utils.cg_parser

Functions

`gen_pbc_box`(psf, pos)	Generates pbc box and adds it to the psf.
`parse_params`(toppar_directory, toppar_str_file)	Use to read in top and par files generated by the CHARMM-GUI.

utils.cg_parser.parse_params(toppar_directory: str, toppar_str_file: str) → openmm.app.charmmparameterset.CharmmParameterSet[source]

Use to read in top and par files generated by the CHARMM-GUI. IMPORTANT: allways give the path to the openmm (created by charmm gui) folder within the charmm-gui folder.

Args:: param_directory (str): folder created by charmm_gui
Returns:: app.charmmparameterset.CharmmParameterSet: [description]

utils.cg_parser.gen_pbc_box(psf: str, pos: openmm.unit.quantity.Quantity) → List[openmm.unit.quantity.Quantity][source]

Generates pbc box and adds it to the psf. returns offset of the box from 0,0,0.

Args:: psf (strorapp.CharmmPsfFile): psf file or path to psf file crd (strorapp.CharmmCrdFile): crd file or path to crd file
Returns:: List[unit.Quantity]: offset of box from 0,0,0