def addAtom(mol, name, ADtype, value, coords, ctr):
    #if debug: print "in addAtom", value,
    res = mol.chains.residues[0]
    chemicalElement = ADtype[0] #???
    childIndex = ctr - 1
    top = mol
    newAt = Atom(name=name, parent=res, top=mol, 
                    chemicalElement=chemicalElement, 
                    childIndex=childIndex)
    newAt.temperatureFactor = value
    newAt.occupancy = value
    newAt.number = ctr
    newAt.conformation = 0
    newAt._coords = [list(coords)]
    newAt.hetatm = 0
    #if debug: print "added ", name, ctr, ':', newAt.full_name(),'-', newAt.parent.children.index(newAt)
    #update allAtoms attribute of this molecule
    mol.allAtoms = mol.chains.residues.atoms
def addAtom(mol, name, ADtype, value, coords, ctr):
    #if debug: print "in addAtom", value,
    res = mol.chains.residues[0]
    chemicalElement = ADtype[0]  #???
    childIndex = ctr - 1
    top = mol
    newAt = Atom(name=name,
                 parent=res,
                 top=mol,
                 chemicalElement=chemicalElement,
                 childIndex=childIndex)
    newAt.temperatureFactor = value
    newAt.occupancy = value
    newAt.number = ctr
    newAt.conformation = 0
    newAt._coords = [list(coords)]
    newAt.hetatm = 0
    #if debug: print "added ", name, ctr, ':', newAt.full_name(),'-', newAt.parent.children.index(newAt)
    #update allAtoms attribute of this molecule
    mol.allAtoms = mol.chains.residues.atoms
Example #3
0
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]
        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)
        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
        newat.segID = at.segID
        newat.hetatm = at.hetatm
        newat.normalname = at.normalname
        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
Example #4
0
    def addHydrogens(self, mol):
        #check for bonds
        if len(mol.allAtoms.bonds[0]) == 0:
            mol.buildBondsByDistance()
        bonds = mol.allAtoms.bonds[0]
        #could have preset babel_types
        #so check if allAtoms are already typed
        try:
            t = mol.allAtoms.babel_type
        except:
            #if all are not pretyped, type them
            babel = AtomHybridization()
            babel.assignHybridization(mol.allAtoms)

        if self.method == 'withBondOrder':
            mol.rings = RingFinder()
            mol.rings.findRings2(mol.allAtoms, mol.allAtoms.bonds[0])
            mol.rings.bondRings = {}
            for ind in xrange(len(mol.rings.rings)):
                r = mol.rings.rings[ind]
                for b in r['bonds']:
                    if not mol.rings.bondRings.has_key(b):
                        mol.rings.bondRings[b] = [
                            ind,
                        ]
                    else:
                        mol.rings.bondRings[b].append(ind)
            bo = BondOrder()
            bo.assignBondOrder(mol.allAtoms, bonds, mol.rings)
            mol.allAtoms._bndtyped = 1
            # do aromatic here
            arom = Aromatic(mol.rings)
            arom.find_aromatic_atoms(mol.allAtoms)

        hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method)
        bondedAtomDict = {}  # key is heavy atom
        for a in hat:
            if bondedAtomDict.has_key(a[1]):
                bondedAtomDict[a[1]].append(a)
            else:
                bondedAtomDict[a[1]] = [a]

        # now create Atom object for hydrogens
        # and add the to the residues's atom list
        molNewHs = AtomSet([])  # list of created H atoms for this molecule
        heavyAtoms = AtomSet([])  # list of atoms that need new radii

        for heavyAtom, HatmsDscr in bondedAtomDict.items():
            #don't add hydrogens to carbons: polar Only!!!
            if self.htype != 'all' and heavyAtom.element == 'C':
                continue
            res = heavyAtom.parent
            # find where to insert H atom
            childIndex = res.children.index(heavyAtom) + 1

            # loop over H atoms description to be added
            # start at the end to number correctly
            l = len(HatmsDscr)
            for i in range(l - 1, -1, -1):
                a = HatmsDscr[i]
                # build H atom's name
                if len(heavyAtom.name) == 1:
                    name = 'H' + heavyAtom.name
                else:
                    name = 'H' + heavyAtom.name[1:]

                # if more than 1 H atom, add H atom index
                # for instance HD11, HD12, Hd13 (index is 1,2,3)
                if l > 1:
                    name = name + str(i + 1)

                # create the H atom object
                atom = Atom(name,
                            res,
                            top=heavyAtom.top,
                            chemicalElement='H',
                            childIndex=childIndex,
                            assignUniqIndex=0)

                # set atoms attributes
                atom._coords = [a[0]]
                if hasattr(a[1], 'segID'): atom.segID = a[1].segID
                atom.hetatm = 0
                atom.alternate = []
                #atom.element = 'H'
                atom.occupancy = 1.0
                atom.conformation = 0
                atom.temperatureFactor = 0.0
                atom.babel_atomic_number = a[2]
                atom.babel_type = a[3]
                atom.babel_organic = 1
                atom.radius = 1.2

                # create the Bond object bonding Hatom to heavyAtom
                bond = Bond(a[1], atom, bondOrder=1)

                # add the created atom the the list
                molNewHs.append(atom)
                # in case this new hydrogen atom ever ends up in pmv
                # HAVE TO CREATE THESE ENTRIES
                # create the color entries for all geoemtries
                # available for the heavyAtom
                for key, value in heavyAtom.colors.items():
                    atom.colors[key] = (0.0, 1.0, 1.0)
                    atom.opacities[key] = 1.0

        mol.allAtoms = mol.chains.residues.atoms
        if self.renumber:
            mol.allAtoms.number = range(1, len(mol.allAtoms) + 1)
        return len(molNewHs)
Example #5
0
    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
Example #6
0
    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 add_oxt(self, catom):
        if catom.element != 'C':
            return
        mol = catom.top
        ##check for bonds
        #if len(mol.allAtoms.bonds[0])==0:
        #    mol.buildBondsByDistance()
        #check whether residue already has OXT
        res = catom.parent
        if 'OXT' in res.atoms.name:
            print('not adding OXT to ', res.full_name(), '\n',
                  'it already has an OXT atom')
            return
        #check whether catom has a hydrogen to delete
        hatoms = catom.parent.atoms.get(lambda x: x.name == 'HC')
        if len(hatoms):
            hatom = hatoms[0]
            #check for hbonds
            if hasattr(hatom, 'hbonds'):
                #remove hbonds
                for b in hatom.hbonds:
                    atList = [b.donAt, b.accAt]
                    if b.hAt is not None:
                        atList.append(b.hAt)
                    for at in atList:
                        #hbonds might already be gone
                        if not hasattr(at, 'hbonds'):
                            continue
                        okhbnds = []
                        for hb in at.hbonds:
                            if hb != b:
                                okhbnds.append(hb)
                        if len(okhbnds):
                            at.hbonds = okhbnds
                        else:
                            delattr(at, 'hbonds')
            #remove covalent bonds
            for b in hatom.bonds:
                at2 = b.atom1
                if at2 == hatom: at2 = b.atom2
                at2.bonds.remove(b)
            hatom.parent.remove(hatom, cleanup=1)

        #have to type atoms before call to add_sp2_hydrogen:
        if not hasattr(catom, 'babel_type'):
            print('catom has no babel_type: calling typeAtoms')
            #self.warningMsg(msg)
            #typeAtoms does whole molecule
            babel = AtomHybridization()
            babel.assignHybridization(mol.allAtoms)

        #NB: bond_length 1.28 measured from OXT-C bond in 1crn
        tup1 = self.addh.add_sp2_hydrogen(catom, 1.28)
        res = catom.parent

        # find where to insert H atom
        childIndex = res.children.index(catom) + 1
        name = 'OXT'

        # create the OXT atom object
        atom = Atom(name,
                    res,
                    top=mol,
                    childIndex=childIndex,
                    assignUniqIndex=0)

        # set atoms attributes
        atom._coords = [tup1[0][0]]
        if hasattr(catom, 'segID'): atom.segID = catom.segID
        atom.hetatm = 0
        atom.alternate = []
        atom.element = 'O'
        atom.occupancy = 1.0
        atom.conformation = 0
        atom.temperatureFactor = 0.0
        atom.babel_atomic_number = 8
        atom.babel_type = 'O-'
        atom.babel_organic = 1

        # create the Bond object bonding Hatom to heavyAtom
        bond = Bond(catom, atom, bondOrder=2)

        # create the color entries for all geometries
        # available for the other oxygen atom attached to 'C'
        oatom = res.atoms.get(lambda x: x.name == 'O')[0]
        if oatom is not None:
            for key, value in list(oatom.colors.items()):
                atom.colors[key] = value
                #atom.opacities[key] = oatom.opacities[key]

                # update the allAtoms set in the molecule
        mol.allAtoms = mol.chains.residues.atoms

        # update numbers of allAtoms
        fst = mol.allAtoms[0].number
        mol.allAtoms.number = list(range(fst, len(mol.allAtoms) + fst))

        # update _uniqIndex of this residues atoms
        res.assignUniqIndex()
        #return AtomSet([atom])
        return atom
Example #8
0
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
Example #9
0
    print "done"
    ##      db = filter(lambda x:x.bondOrder==2, bonds)
    ##      for b in db:
    ##          print b

    addh = AddHydrogens()
    #pdb.run("hat = addh.addHydrogens(allAtoms)")
    hat = addh.addHydrogens(allAtoms)

    from MolKit.molecule import Atom, Bond
    for a in hat:
        atom = Atom('H', a[1].parent, top=a[1].top)
        atom._coords = [a[0]]
        atom.segID = a[1].segID
        atom.hetatm = 0
        atom.alternate = []
        atom.element = 'H'
        atom.number = -1
        atom.occupancy = 1.0
        atom.conformation = 0
        atom.temperatureFactor = 0.0
        atom.babel_atomic_number = a[2]
        atom.babel_type = a[3]
        atom.babel_organic = 1
        bond = Bond(a[1], atom)

    from Pmv.moleculeViewer import MoleculeViewer
    mv = MoleculeViewer()
    mv.addMolecule(mol)
    mv.lines(mol)
Example #10
0
    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
Example #11
0
    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 addHydrogens(self, mol):
        #check for bonds
        if len(mol.allAtoms.bonds[0])==0:
            mol.buildBondsByDistance()
        bonds = mol.allAtoms.bonds[0]
        #could have preset babel_types
        #so check if allAtoms are already typed
        try:
            t = mol.allAtoms.babel_type
        except:
            #if all are not pretyped, type them
            babel = AtomHybridization()
            babel.assignHybridization(mol.allAtoms)

        if self.method=='withBondOrder':
            mol.rings = RingFinder()
            mol.rings.findRings2(mol.allAtoms, mol.allAtoms.bonds[0])
            mol.rings.bondRings = {}
            for ind in xrange(len(mol.rings.rings)):
                r = mol.rings.rings[ind]
                for b in r['bonds']:
                    if not mol.rings.bondRings.has_key(b):
                        mol.rings.bondRings[b] = [ind,]
                    else:
                        mol.rings.bondRings[b].append(ind)
            bo = BondOrder()
            bo.assignBondOrder(mol.allAtoms, bonds, mol.rings)
            mol.allAtoms._bndtyped = 1
            # do aromatic here
            arom = Aromatic(mol.rings)
            arom.find_aromatic_atoms(mol.allAtoms)
            
        hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method)
        bondedAtomDict = {}  # key is heavy atom
        for a in hat:
            if bondedAtomDict.has_key(a[1]):
                bondedAtomDict[a[1]].append(a)
            else:
                bondedAtomDict[a[1]] = [a]

        # now create Atom object for hydrogens
        # and add the to the residues's atom list
        molNewHs = AtomSet([]) # list of created H atoms for this molecule
        heavyAtoms = AtomSet([]) # list of atoms that need new radii
        
        for heavyAtom, HatmsDscr in bondedAtomDict.items():
            #don't add hydrogens to carbons: polar Only!!!
            if self.htype!='all' and heavyAtom.element=='C': 
                continue
            res = heavyAtom.parent
            # find where to insert H atom
            childIndex = res.children.index(heavyAtom)+1

            # loop over H atoms description to be added
            # start at the end to number correctly
            l = len(HatmsDscr)
            for i in range(l-1,-1,-1):
                a = HatmsDscr[i]
                # build H atom's name
                if len(heavyAtom.name)==1:
                    name = 'H' + heavyAtom.name
                else:
                    name = 'H' + heavyAtom.name[1:]

                # if more than 1 H atom, add H atom index
                # for instance HD11, HD12, Hd13 (index is 1,2,3)
                if l > 1:
                    name = name + str(i+1)

                # create the H atom object
                atom = Atom(name, res, top=heavyAtom.top,
                            chemicalElement='H',
                            childIndex=childIndex, assignUniqIndex=0)

                # set atoms attributes
                atom._coords = [ a[0] ]
                if hasattr(a[1], 'segID'): atom.segID = a[1].segID
                atom.hetatm = 0
                atom.alternate = []
                #atom.element = 'H'
                atom.occupancy = 1.0
                atom.conformation = 0
                atom.temperatureFactor = 0.0
                atom.babel_atomic_number = a[2]
                atom.babel_type = a[3]
                atom.babel_organic = 1
                atom.radius = 1.2
                
                # create the Bond object bonding Hatom to heavyAtom
                bond = Bond( a[1], atom, bondOrder=1)

                # add the created atom the the list
                molNewHs.append(atom)
                # in case this new hydrogen atom ever ends up in pmv 
                # HAVE TO CREATE THESE ENTRIES 
                # create the color entries for all geoemtries
                # available for the heavyAtom
                for key, value in heavyAtom.colors.items():
                    atom.colors[key]=(0.0, 1.0, 1.0)
                    atom.opacities[key]=1.0

        mol.allAtoms = mol.chains.residues.atoms
        if self.renumber:
            mol.allAtoms.number = range(1, len(mol.allAtoms)+1)
        return len(molNewHs)
Example #13
0
    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
Example #14
0
    def add_oxt(self, catom):       
        if catom.element!='C':
            return
        mol = catom.top    
        ##check for bonds 
        #if len(mol.allAtoms.bonds[0])==0:
        #    mol.buildBondsByDistance()
        #check whether residue already has OXT
        res = catom.parent
        if 'OXT' in res.atoms.name:
            print 'not adding OXT to ',res.full_name(),'\n', 'it already has an OXT atom'
            return
        #check whether catom has a hydrogen to delete
        hatoms = catom.parent.atoms.get(lambda x: x.name=='HC')
        if len(hatoms):
            hatom = hatoms[0]
            #check for hbonds
            if hasattr(hatom, 'hbonds'):
                #remove hbonds
                for b in hatom.hbonds:
                    atList = [b.donAt, b.accAt]
                    if b.hAt is not None:
                        atList.append(b.hAt)
                    for at in atList:
                        #hbonds might already be gone
                        if not hasattr(at, 'hbonds'):
                            continue
                        okhbnds = []
                        for hb in at.hbonds:
                            if hb!=b:
                                okhbnds.append(hb)
                        if len(okhbnds):
                            at.hbonds = okhbnds
                        else:
                            delattr(at, 'hbonds')
            #remove covalent bonds                
            for b in hatom.bonds:
                at2 = b.atom1
                if at2 == hatom: at2 = b.atom2
                at2.bonds.remove(b)
            hatom.parent.remove(hatom, cleanup=1)

        #have to type atoms before call to add_sp2_hydrogen:
        if not hasattr(catom,'babel_type'):
            print 'catom has no babel_type: calling typeAtoms'
            #self.warningMsg(msg)
            #typeAtoms does whole molecule
            babel = AtomHybridization()
            babel.assignHybridization(mol.allAtoms)

        #NB: bond_length 1.28 measured from OXT-C bond in 1crn
        tup1 = self.addh.add_sp2_hydrogen(catom, 1.28)
        res = catom.parent

        # find where to insert H atom
        childIndex = res.children.index(catom)+1
        name = 'OXT'

        # create the OXT atom object
        atom = Atom(name, res, top=mol,
                    childIndex=childIndex, assignUniqIndex=0)

        # set atoms attributes
        atom._coords = [ tup1[0][0] ]
        if hasattr(catom, 'segID'): atom.segID = catom.segID
        atom.hetatm = 0
        atom.alternate = []
        atom.element = 'O'
        atom.occupancy = 1.0
        atom.conformation = 0
        atom.temperatureFactor = 0.0
        atom.babel_atomic_number = 8
        atom.babel_type = 'O-'
        atom.babel_organic = 1

        # create the Bond object bonding Hatom to heavyAtom
        bond = Bond( catom, atom, bondOrder=2)

        # create the color entries for all geometries
        # available for the other oxygen atom attached to 'C'
        oatom = res.atoms.get(lambda x: x.name=='O')[0]
        if oatom is not None:
            for key, value in oatom.colors.items():
                atom.colors[key] = value
                #atom.opacities[key] = oatom.opacities[key]
                
                # update the allAtoms set in the molecule
        mol.allAtoms = mol.chains.residues.atoms

        # update numbers of allAtoms
        fst = mol.allAtoms[0].number
        mol.allAtoms.number = range(fst, len(mol.allAtoms)+fst)

        # update _uniqIndex of this residues atoms
        res.assignUniqIndex()
        #return AtomSet([atom])
        return atom
Example #15
0
    print "done"
##      db = filter(lambda x:x.bondOrder==2, bonds)
##      for b in db:
##          print b
    
    addh = AddHydrogens()
    #pdb.run("hat = addh.addHydrogens(allAtoms)")
    hat = addh.addHydrogens(allAtoms)
    
    from MolKit.molecule import Atom, Bond
    for a in hat:
        atom = Atom('H', a[1].parent, top=a[1].top)
        atom._coords = [ a[0] ]
        atom.segID = a[1].segID
        atom.hetatm = 0
        atom.alternate = []
        atom.element = 'H'
        atom.number = -1
        atom.occupancy = 1.0
        atom.conformation = 0
        atom.temperatureFactor = 0.0
        atom.babel_atomic_number = a[2]
        atom.babel_type = a[3]
        atom.babel_organic=1
        bond = Bond( a[1], atom )

    from Pmv.moleculeViewer import MoleculeViewer
    mv = MoleculeViewer()
    mv.addMolecule(mol)
    mv.lines( mol )