NAME
indigo-depict - molecule and reaction rendering utility
SYNOPSIS
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
DESCRIPTION
indigo-depict is used for depicting molecules.
OPTIONS
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
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
AUTHOR
This manual page was written by Daniel Leidert <[email protected]>, for the Debian GNU/Linux system (but may be used by others).