"""
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) 2002-2010, Jens Erik Nielsen, University College Dublin;
Nathan A. Baker, Washington University in St. Louis; 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, Washington University in
St. Louis, 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
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------
"""
__date__ = "28 February 2006"
__author__ = "Todd Dolinsky"
BACKBONE = ["N","CA","C","O","O2","HA","HN","H","tN"]
import string
from pdb import *
from utilities import *
from quatfit import *
class Chain:
"""
Chain class
The chain class contains information about each chain within a given
Protein object.
"""
def __init__(self, chainID):
"""
Initialize the class
Parameters
chainID: The chainID for this chain as denoted in
the PDB file (string)
"""
self.chainID = chainID
self.residues = []
def 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
"""
if name == "atoms": self.getAtoms()
else:
try:
item = getattr(self, name)
return item
except AttributeError:
message = "Unable to get object \"%s\" in class Chain" % name
raise ValueError, message
def addResidue(self, residue):
"""
Add a residue to the chain
Parameters
residue: The residue to be added (Residue)
"""
self.residues.append(residue)
def numResidues(self):
"""
Get the number of residues for the chain
Returns
count: Number of residues in the chain (int)
"""
count = 0
for residue in self.residues:
count += 1
return count
def renumberResidues(self):
"""
Renumber Atoms based on actual Residue number and not PDB resSeq
"""
count = 1
for residue in self.residues:
residue.setResSeq(count)
count += 1
def numAtoms(self):
"""
Get the number of atoms for the chain
Returns
count: Number of atoms in the chain (int)
"""
count = len(self.getAtoms())
return count
def getResidues(self):
"""
Return a list of Residue objects in this chain
"""
return self.residues
def getAtoms(self):
"""
Return a list of Atom objects contained in this chain
Returns
atomlist: List of Atom objects (list)
"""
atomlist = []
for residue in self.residues:
myList = residue.get("atoms")
for atom in myList:
atomlist.append(atom)
return atomlist
class Residue:
"""
Residue class
The residue class contains a list of Atom objects associated with that
residue and other helper functions.
"""
def __init__(self, atoms):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
sampleAtom = atoms[-1]
self.atoms = []
self.name = sampleAtom.resName
self.chainID = sampleAtom.chainID
self.resSeq = sampleAtom.resSeq
self.iCode = sampleAtom.iCode
#
#
self.map = {}
self.naname = None
atomclass = ""
for a in atoms:
if isinstance(a,ATOM):
atomclass = "ATOM"
elif isinstance(a, HETATM):
atomclass = "HETATM"
atom = Atom(a, atomclass, self)
atomname = atom.get("name")
if atomname not in self.map:
self.addAtom(atom)
else: # Don't add duplicate atom
oldatom = self.getAtom(atomname)
oldatom.set("altLoc","")
if self.name == "HOH":
self.name = "WAT"
for atom in self.atoms:
atom.set("resName","WAT")
def __str__(self):
"""
Basic string representation for debugging
"""
text = "%s %s %i" % (self.name, self.chainID, self.resSeq)
return text
def 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
"""
try:
item = getattr(self, name)
return item
except AttributeError:
message = "Unable to access object \"%s\" in class Residue" % name
raise ValueError, message
def 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
"""
if name == "resSeq": self.setResSeq(value)
else:
try:
setattr(self, name, value)
except AttributeError:
message = "Unable to set object \"%s\" in class Residue" % name
raise ValueError, message
def update_terminus_status(self):
"""Update the isNterms and isCterm flags"""
#
# If Nterm then update counter of hydrogens
#
if self.isNterm:
count=0
atoms=['H','H2','H3']
for atom in atoms:
for atom2 in self.atoms:
atomname=atom2.get('name')
if atom==atomname:
count=count+1
self.isNterm=count
#
# If Cterm then update counter
#
if self.isCterm:
self.isCterm=None
for atom in self.atoms:
atomname=atom.get('name')
if atomname=='HO':
self.isCterm=2
break
if not self.isCterm:
self.isCterm=1
return
def numAtoms(self):
"""
Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
"""
count = len(self.atoms)
return count
def 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)
"""
self.iCode = ""
self.resSeq = value
for atom in self.atoms:
atom.set("resSeq",value)
#atom.set("iCode","")
def setChainID(self, value):
"""
Set the chainID field to a certain value
"""
self.chainID = value
for atom in self.atoms:
atom.set("chainID", value)
def addAtom(self, atom):
"""
Add the atom object to the residue.
Parameters
atom: The object to be added (ATOM)
"""
self.atoms.append(atom)
self.map[atom.get("name")] = atom
def removeAtom(self, atomname):
"""
Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
"""
# Delete the atom from the map
atom = self.map[atomname]
bonds = atom.bonds
del self.map[atomname]
# Delete the atom from the list
self.atoms.remove(atom)
# Delete all instances of the atom as a bond
for bondatom in bonds:
if atom in bondatom.bonds:
bondatom.bonds.remove(atom)
del atom
def renameAtom(self, oldname, newname):
"""
Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
"""
atom = self.map[oldname]
atom.set("name",newname)
self.map[newname] = atom
del self.map[oldname]
def 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
"""
oldatom = self.atoms[0]
newatom = Atom(oldatom, type, self)
newatom.set("x",newcoords[0])
newatom.set("y",newcoords[1])
newatom.set("z",newcoords[2])
newatom.set("name", name)
newatom.set("occupancy",1.00)
newatom.set("tempFactor",0.00)
self.addAtom(newatom)
def addMissing(self, value):
"""
Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
"""
self.missing.append(value)
def getAtom(self, name):
"""
Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
"""
try:
return self.map[name]
except KeyError:
return None
def getAtoms(self):
return self.atoms
def hasAtom(self, name):
if name in self.map: return 1
else: return 0
def 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)
"""
charge = 0.0
for atom in self.atoms:
atomcharge = atom.get("ffcharge")
if atomcharge != None:
charge = charge + atomcharge
charge = float("%.4f" % charge)
return charge
def renameResidue(self, name):
"""
Rename a given residue
Parameters
name: The new name of the residue
"""
self.name = name
for atom in self.atoms:
atom.resName = name
def 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)
"""
moveatoms = []
movecoords = []
initcoords = subtract(atom2.getCoords(), atom1.getCoords())
# Determine which atoms to rotate
for atom in atom2.bonds:
if atom == atom1: continue
moveatoms.append(atom)
movecoords.append(subtract(atom.getCoords(), atom1.getCoords()))
newcoords = qchichange(initcoords, movecoords, angle)
for i in range(len(moveatoms)):
atom = moveatoms[i]
x = (newcoords[i][0] + atom1.get("x"))
y = (newcoords[i][1] + atom1.get("y"))
z = (newcoords[i][2] + atom1.get("z"))
atom.set("x", x)
atom.set("y", y)
atom.set("z", z)
def setDonorsAndAcceptors(self):
"""
Set the donors and acceptors within the residue
"""
if not hasattr(self, "reference"): return
for atom in self.getAtoms():
atomname = atom.get("name")
resname = self.name
atom.set("hdonor", 0)
atom.set("hacceptor", 0)
if atomname.startswith("N"):
bonded = 0
for bondedatom in atom.bonds:
if bondedatom.isHydrogen():
atom.set("hdonor",1)
bonded = 1
break
if not bonded and self.reference.name == "HIS":
atom.set("hacceptor",1)
elif atomname.startswith("O") or \
(atomname.startswith("S") and self.reference.name == "CYS"):
atom.set("hacceptor",1)
for bondedatom in atom.bonds:
if bondedatom.isHydrogen():
atom.set("hdonor",1)
break
def reorder(self):
"""
Reorder the atoms to start with N, CA, C, O if they exist
"""
templist = []
if self.hasAtom("N"): templist.append(self.getAtom("N"))
if self.hasAtom("CA"): templist.append(self.getAtom("CA"))
if self.hasAtom("C"): templist.append(self.getAtom("C"))
if self.hasAtom("O"): templist.append(self.getAtom("O"))
# Add remaining atoms
for atom in self.atoms:
if atom.name not in ["N", "CA", "C", "O"]:
templist.append(atom)
# Change the list pointer
self.atoms = templist[:]
class Atom(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.
"""
def __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)
"""
if type == "ATOM" or type == "HETATM":
self.type = type
else:
raise ValueError, "Invalid atom type %s (Atom Class IN structures.py)!"
self.serial = atom.serial
self.name = atom.name
self.altLoc = atom.altLoc
self.resName = atom.resName
self.chainID = atom.chainID
self.resSeq = atom.resSeq
self.iCode = atom.iCode
self.x = atom.x
self.y = atom.y
self.z = atom.z
self.occupancy = atom.occupancy
self.tempFactor = atom.tempFactor
self.segID = atom.segID
self.element = atom.element
self.charge = atom.charge
self.bonds = []
self.reference = None
self.residue = residue
self.radius = None
self.ffcharge = None
self.hdonor = 0
self.hacceptor = 0
self.cell = None
self.added = 0
self.optimizeable = 0
self.refdistance = 0
self.id = None
self.mol2charge=None
if hasattr(atom,'mol2charge'):
self.mol2charge=atom.mol2charge
def __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
str: String with ATOM/HETATM field set appropriately
"""
str = ""
tstr = self.type
str = str + string.ljust(tstr, 6)[:6]
tstr = "%d" % self.serial
str = str + string.rjust(tstr, 5)[:5]
str = str + " "
tstr = self.name
if len(tstr) == 4 or len(tstr.strip("FLIP")) == 4:
str = str + string.ljust(tstr, 4)[:4]
else:
str = str + " " + string.ljust(tstr, 3)[:3]
tstr = self.resName
if len(tstr) == 4:
str = str + string.ljust(tstr, 4)[:4]
else:
str = str + " " + string.ljust(tstr, 3)[:3]
str = str + " "
tstr = self.chainID
str = str + string.ljust(tstr, 1)[:1]
tstr = "%d" % self.resSeq
str = str + string.rjust(tstr, 4)[:4]
if self.iCode != "":
str = str + "%s " % self.iCode
else:
str = str + " "
tstr = "%8.3f" % self.x
str = str + string.ljust(tstr, 8)[:8]
tstr = "%8.3f" % self.y
str = str + string.ljust(tstr, 8)[:8]
tstr = "%8.3f" % self.z
str = str + string.ljust(tstr, 8)[:8]
if self.ffcharge != None: ffcharge = "%.4f" % self.ffcharge
else: ffcharge = "0.0000"
str = str + string.rjust(ffcharge, 8)[:8]
if self.radius != None: ffradius = "%.4f" % self.radius
else: ffradius = "0.0000"
str = str + string.rjust(ffradius, 7)[:7]
return str
def 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
"""
try:
item = getattr(self, name)
return item
except AttributeError:
message = "Unable to access object \"%s\" in class Atom" % name
raise ValueError, message
def 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
"""
try:
setattr(self, name, value)
except AttributeError:
message = "Unable to set object \"%s\" in class Atom" % name
raise ValueError, message
def getCoords(self):
"""
Return the x,y,z coordinates of the atom in list form
Returns
List of the coordinates (list)
"""
return [self.x, self.y, self.z]
def addBond(self, bondedatom):
"""
Add a bond to the list of bonds
Parameters:
bondedatom: The atom to bond to (Atom)
"""
self.bonds.append(bondedatom)
def isHydrogen(self):
"""
Is this atom a Hydrogen atom?
Returns
value: 1 if Atom is a Hydrogen, 0 otherwise
"""
value = 0
if self.name[0] == "H": value = 1
return value
def isBackbone(self):
"""
Return true if atom name is in backbone, otherwise false
Returns
state: 1 if true, 0 if false
"""
state = 0
if self.name in BACKBONE:
state = 1
return state
def hasReference(self):
"""
Determine if the atom object has a reference object or not.
All known atoms should have reference objects.
Returns
1 if atom has a reference object, 0 otherwise.
"""
if self.reference != None: return 1
else: return 0
