I want to identify the major torsional angles of a molecule and cluster the conformations according to that. How can I do that?
I’m not quite sure I understand what you mean by “major torsional angles.”
But for clustering conformations, e.g.:
Beyond RDKit, crest also offers clustering options:
Say one has a molecule (to present this at level of a concept, a simple like diethyl ether) for which openbabel can suggest a conformation (vide infra) by
obabel -:"CCOCC" -h --gen3d -O ether.sdf
Openbabel equally can analyze this by a subsequent
obabel ether.sdf -oreport -O analysis.txt
where file analysis.txt includes a section about torsion angles, the atoms which define the angle in question. (As these are depicted by the atom index, see the earlier section about atomic charges to recognize the atom type.)
It is possible to extend this to cover multiple conformers (cf. vide supra) by the request to generate multiple conformers (see openbabel’s documentation here). The systematic search for conformers of a structure equally can be performed outside openbabel by other programs, too.
Similar to Geoffrey’s reply, please elaborate further what you refer to by “cluster the conformations according to that” e.g. a specific publication (link/doi) which showcases the subsequent work ahead.