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 VIDA and the atoms labeled with Name to visually inspect which color atoms are being added.
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
Finally, to generate a report file and an OEB file that can be viewed in VIDA:
prompt> checkcff -in 4cox-neutral.sdf -report color.txt -out checkcff.oeb
The report file would look like:
----------------------------------------------------------- Title: 4cox-ligD self color: -8.0 #1 Type: rings SMARTS Atoms: C1-C2-C8-C9-N1 #2 Type: rings SMARTS Atoms: C1-C2-C3-C4-C5-C6 #3 Type: rings SMARTS Atoms: C11-C16-C15-C14-C13-C12 #4 Type: acceptor SMARTS Atoms: O1 #5 Type: acceptor SMARTS Atoms: O2 #6 Type: acceptor SMARTS Atoms: O3 #7 Type: acceptor SMARTS Atoms: O4 #8 Type: anion SMARTS Atoms: O4-C19-O3
And the view in VIDA might look a bit like:
A description of the command line interface can be obtained by executing CheckCff with the --help option.
> checkcff --help
will generate the following output:
Help functions: checkcff --help simple : Get a list of simple parameters checkcff --help all : Get a complete list of parameters checkcff --help defaults : List the defaults for all parameters checkcff --help <parameter> : Get detailed help on a parameter checkcff --help html : Create an html help file for this program checkcff --help versions : List the toolkits and versions used in the application
checkcff only has 1 required commandline parameter.
There are 3 optional parameters.
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 Color Force Field.
[default = ImplicitMillsDean]
Output OEB file name for 3D structures with color atoms named by the TYPE from the color force field.
[default = checkcff.oeb]
File name for text report. If the special filename, - is used, the report will be written to stdout.