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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 & 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 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) ```  #### 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) ```  ## 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) ```  ### 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") ``` 
