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indigo-depict - Online in the Cloud

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This is the command indigo-depict that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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