Hi, I've come across a subtle bug (or misunderstanding on my part..?) when merging molecules from python... I've attached a minimal example that segfaults (tested on Red Hat Enterprise Linux, python 2.7, openbabel 2.3.1). Essentially, it seems that if I do something like
mol1 += mol2
inside a function, mol1 (or more likely the C++ object underneath) is
no longer valid and doing things like converting it to an output
string fails with a segfault. I'm guessing swig or python has decided
there aren't any more references to it and has triggered deletion of
the C++ object?
e.g something like:
def addNewFragment(obmol):
frag = newFrag() # Create some OBMol instance
obmol += frag
mymol = getMol() # Some function to return OBMol instance
addNewFragment(mymol)
# At this point the mymol object is broken, and calls to many of its
methods fail with a segfault
Storing another reference to it (e.g. by returning the molecule from
the function and assigning it to something ) fixes the problem, e.g:
def addNewFragmentAndReturn(obmol):
frag = newFrag()
obmol += frag
return obmol
mymol =getMol()
foo = addNewFragmentAndReturn(mymol)
# mymol is still valid... (creating the "foo" reference seems to have
kept it alive...)
I think this is a bug - Can anyone else reproduce this (demo script
attached) or is it me not understanding how to use the library :)
Fred
bug_report.py
Description: Binary data
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