Hi. I'm trying to use Openbabel to detect rotatable bonds in a small
molecule.
Here is the code:
pdb="myfile.pdb"
eltab = openbabel.OBElementTable()
mol = openbabel.OBMol()
obConversion = openbabel.OBConversion()
obConversion.SetInFormat("sdf")
obConversion.ReadFile(mol, pdb)
for i in xrange(mol.NumBonds()):
b = mol.GetBond(i)
st = eltab.GetSymbol(b.GetBeginAtom().GetAtomicNum())
en = eltab.GetSymbol(b.GetEndAtom().GetAtomicNum())
if b.IsRotor():
print st, b.GetBeginAtomIdx(), "rot", en, b.GetEndAtomIdx()
As I can see, it treat as a rotatable bond only single bonds. But I know
that in my molecule there are some peptide bonds that could not be treated
as rotatable. How can I make this script to exclude peptide bonds from be
treated as rotatable?
Thanks in advance,
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