Depicting a Single Molecule¶

A program that converts a molecular structure 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 Mol2Img --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
   -ringdict : User-defined 2D ring dictionary

 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

Mol2Img.java and Mol2Img.txt interface file

Examples¶

prompt> java Mol2Img -in nexium.ism -out image.png

will generate the image shown in Figure: Example of using the program with default parameters.

Example of using the program with default parameters¶

prompt> java Mol2Img -in nexium.ism -out image.png -atomcolor WhiteMonochrome

will generate the image shown in Figure: Example of using the program with the white monochrome atom coloring style.

Example of using the program with the white monochrome atom coloring style¶

prompt> java Mol2Img -in nexium.ism -out image.png -aromstyle Circle

will generate the image shown in Figure: Example of using the program with aromaticity style ‘Circle’.

Example of using the program with aromaticity style ‘Circle’¶

prompt> java Mol2Img -in nexium.ism -out image.png -atomstereostyle "AtomStereo|CIPAtomStereo"

will generate the image shown in Figure: Example of the mol2img program with CIP atom stereo option.

Example of using the program with CIP atom stereo option¶

prompt> java Mol2Img -in nexium.ism -out image.png -linewidth 4

will generate the image shown in Figure: Example of using the program with user-defined line width.

Example of using the program with user-defined line width¶

prompt> java Mol2Img -in nexium.ism -out image.png -superdisp All

will generate the image shown in Figure: Example of using the program with superatom style.

Example of using the program with superatom style¶

Note

The above program can generate 2D coordinates with user-defined 2D ring layouts when using the -ringdict parameter.

See also the 2D coordinate generation examples section of the OEChem TK manual that shows examples about how to generate and utilize user-defined ring dictionaries.