forcefield (6 October 2003) | index /home/todd/release/pdb2pqr/forcefield.py

`Forcefield script
This module takes a pdblist as input and replaces the occupancy and
tempfactor fields with charge and radius fields, with values as defined
by a particular forcefield. The forcefield structure is modeled off of
the structures.py file, where each forcefield is considered a chain of
residues of atoms.
Todd Dolinsky (todd@ccb.wustl.edu)
Washington University in St. Louis`

Modules
`` |  |
getopt | string | sys |

Classes
`` |  | Forcefield ForcefieldAtom ForcefieldResidue
class Forcefield
`` | `Forcefield class The forcefield class contains definitions for a given forcefield. Each forcefield object contains a dictionary of residues, with each residue containing a dictionary of atoms. Dictionaries are used instead of lists as the ordering is not important. The forcefield definition files are unedited, directly from the forcefield - all transformations are done within.`
| Methods defined here: __init__(self, ff) `Initialize the class by parsing the definition file Parameters ff: The name of the forcefield (string)` getAmberParams(self, residue, name) `Get the forcefield definitions from the Amber database Parameters residue: The residue (residue) name: The atom name (string) Returns resname: The name of the amber residue atomname: The name of the amber atom` getCharmmParams(self, residue, name) `Get the forcefield definitions from the Charmm database Parameters residue: The residue (residue) name: The atom name (string) Returns resname: The name of the Charmm residue atomname: The name of the Charmm atom` getParams(self, residue, name) `Get the parameters associated with the input fields. The residue itself is needed instead of simply its name because the forcefield may use a different residue name than the standard amino acid name. Parameters residue: The residue (residue) name: The atom name (string) Returns charge: The charge on the atom (float) radius: The radius of the atom (float)` getParseParams(self, residue, name) `Get the forcefield definitions from the Parse database Parameters residue: The residue (residue) name: The atom name (string) Returns resname: The name of the amber residue atomname: The name of the amber atom` getResidue(self, resname) `Return the residue object with the given resname Parameters resname: The name of the residue (string) Returns residue: The residue object (ForcefieldResidue)` Data and non-method functions defined here: __doc__ = '\n Forcefield class\n\n The forcefiel...ll\n transformations are done within.\n\n ' __module__ = 'forcefield'
class ForcefieldAtom
`` | `ForcefieldAtom class The ForcefieldAtom object contains fields that are related to the forcefield at the atom level`
| Methods defined here: __init__(self, name, charge, radius) `Initialize the object Parameters name: The atom name (string) charge: The charge on the atom (float) radius: The radius of the atom (float)` get(self, name) `Get a member of the ForcefieldAtom class Parameters name: The name of the member (string) Possible Values name: The atom name (string) charge: The charge on the atom (float) radius: The radius of the atom (float) epsilon: The epsilon assocaited with the atom (float) Returns item: The value of the member` Data and non-method functions defined here: __doc__ = '\n ForcefieldAtom class\n\n The Force... to the\n forcefield at the atom level\n ' __module__ = 'forcefield'
class ForcefieldResidue
`` | `ForcefieldResidue class The ForceFieldResidue class contains a mapping of all atoms within the residue for easy searching.`
| Methods defined here: __init__(self, name) `Initialize the ForceFieldResidue object Parameters name: The name of the residue (string)` addAtom(self, atom) `Add an atom to the ForcefieldResidue Parameters atom: The atom to be added (atom)` getAtom(self, atomname) `Return the atom object with the given atomname Parameters resname: The name of the atom (string) Returns residue: The atom object (ForcefieldAtom)` Data and non-method functions defined here: __doc__ = '\n ForcefieldResidue class\n\n The Fo...thin\n the residue for easy searching.\n ' __module__ = 'forcefield'

Data
`` |  | AMBER_FILE = 'AMBER.DAT' CHARMM_FILE = 'CHARMM.DAT' PARSE_FILE = 'PARSE.DAT' __author__ = 'Todd Dolinsky' __date__ = '6 October 2003' __file__ = './forcefield.pyc' __name__ = 'forcefield'

Author
`` |  | Todd Dolinsky