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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