OBRMS(1) General Commands Manual (urm) OBRMS(1)

obrms — Calculate the heavy-atom RMSD between two chemically identical structures

obrms [-fmxso] filename1 filename2

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.

, --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)
, --minimize
Compute the minimum RMSD achievable by applying a rigid-body transformation to the test molecule
, --cross
Compute all n^2 RMSDs between molecules of the reference file. Test file is ignored.
, --separate
Separate reference file into constituent molecules (disconnected fragments) and report best RMSD
t, --timeout t
Give up on matching after specified number of seconds
file, --out file
Re-oriented test structure output (used with -m)

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.

obfit(1).

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May 26, 2026 Open Babel 3.2