protein (14 November 2003) | index /home/todd/release/pdb2pqr/protein.py

`Routines for PDB2PQR
This module contains the protein object used in PDB2PQR and associated
methods
Todd Dolinsky (todd@ccb.wustl.edu)
Washington University in St. Louis`

Modules
`` |  |
string | sys |  |

Classes
`` |  | Protein
class Protein
`` | `Protein class The protein class represents the parsed PDB, and provides a hierarchy of information - each Protein contains a list of Chain objects as provided in the PDB file. Each Chain then contains its associated list of Residue objects, and each Residue contains a list of Atom objects, completing the hierarchy.`
| Methods defined here: __init__(self, pdblist) `Initialize using parsed PDB file Parameters pdblist: List of Classes of PDB lines as created by pdb.py->readPDB` createProtein(self, pdblist) `Fill the Protein with chains, residues, and atoms Parameters pdblist: List of Classes of PDB lines as created by pdb.py->readPDB (list) Returns dict: Mapping of chain ID to chain object list: List of chain objects sorted by chain ID (dict)` getAtoms(self) `Return all Atom objects in list format Returns atomlist: List of Atom objects in the protein (list)` getChains(self) `Get the chains object Returns chains: The list of chains in the protein (chain)` getCharge(self) `Get the total charge on the protein NOTE: Since the misslist is used to identify incorrect charge assignments, this routine does not list the 3 and 5 termini of nucleic acid chains as having non-integer charge even though they are (correctly) non-integer. Returns: misslist: List of residues with non-integer charges (list) charge: The total charge on the protein (float)` numAtoms(self) `Get the number of atoms for the entire protein(including multiple chains) Returns count: Number of atoms in the protein (int)` numResidues(self) `Get the number of residues for the entire protein (including multiple chains) Returns count: Number of residues in the protein (int)` printAtoms(self, atomlist) `Get the text for the entire protein Parameters atomlist: The list of atoms to include (list) Returns text: The list of (stringed) atoms (list)` reSerialize(self) `Generate new serial numbers for atoms in the protein` Data and non-method functions defined here: __doc__ = '\n Protein class\n\n The protein clas... of Atom objects, completing the hierarchy.\n ' __module__ = 'protein'

Data
`` |  | BACKBONE = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN'] __author__ = 'Todd Dolinsky' __date__ = '14 November 2003' __file__ = './protein.pyc' __name__ = 'protein'

Author
`` |  | Todd Dolinsky