
+	--vspace-3: calc(0.5 * var(--space) * 1rem);
+}
+
+.app {
+	max-width: 748px !important;
+}
+
+.prose p {
+	margin: var(--vspace) 0;
+	line-height: var(--vspace * 2);
+	font-size: 1rem;
+}
+
+code {
+	font-family: "Inconsolata", sans-serif;
+	font-size: 16px;
+}
+
+h1,
+h1 code {
+	font-weight: 400;
+	line-height: calc(2.5 / var(--space) * var(--vspace));
+}
+
+h1 code {
+	background: none;
+	border: none;
+	letter-spacing: 0.05em;
+	padding-bottom: 5px;
+	position: relative;
+	padding: 0;
+}
+
+h2 {
+	margin: var(--vspace-1) 0 var(--vspace-2) 0;
+	line-height: 1em;
+}
+
+h3,
+h3 code {
+	margin: var(--vspace-1) 0 var(--vspace-2) 0;
+	line-height: 1em;
+}
+
+h4,
+h5,
+h6 {
+	margin: var(--vspace-3) 0 var(--vspace-3) 0;
+	line-height: var(--vspace);
+}
+
+.bigtitle,
+h1,
+h1 code {
+	font-size: calc(8px * 4.5);
+	word-break: break-word;
+}
+
+.title,
+h2,
+h2 code {
+	font-size: calc(8px * 3.375);
+	font-weight: lighter;
+	word-break: break-word;
+	border: none;
+	background: none;
+}
+
+.subheading1,
+h3,
+h3 code {
+	font-size: calc(8px * 1.8);
+	font-weight: 600;
+	border: none;
+	background: none;
+	letter-spacing: 0.1em;
+	text-transform: uppercase;
+}
+
+h2 code {
+	padding: 0;
+	position: relative;
+	letter-spacing: 0.05em;
+}
+
+blockquote {
+	font-size: calc(8px * 1.1667);
+	font-style: italic;
+	line-height: calc(1.1667 * var(--vspace));
+	margin: var(--vspace-2) var(--vspace-2);
+}
+
+.subheading2,
+h4 {
+	font-size: calc(8px * 1.4292);
+	text-transform: uppercase;
+	font-weight: 600;
+}
+
+.subheading3,
+h5 {
+	font-size: calc(8px * 1.2917);
+	line-height: calc(1.2917 * var(--vspace));
+
+	font-weight: lighter;
+	text-transform: uppercase;
+	letter-spacing: 0.15em;
+}
+
+h6 {
+	font-size: calc(8px * 1.1667);
+	font-size: 1.1667em;
+	font-weight: normal;
+	font-style: italic;
+	font-family: "le-monde-livre-classic-byol", serif !important;
+	letter-spacing: 0px !important;
+}
+
+#start .md > *:first-child {
+	margin-top: 0;
+}
+
+h2 + h3 {
+	margin-top: 0;
+}
+
+.md hr {
+	border: none;
+	border-top: 1px solid var(--block-border-color);
+	margin: var(--vspace-2) 0 var(--vspace-2) 0;
+}
+.prose ul {
+	margin: var(--vspace-2) 0 var(--vspace-1) 0;
+}
+
+.gap {
+	gap: 0;
+}

gradio_molecule3d/demo/requirements.txt

@@ -0,0 +1 @@
+gradio_molecule3d

gradio_molecule3d/frontend/Example.svelte

@@ -0,0 +1,30 @@
+<script lang="ts">
+	import type { FileData } from "@gradio/client";
+
+	export let value: FileData | null;
+	export let type: "gallery" | "table";
+	export let selected = false;
+</script>
+
+<div
+	class:table={type === "table"}
+	class:gallery={type === "gallery"}
+	class:selected
+>
+	{value ? (Array.isArray(value) ? value.join(", ") : value) : ""}
+</div>
+
+<style>
+	div {
+		overflow: hidden;
+		text-overflow: ellipsis;
+		white-space: nowrap;
+	}
+	.gallery {
+		display: flex;
+		align-items: center;
+		cursor: pointer;
+		padding: var(--size-1) var(--size-2);
+		text-align: left;
+	}
+</style>

gradio_molecule3d/frontend/Index.svelte

@@ -0,0 +1,339 @@
+<svelte:options accessors={true} />
+
+<script context="module" lang="ts">
+  export { default as FilePreview } from "./shared/FilePreview.svelte";
+  export { default as BaseFileUpload } from "./shared/FileUpload.svelte";
+  export { default as BaseFile } from "./shared/File.svelte";
+  export { default as BaseExample } from "./Example.svelte";
+</script>
+
+<script lang="ts">
+  import "./style.css";
+
+  import type { Gradio, SelectData } from "@gradio/utils";
+  import File from "./shared/File.svelte";
+  import FileUpload from "./shared/FileUpload.svelte";
+  import type { FileData } from "@gradio/client";
+  import { Block, UploadText } from "@gradio/atoms";
+
+  import { StatusTracker } from "@gradio/statustracker";
+  import type { LoadingStatus } from "@gradio/statustracker";
+
+  export let elem_id = "";
+  export let elem_classes: string[] = [];
+  export let visible = true;
+  export let value: null | FileData | FileData[];
+
+  export let interactive: boolean;
+  export let root: string;
+  export let label: string;
+  export let show_label: boolean;
+  export let height: number | undefined = undefined;
+
+  //Molecule3D specific arguments
+  export let reps: any = [];
+  export let config: any = {};
+  export let confidenceLabel: string = "";
+  export let showviewer: boolean = true;
+
+  export let _selectable = false;
+  export let loading_status: LoadingStatus;
+  export let container = true;
+  export let scale: number | null = null;
+  export let min_width: number | undefined = undefined;
+  export let gradio: Gradio<{
+    change: never;
+    error: string;
+    upload: never;
+    clear: never;
+    select: SelectData;
+    clear_status: LoadingStatus;
+    delete: FileData;
+  }>;
+  export let file_count: "single" | "multiple" | "directory";
+  export let file_types: string[] = ["file"];
+
+  let old_value = value;
+  $: if (JSON.stringify(old_value) !== JSON.stringify(value)) {
+    gradio.dispatch("change");
+    old_value = value;
+
+    moldata = null;
+    retrieveContent(value);
+  }
+
+  $: if (JSON.stringify(reps) !== JSON.stringify(reps)) {
+    gradio.dispatch("change");
+    old_value = value;
+
+    // console.log("reps changed");
+    // console.log(reps);
+
+    moldata = null;
+    retrieveContent(value);
+  }
+
+  let dragging = false;
+  let pending_upload = false;
+
+  let keys_for_reps = {
+    model: {
+      type: Number,
+      default: 0,
+    },
+    chain: {
+      type: String,
+      default: "",
+    },
+    resname: {
+      type: String,
+      default: "",
+    },
+    style: {
+      type: String,
+      default: "cartoon",
+      choices: ["cartoon", "stick", "sphere", "surface"],
+    },
+    color: {
+      type: String,
+      default: "whiteCarbon",
+      choices: [
+        "whiteCarbon",
+        "orangeCarbon",
+        "redCarbon",
+        "blackCarbon",
+        "blueCarbon",
+        "grayCarbon",
+        "greenCarbon",
+        "cyanCarbon",
+        "alphafold",
+        "default",
+        "Jmol",
+        "chain",
+        "spectrum",
+      ],
+    },
+    opacity: {
+      type: Number,
+      default: 1,
+    },
+    residue_range: {
+      type: String,
+      default: "",
+    },
+    around: {
+      type: Number,
+      default: 0,
+    },
+    byres: {
+      type: Boolean,
+      default: false,
+    },
+    visible: {
+      type: Boolean,
+      default: true,
+    },
+  };
+  let moldata = null;
+  let allowed_extensions = ["pdb", "sdf", "mol2", "pdb1", "cif", "traj", "xyz"];
+  async function fetchFileContent(url) {
+    const response = await fetch(url);
+    const content = await response.text();
+    return content;
+  }
+  let promise = null;
+  let errors = [];
+  async function retrieveContent(value) {
+    if (value == null) {
+      return [];
+    } else if (Array.isArray(value)) {
+      let tempMoldata = [];
+      // get file extension
+      for (const element of value) {
+        let ext = element.orig_name.split(".").pop();
+        if (!allowed_extensions.includes(ext)) {
+          errors.push(
+            `Invalid file extension for ${
+              element.orig_name
+            }. Expected one of ${allowed_extensions.join(", ")}, got ${ext}`
+          );
+          moldata = null;
+          continue;
+        }
+        tempMoldata.push({
+          data: await fetchFileContent(element.url),
+          name: element.orig_name,
+          format: ext,
+          asFrames: false,
+        });
+      }
+      moldata = tempMoldata;
+    } else if (typeof value === "object" && value !== null) {
+      let ext = value.orig_name.split(".").pop();
+      if (!allowed_extensions.includes(ext)) {
+        errors.push(
+          `Invalid file extension for ${
+            value.orig_name
+          }. Expected one of ${allowed_extensions.join(", ")}, got ${ext}`
+        );
+        moldata = null;
+      } else {
+        let t = await fetchFileContent(value.url);
+        let ext = value.orig_name.split(".").pop();
+        if (ext === "pdb1") {
+          ext = "pdb";
+        }
+        moldata = [
+          { data: t, name: value.orig_name, format: ext, asFrames: false },
+        ];
+      }
+    } else {
+      moldata = null;
+    }
+    // value is object
+  }
+  // go through each rep, do a type check and add missing keys to the rep
+  let lenMoldata = 0;
+  $: lenMoldata = moldata ? moldata.length : 0;
+  let representations = [];
+  //first add all missing keys
+  $: {
+    reps.forEach((rep) => {
+      for (const [key, value] of Object.entries(keys_for_reps)) {
+        if (rep[key] === undefined) {
+          rep[key] = value["default"];
+        }
+        if (rep[key].constructor != value["type"]) {
+          errors.push(
+            `Invalid type for ${key} in reps. Expected ${
+              value["type"]
+            }, got ${typeof rep[key]}`
+          );
+        }
+      }
+    });
+    // then check if model does exist and add to representations
+    reps.forEach((rep) => {
+      if (rep["model"] <= lenMoldata) {
+        representations.push(rep);
+      }
+    });
+  }
+  $: promise = retrieveContent(value);
+</script>
+
+<Block
+  {visible}
+  variant={value ? "solid" : "dashed"}
+  border_mode={dragging ? "focus" : "base"}
+  padding={false}
+  {elem_id}
+  {elem_classes}
+  {container}
+  {scale}
+  {min_width}
+  allow_overflow={false}
+>
+  <StatusTracker
+    autoscroll={gradio.autoscroll}
+    i18n={gradio.i18n}
+    {...loading_status}
+    status={pending_upload
+      ? "generating"
+      : loading_status?.status || "complete"}
+    on:clear_status={() => gradio.dispatch("clear_status", loading_status)}
+  />
+  {#if !interactive}
+    <File
+      on:select={({ detail }) => gradio.dispatch("select", detail)}
+      selectable={_selectable}
+      {value}
+      {label}
+      {show_label}
+      {height}
+      {representations}
+      {config}
+      {confidenceLabel}
+      {moldata}
+      {errors}
+      i18n={gradio.i18n}
+      molviewer={showviewer}
+    />
+  {:else}
+    <FileUpload
+      upload={gradio.client.upload}
+      stream_handler={gradio.client.stream}
+      {label}
+      {show_label}
+      {value}
+      {file_count}
+      {file_types}
+      selectable={_selectable}
+      {root}
+      {height}
+      {representations}
+      {config}
+      {confidenceLabel}
+      {moldata}
+      molviewer={showviewer}
+      max_file_size={gradio.max_file_size}
+      on:change={({ detail }) => {
+        value = detail;
+      }}
+      on:drag={({ detail }) => (dragging = detail)}
+      on:clear={() => gradio.dispatch("clear")}
+      on:select={({ detail }) => gradio.dispatch("select", detail)}
+      on:notfound={() =>
+        gradio.dispatch(
+          "error",
+          "identifier not found in database, check spelling"
+        )}
+      on:upload={() => gradio.dispatch("upload")}
+      on:error={({ detail }) => {
+        loading_status = loading_status || {};
+        loading_status.status = "error";
+        gradio.dispatch("error", detail);
+      }}
+      on:delete={({ detail }) => {
+        gradio.dispatch("delete", detail);
+      }}
+      i18n={gradio.i18n}
+    >
+      <UploadText i18n={gradio.i18n} type="file" />
+    </FileUpload>
+  {/if}
+
+  {#if errors.length > 0 && value !== null}
+    <div
+      class="flex m-2 p-4 mb-4 text-sm text-red-800 rounded-lg bg-red-50 dark:bg-gray-800 dark:text-red-400"
+      role="alert"
+    >
+      <svg
+        class="flex-shrink-0 inline w-4 h-4 mr-3 mt-[2px]"
+        xmlns="http://www.w3.org/2000/svg"
+        fill="none"
+        viewBox="0 0 24 24"
+        stroke-width="1.5"
+        stroke="currentColor"
+      >
+        <path
+          stroke-linecap="round"
+          stroke-linejoin="round"
+          d="M12 9v3.75m-9.303 3.376c-.866 1.5.217 3.374 1.948 3.374h14.71c1.73 0 2.813-1.874 1.948-3.374L13.949 3.378c-.866-1.5-3.032-1.5-3.898 0L2.697 16.126zM12 15.75h.007v.008H12v-.008z"
+        />
+      </svg>
+
+      <span class="sr-only">Error in the representations</span>
+      <div>
+        <span class="font-medium"
+          >Couldn't display Molecule. Fix the following problems:</span
+        >
+        <ul class="mt-1.5 ml-4 list-disc list-inside">
+          {#each errors as error}
+            <li>{error}</li>
+          {/each}
+        </ul>
+      </div>
+    </div>
+  {/if}
+</Block>

gradio_molecule3d/frontend/gradio.config.js

@@ -0,0 +1,11 @@
+import tailwindcss from "@tailwindcss/vite";
+
+export default {
+  plugins: [tailwindcss()],
+  svelte: {
+    preprocess: [],
+  },
+  build: {
+    target: "modules",
+  },
+};

gradio_molecule3d/frontend/package.json

@@ -0,0 +1,36 @@
+{
+  "name": "gradio_molecule3d",
+  "version": "0.9.2",
+  "description": "Gradio UI packages",
+  "type": "module",
+  "author": "",
+  "license": "ISC",
+  "private": false,
+  "dependencies": {
+    "@gradio/atoms": "^0.9.0",
+    "@gradio/client": "^1.6.0",
+    "@gradio/icons": "^0.8.0",
+    "@gradio/markdown": "^0.10.1",
+    "@gradio/statustracker": "^0.8.1",
+    "@gradio/upload": "^0.13.1",
+    "@gradio/utils": "^0.7.0",
+    "@gradio/wasm": "^0.14.1",
+    "@tailwindcss/vite": "^4.0.0-alpha.30",
+    "3dmol": "^2.4.0",
+    "tailwindcss": "^4.0.0-alpha.30"
+  },
+  "devDependencies": {
+    "@gradio/preview": "0.12.0"
+  },
+  "main": "./Index.svelte",
+  "main_changeset": true,
+  "exports": {
+    ".": {
+      "gradio": "./Index.svelte"
+    },
+    "./example": {
+      "gradio": "./Example.svelte"
+    },
+    "./package.json": "./package.json"
+  }
+}

gradio_molecule3d/frontend/shared/File.svelte

@@ -0,0 +1,39 @@
+<script lang="ts">
+  import type { FileData } from "@gradio/client";
+  import { BlockLabel, Empty } from "@gradio/atoms";
+  import { File } from "@gradio/icons";
+  import FilePreview from "./FilePreview.svelte";
+  import type { I18nFormatter } from "@gradio/utils";
+
+  import MolecularViewer from "./MolecularViewer.svelte";
+
+  export let value: FileData | FileData[] | null = null;
+  export let label: string;
+  export let show_label = true;
+  export let selectable = false;
+  export let height: number | undefined = undefined;
+  export let i18n: I18nFormatter;
+
+  export let config = {};
+  export let confidenceLabel = "";
+  export let representations = [];
+  export let moldata = null;
+  export let molviewer = false;
+</script>
+
+<BlockLabel
+  {show_label}
+  float={value === null}
+  Icon={File}
+  label={label || "File"}
+/>
+
+{#if value && (Array.isArray(value) ? value.length > 0 : true)}
+  <!-- <FilePreview {i18n} {selectable} on:select {value} {height} /> -->
+
+  {#if moldata != null && molviewer}
+    <MolecularViewer {moldata} {config} {confidenceLabel} {representations} />
+  {/if}
+{:else}
+  <Empty unpadded_box={true} size="large"><File /></Empty>
+{/if}

gradio_molecule3d/frontend/shared/FilePreview.svelte

@@ -0,0 +1,197 @@
+<script lang="ts">
+	import type { FileData } from "@gradio/client";
+	import { prettyBytes } from "./utils";
+	import { createEventDispatcher } from "svelte";
+	import type { I18nFormatter, SelectData } from "@gradio/utils";
+	import { DownloadLink } from "@gradio/wasm/svelte";
+
+	const dispatch = createEventDispatcher<{
+		select: SelectData;
+		change: FileData[] | FileData;
+		delete: FileData;
+	}>();
+	export let value: FileData | FileData[];
+	export let selectable = false;
+	export let height: number | undefined = undefined;
+	export let i18n: I18nFormatter;
+
+	function split_filename(filename: string): [string, string] {
+		const last_dot = filename.lastIndexOf(".");
+		if (last_dot === -1) {
+			return [filename, ""];
+		}
+		return [filename.slice(0, last_dot), filename.slice(last_dot)];
+	}
+
+	$: normalized_files = (Array.isArray(value) ? value : [value]).map((file) => {
+		const [filename_stem, filename_ext] = split_filename(file.orig_name ?? "");
+		return {
+			...file,
+			filename_stem,
+			filename_ext
+		};
+	});
+
+	function handle_row_click(
+		event: MouseEvent & { currentTarget: HTMLTableRowElement },
+		index: number
+	): void {
+		const tr = event.currentTarget;
+		const should_select =
+			event.target === tr || // Only select if the click is on the row itself
+			(tr &&
+				tr.firstElementChild &&
+				event.composedPath().includes(tr.firstElementChild)); // Or if the click is on the name column
+
+		if (should_select) {
+			dispatch("select", { value: normalized_files[index].orig_name, index });
+		}
+	}
+
+	function remove_file(index: number): void {
+		const removed = normalized_files.splice(index, 1);
+		normalized_files = [...normalized_files];
+		value = normalized_files;
+		dispatch("delete", removed[0]);
+		dispatch("change", normalized_files);
+	}
+</script>
+
+<div
+	class="file-preview-holder"
+	style="max-height: {typeof height === undefined ? 'auto' : height + 'px'};"
+>
+	<table class="file-preview">
+		<tbody>
+			{#each normalized_files as file, i (file)}
+				<tr
+					class="file"
+					class:selectable
+					on:click={(event) => {
+						handle_row_click(event, i);
+					}}
+				>
+					<td class="filename" aria-label={file.orig_name}>
+						<span class="stem">{file.filename_stem}</span>
+						<span class="ext">{file.filename_ext}</span>
+					</td>
+
+					<td class="download">
+						{#if file.url}
+							<DownloadLink
+								href={file.url}
+								download={window.__is_colab__ ? null : file.orig_name}
+							>
+								{@html file.size != null
+									? prettyBytes(file.size)
+									: "(size unknown)"}&nbsp;&#8675;
+							</DownloadLink>
+						{:else}
+							{i18n("file.uploading")}
+						{/if}
+					</td>
+
+					{#if normalized_files.length > 1}
+						<td>
+							<button
+								class="label-clear-button"
+								aria-label="Remove this file"
+								on:click={() => {
+									remove_file(i);
+								}}
+								on:keydown={(event) => {
+									if (event.key === "Enter") {
+										remove_file(i);
+									}
+								}}
+								>×
+							</button>
+						</td>
+					{/if}
+				</tr>
+			{/each}
+		</tbody>
+	</table>
+</div>
+
+<style>
+	.label-clear-button {
+		color: var(--body-text-color-subdued);
+		position: relative;
+		left: -3px;
+	}
+
+	.label-clear-button:hover {
+		color: var(--body-text-color);
+	}
+
+	.file-preview {
+		table-layout: fixed;
+		width: var(--size-full);
+		max-height: var(--size-60);
+		overflow-y: auto;
+		margin-top: var(--size-1);
+		color: var(--body-text-color);
+	}
+
+	.file-preview-holder {
+		overflow: auto;
+	}
+
+	.file {
+		display: flex;
+		width: var(--size-full);
+	}
+
+	.file > * {
+		padding: var(--size-1) var(--size-2-5);
+	}
+
+	.filename {
+		flex-grow: 1;
+		display: flex;
+		overflow: hidden;
+	}
+	.filename .stem {
+		overflow: hidden;
+		text-overflow: ellipsis;
+		white-space: nowrap;
+	}
+	.filename .ext {
+		white-space: nowrap;
+	}
+
+	.download {
+		min-width: 8rem;
+		width: 10%;
+		white-space: nowrap;
+		text-align: right;
+	}
+	.download:hover {
+		text-decoration: underline;
+	}
+	.download > :global(a) {
+		color: var(--link-text-color);
+	}
+
+	.download > :global(a:hover) {
+		color: var(--link-text-color-hover);
+	}
+	.download > :global(a:visited) {
+		color: var(--link-text-color-visited);
+	}
+	.download > :global(a:active) {
+		color: var(--link-text-color-active);
+	}
+	.selectable {
+		cursor: pointer;
+	}
+
+	tbody > tr:nth-child(even) {
+		background: var(--block-background-fill);
+	}
+
+	tbody > tr:nth-child(odd) {
+		background: var(--table-odd-background-fill);
+	}
+</style>

gradio_molecule3d/frontend/shared/FileRetrieval.svelte

@@ -0,0 +1,159 @@
+<script lang="ts">
+  import { createEventDispatcher, tick, getContext } from "svelte";
+
+  import { FileData } from "@gradio/client";
+  import LoadingSpinner from "./loading_spinner.svelte";
+  let uploaded_files;
+  const dispatch = createEventDispatcher();
+
+  import type { Client } from "@Gradio Uptime/client";
+  export let upload: Client["upload"];
+
+  export let root: string;
+  async function handle_upload(file_data: FileData): Promise<void> {
+    await tick();
+    const upload_id = Math.random().toString(36).substring(2, 15);
+    uploaded_files = await upload([file_data], root, upload_id);
+    dispatch("load", uploaded_files[0]);
+  }
+  let loading = false;
+  async function fetchFromDB(identifier, database): Promise<void> {
+    let dbs = {
+      pdb_assym: {
+        url: "https://files.rcsb.org/view/",
+        ext: ".pdb",
+      },
+      pdb_bioass: {
+        url: "https://files.rcsb.org/view/",
+        ext: ".pdb1",
+      },
+      af: {
+        url: "https://alphafold.ebi.ac.uk/files/AF-",
+        ext: "-F1-model_v4.pdb",
+      },
+      esm: {
+        url: "https://api.esmatlas.com/fetchPredictedStructure/",
+        ext: ".pdb",
+      },
+      // pubchem: "pubchem",
+      // text: "text",
+    };
+    let url = dbs[database]["url"];
+    let ext = dbs[database]["ext"];
+    // load the file and save blob
+    // emulate file upload by fetching from the db and triggering upload
+    // check if response status is 200, then return blob
+    loading = true;
+    let file = null;
+    try {
+      file = await fetch(url + identifier + ext)
+        .then((r) => {
+          loading = false;
+          if (r.status == 200) {
+            return r.blob();
+          } else {
+            dispatch("notfound");
+          }
+        })
+        .then((blob) => {
+          return new File([blob], identifier + ".pdb", { type: "text/plain" });
+        });
+    } catch (error) {
+      loading = false;
+      dispatch("notfound");
+    }
+    let file_data = new FileData({
+      path: identifier + ".pdb",
+      orig_name: identifier + ".pdb",
+      blob: file,
+      size: file.size,
+      mime_type: file.type,
+      is_stream: false,
+    });
+    await handle_upload(file_data);
+  }
+  let selectedValue = "pdb_assym";
+  let placeholder = "";
+  let textInput = "";
+  function handleSelect(event) {
+    selectedValue = event.target.value;
+  }
+  let placeholders = {
+    pdb_assym: "Enter PDB identifier",
+    pdb_bioass: "Enter PDB identifier",
+    af: "Enter UniProt identifier",
+    esm: "Enter MGnify protein identifier",
+    // pubchem: "Enter PubChem identifier",
+    // text: "Enter molecule in PDB or mol2 format",
+  };
+  $: placeholder = placeholders[selectedValue];
+  function isEnterPressed(event) {
+    if (event.key === "Enter") {
+      fetchFromDB(textInput, selectedValue);
+    }
+  }
+</script>
+
+<style>
+  .py {
+    padding: 10px 0;
+  }
+  .btn {
+    margin: 0 5px;
+    padding: 3px 15px;
+    border: var(--button-border-width) solid
+      var(--button-secondary-border-color);
+    background: var(--button-secondary-background-fill);
+    color: var(--button-secondary-text-color);
+    border-radius: var(--button-large-radius);
+    padding: var(--button-large-padding);
+    font-weight: var(--button-large-text-weight);
+    font-size: var(--button-large-text-size);
+    cursor: pointer;
+  }
+  .btn:hover {
+    border-color: var(--button-secondary-border-color-hover);
+    background: var(--button-secondary-background-fill-hover);
+    color: var(--button-secondary-text-color-hover);
+    box-shadow: var(--button-shadow-hover);
+  }
+  .or {
+    color: var(--body-text-color-subdued);
+    text-align: center;
+    display: block;
+  }
+  .wfull {
+    width: 100%;
+  }
+  .mt-2 {
+    margin-top: 2rem;
+  }
+  .input {
+    box-shadow: var(--input-shadow);
+    background: var(--input-background-fill);
+    border: var(--input-border-width) solid var(--input-border-color);
+    border-radius: var(--input-radius);
+    margin: 0 5px;
+  }
+  .select {
+    outline: none;
+    border: none;
+  }
+  .flex {
+    display: flex;
+    justify-content: space-between;
+  }
+  .inp {
+    width: 100%;
+    border: 0 #fff !important;
+    outline: none !important;
+  }
+  .inp:focus,
+  .inp:hover {
+    border: 0 !important;
+    outline: none !important;
+  }
+  .text-center {
+    text-align: center;
+  }
+</style>

gradio_molecule3d/frontend/shared/FileUpload.svelte

@@ -0,0 +1,100 @@
+<script lang="ts">
+  import { createEventDispatcher, tick } from "svelte";
+  import { Upload, ModifyUpload } from "@gradio/upload";
+  import type { FileData, Client } from "@gradio/client";
+  import { BlockLabel } from "@gradio/atoms";
+  import { File } from "@gradio/icons";
+  import FileRetrieval from "./FileRetrieval.svelte";
+
+  import FilePreview from "./FilePreview.svelte";
+  import type { I18nFormatter } from "@gradio/utils";
+  import MolecularViewer from "./MolecularViewer.svelte";
+
+  export let value: null | FileData | FileData[];
+
+  export let label: string;
+  export let show_label = true;
+  export let file_count: "single" | "multiple" | "directory" = "single";
+  export let file_types: string[] | null = null;
+  export let selectable = false;
+  export let root: string;
+  export let height: number | undefined = undefined;
+  export let i18n: I18nFormatter;
+  export let max_file_size: number | null = null;
+  export let upload: Client["upload"];
+  export let stream_handler: Client["stream"];
+
+  export let config = {};
+  export let confidenceLabel = "";
+  export let representations = [];
+  export let moldata = null;
+  export let molviewer = false;
+
+  async function handle_upload({
+    detail,
+  }: CustomEvent<FileData | FileData[]>): Promise<void> {
+    value = detail;
+    console.log("upload", detail);
+
+    await tick();
+    dispatch("change", value);
+    dispatch("upload", detail);
+  }
+
+  function handle_clear(): void {
+    value = null;
+    oldata = null;
+    dispatch("change", null);
+    dispatch("clear");
+  }
+
+  const dispatch = createEventDispatcher<{
+    change: FileData[] | FileData | null;
+    clear: undefined;
+    drag: boolean;
+    upload: FileData[] | FileData;
+    load: FileData[] | FileData;
+    error: string;
+  }>();
+
+  let dragging = false;
+  $: dispatch("drag", dragging);
+</script>
+
+<BlockLabel {show_label} Icon={File} float={!value} label={label || "File"} />
+
+{#if value && (Array.isArray(value) ? value.length > 0 : true)}
+  <ModifyUpload {i18n} on:clear={handle_clear} absolute />
+  <FilePreview
+    {i18n}
+    on:select
+    {selectable}
+    {value}
+    {height}
+    on:change
+    on:delete
+  />
+  {#if moldata != null && molviewer}
+    <MolecularViewer {moldata} {config} {confidenceLabel} {representations} />
+  {/if}
+{:else}
+  <FileRetrieval
+    {root}
+    on:load={handle_upload}
+    {upload}
+    on:notfound={() => dispatch("notfound")}
+  />
+  <Upload
+    on:load={handle_upload}
+    filetype={file_types}
+    {file_count}
+    {max_file_size}
+    {root}
+    bind:dragging
+    on:error
+    {stream_handler}
+    {upload}
+  >
+    <slot />
+  </Upload>
+{/if}

gradio_molecule3d/frontend/shared/MolecularViewer.svelte

@@ -0,0 +1,2438 @@
+<script lang="ts">
+  import * as mol from "3dmol/build/3Dmol.js";
+  let TDmol = mol;
+
+  import { onMount, onDestroy, beforeUpdate } from "svelte";
+
+  let viewer;
+  export let confidenceLabel = null;
+
+  export let moldata = null;
+
+  let settings = {
+    backgroundColor: {
+      type: "select",
+      options: ["white", "black", "gray", "lightgray", "beige", "orange"],
+    },
+    orthographic: {
+      type: "toggle",
+    },
+    disableFog: {
+      type: "toggle",
+    },
+  };
+  export let config = {
+    backgroundColor: "white",
+    orthographic: false,
+    disableFog: false,
+  };
+
+  $: {
+    if (view != undefined) {
+      view.setBackgroundColor(config.backgroundColor);
+      view.enableFog(!config.disableFog);
+      view.setCameraParameters({ orthographic: config.orthographic });
+    }
+  }
+
+  let labelHover = true;
+
+  let showCiteTooltip = false;
+
+  function toggleCiteTooltip() {
+    showCiteTooltip = !showCiteTooltip;
+  }
+
+  export let representations = [];
+
+  let showOffCanvas = false;
+  let showOffCanvasReps = false;
+
+  function toggleOffCanvas() {
+    showOffCanvas = !showOffCanvas;
+  }
+
+  function toggleOffCanvasReps() {
+    showOffCanvasReps = !showOffCanvasReps;
+  }
+  function deleteRep(index) {
+    representations.splice(index, 1);
+    representations = representations;
+  }
+  function insertRep() {
+    representations.push({
+      model: 0,
+      chain: "",
+      resname: "",
+      style: "cartoon",
+      color: "grayCarbon",
+      residue_range: "",
+      around: 0,
+      byres: false,
+      visible: true,
+      opacity: 1,
+      scale: 1,
+    });
+    representations = representations;
+  }
+
+  function fade(node, { delay = 0, duration = 50 }) {
+    const o = +getComputedStyle(node).opacity;
+
+    return {
+      delay,
+      duration,
+      css: (t) => `opacity: ${t * o}`,
+    };
+  }
+  let colorAlpha = function (atom) {
+    if (atom.b < 50) {
+      return "OrangeRed";
+    } else if (atom.b < 70) {
+      return "Gold";
+    } else if (atom.b < 90) {
+      return "MediumTurquoise";
+    } else {
+      return "Blue";
+    }
+  };
+
+  let colorHydrophobicity = function (atom) {
+    let kyte_doolittle = {
+      ILE: 4.5,
+      VAL: 4.2,
+      LEU: 3.8,
+      PHE: 2.8,
+      CYS: 2.5,
+      MET: 1.9,
+      ALA: 1.8,
+      GLY: -0.4,
+      THR: -0.7,
+      SER: -0.8,
+      TRP: -0.9,
+      TYR: -1.3,
+      PRO: -1.6,
+      HIS: -3.2,
+      GLU: -3.5,
+      GLN: -3.5,
+      ASP: -3.5,
+      ASN: -3.5,
+      LYS: -3.9,
+      ARG: -4.5,
+    };
+    if (atom.resn in kyte_doolittle) {
+      const value = kyte_doolittle[atom.resn];
+      const min = -4.5;
+      const max = 4.5;
+
+      // Normalize the value to a range of 0 to 1
+      const normalized = (value - min) / (max - min);
+
+      // Interpolate colors between DarkCyan, White, and DarkGoldenRod
+      const interpolateColor = (start, end, factor) => {
+        const startRGB = parseInt(start.slice(1), 16);
+        const endRGB = parseInt(end.slice(1), 16);
+
+        const r = Math.round(
+          ((endRGB >> 16) - (startRGB >> 16)) * factor + (startRGB >> 16),
+        );
+        const g = Math.round(
+          (((endRGB >> 8) & 0xff) - ((startRGB >> 8) & 0xff)) * factor +
+            ((startRGB >> 8) & 0xff),
+        );
+        const b = Math.round(
+          ((endRGB & 0xff) - (startRGB & 0xff)) * factor + (startRGB & 0xff),
+        );
+
+        return `#${((1 << 24) + (r << 16) + (g << 8) + b).toString(16).slice(1)}`;
+      };
+
+      if (normalized <= 0.5) {
+        // Interpolate between DarkCyan and White
+        return interpolateColor("#008B8B", "#FFFFFF", normalized * 2);
+      } else {
+        // Interpolate between White and DarkGoldenRod
+        return interpolateColor("#FFFFFF", "#B8860B", (normalized - 0.5) * 2);
+      }
+    } else {
+      return "#FFFFFF"; // White
+    }
+  };
+
+  let view;
+
+  function resetZoom(rep) {
+    // if is not pointerevent
+    if (rep.type != undefined) {
+      view.zoomTo();
+    } else {
+      let sel = {
+        model: rep.model,
+      };
+      if (rep.chain !== "") {
+        sel.chain = rep.chain;
+      }
+      if (rep.residue_range !== "") {
+        sel.resi = rep.residue_range;
+      }
+      if (rep.resname !== "") {
+        sel.resn = rep.resname;
+      }
+      view.zoomTo(sel);
+    }
+  }
+  function applyStyles(representations) {
+    if (view !== undefined) {
+      view.setStyle();
+      view.removeAllSurfaces();
+      representations.forEach((rep) => {
+        let colorObj;
+
+        if (rep.color === "alphafold") {
+          colorObj = { colorfunc: colorAlpha };
+        } else if (rep.color === "hydrophobicity") {
+          colorObj = { colorfunc: colorHydrophobicity };
+        } else if (rep.color == "spectrum") {
+          colorObj = { color: "spectrum" };
+        } else {
+          colorObj = { colorscheme: rep.color };
+        }
+
+        colorObj.opacity = rep.opacity;
+
+        let selObj = { model: rep.model };
+        if (rep.chain !== "") {
+          selObj.chain = rep.chain;
+        }
+        if (rep.residue_range !== "") {
+          selObj.resi = rep.residue_range;
+        }
+        if (rep.resname !== "") {
+          selObj.resn = rep.resname;
+        }
+        selObj.byres = rep.byres;
+        if (rep.around !== 0) {
+          selObj.expand = rep.around;
+        }
+        if (rep.sidechain) {
+          selObj = {
+            and: [selObj, { atom: ["N", "C", "O"], invert: true }],
+          };
+        }
+
+        if (rep.style == "sphere") {
+          colorObj["scale"] = rep.scale;
+        } else if (rep.style == "stick") {
+          colorObj["scale"] = rep.scale;
+        }
+
+        if (rep.style === "surface") {
+          view.addSurface(TDmol.SurfaceType.VDW, colorObj, selObj);
+        } else {
+          try {
+            if (view.getModel(selObj.model) != null) {
+              view.addStyle(selObj, {
+                [rep.style]: colorObj,
+              });
+            }
+          } catch (error) {
+            console.log(error);
+          }
+        }
+      });
+
+      view.render();
+    }
+  }
+
+  onMount(() => {
+    console.log("MolecularViewer Mounted");
+    let startingConfig = { ...config, cartoonQuality: 7 };
+
+    view = TDmol.createViewer(viewer, startingConfig);
+
+    //filter duplicate representations
+    let uniqueReps = [];
+    representations.forEach((rep) => {
+      if (
+        !uniqueReps.some(
+          (uniqueRep) =>
+            uniqueRep.model === rep.model &&
+            uniqueRep.chain === rep.chain &&
+            uniqueRep.resname === rep.resname &&
+            uniqueRep.style === rep.style &&
+            uniqueRep.color === rep.color &&
+            uniqueRep.residue_range === rep.residue_range &&
+            uniqueRep.around === rep.around &&
+            uniqueRep.byres === rep.byres &&
+            uniqueRep.sidechain === rep.sidechain &&
+            uniqueRep.scale == rep.scale,
+        )
+      ) {
+        uniqueReps.push(rep);
+      }
+    });
+    representations = uniqueReps;
+    if (moldata.length > 0) {
+      moldata.forEach((element) => {
+        view.addModelsAsFrames(element.data, element.format, {
+          keepH: true,
+          multiModel: true,
+        });
+      });
+    }
+
+    view.addUnitCell(view.getModel(), {
+      box: {
+        color: "black", // Set color to black
+        linewidth: 2, // Set line width
+        hidden: false,
+      },
+    });
+
+    applyStyles(representations);
+    view.zoomTo();
+    view.render();
+    view.zoom(0.9, 100);
+
+    representations.forEach((rep) => {
+      if (rep.color === "alphafold") {
+        anyColorAlphaFold = true;
+      }
+      if (rep.color === "hydrophobicity") {
+        anyColorHydrophobic = true;
+      }
+    });
+
+    if (labelHover) {
+      view.setHoverable(
+        {},
+        true,
+        function (atom, view, event, container) {
+          if (!atom.label) {
+            let label;
+            if (anyColorAlphaFold) {
+              label =
+                atom.resn +
+                ":" +
+                atom.resi +
+                ":" +
+                atom.atom +
+                " (" +
+                confidenceLabel +
+                " " +
+                atom.b +
+                ")";
+            } else {
+              label = atom.resn + ":" + atom.resi + ":" + atom.atom;
+            }
+            atom.label = view.addLabel(label, {
+              position: atom,
+              backgroundColor: "#ffffff",
+              borderColor: "#dddddd",
+              fontColor: "black",
+            });
+          }
+        },
+        function (atom, view) {
+          if (atom.label) {
+            view.removeLabel(atom.label);
+            delete atom.label;
+          }
+        },
+      );
+    }
+
+    if (view.getNumFrames() > 1) {
+      toggleAnimation();
+    }
+  });
+
+  beforeUpdate(() => {
+    // console.log("beforeUpdate");
+    // console.log(representations);
+  });
+
+  $: applyStyles(representations);
+  let hasFrames = true;
+  let isAnimated = false;
+
+  let anyColorAlphaFold = false;
+  $: {
+    anyColorAlphaFold = false;
+    representations.forEach((rep) => {
+      if (rep.color === "alphafold") {
+        anyColorAlphaFold = true;
+      }
+    });
+  }
+
+  let anyColorHydrophobic = false;
+  $: {
+    anyColorHydrophobic = false;
+    representations.forEach((rep) => {
+      if (rep.color === "hydrophobicity") {
+        anyColorHydrophobic = true;
+      }
+    });
+  }
+  function toggleAnimation() {
+    console.log(view.isAnimated());
+    if (isAnimated) {
+      view.stopAnimate();
+    } else {
+      view.animate({ loop: "forward", reps: 0 });
+    }
+    isAnimated = !isAnimated;
+  }
+</script>
+
+<div class="bg-white w-full minh">
+  <div class="overflow-hidden flex gap-px w-full h-full flex-wrap">
+    <div class="gr-block gr-box relative w-full overflow-hidden">
+      <div
+        class="absolute z-50 top-0 right-0 mr-2 flex flex-col divide-y border border-gray-200 mt-2 rounded items-center justify-center bg-white dark:bg-gray-800"
+      >
+        <button class="p-2" title="Reset View" on:click={resetZoom}>
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            fill="none"
+            viewBox="0 0 24 24"
+            stroke-width="1.5"
+            stroke="currentColor"
+            class="w-4 h-4 text-gray-500 hover:text-orange-600 cursor-pointer"
+          >
+            <path
+              stroke-linecap="round"
+              stroke-linejoin="round"
+              d="M9 9V4.5M9 9H4.5M9 9L3.75 3.75M9 15v4.5M9 15H4.5M9 15l-5.25 5.25M15 9h4.5M15 9V4.5M15 9l5.25-5.25M15 15h4.5M15 15v4.5m0-4.5l5.25 5.25"
+            />
+          </svg>
+        </button>
+        <button class="p-2" title="Settings" on:click={toggleOffCanvas}>
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            fill="none"
+            viewBox="0 0 24 24"
+            stroke-width="1.5"
+            stroke="currentColor"
+            class="w-5 h-5 text-gray-500 hover:text-orange-600 cursor-pointer"
+          >
+            <path
+              stroke-linecap="round"
+              stroke-linejoin="round"
+              d="M10.5 6h9.75M10.5 6a1.5 1.5 0 11-3 0m3 0a1.5 1.5 0 10-3 0M3.75 6H7.5m3 12h9.75m-9.75 0a1.5 1.5 0 01-3 0m3 0a1.5 1.5 0 00-3 0m-3.75 0H7.5m9-6h3.75m-3.75 0a1.5 1.5 0 01-3 0m3 0a1.5 1.5 0 00-3 0m-9.75 0h9.75"
+            />
+          </svg>
+        </button>
+
+        <button
+          class="p-2"
+          title="Representations"
+          on:click={toggleOffCanvasReps}
+        >
+          <!-- <svg
+            xmlns="http://www.w3.org/2000/svg"
+            fill="none"
+            viewBox="0 0 24 24"
+            stroke-width="1.5"
+            stroke="currentColor"
+            class="w-5 h-5 text-gray-500 hover:text-orange-600 cursor-pointer"
+          >
+            <path
+              stroke-linecap="round"
+              stroke-linejoin="round"
+              d="M21.75 6.75a4.5 4.5 0 01-4.884 4.484c-1.076-.091-2.264.071-2.95.904l-7.152 8.684a2.548 2.548 0 11-3.586-3.586l8.684-7.152c.833-.686.995-1.874.904-2.95a4.5 4.5 0 016.336-4.486l-3.276 3.276a3.004 3.004 0 002.25 2.25l3.276-3.276c.256.565.398 1.192.398 1.852z"
+            />
+            <path
+              stroke-linecap="round"
+              stroke-linejoin="round"
+              d="M4.867 19.125h.008v.008h-.008v-.008z"
+            />
+          </svg> -->
+
+          <!-- CC BY ND  zwicon https://www.zwicon.com -->
+          <svg
+            class="w-5 h-5 text-gray-500 hover:text-orange-600 cursor-pointer"
+            viewBox="0 0 24 24"
+            xmlns="http://www.w3.org/2000/svg"
+          >
+            <path
+              d="M12.0281146,15 L12.5,15 C13.3284271,15 14,15.6715729 14,16.5 L14,20.5 C14,21.3284271 13.3284271,22 12.5,22 L10.5,22 C9.67157288,22 9,21.3284271 9,20.5 L9,16.5 C9,15.6715729 9.67157288,15 10.5,15 L11.0167145,15 C11.1492163,13.8570393 12.0552513,12.9352285 13.2239212,12.8053762 L18.6656473,12.20074 C19.4252963,12.1163346 20,11.4742382 20,10.7099144 L20,8.5 C20,7.67157288 19.3284271,7 18.5,7 C18.2238576,7 18,6.77614237 18,6.5 C18,6.22385763 18.2238576,6 18.5,6 C19.8807119,6 21,7.11928813 21,8.5 L21,10.7099144 C21,11.9837875 20.0421605,13.053948 18.7760788,13.1946238 L13.3343527,13.79926 C12.6731623,13.8727256 12.1520824,14.3686853 12.0281146,15 Z M10.5,16 C10.2238576,16 10,16.2238576 10,16.5 L10,20.5 C10,20.7761424 10.2238576,21 10.5,21 L12.5,21 C12.7761424,21 13,20.7761424 13,20.5 L13,16.5 C13,16.2238576 12.7761424,16 12.5,16 L10.5,16 Z M5.49996942,2.99995128 L16.5,2.99995128 C17.8807119,2.99995128 19,4.11923941 19,5.49995128 L19,7.5 C19,8.88071187 17.8807119,10 16.5,10 L5.49996942,10 C4.11925755,10 2.99996942,8.88071187 2.99996942,7.5 L2.99996942,5.49995128 C2.99996942,4.11923941 4.11925755,2.99995128 5.49996942,2.99995128 Z M5.49996942,3.99995128 C4.6715423,3.99995128 3.99996942,4.67152416 3.99996942,5.49995128 L3.99996942,7.5 C3.99996942,8.32842712 4.6715423,9 5.49996942,9 L16.5,9 C17.3284271,9 18,8.32842712 18,7.5 L18,5.49995128 C18,4.67152416 17.3284271,3.99995128 16.5,3.99995128 L5.49996942,3.99995128 Z"
+            />
+          </svg>
+        </button>
+
+        <!-- <button class="p-2" title="Download files">
+          <svg
+            aria-hidden="true"
+            fill="currentColor"
+            viewBox="0 0 20 20"
+            xmlns="http://www.w3.org/2000/svg"
+            class="w-5 h-5 text-gray-500 hover:text-orange-600 cursor-pointer"
+          >
+            <path
+              d="M10.75 2.75a.75.75 0 00-1.5 0v8.614L6.295 8.235a.75.75 0 10-1.09 1.03l4.25 4.5a.75.75 0 001.09 0l4.25-4.5a.75.75 0 00-1.09-1.03l-2.955 3.129V2.75z"
+            />
+            <path
+              d="M3.5 12.75a.75.75 0 00-1.5 0v2.5A2.75 2.75 0 004.75 18h10.5A2.75 2.75 0 0018 15.25v-2.5a.75.75 0 00-1.5 0v2.5c0 .69-.56 1.25-1.25 1.25H4.75c-.69 0-1.25-.56-1.25-1.25v-2.5z"
+            />
+          </svg>
+        </button> -->
+      </div>
+
+      {#if anyColorAlphaFold}
+        <div class="absolute bottom-0 left-0 z-50 p-2 -mb-2 w-full bg-white">
+          <div class="flex text-sm items-center space-x-2 justify-center">
+            <div class="flex space-x-1 py-1 items-center">
+              <span class="w-4 h-4" style="background-color: rgb(0, 83, 214);"
+                >&nbsp;</span
+              ><span class="legendlabel"
+                >Very high ({confidenceLabel} &gt; 90)</span
+              >
+            </div>
+            <div class="flex space-x-1 py-1 items-center">
+              <span
+                class="w-4 h-4"
+                style="background-color: rgb(101, 203, 243);">&nbsp;</span
+              ><span class="legendlabel"
+                >Confident (90 &gt; {confidenceLabel} &gt; 70)</span
+              >
+            </div>
+            <div class="flex space-x-1 py-1 items-center">
+              <span class="w-4 h-4" style="background-color: rgb(255, 219, 19);"
+                >&nbsp;</span
+              ><span class="legendlabel"
+                >Low (70 &gt; {confidenceLabel} &gt; 50)</span
+              >
+            </div>
+            <div class="flex space-x-1 py-1 items-center">
+              <span class="w-4 h-4" style="background-color: rgb(255, 125, 69);"
+                >&nbsp;</span
+              ><span class="legendlabel"
+                >Very low ({confidenceLabel} &lt; 50)</span
+              >
+            </div>
+          </div>
+        </div>
+      {/if}
+
+      {#if anyColorHydrophobic}
+        <div class="absolute bottom-0 left-0 z-50 p-2 mb-2 w-full bg-white">
+          <div class="flex text-sm items-center space-x-2 justify-center">
+            <div class="flex space-x-1 py-1 items-center">
+              <a
+                class="cursor-pointer"
+                href="https://pubmed.ncbi.nlm.nih.gov/7108955/"
+                >Kyte & Doolittle hydrophobicity scale:</a
+              >
+            </div>
+            <div class="flex space-x-1 py-1 items-center">
+              <span class="w-4 h-4" style="background-color: #B8860B;"
+                >&nbsp;</span
+              ><span class="legendlabel">Hydrophobic</span>
+            </div>
+            <div class="flex space-x-1 py-1 items-center">
+              <span
+                class="w-4 h-4 border border-gray-300"
+                style="background-color: white">&nbsp;</span
+              ><span class="legendlabel">Neutral</span>
+            </div>
+            <div class="flex space-x-1 py-1 items-center">
+              <span class="w-4 h-4" style="background-color: darkcyan;"
+                >&nbsp;</span
+              ><span class="legendlabel">Hydrophilic</span>
+            </div>
+          </div>
+        </div>
+      {/if}
+
+      {#if hasFrames}
+        <div
+          class="absolute z-50 bottom-0 right-0 mr-2 flex divide-x border border-gray-200 mb-2 rounded items-center justify-center"
+        >
+          {#if !isAnimated}
+            <button class="p-2" title="Play" on:click={toggleAnimation}>
+              <svg
+                xmlns="http://www.w3.org/2000/svg"
+                fill="none"
+                viewBox="0 0 24 24"
+                stroke-width="2"
+                stroke="currentColor"
+                class="w-4 h-4 text-gray-500 hover:text-orange-600 cursor-pointer"
+              >
+                <path
+                  stroke-linecap="round"
+                  stroke-linejoin="round"
+                  d="M5.25 5.653c0-.856.917-1.398 1.667-.986l11.54 6.348a1.125 1.125 0 010 1.971l-11.54 6.347a1.125 1.125 0 01-1.667-.985V5.653z"
+                />
+              </svg>
+            </button>
+          {:else}
+            <button class="p-2" title="Pause" on:click={toggleAnimation}>
+              <svg
+                xmlns="http://www.w3.org/2000/svg"
+                fill="none"
+                viewBox="0 0 24 24"
+                stroke-width="2"
+                stroke="currentColor"
+                class="w-4 h-4 text-gray-500 hover:text-orange-600 cursor-pointer"
+              >
+                <path
+                  stroke-linecap="round"
+                  stroke-linejoin="round"
+                  d="M5.25 7.5A2.25 2.25 0 017.5 5.25h9a2.25 2.25 0 012.25 2.25v9a2.25 2.25 0 01-2.25 2.25h-9a2.25 2.25 0 01-2.25-2.25v-9z"
+                />
+              </svg>
+
+              <!-- <svg
+                                xmlns="http://www.w3.org/2000/svg"
+                                fill="none"
+                                viewBox="0 0 24 24"
+                                stroke-width="2"
+                                stroke="currentColor"
+                                class="w-4 h-4 text-gray-500 hover:text-orange-600 cursor-pointer"
+                            >
+                                <path
+                                    stroke-linecap="round"
+                                    stroke-linejoin="round"
+                                    d="M15.75 5.25v13.5m-7.5-13.5v13.5"
+                                />
+                            </svg> -->
+            </button>
+          {/if}
+        </div>
+      {/if}
+
+      <div
+        class="absolute z-50 bottom-0 left-0 ml-2 flex divide-x mb-2 rounded items-center justify-center"
+      >
+        <button
+          class="p-1"
+          title="How to cite 3Dmol.js"
+          on:click={toggleCiteTooltip}
+        >
+          <svg
+            class="w-4 h-4 text-gray-500 hover:text-orange-600 cursor-pointer fill-current"
+            viewBox="0 0 20 20"
+            xmlns="http://www.w3.org/2000/svg"
+            ><g id="SVGRepo_bgCarrier" stroke-width="0" /><g
+              id="SVGRepo_tracerCarrier"
+              stroke-linecap="round"
+              stroke-linejoin="round"
+            /><g id="SVGRepo_iconCarrier"
+              ><path
+                d="M12.6 7.6v3.9h-1.1v4.6h-3v-4.6H7.4V7.6c0-.3.3-.6.6-.6h4c.3 0 .6.3.6.6zM10 6.5c.7 0 1.3-.6 1.3-1.3 0-.7-.6-1.3-1.3-1.3-.7 0-1.3.6-1.3 1.3 0 .7.6 1.3 1.3 1.3zm9.6 3.5c0 2.7-.9 4.9-2.7 6.7-1.9 1.9-4.2 2.9-6.9 2.9-2.6 0-4.9-.9-6.8-2.8C1.3 14.9.4 12.7.4 10c0-2.6.9-4.9 2.8-6.8C5.1 1.3 7.3.4 10 .4s5 .9 6.8 2.8c1.9 1.8 2.8 4.1 2.8 6.8zm-1.7 0c0-2.2-.8-4-2.3-5.6C14 2.9 12.2 2.1 10 2.1c-2.2 0-4 .8-5.5 2.3C2.9 6 2.1 7.9 2.1 10c0 2.1.8 4 2.3 5.5s3.4 2.3 5.6 2.3c2.1 0 4-.8 5.6-2.4 1.5-1.4 2.3-3.2 2.3-5.4z"
+              /></g
+            ></svg
+          >
+        </button>
+
+        <span
+          class=" absolute -top-1 left-6 w-max rounded bg-gray-900 px-2 py-1 text-sm font-medium text-gray-50 opacity-0 shadow transition-opacity"
+          class:opacity-100={showCiteTooltip}
+        >
+          Cite 3dmol.js as Rego & Koes, doi:10/gb5g5n
+        </span>
+      </div>
+
+      <div class="viewer w-full h-full z-10" bind:this={viewer} />
+
+      {#if showOffCanvas}
+        <div
+          id="settings-drawer"
+          class="absolute top-0 right-0 z-50 h-full overflow-y-auto transition-transform bg-gray-100 w-80 dark:bg-gray-800"
+          tabindex="-1"
+          aria-labelledby="settings-drawer-label"
+        >
+          <div class="p-4">
+            <h5
+              id="settings-drawer-label"
+              class="inline-flex items-center mb-4 text-base font-semibold text-gray-500 dark:text-gray-400"
+            >
+              Settings
+            </h5>
+            <button
+              type="button"
+              data-drawer-hide="drawer-example"
+              aria-controls="drawer-example"
+              class="text-gray-400 bg-transparent hover:bg-gray-200 hover:text-gray-900 rounded-lg text-sm p-1.5 absolute top-2.5 right-2.5 inline-flex items-center dark:hover:bg-gray-600 dark:hover:text-white"
+              on:click={toggleOffCanvas}
+            >
+              <svg
+                aria-hidden="true"
+                class="w-5 h-5"
+                fill="currentColor"
+                viewBox="0 0 20 20"
+                xmlns="http://www.w3.org/2000/svg"
+                ><path
+                  fill-rule="evenodd"
+                  d="M4.293 4.293a1 1 0 011.414 0L10 8.586l4.293-4.293a1 1 0 111.414 1.414L11.414 10l4.293 4.293a1 1 0 01-1.414 1.414L10 11.414l-4.293 4.293a1 1 0 01-1.414-1.414L8.586 10 4.293 5.707a1 1 0 010-1.414z"
+                  clip-rule="evenodd"
+                /></svg
+              >
+              <span class="sr-only">Close menu</span>
+            </button>
+          </div>
+          {#each Object.keys(config) as setting}
+            <div class="flex flex-col mb-4 divide-y">
+              <div
+                class="flex items-center border-t border-b border-gray-200 bg-white px-4 py-2 space-x-2"
+              >
+                <label
+                  for={setting}
+                  class="text-sm font-medium text-gray-600 dark:text-gray-400 w-1/2"
+                >
+                  {setting}
+                </label>
+
+                {#if settings[setting].type == "toggle"}
+                  <label
+                    class="relative inline-flex items-center mr-5 cursor-pointer text-center justify-center"
+                  >
+                    <input
+                      type="checkbox"
+                      value=""
+                      class="sr-only peer"
+                      bind:checked={config[setting]}
+                    />
+                    <div
+                      class="w-11 h-6 bg-gray-200 rounded-full peer dark:bg-gray-700 peer-focus:ring-4 peer-focus:ring-orange-300 dark:peer-focus:ring-orange-800 peer-checked:after:translate-x-full peer-checked:after:border-white after:content-[''] after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-orange-400"
+                    />
+                  </label>
+                {/if}
+                {#if settings[setting].type == "range"}
+                  <div class="flex items-center">
+                    <input
+                      id="medium-range"
+                      type="range"
+                      value={config[setting]}
+                      min={settings[setting].min}
+                      max={settings[setting].max}
+                      step={settings[setting].step}
+                      on:change={() => {
+                        config[setting] = event.target.value;
+                      }}
+                      class="w-2/3 h-2 bg-gray-200 rounded-lg appearance-none cursor-pointer dark:bg-gray-700"
+                    />
+                    <span
+                      class="w-1/3 text-center text-sm font-medium text-gray-600 dark:text-gray-400"
+                      >{config[setting]}</span
+                    >
+                  </div>
+                {/if}
+                {#if settings[setting].type == "select"}
+                  <label for={setting} class="sr-only">Select style</label>
+                  <select
+                    id={setting}
+                    class="bg-gray-50 border border-gray-300 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block w-full p-2.5 dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500"
+                    bind:value={config[setting]}
+                  >
+                    {#each settings[setting].options as option}
+                      <option
+                        value={option}
+                        selected={option == config[setting]}
+                      >
+                        {option}
+                      </option>
+                    {/each}
+                  </select>
+                {/if}
+              </div>
+            </div>
+          {/each}
+          <div class="bg-white">
+            <div
+              class="flex items-center border-t border-b border-gray-200 bg-white px-4 py-2 space-x-2"
+            >
+              <label
+                class="text-sm font-medium text-gray-600 dark:text-gray-400 w-1/2"
+              >
+                Label atoms on hover
+              </label>
+              <label
+                class="relative inline-flex items-center mr-5 cursor-pointer text-center justify-center"
+              >
+                <input
+                  type="checkbox"
+                  class="sr-only peer"
+                  bind:value={labelHover}
+                />
+                <div
+                  class="w-11 h-6 bg-gray-200 rounded-full peer dark:bg-gray-700 peer-focus:ring-4 peer-focus:ring-orange-300 dark:peer-focus:ring-orange-800 peer-checked:after:translate-x-full peer-checked:after:border-white after:content-[''] after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-orange-400"
+                />
+              </label>
+            </div>
+          </div>
+        </div>
+      {/if}
+      {#if showOffCanvasReps}
+        <div
+          id="drawer-example"
+          class="absolute top-0 right-0 z-50 h-full overflow-y-auto transition-transform bg-gray-100 w-80 dark:bg-gray-800 border-l border-gray-200"
+          tabindex="-1"
+          aria-labelledby="drawer-label"
+        >
+          <div class="p-4">
+            <h5
+              id="drawer-label"
+              class="inline-flex items-center mb-4 text-base font-semibold text-gray-500 dark:text-gray-400"
+            >
+              Representations
+            </h5>
+            <button
+              type="button"
+              data-drawer-hide="drawer-example"
+              aria-controls="drawer-example"
+              class="text-gray-400 bg-transparent hover:bg-gray-200 hover:text-gray-900 rounded-lg text-sm p-1.5 absolute top-2.5 right-2.5 inline-flex items-center dark:hover:bg-gray-600 dark:hover:text-white"
+              on:click={toggleOffCanvasReps}
+            >
+              <svg
+                aria-hidden="true"
+                class="w-5 h-5"
+                fill="currentColor"
+                viewBox="0 0 20 20"
+                xmlns="http://www.w3.org/2000/svg"
+                ><path
+                  fill-rule="evenodd"
+                  d="M4.293 4.293a1 1 0 011.414 0L10 8.586l4.293-4.293a1 1 0 111.414 1.414L11.414 10l4.293 4.293a1 1 0 01-1.414 1.414L10 11.414l-4.293 4.293a1 1 0 01-1.414-1.414L8.586 10 4.293 5.707a1 1 0 010-1.414z"
+                  clip-rule="evenodd"
+                /></svg
+              >
+              <span class="sr-only">Close menu</span>
+            </button>
+          </div>
+
+          {#each representations as rep, index}
+            <div class="bg-white border-b border-t border-gray-200 py-4 px-2">
+              <div class="">
+                <div class="flex space-x-2 items-center cursor-pointer p-1">
+                  <button
+                    on:click={() => (rep.visible = !rep.visible)}
+                    class="flex items-center space-x-2"
+                  >
+                    <svg
+                      xmlns="http://www.w3.org/2000/svg"
+                      fill="none"
+                      viewBox="0 0 24 24"
+                      stroke-width="1.5"
+                      stroke="currentColor"
+                      class={rep.visible
+                        ? "transform rotate-90 w-5 h-5 "
+                        : "w-5 h-5 "}
+                    >
+                      <path
+                        stroke-linecap="round"
+                        stroke-linejoin="round"
+                        d="M8.25 4.5l7.5 7.5-7.5 7.5"
+                      />
+                    </svg>
+                    <span>Representation #{index}</span>
+                  </button>
+                  <button on:click={() => deleteRep(index)}>
+                    <!---->
+                    <svg
+                      xmlns="http://www.w3.org/2000/svg"
+                      fill="none"
+                      viewBox="0 0 24 24"
+                      stroke-width="1.5"
+                      stroke="currentColor"
+                      class="w-5 h-5"
+                    >
+                      <path
+                        stroke-linecap="round"
+                        stroke-linejoin="round"
+                        d="M14.74 9l-.346 9m-4.788 0L9.26 9m9.968-3.21c.342.052.682.107 1.022.166m-1.022-.165L18.16 19.673a2.25 2.25 0 01-2.244 2.077H8.084a2.25 2.25 0 01-2.244-2.077L4.772 5.79m14.456 0a48.108 48.108 0 00-3.478-.397m-12 .562c.34-.059.68-.114 1.022-.165m0 0a48.11 48.11 0 013.478-.397m7.5 0v-.916c0-1.18-.91-2.164-2.09-2.201a51.964 51.964 0 00-3.32 0c-1.18.037-2.09 1.022-2.09 2.201v.916m7.5 0a48.667 48.667 0 00-7.5 0"
+                      />
+                    </svg>
+                  </button>
+                  <button
+                    title="zoom to selection"
+                    on:click={() => resetZoom(rep)}
+                  >
+                    <svg
+                      xmlns="http://www.w3.org/2000/svg"
+                      fill="none"
+                      viewBox="0 0 24 24"
+                      stroke-width="1.5"
+                      stroke="currentColor"
+                      class="w-4 h-4 text-gray-500 hover:text-orange-600 cursor-pointer"
+                    >
+                      <path
+                        stroke-linecap="round"
+                        stroke-linejoin="round"
+                        d="M9 9V4.5M9 9H4.5M9 9L3.75 3.75M9 15v4.5M9 15H4.5M9 15l-5.25 5.25M15 9h4.5M15 9V4.5M15 9l5.25-5.25M15 15h4.5M15 15v4.5m0-4.5l5.25 5.25"
+                      />
+                    </svg>
+                  </button>
+                </div>
+                {#if rep.visible}
+                  <div in:fade>
+                    <div class="p-1 flex space-x-1">
+                      <select
+                        id="style"
+                        class="bg-gray-50 border border-gray-300 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block w-full p-2.5 dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500"
+                        bind:value={rep.model}
+                      >
+                        {#each moldata as mol, i}
+                          <option value={i}>{mol.name} #{i}</option>
+                        {/each}
+                      </select>
+                      <input
+                        type="text"
+                        id="chain"
+                        class="w-1/2 bg-gray-50 border border-gray-300 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block p-2.5 dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500"
+                        placeholder="Chain"
+                        bind:value={rep.chain}
+                      />
+                    </div>
+                    <div class="p-1 flex space-x-1">
+                      <input
+                        type="text"
+                        id="chain"
+                        class="w-1/2 bg-gray-50 border border-gray-300 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block p-2.5 dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500"
+                        placeholder="Resname"
+                        bind:value={rep.resname}
+                      />
+                      <input
+                        type="text"
+                        id="residue_range"
+                        class="w-full bg-gray-50 border border-gray-300 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block p-2.5 dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500"
+                        placeholder="Residue range"
+                        bind:value={rep.residue_range}
+                      />
+                    </div>
+                    <div class="p-1 flex space-x-1 items-center">
+                      <label
+                        for="countries"
+                        class="block mb-2 text-sm w-1/3 font-medium text-gray-600 dark:text-white"
+                        >Select style</label
+                      >
+                      <select
+                        id="style"
+                        class="bg-gray-50 border border-gray-300 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block w-full p-2.5 dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500"
+                        bind:value={rep.style}
+                      >
+                        <option value="stick">Stick</option>
+                        <option value="cartoon">Cartoon</option>
+                        <option value="surface">Surface</option>$
+                        <option value="sphere">Sphere</option>
+                      </select>
+                    </div>
+                    <div
+                      class="flex p-1 items-center text-gray-700 space-x-1 text-sm"
+                    >
+                      <div class="">Opacity</div>
+                      <input
+                        id="around"
+                        type="range"
+                        value={rep.opacity}
+                        min="0"
+                        max="1"
+                        step="0.1"
+                        on:change={(event) => {
+                          rep.opacity = event.target.value;
+                        }}
+                        class="h-2 w-full bg-gray-200 rounded-lg appearance-none cursor-pointer dark:bg-gray-700"
+                      />
+                      <input type="text" bind:value={rep.opacity} class="w-8" />
+                    </div>
+                    <div
+                      class="flex p-1 items-center text-gray-700 space-x-1 text-sm"
+                    >
+                      <div class="">scale</div>
+                      <input
+                        id="around"
+                        type="range"
+                        value={rep.scale}
+                        min="0"
+                        max="1"
+                        step="0.1"
+                        on:change={(event) => {
+                          rep.scale = event.target.value;
+                        }}
+                        class="h-2 w-full bg-gray-200 rounded-lg appearance-none cursor-pointer dark:bg-gray-700"
+                      />
+                      <input type="text" bind:value={rep.scale} class="w-8" />
+                    </div>
+                    <div
+                      class="flex p-1 items-center text-gray-700 space-x-1 text-sm"
+                    >
+                      <div class="">Expand selection</div>
+                      <input
+                        id="around"
+                        type="range"
+                        value={rep.around}
+                        min="0"
+                        max="10"
+                        step="0.5"
+                        on:change={(event) => {
+                          rep.around = event.target.value;
+                        }}
+                        class="h-2 w-1/3 bg-gray-200 rounded-lg appearance-none cursor-pointer dark:bg-gray-700"
+                      />
+                      <input type="text" bind:value={rep.around} class="w-8" />
+                      <div>Å</div>
+                    </div>
+
+                    <div
+                      class="flex p-1 items-center text-gray-700 space-x-1 text-sm"
+                    >
+                      <div class="flex space-x-1 w-1/2">
+                        <span>Full residue</span>
+                        <label
+                          class="relative inline-flex items-center mr-5 cursor-pointer text-center"
+                        >
+                          <input
+                            type="checkbox"
+                            value=""
+                            class="sr-only peer"
+                            bind:checked={rep.byres}
+                          />
+                          <div
+                            class="w-11 h-6 bg-gray-200 rounded-full peer dark:bg-gray-700 peer-focus:ring-4 peer-focus:ring-orange-300 dark:peer-focus:ring-orange-800 peer-checked:after:translate-x-full peer-checked:after:border-white after:content-[''] after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-orange-400"
+                          />
+                        </label>
+                      </div>
+                      <div class="flex space-x-1 w-1/2">
+                        <span>Only sidechain</span>
+                        <label
+                          class="relative inline-flex items-center mr-5 cursor-pointer text-center"
+                        >
+                          <input
+                            type="checkbox"
+                            value=""
+                            class="sr-only peer"
+                            bind:checked={rep.sidechain}
+                          />
+                          <div
+                            class="w-11 h-6 bg-gray-200 rounded-full peer dark:bg-gray-700 peer-focus:ring-4 peer-focus:ring-orange-300 dark:peer-focus:ring-orange-800 peer-checked:after:translate-x-full peer-checked:after:border-white after:content-[''] after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-orange-400"
+                          />
+                        </label>
+                      </div>
+                    </div>
+
+                    <div class="flex space-x-2 mt-2">
+                      <button
+                        class={rep.color === "orangeCarbon"
+                          ? "bg-orange-600 rounded-full w-8 h-8 border-4 border-gray-300  cursor-pointer"
+                          : "bg-orange-600 rounded-full w-8 h-8 border-4 border-white cursor-pointer"}
+                        on:click={() => (rep.color = "orangeCarbon")}
+                      />
+                      <button
+                        class={rep.color === "redCarbon"
+                          ? "bg-red-600 rounded-full w-8 h-8 border-4 border-gray-300  cursor-pointer"
+                          : "bg-red-600 rounded-full w-8 h-8 border-4 border-white cursor-pointer"}
+                        on:click={() => (rep.color = "redCarbon")}
+                      />
+                      <button
+                        class={rep.color === "blackCarbon"
+                          ? "bg-black rounded-full w-8 h-8 border-4 border-gray-300  cursor-pointer"
+                          : "bg-black rounded-full w-8 h-8 border-4 border-white cursor-pointer"}
+                        on:click={() => (rep.color = "blackCarbon")}
+                      />
+                      <button
+                        class={rep.color === "blueCarbon"
+                          ? "bg-blue-600 rounded-full w-8 h-8 border-4 border-gray-300  cursor-pointer"
+                          : "bg-blue-600 rounded-full w-8 h-8 border-4 border-white cursor-pointer"}
+                        on:click={() => (rep.color = "blueCarbon")}
+                      />
+                      <button
+                        class={rep.color === "grayCarbon"
+                          ? "bg-gray-600 rounded-full w-8 h-8 border-4 border-gray-300  cursor-pointer"
+                          : "bg-gray-600 rounded-full w-8 h-8 border-4 border-white cursor-pointer"}
+                        on:click={() => (rep.color = "grayCarbon")}
+                      />
+                      <button
+                        class={rep.color === "greenCarbon"
+                          ? "bg-green-600 rounded-full w-8 h-8 border-4 border-gray-300  cursor-pointer"
+                          : "bg-green-600 rounded-full w-8 h-8 border-4 border-white cursor-pointer"}
+                        on:click={() => (rep.color = "greenCarbon")}
+                      />
+                      <button
+                        class={rep.color === "cyanCarbon"
+                          ? "bg-cyan-600 rounded-full w-8 h-8 border-4 border-gray-300  cursor-pointer"
+                          : "bg-cyan-600 rounded-full w-8 h-8 border-4 border-white cursor-pointer"}
+                        on:click={() => (rep.color = "cyanCarbon")}
+                      />
+                    </div>
+                    <div class="flex space-x-2 py-2 text-sm">
+                      <button
+                        class={rep.color === "alphafold"
+                          ? "rounded-lg p-1 border border-gray-400 cursor-pointer bg-gray-200"
+                          : "rounded-lg p-1 border border-gray-200 cursor-pointer bg-white"}
+                        on:click={() => (rep.color = "alphafold")}
+                      >
+                        AlphaFold
+                      </button>
+                      <button
+                        class={rep.color === "hydrophobicity"
+                          ? "rounded-lg p-1 border border-gray-400 cursor-pointer bg-gray-200"
+                          : "rounded-lg p-1 border border-gray-200 cursor-pointer bg-white"}
+                        on:click={() => (rep.color = "hydrophobicity")}
+                      >
+                        Hydrophobicity
+                      </button>
+                      <button
+                        class={rep.color === "default"
+                          ? "rounded-lg p-1 border border-gray-400 cursor-pointer bg-gray-200"
+                          : "rounded-lg p-1 border border-gray-200 cursor-pointer bg-white"}
+                        on:click={() => (rep.color = "default")}
+                      >
+                        PyMol
+                      </button>
+                      <button
+                        class={rep.color === "Jmol"
+                          ? "rounded-lg p-1 border border-gray-400 cursor-pointer bg-gray-200"
+                          : "rounded-lg p-1 border border-gray-200 cursor-pointer bg-white"}
+                        on:click={() => (rep.color = "Jmol")}
+                      >
+                        Jmol
+                      </button>
+                    </div>
+                    <div class="flex space-x-2 py-2 text-sm">
+                      <button
+                        class={rep.color === "chain"
+                          ? "rounded-lg p-1 border border-gray-400 cursor-pointer bg-gray-200"
+                          : "rounded-lg p-1 border border-gray-200 cursor-pointer bg-white"}
+                        on:click={() => (rep.color = "chain")}
+                      >
+                        Chain
+                      </button>
+                      <button
+                        class={rep.color === "spectrum"
+                          ? "rounded-lg p-1 border border-gray-400 cursor-pointer bg-gray-200"
+                          : "rounded-lg p-1 border border-gray-200 cursor-pointer bg-white"}
+                        on:click={() => (rep.color = "spectrum")}
+                      >
+                        Spectrum
+                      </button>
+                    </div>
+                  </div>
+                {/if}
+              </div>
+            </div>
+          {/each}
+
+          <button
+            class="w-full flex text-orange-600 justify-center my-2 text-sm space-x-2 items-center hover:text-gray-600 cursor-pointer"
+            on:click={insertRep}
+          >
+            <svg
+              xmlns="http://www.w3.org/2000/svg"
+              fill="none"
+              viewBox="0 0 24 24"
+              stroke-width="2"
+              stroke="currentColor"
+              class="w-4 h-4"
+            >
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                d="M12 9v6m3-3H9m12 0a9 9 0 11-18 0 9 9 0 0118 0z"
+              />
+            </svg>
+
+            <div>Add representation</div>
+          </button>
+        </div>
+      {/if}
+    </div>
+  </div>
+</div>
+
+<style>
+  *,
+  :before,
+  :after {
+    box-sizing: border-box;
+    border-width: 0;
+    border-style: solid;
+    border-color: #e5e7eb;
+  }
+  :before,
+  :after {
+    --tw-content: "";
+  }
+  html {
+    line-height: 1.5;
+    -webkit-text-size-adjust: 100%;
+    -moz-tab-size: 4;
+    -o-tab-size: 4;
+    tab-size: 4;
+    font-family:
+      ui-sans-serif,
+      system-ui,
+      -apple-system,
+      BlinkMacSystemFont,
+      Segoe UI,
+      Roboto,
+      Helvetica Neue,
+      Arial,
+      Noto Sans,
+      sans-serif,
+      "Apple Color Emoji",
+      "Segoe UI Emoji",
+      Segoe UI Symbol,
+      "Noto Color Emoji";
+    font-feature-settings: normal;
+  }
+  body {
+    margin: 0;
+    line-height: inherit;
+  }
+  hr {
+    height: 0;
+    color: inherit;
+    border-top-width: 1px;
+  }
+  abbr:where([title]) {
+    -webkit-text-decoration: underline dotted;
+    text-decoration: underline dotted;
+  }
+  h1,
+  h2,
+  h3,
+  h4,
+  h5,
+  h6 {
+    font-size: inherit;
+    font-weight: inherit;
+  }
+  a {
+    color: inherit;
+    text-decoration: inherit;
+  }
+  b,
+  strong {
+    font-weight: bolder;
+  }
+  code,
+  kbd,
+  samp,
+  pre {
+    font-family:
+      ui-monospace,
+      SFMono-Regular,
+      Menlo,
+      Monaco,
+      Consolas,
+      Liberation Mono,
+      Courier New,
+      monospace;
+    font-size: 1em;
+  }
+  small {
+    font-size: 80%;
+  }
+  sub,
+  sup {
+    font-size: 75%;
+    line-height: 0;
+    position: relative;
+    vertical-align: baseline;
+  }
+  sub {
+    bottom: -0.25em;
+  }
+  sup {
+    top: -0.5em;
+  }
+  table {
+    text-indent: 0;
+    border-color: inherit;
+    border-collapse: collapse;
+  }
+  button,
+  input,
+  optgroup,
+  select,
+  textarea {
+    font-family: inherit;
+    font-size: 100%;
+    font-weight: inherit;
+    line-height: inherit;
+    color: inherit;
+    margin: 0;
+    padding: 0;
+  }
+  button,
+  select {
+    text-transform: none;
+  }
+  button,
+  [type="button"],
+  [type="reset"],
+  [type="submit"] {
+    -webkit-appearance: button;
+    background-color: transparent;
+    background-image: none;
+  }
+  :-moz-focusring {
+    outline: auto;
+  }
+  :-moz-ui-invalid {
+    box-shadow: none;
+  }
+  progress {
+    vertical-align: baseline;
+  }
+  ::-webkit-inner-spin-button,
+  ::-webkit-outer-spin-button {
+    height: auto;
+  }
+  [type="search"] {
+    -webkit-appearance: textfield;
+    outline-offset: -2px;
+  }
+  ::-webkit-search-decoration {
+    -webkit-appearance: none;
+  }
+  ::-webkit-file-upload-button {
+    -webkit-appearance: button;
+    font: inherit;
+  }
+  summary {
+    display: list-item;
+  }
+  blockquote,
+  dl,
+  dd,
+  h1,
+  h2,
+  h3,
+  h4,
+  h5,
+  h6,
+  hr,
+  figure,
+  p,
+  pre {
+    margin: 0;
+  }
+  fieldset {
+    margin: 0;
+    padding: 0;
+  }
+  legend {
+    padding: 0;
+  }
+  ol,
+  ul,
+  menu {
+    list-style: none;
+    margin: 0;
+    padding: 0;
+  }
+  textarea {
+    resize: vertical;
+  }
+  input::-moz-placeholder,
+  textarea::-moz-placeholder {
+    opacity: 1;
+    color: #9ca3af;
+  }
+  input::placeholder,
+  textarea::placeholder {
+    opacity: 1;
+    color: #9ca3af;
+  }
+  button,
+  [role="button"] {
+    cursor: pointer;
+  }
+  :disabled {
+    cursor: default;
+  }
+  img,
+  svg,
+  video,
+  canvas,
+  audio,
+  iframe,
+  embed,
+  object {
+    display: block;
+    vertical-align: middle;
+  }
+  img,
+  video {
+    max-width: 100%;
+    height: auto;
+  }
+  [hidden] {
+    display: none;
+  }
+  *,
+  :before,
+  :after {
+    --tw-border-spacing-x: 0;
+    --tw-border-spacing-y: 0;
+    --tw-translate-x: 0;
+    --tw-translate-y: 0;
+    --tw-rotate: 0;
+    --tw-skew-x: 0;
+    --tw-skew-y: 0;
+    --tw-scale-x: 1;
+    --tw-scale-y: 1;
+    --tw-pan-x: ;
+    --tw-pan-y: ;
+    --tw-pinch-zoom: ;
+    --tw-scroll-snap-strictness: proximity;
+    --tw-ordinal: ;
+    --tw-slashed-zero: ;
+    --tw-numeric-figure: ;
+    --tw-numeric-spacing: ;
+    --tw-numeric-fraction: ;
+    --tw-ring-inset: ;
+    --tw-ring-offset-width: 0px;
+    --tw-ring-offset-color: #fff;
+    --tw-ring-color: rgb(59 130 246 / 0.5);
+    --tw-ring-offset-shadow: 0 0 #0000;
+    --tw-ring-shadow: 0 0 #0000;
+    --tw-shadow: 0 0 #0000;
+    --tw-shadow-colored: 0 0 #0000;
+    --tw-blur: ;
+    --tw-brightness: ;
+    --tw-contrast: ;
+    --tw-grayscale: ;
+    --tw-hue-rotate: ;
+    --tw-invert: ;
+    --tw-saturate: ;
+    --tw-sepia: ;
+    --tw-drop-shadow: ;
+    --tw-backdrop-blur: ;
+    --tw-backdrop-brightness: ;
+    --tw-backdrop-contrast: ;
+    --tw-backdrop-grayscale: ;
+    --tw-backdrop-hue-rotate: ;
+    --tw-backdrop-invert: ;
+    --tw-backdrop-opacity: ;
+    --tw-backdrop-saturate: ;
+    --tw-backdrop-sepia: ;
+  }
+  ::backdrop {
+    --tw-border-spacing-x: 0;
+    --tw-border-spacing-y: 0;
+    --tw-translate-x: 0;
+    --tw-translate-y: 0;
+    --tw-rotate: 0;
+    --tw-skew-x: 0;
+    --tw-skew-y: 0;
+    --tw-scale-x: 1;
+    --tw-scale-y: 1;
+    --tw-pan-x: ;
+    --tw-pan-y: ;
+    --tw-pinch-zoom: ;
+    --tw-scroll-snap-strictness: proximity;
+    --tw-ordinal: ;
+    --tw-slashed-zero: ;
+    --tw-numeric-figure: ;
+    --tw-numeric-spacing: ;
+    --tw-numeric-fraction: ;
+    --tw-ring-inset: ;
+    --tw-ring-offset-width: 0px;
+    --tw-ring-offset-color: #fff;
+    --tw-ring-color: rgb(59 130 246 / 0.5);
+    --tw-ring-offset-shadow: 0 0 #0000;
+    --tw-ring-shadow: 0 0 #0000;
+    --tw-shadow: 0 0 #0000;
+    --tw-shadow-colored: 0 0 #0000;
+    --tw-blur: ;
+    --tw-brightness: ;
+    --tw-contrast: ;
+    --tw-grayscale: ;
+    --tw-hue-rotate: ;
+    --tw-invert: ;
+    --tw-saturate: ;
+    --tw-sepia: ;
+    --tw-drop-shadow: ;
+    --tw-backdrop-blur: ;
+    --tw-backdrop-brightness: ;
+    --tw-backdrop-contrast: ;
+    --tw-backdrop-grayscale: ;
+    --tw-backdrop-hue-rotate: ;
+    --tw-backdrop-invert: ;
+    --tw-backdrop-opacity: ;
+    --tw-backdrop-saturate: ;
+    --tw-backdrop-sepia: ;
+  }
+  .container {
+    width: 100%;
+  }
+  @media (min-width: 640px) {
+    .container {
+      max-width: 640px;
+    }
+  }
+  @media (min-width: 768px) {
+    .container {
+      max-width: 768px;
+    }
+  }
+  @media (min-width: 1024px) {
+    .container {
+      max-width: 1024px;
+    }
+  }
+  @media (min-width: 1280px) {
+    .container {
+      max-width: 1280px;
+    }
+  }
+  @media (min-width: 1536px) {
+    .container {
+      max-width: 1536px;
+    }
+  }
+  .sr-only {
+    position: absolute;
+    width: 1px;
+    height: 1px;
+    padding: 0;
+    margin: -1px;
+    overflow: hidden;
+    clip: rect(0, 0, 0, 0);
+    white-space: nowrap;
+    border-width: 0;
+  }
+  .visible {
+    visibility: visible;
+  }
+  .absolute {
+    position: absolute;
+  }
+  .relative {
+    position: relative;
+  }
+  .bottom-0 {
+    bottom: 0px;
+  }
+  .left-0 {
+    left: 0px;
+  }
+  .right-0 {
+    right: 0px;
+  }
+  .right-2 {
+    right: 0.5rem;
+  }
+  .right-2\.5 {
+    right: 0.625rem;
+  }
+  .top-0 {
+    top: 0px;
+  }
+  .top-2 {
+    top: 0.5rem;
+  }
+  .top-2\.5 {
+    top: 0.625rem;
+  }
+  .z-10 {
+    z-index: 10;
+  }
+  .z-50 {
+    z-index: 50;
+  }
+  .my-2 {
+    margin-top: 0.5rem;
+    margin-bottom: 0.5rem;
+  }
+  .mb-2 {
+    margin-bottom: 0.5rem;
+  }
+  .mb-4 {
+    margin-bottom: 1rem;
+  }
+  .mr-2 {
+    margin-right: 0.5rem;
+  }
+  .ml-1 {
+    margin-left: 0.25rem;
+  }
+  .ml-2 {
+    margin-left: 0.5rem;
+  }
+  .mr-5 {
+    margin-right: 1.25rem;
+  }
+  .mt-2 {
+    margin-top: 0.5rem;
+  }
+  .block {
+    display: block;
+  }
+  .flex {
+    display: flex;
+  }
+  .inline-flex {
+    display: inline-flex;
+  }
+  .contents {
+    display: contents;
+  }
+  .h-2 {
+    height: 0.5rem;
+  }
+  .h-3 {
+    height: 0.75rem;
+  }
+  .h-4 {
+    height: 1rem;
+  }
+  .h-5 {
+    height: 1.25rem;
+  }
+  .h-6 {
+    height: 1.5rem;
+  }
+  .h-8 {
+    height: 2rem;
+  }
+  .h-96 {
+    height: 24rem;
+  }
+  .h-full {
+    height: 100%;
+  }
+  .h-screen {
+    height: 100vh;
+  }
+  .w-1\/2 {
+    width: 50%;
+  }
+  .w-1\/3 {
+    width: 33.333333%;
+  }
+  .w-11 {
+    width: 2.75rem;
+  }
+  .w-2\/3 {
+    width: 66.666667%;
+  }
+  .w-3 {
+    width: 0.75rem;
+  }
+  .w-4 {
+    width: 1rem;
+  }
+  .w-5 {
+    width: 1.25rem;
+  }
+  .w-8 {
+    width: 2rem;
+  }
+  .w-80 {
+    width: 20rem;
+  }
+  .w-full {
+    width: 100%;
+  }
+  .max-w-4xl {
+    max-width: 56rem;
+  }
+  .rotate-90 {
+    --tw-rotate: 90deg;
+    transform: translate(var(--tw-translate-x), var(--tw-translate-y))
+      rotate(var(--tw-rotate)) skew(var(--tw-skew-x)) skewY(var(--tw-skew-y))
+      scaleX(var(--tw-scale-x)) scaleY(var(--tw-scale-y));
+  }
+  .transform {
+    transform: translate(var(--tw-translate-x), var(--tw-translate-y))
+      rotate(var(--tw-rotate)) skew(var(--tw-skew-x)) skewY(var(--tw-skew-y))
+      scaleX(var(--tw-scale-x)) scaleY(var(--tw-scale-y));
+  }
+  .cursor-pointer {
+    cursor: pointer;
+  }
+  .appearance-none {
+    -webkit-appearance: none;
+    -moz-appearance: none;
+    appearance: none;
+  }
+  .flex-col {
+    flex-direction: column;
+  }
+  .fill-current {
+    fill: currentColor;
+  }
+  .flex-wrap {
+    flex-wrap: wrap;
+  }
+  .items-center {
+    align-items: center;
+  }
+  .justify-center {
+    justify-content: center;
+  }
+  .gap-px {
+    gap: 1px;
+  }
+  .space-x-1 > :not([hidden]) ~ :not([hidden]) {
+    --tw-space-x-reverse: 0;
+    margin-right: calc(0.25rem * var(--tw-space-x-reverse));
+    margin-left: calc(0.25rem * calc(1 - var(--tw-space-x-reverse)));
+  }
+  .space-x-2 > :not([hidden]) ~ :not([hidden]) {
+    --tw-space-x-reverse: 0;
+    margin-right: calc(0.5rem * var(--tw-space-x-reverse));
+    margin-left: calc(0.5rem * calc(1 - var(--tw-space-x-reverse)));
+  }
+  .divide-x > :not([hidden]) ~ :not([hidden]) {
+    --tw-divide-x-reverse: 0;
+    border-right-width: calc(1px * var(--tw-divide-x-reverse));
+    border-left-width: calc(1px * calc(1 - var(--tw-divide-x-reverse)));
+  }
+  .divide-y > :not([hidden]) ~ :not([hidden]) {
+    --tw-divide-y-reverse: 0;
+    border-top-width: calc(1px * calc(1 - var(--tw-divide-y-reverse)));
+    border-bottom-width: calc(1px * var(--tw-divide-y-reverse));
+  }
+  .overflow-hidden {
+    overflow: hidden;
+  }
+  .overflow-y-auto {
+    overflow-y: auto;
+  }
+  .rounded {
+    border-radius: 0.25rem;
+  }
+  .rounded-full {
+    border-radius: 9999px;
+  }
+  .rounded-lg {
+    border-radius: 0.5rem;
+  }
+  .rounded-br {
+    border-bottom-right-radius: 0.25rem;
+  }
+  .border {
+    border-width: 1px;
+  }
+  .border-4 {
+    border-width: 4px;
+  }
+  .border-b {
+    border-bottom-width: 1px;
+  }
+  .border-l {
+    border-left-width: 1px;
+  }
+  .border-r {
+    border-right-width: 1px;
+  }
+  .border-t {
+    border-top-width: 1px;
+  }
+  .border-solid {
+    border-style: solid;
+  }
+  .border-dashed {
+    border-style: dashed;
+  }
+  .border-gray-200 {
+    --tw-border-opacity: 1;
+    border-color: rgb(229 231 235 / var(--tw-border-opacity));
+  }
+  .border-gray-300 {
+    --tw-border-opacity: 1;
+    border-color: rgb(209 213 219 / var(--tw-border-opacity));
+  }
+  .border-gray-400 {
+    --tw-border-opacity: 1;
+    border-color: rgb(156 163 175 / var(--tw-border-opacity));
+  }
+  .border-white {
+    --tw-border-opacity: 1;
+    border-color: rgb(255 255 255 / var(--tw-border-opacity));
+  }
+  .bg-black {
+    --tw-bg-opacity: 1;
+    background-color: rgb(0 0 0 / var(--tw-bg-opacity));
+  }
+  .bg-blue-600 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(37 99 235 / var(--tw-bg-opacity));
+  }
+  .bg-cyan-600 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(8 145 178 / var(--tw-bg-opacity));
+  }
+  .bg-gray-100 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(243 244 246 / var(--tw-bg-opacity));
+  }
+  .bg-gray-200 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(229 231 235 / var(--tw-bg-opacity));
+  }
+  .bg-gray-50 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(249 250 251 / var(--tw-bg-opacity));
+  }
+  .bg-gray-600 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(75 85 99 / var(--tw-bg-opacity));
+  }
+  .bg-green-600 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(22 163 74 / var(--tw-bg-opacity));
+  }
+  .bg-orange-600 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(234 88 12 / var(--tw-bg-opacity));
+  }
+  .bg-red-600 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(220 38 38 / var(--tw-bg-opacity));
+  }
+  .bg-transparent {
+    background-color: transparent;
+  }
+  .bg-white {
+    --tw-bg-opacity: 1;
+    background-color: rgb(255 255 255 / var(--tw-bg-opacity));
+  }
+  .p-1 {
+    padding: 0.25rem;
+  }
+  .p-1\.5 {
+    padding: 0.375rem;
+  }
+  .p-2 {
+    padding: 0.5rem;
+  }
+  .p-2\.5 {
+    padding: 0.625rem;
+  }
+  .p-4 {
+    padding: 1rem;
+  }
+  .p-5 {
+    padding: 1.25rem;
+  }
+  .px-2 {
+    padding-left: 0.5rem;
+    padding-right: 0.5rem;
+  }
+  .px-4 {
+    padding-left: 1rem;
+    padding-right: 1rem;
+  }
+  .py-1 {
+    padding-top: 0.25rem;
+    padding-bottom: 0.25rem;
+  }
+  .py-2 {
+    padding-top: 0.5rem;
+    padding-bottom: 0.5rem;
+  }
+  .py-4 {
+    padding-top: 1rem;
+    padding-bottom: 1rem;
+  }
+  .text-center {
+    text-align: center;
+  }
+  .text-base {
+    font-size: 1rem;
+    line-height: 1.5rem;
+  }
+  .text-sm {
+    font-size: 0.875rem;
+    line-height: 1.25rem;
+  }
+  .text-xs {
+    font-size: 0.75rem;
+    line-height: 1rem;
+  }
+  .font-medium {
+    font-weight: 500;
+  }
+  .font-semibold {
+    font-weight: 600;
+  }
+  .text-gray-400 {
+    --tw-text-opacity: 1;
+    color: rgb(156 163 175 / var(--tw-text-opacity));
+  }
+  .text-gray-500 {
+    --tw-text-opacity: 1;
+    color: rgb(107 114 128 / var(--tw-text-opacity));
+  }
+  .text-gray-600 {
+    --tw-text-opacity: 1;
+    color: rgb(75 85 99 / var(--tw-text-opacity));
+  }
+  .text-gray-700 {
+    --tw-text-opacity: 1;
+    color: rgb(55 65 81 / var(--tw-text-opacity));
+  }
+  .text-gray-900 {
+    --tw-text-opacity: 1;
+    color: rgb(17 24 39 / var(--tw-text-opacity));
+  }
+  .text-orange-600 {
+    --tw-text-opacity: 1;
+    color: rgb(234 88 12 / var(--tw-text-opacity));
+  }
+  .invert {
+    --tw-invert: invert(100%);
+    filter: var(--tw-blur) var(--tw-brightness) var(--tw-contrast)
+      var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert)
+      var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow);
+  }
+  .transition-transform {
+    transition-property: transform;
+    transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1);
+    transition-duration: 0.15s;
+  }
+  .scroll-hide {
+    -ms-overflow-style: none;
+    scrollbar-width: none;
+  }
+  .sr-only {
+    clip: rect(0, 0, 0, 0);
+    position: absolute;
+    margin: -1px;
+    border-width: 0;
+    padding: 0;
+    width: 1px;
+    height: 1px;
+    overflow: hidden;
+    white-space: nowrap;
+  }
+  .scroll-hide::-webkit-scrollbar {
+    display: none;
+  }
+  .gradio-container {
+    -webkit-text-size-adjust: 100%;
+    line-height: 1.5;
+    font-family:
+      Source Sans Pro,
+      ui-sans-serif,
+      system-ui,
+      -apple-system,
+      BlinkMacSystemFont,
+      Segoe UI,
+      Roboto,
+      Helvetica Neue,
+      Arial,
+      Noto Sans,
+      sans-serif,
+      "Apple Color Emoji",
+      "Segoe UI Emoji",
+      Segoe UI Symbol,
+      "Noto Color Emoji";
+    -moz-tab-size: 4;
+    -o-tab-size: 4;
+    tab-size: 4;
+  }
+  .cropper-container {
+    position: relative;
+    touch-action: none;
+    font-size: 0;
+    line-height: 0;
+    direction: ltr;
+    -webkit-user-select: none;
+    -moz-user-select: none;
+    user-select: none;
+  }
+  .cropper-container img {
+    display: block;
+    image-orientation: 0deg;
+    width: 100%;
+    min-width: 0 !important;
+    max-width: none !important;
+    height: 100%;
+    min-height: 0 !important;
+    max-height: none !important;
+  }
+  .cropper-wrap-box,
+  .cropper-canvas,
+  .cropper-drag-box,
+  .cropper-crop-box,
+  .cropper-modal {
+    position: absolute;
+    top: 0;
+    right: 0;
+    bottom: 0;
+    left: 0;
+  }
+  .cropper-wrap-box,
+  .cropper-canvas {
+    overflow: hidden;
+  }
+  .cropper-drag-box {
+    opacity: 0;
+    background-color: #fff;
+  }
+  .cropper-modal {
+    opacity: 0.5;
+    background-color: #000;
+  }
+  .cropper-view-box {
+    display: block;
+    outline: 1px solid #39f;
+    outline-color: #3399ffbf;
+    width: 100%;
+    height: 100%;
+    overflow: hidden;
+  }
+  .cropper-dashed {
+    display: block;
+    position: absolute;
+    opacity: 0.5;
+    border: 0 dashed #eee;
+  }
+  .cropper-dashed.dashed-h {
+    top: calc(100% / 3);
+    left: 0;
+    border-top-width: 1px;
+    border-bottom-width: 1px;
+    width: 100%;
+    height: calc(100% / 3);
+  }
+  .cropper-dashed.dashed-v {
+    top: 0;
+    left: calc(100% / 3);
+    border-right-width: 1px;
+    border-left-width: 1px;
+    width: calc(100% / 3);
+    height: 100%;
+  }
+  .cropper-center {
+    display: block;
+    position: absolute;
+    top: 50%;
+    left: 50%;
+    opacity: 0.75;
+    width: 0;
+    height: 0;
+  }
+  .cropper-center:before,
+  .cropper-center:after {
+    display: block;
+    position: absolute;
+    background-color: #eee;
+    content: " ";
+  }
+  .cropper-center:before {
+    top: 0;
+    left: -3px;
+    width: 7px;
+    height: 1px;
+  }
+  .cropper-center:after {
+    top: -3px;
+    left: 0;
+    width: 1px;
+    height: 7px;
+  }
+  .cropper-face,
+  .cropper-line,
+  .cropper-point {
+    display: block;
+    position: absolute;
+    opacity: 0.1;
+    width: 100%;
+    height: 100%;
+  }
+  .cropper-face {
+    top: 0;
+    left: 0;
+    background-color: #fff;
+  }
+  .cropper-line {
+    background-color: #39f;
+  }
+  .cropper-line.line-e {
+    top: 0;
+    right: -3px;
+    cursor: ew-resize;
+    width: 5px;
+  }
+  .cropper-line.line-n {
+    top: -3px;
+    left: 0;
+    cursor: ns-resize;
+    height: 5px;
+  }
+  .cropper-line.line-w {
+    top: 0;
+    left: -3px;
+    cursor: ew-resize;
+    width: 5px;
+  }
+  .cropper-line.line-s {
+    bottom: -3px;
+    left: 0;
+    cursor: ns-resize;
+    height: 5px;
+  }
+  .cropper-point {
+    opacity: 0.75;
+    background-color: #39f;
+    width: 5px;
+    height: 5px;
+  }
+  .cropper-point.point-e {
+    top: 50%;
+    right: -3px;
+    cursor: ew-resize;
+    margin-top: -3px;
+  }
+  .cropper-point.point-n {
+    top: -3px;
+    left: 50%;
+    cursor: ns-resize;
+    margin-left: -3px;
+  }
+  .cropper-point.point-w {
+    top: 50%;
+    left: -3px;
+    cursor: ew-resize;
+    margin-top: -3px;
+  }
+  .cropper-point.point-s {
+    bottom: -3px;
+    left: 50%;
+    cursor: s-resize;
+    margin-left: -3px;
+  }
+  .cropper-point.point-ne {
+    top: -3px;
+    right: -3px;
+    cursor: nesw-resize;
+  }
+  .cropper-point.point-nw {
+    top: -3px;
+    left: -3px;
+    cursor: nwse-resize;
+  }
+  .cropper-point.point-sw {
+    bottom: -3px;
+    left: -3px;
+    cursor: nesw-resize;
+  }
+  .cropper-point.point-se {
+    right: -3px;
+    bottom: -3px;
+    opacity: 1;
+    cursor: nwse-resize;
+    width: 20px;
+    height: 20px;
+  }
+  @media (min-width: 768px) {
+    .cropper-point.point-se {
+      width: 15px;
+      height: 15px;
+    }
+  }
+  @media (min-width: 992px) {
+    .cropper-point.point-se {
+      width: 10px;
+      height: 10px;
+    }
+  }
+  @media (min-width: 1200px) {
+    .cropper-point.point-se {
+      opacity: 0.75;
+      width: 5px;
+      height: 5px;
+    }
+  }
+  .cropper-point.point-se:before {
+    display: block;
+    position: absolute;
+    right: -50%;
+    bottom: -50%;
+    opacity: 0;
+    background-color: #39f;
+    width: 200%;
+    height: 200%;
+    content: " ";
+  }
+  .cropper-invisible {
+    opacity: 0;
+  }
+  .cropper-bg {
+    background-image: url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQAQMAAAAlPW0iAAAAA3NCSVQICAjb4U/gAAAABlBMVEXMzMz////TjRV2AAAACXBIWXMAAArrAAAK6wGCiw1aAAAAHHRFWHRTb2Z0d2FyZQBBZG9iZSBGaXJld29ya3MgQ1M26LyyjAAAABFJREFUCJlj+M/AgBVhF/0PAH6/D/HkDxOGAAAAAElFTkSuQmCC);
+  }
+  .cropper-hide {
+    display: block;
+    position: absolute;
+    width: 0;
+    height: 0;
+  }
+  .cropper-hidden {
+    display: none !important;
+  }
+  .cropper-move {
+    cursor: move;
+  }
+  .cropper-crop {
+    cursor: crosshair;
+  }
+  .cropper-disabled .cropper-drag-box,
+  .cropper-disabled .cropper-face,
+  .cropper-disabled .cropper-line,
+  .cropper-disabled .cropper-point {
+    cursor: not-allowed;
+  }
+  .after\:absolute:after {
+    content: var(--tw-content);
+    position: absolute;
+  }
+  .after\:left-\[2px\]:after {
+    content: var(--tw-content);
+    left: 2px;
+  }
+  .after\:top-0:after {
+    content: var(--tw-content);
+    top: 0px;
+  }
+  .after\:top-0\.5:after {
+    content: var(--tw-content);
+    top: 0.125rem;
+  }
+  .after\:h-5:after {
+    content: var(--tw-content);
+    height: 1.25rem;
+  }
+  .after\:w-5:after {
+    content: var(--tw-content);
+    width: 1.25rem;
+  }
+  .after\:rounded-full:after {
+    content: var(--tw-content);
+    border-radius: 9999px;
+  }
+  .after\:border:after {
+    content: var(--tw-content);
+    border-width: 1px;
+  }
+  .after\:border-gray-300:after {
+    content: var(--tw-content);
+    --tw-border-opacity: 1;
+    border-color: rgb(209 213 219 / var(--tw-border-opacity));
+  }
+  .after\:bg-white:after {
+    content: var(--tw-content);
+    --tw-bg-opacity: 1;
+    background-color: rgb(255 255 255 / var(--tw-bg-opacity));
+  }
+  .after\:transition-all:after {
+    content: var(--tw-content);
+    transition-property: all;
+    transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1);
+    transition-duration: 0.15s;
+  }
+  .after\:content-\[\'\'\]:after {
+    --tw-content: "";
+    content: var(--tw-content);
+  }
+  .hover\:bg-gray-200:hover {
+    --tw-bg-opacity: 1;
+    background-color: rgb(229 231 235 / var(--tw-bg-opacity));
+  }
+  .hover\:text-gray-600:hover {
+    --tw-text-opacity: 1;
+    color: rgb(75 85 99 / var(--tw-text-opacity));
+  }
+  .hover\:text-gray-900:hover {
+    --tw-text-opacity: 1;
+    color: rgb(17 24 39 / var(--tw-text-opacity));
+  }
+  .hover\:text-orange-600:hover {
+    --tw-text-opacity: 1;
+    color: rgb(234 88 12 / var(--tw-text-opacity));
+  }
+  .focus\:border-blue-500:focus {
+    --tw-border-opacity: 1;
+    border-color: rgb(59 130 246 / var(--tw-border-opacity));
+  }
+  .focus\:ring-blue-500:focus {
+    --tw-ring-opacity: 1;
+    --tw-ring-color: rgb(59 130 246 / var(--tw-ring-opacity));
+  }
+  .peer:checked ~ .peer-checked\:bg-orange-400 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(251 146 60 / var(--tw-bg-opacity));
+  }
+  .peer:checked ~ .peer-checked\:after\:translate-x-full:after {
+    content: var(--tw-content);
+    --tw-translate-x: 100%;
+    transform: translate(var(--tw-translate-x), var(--tw-translate-y))
+      rotate(var(--tw-rotate)) skew(var(--tw-skew-x)) skewY(var(--tw-skew-y))
+      scaleX(var(--tw-scale-x)) scaleY(var(--tw-scale-y));
+  }
+  .peer:checked ~ .peer-checked\:after\:border-white:after {
+    content: var(--tw-content);
+    --tw-border-opacity: 1;
+    border-color: rgb(255 255 255 / var(--tw-border-opacity));
+  }
+  .peer:focus ~ .peer-focus\:ring-4 {
+    --tw-ring-offset-shadow: var(--tw-ring-inset) 0 0 0
+      var(--tw-ring-offset-width) var(--tw-ring-offset-color);
+    --tw-ring-shadow: var(--tw-ring-inset) 0 0 0
+      calc(4px + var(--tw-ring-offset-width)) var(--tw-ring-color);
+    box-shadow: var(--tw-ring-offset-shadow), var(--tw-ring-shadow),
+      var(--tw-shadow, 0 0 #0000);
+  }
+  .peer:focus ~ .peer-focus\:ring-orange-300 {
+    --tw-ring-opacity: 1;
+    --tw-ring-color: rgb(253 186 116 / var(--tw-ring-opacity));
+  }
+  @media (prefers-color-scheme: dark) {
+    .dark\:border-gray-600 {
+      --tw-border-opacity: 1;
+      border-color: rgb(75 85 99 / var(--tw-border-opacity));
+    }
+    .dark\:bg-gray-700 {
+      --tw-bg-opacity: 1;
+      background-color: rgb(55 65 81 / var(--tw-bg-opacity));
+    }
+    .dark\:bg-gray-800 {
+      --tw-bg-opacity: 1;
+      background-color: rgb(31 41 55 / var(--tw-bg-opacity));
+    }
+    .dark\:text-gray-400 {
+      --tw-text-opacity: 1;
+      color: rgb(156 163 175 / var(--tw-text-opacity));
+    }
+    .dark\:text-white {
+      --tw-text-opacity: 1;
+      color: rgb(255 255 255 / var(--tw-text-opacity));
+    }
+    .dark\:placeholder-gray-400::-moz-placeholder {
+      --tw-placeholder-opacity: 1;
+      color: rgb(156 163 175 / var(--tw-placeholder-opacity));
+    }
+    .dark\:placeholder-gray-400::placeholder {
+      --tw-placeholder-opacity: 1;
+      color: rgb(156 163 175 / var(--tw-placeholder-opacity));
+    }
+    .dark\:hover\:bg-gray-600:hover {
+      --tw-bg-opacity: 1;
+      background-color: rgb(75 85 99 / var(--tw-bg-opacity));
+    }
+    .dark\:hover\:text-white:hover {
+      --tw-text-opacity: 1;
+      color: rgb(255 255 255 / var(--tw-text-opacity));
+    }
+    .dark\:focus\:border-blue-500:focus {
+      --tw-border-opacity: 1;
+      border-color: rgb(59 130 246 / var(--tw-border-opacity));
+    }
+    .dark\:focus\:ring-blue-500:focus {
+      --tw-ring-opacity: 1;
+      --tw-ring-color: rgb(59 130 246 / var(--tw-ring-opacity));
+    }
+    .peer:focus ~ .dark\:peer-focus\:ring-orange-800 {
+      --tw-ring-opacity: 1;
+      --tw-ring-color: rgb(154 52 18 / var(--tw-ring-opacity));
+    }
+  }
+  .minh {
+    height: 600px;
+  }
+
+  .-top-1 {
+    top: -0.25rem;
+  }
+
+  .left-6 {
+    left: 1.5rem;
+  }
+
+  .h-4 {
+    height: 1rem;
+  }
+
+  .w-4 {
+    width: 1rem;
+  }
+
+  .w-max {
+    width: max-content;
+  }
+
+  .cursor-pointer {
+    cursor: pointer;
+  }
+
+  .rounded {
+    border-radius: 0.25rem;
+  }
+
+  .bg-gray-900 {
+    --tw-bg-opacity: 1;
+    background-color: rgb(17 24 39 / var(--tw-bg-opacity));
+  }
+
+  .fill-current {
+    fill: currentColor;
+  }
+
+  .p-10 {
+    padding: 2.5rem;
+  }
+
+  .px-2 {
+    padding-left: 0.5rem;
+    padding-right: 0.5rem;
+  }
+
+  .py-1 {
+    padding-top: 0.25rem;
+    padding-bottom: 0.25rem;
+  }
+
+  .text-sm {
+    font-size: 0.875rem;
+    line-height: 1.25rem;
+  }
+
+  .font-medium {
+    font-weight: 500;
+  }
+
+  .text-gray-50 {
+    --tw-text-opacity: 1;
+    color: rgb(249 250 251 / var(--tw-text-opacity));
+  }
+
+  .text-gray-500 {
+    --tw-text-opacity: 1;
+    color: rgb(107 114 128 / var(--tw-text-opacity));
+  }
+
+  .opacity-0 {
+    opacity: 0;
+  }
+
+  .opacity-100 {
+    opacity: 1;
+  }
+
+  .shadow {
+    --tw-shadow: 0 1px 3px 0 rgb(0 0 0 / 0.1), 0 1px 2px -1px rgb(0 0 0 / 0.1);
+    --tw-shadow-colored: 0 1px 3px 0 var(--tw-shadow-color),
+      0 1px 2px -1px var(--tw-shadow-color);
+    box-shadow: var(--tw-ring-offset-shadow, 0 0 #0000),
+      var(--tw-ring-shadow, 0 0 #0000), var(--tw-shadow);
+  }
+
+  .transition-opacity {
+    transition-property: opacity;
+    transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1);
+    transition-duration: 150ms;
+  }
+
+  .hover\:text-orange-600:hover {
+    --tw-text-opacity: 1;
+    color: rgb(234 88 12 / var(--tw-text-opacity));
+  }
+</style>

gradio_molecule3d/frontend/shared/loading_spinner.svelte

@@ -0,0 +1,44 @@
+<!-- By Sam Herbert (@sherb), for everyone. More @ http://goo.gl/7AJzbL -->
+<svg
+  width="20"
+  height="20 "
+  viewBox="0 0 38 38"
+  xmlns="http://www.w3.org/2000/svg"
+>
+  <defs>
+    <linearGradient x1="8.042%" y1="0%" x2="65.682%" y2="23.865%" id="a">
+      <stop stop-color="#FF7C00" stop-opacity="0" offset="0%" />
+      <stop stop-color="#FF7C00" stop-opacity=".631" offset="63.146%" />
+      <stop stop-color="#FF7C00" offset="100%" />
+    </linearGradient>
+  </defs>
+  <g fill="none" fill-rule="evenodd">
+    <g transform="translate(1 1)">
+      <path
+        d="M36 18c0-9.94-8.06-18-18-18"
+        id="Oval-2"
+        stroke="url(#a)"
+        stroke-width="2"
+      >
+        <animateTransform
+          attributeName="transform"
+          type="rotate"
+          from="0 18 18"
+          to="360 18 18"
+          dur="0.9s"
+          repeatCount="indefinite"
+        />
+      </path>
+      <circle fill="#FFf" cx="36" cy="18" r="1">
+        <animateTransform
+          attributeName="transform"
+          type="rotate"
+          from="0 18 18"
+          to="360 18 18"
+          dur="0.9s"
+          repeatCount="indefinite"
+        />
+      </circle>
+    </g>
+  </g>
+</svg>

gradio_molecule3d/frontend/shared/utils.ts

@@ -0,0 +1,12 @@
+import type { FileData } from "@gradio/client";
+
+export const prettyBytes = (bytes: number): string => {
+	let units = ["B", "KB", "MB", "GB", "PB"];
+	let i = 0;
+	while (bytes > 1024) {
+		bytes /= 1024;
+		i++;
+	}
+	let unit = units[i];
+	return bytes.toFixed(1) + " " + unit;
+};

gradio_molecule3d/frontend/style.css

@@ -0,0 +1 @@
+@import "tailwindcss";

gradio_molecule3d/package.json

@@ -0,0 +1,5 @@
+{
+  "devDependencies": {
+    "@gradio/preview": "^0.13.0"
+  }
+}

gradio_molecule3d/pyproject.toml

@@ -0,0 +1,50 @@
+[build-system]
+requires = [
+  "hatchling",
+  "hatch-requirements-txt",
+  "hatch-fancy-pypi-readme>=22.5.0",
+]
+build-backend = "hatchling.build"
+
+[project]
+name = "gradio_molecule3d"
+version = "0.0.7"
+description = "Python library for easily interacting with trained machine learning models"
+readme = "README.md"
+license = "Apache-2.0"
+requires-python = ">=3.8"
+authors = [{ name = "YOUR NAME", email = "[email protected]" }]
+keywords = [
+  "machine learning",
+  "reproducibility",
+  "visualization",
+  "gradio",
+  "gradio custom component",
+  "gradio-template-File",
+  "protein"
+]
+# Add dependencies here
+dependencies = ["gradio>=4.0,<6.0"]
+classifiers = [
+  'Development Status :: 3 - Alpha',
+  'Operating System :: OS Independent',
+  'Programming Language :: Python :: 3',
+  'Programming Language :: Python :: 3 :: Only',
+  'Programming Language :: Python :: 3.8',
+  'Programming Language :: Python :: 3.9',
+  'Programming Language :: Python :: 3.10',
+  'Programming Language :: Python :: 3.11',
+  'Topic :: Scientific/Engineering',
+  'Topic :: Scientific/Engineering :: Artificial Intelligence',
+  'Topic :: Scientific/Engineering :: Visualization',
+]
+
+
+[project.optional-dependencies]
+dev = ["build", "twine"]
+
+[tool.hatch.build]
+artifacts = ["/backend/gradio_molecule3d/templates", "*.pyi", "/Users/zulissi/micromamba/envs/gradio/lib/python3.12/site-packages/gradio_molecule3d/templates", "/private/home/zulissi/conda_envs/fairchem_020625/lib/python3.12/site-packages/gradio_molecule3d/templates"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["/backend/gradio_molecule3d"]

hf_calculator.py

@@ -0,0 +1,121 @@
+"""
+Copyright (c) Meta Platforms, Inc. and affiliates.
+
+This source code is licensed under the MIT license found in the
+LICENSE file in the root directory of this source tree.
+"""
+
+import hashlib
+import json
+import os
+from pathlib import Path
+
+import ase
+import gradio as gr
+import huggingface_hub as hf_hub
+from ase.calculators.calculator import Calculator
+from ase.db.core import now
+from ase.db.row import AtomsRow
+from ase.io.jsonio import decode, encode
+
+
+def hash_save_file(atoms: ase.Atoms, task_name, path: Path | str):
+    atoms = atoms.copy()
+    atoms.info["task_name"] = task_name
+    atoms.write(
+        Path(path)
+        / f"{hashlib.md5(atoms_to_json(atoms).encode('utf-8')).hexdigest()}.traj"
+    )
+    return
+
+
+class HFEndpointCalculator(Calculator):
+
+    # A simple calculator that uses the Hugging Face Inference Endpoints to run
+
+    implemented_properties = ["energy", "free_energy", "stress", "forces"]
+
+    def __init__(
+        self,
+        atoms,
+        endpoint_url,
+        oauth_token,
+        task_name,
+        example=False,
+        *args,
+        **kwargs,
+    ):
+        # If we have an example structure, we don't need to check for authentication
+        # Otherwise, we need to check if the user is authenticated and has gated access to the UMA models
+        if not example:
+            try:
+                hf_hub.HfApi().auth_check(
+                    repo_id="facebook/OMAT24", token=oauth_token.token
+                )
+                hash_save_file(atoms, task_name, "/data/custom_inputs/")
+            except (hf_hub.errors.HfHubHTTPError, AttributeError):
+                raise gr.Error(
+                    "You need to log in to HF and have gated model access to UMA before running your own simulations!"
+                )
+
+        self.client = hf_hub.InferenceClient(
+            model=endpoint_url, token=os.environ["HF_TOKEN"]
+        )
+        self.atoms = atoms
+        self.task_name = task_name
+
+        super().__init__(*args, **kwargs)
+
+    def calculate(self, atoms, properties, system_changes):
+        Calculator.calculate(self, atoms, properties, system_changes)
+
+        task_name = self.task_name.lower()
+        if task_name == "omc":
+            task_name = "osc"
+
+        # Run inference via a post request to the endpoint
+        try:
+            response = self.client.post(
+                json={
+                    "inputs": atoms_to_json(atoms, data=atoms.info),
+                    "properties": properties,
+                    "system_changes": system_changes,
+                    "task_name": task_name,
+                }
+            )
+        except hf_hub.errors.BadRequestError:
+            hash_save_file(atoms, task_name, "/data/custom_inputs/errors/")
+            raise gr.Error(
+                "Backend failure during your calculation; if you have continued issues please file an issue in the main FAIR chemistry repo (https://github.com/facebookresearch/fairchem)."
+            )
+
+        # Load the response and store the results in the calc and atoms object
+        response_dict = decode(json.loads(response))
+        self.results = response_dict["results"]
+        atoms.info = response_dict["info"]
+
+
+def atoms_to_json(atoms, data=None):
+    # Similar to ase.db.jsondb
+
+    mtime = now()
+
+    row = AtomsRow(atoms)
+    row.ctime = mtime
+
+    dct = {}
+    for key in row.__dict__:
+        if key[0] == "_" or key in row._keys or key == "id":
+            continue
+        dct[key] = row[key]
+
+    dct["mtime"] = mtime
+
+    if data:
+        dct["data"] = data
+
+    constraints = row.get("constraints")
+    if constraints:
+        dct["constraints"] = constraints
+
+    return encode(dct)

requirements.txt

@@ -0,0 +1,6 @@
+gradio
+numpy
+ase
+
+# Pinned since huggingface_hub>=0.31 does not support custom inference endpoint posts
+huggingface_hub<0.31

simulation_scripts.py

@@ -0,0 +1,345 @@
+"""
+Copyright (c) Meta Platforms, Inc. and affiliates.
+
+This source code is licensed under the MIT license found in the
+LICENSE file in the root directory of this source tree.
+"""
+
+import glob
+import hashlib
+import os
+import tempfile
+
+import ase
+import ase.io
+import gradio as gr
+import numpy as np
+from ase import units
+from ase.filters import FrechetCellFilter
+from ase.io.trajectory import Trajectory
+from ase.md import MDLogger
+from ase.md.nose_hoover_chain import NoseHooverChainNVT
+from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
+from ase.md.verlet import VelocityVerlet
+from ase.optimize import LBFGS
+
+from hf_calculator import HFEndpointCalculator
+
+
+def hash_file(file_path):
+    """Generate MD5 hash for a file."""
+    hasher = hashlib.md5()
+    with open(file_path, "rb") as f:
+        data = f.read()
+    hasher.update(data)
+    return hasher.hexdigest()
+
+
+EXAMPLE_FILE_HASHES = set(
+    [hash_file(file_path) for file_path in glob.glob("examples/*")]
+)
+MAX_ATOMS = os.environ.get("MAX_ATOMS", 2000)
+INFERENCE_ENDPOINT_URL = os.environ["INFERENCE_ENDPOINT_URL"]
+
+
+def load_check_ase_atoms(structure_file):
+    # Validate and write the uploaded file content
+    if not structure_file:
+        raise gr.Error("You need an input structure file to run a simulation!")
+
+    try:
+        atoms = ase.io.read(structure_file)
+
+        if not (all(atoms.pbc) or np.all(~np.array(atoms.pbc))):
+            raise gr.Error(
+                "Mixed PBC are not supported yet - please set PBC all True or False in your structure before uploading"
+            )
+
+        if len(atoms) == 0:
+            raise gr.Error("Error: Structure file contains no atoms.")
+
+        if len(atoms) > MAX_ATOMS:
+            raise gr.Error(
+                f"Error: Structure file contains {len(atoms)}, which is more than {MAX_ATOMS} atoms. Please use a smaller structure for this demo, or run this on a local machine!"
+            )
+
+        atoms.positions -= atoms.get_center_of_mass()
+        cell_center = atoms.get_cell().sum(axis=0) / 2
+        atoms.positions += cell_center
+
+        return atoms
+    except Exception as e:
+        raise gr.Error(f"Error loading structure with ASE: {str(e)}")
+
+
+def run_md_simulation(
+    structure_file,
+    num_steps,
+    num_prerelax_steps,
+    md_timestep,
+    temperature_k,
+    md_ensemble,
+    task_name,
+    total_charge,
+    spin_multiplicity,
+    explanation: str | None = None,
+    oauth_token: gr.OAuthToken | None = None,
+    progress=gr.Progress(),
+):
+    temp_path = None
+    traj_path = None
+    md_log_path = None
+    atoms = None
+
+    if task_name != "OMol":
+        total_charge = 0
+        spin_multiplicity = 0
+
+    try:
+
+        atoms = load_check_ase_atoms(structure_file)
+
+        # Check if the file is an example
+        example = hash_file(structure_file) in EXAMPLE_FILE_HASHES
+
+        atoms.info["charge"] = total_charge
+        atoms.info["spin"] = spin_multiplicity
+
+        atoms.calc = HFEndpointCalculator(
+            atoms,
+            endpoint_url=INFERENCE_ENDPOINT_URL,
+            oauth_token=oauth_token,
+            example=example,
+            task_name=task_name,
+        )
+
+        # Attach a progress callback to track in gradio
+        interval = 1
+        steps = [0]
+        expected_steps = num_steps + num_prerelax_steps
+
+        def update_progress():
+            steps[-1] += interval
+            progress(steps[-1] / expected_steps)
+
+        with tempfile.NamedTemporaryFile(suffix=".traj", delete=False) as traj_f:
+            traj_path = traj_f.name
+        with tempfile.NamedTemporaryFile(suffix=".log", delete=False) as log_f:
+            md_log_path = log_f.name
+
+        # Do a quick pre-relaxation to make sure the system is stable before starting
+        opt = LBFGS(atoms, logfile=md_log_path, trajectory=traj_path)
+        opt.attach(update_progress, interval=interval)
+        opt.run(fmax=0.05, steps=num_prerelax_steps)
+
+        # Initialize the velocity distribution. Since we did a relaxation, half of this
+        # will partition to the potential energy right away, so we double the temperature
+        MaxwellBoltzmannDistribution(atoms, temperature_K=temperature_k * 2)
+
+        # Initialize the MD integrator
+        if md_ensemble == "NVE":
+            dyn = VelocityVerlet(atoms, timestep=md_timestep * units.fs)
+        elif md_ensemble == "NVT":
+            dyn = NoseHooverChainNVT(
+                atoms,
+                timestep=md_timestep * units.fs,
+                temperature_K=temperature_k,
+                tdamp=10 * md_timestep * units.fs,
+            )
+        traj = Trajectory(traj_path, "a", atoms)
+        dyn.attach(traj.write, interval=1)
+        dyn.attach(update_progress, interval=interval)
+        dyn.attach(
+            MDLogger(
+                dyn,
+                atoms,
+                md_log_path,
+                header=True,
+                stress=False,
+                peratom=True,
+                mode="a",
+            ),
+            interval=10,
+        )
+
+        # Run the simulation!
+        dyn.run(num_steps)
+
+        reproduction_script = f"""
+import ase.io
+from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
+from ase.md.verlet import VelocityVerlet
+from ase.optimize import LBFGS
+from ase.io.trajectory import Trajectory
+from ase.md import MDLogger
+from ase import units
+from fairchem.core.common.calculator import FAIRChemCalculator
+
+# Read the atoms object from ASE read-able file
+atoms = ase.io.read('input_file.traj')
+
+# Set the total charge and spin multiplicity if using the OMol task
+atoms.info["charge"] = {total_charge}
+atoms.info["spin"] = {spin_multiplicity}
+
+# Set up the calculator
+atoms.calc = FAIRChemCalculator(name='UMA-SM-Final', hf_hub_repo_id='facebook/UMA', hf_hub_filename = 'UMA-SM-Final', task_name='{task_name}')
+
+# Do a quick pre-relaxation to make sure the system is stable
+opt = LBFGS(atoms, trajectory="relaxation_output.traj")
+opt.run(fmax=0.05, steps={num_prerelax_steps})
+
+# Initialize the velocity distribution; we set twice the temperature since we did a relaxation and
+# much of the kinetic energy will partition to the potential energy right away
+MaxwellBoltzmannDistribution(atoms, temperature_K={temperature_k}*2)
+
+# Initialize the integrator; NVE is shown here as an example, see https://wiki.fysik.dtu.dk/ase/ase/md.html for all options
+dyn = VelocityVerlet(atoms, timestep={md_timestep} * units.fs)
+
+# Set up trajectory and MD logger
+dyn.attach(MDLogger(dyn, atoms, 'md.log', header=True, stress=False, peratom=True, mode="w"), interval=10)
+traj = Trajectory("md_output.traj"', "w", atoms)
+dyn.attach(traj.write, interval=1)
+
+# Run the simulation!
+dyn.run({num_steps})
+        """
+
+        with open(md_log_path, "r") as md_log_file:
+            md_log = md_log_file.read()
+
+        if explanation is None:
+            explanation = f"MD simulation of {len(atoms)} atoms for {num_steps} steps with a timestep of {md_timestep} fs at {temperature_k} K in the {md_ensemble} ensemble using the {task_name} UMA task. You submitted this simulation, so I hope you know what's you're looking for or what it means!"
+
+        return traj_path, md_log, reproduction_script, explanation
+    except Exception as e:
+        raise gr.Error(
+            f"Error running MD simulation: {str(e)}. Please try again or report this error."
+        )
+    finally:
+        if temp_path and os.path.exists(temp_path):
+            os.remove(temp_path)
+
+        if md_log_path and os.path.exists(md_log_path):
+            os.remove(md_log_path)
+
+        if atoms is not None and getattr(atoms, "calc", None) is not None:
+            calc = atoms.calc
+            atoms.calc = None
+            del calc
+
+
+def run_relaxation_simulation(
+    structure_file,
+    num_steps,
+    fmax,
+    task_name,
+    total_charge: float,
+    spin_multiplicity: float,
+    relax_unit_cell,
+    explanation: str | None = None,
+    oauth_token: gr.OAuthToken | None = None,
+    progress=gr.Progress(),
+):
+    temp_path = None
+    traj_path = None
+    opt_log_path = None
+    atoms = None
+
+    if task_name != "OMol":
+        total_charge = 0
+        spin_multiplicity = 0
+
+    try:
+        atoms = load_check_ase_atoms(structure_file)
+
+        # Check if the file is an example
+        example = hash_file(structure_file) in EXAMPLE_FILE_HASHES
+
+        # Center things for consistency in visualization
+        atoms.positions -= atoms.get_center_of_mass()
+        cell_center = atoms.get_cell().sum(axis=0) / 2
+        atoms.positions += cell_center
+
+        atoms.info["charge"] = total_charge
+        atoms.info["spin"] = spin_multiplicity
+
+        atoms.calc = HFEndpointCalculator(
+            atoms,
+            endpoint_url=INFERENCE_ENDPOINT_URL,
+            oauth_token=oauth_token,
+            example=example,
+            task_name=task_name,
+        )
+
+        # Set up a trajectory file to keep the results
+        with tempfile.NamedTemporaryFile(suffix=".traj", delete=False) as traj_f:
+            traj_path = traj_f.name
+        with tempfile.NamedTemporaryFile(suffix=".log", delete=False) as log_f:
+            opt_log_path = log_f.name
+
+        optimizer = LBFGS(
+            FrechetCellFilter(atoms) if relax_unit_cell else atoms,
+            trajectory=traj_path,
+            logfile=opt_log_path,
+        )
+
+        # Attach a progress callback to track in gradio
+        interval = 1
+        steps = [0]
+
+        def update_progress(steps):
+            steps[-1] += interval
+            progress(steps[-1] / num_steps)
+
+        optimizer.attach(update_progress, interval=interval, steps=steps)
+
+        optimizer.run(fmax=fmax, steps=num_steps)
+
+        reproduction_script = f"""
+import ase.io
+from ase.optimize import LBFGS
+from ase.filters import FrechetCellFilter
+from fairchem.core.common.calcaulator import FAIRChemCalculator
+
+# Read the atoms object from ASE read-able file
+atoms = ase.io.read('input_file.traj')
+
+# Set the total charge and spin multiplicity if using the OMol task
+atoms.info["charge"] = {total_charge}
+atoms.info["spin"] = {spin_multiplicity}
+
+# Set up the calculator
+atoms.calc = FAIRChemCalculator(name='UMA-SM-Final', hf_hub_repo_id='facebook/UMA', hf_hub_filename = 'UMA-SM-Final', task_name='{task_name}')
+
+# Initialize the optimizer from ASE
+relax_unit_cell = {relax_unit_cell}
+optimizer = LBFGS(FrechetCellFilter(atoms) if relax_unit_cell else atoms, trajectory="relaxation_output.traj")
+
+# Run the simulation!
+dyn.run({num_steps}, fmax={fmax})
+        """
+
+        with open(opt_log_path, "r") as opt_log_file:
+            opt_log = opt_log_file.read()
+
+        if explanation is None:
+            explanation = f"Relaxation of {len(atoms)} atoms for {num_steps} steps with a force tolerance of {fmax} eV/Å using the {task_name} UMA task. You submitted this simulation, so I hope you know what's you're looking for or what it means!"
+        return traj_path, opt_log, reproduction_script, explanation
+    except Exception as e:
+        raise gr.Error(
+            f"Error running relaxation: {str(e)}. Please try again or report this error."
+        )
+    # Make sure we clean up the temp traj files
+    finally:
+        if temp_path and os.path.exists(temp_path):
+            os.remove(temp_path)
+        # if traj_path and os.path.exists(traj_path):
+        #     os.remove(traj_path)
+        if opt_log_path and os.path.exists(opt_log_path):
+            os.remove(opt_log_path)
+
+        if atoms is not None and getattr(atoms, "calc", None) is not None:
+            calc = atoms.calc
+            atoms.calc = None
+            del calc