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INDIGO-DEPICT(1) User Manual INDIGO-DEPICT(1)

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.

Picture width in pixels
Picture height in pixels
Average bond length in pixels
Horizontal and vertical margins, in pixels. No margins by default
Set relative thickness factor. Default is 1.0
Set bond line width factor. Default is 1.0
Set atom label display mode. Default is terminal-hetero
Show implicit hydrogens. Default is on
-[de]arom
Force [de]aromatization
Stereogroups display mode. Default is old
Center double bonds which have an adjacent stereo bond (disabled by default)
Treat the input as a query molecule or reaction (disabled by default)
Treat the input as a SMARTS query molecule or reaction (disabled by default)
SDF/RDF field to be put in place of '%s' in the names of saved files (default is molecule/reaction number)
Reaction catalysts placement w.r.t. the arrow. Default is above-and-below
Text comment to be put above the molecule or reaction. No default value
Vertical space (in pixels) between the comment and the structure
Use specified SDF/RDF field as a comment
Use molecule/reaction name as a comment
Text comment font size factor relative to bond thickness. Default is 6
Text comment position (bottom by default)
Text comment alignment, a float value: 0 = left, 0.5 = center, 1 = right
Enable/disable coloring. Default is on
Enable highlighting with thick lines and bold characters
Enable highlighting with color. Component values must be in range [0..255]
Set the background color. Component values must be in range [0..255]
Set the default foreground color. Component values must be in range [0..255]
Set the color of AAM indices. Component values must be in range [0..255]
Set the color of data SGroups. Component values must be in range [0..255]
Set the color of the comment. Component values must be in range [0..255]
Show atom numbers (for debugging purposes only)
Show bond numbers (for debugging purposes only)
Start atom and bond indices from one. Default is from zero
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 <dleidert@debian.org>, for the Debian GNU/Linux system (but may be used by others).

29/12/2013 indigo