Next-Generation Organic Chemistry Toolkit from SciTouch LLC
The utility is called dingo-render.exe in Windows distribution or simply dingo-render in Linux or Mac OS X distribution. For Windows, the third-party library libcairo-2.dll and its dependencies are included as well. On Linux and Mac OS X, you should have libcairo installed on your system.
Distributions are offered in 32-bit and 64-bit versions.
The help message from the program is the following:
Usage: dingo-render infile.{mol,rxn,smi} outfile.{png,svg,pdf} [parameters]
dingo-render infile.{sdf,rdf,smi} outfile_%s.{png,svg,pdf} [parameters]
dingo-render infile.{sdf,rdf}.gz outfile_%s.{png,svg,pdf} [parameters]
dingo-render infile.smi outfile.{mol,rxn} [parameters]
dingo-render infile.smi outfile.{sdf,rdf} [parameters]
dingo-render - SMILES outfile.{png,svg,pdf} [parameters]
dingo-render - SMILES outfile.{mol,rxn} [parameters]
Parameters:
-w <number>
Picture width in pixels
-h <number>
Picture height in pixels
-bond <number>
Average bond length in pixels (conflicts with -w and -h)
-marginfactor <number>
Set margin relative to average bond length. Default is 1.0
-thickness <number>
Set relative thickness factor. Default is 1.0
-hydro <none|terminal|hetero|terminalhetero|all>
Set implicit hydrogen display mode (default is terminalhetero)
-label <normal|forceshow|hideterminal|forcehide>
Set atom label display mode (default is normal)
-[de]arom
Force [de]aromatization
-stereo <old|ext>
Stereogroups display mode (default is 'old')
-cdbwsa
Center double bonds which have an adjacent stereo bond (disabled by default)
-id <string>
SDF/RDF field to be put in place of '%s' in the names of saved files
(default is molecule/reaction number)
-coloring <on|off>
Enable/disable coloring (enabled by default)
-hlthick
Enable highlighting with thick lines and bold characters
-hlcolor <red> <green> <blue>
Enable highlighting with color. Component values must be in range [0..255]
-bgcolor <red> <green> <blue>
Set the background color. Component values must be in range [0..255]
-basecolor <red> <green> <blue>
Set the default foreground color. Component values must be in range [0..255]
-aamcolor <red> <green> <blue>
Set the color of AAM indices. Component values must be in range [0..255]
-atomnumbers
Show atom numbers (for debugging purposes only)
-bondnumbers
Show bond numbers (for debugging purposes only)
-help
Print this help message
Examples:
dingo-render infile.mol outfile.png -coloring off -arom
dingo-render database.sdf molecule_%s.png -id cdbregno -thickness 1.1
dingo-render database.smi database.sdf
dingo-render - "CC.[O-][*-]([O-])=O" outfile.png
dingo-render - "OCO>>CC(C)N" reaction.rxn
The illustrations for the Bingo User Manual were rendered on Linux by the following commands:
#!/bin/sh
for F in *rxn; do ./dingo-render $F `basename $F .rxn`.svg -hlcolor 0 0 120 -hlthick \
-bond 30 -coloring off -aamcolor 154 0 255 -hydro none; done
for F in *mol; do ./dingo-render $F `basename $F .mol`.svg -hlcolor 0 0 120 -hlthick \
-bond 30 -coloring off -hydro none; done