parmed.tinker.parameterfile module

This module contains classes regarding the Amoeba potential and loading in a TINKER-based parameter file.

class parmed.tinker.parameterfile.AmoebaParameterSet(fname=None)[source]

Bases: object

Contains all of the parameters found in an Amoeba parameter file from TINKER

Methods

load_parameter_file(fname)

Parses a parameter file and loads all of the parameters found into data structures.
anglere = re.compile('angle([ 345fF])')
atomre = re.compile('atom *(\\d+) *(\\d+) *([A-Za-z\\-\\+\\*0-9]+) *"(.+)" *(\\d+) *(\\d+\\.\\d+) *(\\d+)', re.IGNORECASE)
load_parameter_file(fname)[source]

Parses a parameter file and loads all of the parameters found into data structures.

class parmed.tinker.parameterfile.BookmarkedFile(*args, **kwargs)[source]

Bases: object

Allows setting a bookmark and rewinding to that bookmark

Methods

mark

rewind
mark()[source]
rewind()[source]
parmed.tinker.parameterfile.get_angle_type(typecode, *args, **kwargs)[source]

Factory that returns the appropriate angle type

parmed.tinker.parameterfile.get_atom_type(index, atomic_number, mass, valence)[source]

Factory for getting an _AtomType, but making sure that only one instance of a particular type is created

parmed.tinker.parameterfile.reset()[source]

Resets all of the TypeList instances (without destroying the data inside them) so we can load multiple parameter sets