Can you give us an example file or two? This would help us debug by reproducing
the problem.
Thanks very much,
-Geoff
On Apr 24, 2013, at 11:01 AM, Pascal Muller <pascal.jm.mul...@gmail.com> wrote:
> Hi,
>
> I have a little pybel script for generating Murcko scaffolds, which
> works well with 2.3.1, but fails on a few molecules ("Segmentation
> fault") with 2.3.2.
>
> Depending on code modifications, the fault raises at different points,
> but I have no clue on why the bug is happening.
>
> Below is my code shortened as much as I could.
>
> Regards,
> Pascal
>
>
>
> #!/usr/bin/env python
> # encoding: utf-8
> import sys
> import os, pybel
> import openbabel as ob
>
> def GetMurckoFramework(mol):
> haveAtomWithOneNeighbor,atomsWithOneNeighborList =
> checkIfIsOnlyOneNeighbor(mol)
> while (haveAtomWithOneNeighbor):
> for atomToDel in atomsWithOneNeighborList:
> mol.OBMol.DeleteAtom(atomToDel) # delete atom which are
> not part of a cycle or a linker (terminal atoms)
> haveAtomWithOneNeighbor,atomsWithOneNeighborList =
> checkIfIsOnlyOneNeighbor(mol)
> return mol
>
> def checkIfIsOnlyOneNeighbor(mol):
> isAnAtomWithOneNeighbor = 0
> atomWithOneNeighborList = []
> for atom in ob.OBMolAtomIter(mol.OBMol):
> if not atom.IsInRing():
> neighborsCount = 0
> for neighbor in ob.OBAtomAtomIter(atom):
> neighborsCount = neighborsCount + 1
> if (neighborsCount <= 1): # It is a terminal atom (only
> one neighbor) double bond
> atomWithOneNeighborList.append(atom) # will be deleted
> isAnAtomWithOneNeighbor = 1
> return isAnAtomWithOneNeighbor, atomWithOneNeighborList
>
>
> def main():
> if len(sys.argv) < 2:
> print "No input file provided: Murcko.py filetosprocess.smi"
> sys.exit(1)
>
> mol1 = pybel.readstring("smi", "C1(=Cc2cn(nc2)CC(=O)N)C(=O)NC(=O)S1")
> mol2 = pybel.readstring("smi", "C1(=CC2=C(N=C(C2)C(=O)N)C)C(=O)NC(=O)S1")
> li = [mol1, mol2]
>
> for mol in li:
> mol = GetMurckoFramework(mol)
> print mol
>
> if __name__ == '__main__':
> main()
>
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