AMBIT:Chemical Structure DB&Web Service Files

ambitcli-3.0.3-8096.jar is a prerelease of ambit 3.0.3

java -jar ambitcli-3.0.3-8096.jar
INFO   ambitcli-3.0.3-SNAPSHOT build:8096 1493634845590
http://ambit.sourceforge.net/download_ambitcli.html

    ambitcli -a {command} -m {subcommand} -d {options}
    (use -m help to list subcommands and options per command)

Change log : standardisation bug fixed

ambitcli-3.0.3-8007.jar is a prerelease of ambit 3.0.3

java -jar ambitcli-3.0.3-8007.jar -a help
INFO   ambitcli-3.0.3-SNAPSHOT build:8007 1485240262107
http://ambit.sourceforge.net/download_ambitcli.html
ambitcli -a {command} -m {subcommand} -d {options}
    (use -m help to list subcommands and options per command)

ambitcli-3.0.3-7892.jar is a prerelease of ambit 3.0.3

All options http://ambit.sourceforge.net/download_ambitcli.html

java -jar ambitcli-3.0.3-7892.jar -a help 
INFO   ambitcli-3.0.3-SNAPSHOT build:7892 1476635488693
http://ambit.sourceforge.net/download_ambitcli.html

ambitcli -a {command} -m {subcommand} -d {options}
    (use -m help to list subcommands and options per command)


-a split    Splits an SDF into chunks of predefined size (-i inputfile -o outputfile).
    Example:    ambitcli  -a split -m post -d chunk=1000

-a standardize  Chemical structure standardization (-i inputfile.sdf -o outputfile.sdf , recognized by extensions .sdf , .csv, .cml , .txt)
    Example:    ambitcli  -a standardize -m post -d smirks=null -d neutralise=false -d splitfragments=false -d implicith=false -d generatestereofrom2d=false -d isotopes=false -d generate2D=false -d tautomers=false -d inchi=true -d smiles=true -d smilescanonical=false -d smilesaromatic=false -d page=0 -d pagesize=20000 -d inputtag_smiles=SMILES -d inputtag_inchi=InChI -d inputtag_inchikey=InChIKey -d tag_inchi=InChI -d tag_inchikey=InChIKey -d tag_smiles=SMILES -d tag_rank=RANK -d tag_tokeep= -d sdftitle=null -d debugatomtypes=false

-a fingerprint  Fingerprint calculation. Writes multiple files per fingerprint, all files start with prefix given by -o prefix)
    Example:    ambitcli  -a fingerprint -m post -d fpclass=CircularFingerprinter,PubchemFingerprinter,MACCSFingerprinter -d page=0 -d pagesize=20000 -d inputtag_smiles=SMILES -d inputtag_inchi=InChI -d inputtag_inchikey=InChIKey -d tag_tokeep=InChIKey -d write_count=false -d write_raw=false -d sdftitle=null

-a simmatrix    Similarity matrix from fingerprint files, as generated by the -a fingerprint command
    Example:    ambitcli  -a simmatrix -m post -d sparse=true -d threshold=0.75 -d page=0 -d pagesize=10000

-a dataset  Dataset import into AMBIT database (with normalisation). The database connection settings are read from -c {file}.
    Example:    ambitcli  -a dataset -m post

-a dbmigrate    dbmigrate
    Example:    ambitcli  -a dbmigrate -m get   
    Example:    ambitcli  -a dbmigrate -m put -d sql_log_bin=0

-a import   Quick import into AMBIT database (No normalisation!). Input file (-i file). The database connection settings are read from -c {file}
    Example:    ambitcli  -a import -m post

-a preprocessing    Preprocessing of structures in AMBIT database (depends on options, default inchi). The database connection settings are read from -c {file}
    Example:    ambitcli  -a preprocessing -m post -d inchi=false -d atomprops=false -d fp1024=false -d sk1024=false -d cf1024=false -d smarts=false -d similarity=false -d pagesize=5000000

a atomenvironments  Generates atom environments matrix descriptors from SDF file (-i inputfile -o outputfile)
    Example:    ambitcli  -a atomenvironments -m post -d id_tag=ID -d activity_tag=Activity -d merge_results_file=null -d generate_csv=false -d generate_mm=false -d generate_json=false -d generate_vw=true -d normalize=true -d laplace_smoothing=null -d cost_sensitive=true -d levels_as_namespace=false -d toxtree=false

-a help List all commands

Standardisation

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

java -jar ambitcli-3.0.2-7489.jar -a standardize -m post 
INFO   ambitcli-3.0.2 build:7489 1460964115787
http://ambit.sourceforge.net/download_ambitcli.html
INFO   Running "Chemical structure standardization (-i inputfile.sdf -o outputfile.sdf , recognized by extensions .sdf ,.csv, .cml , .txt)"
ambitcli-3.0.2    -a standardize -m post
 -d smirks=null // JSON file with SMIRKS transformations        
 -d neutralise=false    // If true neutralises the molecule via set of predefined SMIRKS        
 -d splitfragments=false        // If true keeps the largest fragment   
 -d implicith=false     // If true converts hydrogens to implicit       
 -d generatestereofrom2d=false  // If true uses org.openscience.cdk.stereo.StereoElementFactory to generate the stereochemistry from 2D coordinates     
 -d isotopes=false      // If true clears isotopes      
 -d generate2D=false    // Generate 2d coordinates (if no any)  
 -d tautomers=false     // If true generates the top ranked tautomer    
 -d inchi=true  // Generates InChIs. If -d tautomers=true InChI FixedH=true, otherwise generates standard InChI 
 -d smiles=true // Generates SMILES (isomeric, kekule).  Uses CDK SmilesGenerator.isomeric()    
 -d smilescanonical=false       // Generates SMILES (canonical).  Uses CDK SmilesGenerator.absolute()   
 -d smilesaromatic=false        // Generates aromatic SMILES.  Uses CDK SmilesGenerator.aromatic()  
 -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.     
 -d inputtag_smiles=SMILES      // Specifies the name of the column, containing SMILES in the input file        
 -d inputtag_inchi=InChI        // Specifies the name of the column, containing InChI in the input file 
 -d inputtag_inchikey=InChIKey  // Specifies the name of the column, containing InChIKey in the input file      
 -d tag_inchi=InChI     // Specifies the tag to store the generated InChI       
 -d tag_inchikey=InChIKey       // Specifies the tag to store the generated InChIKey    
 -d tag_smiles=SMILES   // Specifies the tag to store the generated SMILES      
 -d tag_rank=RANK       // Specifies the tag to store the tautomer rank (energy based, less is better)  
 -d tag_tokeep= // Specifies which tags to keep, comma delimited list. Everything else will be removed. To keep all thetags, leave this empty. 
 -d sdftitle=null       // Specifies which field to write in the first SDF line null|inchikey|inchi|smiles|any-existing-field   
 -d debugatomtypes=false        // Writes only structures with AtomTypes property set. For debug purposes

Similarity matrix

java -jar ambitcli-3.0.3-8007.jar -a simmatrix -m help
INFO   ambitcli-3.0.3-SNAPSHOT build:8007 1485240262107
http://ambit.sourceforge.net/download_ambitcli.html 
-a simmatrix -m post -d <parameters>

"Similarity matrix from fingerprint files, as generated by the -a fingerprint command"
-a simmatrix -m post
-d sparse=true // Dense or sparse format 
-d delimiter=, // Delimiter character  
-d threshold=0.75      // similarity threshold    
-d page=0      // Start page (first page = 0)
-d pagesize=10000      // Page size (in number of records). Set to -1 to read all records.

Example

-d sparse=true -d delimiter=, -d threshold=0.75 -d page=0 -d pagesize=10000