Table of Contents

1. rmsdModerators
   1. Background
   2. Prerequisites
   3. Parameter setting of calculate_rmsd.py
   4. Typical session

rmsdModerators

Background

Complementary to a manual call of of Jimmy Charnley's calculate_rmsd.py (https://github.com/charnley/rmsd) with two model data A and B providing access to Kabsch and quaternion test, I faced the situation to compare multiple structures (more than 50 per run) where each model contains about a dozen of identical molecules.

An acceleration of the analysis was needed, since the the typical batch wise comparison of such a round Robin tournament with (n) model data has to consider (n (n-1)/2) tests to perform. Specific to Python, the "classical" approach is hampered since the GIL will allow only a linear, sequential testing.

Script multipro.py is a moderator script to address the problem differently, relaying the computation to multiple instances of calculate_rmsd.py working independently from each other in multiple cores of a CPU. Meant as proof of concept only, the script intentionally omits possible extensions (e.g., an os.walk).

Prerequisites

While calculate_rmsd.py (version 1.3.2) is agnostic to either Python2 or Python3, this script was written for Python3 only. Place the moderator script, multipro.py, as well as the two *.py by Jimmy Charnley (calculate_rmsd.py and __init__.py) into the same directory containing the *.xyz to scrutinize. Beside these three files and the five test *.xyz, the project contains this README as *.org and *.md as well as a LICENSE (eleven files in total).

Check the computer to be used. At present, the maximum number of tests performed simultaneously is set to equal 3 (three, line #79) which balances nicely gain in performance with resources still available for other (light weight) interaction with a quadrocore processor computer. Feel free to increase / adapt this number at your own risk. Launch the moderator script from the terminal by

python3 multipro.py

At any time the execution of the script may be aborted (Ctrl + C).

Parameter setting of calculate_rmsd.py

Lines #46 to #48 define how calculate_rmsd.py shall work. In the sub-process initiated, modelA (m0) is compared with modelB (m1). Beside these mandatory parameters, the moderator script relays the optional parameter --reorder to resort the atoms according to the Hungarian algorithm as preparation for the scrutiny.

The following, equally optional, parameter --use-reflections specifies how calculate_rmsd.py shall find an optimal alignment between modelA and modelB. By default, the algorithm attempts the optimization by translation and rotation of modelB in respect to modelA. Calling the additional method --use-reflections allows the script to test orientations obtained by reflection of modelB in respect of modelA's coordinate system. As a word of caution, note that this approach inverts the absolute configuration of stereogenic centres if the number of reflections performed is odd. You may replace this inversion test by the conservative optional parameter --use-reflections-keep-stereo; here, the refined alignment is either obtained by no reflection of modelB, or by an even number of reflections of modelB in respect of the coordinate system of modelA (a.k.a. retention of stereo configuration).

Additional information about parameters calculate_rmsd.py may be engage with may be found by calling the script directly

python calculate_rmsd.py

and on Jimmy Charnley's GitHub page.

Typical session

With the five test *.xyz data provided, aiming to determine the RMSD, the output on the CLI is the following:

user@computer:~/Desktop/test$ python3 multipro.py 
python3 calculate_rmsd.py 00_1-O.xyz 01_2-O.xyz --reorder --use-reflections
python3 calculate_rmsd.py 00_1-O.xyz 02_3-O.xyz --reorder --use-reflections
python3 calculate_rmsd.py 00_1-O.xyz 03_4-O.xyz --reorder --use-reflections
4.33091155461067
python3 calculate_rmsd.py 00_1-O.xyz 04_5-O.xyz --reorder --use-reflections
4.4884719544340745
python3 calculate_rmsd.py 01_2-O.xyz 02_3-O.xyz --reorder --use-reflections
4.444536428221002
python3 calculate_rmsd.py 01_2-O.xyz 03_4-O.xyz --reorder --use-reflections
3.9324928926740563
python3 calculate_rmsd.py 01_2-O.xyz 04_5-O.xyz --reorder --use-reflections
6.009884394622477
python3 calculate_rmsd.py 02_3-O.xyz 03_4-O.xyz --reorder --use-reflections
3.8063118346513205
python3 calculate_rmsd.py 02_3-O.xyz 04_5-O.xyz --reorder --use-reflections
2.7791567741970487
5.657525349751654
python3 calculate_rmsd.py 03_4-O.xyz 04_5-O.xyz --reorder --use-reflections
5.208090413262542
5.4498954394137105