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 VIDA and the atoms labeled with Name to visually inspect which color atoms are being added.

checkcff only has 1 required commandline parameter.

-in <filename>

Input molecule file to be colored. Can be any one of the molecule file formats described in Section The Query File.

There are 3 optional parameters.

-chemff <cff_file>

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]

-out <oebfile>

Output OEB file name for 3D structures with color atoms named by the TYPE from the color force field.

[default = checkcff.oeb]

-report <filename>

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

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:

VIDA view of molecule with color atoms.

VIDA view of 4COX with color atoms attached and labeled.