NAME,CAS,SMILES
Acetic acid,64-19-7,CC(O)=O
Acetoin,513-86-0,CC(O)C(C)=O

 -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

 -a fingerprint -m post  -i "input.txt" -o "fp/Compound_XYZ_" -d pagesize=-1 -d "fpclass=CircularFingerprinter,PubchemFingerprinter" -d tag_tokeep=AMBIT_InChIKey  -d inputtag_smiles=AMBIT_SMILES -d inputtag_inchikey=AMBIT_InChIKey -d inputtag_inchi=AMBIT_InChI

-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 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

$java -jar ambitcli.jar -a {command} help

$java -jar ambitcli.jar -a standardize -m help

    >java -jar ambitcli-3.0.2.jar -a fingerprint -m help
INFO   ambitcli-3.0.2 build:7472 1460532616351
http://ambit.sourceforge.net/download_ambitcli.html
-a fingerprint -m post -d <parameters>

"Fingerprint calculation. Writes multiple files per fingerprint, all files start with prefix given by -o prefix). Fingerpritns are written in a sparse format"
   -a fingerprint -m post
 -d fpclass=CircularFingerprinter,PubchemFingerprinter,MACCSFingerprinter       // Comma delimited list of class names i mplementing org.openscience.cdk.fingerprint.IFingerprinter, e.g. KlekotaRothFingerprinter. If not fully qualified will prepend 'org.openscience.cdk.fingerprint.' 
 -d page=0      // Start page (first page = 0) 
 -d pagesize=20000      // Page size (in number of 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_tokeep=InChIKey // Specifies which tags to keep, comma delimited list. Everything else will be removed. To keep all the tags, leave this empty.
 -d write_count=false   // Whether to write the counts of getCountFingerprint() (in [.vw](http://hunch.net/~vw/) format)
 -d write_raw=false     // Whether to write the raw fingerprint (getRawFingerprint)
 -d sdftitle=null       // Specifies which field to write in the first SDF line


Example
 -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=true 

-a split -m post -d <parameters> -i input.sdf -o outputfolder

"Splits an SDF into chunks of predefined size (-i inputfile -o outputfolder)"
   -a split -m post 
 -d chunk=1000	// 	[type:Integer, mandatory:false]

Example
 -d chunk=1000

-a import -m post -i input.sdf -c config/ambit.properties

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

Database connection:	config/ambit.properties

DriverClassName=com.mysql.jdbc.Driver
Host=host.com
Scheme=jdbc\:mysql
Port=3306
Database=dbname
User=theuser
Password=thepassword

-a dataset -m post -i input.sdf -c config/ambit.properties

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

Database connection:	config/ambit.properties

-a preprocessing -m post -d <parameters>

"Preprocessing of structures in AMBIT database (depends on options, default inchi). The database connection settings are read from -c {file}"
   -a preprocessing -m post
 -d inchi=false	// Generates InChIs in chemicals table	[type:Boolean, mandatory:false]
 -d atomprops=false	// Stores precalculated aromaticity/ring information in the structure table	[type:Boolean, mandatory:false]
 -d fp1024=false	// Hashed 1024 bit fingerprints, used for similarity searching anf substructure search prescreening	[type:Boolean, mandatory:false]
 -d sk1024=false	// Structure fingerprints, used for substructure search prescreening	[type:Boolean, mandatory:false]
 -d cf1024=false	// Pubchem fingerprints	[type:Boolean, mandatory:false]
 -d smarts=false	// Everything needed for substructure search prescreening - atomprops,fp1024,sk1024	[type:Boolean, mandatory:false]
 -d similarity=false	// Everything needed for similarity search - atomprops,fp1024	[type:Boolean, mandatory:false]
 -d pagesize=5000000	// query size	[type:Integer, mandatory:false]


Example
 -d inchi=false -d atomprops=false -d fp1024=false -d sk1024=false -d cf1024=false -d smarts=false -d similarity=false -d pagesize=5000000

Database connection:	config/ambit.properties