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
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)
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
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 )