Depicting MDL Reaction¶

A program that converts an MDL reaction into an image file.

Command Line Interface¶

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> java MDLReaction2Img --help

will generate the following output:

Simple parameter list

 image options :
   -height : Height of output image
   -width : Width of output image

 input/output options :
   -in : Input filename
   -out : Output filename

 molecule display options :
   -aromstyle : Aromatic ring display style
   -atomcolor : Atom coloring style
   -atomlabelfontscale : Atom label font scale
   -atomprop : Atom property display
   -atomstereostyle : Atom stereo display style
   -bondcolor : Bond coloring style
   -bondprop : Bond property display
   -bondstereostyle : Bond stereo display style
   -hydrstyle : Hydrogen display style
   -linewidth : Default bond line width
   -protgroupdisp : Protective group display style
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

Code¶

Download code

MDLReaction2Img.java and MDLReaction2Img.txt interface file

Examples¶

prompt> java MDLReaction2Img -in mdlreaction.sdf -out image.png

will generate the following image: Figure: Example of depicting an MDL reaction

Example of depicting an MDL reaction¶

prompt> java MDLReaction2img -in mdlreaction.sdf -out image.png -atomprop MapIdx

will generate the following image: Figure: Example of depicting an MDL reaction with atom map indices

Example of depicting an MDL reaction with atom map indices¶