"""
Nucleic Acid Structures for PDB2PQR
This module contains the base nucleic 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,
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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"
import string
from structures import *
class Nucleic(Residue):
"""
Nucleic class
This class provides standard features of the nucleic 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.is3term = 0
self.is5term = 0
self.isCterm = 0
self.isNterm = 0
self.missing = []
self.reference = ref
# 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. Overrides the generic residue's createAtom().
Parameters
atomname: The name of the atom to add (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):
"""
Adds the termini for all inherited objects
"""
if self.is5term: self.ffname = self.ffname + "5"
if self.is3term: self.ffname = self.ffname + "3"
class A(Nucleic):
"""
Adenosine class
This class gives data about the Adenosine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA.
"""
if self.hasAtom("O2'"): self.ffname = "RA"
else: self.ffname = "DA"
Nucleic.setState(self)
class C(Nucleic):
"""
Cytidine class
This class gives data about the Cytidine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA.
"""
if self.hasAtom("O2'"): self.ffname = "RC"
else: self.ffname = "DC"
Nucleic.setState(self)
class G(Nucleic):
"""
Guanosine class
This class gives data about the Guanosine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA.
"""
if self.hasAtom("O2'"): self.ffname = "RG"
else: self.ffname = "DG"
Nucleic.setState(self)
class T(Nucleic):
"""
Thymine class
This class gives data about the Thymine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA. In this case it is
always DNA.
"""
self.ffname = "DT"
Nucleic.setState(self)
class U(Nucleic):
"""
Uridine class
This class gives data about the Uridine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA. In this case it is
always RNA.
"""
self.ffname = "RU"
Nucleic.setState(self)
class ADE(Nucleic):
"""
Adenosine class
This class gives data about the Adenosine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA.
"""
if self.hasAtom("O2'"): self.ffname = "RA"
else: self.ffname = "DA"
Nucleic.setState(self)
class CYT(Nucleic):
"""
Cytidine class
This class gives data about the Cytidine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA.
"""
if self.hasAtom("O2'"): self.ffname = "RC"
else: self.ffname = "DC"
Nucleic.setState(self)
class GUA(Nucleic):
"""
Guanosine class
This class gives data about the Guanosine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA.
"""
if self.hasAtom("O2'"): self.ffname = "RG"
else: self.ffname = "DG"
Nucleic.setState(self)
class THY(Nucleic):
"""
Thymine class
This class gives data about the Thymine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA. In this case it is
always DNA.
"""
self.ffname = "DT"
Nucleic.setState(self)
class URA(Nucleic):
"""
Uridine class
This class gives data about the Uridine 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)
"""
Nucleic.__init__(self, atoms, ref)
self.reference = ref
def setState(self):
"""
Set the state to distinguish RNA from DNA. In this case it is
always RNA.
"""
self.ffname = "RU"
Nucleic.setState(self)
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