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 <comcona...@gmail.com> 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® 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
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
------------------------------------------------------------------------------
Download Intel® 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
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
