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_PDB_ATOM_record(self, rec): """Parse PDB ATOM records using the pdb columns specifications""" self.atomCounter = self.atomCounter + 1 # not sure about altLoc if self.specType == 'i': rec = rec.split() # Handle the alternate location using a flag. altLoc = self.get_Field_Value(rec, 'altLoc') if altLoc != ' ': self.altLoc = altLoc else: self.altLoc = '' # changed from None to '' # check for chains break # self.modlflag = modlflag # chainID = rec[21]+ modlflag hascid = 1 chainID = self.get_Field_Value(rec, 'chainID') if not chainID: hascid = 0 chainID = str(self.chaincounter) ## should be unk??? if chainID != self.mol.curChain.id: # has to check if the chain exists already or not !!! if not self.mol.chains.id or chainID not in self.mol.chains.id or hascid == 0: self.chaincounter = self.chaincounter + 1 if hascid == 0: chainID = str(self.chaincounter) self.mol.curChain = Chain(chainID, self.mol, top=self.mol) self.residueCounter = 0 else: self.mol.curChain = self.mol.chains.get(chainID)[0] # check for residue break resName = self.get_Field_Value(rec, 'resName') resSeq = self.get_Field_Value(rec, 'resSeq').strip() # WARNING reSeq is a STRING noresSeq = 0 if not resSeq and resName == self.mol.curRes.type and resName != 'HOH': noresSeq = 1 resSeq = self.mol.curRes.number if resSeq != self.mol.curRes.number or \ resName != self.mol.curRes.type: # check if this residue already exists na = resName.strip() + resSeq.strip() res = self.mol.curChain.get(na) if res: self.mol.curRes = res[0] else: self.residueCounter = self.residueCounter + 1 if resName == 'HOH': self.HOHCounter = self.HOHCounter + 1 if not resSeq: if resName == 'HOH': resSeq = self.HOHCounter else: resSeq = self.residueCounter ## FIXME icodes are ignored self.mol.curRes = Residue(resName, resSeq, '', self.mol.curChain, top=self.mol) icode = self.get_Field_Value(rec, 'iCode') if not icode: pass elif icode != ' ': self.mol.curRes.icode = icode # parse atom info # handle atom names (calcium, hydrogen) and find element type # check validity of chemical element column and charge column ## only works if 'name' is in the pdb format! FIX! n = self.get_Field_Value(rec, 'name') el = self.get_Field_Value(rec, 'element') if n: name, element = self.getPDBAtomName(n, el) # if there is not resSeq spec, use first N to figure out new res if noresSeq and name == 'N': At = self.mol.curRes.get('N') if At: self.residueCounter = self.residueCounter + 1 resSeq = self.residueCounter self.mol.curRes = Residue(resName, resSeq, self.mol.curChain, top=self.mol) atom = Atom(name, self.mol.curRes, element, top=self.mol) else: element = el if element: atom = Atom(parent=self.mol.curRes, chemicalElement=element, top=self.mol) else: atom = Atom(parent=self.mol.curRes, top=self.mol) ## elem = string.lower(element) # moved to getPDBAtomName ## if elem =='lp' or elem =='ld': ## element = 'Xx' atom.charge = self.get_Field_Value(rec, 'charge') # should have atom.charge if no charge? # coords are required; where to set default or check? xcoord = self.get_Field_Value(rec, 'x') ycoord = self.get_Field_Value(rec, 'y') zcoord = self.get_Field_Value(rec, 'z') assert xcoord and ycoord and zcoord atom._coords = [[float(xcoord), float(ycoord), float(zcoord)]] atom.segID = self.get_Field_Value(rec, 'segID').strip() if rec[:4] == 'ATOM' or rec[0] == 'ATOM': atom.hetatm = 0 else: atom.hetatm = 1 # atom.alternate = [] atom.element = element num = self.get_Field_Value(rec, 'serial') if num: atom.number = int(num) else: atom.number = self.atomCounter occupancy = self.get_Field_Value(rec, 'occupancy') if occupancy: atom.occupancy = float(occupancy) # must check that it is a number atom.conformation = 0 tempFactor = self.get_Field_Value(rec, 'tempFactor') if tempFactor: atom.temperatureFactor = float(tempFactor) # add in user defined fields to atom attributes for field_name in list(self.recSpecs.UserFieldsDict.keys()): value = self.get_Field_Value(rec, field_name) type = self.recSpecs.get(field_name, 'var_type') if value: if type == 'int': atom.__setattr__(field_name, int(value)) elif type == 'float': atom.__setattr__(field_name, float(value)) else: atom.__setattr__(field_name, value) else: atom.__setattr__(field_name, value) if self.altLoc: # check if the name of the atom is the same than the # name of the previous atom . name = name + '@' + self.altLoc atom.name = name if len(self.mol.curRes.atoms) > 1: # the new atom has been add to the current residue # You have to go to the one before. lastAtom = self.mol.curRes.atoms[-2] altname = lastAtom.name.split('@')[0] if name.split('@')[0] == altname: # Add the new alternate atom to the LastAtom.alternate and # add the lastAtom to the atom.alternate. lastAtom.alternate.append(atom) atom.alternate.append(lastAtom) for l in lastAtom.alternate: if atom.name != l.name: atom.alternate.append(l) l.alternate.append(atom) return atom
def parse_PDB_ATOM_record(self, rec): """Parse PDB ATOM records using the pdb columns specifications""" self.atomCounter = self.atomCounter + 1 # not sure about altLoc if self.specType=='i': rec = string.split(rec) # Handle the alternate location using a flag. altLoc = self.get_Field_Value(rec, 'altLoc') if altLoc!= ' ': self.altLoc = altLoc else: self.altLoc = '' # changed from None to '' # check for chains break #self.modlflag = modlflag #chainID = rec[21]+ modlflag hascid = 1 chainID = self.get_Field_Value(rec, 'chainID') if not chainID: hascid = 0 chainID = str(self.chaincounter) ## should be unk??? if chainID != self.mol.curChain.id : # has to check if the chain exists already or not !!! if not self.mol.chains.id or not chainID in self.mol.chains.id or \ hascid==0: self.chaincounter = self.chaincounter + 1 if hascid==0: chainID = str(self.chaincounter) self.mol.curChain = Chain(chainID, self.mol, top=self.mol) self.residueCounter = 0 else: self.mol.curChain = self.mol.chains.get(chainID)[0] # check for residue break resName = self.get_Field_Value(rec, 'resName') resSeq = string.strip(self.get_Field_Value(rec, 'resSeq')) #WARNING reSeq is a STRING noresSeq = 0 if not resSeq and resName==self.mol.curRes.type and resName!='HOH': noresSeq = 1 resSeq = self.mol.curRes.number 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.residueCounter = self.residueCounter + 1 if resName=='HOH': self.HOHCounter = self.HOHCounter + 1 if not resSeq: if resName=='HOH': resSeq = self.HOHCounter else: resSeq = self.residueCounter ## FIXME icodes are ignored self.mol.curRes = Residue(resName, resSeq, '', self.mol.curChain, top=self.mol) icode = self.get_Field_Value(rec, 'iCode') if not icode: pass elif icode != ' ': self.mol.curRes.icode = icode # parse atom info # handle atom names (calcium, hydrogen) and find element type # check validity of chemical element column and charge column ## only works if 'name' is in the pdb format! FIX! n = self.get_Field_Value(rec, 'name') el = self.get_Field_Value(rec, 'element') if n: name, element = self.getPDBAtomName(n, el) # if there is not resSeq spec, use first N to figure out new res if noresSeq and name=='N': At = self.mol.curRes.get('N') if At: self.residueCounter = self.residueCounter + 1 resSeq = self.residueCounter self.mol.curRes = Residue(resName, resSeq, self.mol.curChain, top=self.mol) atom = Atom(name, self.mol.curRes, element, top=self.mol) else: element = el if element: atom = Atom(parent = self.mol.curRes, chemicalElement = element, top=self.mol) else: atom = Atom(parent = self.mol.curRes, top=self.mol) ## elem = string.lower(element) # moved to getPDBAtomName ## if elem =='lp' or elem =='ld': ## element = 'Xx' atom.charge = self.get_Field_Value(rec, 'charge') #should have atom.charge if no charge? # coords are required; where to set default or check? xcoord = self.get_Field_Value(rec, 'x') ycoord = self.get_Field_Value(rec, 'y') zcoord = self.get_Field_Value(rec, 'z') assert xcoord and ycoord and zcoord atom._coords = [ [ float(xcoord), float(ycoord), float(zcoord) ] ] atom.segID = string.strip(self.get_Field_Value(rec, 'segID')) if rec[:4]=='ATOM' or rec[0]=='ATOM': atom.hetatm = 0 else: atom.hetatm = 1 #atom.alternate = [] atom.element = element num = self.get_Field_Value(rec, 'serial') if num: atom.number = int(num) else: atom.number = self.atomCounter occupancy = self.get_Field_Value(rec, 'occupancy') if occupancy: atom.occupancy = float(occupancy) # must check that it is a number atom.conformation = 0 tempFactor = self.get_Field_Value(rec, 'tempFactor') if tempFactor: atom.temperatureFactor = float(tempFactor) # add in user defined fields to atom attributes for field_name in self.recSpecs.UserFieldsDict.keys(): value = self.get_Field_Value(rec, field_name) type = self.recSpecs.get(field_name, 'var_type') if value: if type=='int': atom.__setattr__(field_name, int(value)) elif type=='float': atom.__setattr__(field_name, float(value)) else: atom.__setattr__(field_name, value) else: atom.__setattr__(field_name, value) if self.altLoc : # check if the name of the atom is the same than the #name of the previous atom . name = name + '@'+self.altLoc atom.name = name if len(self.mol.curRes.atoms)>1: # the new atom has been add to the current residue # You have to go to the one before. lastAtom = self.mol.curRes.atoms[-2] altname = string.split(lastAtom.name, '@')[0] if string.split(name, '@')[0] == altname: # Add the new alternate atom to the LastAtom.alternate and # add the lastAtom to the atom.alternate. lastAtom.alternate.append(atom) atom.alternate.append(lastAtom) for l in lastAtom.alternate: if atom.name != l.name: atom.alternate.append(l) l.alternate.append(atom) return atom
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