Gensign¶
The gensign program 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.
Table of Contents
Parameters¶
The full usage menu can be retrieved by running command:
> java -jar cpsign-[version].jar gensign
gensign
SYNOPSIS
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gensign [options]
gensign @/tmp/runconfigs/parameters.txt [options]
gensign @C:\Users\User\runconfigs\parameters.txt [options]
DESCRIPTION
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Gensign generates the signatures for given molecules. Signature generation is automatic
within CPSign when running all other programs, this program is only intended to give the
user a grasp of how signature descriptors will be generated and how signature heights
affect the generated descriptors.
OPTIONS
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Input:
-sm | --smiles [SMILES]
SMILES string to generate signatures of
-i | --input [format] [opt args] [URI | path]
Path or URI to a SDF, CSV or json-file
Signature generation:
-hs | --height-start [integer]
Signatures start height
Default: 1
-he | --height-end [integer]
Signatures end height
Default: 3
-sg | --signatures-generator [id | text]
Type of signatures that should be used, note that stereo-signatures take much
longer time to compute. Stereo signatures also requires input data to have stereo
information explicitly given in the file. Options:
(1) default | normal
(2) stereo (experimental mode)
Default: 1
Output:
-of | --output-format [id | text]
Output format of predictions, options:
(1) json
(2) smiles | plain
(3) sdf | sdf-v2000
(4) sdf-v3000
Default: 1
-o | --output [path]
File to write output to (default is printing to screen)
--output-inchi
Generate InChI and InChIKey in the output
--compress
If the outputfile should be compressed (only possible when writing to file)
General:
* --license [URI | path]
Path or URI to license file
-h | --help | man
Get help text
--short
Use shorter help text (used together with the --help argument)
--logfile [path]
Path to a user-set logfile, will be specific for this run
--silent
Silent mode (only print output to logfile)
--echo
Echo the input arguments given to CPSign
--seed [integer]
Set this flag if an explicit RNG seed should be used in tasks that require a RNG
(randomization of training data, splitting in cross-validation, learning algorithms
etc). Not used by all programs.
--progress-bar
Add a Progress bar in the system error output
--progress-bar-ascii
Add a Progress bar in ASCII in the system error output
--time
Print wall-time for all individual steps in execution
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Gensign requires a valid Standard or PRO license as stated in the usage manual, but it will also require to use –smiles, –input or both flags.
Example Usage¶
> java -jar cpsign-[version].jar gensign \
--smiles CC(=O)NCCC1=CNc2c1cc(OC)cc2 \
--license /path/to/Standard-license.license
Running with Standard License registered to [Name] at [Company]. Expiry
date is [Date]
Starting signature generation..
{
"molecule": {
"SMILES": "CC(=O)NCCC1=CNc2c1cc(OC)cc2"
},
"generatedSignatures": {
"[N]([C]([C])[C]([C]=[O]))": 1.0,
"[C](p[C](p[C](p[C,0][O]))p[C]([C]([C])p[C](p[N,1]))p[C](p[C](p[C,0])p[N,1]))": 1.0,
"[C](p[C]([C]p[C])p[N](p[C]))": 1.0,
"[C]([C][N])": 1.0,
"[C](p[C](p[C])p[C](p[C])[O]([C]))": 1.0,
"[C]([C][N]([C]([C]))=[O])": 1.0,
"[C]([O]([C](p[C]p[C])))": 1.0,
"[C]([C]([C])p[C](p[N])p[C](p[C]p[C]))": 1.0,
"[O]([C][C](p[C](p[C])p[C](p[C])))": 1.0,
"[C]([C]p[C]p[C])": 1.0,
"[C]([C]([N])[C](p[C]p[C]))": 1.0,
"[N]([C]([C]([C]))[C]([C]=[O]))": 1.0,
"[C](p[C](p[C])p[C](p[C][O]))": 1.0,
"[C](p[C]p[C]p[N])": 1.0,
"[O](=[C]([C][N]))": 1.0,
"[N]([C][C])": 1.0,
"[O]([C][C](p[C]p[C]))": 1.0,
"[C](p[C]p[C])": 3.0,
"[O](=[C])": 1.0,
"[C](p[C](p[C](p[C,0]))p[C](p[C](p[C]p[C,0]))[O]([C]))": 1.0,
"[C]([O])": 1.0,
"[C]([C][C])": 1.0,
"[C](p[C](p[C]p[C])p[C](p[C][O]))": 1.0,
"[C]([C])": 1.0,
"[C]([O]([C]))": 1.0,
"[N](p[C](p[C]([C]p[C,0]))p[C](p[C](p[C])p[C,0](p[C])))": 1.0,
"[C](p[C](p[C])p[C]([C]p[C])p[C](p[C]p[N]))": 1.0,
"[C](p[C](p[C](p[C,0]p[N]))p[C](p[C](p[C,0])[O]([C])))": 1.0,
"[C](p[C](p[C](p[C,0]))p[C](p[C](p[C,0])p[C]([C]p[C,1]))p[N](p[C,1]))": 1.0,
"[C]([C]([N]=[O]))": 1.0,
"[C](p[C](p[C])p[C](p[C]p[C])p[N](p[C]))": 1.0,
"[C]([C]([N]([C]))[C](p[C](p[N])p[C](p[C]p[C])))": 1.0,
"[C](p[C]p[C][O])": 1.0,
"[O]([C][C])": 1.0,
"[C]([C]([C]([N]))p[C](p[N](p[C,0]))p[C](p[C](p[C])p[C,0](p[C])))": 1.0,
"[C]([C][N]=[O])": 1.0,
"[N](p[C]p[C])": 1.0,
"[O](=[C]([C][N]([C])))": 1.0,
"[C]([C]([C])[N]([C]))": 1.0,
"[C]([C]([N]([C])=[O]))": 1.0,
"[C]([C][N]([C])=[O])": 1.0,
"[C](p[C](p[C](p[C,0])[O]([C]))p[C](p[C]([C]p[C])p[C](p[C,0]p[N])))": 1.0,
"[C](p[C]p[N])": 1.0,
"[C]([C]([C](p[C]p[C]))[N]([C]([C]=[O])))": 1.0,
"[C](p[C]p[C]p[C])": 1.0,
"[C](p[C](p[C])p[C](p[C]p[N]))": 1.0,
"[C](p[C](p[C](p[C,0][O]))p[C](p[C](p[C]p[C,0])p[N](p[C])))": 1.0,
"[C](p[C]([C]([C])p[C](p[C]p[C,0]))p[N](p[C,0](p[C])))": 1.0,
"[N](p[C](p[C])p[C](p[C]p[C]))": 1.0
}
}