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StructureBuilder.py
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.  

"""Consumer class that builds a Structure object.

This is used by the PDBParser and MMCIFparser classes.
"""

import warnings

# SMCRA hierarchy
from Bio.PDB.Structure import Structure
from Bio.PDB.Model import Model
from Bio.PDB.Chain import Chain
from Bio.PDB.Residue import Residue, DisorderedResidue
from Bio.PDB.Atom import Atom, DisorderedAtom 

from Bio.PDB.PDBExceptions import \
        PDBConstructionException, PDBConstructionWarning


00024 class StructureBuilder(object):
    """
    Deals with contructing the Structure object. The StructureBuilder class is used
    by the PDBParser classes to translate a file to a Structure object.
    """
    def __init__(self):
        self.line_counter=0
        self.header={}

    def _is_completely_disordered(self, residue):
        "Return 1 if all atoms in the residue have a non blank altloc."
        atom_list=residue.get_unpacked_list()
        for atom in atom_list:
            altloc=atom.get_altloc()
            if altloc==" ":
                return 0
        return 1

    # Public methods called by the Parser classes

    def set_header(self, header):
        self.header=header

00047     def set_line_counter(self, line_counter):
        """
        The line counter keeps track of the line in the PDB file that 
        is being parsed.
        
        Arguments:
        o line_counter - int
        """
        self.line_counter=line_counter

00057     def init_structure(self, structure_id):
        """Initiate a new Structure object with given id.

        Arguments:
        o id - string
        """
        self.structure=Structure(structure_id)

00065     def init_model(self, model_id, serial_num = None):
        """Initiate a new Model object with given id.
        
        Arguments:
        o id - int
        o serial_num - int
        """
        self.model=Model(model_id,serial_num)
        self.structure.add(self.model)

00075     def init_chain(self, chain_id):
        """Initiate a new Chain object with given id.

        Arguments:
        o chain_id - string
        """
        if self.model.has_id(chain_id):
            self.chain=self.model[chain_id]
            warnings.warn("WARNING: Chain %s is discontinuous at line %i."
                          % (chain_id, self.line_counter),
                          PDBConstructionWarning)
        else:
            self.chain=Chain(chain_id)
            self.model.add(self.chain)

00090     def init_seg(self, segid):
        """Flag a change in segid.
        
        Arguments:
        o segid - string
        """
        self.segid=segid

00098     def init_residue(self, resname, field, resseq, icode):
        """
        Initiate a new Residue object.

        Arguments:
        o resname - string, e.g. "ASN"
        o field - hetero flag, "W" for waters, "H" for 
            hetero residues, otherwise blank.
        o resseq - int, sequence identifier
        o icode - string, insertion code
        """
        if field!=" ":
            if field=="H":
                # The hetero field consists of H_ + the residue name (e.g. H_FUC)
                field="H_"+resname 
        res_id=(field, resseq, icode) 
        if field==" ":
            if self.chain.has_id(res_id):
                # There already is a residue with the id (field, resseq, icode).
                # This only makes sense in the case of a point mutation.
                warnings.warn("WARNING: Residue ('%s', %i, '%s') "
                              "redefined at line %i."
                              % (field, resseq, icode, self.line_counter),
                              PDBConstructionWarning)
                duplicate_residue=self.chain[res_id]
                if duplicate_residue.is_disordered()==2:
                    # The residue in the chain is a DisorderedResidue object.
                    # So just add the last Residue object. 
                    if duplicate_residue.disordered_has_id(resname):
                        # The residue was already made
                        self.residue=duplicate_residue
                        duplicate_residue.disordered_select(resname)
                    else:
                        # Make a new residue and add it to the already
                        # present DisorderedResidue
                        new_residue=Residue(res_id, resname, self.segid)
                        duplicate_residue.disordered_add(new_residue)
                        self.residue=duplicate_residue
                        return
                else:
                    # Make a new DisorderedResidue object and put all
                    # the Residue objects with the id (field, resseq, icode) in it.
                    # These residues each should have non-blank altlocs for all their atoms.
                    # If not, the PDB file probably contains an error. 
                    if not self._is_completely_disordered(duplicate_residue):
                        # if this exception is ignored, a residue will be missing
                        self.residue=None
                        raise PDBConstructionException(\
                            "Blank altlocs in duplicate residue %s ('%s', %i, '%s')" \
                            % (resname, field, resseq, icode))
                    self.chain.detach_child(res_id)
                    new_residue=Residue(res_id, resname, self.segid)
                    disordered_residue=DisorderedResidue(res_id)
                    self.chain.add(disordered_residue)
                    disordered_residue.disordered_add(duplicate_residue)
                    disordered_residue.disordered_add(new_residue)
                    self.residue=disordered_residue
                    return
        residue=Residue(res_id, resname, self.segid)
        self.chain.add(residue)
        self.residue=residue

00160     def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname,
                  serial_number=None, element=None):
        """
        Initiate a new Atom object.

        Arguments:
        o name - string, atom name, e.g. CA, spaces should be stripped
        o coord - Numeric array (Float0, size 3), atomic coordinates
        o b_factor - float, B factor
        o occupancy - float
        o altloc - string, alternative location specifier
        o fullname - string, atom name including spaces, e.g. " CA "
        o element - string, upper case, e.g. "HG" for mercury
        """
        residue=self.residue
        # if residue is None, an exception was generated during
        # the construction of the residue
        if residue is None:
            return
        # First check if this atom is already present in the residue. 
        # If it is, it might be due to the fact that the two atoms have atom 
        # names that differ only in spaces (e.g. "CA.." and ".CA.",
        # where the dots are spaces). If that is so, use all spaces
        # in the atom name of the current atom. 
        if residue.has_id(name):
                duplicate_atom=residue[name]
                # atom name with spaces of duplicate atom
                duplicate_fullname=duplicate_atom.get_fullname()
                if duplicate_fullname!=fullname:
                    # name of current atom now includes spaces
                    name=fullname
                    warnings.warn("Atom names %r and %r differ "
                                  "only in spaces at line %i."
                                  % (duplicate_fullname, fullname,
                                     self.line_counter),
                                  PDBConstructionWarning)
        atom=self.atom=Atom(name, coord, b_factor, occupancy, altloc,
                            fullname, serial_number, element)
        if altloc!=" ":
            # The atom is disordered
            if residue.has_id(name):
                # Residue already contains this atom
                duplicate_atom=residue[name]
                if duplicate_atom.is_disordered()==2:
                    duplicate_atom.disordered_add(atom)     
                else:
                    # This is an error in the PDB file:
                    # a disordered atom is found with a blank altloc
                    # Detach the duplicate atom, and put it in a 
                    # DisorderedAtom object together with the current 
                    # atom.
                    residue.detach_child(name)
                    disordered_atom=DisorderedAtom(name)
                    residue.add(disordered_atom)
                    disordered_atom.disordered_add(atom)
                    disordered_atom.disordered_add(duplicate_atom)
                    residue.flag_disordered()
                    warnings.warn("WARNING: disordered atom found "
                                  "with blank altloc before line %i.\n"
                                  % self.line_counter,
                                  PDBConstructionWarning)
            else:
                # The residue does not contain this disordered atom
                # so we create a new one.
                disordered_atom=DisorderedAtom(name)
                residue.add(disordered_atom)
                # Add the real atom to the disordered atom, and the 
                # disordered atom to the residue
                disordered_atom.disordered_add(atom)
                residue.flag_disordered()
        else:   
            # The atom is not disordered
            residue.add(atom)

    def set_anisou(self, anisou_array):
        "Set anisotropic B factor of current Atom."
        self.atom.set_anisou(anisou_array)

    def set_siguij(self, siguij_array):
        "Set standard deviation of anisotropic B factor of current Atom."
        self.atom.set_siguij(siguij_array)

    def set_sigatm(self, sigatm_array):
        "Set standard deviation of atom position of current Atom."
        self.atom.set_sigatm(sigatm_array)

    def get_structure(self):
        "Return the structure."
        # first sort everything
        # self.structure.sort()
        # Add the header dict
        self.structure.header=self.header
        return self.structure

    def set_symmetry(self, spacegroup, cell):
        pass



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