parmed.charmm.CharmmParameterSet

class parmed.charmm.CharmmParameterSet(*args)

Stores a parameter set defined by CHARMM files. It stores the equivalent of the information found in the MASS section of the CHARMM topology file (TOP/RTF) and all of the information in the parameter files (PAR)

Parameters

*filenamesvariable length arguments of str

The list of topology, parameter, and stream files to load into the parameter set. The following file type suffixes are recognized:

.rtf, .top – Residue topology file .par, .prm – Parameter file .str – Stream file .inp – If “par” is in the file name, it is a parameter file. If

“top” is in the file name, it is a topology file. Otherwise, ValueError is raised.

See also

parmed.parameters.ParameterSet

Attributes

combining_rule

Methods

condense([do_dihedrals])	This function goes through each of the parameter type dicts and eliminates duplicate types.
from_parameterset(params[, copy])	Instantiates a CharmmParameterSet from another ParameterSet (or subclass).
from_structure(struct)	Extracts known parameters from a Structure instance
load_set([tfile, pfile, sfiles])	Instantiates a CharmmParameterSet from a Topology file and a Parameter file (or just a Parameter file if it has all information)
match_improper_type(a1, a2, a3, a4)	Matches an improper type based on atom type names
read_parameter_file(pfile[, comments])	Reads all of the parameters from a parameter file.
read_stream_file(sfile)	Reads RTF and PAR sections from a stream file and dispatches the sections to read_topology_file or read_parameter_file
read_topology_file(tfile)	Reads _only_ the atom type definitions from a topology file.
typeify_templates()	Assign atom types to atom names in templates
write([top, par, str])	Write a CHARMM parameter set to a file

__init__(*args)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(*args)	Initialize self.
condense([do_dihedrals])	This function goes through each of the parameter type dicts and eliminates duplicate types.
from_parameterset(params[, copy])	Instantiates a CharmmParameterSet from another ParameterSet (or subclass).
from_structure(struct)	Extracts known parameters from a Structure instance
load_set([tfile, pfile, sfiles])	Instantiates a CharmmParameterSet from a Topology file and a Parameter file (or just a Parameter file if it has all information)
match_improper_type(a1, a2, a3, a4)	Matches an improper type based on atom type names
read_parameter_file(pfile[, comments])	Reads all of the parameters from a parameter file.
read_stream_file(sfile)	Reads RTF and PAR sections from a stream file and dispatches the sections to read_topology_file or read_parameter_file
read_topology_file(tfile)	Reads _only_ the atom type definitions from a topology file.
typeify_templates()	Assign atom types to atom names in templates
write([top, par, str])	Write a CHARMM parameter set to a file

Attributes

combining_rule