def buildPdb(map_dict, npts, name='DlgBuilt', ctr=0, outputfile='results.pdb', scale=1.0): if debug: print "in buildPdb: tolerance=", tolerance name = 'DlgBuilt' mol = Protein(name=name) mol.curChain = Chain() mol.chains = ChainSet([mol.curChain]) mol.curRes = Residue() mol.curChain.adopt(mol.curRes) mol.allAtoms = AtomSet() mol.curRes.atoms = mol.allAtoms nzpts = nypts = nxpts = npts #nxpts, nypts, nzpts = npts ctr = 0 for ADtype, m in map_dict.items(): if debug: print "PROCESSING ", ADtype, " array:", max(m.ravel()), ':', min( m.ravel()) vals = [] tctr = 0 #for number of each type for z in range(nzpts): for y in range(nypts): for x in range(nxpts): val = scale * abs(m[x, y, z]) vals.append(val) #if abs(val)>.005: if val > tolerance * scale: ctr += 1 name = ADtype + str(ctr) #version3: #info_lo = (xcen - numxcells*spacing, # ycen - numycells*spacing, # zcen - numzcells *spacing) #using lower back pt of cube, i think #xcoord = (x-info_lo[0])/spacing #ycoord = (y-info_lo[1])/spacing #zcoord = (z-info_lo[2])/spacing #version2: xcoord = (x - numxcells) * spacing + xcen ycoord = (y - numycells) * spacing + ycen zcoord = (z - numzcells) * spacing + zcen coords = (xcoord, ycoord, zcoord) tctr += 1 # #print "addAtom: name=",name,"ADtype=", ADtype," val=", val, "coords=", coords,"ctr=", ctr addAtom(mol, name, ADtype, val, coords, ctr) print "added ", tctr, '<-', ADtype, " atoms" if debug: print ADtype, ':', tctr, ' ', ctr print "total atoms=", ctr writer = PdbWriter() writer.write(outputfile, mol.allAtoms, records=['ATOM'])
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): """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 makeMoleculeFromAtoms(molname, atomSet): """ create a new molecule from a list of atoms mol <- makeMoleculeFromAtoms(molname, atomSet) """ from MolKit.molecule import Atom, AtomSet from MolKit.protein import Protein, Chain, Residue # create the top object mol = Protein(name=molname) # find out all residues residues = atomSet.parent.uniq() # find out all chains chains = residues.parent.uniq() # create all chains chainsd = {} for c in chains: newchain = Chain(c.id, mol, top=mol) chainsd[c] = newchain # create all residues resd = {} for res in residues: newres = Residue(res.name[:3], res.name[3:], res.icode, chainsd[res.parent], top=mol) resd[res] = newres newres.hasCA = 0 newres.hasO = 0 # create all the atoms newats = [] for num, at in enumerate(atomSet): name = at.name res = resd[at.parent] name1 = name if hasattr(at, "altname") and at.altname != None: name = at.name.split("@")[0] if name == 'CA': res.hasCA = 1 if name == 'O' or name == 'OXT' or (len(name) > 3 and name[:3] == 'OCT'): res.hasO = 2 newat = Atom(name, res, at.element, top=mol) if name != name1: newat.name = name1 newat.altname = at.altname newats.append(newat) # set constructotr attributes newat._coords = [] for coords in at._coords: newat._coords.append(coords[:]) newat.conformation = at.conformation newat.chemElem = at.chemElem newat.atomicNumber = at.atomicNumber newat.bondOrderRadius = at.bondOrderRadius newat.covalentRadius = at.covalentRadius newat.vdwRadius = at.vdwRadius newat.maxBonds = at.maxBonds newat.organic = at.organic newat.colors = at.colors.copy() newat.opacities = at.opacities.copy() newat._charges = at._charges.copy() newat.chargeSet = at.chargeSet # set attributes from PDB parser try: # pdbqs do not have this newat.segID = at.segID except AttributeError: pass newat.hetatm = at.hetatm try: # pdbqs do not have this newat.normalname = at.normalname except AttributeError: pass newat.number = num #at.number newat.occupancy = at.occupancy newat.temperatureFactor = at.temperatureFactor newat.altname = at.altname # attribute created by PQR parser if hasattr(at, 'pqrRadius'): newat.pqrRadius = at.pqrRadius # attribute created by F2D parser if hasattr(at, 'hbstatus'): newat.hbstatus = at.hbstatus # attribute created by PDBQ parser if hasattr(at, 'autodock_element'): newat.autodock_element = at.autodock_element # attribute created by PDBQT parser #if hasattr(at, ''): # newat. = at. # attribute created by PDBQS parser if hasattr(at, 'AtVol'): newat.AtVol = at.AtVol newat.AtSolPar = at.AtSolPar mol.allAtoms = AtomSet(newats) return mol
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
def build4LevelsTree(self, subst_chain, atomlines): """ Function to build a 4 level hierarchy Protein-Chain-Residue-Atom. """ self.mol = Protein() self.mol.allAtoms = AtomSet() self.mol.atmNum = {} self.mol.parser = self if self.mol.name == 'NoName': self.mol.name = os.path.basename( os.path.splitext(self.filename)[0]) self.mol.curChain = Chain() self.mol.curRes = Residue() self.mol.levels = [Protein, Chain, Residue, Atom] i = 1 for atmline in atomlines: if len(atmline) >= 10: status = string.split(atmline[9], '|') else: status = None if len(atmline) == 8: tmp = [atmline[5][:5], atmline[5][5:]] atmline[5] = tmp[0] atmline.insert(6, tmp[1]) if status and status[0] == 'WATER': chainID = 'W' atmline[7] = 'HOH' + str(i) subst_chain[atmline[7]] = chainID i = i + 1 if subst_chain == {}: chainID = 'default' elif not subst_chain.has_key(atmline[7]): if subst_chain.has_key('****'): try: chainID = subst_chain[atmline[7]] except: chainID = 'default' else: chainID = 'default' elif type(subst_chain[atmline[7]]) is types.StringType: # that is to say that only chains has this substructure name. chainID = subst_chain[atmline[7]] elif type(subst_chain[atmline[7]]) is types.ListType: # That is to say that several chains have the same substructure. chainID = subst_chain[atmline[7]][0] subst_chain[atmline[7]] = subst_chain[atmline[7]].remove( chainID) if chainID != self.mol.curChain.id: if not self.mol.chains.id or not chainID in self.mol.chains.id: self.mol.curChain = Chain(chainID, self.mol, top=self.mol) else: self.mol.curChain = self.mol.chains.get(chainID)[0] if len(atmline) < 7: # test if the atmline has a res name and resseq: resName = 'RES' resSeq = '1' else: resName = atmline[7][:3] resSeq = atmline[7][3:] if resSeq != self.mol.curRes.number or \ resName != self.mol.curRes.type: # check if this residue already exists na = string.strip(resName) + string.strip(resSeq) res = self.mol.curChain.get(na) if res: self.mol.curRes = res[0] else: self.mol.curRes = Residue(resName, resSeq, '', self.mol.curChain, top=self.mol) name = atmline[1] if name == 'CA': self.mol.curRes.hasCA = 1 if name == 'O': self.mol.curRes.hasO = 2 atom = Atom(name, self.mol.curRes, top=self.mol, chemicalElement=string.split(atmline[5], '.')[0]) #atom.element = atmline[5][0] atom.element = atom.chemElem atom.number = int(atmline[0]) self.mol.atmNum[atom.number] = atom atom._coords = [[ float(atmline[2]), float(atmline[3]), float(atmline[4]) ]] if len(atmline) >= 9: atom._charges['mol2'] = float(atmline[8]) atom.chargeSet = 'mol2' # atom.conformation = 0 atom.hetatm = 0 #Add a data member containing a list of string describing # the Sybyl status bis of the atoms. atom.status = status #add altname so buildBondsByDist doesn't croak atom.altname = None self.mol.allAtoms.append(atom) delattr(self.mol, 'curRes') delattr(self.mol, 'curChain')
def build3LevelsTree(self, atomlines): """ Function to build a 3 levels hierarchy Molecule-substructure-atoms.""" self.mol = Protein() self.mol.allAtoms = AtomSet() self.mol.atmNum = {} self.mol.parser = self if self.mol.name == 'NoName': self.mol.name = os.path.basename( os.path.splitext(self.filename)[0]) self.mol.children = ResidueSet([]) self.mol.childrenName = 'residues' self.mol.childrenSetClass = ResidueSet self.mol.elementType = Residue self.mol.curRes = Residue() self.mol.curRes.hasCA = 0 self.mol.curRes.hasO = 0 self.mol.levels = [Protein, Residue, Atom] for atmline in atomlines: if len(atmline) >= 10: status = string.split(atmline[9], '|') else: status = None resName = atmline[7][:3] resSeq = atmline[7][3:] if resSeq != self.mol.curRes.number or \ resName != self.mol.curRes.type: # check if this residue already exists na = string.strip(resName) + string.strip(resSeq) res = self.mol.get(na) if res: self.mol.curRes = res[0] else: self.mol.curRes = Residue(resName, resSeq, '', self.mol, top=self.mol) name = atmline[1] if name == 'CA': self.mol.curRes.hasCA = 1 if name == 'O': self.mol.curRes.hasO = 2 atom = Atom(name, self.mol.curRes, top=self.mol, chemicalElement=string.split(atmline[5], '.')[0]) #atom.element = atmline[5][0] atom.element = atom.chemElem atom.number = int(atmline[0]) self.mol.atmNum[atom.number] = atom atom._coords = [[ float(atmline[2]), float(atmline[3]), float(atmline[4]) ]] atom._charges['mol2'] = float(atmline[8]) atom.chargeSet = mol2 # atom.conformation = 0 atom.hetatm = 0 #Add a data member containing a list of string describing # the Sybyl status bis of the atoms. atom.status = status #add altname so buildBondsByDist doesn't croak atom.altname = None self.mol.allAtoms.append(atom) self.mol.residues = self.mol.children assert hasattr(self.mol, 'chains') delattr(self.mol, 'chains') delattr(self.mol, 'curRes')
class FloodPlayer(Player): def __init__(self, command, file): master = command.vf.GUI.ROOT self.autoLigandCommand = command.vf.AutoLigandCommand self.autoLigandCommand.spheres.Set(visible=1) self.autoLigandCommand.halo.Set(visible=1) pkl_file = open(file, 'rb') self.floods = [] try: data = cPickle.load(pkl_file) except Exception, inst: print "Error loading ", __file__, "\n", inst self.xcent = data[0] self.ycent = data[1] self.zcent = data[2] self.centerx = data[3] self.centery = data[4] self.centerz = data[5] self.spacing = data[6] self.centers = [] data = cPickle.load(pkl_file) self.floods.append(data[1]) try: while data: data = cPickle.load(pkl_file) flood = copy.copy(self.floods[-1]) for item in data[0]: flood.remove(item) for item in data[1]: flood.append(item) self.floods.append(flood) except EOFError: pass pkl_file.close() fileName = os.path.splitext(os.path.split(file)[-1])[0] self.mol = Protein(fileName) self.mol.allAtoms = AtomSet([]) chain = Chain() self.residue = Residue(type="UNK") chain.adopt(self.residue, setChildrenTop=1) self.mol.adopt(chain, setChildrenTop=1) self.mol.parser = None self.filename = file fl = self.floods[0][0] x = (fl[1] - self.xcent) * self.spacing + self.centerx y = (fl[2] - self.ycent) * self.spacing + self.centery z = (fl[3] - self.zcent) * self.spacing + self.centerz if fl[4] == 7: atomchr = 'P' # note, this will color the NA atom pink (the PDB color for Phosphorus) radius = AAradii[13][0] if fl[4] == 6: atomchr = 'S' radius = AAradii[13][0] if fl[4] == 5: atomchr = 'A' radius = AAradii[10][0] if fl[4] == 4: atomchr = 'O' radius = AAradii[1][0] if fl[4] == 3: atomchr = 'N' radius = AAradii[4][0] if fl[4] == 2: atomchr = 'C' radius = AAradii[10][0] if fl[4] == 1: atomchr = 'H' radius = AAradii[15][0] a = Atom(atomchr, self.residue, atomchr, top=self.mol) a._coords = [[x, y, z]] a._charges = {} a.hetatm = 1 a.number = 0 a.radius = radius self.mol.allAtoms = self.residue.atoms self.mol = self.autoLigandCommand.vf.addMolecule(self.mol, False) self.mol.levels = [Protein, Chain, Residue, Atom] self.autoLigandCommand.vf.displayCPK(self.mol, scaleFactor=0.4) self.autoLigandCommand.vf.colorByAtomType(self.mol, ['cpk'], log=0) self.autoLigandCommand.vf.displayLines(self.mol, negate=True, displayBO=False, lineWidth=2, log=0, only=False) self.colorKeys = a.colors.keys() maxLen = len(self.floods) - 1 Player.__init__(self, master=master, endFrame=maxLen, maxFrame=maxLen, titleStr="AutoLigand Flood Player", hasSlider=True) try: # withdrew SetAnim button self.form.ifd.entryByName['setanimB']['widget'].grid_forget() self.form.autoSize() except: pass self.nextFrame(0) self.form.root.protocol('WM_DELETE_WINDOW', self.hide_cb)
#5/19: rec = rec + ' %-2.2s' % atm.autodock_element #rec = rec + ' %-2.2s'%atm.autodock_element.upper() ## #NB: write 'A' in element slot for aromatic carbons ## if atm.autodock_element=='A': ## #in this case, columns 78+79 are blanks ## rec = rec + 'A ' ## else: ## #rec = rec + '%2.2s'%atm.element ## #5/19: ## #columns 78+79: autodock_element ## rec = rec + '%s '%atm.autodock_element ## #if atm.element!=atm.autodock_element: ## # #eg HD or NA or SA or OA, always 2 chars ## # rec = rec + '%s '%atm.autodock_element[1] ## #else: ## # rec = rec + ' ' rec = rec + '\n' return rec if __name__ == '__main__': from MolKit.protein import Protein from MolKit.pdbParser import PdbParser mol = Protein() mol.read('/tsri/pdb/struct/4tpi.pdb', PdbParser()) writer = PdbWriter() writer.add_userRecord('REMARK', ) writer.add_userRecord('TITLE ', [('', 'This is the title record\n')]) writer.write('/home/ktchan/jumble.pdb', mol)