def getHBAtoms(mol):
"""
Function to identify donor and acceptor atoms for hydrogen bonds
d2, d3, a2, a3 <- getHBAtoms(mol)
The function will first build bonds then assign atom hybridization
and bond orders. Next it will use a HydrogenBondBuilder to identify and'
report donor and acceptor atoms in sets corresponding to Sp2 and Sp3
hybridization.
A .hbstatus is added to all atoms. The value can be:
NE: NEutral
D2: Sp2 donor
D3: Sp3 donor
A2: Sp2 acceptor
A3: Sp3 acceptor
B2: Sp2 acceptor and donor
B3: Sp3 acceptor and donor
"""
# add bonds
mol.buildBondsByDistance()
atoms = mol.allAtoms
# assign .babel_type
from PyBabel.atomTypes import AtomHybridization
atyper = AtomHybridization()
atyper.assignHybridization(atoms)
# assign bond order
from PyBabel.bo import BondOrder
bond_orderer = BondOrder()
bond_orderer.assignBondOrder(atoms, atoms.bonds[0])
# get donors
from MolKit.hydrogenBondBuilder import HydrogenBondBuilder
hbbuilder = HydrogenBondBuilder()
donorTypes = hbbuilder.paramDict['donorTypes']
donorsp2Ats, donorsp3Ats = hbbuilder.getHBDonors(atoms, donorTypes)
# get acceptors
acceptorTypes = hbbuilder.paramDict['acceptorTypes']
acceptorsp2Ats, acceptorsp3Ats = hbbuilder.getHBAcceptors(atoms, acceptorTypes)
# create hbstatus attribute
atoms.hbstatus = 'NE'
for a in donorsp2Ats:
a.hbstatus = 'D2'
for a in donorsp3Ats:
a.hbstatus = 'D3'
for a in acceptorsp2Ats:
a.hbstatus = 'A2'
for a in acceptorsp3Ats:
a.hbstatus = 'A3'
# handle atoms that are both donors and acceptor
for a in donorsp2Ats.inter(acceptorsp2Ats):
a.hbstatus = 'B2'
for a in donorsp3Ats.inter(acceptorsp3Ats):
a.hbstatus = 'B3'
return donorsp2Ats, donorsp3Ats, acceptorsp2Ats, acceptorsp3Ats
def check_babel_types(self, ats):
num_ats = len(ats)
num_babel_type = len(ats.get(lambda x: hasattr(x, 'babel_type')))
num_bnd_type = len(ats.get(lambda x: hasattr(x, 'bnd_type')))
if (num_babel_type!=num_ats) or (num_bnd_type!=num_ats):
babel = AtomHybridization()
bond_orderer = BondOrder()
tops = ats.top.uniq()
for mol in tops:
babel.assignHybridization(mol.allAtoms)
bond_orderer.assignBondOrder(mol.allAtoms, mol.allAtoms.bonds[0])
mol.allAtoms._bndtyped = 1
def check_babel_types(self, ats):
try:
ats.babel_type
ats._bndtyped
except AttributeError:
babel = AtomHybridization()
bond_orderer = BondOrder()
tops = ats.top.uniq()
for mol in tops:
babel.assignHybridization(mol.allAtoms)
bond_orderer.assignBondOrder(mol.allAtoms, mol.allAtoms.bonds[0])
mol.allAtoms._bndtyped = 1
def check_babel_types(self, ats):
num_ats = len(ats)
num_babel_type = len(ats.get(lambda x: hasattr(x, 'babel_type')))
num_bnd_type = len(ats.get(lambda x: hasattr(x, 'bnd_type')))
if (num_babel_type != num_ats) or (num_bnd_type != num_ats):
babel = AtomHybridization()
bond_orderer = BondOrder()
tops = ats.top.uniq()
for mol in tops:
babel.assignHybridization(mol.allAtoms)
bond_orderer.assignBondOrder(mol.allAtoms,
mol.allAtoms.bonds[0])
mol.allAtoms._bndtyped = 1
def select(self, bnds, bondOrder=1):
ats = self.getAtoms(bnds)
mols = ats.top.uniq()
atype = AtomHybridization()
for m in mols:
if not m.chains[0].hasBonds:
m.buildBondsByDistance()
allAts = m.chains.residues.atoms
atype.assignHybridization(allAts)
rf = RingFinder()
rf.findRings2(allAts, allAts.bonds[0])
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
return BondSet(bnds.get(lambda x, ord=bondOrder: x.bondOrder==ord))
def select(self, bnds, bondOrder=1):
ats = self.getAtoms(bnds)
mols = ats.top.uniq()
atype = AtomHybridization()
for m in mols:
if not m.chains[0].hasBonds:
m.buildBondsByDistance()
allAts = m.chains.residues.atoms
atype.assignHybridization(allAts)
rf = RingFinder()
rf.findRings2(allAts, allAts.bonds[0])
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
return BondSet(bnds.get(lambda x, ord=bondOrder: x.bondOrder == ord))
def select(self, bnds):
ats = self.getAtoms(bnds)
rf = RingFinder()
#nb maxSize of ring is 20 by default
rf.findRings2(ats, bnds, maxSize=len(ats))
ats = self.getAtoms(rf.allRingBonds)
allAts = ats.top.uniq().allAtoms
atype = AtomHybridization()
atype.assignHybridization(allAts)
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
arom = Aromatic(rf)
arom.find_aromatic_atoms(ats)
aromatic_bnds = ats.bonds[0].get(lambda x: x.bondOrder=='aromatic')
aromatic_ats = self.getAtoms(aromatic_bnds)
aromatic_ats.aromatic = 1
return aromatic_bnds
def select(self, bnds):
ats = self.getAtoms(bnds)
rf = RingFinder()
#nb maxSize of ring is 20 by default
rf.findRings2(ats, bnds, maxSize=len(ats))
ats = self.getAtoms(rf.allRingBonds)
allAts = ats.top.uniq().allAtoms
atype = AtomHybridization()
atype.assignHybridization(allAts)
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
arom = Aromatic(rf)
arom.find_aromatic_atoms(ats)
aromatic_bnds = ats.bonds[0].get(lambda x: x.bondOrder == 'aromatic')
aromatic_ats = self.getAtoms(aromatic_bnds)
aromatic_ats.aromatic = 1
return aromatic_bnds
def getHBAtoms(mol):
"""
Function to identify donor and acceptor atoms for hydrogen bonds
d2, d3, a2, a3 <- getHBAtoms(mol)
The function will first build bonds then assign atom hybridization
and bond orders. Next it will use a HydrogenBondBuilder to identify and'
report donor and acceptor atoms in sets corresponding to Sp2 and Sp3
hybridization.
A .hbstatus is added to all atoms. The value can be:
NE: NEutral
D2: Sp2 donor
D3: Sp3 donor
A2: Sp2 acceptor
A3: Sp3 acceptor
B2: Sp2 acceptor and donor
B3: Sp3 acceptor and donor
"""
# add bonds
mol.buildBondsByDistance()
atoms = mol.allAtoms
# assign .babel_type
from PyBabel.atomTypes import AtomHybridization
atyper = AtomHybridization()
atyper.assignHybridization(atoms)
# assign bond order
from PyBabel.bo import BondOrder
bond_orderer = BondOrder()
bond_orderer.assignBondOrder(atoms, atoms.bonds[0])
# get donors
hbbuilder = HydrogenBondBuilder()
donorTypes = hbbuilder.paramDict['donorTypes']
donorsp2Ats, donorsp3Ats = hbbuilder.getHBDonors(atoms, donorTypes)
# get acceptors
acceptorTypes = hbbuilder.paramDict['acceptorTypes']
acceptorsp2Ats, acceptorsp3Ats = hbbuilder.getHBAcceptors(
atoms, acceptorTypes)
# create hbstatus attribute
atoms.hbstatus = 'NE'
for a in donorsp2Ats:
a.hbstatus = 'D2'
for a in donorsp3Ats:
a.hbstatus = 'D3'
for a in acceptorsp2Ats:
a.hbstatus = 'A2'
for a in acceptorsp3Ats:
a.hbstatus = 'A3'
# handle atoms that are both donors and acceptor
for a in donorsp2Ats.inter(acceptorsp2Ats):
a.hbstatus = 'B2'
for a in donorsp3Ats.inter(acceptorsp3Ats):
a.hbstatus = 'B3'
return donorsp2Ats, donorsp3Ats, acceptorsp2Ats, acceptorsp3Ats
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 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)
