def getMolecule(self, molInd): molecules = [] if molInd == len(self.molIndex) - 1: lastLine = -1 else: lastLine = self.molIndex[molInd + 1] # lines fotr that molecule lines = self.allLines[self.molIndex[molInd]:lastLine] lineIndex = 0 atomsSeen = {} # dict of atom types and number of atoms seen # parser header molName = lines[lineIndex].strip() lineIndex += 3 # create molecule mol = Protein(name=molName) mol.info = lines[lineIndex + 1] mol.comment = lines[lineIndex + 1] #self.mol.parser = self chain = Chain(id='1', parent=mol, top=mol) res = Residue(type='UNK', number='1', parent=chain, top=mol) mol.levels = [Protein, Chain, Residue, Atom] # parse count line line = lines[lineIndex] assert line[ 33: 39] == " V2000", "Format error: only V2000 is suported, got %s" % line[ 33:39] nba = int(line[0:3]) # number of atoms nbb = int(line[3:6]) # number of bonds nbal = int(line[6:9]) # number of atom lists ccc = int(line[12:15]) # chiral flag: 0=not chiral, 1=chiral sss = int(line[15:18]) # number of stext entries lineIndex += 1 # parse atoms for anum in range(nba): line = lines[lineIndex] element = line[31:34].strip() if element in atomsSeen: atomsSeen[element] += 1 else: atomsSeen[element] = 1 atom = Atom(name='%s_%s' % (element, atomsSeen[element]), parent=res, chemicalElement=element, top=mol) atom._coords = [[ float(line[0:10]), float(line[10:20]), float(line[20:30]) ]] atom._charges['sdf'] = int(line[35:38]) atom.chargeSet = 'sdf' mol.allAtoms.append(atom) atom.massDiff = int(line[34:36]) atom.stereo = int(line[38:41]) atom.hcount = line[41:44] atom.valence = int(line[47:50]) atom.hetatm = 1 atom.occupancy = 0.0 atom.temperatureFactor = 0.0 lineIndex += 1 # parse bonds for bnum in range(nba): line = lines[lineIndex] at1 = mol.allAtoms[int(line[0:3]) - 1] at2 = mol.allAtoms[int(line[3:6]) - 1] if at1.isBonded(at2): continue bond = Bond(at1, at2, check=0) bond.bondOrder = int(line[6:9]) #1 = Single, 2 = Double, #3 = Triple, 4 = Aromatic, #5 = Single or Double, #6 = Single or Aromatic, #7 = Double or Aromatic, 8 = Any bond.stereo = int(line[9:12]) #Single bonds: 0 = not stereo, #1 = Up, 4 = Either, #6 = Down, Double bonds: 0 = Use x-, y-, z-coords #from atom block to determine cis or trans, #3 = Cis or trans (either) double bond bond.topo = int(line[15:18]) # 0 = Either, 1 = Ring, 2 = Chain try: bond.ReactionCenter = int(line[18:21]) except ValueError: bond.ReactionCenter = 0 #0 = unmarked, 1 = a center, -1 = not a center, #Additional: 2 = no change, #4 = bond made/broken, #8 = bond order changes #12 = 4+8 (both made/broken and changes); #5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1) # "M END" and properties are not parsed at this point self.mol = mol mname = mol.name strRpr = mname + ':::' mol.allAtoms.setStringRepr(strRpr) strRpr = mname + ':' mol.chains.setStringRepr(strRpr) for c in mol.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) molList = mol.setClass() molList.append(mol) mol.parser = self for n in molList.name: name = n + ',' name = name[:-1] molList.setStringRepr(name) strRpr = name + ':::' molList.allAtoms.setStringRepr(strRpr) return molList
def parse( self, objClass=Protein ): if self.allLines is None and self.filename: self.readFile() if self.allLines is None or len(self.allLines)==0: return mol = Protein() self.mol = mol molList = mol.setClass() molList.append( mol ) current_residue_number = None current_chain = None current_residue = None number_of_atoms = int(self.allLines[1][:5]) self.configureProgressBar( init=1, mode='increment', authtext='parse atoms', max=number_of_atoms ) current_chain = Chain( id='GRO',) #FIX this: The existence of allAtoms attribute (and the fact that it is an empty set rather than all atoms in the chain) causes getNodesByMolecule() to return wrong values if hasattr(current_chain, "allAtoms"): del(current_chain.allAtoms) #current_chain = Chain( id='GRO',parent = mol) mol.adopt( current_chain, setChildrenTop=1 ) for index in range( 2,number_of_atoms+2 ): residue_number = int(self.allLines[index][:5]) if residue_number!=current_residue_number:# #current_chain should adopt the current residue if there is one #create new residue res_type = self.allLines[index][5:10] residue_type = res_type.split(' ')[0] 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 ) n = self.allLines[index][10:15] name = n.split(' ')[-1] element = name if element in babel_elements.keys(): element = element else: if residue_type == "System" or residue_type == "SOL": #if element[1] == 'W': # element = 'H' # group is treated as one particle #else: element = element[0] elif element[:2] == 'Me': element = 'C' else: element = element[0] #if len(element)>1: # if type(element[1]) == types.StringType: # # if element[1] == element[1].lower(): # element =element # else: # element = element[0] # # else: # element = element[0] atom = Atom( name, current_residue, element, top=mol ) c = self.allLines[index][15:20] cx = self.allLines[index][20:28] cy = self.allLines[index][28:36] cz = self.allLines[index][36:44] x = float(cx)*10 y = float(cy)*10 z = float(cz)*10 atom._coords = [[x, y, z]] atom._charges = [] atom.segID = mol.name atom.normalname = name atom.number = int(self.allLines[index][15:20]) atom.elementType = name[0] mol.atmNum[atom.number] = atom atom.altname = None atom.hetatm = 0 mol.name = os.path.split(os.path.splitext(self.filename)[0])[-1] 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 ) 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
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): if self.allLines is None and self.filename: self.readFile() if self.allLines is None or len(self.allLines) == 0: return mol = Protein() self.mol = mol molList = mol.setClass() molList.append(mol) current_residue_number = None current_chain = None current_residue = None number_of_atoms = int(self.allLines[1][:5]) self.configureProgressBar(init=1, mode='increment', authtext='parse atoms', max=number_of_atoms) current_chain = Chain(id='GRO', ) # FIX this: The existence of allAtoms attribute (and the fact that it is an empty set rather than all atoms in # the chain) causes getNodesByMolecule() to return wrong values if hasattr(current_chain, "allAtoms"): del current_chain.allAtoms # current_chain = Chain( id='GRO',parent = mol) mol.adopt(current_chain, setChildrenTop=1) for index in range(2, number_of_atoms + 2): residue_number = int(self.allLines[index][:5]) if residue_number != current_residue_number: # # current_chain should adopt the current residue if there is one # create new residue res_type = self.allLines[index][5:10] residue_type = res_type.split(' ')[0] 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) n = self.allLines[index][10:15] name = n.split(' ')[-1] element = name if element in list(babel_elements.keys()): element = element else: if residue_type == "System" or residue_type == "SOL": # if element[1] == 'W': # element = 'H' # group is treated as one particle # else: element = element[0] elif element[:2] == 'Me': element = 'C' else: element = element[0] # if len(element)>1: # if type(element[1]) == types.StringType: # # if element[1] == element[1].lower(): # element =element # else: # element = element[0] # # else: # element = element[0] atom = Atom(name, current_residue, element, top=mol) c = self.allLines[index][15:20] cx = self.allLines[index][20:28] cy = self.allLines[index][28:36] cz = self.allLines[index][36:44] x = float(cx) * 10 y = float(cy) * 10 z = float(cz) * 10 atom._coords = [[x, y, z]] atom._charges = [] atom.segID = mol.name atom.normalname = name atom.number = int(self.allLines[index][15:20]) atom.elementType = name[0] mol.atmNum[atom.number] = atom atom.altname = None atom.hetatm = 0 mol.name = os.path.split(os.path.splitext(self.filename)[0])[-1] 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) return molList