This is the command obfit that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
obfit — superimpose two molecules based on a pattern
SYNOPSIS
obfit SMARTS-pattern fixed-file outfile
DESCRIPTION
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
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