streamlit-molstar

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streamlit-molstar

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# streamlit-molstar

[Mol*](https://molstar.org/) (/'molstar/) is a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data.

## Install
`pip install streamlit-molstar`

## License Information

This project is distributed under the MIT License. However, it incorporates code snippets from various visualization projects due to Streamlit's functionality. As a result, certain parts of the project are subject to the original licenses of these snippets. During the project's rapid development, tracking the source of all excerpts proved challenging, leading to uncertainties regarding the need for specific attributions.

- For updates on license clarification, see issue https://github.com/pragmatic-streamlit/streamlit-molstar/issues/21 .
- For the pocket visualization component, refer to the license of [p2rankweb](https://github.com/pragmatic-streamlit/streamlit-molstar/pull/23).

## Usage

### Show Molecule

#### Protein with Traj

```python
    import streamlit as st
    from streamlit_molstar import st_molstar, st_molstar_rcsb, st_molstar_remote

#st_molstar_rcsb('1LOL', key='xx')
    #st_molstar_remote("https://files.rcsb.org/view/1LOL.cif", key='sds')
    #st_molstar('examples/complex.pdb',key='3')
    st_molstar('examples/complex.pdb', 'examples/complex.xtc', key='4')
```

![Protein with Traj](https://raw.githubusercontent.com/pragmatic-streamlit/streamlit-molstar/main/examples/example.png)

### Protein & Pocket

#### Select pocket from local protein (pockets predicted using p2rank and visualized using [PrankWeb](https://github.com/cusbg/prankweb))

```python
    import streamlit as st
    from streamlit_molstar.pocket import select_pocket_from_local_protein

selected = select_pocket_from_local_protein("examples/pocket/protein.pdb", prank_home='/Users/wfluo/Downloads/p2rank_2.4/')
    if selected:
        protein_file_path, pocket = selected
        st.write('Protein Path: ', protein_file_path)
        st.write('Selected Pocket: ', pocket)
```

![Select Pocket](https://raw.githubusercontent.com/pragmatic-streamlit/streamlit-molstar/main/examples/pocket/pocket_select.png)

#### Select pocket from uploaded protein (pockets predicted using p2rank and visualized using [PrankWeb](https://github.com/cusbg/prankweb))

```python
    import streamlit as st
    from streamlit_molstar import st_molstar, st_molstar_rcsb, st_molstar_remote

selected = select_pocket_from_upload_protein(prank_home='/Users/wfluo/Downloads/p2rank_2.4/')
    if selected:
        protein_file_path, pocket = selected
        st.write('Protein Path: ', protein_file_path)
        st.write('Selected Pocket: ', pocket)
```

![Upload & Select Pocket](https://raw.githubusercontent.com/pragmatic-streamlit/streamlit-molstar/main/examples/pocket/upload_select.png)

#### Show Pockets (pockets predicted using p2rank and visualized using [PrankWeb](https://github.com/cusbg/prankweb))

```python
    import streamlit as st
    from streamlit_molstar import st_molstar_pockets

st_molstar_pockets(protein_file_path, structure_file_path, pockets_file_path)
```

![Show Pocket](https://raw.githubusercontent.com/pragmatic-streamlit/streamlit-molstar/main/examples/pocket/show_pocket.png)

## Docking

### Show docking result with ground truth

```python
    import streamlit as st
    from streamlit_molstar.docking import st_molstar_docking

st_molstar_docking('examples/docking/2zy1_protein.pdb', 
                       'examples/docking/docking.2zy1.0.sdf',  gt_ligand_file_path='examples/docking/2zy1_ligand.sdf', key="5", height=240)

```

![Show docking with gt](https://raw.githubusercontent.com/pragmatic-streamlit/streamlit-molstar/main/examples/docking/docking_with_gt.png)

### Auto files

```python
    import streamlit as st
    from streamlit_molstar.auto import st_molstar_auto

import streamlit as st

st.set_page_config(layout="wide")

st.write("from remote url")
    files = ["https://files.rcsb.org/download/3PTB.pdb", "https://files.rcsb.org/download/1LOL.pdb"]
    st_molstar_auto(files, key="6", height="320px")

st.write("from local file")
    files = ['examples/7bcq.pdb', "examples/7bcq.mrc"]

st_molstar_auto(files, key="7", height="320px")
```

![Auto Show](https://raw.githubusercontent.com/pragmatic-streamlit/streamlit-molstar/main/examples/auto.png)

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