AMBIT:Chemical Structure DB&Web Service Files

ambitcli-3.0.2.jar is the stable release (build 7472)

See http://ambit.sourceforge.net/ambitcli_standardisation.html

ambitcli-3.0.2-7433.jar is a prerelease of ambit 3.0.2 (build 7433)

• Dense hashed fingerprint format replaced with sparse one, same as for non-hashed fingerprints
• Changed to false the default option for storing the transformation info as properties
• Assign rank property even if tautomerisation is not applicable
• logging improvements

ambitcli-3.0.2-7385.jar is a prerelease of ambit 3.0.2 (build 7385)

• Neutralisation SMIRKS added for N oxides
• logging improvements

ambitcli-3.0.2-7354.jar is a prerelease of ambit 3.0.2 (build 7354)

• Bug fixes b7346 - Fixed a bug caused by the stereo info left from the tautomer structure cloning.
• Fingerprint calculation
• input tag option -d inputtag_smiles
• ensure RANK column is always present

Usage

a standardize -m post -d <parameters>

"Chemical structure standardization (-i inputfile.sdf -o outputfile.sdf , recognized by extensions .sdf , .csv, .cml , .txt)"
-a standardize -m post
-d smirks=null  // JSON file with SMIRKS transformations    [type:String, mandatory:false]
-d neutralise=false // If true neutralises the molecule via set of predefined SMIRKS    [type:Boolean, mandatory:false]
-d splitfragments=false // If true keeps the largest fragment   [type:Boolean, mandatory:false]
-d implicith=false  // If true converts hydrogens to implicit   [type:Boolean, mandatory:false]
-d generatestereofrom2d=false   // If true uses org.openscience.cdk.stereo.StereoElementFactory to generate the stereochemistry from 2D coordinates [type:Boolean, mandatory:false]
-d isotopes=false   // If true clears isotopes  [type:Boolean, mandatory:false]
-d generate2D=false // Generate 2d coordinates (if no any)  [type:Boolean, mandatory:false]
-d tautomers=false  // If true generates the top ranked tautomer    [type:Boolean, mandatory:false]
-d inchi=true   // Generates InChIs. If -d tautomers=true InChI FixedH=true, otherwise generates standard InChI [type:Boolean, mandatory:false]
-d smiles=true  // Generates SMILES (isomeric, kekule).  Uses CDK SmilesGenerator.isomeric()    [type:Boolean, mandatory:false]
-d smilescanonical=false    // Generates SMILES (canonical).  Uses CDK SmilesGenerator.absolute()   [type:Boolean, mandatory:false]
-d smilesaromatic=false // Generates aromatic SMILES.  Uses CDK SmilesGenerator.aromatic()  [type:Boolean, mandatory:false]
-d page=0   // Start page (first page = 0)  [type:Integer, mandatory:false]
-d pagesize=20000   // Page size (in number of records). Set to -1 to read all records. [type:Integer, mandatory:false]
-d inputtag_smiles=SMILES   // Specifies the name of the column, containing SMILES  [type:String, mandatory: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]
-d tag_smiles=SMILES    // Specifies the SMILES tag [type:String, mandatory:false]
-d tag_rank=RANK    // Specifies the tag to store the tautomer rank (energy based, less is better)  [type:String, mandatory:false]
-d tag_tokeep=  // Specifies which tags to keep, comma delimited list. Everything else will be removed. To keep all the tags, leave this empty. [type:String, mandatory:false]
-d sdftitle=null    // Specifies which field to write in the first SDF line null|inchikey|inchi|smiles|any-existing-field   [type:String, mandatory:false]
-d debugatomtypes=false // Writes only structures with AtomTypes property set. For debug purposes   [type:boolean, mandatory:false]

Generate SMILES, InChI and InChI key, retain only the PUBCHEM_CID from the fields in the input file

java -jar ambitcli-3.0.2-7354.jar -a standardize -m post -a standardize -m post -d page=0 -d pagesize=-1 -d tautomers=false -d tag_tokeep=PUBCHEM_CID -d smilescanonical=false -d smiles=true -d inchi=true -i inputfile -o outputfile

Full standardisation, write SMILES, InChI and InChI key into AMBIT_SMILES, AMBIT_InChI, AMBIT_InChIKey, retain only the PUBCHEM_CID from the fields in the input file

java -jar ambitcli-3.0.2-7354.jar -a standardize -m post -a standardize -m post -d page=0 -d pagesize=-1 -d tag_smiles=AMBIT_SMILES -d tag_inchi=AMBIT_InChI -d tag_inchikey=AMBIT_InChIKey -d tautomers=true -d splitfragments=true -d implicith=true -d smiles=true -d smilescanonical=false -d inchi=true -d neutralise=true -d isotopes=true -d tag_tokeep=PUBCHEM_CID

New command to generate fingerprints

-a fingerprint -m post -d <parameters>

"Fingerprint calculation. Writes multiple files per fingerprint, all files start with prefix given by -o prefix)"
-a fingerprint -m post
-d fpclass=CircularFingerprinter,PubchemFingerprinter,MACCSFingerprinter    // Comma delimited list of class names implementing org.openscience.cdk.fingerprint.IFingerprinter, e.g. KlekotaRothFingerprinter. If not fully qualified will prepend 'org.openscience.cdk.fingerprint.'   [type:String, mandatory:false]
-d page=0   // Start page (first page = 0)  [type:Integer, mandatory:false]
-d pagesize=20000   // Page size (in number of records) [type:Integer, mandatory:false]
-d inputtag_smiles=SMILES   // Specifies the name of the column, containing SMILES  [type:String, mandatory:false]
-d tag_tokeep=InChIKey  // Specifies which tags to keep, comma delimited list. Everything else will be removed. To keep all the tags, leave this empty. [type:String, mandatory:false]
-d write_count=false    // Whether to write the counts of getCountFingerprint() [type:Boolean, mandatory:false]
-d write_raw=false  // Whether to write the raw fingerprint (getRawFingerprint) [type:Boolean, mandatory:false]
-d sdftitle=null    // Specifies which field to write in the first SDF line [type:String, mandatory:false]

Example -d fpclass=CircularFingerprinter,PubchemFingerprinter,MACCSFingerprinter -d page=0 -d pagesize=20000 -d inputtag_smiles=SMILES -d tag_tokeep=InChIKey -d write_count=false -d write_raw=false -d sdftitle=null

ambitcli-3.0.2-7315.jar is a prerelease of ambit 3.0.2 (build 7315)

with new option added to specify which fields to be retained

    -d tag_tokeep=comma_delimited_list

Usage

>java -jar ambitcli-3.0.2-7315.jar -help
INFO   ambitcli-3.0.2-SNAPSHOT build:7315 1456509922527
http://ambit.sourceforge.net/download_ambitcli.html



>java -jar ambitcli-3.0.2-7315.jar -a standardize -m help
INFO   ambitcli-3.0.2-SNAPSHOT build:7315 1456509922527
http://ambit.sourceforge.net/download_ambitcli.html
-a standardize -m post -d <parameters>
"Chemical structure standardization (-i inputfile.sdf -o outputfile.sdf , recognized by extensions .sdf , .csv, .cml , .txt)"
-a standardize -m post
-d smirks=null // JSON file with SMIRKS transformations        [type:String, mandatory:false]
-d neutralise=false    // If true neutralises the molecule via set of predefined SMIRKS        [type:Boolean, mandatory:false]
-d splitfragments=false        // If true keeps the largest fragment   [type:Boolean, mandatory:false]
-d implicith=false     // If true converts hydrogens to implicit       [type:Boolean, mandatory:false]
-d generatestereofrom2d=false  // If true uses org.openscience.cdk.stereo.StereoElementFactory to generate the stereochemistry from 2D coordinates     [type:Boolean, mandatory:false]
-d isotopes=false      // If true clears isotopes      [type:Boolean, mandatory:false]
-d generate2D=false    // Generate 2d coordinates (if no any)  [type:Boolean, mandatory:false]
-d tautomers=true      // If true generates the top ranked tautomer    [type:Boolean, mandatory:false]
-d inchi=true  // Generates InChIs. If -d tautomers=true InChI FixedH=true, otherwise generates standard InChI [type:Boolean, mandatory:false]
-d smiles=false        // Generates SMILES (isomeric, kekule)  Uses CDK SmilesGenerator.isomeric() [type:Boolean, mandatory:false]
-d smilescanonical=true        // Generates SMILES (canonical). Uses CDK SmilesGenerator.absolute()  [type:Boolean, mandatory:false]
-d page=0      // Start page (first page = 0)  [type:Integer, mandatory:false]
-d pagesize=20000      // Page size (in number of records)     [type:Integer, mandatory: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]
-d tag_smiles=SMILES   // Specifies the SMILES tag     [type:String, mandatory:false]
-d tag_rank=RANK       // Specifies the tag to store the tautomer rank (energy based, less is better)  [type:String, mandatory:false]
-d tag_tokeep= // Specifies which tags to keep, comma delimited list. Everything else will be removed. To keep all thetags, leave this empty. [type:String, mandatory:false]
-d sdftitle=null       // Specifies which field to write in the first SDF line null|inchikey|inchi|smiles|any-existing-field   [type:String, mandatory:false]
-d debugatomtypes=false        // Writes only structures with AtomTypes property set. For debug purposes       [type:boolean, mandatory:false]

Examples:

Generate SMILES, InChI and InChI key, retain only the PUBCHEM_CID from the fields in the input file

java -jar ambitcli-3.0.2-7315.jar -a standardize -m post -a standardize -m post -d page=0 -d pagesize=-1 -d tautomers=false -d tag_tokeep=PUBCHEM_CID -d smilescanonical=false -d smiles=true -d inchi=true -i inputfile -o outputfile

Full standardisation, write SMILES, InChI and InChI key into AMBIT_SMILES, AMBIT_InChI, AMBIT_InChIKey, retain only the PUBCHEM_CID from the fields in the input file

java -jar ambitcli-3.0.2-7315.jar -a standardize -m post -a standardize -m post -d page=0 -d pagesize=-1 -d tag_smiles=AMBIT_SMILES -d tag_inchi=AMBIT_InChI -d tag_inchikey=AMBIT_InChIKey -d tautomers=true -d splitfragments=true -d implicith=true -d smiles=true -d smilescanonical=false -d inchi=true -d neutralise=true -d isotopes=true -d tag_tokeep=PUBCHEM_CID