"""
Amino Acid Structures for PDB2PQR
This module contains the base amino acid structures for
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__ = "28 December 2006"
__author__ = "Todd Dolinsky"
import string
from structures import *
class Amino(Residue):
"""
Amino class
This class provides standard features of the amino acids listed
below
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
ref: The reference object for the amino acid. Used to
convert from the alternate naming scheme to the
main naming scheme.
"""
def __init__(self, atoms, ref):
sampleAtom = atoms[-1]
self.atoms = []
self.name = sampleAtom.resName
self.chainID = sampleAtom.chainID
self.resSeq = sampleAtom.resSeq
self.iCode = sampleAtom.iCode
self.ffname = self.name
self.map = {}
self.dihedrals = []
self.patches = []
self.peptideC = None
self.peptideN = None
self.isNterm = 0
self.isCterm = 0
self.is5term = 0
self.is3term = 0
self.missing = []
self.reference = ref
self.fixed = 0
self.stateboolean = {}
# Create each atom
for a in atoms:
if a.name in ref.altnames: # Rename atoms
a.name = ref.altnames[a.name]
if a.name not in self.map:
atom = Atom(a, "ATOM", self)
self.addAtom(atom)
def createAtom(self, atomname, newcoords):
"""
Create an atom. Override the generic residue's version of
createAtom().
Parameters
atomname: The name of the atom (string)
newcoords: The coordinates of the atom (list).
"""
oldatom = self.atoms[0]
newatom = Atom(oldatom, "ATOM", self)
newatom.set("x",newcoords[0])
newatom.set("y",newcoords[1])
newatom.set("z",newcoords[2])
newatom.set("name", atomname)
newatom.set("occupancy",1.00)
newatom.set("tempFactor",0.00)
newatom.added = 1
self.addAtom(newatom)
def addAtom(self, atom):
"""
Override the existing addAtom - include the link to the
reference object
"""
self.atoms.append(atom)
atomname = atom.get("name")
self.map[atomname] = atom
try:
atom.reference = self.reference.map[atomname]
for bond in atom.reference.bonds:
if self.hasAtom(bond):
bondatom = self.map[bond]
if bondatom not in atom.bonds: atom.bonds.append(bondatom)
if atom not in bondatom.bonds: bondatom.bonds.append(atom)
except KeyError:
atom.reference = None
def addDihedralAngle(self, value):
"""
Add the value to the list of chiangles
Parameters
value: The value to be added (float)
"""
self.dihedrals.append(value)
def setState(self):
"""
Set the name to use for the forcefield based on the current
state. Uses N* and C* for termini.
"""
if self.isNterm:
if "NEUTRAL-NTERM" in self.patches:
self.ffname = "NEUTRAL-N%s" % self.ffname
else:
self.ffname = "N%s" % self.ffname
elif self.isCterm:
if "NEUTRAL-CTERM" in self.patches:
self.ffname = "NEUTRAL-C%s" % self.ffname
else:
self.ffname = "C%s" % self.ffname
return
class ALA(Amino):
"""
Alanine class
This class gives data about the Alanine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class ARG(Amino):
"""
Arginine class
This class gives data about the Arginine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the name to use for the forcefield based on the current
state.
"""
if "AR0" in self.patches or self.name == "AR0": self.ffname = "AR0"
Amino.setState(self)
class ASN(Amino):
"""
Asparagine class
This class gives data about the Asparagine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class ASP(Amino):
"""
Aspartic Acid class
This class gives data about the Aspartic Acid object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the name to use for the forcefield based on the current
state.
"""
if "ASH" in self.patches or self.name == "ASH": self.ffname = "ASH"
Amino.setState(self)
class CYS(Amino):
"""
Cysteine class
This class gives data about the Cysteine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
self.SSbonded = 0
self.SSbondedpartner = None
def setState(self):
"""
Set the state of the CYS object. If SS-bonded, use CYX. If
negatively charged, use CYM. If HG is not present, use CYX.
"""
if "CYX" in self.patches or self.name == "CYX": self.ffname = "CYX"
elif self.SSbonded: self.ffname = "CYX"
elif "CYM" in self.patches or self.name == "CYM": self.ffname = "CYM"
elif not self.hasAtom("HG"): self.ffname = "CYX"
Amino.setState(self)
class GLN(Amino):
"""
Glutamine class
This class gives data about the Glutamine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class GLU(Amino):
"""
Glutamic Acid class
This class gives data about the Glutamic Acid object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the name to use for the forcefield based on the current
state.
"""
if "GLH" in self.patches or self.name == "GLH": self.ffname = "GLH"
Amino.setState(self)
class GLY(Amino):
"""
Glycine class
This class gives data about the Glycine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class HIS(Amino):
"""
Histidine class
This class gives data about the Histidine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Histidines are a special case due to the presence of
several different forms. This function sets all non-
positive incarnations of HIS to neutral HIS by
checking to see if optimization removed hacceptor or
hdonor flags. Otherwise HID is used as the default.
"""
if "HIP" not in self.patches and self.name not in ["HIP", "HSP"]:
if self.getAtom("ND1").hdonor and not \
self.getAtom("ND1").hacceptor:
if self.hasAtom("HE2"): self.removeAtom("HE2")
elif self.getAtom("NE2").hdonor and not \
self.getAtom("NE2").hacceptor:
if self.hasAtom("HD1"): self.removeAtom("HD1")
elif self.getAtom("ND1").hacceptor and not \
self.getAtom("ND1").hdonor:
if self.hasAtom("HD1"): self.removeAtom("HD1")
else: # Default to HID
if self.hasAtom("HE2"): self.removeAtom("HE2")
if self.hasAtom("HD1") and self.hasAtom("HE2"): self.ffname = "HIP"
elif self.hasAtom("HD1"): self.ffname = "HID"
elif self.hasAtom("HE2"): self.ffname = "HIE"
else:
raise ValueError, "Invalid type for %s!" % str(self)
Amino.setState(self)
class ILE(Amino):
"""
Isoleucine class
This class gives data about the Isoleucine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class LEU(Amino):
"""
Leucine class
This class gives data about the Leucine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class LYS(Amino):
"""
Lysine class
This class gives data about the Lysine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Determine if this is LYN or not
"""
if "LYN" in self.patches or self.name == "LYN": self.ffname = "LYN"
Amino.setState(self)
class MET(Amino):
"""
Methionine class
This class gives data about the Methionine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class PHE(Amino):
"""
Phenylalanine class
This class gives data about the Phenylalanine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class PRO(Amino):
"""
Proline class
This class gives data about the Proline object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the name to use for the forcefield based on the current
state. Uses N* and C* for termini.
"""
if self.isNterm:
self.ffname = "N%s" % self.ffname
elif self.isCterm:
if "NEUTRAL-CTERM" in self.patches:
self.ffname = "NEUTRAL-C%s" % self.ffname
else:
self.ffname = "C%s" % self.ffname
class SER(Amino):
"""
Serine class
This class gives data about the Serine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class THR(Amino):
"""
Threonine class
This class gives data about the Threonine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class TRP(Amino):
"""
Tryptophan class
This class gives data about the Tryptophan object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class TYR(Amino):
"""
Tyrosine class
This class gives data about the Tyrosine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
See if the TYR is negative or not
"""
if "TYM" in self.patches or self.name == "TYM": self.ffname = "TYM"
Amino.setState(self)
class VAL(Amino):
"""
Valine class
This class gives data about the Valine object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
Initialize the class
Parameters
atoms: A list of Atom objects to be stored in this class
(list)
"""
Amino.__init__(self, atoms, ref)
self.reference = ref
class WAT(Residue):
"""
Water class
This class gives data about the Water object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
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.fixed = 0
self.ffname = "WAT"
self.map = {}
self.reference = ref
# Create each atom
for a in atoms:
if a.name in ref.altnames: # Rename atoms
a.name = ref.altnames[a.name]
atom = Atom(a, "HETATM", self)
atomname = atom.get("name")
if atomname not in self.map:
self.addAtom(atom)
else: # Don't add duplicate atom with altLoc field
oldatom = self.getAtom(atomname)
oldatom.set("altLoc","")
def createAtom(self, atomname, newcoords):
"""
Create a water atom. Note the HETATM field.
Parameters
atomname: The name of the atom (string)
newcoords: The new coordinates of the atom (list)
"""
oldatom = self.atoms[0]
newatom = Atom(oldatom, "HETATM", self)
newatom.set("x",newcoords[0])
newatom.set("y",newcoords[1])
newatom.set("z",newcoords[2])
newatom.set("name", atomname)
newatom.set("occupancy",1.00)
newatom.set("tempFactor",0.00)
newatom.added = 1
self.addAtom(newatom)
def addAtom(self, atom):
"""
Override the existing addAtom - include the link to the
reference object
"""
self.atoms.append(atom)
atomname = atom.get("name")
self.map[atomname] = atom
try:
atom.reference = self.reference.map[atomname]
for bond in atom.reference.bonds:
if self.hasAtom(bond):
bondatom = self.map[bond]
if bondatom not in atom.bonds: atom.bonds.append(bondatom)
if atom not in bondatom.bonds: bondatom.bonds.append(atom)
except KeyError:
atom.reference = None
class LIG(Residue):
"""
Generic ligand class
This class gives data about the generic ligand object, and inherits
off the base residue class.
"""
def __init__(self, atoms, ref):
"""
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.fixed = 0
self.ffname = "WAT"
self.map = {}
self.reference = ref
self.isNterm = 0
self.isCterm = 0
# Create each atom
for a in atoms:
if a.name in ref.altnames: # Rename atoms
a.name = ref.altnames[a.name]
atom = Atom(a, "HETATM", self)
atomname = atom.get("name")
if atomname not in self.map:
self.addAtom(atom)
else: # Don't add duplicate atom with altLoc field
oldatom = self.getAtom(atomname)
oldatom.set("altLoc","")
def createAtom(self, atomname, newcoords):
"""
Create a water atom. Note the HETATM field.
Parameters
atomname: The name of the atom (string)
newcoords: The new coordinates of the atom (list)
"""
oldatom = self.atoms[0]
newatom = Atom(oldatom, "HETATM", self)
newatom.set("x",newcoords[0])
newatom.set("y",newcoords[1])
newatom.set("z",newcoords[2])
newatom.set("name", atomname)
newatom.set("occupancy",1.00)
newatom.set("tempFactor",0.00)
newatom.added = 1
self.addAtom(newatom)
def addAtom(self, atom):
"""
Override the existing addAtom - include the link to the
reference object
"""
self.atoms.append(atom)
atomname = atom.get("name")
self.map[atomname] = atom
try:
atom.reference = self.reference.map[atomname]
for bond in atom.reference.bonds:
if self.hasAtom(bond):
bondatom = self.map[bond]
if bondatom not in atom.bonds: atom.bonds.append(bondatom)
if atom not in bondatom.bonds: bondatom.bonds.append(atom)
except KeyError:
atom.reference = None
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