> 1) Is it possible to compare two databases using obgrep, I mean if I have > not only SMARTS pattern, but for example > the datasets of ligands which I want to use against other dataset?
It sounds like you want to perform some sort of "diff" between two databases? That's an interesting use, but it's not what obgrep does. > 2) obconformer generates conformers by Monte Carlo search, what is the > difference with 3D obgen in the provided results?? It is just in methods, > right? > But in obgen Monte Carlo conformational search is performed too, so obgen is > like obconf, just the molecular mechanics minimization is also performed? The "obconformer" program starts from an existing 3D structure, while obgen is designed to start from a SMILES or other "no-coordinate" format, generate rough 3D coordinates, and then yes perform some conformer searching and molecular mechanics optimization. > And obminize also makes optimization of the conformation by moilecular > mechanics right? Yes. > Is it possible to get a series of conformers using OpenBabel like in omega2 > software? That's not currently the aim of the programs, no. > 3) As I understand in GUI by conversion into 3D it is supposed that OpenBabel > generates 3D structure like it is done in some conformation generators like > Corina, Concord etc, or what does that 3D conversion mean? Yes, it generates an approximate 3D structure. Hope that helps, -Geoff ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
