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
See also
- MDL Reaction Depiction chapter
- OEConfigureImageOptions function
- OEConfigure2DMolDisplayOptions function
- OEIsRegisteredImageFile function
- OEReadMDLReactionQueryFile function
- OEPrepareDepiction function
- OEGetImageWidth and OEGetImageHeight functions
- OE2DMolDisplayOptions class
- OESetup2DMolDisplayOptions function
- OE2DMolDisplay class
- OERenderMolecule function
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
See also
- MDL Reaction Depiction chapter