On 8 July 2010 08:08, Hans De Winter <hans.dewin...@silicos.com> wrote: >> On Wed, Jul 7, 2010 at 6:54 PM, Geoffrey Hutchison >> <ge...@geoffhutchison.net> wrote: >>>> >>>> isomorph code (identity checking), so in the meanwhile we would have >>>> to specify a convention such as all molecules with the same title are >>>> the same. >>> >>> I've been thinking about this for a while. The easiest detection is that: >>> a) The number of atoms is the same >>> b) The element list is the same (and in the same order) >> >> Another option is to keep track of canonical smiles. a & b don't >> guarantee the molecules are the same (especially binding). However, >> the symmetry classes encode a variety of properties (connectivity, >> element, aromaticity, formal charge, in ring, bond orders) and can be >> used for this purpose. > > I agree that keeping track of the canonical smiles would be the most robust > way of doing it, and also easy to implement > if one imposes the requirement that different conformers of the same > molecule should be subsequent to each other in > the input file.
Not to prolong this thread, but I think regular SMILES is more appropriate here. We want to keep the atoms in the input order. > >> >> We actually have an implementation using a & b in avogadro. It's in >> the ReafFileThread in libavogadro/src/moleculefile.cpp >> >> (http://github.com/cryos/avogadro/blob/master/libavogadro/src/moleculefile.cpp). >> This implementation assumes you have a file with different molecules >> or all the same. It doesn't support N conformers of different >> molecules in the same file but this should not be hard to write. There >> is much extra code here though. >> >> My suggestion would be to add an option to OBConversion to enable >> conformer reading. When enabled, a Read call will read the same >> molecules until it finds a different molecule. The first molecule is >> kept and coordinates of the following conformers are added to it. > > Right > >> >>> I don't think I'd want it to be automatic, though. There has to be a >>> mechanism to "turn off" (or "turn on") the feature in case you want to >>> splice out a particular frame or conformer, much like we do with >>> multi-molecule files. >> >> Yes, usually when you need it the user will know. Or a program that >> uses it (e.g. obspectrophore) can always enable it. > > Yes > > Bye, > Hans > > ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
