"""
Definitions for PDB2PQR
This file contains classes associated with Amino Acid and Rotamer
definitions as used by PDB2PQR.
----------------------------
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,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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__ = "15 May 2008"
__author__ = "Jens Erik Nielsen, Todd Dolinsky, Yong Huang"
AAPATH = "dat/AA.xml"
NAPATH = "dat/NA.xml"
PATCHPATH = "dat/PATCHES.xml"
import os
import copy
import re
from xml import sax
from pdb import *
from utilities import *
from structures import *
from routines import *
class DefinitionHandler(sax.ContentHandler):
def __init__(self):
self.curelement = ""
self.curatom = None
self.curholder = None
self.curobj = None
self.map = {}
self.patches = []
return
def startElement(self, name, attributes):
if name == "residue":
obj = DefinitionResidue()
self.curholder = obj
self.curobj = obj
elif name == "patch":
obj = Patch()
self.curholder = obj
self.curobj = obj
elif name == "atom":
obj = DefinitionAtom()
self.curatom = obj
self.curobj = obj
else:
self.curelement = name
return
def endElement(self, name):
if name == "residue": # Complete Residue object
residue = self.curholder
if not isinstance(residue, DefinitionResidue):
raise ValueError, "Internal error parsing XML!"
resname = residue.name
if resname == "":
raise ValueError, "Residue name not set in XML!"
else:
self.map[resname] = residue
self.curholder = None
self.curobj = None
elif name == "patch": # Complete patch object
patch = self.curholder
if not isinstance(patch, Patch):
raise ValueError, "Internal error parsing XML!"
patchname = patch.name
if patchname == "":
raise ValueError, "Residue name not set in XML!"
else:
self.patches.append(patch)
self.curholder = None
self.curobj = None
elif name == "atom": # Complete atom object
atom = self.curatom
if not isinstance(atom, DefinitionAtom):
raise ValueError, "Internal error parsing XML!"
atomname = atom.name
if atomname == "":
raise ValueError, "Atom name not set in XML!"
else:
self.curholder.map[atomname] = atom
self.curatom = None
self.curobj = self.curholder
else: # Just free the current element namespace
self.curelement = ""
return self.map
def characters(self, text):
if text.isspace(): return
# If this is a float, make it so
try:
value = float(str(text))
except ValueError:
value = str(text)
# Special cases - lists and dictionaries
if self.curelement == "bond":
self.curobj.bonds.append(value)
elif self.curelement == "dihedral":
self.curobj.dihedrals.append(value)
elif self.curelement == "altname":
self.curholder.altnames[value] = self.curatom.name
elif self.curelement == "remove":
self.curobj.remove.append(value)
else:
setattr(self.curobj, self.curelement, value)
return
class Definition:
"""
Definition class
The Definition class contains the structured definitions found
in the files and several mappings for easy access to the information.
"""
def __init__(self):
"""
Create a new Definition Object
"""
self.map = {}
self.patches = {}
handler = DefinitionHandler()
sax.make_parser()
for path in [AAPATH, NAPATH]:
defpath = getDatFile(path)
if defpath == "":
raise ValueError, "%s not found!" % path
file = open(defpath)
sax.parseString(file.read(), handler)
file.close()
self.map.update(handler.map)
# Now handle patches
defpath = getDatFile(PATCHPATH)
if defpath == "":
raise ValueError, "%s not found!" % PATCHPATH
handler.map = {}
file = open(defpath)
sax.parseString(file.read(), handler)
file.close()
# Apply specific patches to the reference object, allowing users
# to specify protonation states in the PDB file
for patch in handler.patches:
if patch.newname != "":
# Find all residues matching applyto
resnames = self.map.keys()
for name in resnames:
regexp = re.compile(patch.applyto).match(name)
if not regexp: continue
newname = patch.newname.replace("*", name)
self.addPatch(patch, name, newname)
# Either way, make sure the main patch name is available
self.addPatch(patch, patch.applyto, patch.name)
def addPatch(self, patch, refname, newname):
"""
Add a patch to a definition residue.
Parameters
patch: The patch object to add (Patch)
refname: The name of the object to add the patch to (string)
newname: The name of the new (patched) object (string)
"""
try:
aadef = self.map[refname] # The reference
patchResidue = copy.deepcopy(aadef)
# Add atoms from patch
for atomname in patch.map:
patchResidue.map[atomname] = patch.map[atomname]
for bond in patch.map[atomname].bonds:
if bond not in patchResidue.map: continue
if atomname not in patchResidue.map[bond].bonds:
patchResidue.map[bond].bonds.append(atomname)
# Rename atoms as directed
for key in patch.altnames:
patchResidue.altnames[key] = patch.altnames[key]
# Remove atoms as directed
for remove in patch.remove:
if not patchResidue.hasAtom(remove): continue
removebonds = patchResidue.map[remove].bonds
del patchResidue.map[remove]
for bond in removebonds:
if remove in patchResidue.map[bond].bonds:
patchResidue.map[bond].bonds.remove(remove)
# Add the new dihedrals
for dihedral in patch.dihedrals:
patchResidue.dihedrals.append(dihedral)
# Point at the new reference
self.map[newname] = patchResidue
# Store the patch
self.patches[newname] = patch
except KeyError: # Just store the patch
self.patches[newname] = patch
class Patch:
"""
Patch the definitionResidue class
"""
def __init__(self):
"""
Initialize the Patch object.
"""
self.name = ""
self.applyto = ""
self.map = {}
self.remove = []
self.altnames = {}
self.dihedrals = []
self.newname = ""
def __str__(self):
"""
A basic string representation for debugging
"""
text = "%s\n" % self.name
text += "Apply to: %s\n" % self.applyto
text += "Atoms to add: \n"
for atom in self.map:
text += "\t%s\n" % str(self.map[atom])
text += "Atoms to remove: \n"
for remove in self.remove:
text += "\t%s\n" % remove
text += "Alternate naming map: \n"
text += "\t%s\n" % self.altnames
return text
class DefinitionResidue(Residue):
"""
DefinitionResidue class
The DefinitionResidue class extends the Residue class to allow for a
trimmed down initializing function.
"""
def __init__(self):
"""
Initialize the class using a few parameters
Parameters:
name: The abbreviated amino acid name of the DefinitionResidue
"""
self.name = ""
self.dihedrals = []
self.map = {}
self.altnames = {}
def __str__(self):
"""
A basic string representation for debugging
"""
text = "%s\n" % self.name
text += "Atoms: \n"
for atom in self.map:
text += "\t%s\n" % str(self.map[atom])
text += "Dihedrals: \n"
for dihedral in self.dihedrals:
text += "\t%s\n" % dihedral
text += "Alternate naming map: \n"
text += "\t%s\n" % self.altnames
return text
def addDihedral(self, atom):
"""
Add the atom to the list of dihedral bonds
Parameters:
atom: The atom to be added
"""
self.dihedralatoms.append(atom)
def getNearestBonds(self, atomname):
"""
Parameters
number: The number of bonds to get
Returns
bonds: A list of atomnames that are within three bonds of
the atom and present in residue (list)
"""
bonds = []
lev2bonds = []
atom = self.map[atomname]
# Get directly bonded (length = 1) atoms
for bondedatom in atom.bonds:
if bondedatom not in bonds:
bonds.append(bondedatom)
# Get bonded atoms 2 bond lengths away
for bondedatom in atom.bonds:
for bond2 in self.map[bondedatom].bonds:
if bond2 not in bonds and bond2 != atomname:
bonds.append(bond2)
lev2bonds.append(bond2)
# Get bonded atoms 3 bond lengths away
for lev2atom in lev2bonds:
for bond3 in self.map[lev2atom].bonds:
if bond3 not in bonds:
bonds.append(bond3)
return bonds
class DefinitionAtom(Atom):
"""
A trimmed down version of the Atom class
"""
def __init__(self, name=None, x=None, y=None, z=None):
"""
Initialize the class
"""
self.name = name
self.x = x
self.y = y
self.z = z
if name == None:
self.name = ""
if x == None:
self.x = 0.0
if y == None:
self.y = 0.0
if z == None:
self.z = 0.0
self.bonds = []
def __str__(self):
"""
A basic string representation for debugging
"""
text = "%s: %.3f %.3f %.3f" % (self.name, self.x, self.y, self.z)
for bond in self.bonds:
text += " %s" % bond
return text
def isBackbone(self):
"""
Return true if atom name is in backbone, otherwise false
Returns
state: 1 if true, 0 if false
"""
if self.name in BACKBONE: return 1
else: return 0
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