Gensign command

The gensign command is not something that is normally part of the workflow, but a way to validate the resulting signature descriptors for molecules without starting any heavy jobs.

Parameters

The full usage menu can be retrieved by running command:

> java -jar cpsign-[version].jar gensign -h

                                               gensign
SYNOPSIS
----------------------------------------------------------------------------------------------------
   gensign [options]
   gensign @/tmp/runconfigs/parameters.txt [options]
   gensign @C:\Users\User\runconfigs\parameters.txt [options]


DESCRIPTION
----------------------------------------------------------------------------------------------------
   Command gensign generates the signatures for given molecules. Signature generation is automatic
   within CPSign when running all other commands, this method is only intended to give the user a
   grasp of how signatures will be generated and how signature heights affect the generated
   signatures.


OPTIONS
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   Input options:
      -sm, --smiles  [SMILES]
         SMILES string to generate signatures of
      -p, --predictfile  [URI] or [path]
         File to generate signatures of. Accepted formats are SMILES-file (one SMILES per line,
         optionally including tab-delimited data), SDFfile

   Signature generation options:
      -hs, --height-start  [integer]
         Signatures start height
         Default: 1
      -he, --height-end  [integer]
         Signatures end height
         Default: 3
      -sg, --signatures-generator  [text]
         Type of signatures that should be used, note that stereo-signatures take much longer time to
         compute. Options:
           normal (default)
           stereo (experimental mode)
         Default: default

   Output options:
      -of, --output-format  [text value]
         output format of predictions, options:
           json
           smiles/plain
           sdf/sdf-v2000
           sdf-v3000
         Default: json
      -o, --output  [path]
         File to write output to (default is printing to screen)
      --output-inchi
             Generate InChI and InChIKey in the output
             Default: false
      --compress
         If the outputfile should be compressed
         Default: false

   General options:
    * --license  [path]
         Path to license file
      --logfile  [path]
         Path to a user set logfile, will be specific for this run
      --silent
         Silent mode (only print output to logfile)
         Default: false
      --echo
         Echo the input arguments given to CPSign
         Default: false
      -h, --help
         Get help for this command
         Default: false
      --time
         Print wall-time for all individual steps in execution
         Default: false

Gensign requires a valid Standard or PRO license as stated in the usage manual, but it will also require to use --smiles, -p or both flags.

Example Usage

> java -jar cpsign-[version].jar gensign \
   --smiles CC(=O)OC1=CC=CC=C1C(=O)O \
   --license /path/to/Standard-license.license

Running with Standard license: License registered to: [Name] [Company] . Expiry date is: [Date]

Starting signature generation..
{
   "Molecule":{
      "SMILES":"CC(=O)OC1=CC=CC=C1C(=O)O"
      },
   "Generated Signatures":["[C]([C])","[C]([C][O]=[O])","[O](=[C])","[O]([C][C])","[C](p[C]p[C][O])",
      "[C](p[C]p[C])","[C](p[C]p[C])","[C](p[C]p[C])","[C](p[C]p[C])","[C]([C]p[C]p[C])","[C]([C][O]=[O])",
      "[O](=[C])","[O]([C])","[C]([C]([O]=[O]))","[C]([C]=[O][O]([C]))","[O](=[C]([C][O]))",
      "[O]([C](p[C]p[C])[C]([C]=[O]))","[C](p[C](p[C])p[C]([C]p[C])[O]([C]))","[C](p[C](p[C])p[C](p[C][O]))",
      "[C](p[C](p[C])p[C](p[C]))","[C](p[C](p[C])p[C](p[C]))","[C](p[C](p[C])p[C]([C]p[C]))",
      "[C](p[C](p[C])p[C](p[C][O])[C]([O]=[O]))","[C]([C](p[C]p[C])[O]=[O])","[O](=[C]([C][O]))",
      "[O]([C]([C]=[O]))","[C]([C](=[O][O]([C])))","[C]([C]=[O][O]([C](p[C]p[C])))","[O](=[C]([C][O]([C])))",
      "[C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0])[C]([O]=[O]))[O]([C]([C]=[O])))",
      "[C](p[C](p[C](p[C,0]))p[C](p[C]([C]p[C,0])[O]([C])))","[C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0][O])))",
      "[C](p[C](p[C](p[C,0]))p[C](p[C]([C]p[C,0])))","[C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0][O])[C]([O]=[O])))",
      "[C](p[C](p[C](p[C,0]))[C]([O]=[O])p[C](p[C](p[C,0])[O]([C])))","[C]([C](p[C](p[C])p[C](p[C][O]))[O]=[O])",
      "[O](=[C]([C](p[C]p[C])[O]))","[O]([C]([C](p[C]p[C])=[O]))"]
}
Finished Signature Generation