AlloViz.AlloViz.trajutils.process_input#
- AlloViz.AlloViz.trajutils.process_input(GPCR, pdb, protein_sel, pdbf, psf, psff, trajs, trajsf, **kwargs)[source]#
Process the input structure and trajectory(ies) files
Only the passed selection is used from the whole input structure file. Its residue names are standardized to the usual 3-letter residue codes (
AlloViz.AlloViz.trajutils.standardize_resnames()) and, if the structure is a GPCR, the generic numbers are retrieved from GPCRdb (AlloViz.AlloViz.trajutils.get_GPCRdb_numbering()). PDB files of the selection and its CA atoms are written, and also a PSF file with the selection if applicable. The trajectory(ies) of the selection and its CA atoms in xtc format are also generated.- Parameters:
- GPCRbool or int
Use True if the structure is a GPCR, or the ID of a GPCRmd database dynamics entry if it was used originally to download the files from it.
- pdbstr
Filename of the PDB structure to read, process and use.
- protein_selstr
MDAnalysis atom selection string to select the protein structure from the Universe (e.g., in case simulations in biological conditions are used, to avoid selecting extra chains, water molecules, ions…).
- pdbfstr
Complete relative filename of the processed PDB structure to save.
- psfstr
Filename of the .psf file corresponding to the pdb used to read, process and use.
- psffstr
Complete relative filename of the processed PSF structure to save.
- trajslist
Filename(s) of the MD trajectory (or trajectories) to read and use. File format must be recognized by MDAnalysis (e.g., xtc).
- trajsfdict
Complete relative filename(s) of the processed MD trajectory (or trajectories) to save.
- **kwargs
special_res can be passed as an optional kwarg, and it should be a dictionary containing a mapping of special residue 3/4-letter code(s) present in the structure to the corresponding standard 1-letter code(s).