Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

Hi all, here the code for Open3DALIGN: cids = generateConformers(mol, numConformers) prbPyMP = AllChem.MMFFGetMoleculeProperties(mol) maxScore = 0; for refCid in refCids: for cid in cids: alignment =

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

Dear Thomas, if you wish to align two structures by their MCS, O3A is probably not the tool for you. O3A is meant for unsupervised alignment, and it will attempt to align two structures matching the most similar pairs of atoms between the two. Similarity is defined by the closeness of their

[Rdkit-discuss] chirality doxygen tweak

Hi Greg, I don't know if you care about this sort of thing, but if you do, then you should escape - i.e. \@ - (at least) one of the @s here (in Atom.h) //! tetrahedral: clockwise rotation (SMILES @@) So that the output html makes more sense. Currently see

Re: [Rdkit-discuss] chirality doxygen tweak

On Tue, Jul 1, 2014 at 12:53 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: I don't know if you care about this sort of thing, but if you do, then you should escape - i.e. \@ - (at least) one of the @s here (in Atom.h) //! tetrahedral: clockwise rotation (SMILES @@) So that the output