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 <dleidert@debian.org>, for the Debian
       GNU/Linux system (but may be used by others).