On 16/09/2011 22:34, andi wrote: > I'm trying to see if a one fragment is a sub-structure of a molecule and am > using *OBIsomorphismMapper*, however when I start modifying the molecule > (deleting atoms etc..), i start getting strange results, including some > segmentation faults. > > First I want to verify that the *map object* contains the atom *index* and > not *idx*, is this correct? > > Also, right now the way I access the matched atoms in the molecule/fragment, > I add 1 to the element in the *map object * > i.e.) > map.at[0].first+1 or map.at[0].second+1 > OBAtom* atom = m->GetAtom( map.at[0].first+1 ) > > Is this a good way to access the matched atoms, or is there a better way to > access them in order to modify, delete etc..?
It is my understanding that the zero-based index (rather than the one-based idx) is used in the mappings, although the documentation is not very clear on this. The atom indices (both zero or one based) are not valid after an atom deletion. This may be what is causing your problem. You may be able to work around this by deleting atoms in decreasing order of their indices. Incidentally, the third type of atom index from OBAtom::GetId() remains valid after a deletion. Chris ------------------------------------------------------------------------------ BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA http://p.sf.net/sfu/rim-devcon-copy2 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
