text: """
      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) 2002-2011, Jens Erik Nielsen, University College Dublin;
      Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific
      Northwest National Laboratory, operated by Battelle Memorial Institute,
      Pacific Northwest Division for the U.S. Department Energy.;
      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, Battelle Memorial Institute,
            Pacific Northwest National Laboratory, US Department of Energy, 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 *
  from src.errors import PDBInputError
  
  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
  
      def letterCode(self):
          return 'A'
  
  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 letterCode(self):
          return 'R'
  
      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
  
      def letterCode(self):
          return 'N'
  
  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 letterCode(self):
          return 'D'
  
      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 letterCode(self):
          return 'C'
  
      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
  
      def letterCode(self):
          return 'Q'
  
  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 letterCode(self):
          return 'E'
  
      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
  
      def letterCode(self):
          return 'G'
  
  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 letterCode(self):
          return 'H'
  
      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")
  
          self.ffname = "HIP"
          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
  
      def letterCode(self):
          return 'I'
  
  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
  
      def letterCode(self):
          return 'L'
  
  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 letterCode(self):
          return 'K'
  
      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
  
      def letterCode(self):
          return 'M'
  
  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
  
      def letterCode(self):
          return 'F'
  
  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 letterCode(self):
          return 'P'
  
      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
  
      def letterCode(self):
          return 'S'
  
  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
  
      def letterCode(self):
          return 'T'
  
  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
  
      def letterCode(self):
          return 'W'
  
  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 letterCode(self):
          return 'Y'
  
      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
  
      def letterCode(self):
          return 'V'
  
  
  class WAT(Residue):
      """
          Water class
  
          This class gives data about the Water object, and inherits
          off the base residue class.
      """
      water_residue_names = ['HOH', 'WAT']
  
      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
  