Welcome to VRProt’s documentation!
VRProt The main purpose of this project is to serve as an easy to use pipeline to facilitate the processing of protein structures for presentation on the VRNetzer. It is mainly used in a the ProteinStructureFetch Extension an extension for the VRNetzer to visualize protein structures in virtual reality.
For everyone who wants to analyze their own protein structures, with your desired highlighting and coloring, this project is the right place to start. For easy usage of this project, we provide a one file executable which allows to use the program without further installation of python and any dependencies. Nevertheless, a ChimeraX installation is mandatory to use the full potential of this project. Without ChimeraX this software only provides a fetcher with which you can easily fetch PDB files from the AlphaFold Database as well as some converter functions.
Indices and tables
Contents
- Usage
- VRProt
- vrprot.alphafold_db_parser module
AlphafoldDBParser
AlphafoldDBParser.WD
AlphafoldDBParser.alphafold_ver
AlphafoldDBParser.batch_size
AlphafoldDBParser.check_dirs()
AlphafoldDBParser.chimerax
AlphafoldDBParser.chimerax_process()
AlphafoldDBParser.clear_default_dirs()
AlphafoldDBParser.convert_glbs()
AlphafoldDBParser.db
AlphafoldDBParser.execute_fetch()
AlphafoldDBParser.execute_from_bulk()
AlphafoldDBParser.execute_from_object()
AlphafoldDBParser.execute_local()
AlphafoldDBParser.fetch_pdb()
AlphafoldDBParser.fetch_pipeline()
AlphafoldDBParser.filter_already_processed()
AlphafoldDBParser.gen_maps()
AlphafoldDBParser.get_filename()
AlphafoldDBParser.img_size
AlphafoldDBParser.init_dirs()
AlphafoldDBParser.init_structures_dict()
AlphafoldDBParser.keep_temp
AlphafoldDBParser.log
AlphafoldDBParser.not_fetched
AlphafoldDBParser.output_exists()
AlphafoldDBParser.overview_file
AlphafoldDBParser.overwrite
AlphafoldDBParser.pdb_pipeline()
AlphafoldDBParser.processing
AlphafoldDBParser.proteins_from_dir()
AlphafoldDBParser.proteins_from_list()
AlphafoldDBParser.sample_pcd()
AlphafoldDBParser.set_alphafold_version()
AlphafoldDBParser.set_batch_size()
AlphafoldDBParser.set_chimerax()
AlphafoldDBParser.set_coloring_mode()
AlphafoldDBParser.set_database()
AlphafoldDBParser.set_dirs()
AlphafoldDBParser.set_img_size()
AlphafoldDBParser.set_keep_tmp()
AlphafoldDBParser.set_version_from_filenames()
AlphafoldDBParser.structures
AlphafoldDBParser.update_existence()
AlphafoldDBParser.update_output_dir()
AlphafoldDBParser.write_scale()
- vrprot.argument_parser module
- vrprot.batcher module
- vrprot.exceptions module
- vrprot.overview_util module
- vrprot.pointcloud2map_8bit module
- vrprot.sample_pointcloud module
- vrprot.util module
- Module contents
- vrprot.alphafold_db_parser module
Citation
Please cite our work if you use VRProt.
Note
@software{VRProt2022, author = {Oblau, Till Pascal and Fischer, Felix}, title = {{VRProt}: {A} Libary for preparing protein structure point clouds}, url = {https://VRProt.org/}, version = {1.0.0}, year = {2022}, }