obfit1
Superimpose two molecules based on a pattern
Usage
obfit SMARTS-pattern
fixed-file
outfile
Overview
Superimpose two molecules using a quaternion fit. The atoms used to fit the two molecules are defined by the SMARTS-pattern given by the user. It is useful to align congeneric series of molecules on a common structural scaffold for 3D-QSAR studies. It can also be useful for displaying the results of conformational generation.
Any molecules matching the supplied SMARTS-pattern will be rotated and translated to provide the smallest possible RMSD between the matching regions. If a molecule does not match the SMARTS-pattern, it will be output with no transformation.
Examples
Align all the molecules in 'testmv.sdf' on a single molecule of 'testref.sdf' by superimposing them on its N-methylpiperidyl portion (and outputting a new SD file to the standard output):
obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf
Releases
11 releases since Debian 4.0 (Etch); the text changed 4 times.