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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 

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


-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.


-d splitfragments=true|false

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


-d isotopes=true|false

If true clears isotopes.


-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.


-d generatestereofrom2d=true|false

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


-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


11. SDF file molecule name

12. Input tags

More information at


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This project has received fundting from CEFIC Long Range Research Initiative
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