parmed.charmm.CharmmParameterSet

class parmed.charmm.CharmmParameterSet(*args)[source]

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.

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)[source]

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