On Mon, May 7, 2012 at 10:09 AM, Geoffrey Hutchison <geo...@pitt.edu> wrote:
>
> On May 4, 2012, at 10:45 PM, Craig James wrote:
>
> > But it seems to be the atom iterator, not the ring iterator, that's
> causing the problem.
>
> Huh. Here's comparable code in forcefieldmmff94.cpp:
>
> for(rj = (*ri)->_path.begin();rj != (*ri)->_path.end();rj++) { // for
> each ring atom
> index = *rj;
> ringatom = _mol.GetAtom(index);
>
> Granted, like Igor's comment the code gets the rings like so:
>
> vector<OBRing*> vr;
> vr = _mol.GetSSSR();
>
> Have you checked the path size?
>
It's a random number. Here is a more concise version of the code ... it's
extracted from a much larger body of code, but I think I got all the
relevant parts.
OBMol *pmol;
OBConversion conv;
conv.SetInAndOutFormats("sdf", "smi");
pmol = new OBMol;
pmol->Clear();
conv.ReadString(pmol, molData_str);
natoms = pmol->NumAtoms();
nbonds = pmol->NumBonds();
if (natoms <= 0) { // No atoms? (shouldn't happen...)
return 0;
}
for (atom = pmol->BeginAtom(ai); atom; atom = pmol->NextAtom(ai)) {
float x = atom->GetX();
float y = atom->GetY();
// --- snip --- code to draw atom labels into image
}
// --- snip --- initialize code for GIF/JPG/PNG library
vector<OBRing*> rlist = mol->GetSSSR();
vector<OBRing*>::iterator ri;
for (ri = rlist.begin(); ri != rlist.end(); ++ri) {
fprintf(stderr, "_path.size() = %d\n", (*ri)->_path.size());
// Prints out a big random negative number
vector<int>::iterator j;
for (j = (*ri)->_path.begin(); j != (*ri)->_path.end(); j++) {
OBAtom *atom = mol->GetAtom(*j);
// .... crashes because j is NULL
}
}
I ran valgrind on it which is usually very good at finding problems. When
it gets to where I print _path.size(), valgrind complains that I'm printing
uninitialized memory, and the value that comes out is indeed a random value
(-1067674809 or 0x3FA36CB9). valgrind doesn't report any other errors at
all.
I'm stumped, but I'm happy to help,
>
Thanks ... I suspect this will turn out to be a bug somewhere else in the
program (overwriting a buffer or something, but in a way that valgrind
can't detect), but for the life of me I can't find it. It worked for
OpenBabel 2.2.x and now fails for OpenBabel 2.3.x.
Mostly I'm just asking if I'm calling the OpenBabel functions correctly.
It sounds like I am. That being the case, I'll start digging around in the
rest of my code to find the bug.
Craig
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