Tangram SubAlign

Align two, potentially different, molecules based on partial matches of substructures

Features

[WIP]

Usage

In general:

subalign <reference> <probe> [methods <method>]

• reference, probe: must be Chimera selections (e.g. #0 or sel).

• methods (optional): the alignment method(s) to use. If you specify several ones (separate by commas), subalign will try all of them until one succeeds. Choose between:

  • fast: identify the best submatch of the naive one-to-one corresponding atom pairs.
  • best (default): iterate over all possible atom pair correspondences, trying fast over each one, and returns the one with best RMSD.
  • o3a: identifies atom pair correspondences by MM-like atom typing.
  • com: simply overlap centers of mass (great as a fallback method; e.g. methods best,com)

Note

The passed Chimera selections must corresponde to a single molecule. If you only specify a subset of atoms, it will be expanded to the containing molecule. With protein-ligand systems, this can be costly. The current recommendation is to split the molecule in submodels beforehand with split (see Chimera docs) and then specify the desired submodel.

Requirements

• libtangram, pychimera
• rdkit

Note

conda install -c insilichem/label/dev -c insilichem -c rdkit tangram_subalign

Note

This package might need that you launch UCSF Chimera with pychimera --gui