"""
    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

    <NAME> (<EMAIL>)
    <NAME> (<EMAIL>)
    Dept. of Biochemistry and Molecular Biophysics
    Center for Computational Biology
    Washington University in St. Louis

    <NAME> (<EMAIL>)
    University College Dublin

    Additional contributing authors listed in documentation and supporting
    package licenses.

    Copyright (c) 2003-2007.  Washington University in St. Louis.  
    All Rights Reserved.

    This file is part of PDB2PQR.

    PDB2PQR is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.
 
    PDB2PQR is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
   
    You should have received a copy of the GNU General Public License
    along with PDB2PQR; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA

    ----------------------------

"""

__date__ = "28 December 2006"
__author__ = "<NAME>"

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
        
        # 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

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")
            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
        
        # 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

"""
    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

    <NAME> (<EMAIL>)
    <NAME> (<EMAIL>)
    Dept. of Biochemistry and Molecular Biophysics
    Center for Computational Biology
    Washington University in St. Louis

    <NAME> (<EMAIL>)
    University College Dublin

    Additional contributing authors listed in documentation and supporting
    package licenses.

    Copyright (c) 2003-2007.  Washington University in St. Louis.  
    All Rights Reserved.

    This file is part of PDB2PQR.

    PDB2PQR is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.
 
    PDB2PQR is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
   
    You should have received a copy of the GNU General Public License
    along with PDB2PQR; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA

    ----------------------------

"""

__date__ = "28 December 2006"
__author__ = "<NAME>"

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
        
        # 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

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")
            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
        
        # 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

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      <NAME> (<EMAIL>)     <NAME> (<EMAIL>)     Dept. of Biochemistry and Molecular Biophysics     Center for Computational Biology     Washington University in St. Louis      <NAME> (<EMAIL>)     University College Dublin      Additional contributing authors listed in documentation and supporting     package licenses.      Copyright (c) 2003-2007.  Washington University in St. Louis.       All Rights Reserved.      This file is part of PDB2PQR.      PDB2PQR is free software; you can redistribute it and/or modify     it under the terms of the GNU General Public License as published by     the Free Software Foundation; either version 2 of the License, or     (at your option) any later version.       PDB2PQR is distributed in the hope that it will be useful,     but WITHOUT ANY WARRANTY; without even the implied warranty of     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the     GNU General Public License for more details.         You should have received a copy of the GNU General Public License     along with PDB2PQR; if not, write to the Free Software     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA      ---------------------------- 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. # Create each atom # Rename atoms 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). Override the existing addAtom - include the link to the             reference object Add the value to the list of chiangles              Parameters                 value: The value to be added (float) Set the name to use for the forcefield based on the current            state.  Uses N* and C* for termini. Alanine class          This class gives data about the Alanine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Arginine class          This class gives data about the Arginine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Asparagine class          This class gives data about the Asparagine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Aspartic Acid class          This class gives data about the Aspartic Acid object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Set the name to use for the forcefield based on the current            state. Cysteine class          This class gives data about the Cysteine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Set the state of the CYS object.  If SS-bonded, use CYX.  If             negatively charged, use CYM.  If HG is not present, use CYX. Glutamine class          This class gives data about the Glutamine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Glutamic Acid class          This class gives data about the Glutamic Acid object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Set the name to use for the forcefield based on the current            state. Glycine class          This class gives data about the Glycine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Histidine class          This class gives data about the Histidine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) 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. # Default to HID Isoleucine class          This class gives data about the Isoleucine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Leucine class          This class gives data about the Leucine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Lysine class          This class gives data about the Lysine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Determine if this is LYN or not Methionine class          This class gives data about the Methionine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Phenylalanine class          This class gives data about the Phenylalanine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Proline class          This class gives data about the Proline object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Set the name to use for the forcefield based on the current            state.  Uses N* and C* for termini. Serine class          This class gives data about the Serine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Threonine class          This class gives data about the Threonine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Tryptophan class          This class gives data about the Tryptophan object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Tyrosine class          This class gives data about the Tyrosine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) See if the TYR is negative or not Valine class          This class gives data about the Valine object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) Water class          This class gives data about the Water object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) # Create each atom # Rename atoms # Don't add duplicate atom with altLoc field Create a water atom.  Note the HETATM field.              Parameters                 atomname: The name of the atom (string)                 newcoords:  The new coordinates of the atom (list) Override the existing addAtom - include the link to the             reference object Generic ligand class          This class gives data about the generic ligand object, and inherits         off the base residue class. Initialize the class              Parameters                 atoms:      A list of Atom objects to be stored in this class                             (list) # Create each atom # Rename atoms # Don't add duplicate atom with altLoc field Create a water atom.  Note the HETATM field.              Parameters                 atomname: The name of the atom (string)                 newcoords:  The new coordinates of the atom (list) Override the existing addAtom - include the link to the             reference object