def get_pdb_ccd_open_babel_mol(pdb_mol):
""" Generate an Open Babel representation of a PDB CCD entry
Args:
pdb_mol (:obj:`dict`): structure of a entry
Returns:
:obj:`openbabel.OBMol`: structure of a entry
"""
if not pdb_mol['complete']:
return None
mol = openbabel.OBMol()
for pdb_atom in pdb_mol['atoms']:
atom = openbabel.OBAtom()
atom.SetAtomicNum(pdb_atom['atomic_num'])
atom.SetFormalCharge(pdb_atom['charge'])
mol.AddAtom(atom)
for pdb_bond in pdb_mol['bonds']:
bond = openbabel.OBBond()
bond.SetBegin(mol.GetAtom(pdb_bond['begin']))
bond.SetEnd(mol.GetAtom(pdb_bond['end']))
bond.SetBondOrder(pdb_bond['order'])
assert mol.AddBond(bond)
return mol
def exchangeAtom(C, H, molTS, molFG, outfile, bondLength):
# read write xyz file
convTS, convFG = [ob.OBConversion() for i in range(2)]
convTS.SetInAndOutFormats("xyz", "xyz")
convFG.SetInAndOutFormats("xyz", "xyz")
# builder
builder = ob.OBBuilder()
# define molecules, atoms and bond classes
TS, FG = [ob.OBMol() for i in range(2)]
atomH = ob.OBAtom()
atomC = ob.OBAtom()
bond = ob.OBBond()
# read in xyz files
convTS.ReadFile(TS, molTS)
convFG.ReadFile(FG, molFG)
# number of atoms in TS molecule
numAtoms = TS.NumAtoms()
# get hydrogen atom and its vector
atomH = TS.GetAtom(H)
atomC = TS.GetAtom(C)
vec = ob.vector3(float(atomH.GetX()), float(atomH.GetY()),
float(atomH.GetZ()))
# delete hydrogen atom
TS.DeleteAtom(atomH)
# put both molecules together (same coord system)
TS += FG
# making the bond
builder.Connect(TS, C, numAtoms, vec, 1)
bond = TS.GetBond(C, numAtoms)
bond.SetLength(atomC, bondLength)
# call opimizer
#opt_mmff_FG(TS, numAtoms, outfile)
convTS.WriteFile(TS, "single/" + outfile)
# clear TS and FG molecule classes
TS.Clear()
FG.Clear()
def oasa_to_ob_bond(self, obond):
pbond = openbabel.OBBond()
pbond.SetBondOrder(obond.order)
return pbond
def pic(self, filename, picformat='svg'):
"""
Generates a graphical file with 2D-representation of the resonance structure
"""
try:
import openbabel as ob
except:
print "Cannot import openbabel"
return
#ValEl = {'H':1, 'B':3,'C':4,'N':5,'O':6,'F':7,'S':6}
#ValEl = {'1':1, '5':3,'6':4,'7':5,'8':6,'9':7,'16':6}
# Import Element Numbers
ati = []
Sym2Num = ob.OBElementTable()
for a in self.symbols:
ElNum = Sym2Num.GetAtomicNum(a)
ati.append(ElNum)
# Import connections
conn = self.data
mol = ob.OBMol()
# Create atoms
for a in ati:
at = ob.OBAtom()
at.SetAtomicNum(a)
mol.AddAtom(at)
# Create connections
val = []
total_LP = 0
for i in range(len(conn)):
total_LP += conn[i][i]
for i in range(len(conn)):
val.append(conn[i][i] * 2)
for j in range(i):
if conn[i][j] == 0:
continue
val[i] += conn[i][j]
val[j] += conn[i][j]
atA = mol.GetAtomById(i)
atB = mol.GetAtomById(j)
b = ob.OBBond()
b.SetBegin(atA)
b.SetEnd(atB)
b.SetBO(int(conn[i][j]))
mol.AddBond(b)
for i in range(len(conn)):
atA = mol.GetAtomById(i)
atAN = atA.GetAtomicNum()
FormValEl = CountValenceEl(atAN)
#if total_LP == 0:
# if atAN == 1:
# FullShell = 2
# else:
# FullShell = 8
# FormCharge = FormValEl + int(val[i]) - FullShell
#else:
FormCharge = int(FormValEl - val[i])
#print "atAN, FormValEl, val[i], FullShell"
#print atAN, FormValEl, val[i], FullShell
#FormCharge = FormCharge % 2
atA.SetFormalCharge(FormCharge)
# Export file
mol.DeleteNonPolarHydrogens()
conv = ob.OBConversion()
conv.SetOutFormat(picformat)
conv.AddOption('C')
conv.WriteFile(mol, filename)
def is_c_terminus(self, mol, atom, residue=True, convert_to_aa=False):
""" Determine if an atom is an C-terminus
Args:
mol (:obj:`openbabel.OBMol`): molecule
atom (:obj:`openbabel.OBAtom`): atom
residue (:obj:`bool`, optional): if :obj:`True`, search for a residue (H instead of O- at C terminus)
convert_to_aa (:obj:`bool`, optional): if :obj:`True`, convert COH to COOH
Returns:
:obj:`bool`: :obj:`True` if the atom is an C-terminus
"""
if atom is None:
return False
# check atom is carbon
if atom.GetAtomicNum() != 6:
return False
# check atom has charge 0
if atom.GetFormalCharge() != 0:
return False
# check atom is bonded to 1 oxygen, 1 carbon, and 1 hydrogen atom (residue=True) or 1 oxygen (residue=False) atom
other_atoms = [
other_atom.GetAtomicNum()
for other_atom in openbabel.OBAtomAtomIter(atom)
]
tot_bond_order = sum(
[bond.GetBondOrder() for bond in openbabel.OBAtomBondIter(atom)])
other_atoms += [1] * (4 + atom.GetFormalCharge() - tot_bond_order)
other_atoms.sort()
if set(other_atoms).difference(set([1, 6, 8])):
return False
if 6 not in other_atoms or 8 not in other_atoms:
return False
if len(other_atoms) != 3:
return False
if residue and other_atoms[0] != 1:
return False
if not residue and other_atoms[1] != 8:
return False
# check bonds to carbon and hydrogen are single bonds and bond to oxygen is a double bond
o_single_bonds = []
o_double_bonds = []
for bond in openbabel.OBAtomBondIter(atom):
other_atom = bond.GetBeginAtom()
if other_atom == atom:
other_atom = bond.GetEndAtom()
if other_atom.GetAtomicNum() == 8:
if bond.GetBondOrder() == 1:
o_single_bonds.append((bond, other_atom))
elif bond.GetBondOrder() == 2:
o_double_bonds.append((bond, other_atom))
else:
return False
elif bond.GetBondOrder() != 1:
return False
if residue and (len(o_single_bonds) != 0 or len(o_double_bonds) != 1):
return False
if not residue and (len(o_single_bonds) != 1
or len(o_double_bonds) != 1):
return False
# if not residue, check that single oxygen is bound to H
if not residue:
oxygen_atom = o_single_bonds[0][1]
for bond in openbabel.OBAtomBondIter(oxygen_atom):
other_atom = bond.GetBeginAtom()
if other_atom == oxygen_atom:
other_atom = bond.GetEndAtom()
if other_atom.GetIdx() != atom.GetIdx(
) and other_atom.GetAtomicNum() != 1:
return False
# correct residue to amino acid
if convert_to_aa:
h_atom = None
for other_atom in openbabel.OBAtomAtomIter(atom):
if other_atom.GetAtomicNum() == 1:
h_atom = other_atom
break
if h_atom is not None:
h_atom.SetAtomicNum(8)
else:
o_atom = mol.NewAtom()
o_atom.SetAtomicNum(8)
o_atom.SetFormalCharge(0)
bond = openbabel.OBBond()
bond.SetBegin(atom)
bond.SetEnd(o_atom)
bond.SetBondOrder(1)
assert mol.AddBond(bond)
# return True
return True