Title: ambitcli-3.0.2
Type Software Jeliazkova, Nina, Kochev, Nikolay, Jeliazkov, Vedrin (2016): ambitcli-3.0.2. Zenodo. Software. https://zenodo.org/record/173560
Links
- Item record in Zenodo
- Digital object URL
Summary
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/
More information
- DOI: 10.5281/zenodo.173560
Subjects
- chemical structure standartization, chemical descriptors, chemical database
Dates
- Publication date: 2016
- Issued: April 14, 2016
Notes
Other: This project has received fundting from CEFIC Long Range Research Initiative http://cefic-lri.org/Rights
- https://opensource.org/licenses/LGPL-3.0 GNU Lesser General Public License v3.0 only
- info:eu-repo/semantics/openAccess Open Access
Funding Information
| Awardnumber | Awarduri | Funderidentifier | Funderidentifiertype | Fundername |
|---|---|---|---|---|
| 671555 | info:eu-repo/grantAgreement/EC/H2020/671555/ | 10.13039/100010661 | Crossref Funder ID | European Commission |
Format
electronic resource
Relateditems
| Description | Item type | Relationship | Uri |
|---|---|---|---|
| Compiles | https://doi.org/10.5281/zenodo.173258 | ||
| Cites | https://doi.org/10.1186/1758-2946-3-18 | ||
| HasPart | https://doi.org/10.1002/minf.201200133 | ||
| IsVersionOf | https://doi.org/10.5281/zenodo.676504 | ||
| IsPartOf | https://zenodo.org/communities/ambit | ||
| IsPartOf | https://zenodo.org/communities/ecfunded | ||
| IsPartOf | https://zenodo.org/communities/zenodo |