Calculate RMSD between two sets of molecules (eg, Crystal pose vs. docked pose)

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10/21/2020 Ying

Script to calculate RMSD between two sets of molecules (mol2 format), modified from the openeye rmsd.py (https://docs.eyesopen.com/toolkits/python/_downloads/rmsd.py).

To use it, you just need two mol2 files but with match names for the same molecule.

 /nfs/home/yingyang/programs/miniconda3/envs/teachopencadd/bin/python \
 /nfs/home/yingyang/scripts/rmsd_oe_multi.py -ref <xtal_ligs.mol2> -in <poses.mol2>
  • make sure the other conda/python environment is not activated