indigo-depict

Usage: indigo-depict infile.{mol,rxn,smi} outfile.{png,svg,pdf} [parameters]
       indigo-depict infile.{sdf,rdf,smi} outfile_%s.{png,svg,pdf} [parameters]
       indigo-depict infile.{sdf,rdf}.gz outfile_%s.{png,svg,pdf} [parameters]
       indigo-depict infile.smi outfile.{mol,rxn} [parameters]
       indigo-depict infile.smi outfile.{sdf} [parameters]
       indigo-depict - SMILES outfile.{png,svg,pdf} [parameters]
       indigo-depict - SMILES outfile.{mol,rxn} [parameters]

Parameters:
-w
   Picture width in pixels
-h
   Picture height in pixels
-bond
   Average bond length in pixels (conflicts with -w and -h)
-margins
   Horizontal and vertical margins, in pixels. No margins by default
-commentmargins
   Horizontal and vertical margins around comment. No margins by default
-thickness
   Set relative thickness factor. Default is 1.0
-hydro
   Set implicit hydrogen display mode (default is terminalhetero)
-label
   Set atom label display mode (default is normal)
-[de]arom
   Force [de]aromatization
-stereo
   Stereogroups display mode (default is 'old')
-cdbwsa
   Center double bonds which have an adjacent stereo bond (disabled by default)
-query
   Treat the input as a query molecule or reaction (disabled by default)
-idfield
   SDF/RDF field to be put in place of '%s' in the names of saved files
   (default is molecule/reaction number)
-comment
   Text comment to be put above the molecule or reaction. No default value
-commentfield
   Use specified SDF/RDF field as a comment
-commentname
   Use molecule/reaction name as a comment
-commentsize
   Text comment font size factor relative to bond thickness (default 6)
-commentpos
   Text comment position (bottom by default)
-commentalign
   Text comment alignment (center by default)
-coloring
   Enable/disable coloring (enabled by default)
-hlthick
   Enable highlighting with thick lines and bold characters
-hlcolor
   Enable highlighting with color. Component values must be in range [0..255]
-bgcolor
   Set the background color. Component values must be in range [0..255]
-basecolor
   Set the default foreground color. Component values must be in range [0..255]
-aamcolor
   Set the color of AAM indices. Component values must be in range [0..255]
-commentcolor
   Set the color of the comment. Component values must be in range [0..255]
-atomnumbers
   Show atom numbers (for debugging purposes only)
-bondnumbers
   Show bond numbers (for debugging purposes only)
-help
   Print this help message

Examples:
   indigo-depict infile.mol outfile.png -coloring off -arom
   indigo-depict database.sdf molecule_%s.png -idfield cdbregno -thickness 1.1
   indigo-depict database.smi database.sdf
   indigo-depict - "CC.[O-][*-]([O-])=O" query.png -query
   indigo-depict - "OCO>>CC(C)N" reaction.rxn