Depicting MDL Query Substructure Search Hits

A program that performs substructure search on a molecule using an MDL query and generates an image file one match per molecule.

Command Line Interface

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

prompt> java ViewMDLSearch --help

Will generate the following output:

Simple parameter list
 general options :
   -align : Align hits to query

 highlight options :
   -highlightcolor : Highlighting color
   -highlightstyle : Highlighting style

 input/output options :
   -out : Output image filename
   -query : Input query filename
   -target : Input target 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
   -scale : Scaling of the depicted molecule
   -superdisp : Super atom display style
   -titleloc : Location of the molecule title

 report options :
   -colsperpage : Number of columns per page
   -pageheight : Page height
   -pageorientation : Page orientation
   -pagesize : Page size
   -pagewidth : Page width
   -rowsperpage : Number of rows per page

See also