On Thu, Oct 22, 2009 at 11:51 PM, Craig A. James <cja...@emolecules.com> wrote:
> 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);
GetAtomById is meant to be used together with the unique ids (GetId),
not indexes (1...N). These unique ids initially go from 0 to N-1 but
there can be gaps.
Using (the old) GetAtom with the values in _path (result from GetIdx,
1...N) would give you the correct behaviour. This function could be
renamed to make it more clear though.
Tim
> 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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