RMSDFlow

Description

RMSDFlow is a Python 3 script that computes the Root Mean Squared Deviation (RMSD) between one or several input molecular structures and one or more references.

RMSDFlow's force relies on its implementation of the Hungarian Algorithm to correctly account for poses related by symmetry operations.
It is also capable of using more classical algorithms to compute the RMSD.

Usage

All input structures must be MOL2 files, with a single molecule per file.

RMSDFlow

• -r|--reference FILE(S) : Path to 1 or several reference mol2 file(s).
• -i|--input FILE(S) : Path to 1 or several input mol2 file(s).
• -a|--algorithm ALGO :
  • ha : Hungarian Algorithm (Recommended)
  • std : Standard, matches atom names. Compatible with --cutoff and --outliers
  • mda : Minimal Distance Algorithm. Compatible with --cutoff and --outliers
• --hydrogen : Read hydrogen atoms.
• --cutoff DISTANCE : Atomic distance cut-off. Used to ignore outliers and do MDA optimization. Default : 2.0
• --outliers : Ignore outliers (atoms that cannot find a match while having a pairwise distance below CUTOFF).
• -o|--output NAME : Output a CSV file containing RMSD between reference and input molecules.
• -p|--plot : Plot RMSD by input molecule, show the plot and save as a PNG image. The input molecules are sorted according to their RMSD with the first reference molecule given, before plotting.
• -v|--verbose : Increase output verbosity
• -s|--silent : Don't output RMSD results on the terminal.

Example

RMSDFlow -r ref.mol2 -i ref_conf_*.mol2 -a ha -v -p

Output :

RMSD (46/84 atoms) ref - ref_conf_01 : 0.510324
RMSD (46/84 atoms) ref - ref_conf_02 : 0.534447
RMSD (46/84 atoms) ref - ref_conf_03 : 1.865758
RMSD (46/84 atoms) ref - ref_conf_04 : 1.655034
RMSD (46/84 atoms) ref - ref_conf_05 : 1.565401
RMSD (46/84 atoms) ref - ref_conf_06 : 2.358195
RMSD (46/84 atoms) ref - ref_conf_07 : 1.518066
RMSD (46/84 atoms) ref - ref_conf_08 : 2.415969
RMSD (46/84 atoms) ref - ref_conf_09 : 2.985259
RMSD (46/84 atoms) ref - ref_conf_10 : 1.793072
RMSD (46/84 atoms) ref - ref_conf_11 : 3.017879
RMSD (46/84 atoms) ref - ref_conf_12 : 2.105146
RMSD (46/84 atoms) ref - ref_conf_13 : 2.979824
RMSD (46/84 atoms) ref - ref_conf_14 : 1.730604
RMSD (46/84 atoms) ref - ref_conf_15 : 1.246444
RMSD (46/84 atoms) ref - ref_conf_16 : 2.717990
RMSD (46/84 atoms) ref - ref_conf_17 : 1.571292
RMSD (46/84 atoms) ref - ref_conf_18 : 2.225690
RMSD (46/84 atoms) ref - ref_conf_19 : 1.385847
RMSD (46/84 atoms) ref - ref_conf_20 : 2.959397
Saved figure rmsd_plot.png