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ambitcli-3.0.2

Jeliazkova, Nina; Kochev, Nikolay; Jeliazkov, Vedrin

A command line Java application used for processing chemical files, structure standardization, import into AMBIT database and processing AMBIT database entries.  More information at http://ambit.sourceforge.net/download_ambitcli.html 

Chemical structure standardization option available since AMBIT 3.0.0.

 

java -Xmx1536m -jar ambitcli{version}.jar -a standardize -i <inputfile> -m post -d page=page num -d pagesize=-1|page_size -o <output> -d tautomers=true -d splitfragments=true -d implicith=true -d smiles=false -d smilescanonical=true -d inchi=true -d neutralise=true -d isotopes=true

1.Transformation

-d smirks=null|file.json

Chemical structure transformation by SMIRKS, implemented by ambit2-smirks package. The option expects either null (default) or a JSON file defining SMIRKS in the following format. Any number of transformations could be specified.

2.Fragments

-d splitfragments=true|false

If true keeps the largest fragment. If false keeps the entire molecule, even if disconnected. Default is false.

3.Isotopes

-d isotopes=true|false

If true clears isotopes.

4.Neutralisation

-d neutralise=true|false

If true neutralises the molecule via set of predefined SMIRKS. This is an option for convenience only. Using the transformation option -d smirkswith the same SMIRKS file will have the same effect.

5.Implicit hydrogens

-d implicith=true|false

If true converts hydrogens to implicit. If false leaves the structure as it is. Default is false.

6.Stereochemistry

-d generatestereofrom2d=true|false

If true uses org.openscience.cdk.stereo.StereoElementFactory to generate the stereochemistry from 2D (stereo elements derived from 2D coordinates).

7.Tautomers

-d tautomers=true|false -d tag_rank=RANK

If true generates the top ranked tautomer via ambit-tautomers package doi:10.1002/minf.201200133. Default is false. The tag_rank option specifies the tag to store the tautomer rank (energy based, less is better).

8.InChI generation

-d inchi=true|false -d tag_inchi=InChI // Specifies the InChI tag [type:String, mandatory:false] -d tag_inchikey=InChIKey // Specifies the InChIKey tag [type:String, mandatory:false]

Generates InChIs. If -d tautomers=true uses InChI option FixedH=true, otherwise generates standard InChI. If false does not generate InChI. Default is true.

9.SMILES generation

10.Page/Pagesize

11. SDF file molecule name

12. Input tags

More information at  http://ambit.sourceforge.net/ambitcli_standardisation.html

 

Sourceforge download https://sourceforge.net/projects/ambit/files/Ambit2/AMBIT%20applications/ambitcli/ambitcli-3.0.2/

This project has received fundting from CEFIC Long Range Research Initiative http://cefic-lri.org/
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ambitcli-3.0.2.jar md5:876c01438c618c86fe26e3889f103ccc 36.3 MB Download

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