src.structures (28 February 2006) | index /Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/structures.py

`Structures for PDB2PQR
This module contains the structure objects used in PDB2PQR and their
associated methods.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Copyright (c) 2002-2011, Jens Erik Nielsen, University College Dublin;
Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific
Northwest National Laboratory, operated by Battelle Memorial Institute,
Pacific Northwest Division for the U.S. Department Energy.;
Paul Czodrowski & Gerhard Klebe, University of Marburg.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the names of University College Dublin, Battelle Memorial Institute,
Pacific Northwest National Laboratory, US Department of Energy, or University
of Marburg nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
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OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------`

Modules
`` |  |
copy math | os string | sys |

Classes
`` |  | src.pdb.ATOM(src.pdb.BaseRecord) Atom Chain Residue
class Atom(src.pdb.ATOM)
`` | `Class Atom The Atom class inherits off the ATOM object in pdb.py. It is used for adding fields not found in the pdb that may be useful for analysis. Also simplifies code by combining ATOM and HETATM objects into a single class.`
| Method resolution order: Atom src.pdb.ATOM src.pdb.BaseRecord __builtin__.object Methods defined here: __init__(self, atom, type, residue) `Initialize the new Atom object by using the old object. Parameters atom: The original ATOM object (ATOM) type: Either ATOM or HETATM (string) residue: A pointer back to the parent residue object (Residue)` __str__(self) `Returns a string of the new atom type. Uses the ATOM string output but changes the first field to either by ATOM or HETATM as necessary. This is used to create the output for pqr files! No touchy! Returns str: String with ATOM/HETATM field set appropriately` addBond(self, bondedatom) `Add a bond to the list of bonds Parameters: bondedatom: The atom to bond to (Atom)` get(self, name) `Get a member of the Atom class Parameters name: The name of the member (string) Possible Values type: The type of Atom (either ATOM or HETATM) serial: Atom serial number name: Atom name altLoc: Alternate location resName: Residue name chainID: Chain identifier resSeq: Residue sequence number iCode: Code for insertion of residues x: Orthogonal coordinates for X in Angstroms. y: Orthogonal coordinates for Y in Angstroms. z: Orthogonal coordinates for Z in Angstroms. occupancy: Occupancy tempFactor: Temperature Factor segID: Segment identifier element: Element symbol charge: Charge on the atom bonds: The bonds associated with the atom interbonds: The intrabonds associated with the atom extrabonds: The extrabonds assocaited with the atom residue: The parent residue of the atom radius: The radius of the atom ffcharge: The forcefield charge on the atom hdonor: Whether the atom is a hydrogen donor hacceptor: Whether the atom is a hydrogen acceptor Returns item: The value of the member` getCommonStringRep(self, chainflag=False) `Returns a string of the common column of the new atom type. Uses the ATOM string output but changes the first field to either by ATOM or HETATM as necessary. This is used to create the output for pqr and pdb files! No touchy! Returns outstr: String with ATOM/HETATM field set appropriately` getCoords(self) `Return the x,y,z coordinates of the atom in list form Returns List of the coordinates (list)` getPDBString(self) `Returns a string of the new atom type. Uses the ATOM string output but changes the first field to either by ATOM or HETATM as necessary. This is for the pdb representation of the atom. The propka30 module depends on this being correct. No touchy! Returns str: String with ATOM/HETATM field set appropriately` getPQRString(self, chainflag=False) `Returns a string of the new atom type. Uses the ATOM string output but changes the first field to either by ATOM or HETATM as necessary. This is used to create the output for pqr files! No touchy! Returns str: String with ATOM/HETATM field set appropriately` hasReference(self) `Determine if the atom object has a reference object or not. All known atoms should have reference objects. Returns True if atom has a reference object, False otherwise.` isBackbone(self) `Return true if atom name is in backbone, otherwise false Returns state: 1 if true, 0 if false` isHydrogen(self) `Is this atom a Hydrogen atom? Returns value: 1 if Atom is a Hydrogen, 0 otherwise` set(self, name, value) `Set a member of the Atom class Parameters name: The name of the member (string) value: The value to set the member to Possible Values type: The type of Atom (either ATOM or HETATM) serial: Atom serial number name: Atom name altLoc: Alternate location resName: Residue name chainID: Chain identifier resSeq: Residue sequence number iCode: Code for insertion of residues x: Orthogonal coordinates for X in Angstroms. y: Orthogonal coordinates for Y in Angstroms. z: Orthogonal coordinates for Z in Angstroms. occupancy: Occupancy tempFactor: Temperature Factor segID: Segment identifier element: Element symbol charge: Charge on the atom residue: The parent residue of the atom radius: The radius of the atom ffcharge: The forcefield charge on the atom hdonor: Whether the atom is a hydrogen donor hacceptor: Whether the atom is a hydrogen acceptor` Data descriptors inherited from src.pdb.BaseRecord: __dict__ `dictionary for instance variables (if defined)` __weakref__ `list of weak references to the object (if defined)`
class Chain
`` | `Chain class The chain class contains information about each chain within a given Protein object.`
| Methods defined here: __init__(self, chainID) `Initialize the class Parameters chainID: The chainID for this chain as denoted in the PDB file (string)` addResidue(self, residue) `Add a residue to the chain Parameters residue: The residue to be added (Residue)` get(self, name) `Get a member of the Chain class Parameters name: The name of the member Possible Values ID: The ID of the chain Residues: The list of residues within the Chain Returns item: The value of the member` getAtoms(self) `Return a list of Atom objects contained in this chain Returns atomlist: List of Atom objects (list)` getResidues(self) `Return a list of Residue objects in this chain` getSummary(self) numAtoms(self) `Get the number of atoms for the chain Returns count: Number of atoms in the chain (int)` numResidues(self) `Get the number of residues for the chain Returns count: Number of residues in the chain (int)` renumberResidues(self) `Renumber Atoms based on actual Residue number and not PDB resSeq`
class Residue
`` | `Residue class The residue class contains a list of Atom objects associated with that residue and other helper functions.`
| Methods defined here: __init__(self, atoms) `Initialize the class Parameters atoms: A list of Atom objects to be stored in this class (list)` __str__(self) `Basic string representation` addAtom(self, atom) `Add the atom object to the residue. Parameters atom: The object to be added (ATOM)` addMissing(self, value) `Add the value to the list of missing atoms Parameters value: The name of the missing atom (string)` createAtom(self, name, newcoords, type) `Add a new atom object to the residue. Uses an atom currently in the residue to seed the new atom object, then replaces the coordinates and name accordingly. Parameters name: The name of the new atom (string) newcoords: The x,y,z coordinates of the new atom (list) type: The type of atom, ATOM or HETATM` get(self, name) `Get a member of the Residue class Parameters name: The name of the member (string) Possible Values atoms: The atoms in the residue name: The name of the residue chainID: The chainID associated with the residue resSeq: The sequence number of the residue icode: The iCode of the residue SSbonded: 1 if the residue has a SS bond, 0 otherwise SSbondpartner: The residue of the bond partner type: The type associated with this residue isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise isCterm: 1 if the residue is the C-Terminus, 0 otherwise missing: List of missing atoms of the residue Returns item: The value of the member` getAtom(self, name) `Retrieve an atom from the mapping Parameters resname: The name of the residue to retrieve (string)` getAtoms(self) getCharge(self) `Get the total charge of the residue. In order to get rid of floating point rounding error, do the string transformation. Returns: charge: The charge of the residue (float)` hasAtom(self, name) letterCode(self) numAtoms(self) `Get the number of atoms for the residue Returns Number of atoms in the residue (int)` removeAtom(self, atomname) `Remove an atom from the residue object. Parameters atomname: The name of the atom to be removed (string)` renameAtom(self, oldname, newname) `Rename an atom to a new name Parameters oldname: The old atom name (string) newname: The new atom name (string)` renameResidue(self, name) `Rename a given residue Parameters name: The new name of the residue` reorder(self) `Reorder the atoms to start with N, CA, C, O if they exist` rotateTetrahedral(self, atom1, atom2, angle) `Rotate about the atom1-atom2 bond by a given angle All atoms connected to atom2 will rotate. Parameters: atom1: The first atom of the bond to rotate about (atom) atom2: The second atom of the bond to rotate about (atom) angle: The number of degrees to rotate (float)` set(self, name, value) `Set a member of the Residue class to a specific value Parameters name: The name of the object to set (string) value: The object to append Possible Values atoms: The atoms in the residue name: The name of the residue chain: The chainID associated with the residue resSeq: The sequence number of the residue icode: The iCode of the residue SSbonded: 1 if the residue has a SS bond, 0 otherwise SSbondpartner: The residue of the bond partner type: The type associated with this residue isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise isCterm: 1 if the residue is the C-Terminus, 0 otherwise isDirty: 1 if the residue is not missing atoms, 0 otherwise Notes resSeq points to the residue.setResSeq function Returns item: The value of the member` setChainID(self, value) `Set the chainID field to a certain value` setDonorsAndAcceptors(self) `Set the donors and acceptors within the residue` setResSeq(self, value) `Set the atom field resSeq to a certain value and change the residue's information. The icode field is no longer useful. Parameters value: The new value of resSeq (int)` update_terminus_status(self) `Update the isNterms and isCterm flags`

Data
`` |  | BACKBONE = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN'] DIHEDRAL = 57.2958 INSTALLDIR = '/Users/d3y382/pdb2pqr/' SMALL = 1e-07 TMPDIR = 'tmp/' __author__ = 'Todd Dolinsky' __date__ = '28 February 2006' lineParsers = {'ANISOU': <class 'src.pdb.ANISOU'>, 'ATOM': <class 'src.pdb.ATOM'>, 'AUTHOR': <class 'src.pdb.AUTHOR'>, 'CAVEAT': <class 'src.pdb.CAVEAT'>, 'CISPEP': <class 'src.pdb.CISPEP'>, 'COMPND': <class 'src.pdb.COMPND'>, 'CONECT': <class 'src.pdb.CONECT'>, 'CRYST1': <class 'src.pdb.CRYST1'>, 'DBREF': <class 'src.pdb.DBREF'>, 'END': <class 'src.pdb.END'>, ...}

Author
`` |  | Todd Dolinsky