I'm baffled by the following, and can only assume I have some misunderstanding
of how atom Idx's are stored.
I asked for an SSSR using GetSSSR(), then take the first ring from the SSSR.
Then I wanted something simple: one atom from that ring. So I take the first
IDX from ring->_path, like this:
int start_idx = ring->_path[0];
OBAtom *start_atom = GetAtomById(start_idx);
Segmentation fault.
Hmmm... so after digging around in mol.cpp, I can't see why this should be.
Adding a bit of debugging to see what the heck is going on, I find:
int start_idx = ring->_path[0];
cout << " start_idx: " << start_idx << ", _atomIds.size: " <<
_atomIds.size() << endl;
for (int i = 0; i < _atomIds.size(); i++)
cout << " " << i << ":" << _atomIds[i] << "(" << _atomIds[i]->GetId()
<<") ";
cout << endl;
OBAtom *start_atom = GetAtomById(start_idx);
And it prints:
start_idx: 10, _atomIds.size: 10
0:0x624ef0(0) 1:0x626ae0(1) 2:0x625350(2) 3:0x6254c0(3) 4:0x624700(4)
5:0x624610(5)
6:0x654e50(6) 7:0x654f60(7) 8:0x624ac0(8) 9:0x656d10(9)
So what gives here? I thought Atom Idx's were from 1..N, but this looks like
in OBMol::_atomIds, they're 0 to N-1, and the same in ring->_path. I expected
_atomIds[0] to be NULL.
BTW, all I'm really trying to do is get one atom from each ring in the SSSR as
a starting point for assigning the single/double bonds in kekule.cpp, so if
someone could point out how to do this seemingly-simple code, I'd appreciate
it. I probably just need more sleep or something...
Thanks!
Craig
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