Ejemplo n.º 1
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)
    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
Ejemplo n.º 3
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)
    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)
Ejemplo n.º 5
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
Ejemplo n.º 6
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 )