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
