Python: module definitions

definitions (8 September 2004)

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/home/todd/release/pdb2pqr/definitions.py

Definitions for PDB2PQR This file contains classes associated with Amino Acid and Rotamer definitions as used by PDB2PQR. Definition Files Created by Jens Erik Nielsen Ported to Python by Todd Dolinsky (todd@ccb.wustl.edu) Washington University in St. Louis

Modules

getopt
math

os
random

string
sys

Classes

structures.Atom(pdb.ATOM)

DefinitionAtom

structures.Chain

DefinitionChain

Definition

structures.Residue

DefinitionResidue

class Definition

Definition class The Definition class contains the structured definitions found in the files and several mappings for easy access to the information.

Methods defined here:

__init__(self): Create a new Definition Object

getAA(self): Get the Amino Acid definition Returns The Amino Acid definition in self.chains[0]

getNA(self): Get the Nucleic Acid definition Returns The Nucleic Acid definition - a list of Nucleic Acid residues

parseDefinition(self, reslines, name, restype): Parse the definition file, obtaining information about each atom, its position, and its bonding information. Parameters reslines: A list of lines containing each of the atoms of the residue (list) name: The name of the Residue (string) restype: The type of the residue (int) Returns myResidue: The parsed residue (DefinitionResidue)

parseRotamer(self, reslines): Parse ROTAMER.DAT, obtaining information about each atom and its position. Parameters reslines: A list of lines containing each of the atoms of the residue (list) Returns myResidue: The parsed residue (DefinitionResidue)

readDefinition(self, defpath): Read a definition file Parameters deffile: The path to the definition file (string) Returns def: The definition chain (AADefinition)

readRotamerDefinition(self): Read the Rotamer definitions

Data and non-method functions defined here:

__doc__ = '\n Definition class\n\n The Definitio...mappings for easy access to the information.\n '

__module__ = 'definitions'

class DefinitionAtom(structures.Atom)

Class DefinitionAtom The DefinitionAtom class inherits off the Atom class. It provides a trimmed down version of the initializating function from the Atom class for the definition files.

Method resolution order:: DefinitionAtom; structures.Atom; pdb.ATOM

Methods defined here:

__init__(self, serial, name, resName, x, y, z): Initialize using a few basic parameters - set all other fields to null, which is necessary for debugging output by using the string function in the parent class. Parameters serial: Atom serial number (int) name: Atom name. (string) resName: Residue name. (string) resSeq: Residue sequence number. (int) x: Orthogonal coordinates for X in Angstroms. (float) y: Orthogonal coordinates for Y in Angstroms. (float) z: Orthogonal coordinates for Z in Angstroms. (float)

isBackbone(self): Return true if atom name is in backbone, otherwise false Returns state: 1 if true, 0 if false

Data and non-method functions defined here:

__doc__ = '\n Class DefinitionAtom\n\n The Defin...Atom\n class for the definition files.\n '

__module__ = 'definitions'

Methods inherited from structures.Atom:

__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. Returns out: String with ATOM/HETATM field set appropriately

addExtraBond(self, bondedatom): Add a bond to the list of extrabonds Parameters: bondedatom: The atom to bond to (Atom)

addIntraBond(self, bondedatom): Add a bond to the list of intrabonds 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

getCoords(self): Return the x,y,z coordinates of the atom in list form Returns List of the coordinates (list)

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 Returns item: The value of the member

class DefinitionChain(structures.Chain)

DefinitionChain class The DefinitionChain class extends the chain class to provide lookups for atom information.

Methods defined here:

__init__(self, ID): Initialize like the Chain constructor, but add necessary features Parameters ID: The ID of the chain

addResidue(self, residue): Add a residue to the chain Parameters residue: The residue to be added (Residue)

getResidue(self, name): Retrieve a residue from the mapping Parameters name: The name of the residue to retrieve (string)

Data and non-method functions defined here:

__doc__ = '\n DefinitionChain class\n\n The Defi...rovide\n lookups for atom information.\n '

__module__ = 'definitions'

Methods inherited from structures.Chain:

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)

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 DefinitionResidue(structures.Residue)

DefinitionResidue class The DefinitionResidue class extends the Residue class to allow for a trimmed down initializing function.

Methods defined here:

__init__(self, name, type): Initialize the class using a few parameters Parameters: name: The abbreviated amino acid name of the DefinitionResidue type: The typecode associated with the residue Available typecodes are: 1: Protein residue 2: Drug/small-molecule 3: Water number: ID number for residue

addDihedral(self, atom): Add the atom to the list of dihedral bonds Parameters: atom: The atom to be added

makeBondList(self, residue, atomname): For the given atomname, make a list of bonded atoms. First get all atoms present in the residue that are directly bonded to the atom - if this number is less than REFATOM_SIZE, take those atoms that are present and bonded to initial bond list and use them. Parameters residue: The residue to check for present atoms (Residue) atomname: The atom name to sedd the list of bonds (string) Returns bonds: A list of atomnames that are within two bonds of the atom and present in residue (list)

Data and non-method functions defined here:

__doc__ = '\n DefinitionResidue class\n\n The De...\n trimmed down initializing function.\n '

__module__ = 'definitions'

Methods inherited from structures.Residue:

addAtom(self, atom): Add the atom object to the residue. Parameters atom: The object to be added (ATOM)

addChiangle(self, value): Add the value to the list of chiangles Parameters value: The value to be added (float)

addDebumpAtom(self, atom): Add an atom to the check for debumping Parameters atom: The atom to add to the list

addMissing(self, value): Add the value to the list of missing atoms Parameters value: The name of the missing atom (string)

checkAtomNames(self): Check to see if there are any misnamed hydrogens within the residue. Converts hydrogens of type 1HH1 and 2H* to HH11 and H*2 to easily compare with the Amino Acid definition file. Also converts H*1 and H*2 to H*2 and H*3 when necessary. Rename the atom and update the residue.

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: 1 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)

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)

numAtoms(self): Get the number of atoms for the residue Returns count: 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)

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: 1 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

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)

updateIntraBonds(self, defresidue): Update the IntraBonds for each atom in the residue Parameters defresidue: The definition residue (DefinitionResidue)

Functions

acos(...): acos(x) Return the arc cosine (measured in radians) of x.

asin(...): asin(x) Return the arc sine (measured in radians) of x.

atan(...): atan(x) Return the arc tangent (measured in radians) of x.

atan2(...): atan2(y, x) Return the arc tangent (measured in radians) of y/x. Unlike atan(y/x), the signs of both x and y are considered.

ceil(...): ceil(x) Return the ceiling of x as a float. This is the smallest integral value >= x.

cos(...): cos(x) Return the cosine of x (measured in radians).

cosh(...): cosh(x) Return the hyperbolic cosine of x.

exp(...): exp(x) Return e raised to the power of x.

fabs(...): fabs(x) Return the absolute value of the float x.

floor(...): floor(x) Return the floor of x as a float. This is the largest integral value <= x.

fmod(...): fmod(x,y) Return fmod(x, y), according to platform C. x % y may differ.

frexp(...): frexp(x) Return the mantissa and exponent of x, as pair (m, e). m is a float and e is an int, such that x = m * 2.**e. If x is 0, m and e are both 0. Else 0.5 <= abs(m) < 1.0.

hypot(...): hypot(x,y) Return the Euclidean distance, sqrt(x*x + y*y).

ldexp(...): ldexp(x, i) -> x * (2**i)

log(...): log(x) -> the natural logarithm (base e) of x.

log10(...): log10(x) -> the base 10 logarithm of x.

modf(...): modf(x) Return the fractional and integer parts of x. Both results carry the sign of x. The integer part is returned as a real.

pow(...): pow(x,y) Return x**y (x to the power of y).

sin(...): sin(x) Return the sine of x (measured in radians).

sinh(...): sinh(x) Return the hyperbolic sine of x.

sqrt(...): sqrt(x) Return the square root of x.

tan(...): tan(x) Return the tangent of x (measured in radians).

tanh(...): tanh(x) Return the hyperbolic tangent of x.

Data
		AAFILE = 'AA.DAT' AAS = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLH', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'MET', ...] AMBER_FILE = 'AMBER.DAT' BACKBONE = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN'] BONDED_SS_LIMIT = 2.5 BUMP_DIST = 2.0 BUMP_HDIST = 1.5 CELL_SIZE = 2 CHARMM_FILE = 'CHARMM.DAT' DIHEDRAL = 57.2958 HYDRO_BONDCOORDS = [[7.5810000000000004, 2.0899999999999999, 12.506], [6.4580000000000002, 2.1619999999999999, 13.159000000000001], [5.1449999999999996, 2.2090000000000001, 12.452999999999999]] HYDRO_COORDS = [6.476, 2.1859999999999999, 14.159000000000001] LARGE_TORSION_ANGLE = 1000.0 NAFILE = 'NA.DAT' NAS = ['A', 'A5', 'A3', 'C', 'C5', 'C3', 'G', 'G5', 'G3', 'T', 'T5', 'T3', 'U', 'U5', 'U3'] NTERM2_COORDS = [-24.001000000000001, 50.223999999999997, -22.225999999999999] NTERM3_COORDS = [-24.869, 48.845999999999997, -22.77] NTERM_COORDS = [[-24.196000000000002, 48.789999999999999, -20.800000000000001], [-25.552, 49.881, -21.847999999999999], [-24.645, 49.491, -22.007000000000001]] OXT_COORDS = [-1.5289999999999999, 1.8580000000000001, 0.69499999999999995] PARSE_FILE = 'PARSE.DAT' PEPTIDE_DIST = 1.7 PEP_TRANS_CA = [-2.3130000000000002, 2.7839999999999998, 1.0229999999999999] PEP_TRANS_N = [-1.252, 1.877, 0.88300000000000001] REFATOM_SIZE = 3 REPAIR_LIMIT = 10 ROTAMERFILE = 'ROTAMER.DAT' SMALL = 9.9999999999999995e-08 __author__ = 'Jens Erik Nielsen, Todd Dolinsky' __date__ = '8 September 2004' __file__ = './definitions.pyc' __name__ = 'definitions' e = 2.7182818284590451 pi = 3.1415926535897931

Author
		Jens Erik Nielsen, Todd Dolinsky