On 19/09/10 04:44, Greg Landrum wrote: > On Sat, Sep 18, 2010 at 4:03 PM, Paul Emsley<paul.ems...@bioch.ox.ac.uk> > wrote: > >> The (additional) useful thing libcheck can do is generate esd geometry >> restraints for crystallographic refinement (something like the "spring >> constants", e.g. 0.02A for a C-C single bonds, 3 degrees for C-C-C >> angles etc. (atom type dependent, of course) - also planes and >> torsions). I wonder how hard that would be to get >> similar/compatible/corresponding numbers by digging into RDKit's UFF >> (presumably that would be the way to do it). Any thoughts/advice? >> > Apologies for my ignorance about things crystallographic, but I'm not > quite sure what you mean. Are you talking about accessing the > geometric parameters themselves or adding special terms to the > forcefield? Either is pretty straightforward. >
Hi Greg, Sorry for the hand-waving question. Thanks for your encouraging answer. The interchange of information between the chemical model/restraints generation programs and modern programs that do refinement using X-ray data is in the form of macromolecular Crystallographic Information File, mmCIF (STAR-formatted) files, e.g. http://lmb.bioch.ox.ac.uk/emsley/ccp4/PHE.cif I was hoping that the tools of RDKit can be used in the generation of such files (starting from SMILES or a 2D mol2 description [1]). It seems to me that many of the data items *can* be generated. The question I had was (something like): how hard would it be to fill the data for these columns: _chem_comp_bond.value_dist_esd, _chem_comp_angle.value_angle_esd _chem_comp_tor.value_angle_esd and _chem_comp_plane_atom.dist_esd? (I am not sure that this needs an answer any more than you have already given - I'll start digging). Thanks, Paul. [1] people in our community currently use libcheck, PRODRG or CORINA to do this (those are non-Free programs). ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
