Looks like a Builder bug. The stochastic issue is due to the use of a
random vector in there. I don't think we should be using that.
Regarding gen3d versus Python code, gen3d does a forcefield
optimisation after calling the Builder. You should look at its code,
gen3d.cpp.
- Noel
On 16 September 2012 18:55, Чугунов Антон <batc...@yandex.ru> wrote:
> Hello All!
> I encounter a very strange problem when I convert peptides from smiles to
> 3D. This problem persists for Phe and Tyr residues, but it's stochastic: it
> appears approx. in one case in ten. The problem is that CB-CG-CD1 valence
> angle is about 0 degrees, and the ring "folds back" to CB atom (see picture
> and two PDB files). Here's the code:
>
> #!/usr/bin/python
> import pybel, openbabel
> Smiles = {
> 'F': 'N[C@@H](CC1=CC=CC=C1)C(=O)',
> 'I': 'N[C@@H]([C@@H](C)CC)C(=O)',
> 'Y': 'N[C@@H](CC1=CC=C(C=C1)O)C(=O)'
> }
> seq = 'FIIFIIIYIIIIFIIY'
> def make_3d(pep_seq):
> pep_smiles = ''
> for aa in pep_seq:
> pep_smiles = pep_smiles + Smiles[aa]
> pep = pybel.readstring("smi", pep_smiles)
> openbabel.OBBuilder().Build(pep.OBMol)# Make 3D-coordinates
> return pep
>
> for i in range(20): # This makes 20 different peptides
> print i
> pep = make_3d(seq)
> pep.write('pdb', 'pep{:d}.pdb'.format(i), overwrite = True)
>
> This problem is still with me if I use a single Phe or Tyr residue; at the
> same time, command line obabel tool does not seem to have this; at least
> after 20 trials of obabel -:"N[C@@H](CC1=CC=CC=C1)C(=O)" -O pep${i}.pdb
> --gen3d I didn't notice any problems.
> Does anyone have idea, how to overcome this problem? Minimization corrects
> this to some extent, but you'll still have different conformations of side
> chains => there's no reproductivity in generated structures.
>
> Chugunov Anton.
>
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