Description

References:

• Eric W. Bell & Yang Zhang DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of Cheminformatics volume 11, Article number: 40 (2019)

• pyDockRMSD Main Site

• Module Name: pydockrmsd (see the modules page for more information)
• singlethreaded
• Example files in $PYDOCKRMSD_EXAMPLES

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pydockrmsd

[user@cn3144 ~]$  

[user@cn3144 ~]$ mkdir test && cd test
[user@cn3144 ~]$ cp -Rp ../github/pyDockRMSD/examples/data .
[user@cn3144 ~]$ cat << EOF > z.py
from pydockrmsd.dockrmsd import PyDockRMSD
import pydockrmsd.hungarian as hungarian
dockrmsd = PyDockRMSD("./data/targets/1a8i/crystal.mol2",
                      "./data/targets/1a8i/vina1.mol2")
print(dockrmsd.rmsd)
print(dockrmsd.total_of_possible_mappings)
print(dockrmsd.optimal_mapping)
print(dockrmsd.error)
print(hungarian("./data/targets/1a8i/crystal.mol2",
                "./data/targets/1a8i/vina1.mol2"))
EOF
[user@cn3144 ~]$ python z.py
0.692337048145839
108.0
Optimal mapping (First file -> Second file, * indicates correspondence is not one-to-one):
C  1 -> C  1
C  2 -> C  2
O  3 -> O 15 *
C  4 -> C  3 *
O  5 -> O 17 *
C  6 -> C  4 *
O  7 -> O 22 *
C  8 -> C  5 *
C  9 -> C 19 *
O 10 -> O 20 *
O 11 -> O  6 *
N 12 -> N  7 *
C 13 -> C  8 *
O 14 -> O  9 *
N 15 -> N 10 *
C 16 -> C 11 *
O 17 -> O 12 *

0.6923022121452281

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. pydockrmsd.sh). For example:

#!/bin/bash
set -e
module load pydockrmsd
python my_pydockrmsd_script.py

Submit this job using the Slurm sbatch command.

sbatch pydockrmsd.sh