Ask the bond whether it's an amide, using "b.IsAmide()". See the docs
at
http://openbabel.org/api/2.3/classOpenBabel_1_1OBBond.shtml#a86eb2acbb9c5811e645df18b8b0bacf7
I think that the reason it's regarded as rotatable is that trans amide
bonds do exist, even in peptides.
- Noel
On 14 March 2013 09:12, annndrey <gontc...@gmail.com> wrote:
> 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,
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Openbabel-rotation-bonds-search-tp4656052.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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