4.2 checkcff

This is a simple utility that will simply apply a color force field to one or more input molecules and output a report of color atoms added, the TYPE of the added atom and the corresponding input molecule atoms that matched the SMARTS defining that TYPE. Additionally, checkcff will output an OEB file containing molecules with the color atoms added. This file can be loaded into Vida2 and the atoms labeled with ``Name" to see visually inspect which color atoms are being added.

checkcff only has 1 required commandline parameter.

-in: Input molecule file to be colored. Can be any one of the molecule file formats described in Section 2.2.2.

There are 3 optional parameters.

-chemff: Color-force-field name. Either the name of one of the built-in color force fields (ImplicitMillsDean or ExplicitMillsDean) or the name of a user-defined color force field file. The format of this file is given in section 2.6. [default = ImplicitMillsDean]
-out: Output OEB file name for 3D structures with color atoms named by the TYPE from the color force field. [default = checkcff.oeb]
-report: File name for text report. If the special filename, '-' is used, the report will be written to stdout.

By default, checkcff will use the ImplicitMillsDean color force field. This can be over-ridden by using the -chemff option and providing either a name of one of the built-in color force fields (ImplicitMillsDean or ExplicitMillsDean) or the name of a user-defined color force field file.

So to see which atoms are considered color atoms using the ImplicitMillsDean force field:

prompt> checkcff -in mymolecules.sdf -report color.txt

To use the ExplicitMillsDean force field to see which atoms are considered to be color atoms:

prompt> checkcff -in molecules.sdf -report color.txt -chemff ExplicitMillsDean

Both of the above examples will write an output file called ``checkcff.oeb" that can be loaded into Vida2 to visualize the placement of color atoms.

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