pygromos.files.simulation_parameters package¶

Submodules¶

pygromos.files.simulation_parameters.imd module¶

FUNCTIONLIB: gromos++ input file functions Description:

in this lib, gromosXX input file mainpulating functions are gathered

Author: Kay Schaller & Benjamin Schroeder

class pygromos.files.simulation_parameters.imd.Imd(in_value: str, _future_file: bool = False)[source]¶

Bases: pygromos.files._basics._general_gromos_file._general_gromos_file

BOUNDCOND: pygromos.files.blocks.imd_blocks.BOUNDCOND¶

COMTRANSROT: pygromos.files.blocks.imd_blocks.COMTRANSROT¶

CONSTRAINT: pygromos.files.blocks.imd_blocks.CONSTRAINT¶

DISTANCERES: pygromos.files.blocks.imd_blocks.DISTANCERES¶

EDS: pygromos.files.blocks.imd_blocks.EDS¶

ENERGYMIN: pygromos.files.blocks.imd_blocks.ENERGYMIN¶

FORCE: pygromos.files.blocks.imd_blocks.FORCE¶

INITIALISE: pygromos.files.blocks.imd_blocks.INITIALISE¶

MULTIBATH: pygromos.files.blocks.imd_blocks.MULTIBATH¶

NEW_REPLICA_EDS: pygromos.files.blocks.imd_blocks.NEW_REPLICA_EDS¶

NONBONDED: pygromos.files.blocks.imd_blocks.NONBONDED¶

PAIRLIST: pygromos.files.blocks.imd_blocks.PAIRLIST¶

POSITIONRES: pygromos.files.blocks.imd_blocks.POSITIONRES¶

PRESSURESCALE: pygromos.files.blocks.imd_blocks.PRESSURESCALE¶

PRINTOUT: pygromos.files.blocks.imd_blocks.PRINTOUT¶

QMMM: pygromos.files.blocks.imd_blocks.QMMM¶

REPLICA: pygromos.files.blocks.imd_blocks.REPLICA¶

REPLICA_EDS: pygromos.files.blocks.imd_blocks.REPLICA_EDS¶

STEP: pygromos.files.blocks.imd_blocks.STEP¶

SYSTEM: pygromos.files.blocks.imd_blocks.SYSTEM¶

TITLE: pygromos.files.blocks._general_blocks.TITLE¶

WRITETRAJ: pygromos.files.blocks.imd_blocks.WRITETRAJ¶

edit_EDS(NUMSTATES: int, S: float, EIR: list, EDS: int = 1, ALPHLJ: float = 0.0, ALPHC: float = 0.0, FUNCTIONAL: int = 1)[source]¶

edit_REEDS(REEDS: Optional[int] = None, NUMSTATES: Optional[int] = None, SVALS: Optional[Union[numbers.Number, List[numbers.Number]]] = None, EIR: Optional[Union[numbers.Number, Iterable[numbers.Number]]] = None, NRETRIAL: Optional[int] = None, NREQUIL: Optional[int] = None, CONT: Optional[Union[bool, int]] = None, EDS_STAT_OUT: Optional[Union[bool, int]] = None)[source]¶

path: str¶

randomize_seed()[source]¶

read_file()[source]¶

give back the content. WARNING DEAPRECEATED.

Warning

DEAPRECEATED

Returns: key is the block name of the gromos file, any is the content of a block
Return type: Dict[str, any]

write_json(out_path: str)[source]¶

Module contents¶