Dear Greg, and rdkit-discuss members. Thank you for your advice. That code is very useful for me !
And I have one question. Can I get selected pharmacophore feature positions from AtomIds? Or how can I get selected pharmacophore features from AtomIds? >From feature object, it is easy to do that by useing "feature.GetPos()" method. I want to do same thing by using AtomIds. Sincerely. Taka 2012/7/20 Greg Landrum <greg.land...@gmail.com>: > Dear Taka, > > On Thu, Jul 19, 2012 at 9:44 AM, Taka Seri <serit...@gmail.com> wrote: >> Dear all. >> I have some questions about Pharmacophore. >> I want to align molecules that from SDF files, by Pharmacophore. >> At first, I set Pharmacophore by using "EmbedPharmacophore()" method. >> And checked molecules by "EmbedPharmacophore()" method. >> Then, generated 3D structures by "EmbedPharmacophore()" method. >> Finally, I want to align these conformers to the Pharmacophore. >> Could anyone give me a small example? > > There is unfortunately no really good sample code available for this. > There is some very old code from a GUI application that was built with > the RDKit but that is no longer supported (or part of the current SVN > app) here: > http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Python/qtGui/Search3D/SearchUtils.py?revision=2&view=markup&pathrev=5 > in the function AlignMatchToReference() > > > Here's an attempt to distill that information down: > > First you need the alignment package: > > from rdkit.Numerics import rdAlignment > > which contains the function GetAlignmentTransform: > > In [5]: rdAlignment.GetAlignmentTransform? > Type: function > Base Class: <type 'builtin_function_or_method'> > String Form:<Boost.Python.function object at 0x102fe0dc0> > Namespace: Interactive > Docstring: > GetAlignmentTransform( (object)refPoints, (object)probePoints [, > (object)weights=[] [, (bool)reflect=False [, (int)maxIterations=50]]]) > -> object : > Compute the optimal alignment (minimum RMSD) between two set of points > > > ARGUMENTS: > > - refPoints : reference points sepcified as a N by 3 Numeric array or > sequence of 3-sequences or sequence of Point3Ds > - probePoints : probe points to align to reference points - same > format > restrictions as reference points apply here > - weights : optional numeric vector or list of weights to > associate to each pair of points > - reflect : reflect the probe points before attempting alignment > - maxIteration : maximum number of iterations to try to minimize RMSD > > RETURNS: > > a 2-tuple: > - SSD value for the alignment > - the 4x4 transform matrix, as a Numeric array > > > This will give the transformation required to align one set of points > (the ph4 points from your embedded molecule) to another set of points > (the ph4 points from your reference ph4). > > To do this you need the positions of each of the features: > probePts = [list(x.GetPos()) for x in probeFeats] > refPts = [list(x.GetPos()) for x in refFeats] > > And then you align them: > ssd,tform = Aligner.GetAlignmentTransform(refArr,probeArr,weights=weights) > > If your molecule has no chiral centers, it's a good idea to try > reflecting the alignment: > ssd2,tform2 = > Aligner.GetAlignmentTransform(refArr,probeArr,weights=weights,reflect=True) > if ssd2<ssd: > tform = tform2 > ssd = ssd2 > > > the two return values are the sum of squared deviations of the atomic > positions (easily convertible to the RMSD) and the transformation > matrix. You can apply the transformation matrix to your embedded probe > molecule (to align it to the ph4) with the function > AllChem.TransformMol: > AllChem.TransformMol(probeMol,tform) > > I hope this helps. > > -greg ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
