Python-openbabel code crashes definitely on program finish

> This is the part of program, which also crashes in the same way:
>
> #!/usr/bin/python -d
> import openbabel, sys, math, random
> import numpy
>
> try:
>        def add(x, y): return x+y
>        obC = openbabel.OBConversion()
>        obC.SetInAndOutFormats("pdb", "pdb")
>
>        mols = []
>        verts = []
>        probs = []
>
>        # initializing structures
>        if True:
>          nmol = openbabel.OBMol()
>          obC.ReadFile(nmol, "dppsnew.pdb")
>          mols.append( nmol )
>          nmol = openbabel.OBMol()
>          obC.ReadFile( nmol, "chlnew.pdb")
>          mols.append( nmol )
>
>        # init values for grid
>        numconformers = 50
>
> # =================================================
> #           crashes because of this block!!!
> # =================================================
>        for mol in mols:
>                for i in range(0,numconformers):
>                        nmol = openbabel.OBMol(mol)
>                        for torl in openbabel.OBMolTorsionIter(nmol):
>                                atlist = [nmol.GetAtom(torl[0]+1),
> nmol.GetAtom(torl[1]+1), nmol.GetAtom(torl[2]+1),
> nmol.GetAtom(torl[3]+1)]
>                                if (atlist[1].IsInRing() and
> atlist[2].IsInRing() ):
>                                        continue
>                                tor = nmol.GetTorsion(atlist[0],
> atlist[1], atlist[2], atlist[3])
>                                tor = random.gauss(tor, 3)*math.pi/180
>                                nmol.SetTorsion(atlist[0], atlist[1],
> atlist[2], atlist[3], tor)
>                        mol.AddConformer(nmol.GetConformer(0))
> # =================================================
> #           end of block
> # =================================================
> finally:
>        print 'Bue!'
>
>
>
> crash message:
>
> *** glibc detected *** /usr/bin/python2.6: double free or corruption
> (out): 0x0000000000d4bd20 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0x7f5f621f14ce]
> /lib/libc.so.6(cfree+0x75)[0x7f5f621f2dbb]
> /usr/local/lib/libopenbabel.so.3(_ZN9OpenBabel5OBMolD0Ev+0xd0)[0x7f5f61a135e0]
>
>
> Program crashes at end everywhere - in debian, gento and cygwin.
> Program works absolutely normally. The only error - is the crush on
> the end, while destructing. What I does wrong with conformers?
>
> Thank you.
>
> ------------------------------------------------------------------------------
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>

> Hello Alexey,
>
> To make it easier for us to identify the problem, could you provide
> the simplest possible program that causes the program? Could you name
> a PDB file that causes the problem?
>
> - Noel
>
> On 22 February 2010 17:32, Alexey Nesternko <[hidden email]> wrote:
>> This is the part of program, which also crashes in the same way:
>>
>> #!/usr/bin/python -d
>> import openbabel, sys, math, random
>> import numpy
>>
>> try:
>>        def add(x, y): return x+y
>>        obC = openbabel.OBConversion()
>>        obC.SetInAndOutFormats("pdb", "pdb")
>>
>>        mols = []
>>        verts = []
>>        probs = []
>>
>>        # initializing structures
>>        if True:
>>          nmol = openbabel.OBMol()
>>          obC.ReadFile(nmol, "dppsnew.pdb")
>>          mols.append( nmol )
>>          nmol = openbabel.OBMol()
>>          obC.ReadFile( nmol, "chlnew.pdb")
>>          mols.append( nmol )
>>
>>        # init values for grid
>>        numconformers = 50
>>
>> # =================================================
>> #           crashes because of this block!!!
>> # =================================================
>>        for mol in mols:
>>                for i in range(0,numconformers):
>>                        nmol = openbabel.OBMol(mol)
>>                        for torl in openbabel.OBMolTorsionIter(nmol):
>>                                atlist = [nmol.GetAtom(torl[0]+1),
>> nmol.GetAtom(torl[1]+1), nmol.GetAtom(torl[2]+1),
>> nmol.GetAtom(torl[3]+1)]
>>                                if (atlist[1].IsInRing() and
>> atlist[2].IsInRing() ):
>>                                        continue
>>                                tor = nmol.GetTorsion(atlist[0],
>> atlist[1], atlist[2], atlist[3])
>>                                tor = random.gauss(tor, 3)*math.pi/180
>>                                nmol.SetTorsion(atlist[0], atlist[1],
>> atlist[2], atlist[3], tor)
>>                        mol.AddConformer(nmol.GetConformer(0))
>> # =================================================
>> #           end of block
>> # =================================================
>> finally:
>>        print 'Bue!'
>>
>>
>>
>> crash message:
>>
>> *** glibc detected *** /usr/bin/python2.6: double free or corruption
>> (out): 0x0000000000d4bd20 ***
>> ======= Backtrace: =========
>> /lib/libc.so.6[0x7f5f621f14ce]
>> /lib/libc.so.6(cfree+0x75)[0x7f5f621f2dbb]
>> /usr/local/lib/libopenbabel.so.3(_ZN9OpenBabel5OBMolD0Ev+0xd0)[0x7f5f61a135e0]
>>
>>
>> Program crashes at end everywhere - in debian, gento and cygwin.
>> Program works absolutely normally. The only error - is the crush on
>> the end, while destructing. What I does wrong with conformers?
>>
>> Thank you.
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>

> The code, I has written in the post in eough to reproduce a problem. Problem
> doesn't depends on what PDB files i use. For example, it was cholesterol. In
> my case it was 2 lipids, I can The problem is memory leak during destructing
> mols array.
> ________________________________
> View this message in context: Re: Python-openbabel code crashes definitely
> on program finish
> Sent from the openbabel-discuss mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>