obrms1
Calculate the heavy-atom rmsd between two chemically identical structures
Usage
obrms [-fmxso]
filename1
filename2
Overview
Computes the heavy-atom RMSD of identical compound structures. Structures in multi-structure files are compared one-by-one unless --firstonly is passed, in which case only the first structure in the reference file is used.
Options
-
-f, --firstonly -
use only the first structure in the reference file (otherwise the n-th molecule in the reference file is compared to the n-th molecule in the test file)
-
-m, --minimize -
Compute the minimum RMSD achievable by applying a rigid-body transformation to the test molecule
-
-x, --cross -
Compute all n^2 RMSDs between molecules of the reference file. Test file is ignored.
-
-s, --separate -
Separate reference file into constituent molecules (disconnected fragments) and report best RMSD
-
-t t, --timeout t -
Give up on matching after specified number of seconds
-
-o file, --out file -
Re-oriented test structure output (used with
-m)
Examples
obrms ref.sdf test.sdf
Calculate the RMSD between ref.sdf and test.sdf. Both files should have the same number of molecules.
obrms -f ref.sdf test.sdf
Calculate the RMSD between the first molecule in ref.sdf and each molecule in test.sdf.
History
- Arch Linux 2026-11-01: the text shown here
- Debian 13 (Trixie) to Debian 11 (Bullseye)
- Debian 10 (Buster)
--cross since Debian 11 (Bullseye);
--firstonly since Debian 11 (Bullseye);
--minimize since Debian 11 (Bullseye);
--out since Debian 11 (Bullseye);
--separate since Debian 11 (Bullseye);
--timeout since Arch Linux 2026-11-01;
-f since Debian 11 (Bullseye);
-m since Debian 11 (Bullseye);
-o since Debian 11 (Bullseye);
-s since Debian 11 (Bullseye);
-t since Arch Linux 2026-11-01;
-x since Debian 11 (Bullseye).