An automatic algorithm of RMSD

usage: CanonizedRMSD.py [-h] [-s] [-m] [-i] [-q] [-r] file1 file2

to calculate the RMSD of two molecules after canonizing them.

supported file types: .mol | .sdf | .rxn | .mol2 | .ml2 | .pdb

positional arguments: file1 file2

optional arguments:

-h, --help show this help message and exit

-s, --save save intermediate results

-m, --mapping output atom mapping relationship with two molecules

-i, --ignore_isomerism ignore geometric and stereometric isomerism when canonizing

-a, --no_alignment do not apply molecule alignment by Kabsch algorithm or QCP algorithm when calculating RMSD

-q, --use QCP algorithm instead of Kabsch algorithm

-r, --remove H atoms