{"id":22794813,"url":"https://github.com/menchelab/proteinstructurefetch","last_synced_at":"2025-03-30T17:44:02.081Z","repository":{"id":178672827,"uuid":"566095587","full_name":"menchelab/ProteinStructureFetch","owner":"menchelab","description":"Repository for the ProteinStructureFetch extensions. 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This extension is built around the Python package\n[vrprot](https://test.pypi.org/project/vrprot/0.0.6/). As\n[vrprot](https://test.pypi.org/project/vrprot/0.0.6/) uses\n[ChimeraX](https://www.cgl.ucsf.edu/chimerax/download.html) it is mandatory to\ninstall it before using this extension.\n\n## **Installation**\n\n1. Download and install the latest version of\n   [ChimeraX](https://www.cgl.ucsf.edu/chimerax/download.html).\n2. Add the `ProteinStructureFetch` directory to your VRNetzer backend directory.\n   The directory should be located at `\"extensions/ProteinStructureFetch\"`.\n3. Before the line:\n   ```\n   python -m pip install -r requirements.txt\n   ```\n   add the following line to the VRNetzer backend's `build and run` script\n   (Windows: `buildandRUN.ps`, Linux: `linux_buildandrun.sh`, Mac:\n   `mac_buildandrun.sh`) :\n   ```\n   python -m pip install -r extensions/ProteinStructureFetch/requirements.txt\n   ```\n   It should now look something like this:\n   ```\n   python -m pip install -r extensions/ProteinStructureFetch/requirements.txt\n   python -m pip install -r requirements.txt\n   ```\n\n## **Usage**\n\n### **Automatically fetch structures**\n\n---\n\nIf you are in the VR of the VRNetzer and the network you are exploring is a PPI,\nyou can select a node label. On the node panel, you'll see a second tab:\n\n\u003cimg src=\"./pictures/nodepanel_example.png\" alt=\"interactive config panel\" style=\"width:50%;margin-left:auto;margin-right:auto;display:block;margin-top:20px;margin-bottom:20px;\"\u003e\n\nBy selecting a protein structure in the dropdown menu, a fetching process is\nstarted in the background. If the structure has not yet been processed\nbeforehand, the extension will fetch the structure from the AlphaFold DB and\nprocess it. This process takes some seconds. After the process is finished, the\nstructure should rendered in the VR.\n\n---\n\n# API-References\n\n### **Manually fetch structures**\n\n---\n\nTo manually fetch a certain structure, you can navigate to:\n\nhttp://localhost:5000/vrprot/fetch (Windows/Linux)\n\nhttp://localhost:3000/vrprot/fetch (MacOS)\n\nYou define the protein structure you want to fetch by adding:\n\n`?id=\u003cUniProtID_ID\u003e` to the URL.\n\nFor example, to fetch the structure with the UniProt ID `P68871`, you would\nnavigate to:\n\nhttp://localhost:5000/vrprot/fetch?id=P68871\n\nFurthermore, you can define the mode in which the structure will be preprocessed\nin ChimarX by adding `\u0026mode=\u003cMODE\u003e` to the URL.\n\nTo get a list of available modes you navigate to:\n\nhttp://localhost:5000/vrprot/fetch?id=P68871\u0026mode=help\n\n---\n\n### **Fetch all structures of a project**\n\n---\n\nTo fetch all structures of a project, you can navigate to:\n\nhttp://localhost:5000/vrprot/project (Windows/Linux)\n\nhttp://localhost:3000/vrprot/project (MacOS).\n\nYou define the project you want to fetch by adding:\n\n`/\u003cPROJECT_NAME\u003e` to the URL.\n\nFor example, to fetch the project with the project name `my_project`, you would\nnavigate to:\n\nhttp://localhost:5000/vrprot/project/my_project\n\nHere you can also define the mode as described\n[above](#manually-fetch-structures.)\n\nFor this to work, each node has to have a `uniprot` attribute which is a list of\nUniProt IDs. If a node has multiple UniProt IDs, all of them will be fetched and\nprocessed\n\n---\n\n### Fetch a list of structures\n\n---\n\nTo fetch a list of structures, you can navigate to:\n\nhttp://localhost:5000/vrprot/list (Windows/Linux)\n\nhttp://localhost:3000/vrprot/list (MacOS).\n\nYou define the list of structures by adding:\n\n`?ids=\u003cUniProtID_1\u003e,\u003cUniProtID_2\u003e,...,\u003cUniProtID_N\u003e` to the URL.\n\nFor example, to fetch the structures with the UniProt IDs `P68871` and `P68872`,\nyou would navigate to:\n\nhttp://localhost:5000/vrprot/list?ids=P68871,P68872\n\nHere you can also define the mode as described\n[above](#manually-fetch-structures).\n\n---\n\n## **Configuration**\n\n---\n\nThe extension can be configured by editing the `config.ini` file in the\n`ProteinStructureFetch` directory. For every value in this config file there is\na explanation provided. When this config file is not present, the extension will\ncreate a default config file. The coloring mode, AlphaFold DB version, and the overwrite mode can be changed in VR using the interactive panel which is added by this extension:\n\n\u003cimg src=\"./pictures/config_panel.png\" alt=\"interactive config panel\" style=\"width:50%;margin-left:auto;margin-right:auto;display:block;margin-top:20px;margin-bottom:20px;\"\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fproteinstructurefetch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmenchelab%2Fproteinstructurefetch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fproteinstructurefetch/lists"}