Is it possible to colour whole molecules using terminal?

I have generated such a command:

/Applications/ChemAxon/JChem/bin/molconvert png:scale500,H_off,#ffffffff,setcolors:a:#fff67e,b:#fff67e /Users/User/Desktop/123/1461.smi -o /Users/User/Desktop/genImages/asn/1461.png

Though for (a) and (b) I have to write a set of atoms/bonds. Is it possible to write somewhat like 'all', to colour all bonds and atoms?

Hi Anastasia,

according to our documentation there is an additional value within "setcolors" parameter. It says the following: "Use "ak:#rrggbb" for atom set k, "bk:#rrggbb" for bond set k."

Since the default atom and bond set value is zero, the following line might works.

molconvert "png:scale500,H_off,setcolors:a0:#fff67e:b0:#fff67e" /Users/User/Desktop/123/1461.smi -o /Users/User/Desktop/genImages/asn/1461.png

Sincerelly, Zoltan.

It doesn't work

Here is the command:

/Applications/ChemAxon/JChemSuite/bin/molconvert png:scale500,H_off,#ffffffff,setcolors:a0:#fff67e,b0:#fff67e /Users/user/Desktop/FolderForAnalysis/IMAGES_GEN/SMI/mol3647.smi -o /Users/user/Desktop/FolderForAnalysis/IMAGES_GEN/img/mol3647.png

And here is the output:

Invalid bits/pixel option "b0". Valid values are 1, 2, 4, 8, 24, 32

Hi Anastasia,

try it out with colon before b0 rather than a comma:

/Applications/ChemAxon/JChemSuite/bin/molconvert "png:scale500,H_off,#ffffffff,setcolors:a0:#fff67e:b0:#fff67e" /Users/user/Desktop/FolderForAnalysis/IMAGES_GEN/SMI/mol3647.smi -o /Users/user/Desktop/FolderForAnalysis/IMAGES_GEN/img/mol3647.png

Regards, Zoltan

Thank you! It has finally worked out)