Re: [Open Babel] generate 3D coordinates based on a scaffold

2012-04-14 Thread Matthew Ketterer
You probably are aware of this, but OBfit can probably start you if you can manipulate the smarts pattern to include what you want as the scaffold in a more generalized SMARTS pattern? Maybe you could generate a list of possible substitutions for a functional group in the pattern, and then it woul

[Open Babel] InChi notation of a small molecule

2012-04-14 Thread prasun kumar
Dear all I am using Openbabel for converting pdb file to its corresponding inchi notation. Its working well, but problem is coming in identifying the real number of the atoms in the pdb files as Inchi notation is gives its own identifying number. Can some body help me in getting this information. T