Molecule and reaction rendering utility
indigo-depict infile.{mol,rxn,cml,smi} outfile.{png,svg,pdf} [parameters]
indigo-depict infile.{cml,rdf,rdf.gz,sdf,sdf.gz,smi} outfile_%s.{png,svg,pdf} [parameters]
indigo-depict infile.smi outfile.{cml,mol,rdf,rxn,sdf} [parameters]
indigo-depict - SMILES outfile.{cml,mol,pdf,png,rxn,svg} [parameters]
indigo-depict -help
indigo-depict is used for depicting molecules.
indigo-depict can read input files or SMILES code from the standard input. These can be followed by one or more of the following parameters.
-w <number>
Picture width in pixels
-h <number>
Picture height in pixels
-bond <number>
Average bond length in pixels
-margins <number> <number>
Horizontal and vertical margins, in pixels. No margins by default
-thickness <number>
Set relative thickness factor. Default is 1.0
-linewidth <number>
Set bond line width factor. Default is 1.0
-label <none|hetero|terminal-hetero|all>
Set atom label display mode. Default is terminal-hetero
-hydro <on|off>
Show implicit hydrogens. Default is on
-[de]arom
Force [de]aromatization
-stereo <old|ext|none>
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)
-smarts
Treat the input as a SMARTS query molecule or reaction (disabled by default)
-idfield <string>
SDF/RDF field to be put in place of '%s' in the names of saved files (default is molecule/reaction number)
-catalysts <above|above-and-below>
Reaction catalysts placement w.r.t. the arrow. Default is above-and-below
-comment <string>
Text comment to be put above the molecule or reaction. No default value
-commentoffset <number>
Vertical space (in pixels) between the comment and the structure
-commentfield <string>
Use specified SDF/RDF field as a comment
-commentname
Use molecule/reaction name as a comment
-commentsize <number>
Text comment font size factor relative to bond thickness. Default is 6
-commentpos <top|bottom>
Text comment position (bottom by default)
-commentalign <0..1>
Text comment alignment, a float value: 0 = left, 0.5 = center, 1 = right
-coloring <on|off>
Enable/disable coloring. Default is on
-hlthick
Enable highlighting with thick lines and bold characters
-hlcolor <red> <green> <blue>
Enable highlighting with color. Component values must be in range [0..255]
-bgcolor <red> <green> <blue>
Set the background color. Component values must be in range [0..255]
-basecolor <red> <green> <blue>
Set the default foreground color. Component values must be in range [0..255]
-aamcolor <red> <green> <blue>
Set the color of AAM indices. Component values must be in range [0..255]
-dsgcolor <red> <green> <blue>
Set the color of data SGroups. Component values must be in range [0..255]
-commentcolor <red> <green> <blue>
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)
-onebased
Start atom and bond indices from one. Default is from zero
-help
Print this help message
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
This manual page was written by Daniel Leidert <[email protected]>, for the Debian GNU/Linux system (but may be used by others).