def instanceMatricesFromGroup(molecule): returnMatrices = [numpy.eye(4, 4)] crystal = Crystal(molecule.cellLength, molecule.cellAngles) matrices = spaceGroups[molecule.spaceGroup] for matrix in matrices: tmpMatix = numpy.eye(4, 4) tmpMatix[:3, :3] = matrix[0] tmpMatix[:3, 3] = crystal.toCartesian(matrix[1]) returnMatrices.append(tmpMatix) molecule.crystal = crystal return returnMatrices
def instanceMatricesFromGroup(molecule): returnMatrices = [numpy.eye(4,4)] crystal = Crystal(molecule.cellLength, molecule.cellAngles) matrices = spaceGroups[molecule.spaceGroup] for matrix in matrices: tmpMatix = numpy.eye(4,4) tmpMatix[:3, :3] = matrix[0] tmpMatix[:3, 3] = crystal.toCartesian(matrix[1]) returnMatrices.append(tmpMatix) molecule.crystal = crystal return returnMatrices
def parse(self, objClass=Protein): """Parses mmCIF dictionary (self.mmCIF_dict) into MolKit object""" if self.allLines is None and self.filename: self.readFile() if self.allLines is None or len(self.allLines)==0: return self.mmCIF2Dict() type_symbol = None B_iso_or_equiv = None mmCIF_dict = self.mmCIF_dict fileName, fileExtension = os.path.splitext(self.filename) molName = os.path.basename(fileName) if mmCIF_dict.has_key('_entry.id'): molName = mmCIF_dict['_entry.id'] if mmCIF_dict.has_key('_atom_site.id'): #The description of the data names can be found in the following link #http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items ids = mmCIF_dict['_atom_site.id'] #1 number group_PDB = mmCIF_dict['_atom_site.group_PDB'] #2 atom/hetatm atom_id = mmCIF_dict['_atom_site.label_atom_id'] #3 name comp_id = mmCIF_dict['_atom_site.label_comp_id'] #4 residue type label_asym_id = mmCIF_dict['_atom_site.label_asym_id'] #5 chain #Note: chain ID from mmCIF file might be different from PDB file seq_id = mmCIF_dict['_atom_site.label_seq_id'] #6 residue number x_coords = mmCIF_dict['_atom_site.Cartn_x'] #7 xcoord y_coords = mmCIF_dict['_atom_site.Cartn_y'] #8 ycoord z_coords = mmCIF_dict['_atom_site.Cartn_z'] #9 zcoord occupancy = mmCIF_dict['_atom_site.occupancy'] #10 B_iso_or_equiv = mmCIF_dict['_atom_site.B_iso_or_equiv']#11 type_symbol = mmCIF_dict['_atom_site.type_symbol'] elif mmCIF_dict.has_key('_atom_site_label'): #ftp://ftp.iucr.org/pub/cif_core.dic atom_id = mmCIF_dict['_atom_site_label'] len_atoms = len(atom_id) ids = range(len_atoms) group_PDB = len_atoms*['HETATM'] comp_id = len_atoms*["CIF"] label_asym_id = len_atoms*['1'] seq_id = len_atoms*[1] from mglutil.math.crystal import Crystal a = mmCIF_dict['_cell.length_a'] = float(mmCIF_dict['_cell_length_a'].split('(')[0]) b = mmCIF_dict['_cell.length_b'] = float(mmCIF_dict['_cell_length_b'].split('(')[0]) c = mmCIF_dict['_cell.length_c'] = float(mmCIF_dict['_cell_length_c'].split('(')[0]) alpha = mmCIF_dict['_cell.angle_alpha'] = float(mmCIF_dict['_cell_angle_alpha'].split('(')[0]) beta = mmCIF_dict['_cell.angle_beta'] = float(mmCIF_dict['_cell_angle_beta'].split('(')[0]) gamma = mmCIF_dict['_cell.angle_gamma'] = float(mmCIF_dict['_cell_angle_gamma'].split('(')[0]) cryst = Crystal((a, b, c), (alpha, beta, gamma)) x = [] for item in mmCIF_dict['_atom_site_fract_x']: x.append(float(item.split('(')[0])) y = [] for item in mmCIF_dict['_atom_site_fract_y']: y.append(float(item.split('(')[0])) z = [] for item in mmCIF_dict['_atom_site_fract_z']: z.append(float(item.split('(')[0])) x_coords = [] y_coords = [] z_coords = [] B_iso_or_equiv = [] for i in ids: trans = cryst.toCartesian([x[i], y[i], z[i]]) x_coords.append(trans[0]) y_coords.append(trans[1]) z_coords.append(trans[2]) if mmCIF_dict.has_key('_atom_site_U_iso_or_equiv'): B_iso_or_equiv.append(mmCIF_dict['_atom_site_U_iso_or_equiv'][i].split('(')[0]) if mmCIF_dict.has_key('_atom_site_type_symbol'): type_symbol = mmCIF_dict['_atom_site_type_symbol'] if mmCIF_dict.has_key('_atom_site_occupancy'): occupancy = mmCIF_dict['_atom_site_occupancy'] if mmCIF_dict.has_key('_chemical_name_common'): molName = mmCIF_dict['_chemical_name_common'] elif mmCIF_dict.has_key('_chemical_name_mineral'): molName = mmCIF_dict['_chemical_name_mineral'] if mmCIF_dict.has_key('_symmetry_space_group_name_H-M'): mmCIF_dict['_symmetry.space_group_name_H-M'] = mmCIF_dict['_symmetry_space_group_name_H-M'] else: print 'No _atom_site.id or _atom_site_label record is available in %s' % self.filename return None mol = Protein() self.mol = mol self.mol.allAtoms = AtomSet([]) molList = mol.setClass() molList.append( mol ) current_chain_id = None current_residue_number = None current_chain = None current_residue = None number_of_atoms = len(ids) self.configureProgressBar(init=1, mode='increment', authtext='parse atoms', max=number_of_atoms) for index in range(number_of_atoms): #make a new atom for the current index chain_id = label_asym_id[index] if chain_id != current_chain_id: #make a new chain #molecule should adopt the current chain if there is one current_chain = Chain(id=chain_id) # FIXME: current_chain should not have allAtoms attribute delattr(current_chain, "allAtoms") current_chain_id = chain_id if current_chain is not None: #REMEMBER TO ADOPT THE LAST ONE!!! mol.adopt(current_chain, setChildrenTop=1) residue_number = seq_id[index] if residue_number != current_residue_number or chain_id != label_asym_id[index-1]: #make a new chain: #current_chain should adopt the current residue if there is one #create new residue residue_type = comp_id[index] current_residue = Residue(type=residue_type, number=residue_number) current_residue_number = residue_number if current_residue is not None: #REMEMBER TO ADOPT THE LAST ONE!!! current_chain.adopt(current_residue, setChildrenTop=1) name = atom_id[index] if type_symbol: element = type_symbol[index] else: element = None atom = Atom( name, current_residue, element, top=mol ) atom._coords = [[float(x_coords[index]), float(y_coords[index]), float(z_coords[index])]] atom._charges = {} atom.segID = mol.name atom.normalname = name atom.number = int(ids[index]) mol.atmNum[atom.number] = atom atom.occupancy = float(occupancy[index]) if B_iso_or_equiv: atom.temperatureFactor = float(B_iso_or_equiv[index]) atom.altname = None atom.hetatm = 0 if group_PDB[index]=='HETATM': atom.hetatm = 1 self.updateProgressBar() self.parse_MMCIF_CELL() try: self.parse_MMCIF_HYDBND() except: print >>sys.stderr,"Parsing Hydrogen Bond Record Failed in",self.filename mol.name = molName mol.allAtoms = mol.chains.residues.atoms mol.parser = self mol.levels = [Protein, Chain, Residue, Atom] name = '' for n in molList.name: name = n + ',' name = name[:-1] molList.setStringRepr(name) strRpr = name + ':::' molList.allAtoms.setStringRepr(strRpr) for m in molList: mname = m.name strRpr = mname + ':::' m.allAtoms.setStringRepr(strRpr) strRpr = mname + ':' m.chains.setStringRepr(strRpr) for c in m.chains: cname = c.id strRpr = mname + ':' + cname + ':' c.residues.setStringRepr(strRpr) for r in c.residues: rname = r.name strRpr = mname + ':' + cname + ':' + rname + ':' r.atoms.setStringRepr(strRpr) self.buildBonds() return molList
def parse(self, objClass=Protein): """Parses mmCIF dictionary (self.mmCIF_dict) into MolKit object""" if self.allLines is None and self.filename: self.readFile() if self.allLines is None or len(self.allLines) == 0: return self.mmCIF2Dict() type_symbol = None B_iso_or_equiv = None mmCIF_dict = self.mmCIF_dict fileName, fileExtension = os.path.splitext(self.filename) molName = os.path.basename(fileName) if mmCIF_dict.has_key('_entry.id'): molName = mmCIF_dict['_entry.id'] if mmCIF_dict.has_key('_atom_site.id'): #The description of the data names can be found in the following link #http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items ids = mmCIF_dict['_atom_site.id'] #1 number group_PDB = mmCIF_dict['_atom_site.group_PDB'] #2 atom/hetatm atom_id = mmCIF_dict['_atom_site.label_atom_id'] #3 name comp_id = mmCIF_dict['_atom_site.label_comp_id'] #4 residue type label_asym_id = mmCIF_dict['_atom_site.label_asym_id'] #5 chain #Note: chain ID from mmCIF file might be different from PDB file seq_id = mmCIF_dict['_atom_site.label_seq_id'] #6 residue number x_coords = mmCIF_dict['_atom_site.Cartn_x'] #7 xcoord y_coords = mmCIF_dict['_atom_site.Cartn_y'] #8 ycoord z_coords = mmCIF_dict['_atom_site.Cartn_z'] #9 zcoord occupancy = mmCIF_dict['_atom_site.occupancy'] #10 B_iso_or_equiv = mmCIF_dict['_atom_site.B_iso_or_equiv'] #11 type_symbol = mmCIF_dict['_atom_site.type_symbol'] elif mmCIF_dict.has_key('_atom_site_label'): #ftp://ftp.iucr.org/pub/cif_core.dic atom_id = mmCIF_dict['_atom_site_label'] len_atoms = len(atom_id) ids = range(len_atoms) group_PDB = len_atoms * ['HETATM'] comp_id = len_atoms * ["CIF"] label_asym_id = len_atoms * ['1'] seq_id = len_atoms * [1] from mglutil.math.crystal import Crystal a = mmCIF_dict['_cell.length_a'] = float( mmCIF_dict['_cell_length_a'].split('(')[0]) b = mmCIF_dict['_cell.length_b'] = float( mmCIF_dict['_cell_length_b'].split('(')[0]) c = mmCIF_dict['_cell.length_c'] = float( mmCIF_dict['_cell_length_c'].split('(')[0]) alpha = mmCIF_dict['_cell.angle_alpha'] = float( mmCIF_dict['_cell_angle_alpha'].split('(')[0]) beta = mmCIF_dict['_cell.angle_beta'] = float( mmCIF_dict['_cell_angle_beta'].split('(')[0]) gamma = mmCIF_dict['_cell.angle_gamma'] = float( mmCIF_dict['_cell_angle_gamma'].split('(')[0]) cryst = Crystal((a, b, c), (alpha, beta, gamma)) x = [] for item in mmCIF_dict['_atom_site_fract_x']: x.append(float(item.split('(')[0])) y = [] for item in mmCIF_dict['_atom_site_fract_y']: y.append(float(item.split('(')[0])) z = [] for item in mmCIF_dict['_atom_site_fract_z']: z.append(float(item.split('(')[0])) x_coords = [] y_coords = [] z_coords = [] B_iso_or_equiv = [] for i in ids: trans = cryst.toCartesian([x[i], y[i], z[i]]) x_coords.append(trans[0]) y_coords.append(trans[1]) z_coords.append(trans[2]) if mmCIF_dict.has_key('_atom_site_U_iso_or_equiv'): B_iso_or_equiv.append( mmCIF_dict['_atom_site_U_iso_or_equiv'][i].split( '(')[0]) if mmCIF_dict.has_key('_atom_site_type_symbol'): type_symbol = mmCIF_dict['_atom_site_type_symbol'] if mmCIF_dict.has_key('_atom_site_occupancy'): occupancy = mmCIF_dict['_atom_site_occupancy'] if mmCIF_dict.has_key('_chemical_name_common'): molName = mmCIF_dict['_chemical_name_common'] elif mmCIF_dict.has_key('_chemical_name_mineral'): molName = mmCIF_dict['_chemical_name_mineral'] if mmCIF_dict.has_key('_symmetry_space_group_name_H-M'): mmCIF_dict['_symmetry.space_group_name_H-M'] = mmCIF_dict[ '_symmetry_space_group_name_H-M'] else: print 'No _atom_site.id or _atom_site_label record is available in %s' % self.filename return None mol = Protein() self.mol = mol self.mol.allAtoms = AtomSet([]) molList = mol.setClass() molList.append(mol) current_chain_id = None current_residue_number = None current_chain = None current_residue = None number_of_atoms = len(ids) self.configureProgressBar(init=1, mode='increment', authtext='parse atoms', max=number_of_atoms) for index in range(number_of_atoms): #make a new atom for the current index chain_id = label_asym_id[index] if chain_id != current_chain_id: #make a new chain #molecule should adopt the current chain if there is one current_chain = Chain(id=chain_id) # FIXME: current_chain should not have allAtoms attribute delattr(current_chain, "allAtoms") current_chain_id = chain_id if current_chain is not None: #REMEMBER TO ADOPT THE LAST ONE!!! mol.adopt(current_chain, setChildrenTop=1) residue_number = seq_id[index] if residue_number != current_residue_number or chain_id != label_asym_id[ index - 1]: #make a new chain: #current_chain should adopt the current residue if there is one #create new residue residue_type = comp_id[index] current_residue = Residue(type=residue_type, number=residue_number) current_residue_number = residue_number if current_residue is not None: #REMEMBER TO ADOPT THE LAST ONE!!! current_chain.adopt(current_residue, setChildrenTop=1) name = atom_id[index] if type_symbol: element = type_symbol[index] else: element = None atom = Atom(name, current_residue, element, top=mol) atom._coords = [[ float(x_coords[index]), float(y_coords[index]), float(z_coords[index]) ]] atom._charges = {} atom.segID = mol.name atom.normalname = name atom.number = int(ids[index]) mol.atmNum[atom.number] = atom atom.occupancy = float(occupancy[index]) if B_iso_or_equiv: atom.temperatureFactor = float(B_iso_or_equiv[index]) atom.altname = None atom.hetatm = 0 if group_PDB[index] == 'HETATM': atom.hetatm = 1 self.updateProgressBar() self.parse_MMCIF_CELL() try: self.parse_MMCIF_HYDBND() except: print >> sys.stderr, "Parsing Hydrogen Bond Record Failed in", self.filename mol.name = molName mol.allAtoms = mol.chains.residues.atoms mol.parser = self mol.levels = [Protein, Chain, Residue, Atom] name = '' for n in molList.name: name = n + ',' name = name[:-1] molList.setStringRepr(name) strRpr = name + ':::' molList.allAtoms.setStringRepr(strRpr) for m in molList: mname = m.name strRpr = mname + ':::' m.allAtoms.setStringRepr(strRpr) strRpr = mname + ':' m.chains.setStringRepr(strRpr) for c in m.chains: cname = c.id strRpr = mname + ':' + cname + ':' c.residues.setStringRepr(strRpr) for r in c.residues: rname = r.name strRpr = mname + ':' + cname + ':' + rname + ':' r.atoms.setStringRepr(strRpr) self.buildBonds() return molList