indigo-depict - molecule and reaction rendering utility

       This manual page was written by Daniel Leidert <dleidert@debian.org>, for  the  Debian  GNU/Linux  system
       (but may be used by others).

indigo                                             29/12/2013                                   INDIGO-DEPICT(1)

indigo-depict is used for depicting molecules.

indigo-depictinfile.moloutfile.png-coloringoff-aromindigo-depictdatabase.sdfmolecule_%s.png-idfieldcdbregno-thickness1.1indigo-depictdatabase.smidatabase.sdfindigo-depict-CC.[O-][*-]([O-])=Oquery.png-queryindigo-depict-OCO>>CC(C)Nreaction.rxn

       indigo-depict - molecule and reaction rendering utility

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-depictinfile.{mol,rxn,cml,smi}outfile.{png,svg,pdf} [parameters]

       indigo-depictinfile.{cml,rdf,rdf.gz,sdf,sdf.gz,smi}outfile_%s.{png,svg,pdf} [parameters]

       indigo-depictinfile.smioutfile.{cml,mol,rdf,rxn,sdf} [parameters]

       indigo-depict-SMILESoutfile.{cml,mol,pdf,png,rxn,svg} [parameters]

       indigo-depict-help