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