Depicting Substructure Search Match¶
A program that performs a substructure search initialized with the given SMARTS pattern and highlights the identified matches on the depicted molecule.
Command Line Interface¶
A description of the command line interface can be obtained by executing the program with the –help argument.
prompt> Match2Img --help
will generate the following output:
Simple parameter list
highlight options :
-highlightcolor : Highlighting color
-highlightstyle : Highlighting style
image options :
-height : Height of output image
-width : Width of output image
input/output options :
-in : Input filename
-out : Output filename
-smarts : SMARTS pattern
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
prepare depiction options :
-clearcoords : Clear and regenerate 2D coordinates of molecule(s)
-orientation : Set the preferred orientation of 2D coordinates
-suppressH : Suppress explicit hydrogens of molecule(s)
Code¶
Download code
See also
- OEConfigureImageOptions function
- OEConfigurePrepareDepictionOptions function
- OEConfigure2DMolDisplayOptions function
- OEConfigureHighlightParams function
- OESetup2DMolDisplayOptions function
- OESubSearch class
- OEPrepareDepictionOptions class
- OESetupPrepareDepictionOptions function
- OEPrepareDepiction function
- OEGetImageWidth and OEGetImageHeight functions
- OE2DMolDisplayOptions class
- OESetup2DMolDisplayOptions function
- OE2DMolDisplay class
- OEGetHighlightStyle and OEGetHighlightColor functions
- OEPrepareSearch function
- OEAddHighlighting function
- OERenderMolecule function
Examples¶
prompt> Match2Img -in indole.ism -out image.png -smarts "c1ccccc1"
will generate the image shown in Figure: Example of using the program with default highlighting

Example of using the program with default highlighting
prompt> Match2Img -in indole.ism -out image.png -smarts "c1ccccc1" -highlightcolor green
will generate the image shown in Figure: Example of using the program with green highlighting

Example of using the program with green highlighting
prompt> Match2Img -in indole.ism -out image.png -smarts "c1ccccc1" -highlightstyle BallAndStick
will generate the image shown in Figure: Example of using the program with ball and stick

Example of using the program with ball and stick highlighting
See also
- Highlighting chapter