|obrms(1)||General Commands Manual (urm)||obrms(1)|
obrms — Calculate
the heavy-atom RMSD between two chemically identical structures
||[-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.
- use only the first structure in the reference file (otherwise the nth molecule in the reference file is compared to the nth molecule in the test file)
- Compute the minimum RMSD achievable by applying a rigid-body transformation to the test molecule
- Compute all n^2 RMSDs between molecules of the reference file. Test file is ignored.
- Separate reference file into constituent molecules (disconnected fragments) and report best RMSD
- 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.
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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|October 10, 2019||Open Babel 3.1|