Constant Field Values

Contents

• ambit2.balloon.*
• ambit2.base.*
• ambit2.core.*
• ambit2.db.*
• ambit2.descriptors.*
• ambit2.dragon.*
• ambit2.export.*
• ambit2.groupcontribution.*
• ambit2.model.*
• ambit2.mopac.*
• ambit2.pubchem.*
• ambit2.reactions.*
• ambit2.rendering.*
• ambit2.rest.*
• ambit2.search.*
• ambit2.similarity.*
• ambit2.sln.*
• ambit2.smarts.*
• ambit2.some.*
• ambit2.tautomers.*
• ambit2.ui.*
• ambit2.vega.*

ambit2.balloon.*

ambit2.balloon.ShellBalloon

Modifier and Type	Constant Field	Value
public static final String	BALLOON_EXE	"balloon"
public static final String	BALLOON_HOME	"BALLOON_HOME"

ambit2.base.*

ambit2.base.config.AMBITConfigProperties

Modifier and Type	Constant Field	Value
public static final String	ambitProperties	"ambit2/rest/config/ambit2.pref"
public static final String	configProperties	"ambit2/rest/config/config.prop"
public static final String	loggingProperties	"ambit2/rest/config/logging.prop"
public static final String	templateProperties	"ambit2/rest/config/ambit2.assay.properties"

ambit2.base.data.ChEMBLProperties

Modifier and Type	Constant Field	Value
public static final String	biboPrefix	"http://purl.org/ontology/bibo/"
public static final String	chembl	"ChEMBL"
public static final String	chemblPrefix	"http://rdf.farmbio.uu.se/chembl/onto/#"
public static final String	chemblSparql	"http://rdf.farmbio.uu.se/chembl/"
public static final String	dcPrefix	"http://purl.org/dc/elements/1.1/"

ambit2.base.data.LiteratureEntry

Modifier and Type	Constant Field	Value
public static final String	p_title	"title"
public static final String	p_url	"URL"

ambit2.base.data.Property

Modifier and Type	Constant Field	Value
public static final String	CAS	"CasRN"
public static final String	EC	"EC"
public static final String	IUCLID5_UUID	"I5UUID"
public static final String	link_WikiPathway	"http://www.wikipathways.org/index.php/Pathway"
public static final String	Names	"Names"
public static final String	opentox_CAS	"http://www.opentox.org/api/1.1#CASRN"
public static final String	opentox_ChEBI	"http://www.opentox.org/api/dblinks#ChEBI"
public static final String	opentox_ChEMBL	"http://www.opentox.org/api/dblinks#ChEMBL"
public static final String	opentox_ChemSpider	"http://www.opentox.org/api/dblinks#ChemSpider"
public static final String	opentox_CMS	"http://www.opentox.org/api/dblinks#CMS"
public static final String	opentox_ConfidenceFeature	"http://www.opentox.org/api/1.1#ConfidenceFeature"
public static final String	opentox_DrugBank	"http://www.opentox.org/api/dblinks#DrugBank"
public static final String	opentox_EC	"http://www.opentox.org/api/1.1#EINECS"
public static final String	opentox_InChI	"http://www.opentox.org/api/1.1#InChI"
public static final String	opentox_InChI_std	"http://www.opentox.org/api/1.1#InChI_std"
public static final String	opentox_InChIAuxInfo	"http://www.opentox.org/api/1.1#InChI_AuxInfo"
public static final String	opentox_InChIAuxInfo_std	"http://www.opentox.org/api/1.1#InChI_AuxInfo_std"
public static final String	opentox_InChIKey	"http://www.opentox.org/api/1.1#InChIKey"
public static final String	opentox_InChIKey_std	"http://www.opentox.org/api/1.1#InChIKey_std"
public static final String	opentox_IUCLID5_UUID	"http://www.opentox.org/api/1.1#IUCLID5_UUID"
public static final String	opentox_IupacName	"http://www.opentox.org/api/1.1#IUPACName"
public static final String	opentox_KEGG	"http://www.opentox.org/api/dblinks#KEGG"
public static final String	opentox_LS	"http://www.opentox.org/api/dblinks#LS"
public static final String	opentox_Name	"http://www.opentox.org/api/1.1#ChemicalName"
public static final String	opentox_Pubchem	"http://www.opentox.org/api/dblinks#Pubchem"
public static final String	opentox_REACHDATE	"http://www.opentox.org/api/1.1#REACHRegistrationDate"
public static final String	opentox_SigmaAldrich	"http://www.opentox.org/api/dblinks#SigmaAldrich"
public static final String	opentox_SMILES	"http://www.opentox.org/api/1.1#SMILES"
public static final String	opentox_SubstanceDataSource	"http://www.opentox.org/api/1.1#SubstanceDataSource"
public static final String	opentox_ToxbankWiki	"http://www.opentox.org/api/dblinks#ToxbankWiki"
public static final String	opentox_TradeName	"http://www.opentox.org/api/1.1#TradeName"
public static final String	opentox_TupleFeature	"http://www.opentox.org/api/1.1#TupleFeature"

ambit2.base.exceptions.PropertyNotInTemplateException

Modifier and Type	Constant Field	Value
public static final String	MESSAGE	"Property not in template!"

ambit2.base.external.CommandShell<INPUT,OUTPUT>

Modifier and Type	Constant Field	Value
public static final String	os_FreeBSD	"FreeBSD"
public static final String	os_LINUX	"Linux"
public static final String	os_LINUX64	"Linux64"
public static final String	os_MAC	"Mac OS"
public static final String	os_WINDOWS	"Windows"
public static final String	os_WINDOWS7	"Windows 7"
public static final String	os_WINDOWSVISTA	"Windows Vista"

ambit2.base.processors.CASProcessor

Modifier and Type	Constant Field	Value
protected static final String	dash	"-"
protected static final String	zero	"0"

ambit2.base.ro.I5CONSTANTS

Modifier and Type	Constant Field	Value
public static final String	AGGLO_AGGR_DIAM	"AGGLO_AGGR_DIAM"
public static final String	AGGLO_AGGR_SIZE	"AGGLO_AGGR_SIZE"
public static final String	AGGLO_AGGR_SIZE_DIST	"AGGLO_AGGR_SIZE_DIST"
public static final String	AGGLO_AGGREGATION_IDX	"AGGLO_AGGREGATION_IDX"
public static final String	AtmPressure	"Atm. Pressure"
public static final String	BOILINGPOINT	"Boiling point"
public static final String	cBasisForEffect	"Basis for effect"
public static final String	cBioaccBasis	"Bioacc. basis"
public static final String	cConcType	"Based on"
public static final String	cDegradationParameter	"Degradation Parameter"
public static final String	cDoses	"Doses/concentrations"
public static final String	cEffect	"Effect"
public static final String	cEffectType	"Effect type"
public static final String	cExposure	"Exposure"
public static final String	cGeneration	"Generation"
public static final String	cMaxScore	"MaxScore"
public static final String	cMeasuredConcentration	"Measured concentration"
public static final String	cMEDIUM	"MEDIUM"
public static final String	cMetabolicActivation	"Metabolic activation"
public static final String	cMetabolicActivationSystem	"Metabolic activation system"
public static final String	cOCContent	"OC content"
public static final String	Color	"Color"
public static final String	cPERCENTILE	"PERCENTILE"
public static final String	cReference	"Reference"
public static final String	cReversibility	"Reversibility"
public static final String	CriticalEffectsObserved	"CriticalEffectsObserved"
public static final String	cRoute	"Route"
public static final String	cRouteAdm	"Route of administration"
public static final String	cSalinity	"Salinity"
public static final String	cSEQ_NUM	"SEQ_NUM"
public static final String	cSex	"Sex"
public static final String	cSoilNo	"Soil No."
public static final String	cSoilType	"Soil type"
public static final String	cSolvent	"Solvent"
public static final String	cSpecies	"Species"
public static final String	cTargetGene	"Target gene"
public static final String	cTemperature	"Temperature"
public static final String	cTestMedium	"Test Medium"
public static final String	cTestOrganism	"Test organism"
public static final String	cTestType	"Test type"
public static final String	cTimePoint	"Sampling time"
public static final String	cToxicity	"Toxicity"
public static final String	cTypeCoverage	"TYPE_COVERAGE"
public static final String	cTypeGenotoxicity	"Type of genotoxicity"
public static final String	cTypeMethod	"Type of method"
public static final String	cTypeStudy	"Type of study"
public static final String	cYear	"Study year"
public static final String	DevelopmentalEffectsObserved	"DevelopmentalEffectsObserved"
public static final String	DoseResponseRelationship	"DoseResponseRelationship"
public static final String	eAERODYNAMIC_DIAMETER	"AERODYNAMIC_DIAMETER"
public static final String	eAGGLO_AGGR_DIAM	"AGGLOMERATION AGGREGATION DIAMETER"
public static final String	eAGGLO_AGGR_DISTRIBUTION	"AGGLOMERATION AGGREGATION SIZE DISTRIBUTION"
public static final String	eAGGLO_AGGR_SIZE	"AGGLOMERATION AGGREGATION SIZE"
public static final String	eAGGLO_AGGR_SIZE_DIST	"AGGLOMERATION AGGREGATION SIZE DIST"
public static final String	eAGGLO_AGGREGATION_ID	"AGGLOMERATION AGGREGATION INDEX"
public static final String	eASPECT_RATIO	"ASPECT RATIO"
public static final String	eASPECT_RATIO_X	"X"
public static final String	eASPECT_RATIO_Y	"Y"
public static final String	eASPECT_RATIO_Z	"Z"
public static final String	eATOMIC_COMPOSITION	"ATOMIC COMPOSITION"
public static final String	eBCF	"BCF"
public static final String	eCATALYTIC_ACTIVITY	"CATALYTIC_ACTIVITY"
public static final String	eCRYSTALLINE_PHASE	"CRYSTALLINE_PHASE"
public static final String	eCRYSTALLITE_SIZE	"CRYSTALLITE_SIZE"
public static final String	eDUSTINEX	"DUSTINESS INDEX"
public static final String	effect_stdev	"sd"
public static final String	eFRACTION	"CONTRIBUTION"
public static final String	eFUNCTIONAL_GROUP	"FUNCTIONAL GROUP"
public static final String	eGenotoxicity	"GENOTOXICITY"
public static final String	eISOELECTRIC_POINT	"ISOELECTRIC POINT"
public static final String	eMELTINGPOINT	"Melting Point"
public static final String	eMODAL_PORE_VOLUME	"MODAL_PORE_VOLUME"
public static final String	endpoint_type_MEAN	"MEAN"
public static final String	endpoint_type_MEDIAN	"MEDIAN"
public static final String	endpoint_type_MEDIAN_MASS	"MEDIAN MASS"
public static final String	endpoint_type_PERCENT	"PERCENT"
public static final String	ePercentDegradation	"% Degradation"
public static final String	ePHOTOCATALYTIC_ACTIVITY	"PHOTOCATALYTIC_ACTIVITY"
public static final String	ePOROSITY	"POROSITY"
public static final String	ePOUR_DENSITY	"POUR DENSITY"
public static final String	eRadicalFormation_Observations	"RADICAL_FORMATION_OBSERVATION"
public static final String	eRadicalFormation_Quantitative	"RADICAL_FORMATION_QUANTITATIVE"
public static final String	eSHAPE	"SHAPE_PERCENTAGE"
public static final String	eSHAPE_DESCRIPTIVE	"SHAPE"
public static final String	eSOLUBILITY_ORG_SOLVENT	"Solubility org. solvents"
public static final String	eSPECIFIC_PORE_VOLUME	"SPECIFIC_PORE_VOLUME"
public static final String	eTURNOVERFREQUENCY	"TURN_OVER_FREQUENCY"
public static final String	eVapourPressure	"Vapour Pressure"
public static final String	eWaterSolubility	"Water solubility"
public static final String	eZETA_POTENTIAL	"ZETA POTENTIAL"
public static final String	Form	"Form"
public static final String	HLC	"Henry\'s Law const."
public static final String	I5_STUDY_SECTION	"eu.europa.echa.schemas.iuclid5._%s.studyrecord.%s_SECTION"
public static final String	KeyResult	"KeyResult"
public static final String	MEAN_DIAMETER	"MEAN DIAMETER"
public static final String	methodType	"Method type"
public static final String	Odor	"Odor"
public static final String	Organ	"Organ"
public static final String	pCOATING	"COATING"
public static final String	pCOATING_DESCRIPTION	"COATING_DESCRIPTION"
public static final String	pDATA_GATHERING_INSTRUMENTS	"DATA_GATHERING_INSTRUMENTS"
public static final String	pDESCRIPTION	"DESCRIPTION"
public static final String	pDISTRIBUTION	"DISTRIBUTION"
public static final String	pDISTRIBUTION_TYPE	"DISTRIBUTION_TYPE"
public static final String	pELEMENT_OR_GROUP	"ELEMENT_OR_GROUP"
public static final String	pFUNCTIONALIZATION	"FUNCTIONALIZATION"
public static final String	pGSD	"GEOMETRIC STANDARD DEVIATION"
public static final String	pH	"pH"
public static final String	Physstate	"Physical state"
public static final String	pKa	"pKa"
public static final String	pMATERIAL_ISOTROPIC	"MATERIAL_ISOTROPIC"
public static final String	pMETHODDETAILS	"Method details"
public static final String	pMMAD	"MASS_MEDIAN_AERODYNAMIC_DIAMETER"
public static final String	pMMD	"MASS MEDIAN DIAMETER"
public static final String	pPARTICLESIZE	"PARTICLE SIZE"
public static final String	pReactant	"Reactant"
public static final String	Pressure	"Pressure"
public static final String	pSAMPLING	"SAMPLING"
public static final String	pTESTMAT_FORM	"TESTMAT_FORM"
public static final String	pTYPE	"TYPE"
public static final String	rCRYSTALLINE_PHASE_BRAVAIS_LATTICE	"BRAVAIS_LATTICE"
public static final String	rCRYSTALLINE_PHASE_COMMON_NAME	"COMMON NAME"
public static final String	rCRYSTALLINE_PHASE_CRYSTAL_SYSTEM	"CRYSTAL_SYSTEM"
public static final String	rCRYSTALLINE_PHASE_CRYSTGRPH_PLANES	"CRYSTALLOGRAPHIC_PLANES"
public static final String	rCRYSTALLINE_PHASE_POINT_GROUP	"POINT_GROUP"
public static final String	rCRYSTALLINE_PHASE_SPACE_GROUP	"SPACE_GROUP"
public static final String	rDECOMPOSITION	"Decomposition"
public static final String	rDegradation	"Degradation"
public static final String	rDegradationRateConstant	"DegradationRateConstant"
public static final String	RelationToOtherToxicEffects	"RelationToOtherToxicEffects"
public static final String	Remark	"Remark"
public static final String	ReproductiveEffectsObserved	"ReproductiveEffectsObserved"
public static final String	rNo	"No."
public static final String	rOrgCarbonPercent	"% Org.Carbon"
public static final String	rPERCENTILE_DT50	"DT50"
public static final String	rSTD_DEV	"STD_DEV"
public static final String	rSUBLIMATION	"Sublimation"
public static final String	SPECIFIC_SURFACE_AREA	"SPECIFIC_SURFACE_AREA"
public static final String	System	"System"
public static final String	TestCondition	"Test condition"
public static final String	TreatmentRelated	"TreatmentRelated"
public static final String	X	"X"
public static final String	Y	"Y"
public static final String	Z	"Z"

ambit2.core.*

ambit2.core.config.AmbitCONSTANTS

Modifier and Type	Constant Field	Value
public static final String	AESimilarity	"Atom environment similarity"
public static final String	AMBIT_IDSTRUCTURE	"AMBIT_ID"
public static final String	AMBIT_IDSUBSTANCE	"AMBIT_IDSUBSTANCE"
public static final String	AtomEnvironment	"ambit2.data.molecule.AtomEnvironmentDescriptor"
public static final String	CASRN	"CasRN"
public static final String	DATASET	"SOURCE"
public static final String	EXPERIMENT	"EXPERIMENT"
public static final String	EXPERIMENT_LIST	"EXPERIMENT_LIST"
public static final String	Fingerprint	"org.openscience.cdk.fingerprint.Fingerprinter"
public static final String	FingerprintSTATUS	"FP_STATUS"
public static final String	FingerprintTIME	"FP_TIME"
public static final String	FORMULA	"FORMULA"
public static final String	INCHI	"InChI"
public static final int	maxCyclicBonds	37
public static final int	maxHAtoms	70
public static final int	maxHeavyAtoms	70
public static final String	MOLWEIGHT	"MolWeigth"
public static final String	NAMES	"Names"
public static final String	PairwiseSimilarity	"PairwiseSimilarity"
public static final String	PREDICTED	"PREDICTED"
public static final String	QSARPOINT	"QSARPOINT"
public static final String	SMARTSQuery	"SMARTSQuery"
public static final String	SMILES	"SMILES"
public static final String	StructuralKey	"ambit2.smarts.SmartsScreeningKeys.key"
public static final String	StructuralKey_STATUS	"ambit2.smarts.SmartsScreeningKeys.status"
public static final String	StructuralKey_TIME	"ambit2.smarts.SmartsScreeningKeys.time"
public static final String	STRUCTURETYPE	"STRUCTURE_TYPE"
public static final String	SUBSTANCETYPE	"SUBSTANCE_TYPE"
public static final String	Tanimoto	"Tanimoto"
public static final String	UNIQUE_SMILES	"USMILES"
public static final String	UNIQUE_SMILES_TIME	"USMILESTIME"
public static final String	version	" v2.0 "

ambit2.core.config.Resources

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_DIR	"DEFAULT_DIR"
public static final String	err_invalidcas	"err_invalidcas"
public static final String	GENERATE2D	"GENERATE2D"
public static final String	MSG_EMPTYFILE	"MSG_EMPTYFILE"
public static final String	MSG_ERRORONOPEN	"MSG_ERRORONOPEN"
public static final String	MSG_ERRORONSAVE	"MSG_ERRORONSAVE"
public static final String	msg_exit	"msg_exit"
public static final String	msg_notallowed	"msg_notallowed"
public static final String	MSG_OPENSUCCESS	"MSG_OPENSUCCESS"
public static final String	MSG_SAVESUCCESS	"MSG_SAVESUCCESS"
public static final String	MSG_UNSUPPORTEDFORMAT	"MSG_UNSUPPORTEDFORMAT"
public static final String	SHOW_AROMATICITY	"SHOW_AROMATICITY"
public static final String	SMARTS_UNDEFINED	"SMARTS_UNDEFINED"
public static final String	SMILESPARSER	"SMILESPARSER"

ambit2.core.data.MoleculeTools

Modifier and Type	Constant Field	Value
public static final int	_FPLength	1024
public static final int	substTypeInorganic	2
public static final int	substTypeMetallic	4
public static final int	substTypeMixture	3
public static final int	substTypeOrganic	1

ambit2.core.filter.MoleculeFilter

Modifier and Type	Constant Field	Value
public static final int	BIG_INTEGER	1000000000
public static final char	closeBracket	93
public static final char	intervalSep	44
public static final char	openBracket	91

ambit2.core.groups.ComponentGroup

Modifier and Type	Constant Field	Value
protected static final String	mainsubscript	"c"

ambit2.core.groups.ISGroup

Modifier and Type	Constant Field	Value
public static final String	SGROUP_CONNECTIVITY	"ambit2.groups.ISGroup.SGROUP_CONNECTIVITY"
public static final String	SGROUP_VISIBLE	"ambit2.groups.ISGroup.visible"

ambit2.core.io.IteratingFilesWithHeaderReader<COLUMN>

Modifier and Type	Constant Field	Value
public static final String	defaultSMILESHeader	"SMILES"

ambit2.core.io.RawIteratingSDFReader

Modifier and Type	Constant Field	Value
public static final String	delimiter	"$$$$"

ambit2.core.io.ToxcastAssayReader

Modifier and Type	Constant Field	Value
protected static final String	DSSTox_RID	"DSSTox_RID"
protected static final String	prefix	"DSSTOX_"
protected static final String	ToxCast_signature	"# EPA ToxCast Phase I Data"

ambit2.core.io.ToXMLReaderSimple

Modifier and Type	Constant Field	Value
protected final String	URI	"http://opentox.org/toxml.owl#"

ambit2.core.io.dx.DXParser

Modifier and Type	Constant Field	Value
public static final String	DXTAG	"> <DX."

ambit2.core.io.sj.MalariaHTSDataDelimitedReader

Modifier and Type	Constant Field	Value
protected static final String	col_batch	"batch"
protected static final String	col_SAMPLE	"SAMPLE"

ambit2.core.io.study.StudyFormatter

Modifier and Type	Constant Field	Value
public static final int	_MAX_COL	16383

ambit2.core.processors.AbstractStructureProcessor

Modifier and Type	Constant Field	Value
protected static final String	at_property	"AtomTypes"
protected static final String	at_property_added	"AtomTypes.added"
protected static final String	at_property_removed	"AtomTypes.removed"

ambit2.core.smiles.OpenBabelAbstractShell<X>

Modifier and Type	Constant Field	Value
public static final String	OBABEL_EXE	"obabel"
public static final String	OBABEL_HOME	"OBABEL_HOME"

ambit2.db.*

ambit2.db.DBVersion

Modifier and Type	Constant Field	Value
public static final int	AMBITDB_VERSION_MAJOR	10
public static final int	AMBITDB_VERSION_MINOR	5

ambit2.db.RepositoryReader<Target>

Modifier and Type	Constant Field	Value
protected static final String	read_structurebyid	"SELECT uncompress(structure) FROM structure where idstructure=?"
protected static final String	read_structures	"SELECT idstructure,idchemical,format FROM structure"

ambit2.db.cache.QueryCachedResults<T>

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select %s from query_results join query using(idquery) join sessions using(idsessions) where sessions.title=? and query.name=? and idchemical=?"

ambit2.db.cache.RetrieveStructureImagePath

Modifier and Type	Constant Field	Value
public static final String	IMAGES	"IMAGES"
public static final String	sqlField	"select structure.idstructure,idchemical,uncompress(structure) as ustructure,format,type_structure,atomproperties,text,idquery,1 as selected from structure\njoin query_results using(idchemical,idstructure)\njoin `query` using(idquery)\njoin sessions using(idsessions)\nwhere\nsessions.title=? and\nquery.name=? and\nstructure.%s =?\nunion\nSELECT idstructure,idchemical,uncompress(structure) as ustructure,format,type_structure,atomproperties,null,null,1 as selected FROM structure\nwhere\nstructure.%s =?\norder by type_structure desc"

ambit2.db.chart.BarChartGeneratorDataset

Modifier and Type	Constant Field	Value
protected static final String	sql_dataset	"SELECT ifnull(value_num,value) as v,count(distinct(idstructure)) as num_chemicals\nFROM struc_dataset join property_values using(idstructure) left join property_string using(idvalue_string) join properties using(idproperty)\nwhere idproperty=%d and id_srcdataset=%d\ngroup by v\n"
protected static final String	sql_query	"SELECT ifnull(value_num,value) as v,count(distinct(idstructure)) as num_chemicals\nFROM query_results join property_values using(idstructure) left join property_string using(idvalue_string) join properties using(idproperty)\nwhere idproperty=%d and idquery=%d\ngroup by v\n"

ambit2.db.chart.HistogramChartGenerator

Modifier and Type	Constant Field	Value
protected static final String	histogram_dataset	"select format(a,2) ,sum(if(((%s>=a) and (%s < b)),1,0)) as num_chemicals from property_values\njoin struc_dataset using(idstructure)\njoin\n(\nselect m1+d*(m2-m1)/19 as a, m1+(d+1)*(m2-m1)/19 as b,d from\n(select min(%s) as m1,max(%s) as m2 from property_values\njoin struc_dataset using(idstructure)\nwhere idproperty=%d and value_num is not null and id_srcdataset=%d\n)\nas L\njoin (\nselect 0 as d\nunion select 1 as d\nunion select 2 as d\nunion select 3 as d\nunion select 4 as d\nunion select 5 as d\nunion select 6 as d\nunion select 7 as d\nunion select 8 as d\nunion select 9 as d\nunion select 10 as d\nunion select 11 as d\nunion select 12 as d\nunion select 13 as d\nunion select 14 as d\nunion select 15 as d\nunion select 16 as d\nunion select 17 as d\nunion select 18 as d\nunion select 19 as d\nunion select 20 as d\n) as M\n) as BINS\nwhere idproperty=%d and value_num is not null and id_srcdataset=%d\ngroup by d\n"
protected static final String	histogram_query	"select format(a,2),sum(if(((%s>=a) and (%s < b)),1,0)) as num_chemicals from property_values\njoin query_results using(idstructure)\njoin\n(\nselect m1+d*(m2-m1)/19 as a, m1+(d+1)*(m2-m1)/19 as b,d from\n(select min(%s) as m1,max(%s) as m2 from property_values\njoin query_results using(idstructure)\nwhere idproperty=%d and value_num is not null and idquery=%d\n)\nas L\njoin (\nselect 0 as d\nunion select 1 as d\nunion select 2 as d\nunion select 3 as d\nunion select 4 as d\nunion select 5 as d\nunion select 6 as d\nunion select 7 as d\nunion select 8 as d\nunion select 9 as d\nunion select 10 as d\nunion select 11 as d\nunion select 12 as d\nunion select 13 as d\nunion select 14 as d\nunion select 15 as d\nunion select 16 as d\nunion select 17 as d\nunion select 18 as d\nunion select 19 as d\nunion select 20 as d\n) as M\n) as BINS\nwhere idproperty=%d and value_num is not null and idquery=%d\ngroup by d\n"

ambit2.db.chart.Nominal2SimilarityChartGenerator

Modifier and Type	Constant Field	Value
protected static final String	sql	"select value,min(metric),max(metric) FROM query_results join property_values using(idstructure) join property_string using(idvalue_string) join properties using(idproperty)\nwhere name=\'%s\' and idquery=%d\ngroup by value"

ambit2.db.chart.Numeric2SimilarityChartGenerator

Modifier and Type	Constant Field	Value
protected static final String	sql	"select metric,value_num from query_results\njoin property_values using(idstructure) join properties using(idproperty)\nwhere name = \'%s\' and idquery=%d and value_num is not null\n"

ambit2.db.chart.PieChartGenerator<T extends ISourceDataset>

Modifier and Type	Constant Field	Value
protected static final String	sql_dataset	"SELECT ifnull(value_num,value) as v,count(distinct(property_values.idchemical)) as num_chemicals\nFROM struc_dataset join property_values using(idstructure) left join property_string using(idvalue_string) join properties using(idproperty)\nwhere idproperty=%d and id_srcdataset=%d\ngroup by v\n"
protected static final String	sql_query	"SELECT ifnull(value_num,value) as v,count(distinct(property_values.idchemical)) as num_chemicals\nFROM query_results join property_values using(idstructure) left join property_string using(idvalue_string) join properties using(idproperty)\nwhere idproperty=%d and idquery=%d\ngroup by v\n"

ambit2.db.chart.PropertiesChartGenerator

Modifier and Type	Constant Field	Value
protected static final String	sql_dataset	"select a,b from\n(\nselect %s as a,idstructure from struc_dataset \njoin property_values using(idstructure) join properties using(idproperty)\nwhere idproperty = %d and id_srcdataset=%d\nand value_num is not null\n) as X\njoin\n(\nselect %s as b,idstructure from struc_dataset \njoin property_values using(idstructure) join properties using(idproperty)\nwhere idproperty = %d and id_srcdataset=%d\nand value_num is not null\n) as Y\nusing(idstructure)\n"
protected static final String	sql_query	"select a,b from\n(\nselect %s as a,idstructure from query_results\njoin property_values using(idstructure) join properties using(idproperty)\nwhere idproperty = %d and idquery=%d\n) as X\njoin\n(\nselect %s as b,idstructure from query_results\njoin property_values using(idstructure) join properties using(idproperty)\nwhere idproperty = %d and idquery=%d\n) as Y\nusing(idstructure)\n"

ambit2.db.chart.XTabChartGenerator

Modifier and Type	Constant Field	Value
protected static final String	sql	"select sql_dataset_xtab(%d,%d,%d,%f)"

ambit2.db.chemrelation.ReadDatasetRelation

Modifier and Type	Constant Field	Value
public static final String	sql_dataset	"select idchemical1,idchemical2,metric,relation from chem_relation r join structure s on s.idchemical = r.idchemical1\njoin struc_dataset using(idstructure)\nwhere id_srcdataset=? and relation=? group by idchemical1,idchemical2,relation order by idchemical1,idchemical2,relation"
public static final String	sql_query	"select idchemical1,idchemical2,metric,relation from chem_relation r join structure s on s.idchemical = r.idchemical1\njoin query_results using(idstructure)\nwhere idquery=? and relation=? group by idchemical1,idchemical2,relation order by idchemical1,idchemical2,relation"

ambit2.db.chemrelation.ReadStructureRelation

Modifier and Type	Constant Field	Value
public static final String	sql	"select idchemical1,idchemical2,-1,1,metric,relation as text from chem_relation where idchemical1=? and relation=?"

ambit2.db.facets.datasets.DatasetByPrefixNameFacetQuery

Modifier and Type	Constant Field	Value
protected static final String	sql	"select substring(name,1,?) as prefix, count(*) from src_dataset\n%s\n%s\ngroup by prefix order by prefix"
protected static final String	sql_compound	"select substring(name,1,?) as prefix, count(*) from src_dataset\njoin struc_dataset using(id_srcdataset)\njoin structure using(idstructure)\nwhere \n%s\n%s\nidchemical=?\ngroup by prefix order by prefix"
protected static final String	sql_structure	"select substring(name,1,?) as prefix, count(*) from src_dataset\njoin struc_dataset using(id_srcdataset)\nwhere \n%s\n%s\nidstructure=?\ngroup by prefix order by prefix"

ambit2.db.facets.datasets.PrefixFacetQuery<PARAM,FACET extends net.idea.modbcum.i.facet.IFacet<String>>

Modifier and Type	Constant Field	Value
protected static final String	where_name	" name regexp ?"

ambit2.db.facets.propertyvalue.PropertyDatasetFacetQuery

Modifier and Type	Constant Field	Value
protected static final String	sql	"SELECT ifnull(value_num,value) as v,count(distinct(property_values.idchemical)) as num_chemicals\nFROM struc_dataset join property_values using(idstructure) left join property_string using(idvalue_string) join properties using(idproperty)\nwhere idproperty=? and id_srcdataset=?\ngroup by v\n"

ambit2.db.facets.qlabel.DatasetChemicalsQualityStats

Modifier and Type	Constant Field	Value
protected static final String	sql	"SELECT id_srcdataset,name,count(distinct(idchemical)),q.label,q.text FROM src_dataset\njoin struc_dataset using(id_srcdataset)\njoin structure using(idstructure)\njoin quality_chemicals q using(idchemical)\n%s\ngroup by id_srcdataset,label,text with rollup\n"
protected static final String	sql_summary	"SELECT null,null,count(idchemical),label,text FROM quality_chemicals\ngroup by label,text with rollup\n"

ambit2.db.facets.qlabel.DatasetStructureQualityStats

Modifier and Type	Constant Field	Value
protected static final String	sql	"SELECT id_srcdataset,name,label,count(idstructure),quality_structure.user_name FROM quality_structure\njoin struc_dataset using(idstructure)\njoin src_dataset using(id_srcdataset)\n%s\ngroup by id_srcdataset,user_name,label with rollup\n"

ambit2.db.facets.qlabel.DatasetStrucTypeStats

Modifier and Type	Constant Field	Value
protected static final String	sql	"SELECT id_srcdataset,name,type_structure,count(idstructure),src_dataset.user_name FROM structure\njoin struc_dataset using(idstructure)\njoin src_dataset using(id_srcdataset)\n%s\ngroup by id_srcdataset,user_name,type_structure with rollup\n"

ambit2.db.processors.FP1024Writer

Modifier and Type	Constant Field	Value
protected static final String	insert_bitset	"INSERT INTO %s (idchemical,time,bc,status,fp1,fp2,fp3,fp4,fp5,fp6,fp7,fp8,fp9,fp10,fp11,fp12,fp13,fp14,fp15,fp16) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?) ON DUPLICATE KEY UPDATE time=?,bc=?,status=?,fp1=?,fp2=?,fp3=?,fp4=?,fp5=?,fp6=?,fp7=?,fp8=?,fp9=?,fp10=?,fp11=?,fp12=?,fp13=?,fp14=?,fp15=?,fp16=?,updated=CURRENT_TIMESTAMP()"

ambit2.db.processors.processorCloseSession

Modifier and Type	Constant Field	Value
protected final String	sql	"update sessions set completed=current_timestamp where idsessions=? and user_name=(SUBSTRING_INDEX(user(),\'@\',1))"

ambit2.db.processors.RepositoryWriter

Modifier and Type	Constant Field	Value
protected final String	idchemical_tag	"idchemical"
protected static final String	seek_dataset	"SELECT idstructure,uncompress(structure) as s,format FROM structure join struc_dataset using(idstructure) join src_dataset using(id_srcdataset) where name=? and idchemical=?"

ambit2.db.processors.ValueWriter<Target,Result>

Modifier and Type	Constant Field	Value
public static final int	n_error	4
public static final int	n_idchemical	2
public static final int	n_idproperty	1
public static final int	n_idstructure	3
public static final int	n_text	5
public static final int	n_value	6
public static final int	n_value_num	5
public static final String	onduplicate_number	" on duplicate key update value_num=values(value_num), status=values(status), idvalue_string=null,text=null,idtype=\'NUMERIC\',user_name=values(user_name) "

ambit2.db.readers.AbstractStructureRetrieval<R>

Modifier and Type	Constant Field	Value
public static final String	sql	"select structure.idstructure,idchemical,uncompress(structure) as ustructure,format,type_structure,atomproperties,1 as selected from structure where structure.%s =? order by type_structure desc"

ambit2.db.readers.RetrieveDatasets

Modifier and Type	Constant Field	Value
public static final String	select_AND	" name %s ?"
public static final String	select_chemical	" idchemical = ? "
public static final String	select_datasets_bystruc	"SELECT id_srcdataset,name,src_dataset.user_name,idreference,title,url,licenseURI,rightsHolder,stars,maintainer FROM structure join struc_dataset using(idstructure) join src_dataset using(id_srcdataset) join catalog_references using(idreference) where %s order by name"
public static final String	select_structure	" idstructure = ? "
public static final String	select_WHERE	"where name %s ?"

ambit2.db.readers.RetrieveDescriptor

Modifier and Type	Constant Field	Value
public static final String	sql	"SELECT idproperty,title,url,name,value_num,user_name FROM property_values join properties using(idproperty) join catalog_references using(idreference) where idstructure=? and value_num is not null"

ambit2.db.readers.RetrieveField<ResultType>

Modifier and Type	Constant Field	Value
protected final String	sql_chemical	"select name,idreference,idproperty,idstructure,ifnull(text,value) as value_string,value_num,title,url,idchemical,id,units,comments from property_values \nleft join property_string using(idvalue_string) \njoin properties using(idproperty) join catalog_references using(idreference) \nwhere idchemical=? %s group by comments,idvalue_string"
protected final String	sql_chemical_novalue	"select name,idreference,idproperty,idstructure,null,null,title,url,idchemical,null,units,comments from structure \njoin properties join catalog_references using(idreference)\nwhere idchemical=? %s order by idstructure limit 1"
protected final String	sql_structure	"select name,idreference,idproperty,idstructure,ifnull(text,value) as value_string,value_num,title,url,-1,id,units,comments from property_values \nleft join property_string using(idvalue_string) \njoin properties using(idproperty) join catalog_references using(idreference) \nwhere idstructure=? %s"
protected final String	sql_structure_novalue	"select name,idreference,idproperty,idstructure,null,null,title,url,idchemical,null,units,comments from structure \njoin properties join catalog_references using(idreference)\nwhere idstructure=? %s"
protected final String	where	"and %s=?"

ambit2.db.readers.RetrieveGroupedValuesByAlias

Modifier and Type	Constant Field	Value
protected final String	sql_grouped	"select idchemical,idstructure,comments,group_concat(distinct(if(status=\'TRUNCATED\',text,value)) SEPARATOR \'\n\'),group_concat(distinct(value_num)),group_concat(distinct(title)),group_concat(distinct(url))\nfrom property_values left join property_string using(idvalue_string) \njoin properties using(idproperty)\njoin catalog_references using(idreference) where idchemical = ? and comments in\n(%s) group by comments order by comments\n"

ambit2.db.readers.RetrieveProfileValues

Modifier and Type	Constant Field	Value
public static final String	NaN	"NaN"
protected final String	sql_alias	"and comments in (%s)"
protected final String	sql_chemical	"select name,idreference,idproperty,idstructure,ifnull(text,value) as value_string,value_num,title,url,idchemical,id,units\nfrom property_values\nleft join property_string using(idvalue_string)\njoin properties using(idproperty) join catalog_references using(idreference)\nwhere status != \'ERROR\'\n%s\nand idchemical=?\n"
protected final String	sql_chemical_novalue	"select name,idreference,idproperty,idstructure,null,null,title,url,idchemical,null,units from structure \njoin properties join catalog_references using(idreference)\nwhere status != \'ERROR\' %s and idchemical=? order by idstructure limit 1"
protected final String	sql_name	"and properties.name in (%s)"
protected final String	sql_propery	"and idproperty in (%s)"
protected final String	sql_structure	"select name,idreference,idproperty,idstructure,ifnull(text,value) as value_string,value_num,title,url,idchemical,id,units\nfrom property_values\nleft join property_string using(idvalue_string)\njoin properties using(idproperty) join catalog_references using(idreference)\nwhere status != \'ERROR\'\n%s\nand idstructure=?\norder by idproperty"
protected final String	sql_structure_novalue	"select name,idreference,idproperty,idstructure,null,null,title,url,idchemical,null,units from structure \njoin properties join catalog_references using(idreference)\nwhere status != \'ERROR\' %s and idstructure=?"

ambit2.db.readers.RetrieveProfileValuesAsRow

Modifier and Type	Constant Field	Value
public static final String	NaN	"NaN"
protected final String	sql_chemical	"SELECT idchemical,idstructure \n%s\nFROM\nproperty_values AS pv\nLEFT JOIN property_string s ON s.idvalue_string=pv.idvalue_string\nWHERE idchemical %s %s\nAND idproperty in (%s)\nGROUP BY idchemical\n"
protected final String	sql_property	"MAX(CASE WHEN pv.idproperty = ? THEN value ELSE NULL END) AS v%d,\nMAX(CASE WHEN pv.idproperty = ? THEN value_num ELSE NULL END) AS n%d\n"
protected final String	sql_structure	"SELECT pv.idchemical,pv.idstructure \n%s\nFROM\nproperty_values AS pv\nLEFT JOIN property_string s ON s.idvalue_string=pv.idvalue_string\nWHERE idstructure %s %s\nAND idproperty in (%s)\nGROUP BY pv.idstructure\n"

ambit2.db.reporters.xlsx.AddDimensionedImage

Modifier and Type	Constant Field	Value
public static final int	EXPAND_COLUMN	2
public static final int	EXPAND_ROW	1
public static final int	EXPAND_ROW_AND_COLUMN	3
public static final int	OVERLAY_ROW_AND_COLUMN	7

ambit2.db.reporters.xlsx.AddDimensionedImage.ConvertImageUnits

Modifier and Type	Constant Field	Value
public static final double	CELL_BORDER_WIDTH_MILLIMETRES	2.0
public static final short	EXCEL_COLUMN_WIDTH_FACTOR	256
public static final int	PIXELS_PER_INCH	96
public static final double	PIXELS_PER_MILLIMETRES	3.78
public static final double	POINTS_PER_MILLIMETRE	2.83
public static final int	TOTAL_COLUMN_COORDINATE_POSITIONS	1023
public static final int	TOTAL_ROW_COORDINATE_POSITIONS	255
public static final int	UNIT_OFFSET_LENGTH	7

ambit2.db.search.DictionaryQuery<T extends Dictionary>

Modifier and Type	Constant Field	Value
public static final String	SQL	"select tObject.name as category,tSubject.name as field,relationship from dictionary d join template as tSubject on d.idsubject=tSubject.idtemplate join template as tObject on d.idobject=tObject.idtemplate where `%s`.name %s ? order by tObject.idtemplate"

ambit2.db.search.IStoredQuery

Modifier and Type	Constant Field	Value
public static final String	SQL_INSERT	"insert ignore into query_results (idquery,idchemical,idstructure,selected,metric,text) "

ambit2.db.search.QueryCombined<T>

Modifier and Type	Constant Field	Value
protected static final String	join	"\njoin\n"
protected static final String	union	"\nunion\n"

ambit2.db.search.QueryInfo

Modifier and Type	Constant Field	Value
public static final String	PROPERTYNAME_DATASET_ENABLED	"datasetEnabled"

ambit2.db.search.QuerySmilesByID

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select idchemical,idstructure,smiles,inchi,inchikey from structure join chemicals using(idchemical) where idstructure "

ambit2.db.search.QueryUser

Modifier and Type	Constant Field	Value
public static final String	SQL	"SELECT user_name,email,title,firstname,lastname,address,country,homepage,institute,keywords,reviewer FROM ausers "
public static final String	WHERE	" where %s %s ?"

ambit2.db.search.property.AbstractPropertyRetrieval<F,T,C extends net.idea.modbcum.i.IQueryCondition>

Modifier and Type	Constant Field	Value
protected static final String	XSDDouble	"http://www.w3.org/2001/XMLSchema#double"
protected static final String	XSDInt	"http://www.w3.org/2001/XMLSchema#int"
protected static final String	XSDString	"http://www.w3.org/2001/XMLSchema#string"

ambit2.db.search.property.FreeTextPropertyQuery

Modifier and Type	Constant Field	Value
protected static final String	pairSQL	"(select idproperty,name,units,title,url,idreference,comments,null,islocal,type from catalog_references join properties using(idreference) join property_values using(idproperty)\njoin property_string using(idvalue_string)\n join structure using(idstructure)\n where name like ? and `value` like ?\n)\nunion\n(select idproperty,name,units,title,url,idreference,comments,null,islocal,type from catalog_references join properties using(idreference) join property_values using(idproperty)\njoin property_string using(idvalue_string)\n join structure using(idstructure)\n where `value` like ? and name like ?\n)\n"
protected static final String	singleSQLName	"(select idproperty,name,units,title,url,idreference,comments,null,islocal,type from catalog_references join properties using(idreference)\njoin property_values using(idproperty) join structure using(idstructure) where name like ?)\n"
protected static final String	singleSQLValue	"(select idproperty,name,units,title,url,idreference,comments,null,islocal,type from catalog_references join properties using(idreference) join property_values using(idproperty)\njoin property_string using(idvalue_string) join structure using(idstructure) where `value` like ?)\n"
protected static final String	sql	"%s"

ambit2.db.search.property.PropertyCount

Modifier and Type	Constant Field	Value
public static final String	SQL	"select properties.name,properties.units,properties.comments,title,url,template.name,count(distinct(idstructure)) from\nproperty_values\njoin properties using(idproperty)\njoin catalog_references using(idreference)\njoin template_def using(idproperty)\njoin template using(idtemplate)\n%sgroup by idproperty"
public static final String	where	"where `%s`.name %s ?\n"

ambit2.db.search.property.TemplateQuery

Modifier and Type	Constant Field	Value
public static final String	SQL_WHERE	"where template.name=?"

ambit2.db.search.structure.AbstractStructureQuery<F,T,C extends net.idea.modbcum.i.IQueryCondition>

Modifier and Type	Constant Field	Value
protected static final String	group	"inner join (select min(preference) as p ,idchemical from structure group by idchemical) ids using(idchemical)"
protected static final String	where_group	" structure.preference=ids.p and "

ambit2.db.search.structure.ChemicalByQueryFolder

Modifier and Type	Constant Field	Value
public static final String	sql	"select idchemical,idstructure from query_results join query using(idquery) join sessions using(idsessions) where title in (%s)"

ambit2.db.search.structure.FingerprintsByStatus

Modifier and Type	Constant Field	Value
public static final String	sql	"select idchemical from chemicals where idchemical not in (select idchemical from %s where status %s ? or status = \'error\')\n"

ambit2.db.search.structure.FreeTextQuery

Modifier and Type	Constant Field	Value
protected static final String	pairSQL	"(select idchemical,1 as metric from properties join property_values using(idproperty)\njoin property_string using(idvalue_string)\n where name like ? and `value` like ?\n)\nunion\n(select idchemical,1 as metric from properties join property_values using(idproperty)\njoin property_string using(idvalue_string)\n where `value` like ? and name like ?\n)\n"
protected static final String	singleSQLName	"(select idchemical,1 as metric from properties\njoin property_values using(idproperty) where name like ?)\n"
protected static final String	singleSQLValue	"(select idchemical,1 as metric from property_values\njoin property_string using(idvalue_string) where `value` like ?)\n"
protected static final String	sql	"%s"

ambit2.db.search.structure.MissingFingerprintsQuery

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select ? as idquery, chemicals.idchemical,idstructure,1 as selected,1 as metric,null as text\nfrom structure join chemicals using(idchemical)\nleft join %s as fingerprints using(idchemical)\nwhere (structure.type_structure != \'NA\') and\n(\n(fingerprints.status is null) or (structure.updated > fingerprints.updated) or (fingerprints.status = \'invalid\')\n)\norder by idchemical\n"
public static final String	sqlFieldStruc	"select ? as idquery, idchemical,idstructure,1 as selected,1 as metric,null as text\nfrom structure\nleft join %s as fingerprint using(idchemical,idstructure)\nwhere (structure.type_structure != \'NA\') &&\n(\n(fingerprint.status is null) or (structure.updated > fingerprint.updated) or (fingerprint.status = \'invalid\')\n) order by idchemical,idstructure\n"
public static final String	sqlINCHI	"select ? as idquery, idchemical,-1,1 as selected,1 as metric,null as text from chemicals where (inchi is null) and ((inchikey is null) or (inchikey is not null) and (inchikey != \'ERROR\'))\n"
public static final String	sqlSMARTS	"select ? as idquery, structure.idchemical,idstructure,1 as selected,1 as metric,null as text\nfrom structure\nwhere (structure.type_structure != \'NA\') and atomproperties is null"

ambit2.db.search.structure.MissingInChIsQuery

Modifier and Type	Constant Field	Value
public static final String	sql	"select ? as idquery, chemicals.idchemical,-1,1 as selected,1 as metric,null as text\nfrom chemicals where label = ?\n"

ambit2.db.search.structure.QueryByIdentifierWithStructureFallback

Modifier and Type	Constant Field	Value
protected final String	sql	"{call findByProperty(?,?,?,?,?,?,?,?,?)}"

ambit2.db.search.structure.QueryDataset

Modifier and Type	Constant Field	Value
public static final String	sql	"select ? as idquery,idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,1 as metric,null as text,id_srcdataset from structure join struc_dataset using(idstructure) join src_dataset using (id_srcdataset) "
public static final String	where	" where src_dataset.name %s ?"

ambit2.db.search.structure.QueryDatasetByID

Modifier and Type	Constant Field	Value
public static final String	sql	"select ? as idquery,idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,1 as metric,null as text from structure join struc_dataset using(idstructure) where id_srcdataset %s %s"

ambit2.db.search.structure.QueryDistance

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select ? as idquery,-1,idstructure,1 as selected,1 as metric,null as text from atom_structure join atom_distance using(iddistance) where atom1 = ? and atom2 = ? and distance "

ambit2.db.search.structure.QueryExactStructure

Modifier and Type	Constant Field	Value
protected static final String	EXACT	"EXACT"

ambit2.db.search.structure.QueryFieldAbstract<T,C extends net.idea.modbcum.i.IQueryCondition,NC extends net.idea.modbcum.i.IQueryCondition>

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select ? as idquery,s1.idchemical,s1.idstructure,if(s1.type_structure=\'NA\',0,1) as selected,s1.preference as metric,null as text\nFROM structure s1\nLEFT JOIN structure s2 ON s1.idchemical = s2.idchemical AND (1E10*s1.preference+s1.idstructure) > (1E10*s2.preference+s2.idstructure)\njoin (\nselect distinct(structure.idchemical)\nfrom structure\njoin property_values using(idstructure)\njoin property_string using (idvalue_string)\njoin properties using(idproperty)\nwhere %s %s\n) a on a.idchemical=s1.idchemical\nwhere s2.idchemical is null\n"
public static final String	sqlField_ci	"select ? as idquery,s1.idchemical,s1.idstructure,if(s1.type_structure=\'NA\',0,1) as selected,s1.preference as metric,null as text\nFROM structure s1\nLEFT JOIN structure s2 ON s1.idchemical = s2.idchemical AND (1E10*s1.preference+s1.idstructure) > (1E10*s2.preference+s2.idstructure)\njoin (\nselect distinct(idchemical)\nfrom summary_property_chemicals\njoin property_ci using (id_ci)\njoin properties using(idproperty)\nwhere %s %s\n) a on a.idchemical=s1.idchemical\nwhere s2.idchemical is null\n"
public static final String	sqlFieldProperties	"select ? as idquery,s1.idchemical,s1.idstructure,if(s1.type_structure=\'NA\',0,1) as selected,s1.preference as metric,null as text,-1 as idproperty,name,comments,value\nFROM structure s1\nLEFT JOIN structure s2 ON s1.idchemical = s2.idchemical AND (1E10*s1.preference+s1.idstructure) > (1E10*s2.preference+s2.idstructure)\njoin (\nselect idchemical,group_concat(distinct value_ci SEPARATOR \';\') as value,group_concat(distinct name) as name,group_concat(distinct comments) as comments\nfrom summary_property_chemicals\njoin properties using(idproperty)\njoin property_ci using (id_ci)\nwhere %s %s \ngroup by idchemical\n) a on a.idchemical=s1.idchemical\nwhere s2.idchemical is null\n"

ambit2.db.search.structure.QueryFieldNumeric

Modifier and Type	Constant Field	Value
public static final String	sqlField	"SELECT ? as idquery,idchemical,idstructure,1 as selected,value_num as metric,null as text FROM properties join property_values using(idproperty)\n"
public final String	where_all	"where value_num is not null and value_num %s ? %s %s \n"
public final String	where_equal	"where value_num is not null and value_num = ? %s\n"
public final String	where_name	"and %s=?"

ambit2.db.search.structure.QuerySimilarityBitset

Modifier and Type	Constant Field	Value
protected final String	order	"order by metric desc"
protected final String	sql_similarity	"select ? as idquery,idchemical,-1,1 as selected,round(cbits/(bc+?-cbits),2) as metric,null as text\nfrom (\nselect %s.idchemical,(bit_count(? & fp1) + bit_count(? & fp2) + bit_count(? & fp3) + bit_count(? & fp4) +\nbit_count(? & fp5) + bit_count(? & fp6) + bit_count(? & fp7) + bit_count(? & fp8) + bit_count(? & fp9) + bit_count(? & fp10) +\nbit_count(? & fp11) + bit_count(? & fp12) + bit_count(? & fp13) + bit_count(? & fp14) + bit_count(? & fp15) + bit_count(? & fp16))\n as cbits,bc from %s\n) as a\nwhere\n(cbits/(bc+?-cbits)>?)\n%s"

ambit2.db.search.structure.QuerySMARTS

Modifier and Type	Constant Field	Value
protected static final String	SMARTS	"SMARTS"

ambit2.db.search.structure.QueryStoredResults

Modifier and Type	Constant Field	Value
public static final String	join	""
public static final String	sqlField	"select %s,idchemical,idstructure,selected, %s,text from query_results %s where %s %s %s %s order by metric %s"
public static final String	where_name	"selected = ?"
public static final String	where_query	"idquery=?"

ambit2.db.search.structure.QueryStoredResultsByName

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select idquery,idchemical,idstructure,selected, %s,text from query_results join query using(idquery) join sessions using(idsessions) where name=? and title=? %s"

ambit2.db.search.structure.QueryStructure

Modifier and Type	Constant Field	Value
protected static final String	sql_chemical	"select ? as idquery,idchemical,-1 as idstructure,0 as selected,1 as metric,inchi as text from chemicals where (%s %s ?) %s"
protected static final String	sql_prefered	"select ? as idquery,idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,preference as metric,null as text\nfrom structure where idchemical = (select idchemical from chemicals where (%s %s ?) %s limit 1)\norder by idchemical,preference,idstructure"

ambit2.db.search.structure.QueryStructureByID

Modifier and Type	Constant Field	Value
public static final String	sqlDataset	"select ? as idquery,idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,? as metric,? as text from structure\njoin struc_dataset using(idstructure) where %s %s %s and id_srcdataset=? order by idchemical,preference,idstructure"
public static final String	sqlField	"select ? as idquery,idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,? as metric,? as text from structure where %s %s %s order by idchemical,preference,idstructure"
public static final String	sqlQuery	"select ? as idquery,structure.idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,? as metric,? as text from structure\njoin query_results q using(idstructure) where %s %s %s and q.idquery=? order by structure.idchemical,preference,idstructure"

ambit2.db.search.structure.QueryStructureByQuality

Modifier and Type	Constant Field	Value
protected static final String	join_struc_dataset	"join struc_dataset using(idstructure)\n"
protected static final String	join_struc_query	"join query_results using(idstructure)\n"
public static final String	sql	"select ? as idquery,structure.idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,cast(quality_structure.label as unsigned) as metric,quality_structure.label as text from structure %sleft join quality_structure using(idstructure)\n %s %s"
public static final String	where	" where quality_structure.label %s ?"
public static final String	where_null	" where quality_structure.label is null"
protected static final String	where_struc_dataset	"and id_srcdataset = ?\n"
protected static final String	where_struc_query	"and idquery = ?\n"

ambit2.db.search.structure.QueryStructureByQualityPairLabel

Modifier and Type	Constant Field	Value
protected static final String	join_struc_query	"join query_results using(idstructure)\n"
public static final String	sql	"select ? as idquery,structure.idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,cast(quality_chemicals.label as unsigned) as metric,quality_chemicals.label as text,id_srcdataset from structure join struc_dataset using(idstructure)%sleft join quality_chemicals using(idchemical)\n %s %s %s"
public static final String	sql_chemical	"select ? as idquery,idchemical,-1,1,cast(quality_chemicals.label as unsigned) as metric,quality_chemicals.label as text from quality_chemicals %s %s %s"
public static final String	where	" where quality_chemicals.label %s ? "
public static final String	where_null	" where quality_chemicals.label is null "
protected static final String	where_struc_dataset	"and id_srcdataset = ?\n"
protected static final String	where_struc_query	"and idquery = ?\n"
public static final String	where_text	" and text = ?"

ambit2.db.search.structure.QueryStructureByValueQuality

Modifier and Type	Constant Field	Value
public static final String	sql	"select ? as idquery,idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,cast(label as unsigned) as metric,label as text from structure\nwhere idstructure in\n(\nselect idstructure from properties join property_values using(idproperty) left join quality_labels using(id) where sameas=? %s\n)\n"
public static final String	where	" and label %s ?"
public static final String	where_null	" and label is null"

ambit2.db.search.structure.QueryStructureType

Modifier and Type	Constant Field	Value
protected static final String	join_struc_dataset	"join struc_dataset using(idstructure)\n"
protected static final String	join_struc_query	"join query_results using(idstructure)\n"
public static final String	sql	"select ? as idquery,structure.idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,cast(type_structure as unsigned) as metric,type_structure as text from structure %s%s %s"
public static final String	where	" where type_structure %s ?"
public static final String	where_null	" where type_structure is null"
protected static final String	where_struc_dataset	"and id_srcdataset = ?\n"
protected static final String	where_struc_query	"and idquery = ?\n"

ambit2.db.search.structure.QueryStrucType

Modifier and Type	Constant Field	Value
public static final String	sql	"select ? as idquery,idchemical,idstructure,if(type_structure=\'NA\',0,1) as selected,cast(type_structure as unsigned) as metric,type_structure from structure where %s"
public static final String	where	" type_structure %s ?"

ambit2.db.search.structure.pairwise.ChemicalSpaceQuery

Modifier and Type	Constant Field	Value
protected final String	sql	"{call tanimotoBinnedSpace(?,?,?,?,?,?)}"

ambit2.db.search.structure.pairwise.QueryStructurePairsDataset

Modifier and Type	Constant Field	Value
protected final String	sql	"SELECT\nif(s1.idstructure <s2.idstructure,s1.idstructure,s2.idstructure) id1,\nif(s1.idstructure >s2.idstructure,s1.idstructure,s2.idstructure) id2\nFROM struc_dataset s1\njoin\nstruc_dataset s2\nwhere\ns1.id_srcdataset=?\nand\ns2.id_srcdataset=?\nand\ns1.idstructure != s2.idstructure\ngroup by id1,id2\norder by id1"

ambit2.db.search.structure.pairwise.QueryStructurePairsMixed

Modifier and Type	Constant Field	Value
protected final String	sql	"SELECT\nif(s1.idstructure <s2.idstructure,s1.idstructure,s2.idstructure) id1,\nif(s1.idstructure >s2.idstructure,s1.idstructure,s2.idstructure) id2\nFROM struc_dataset s1\njoin\nquery_results s2\nwhere\ns1.id_srcdataset=?\nand\ns2.idquery=?\nand\ns1.idstructure != s2.idstructure\ngroup by id1,id2\norder by id1"

ambit2.db.search.structure.pairwise.QueryStructurePairsRDataset

Modifier and Type	Constant Field	Value
protected final String	sql	"SELECT\nif(s1.idstructure <s2.idstructure,s1.idstructure,s2.idstructure) id1,\nif(s1.idstructure >s2.idstructure,s1.idstructure,s2.idstructure) id2\nFROM query_results s1\njoin\nquery_results s2\nwhere\ns1.idquery=?\nand\ns2.idquery=?\nand\ns1.idstructure != s2.idstructure\ngroup by id1,id2\norder by id1"

ambit2.db.simiparity.space.QueryQMapStructures

Modifier and Type	Constant Field	Value
public static final String	sql	"select idsasmap,idchemical,-1,1,g2 as metric,null as text,a,b,c,d,fisher from qsasmap4 where idsasmap=? order by g2 desc "

ambit2.db.substance.relation.ChemicalBySubstanceRelation

Modifier and Type	Constant Field	Value
public static final String	sql	"select idchemical from substance_relation where relation != \'HAS_STRUCTURE\'"

ambit2.db.substance.study.ReadEffectRecordAbstract<F,ER extends EffectRecord<String,String,String>>

Modifier and Type	Constant Field	Value
protected static final String	sql	"SELECT idresult,endpoint as effectendpoint,hex(endpointhash) as hash,conditions,unit,loQualifier,loValue,upQualifier,upValue,errQualifier,err,textValue,resulttype,resultgroup from substance_experiment where document_prefix =? and document_uuid =unhex(?)"

ambit2.db.update.bookmark.CreateBookmark

Modifier and Type	Constant Field	Value
public static final String	create_sql	"INSERT INTO bookmark (idbookmark,creator,recalls,hasTopic,title,description,created,date) values (?,?,?,?,?,?,NOW(),NOW()) ON DUPLICATE KEY UPDATE recalls=values(recalls),hasTopic=values(hasTopic),title=values(title),description=values(description),date=now()"

ambit2.db.update.bookmark.DeleteBookmark

Modifier and Type	Constant Field	Value
public static final String	delete_sql	"delete from bookmark where idbookmark=?"

ambit2.db.update.bookmark.ReadAnnotation

Modifier and Type	Constant Field	Value
protected static final String	sql	"SELECT null,b1.s_source,b1.s_id,b1.o_id,b2.label,b3.label,b1.label,b1.relation,match (b1.s_id,b1.o_id,b1.label) against (? %s) as relevance,hex(b1.uuid) as huuid\nFROM ontobucket b1 left join\n(select label,s_id from ontobucket where relation!=\'subclass\' limit 1) b2 on b1.s_id = b2.s_id\nleft join (select label,s_id from ontobucket where relation!=\'subclass\' limit 1) b3 on b1.o_id = b3.s_id\nwhere match (b1.s_id,b1.o_id,b1.label) against (? %s)"
protected static final String	sql_labelsonly	"SELECT null,b1.s_source,b1.s_id,b1.o_id,b1.label,null,null,b1.relation,match (b1.s_id,b1.o_id,b1.label) against (? %s) as relevance,hex(b1.uuid) as huuid\nFROM ontobucket b1\nwhere match (b1.s_id,b1.o_id,b1.label) against (? %s)"

ambit2.db.update.bookmark.UpdateBookmark

Modifier and Type	Constant Field	Value
public static final String	update_sql	"update bookmark set recalls=?,hasTopic=?,title=?,description=?,date=now() where idbookmark=? and creator=?"

ambit2.db.update.bundle.ReadBundle

Modifier and Type	Constant Field	Value
public static final String	select_datasets	"SELECT idbundle as id_srcdataset,name,user_name,idreference,title,url,licenseURI,rightsHolder,stars,maintainer,created,description,hex(bundle_number) bn,version,user_name,published_status,updated FROM bundle join catalog_references using(idreference) %s %s\n"

ambit2.db.update.bundle.ReadBundleVersion

Modifier and Type	Constant Field	Value
public static final String	select_datasets	"SELECT idbundle as id_srcdataset,name,user_name,idreference,title,url,licenseURI,rightsHolder,stars,maintainer,created,description,hex(bundle_number) bn,version,user_name,published_status,updated FROM bundle join catalog_references using(idreference) where bundle_number in (select bundle_number from bundle where idbundle=?)\n"

ambit2.db.update.chemical.UpdateChemical<C extends IChemical>

Modifier and Type	Constant Field	Value
public static final String	update_sql	"update chemicals set %s,label=?,lastmodified=now() where idchemical=?"

ambit2.db.update.dataset.DatasetAddStructure

Modifier and Type	Constant Field	Value
public static final String	create_sql_byid	"insert ignore into struc_dataset (idstructure,id_srcdataset) values (?,?)"
public static final String	create_sql_byname	"insert ignore into struc_dataset (idstructure,id_srcdataset) SELECT ?,id_srcdataset from src_dataset where name=?"

ambit2.db.update.dataset.DatasetQueryFieldNumeric

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select ? as idquery,s1.idchemical,s1.idstructure,if(s1.type_structure=\'NA\',0,1) as selected,s1.preference as metric,null as text\nFROM structure s1\njoin struc_dataset using(idstructure) join property_values using(idstructure)\nwhere\n id_srcdataset = ? and idproperty = ? and value_num %s ?"
public static final String	sqlField_Rdatasets	"select ? as idquery,s1.idchemical,s1.idstructure,if(s1.type_structure=\'NA\',0,1) as selected,s1.preference as metric,null as text\nFROM structure s1\njoin query_results using(idstructure) join property_values using(idstructure)\nwhere\nidquery = ? and idproperty = ? and value_num %s ?"

ambit2.db.update.dataset.DatasetQueryFieldString

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select ? as idquery,s1.idchemical,s1.idstructure,if(s1.type_structure=\'NA\',0,1) as selected,s1.preference as metric,null as text\nFROM structure s1\njoin struc_dataset using(idstructure) join property_values using(idstructure)\njoin property_string using(idvalue_string) where\n id_srcdataset = ? and idproperty = ? and value = ?"
public static final String	sqlField_Rdatasets	"select ? as idquery,s1.idchemical,s1.idstructure,if(s1.type_structure=\'NA\',0,1) as selected,s1.preference as metric,null as text\nFROM structure s1\njoin query_results using(idstructure) join property_values using(idstructure)\njoin property_string using(idvalue_string) where\nidquery = ? and idproperty = ? and value = ?"

ambit2.db.update.dataset.ReadDataset

Modifier and Type	Constant Field	Value
public static final String	select_datasets	"SELECT id_srcdataset,name,user_name,idreference,title,url,licenseURI,rightsHolder,stars,maintainer FROM src_dataset join catalog_references using(idreference) %s order by stars desc\n"

ambit2.db.update.dataset.ReadDatasetLicense

Modifier and Type	Constant Field	Value
public static final String	select_license_byid	"SELECT licenseURI FROM src_dataset where id_srcdataset = ?"
public static final String	select_license_byname	"SELECT licenseURI FROM src_dataset where name = ?"

ambit2.db.update.dataset.UpdateDataset

Modifier and Type	Constant Field	Value
public static final String	MSG_EMPTY	"No name, license or rightsHolder to update!"

ambit2.db.update.dictionary.TemplateAddProperty

Modifier and Type	Constant Field	Value
public static final String	create_sql	"INSERT IGNORE INTO template_def (idtemplate,idproperty,`order`) SELECT idtemplate,idproperty,idproperty FROM template join properties join catalog_references using(idreference) where properties.name=? and catalog_references.title=? and template.name=?"

ambit2.db.update.fp.ReadStructuresByFingerprint

Modifier and Type	Constant Field	Value
public static final String	sql	"select ? as idquery,idchemical,-1,null,bc,null\nfrom %s where concat(\nhex(fp1),\'-\',\nhex(fp2),\'-\',\nhex(fp3),\'-\',\nhex(fp4),\'-\',\nhex(fp5),\'-\',\nhex(fp6),\'-\',\nhex(fp7),\'-\',\nhex(fp8),\'-\',\nhex(fp9),\'-\',\nhex(fp10),\'-\',\nhex(fp11),\'-\',\nhex(fp12),\'-\',\nhex(fp13),\'-\',\nhex(fp14),\'-\',\nhex(fp15),\'-\',\nhex(fp16)\n) = ?"

ambit2.db.update.model.CreateModel

Modifier and Type	Constant Field	Value
public static final String	create_sql	"INSERT IGNORE INTO models (idmodel,name,dataset,predictors,dependent,predicted,content,mediatype,algorithm,parameters,hidden,creator) SELECT null,?,?,t1.idtemplate,t2.idtemplate,t3.idtemplate,?,?,?,?,?,? from template t1 join template t2 join template t3 where t1.name=? and t2.name =? and t3.name=?"

ambit2.db.update.model.DeleteModel

Modifier and Type	Constant Field	Value
public static final String	delete_sql	"delete from models where %s and user_name=(SUBSTRING_INDEX(user(),\'@\',1))"

ambit2.db.update.model.UpdateModel

Modifier and Type	Constant Field	Value
public static final String	update_sql	"update models set content=?,mediatype=? where %s"

ambit2.db.update.property.CreateProperty

Modifier and Type	Constant Field	Value
public static final String	create_sql	"INSERT IGNORE INTO properties (idproperty,idreference,name,units,comments,islocal,ptype) SELECT ?,idreference,?,?,?,?,? from catalog_references where title=?"

ambit2.db.update.property.CreatePropertyReferenceID

Modifier and Type	Constant Field	Value
public static final String	create_sql	"INSERT IGNORE INTO properties (idproperty,idreference,name,units,comments,islocal) SELECT ?,idreference,?,?,?,? from catalog_references where idreference=?"

ambit2.db.update.property.UpdateProperty

Modifier and Type	Constant Field	Value
public static final String	update_sql	"update properties,catalog_references set %s where idproperty=? and properties.idreference=catalog_references.idreference"

ambit2.db.update.propertyannotations.CreatePropertyAnnotations

Modifier and Type	Constant Field	Value
protected final String	sql	"INSERT ignore into property_annotation (idproperty,rdf_type,predicate,object) values %s"

ambit2.db.update.propertyannotations.ReadPropertyAnnotations

Modifier and Type	Constant Field	Value
protected final String	sql	"SELECT idproperty,rdf_type,predicate,object FROM property_annotation where idproperty=?"

ambit2.db.update.queryfolder.CreateQueryFolder

Modifier and Type	Constant Field	Value
public static final String	sql	"insert into sessions (idsessions,user_name,title,completed) values (?,?,?,current_timestamp) on duplicate key update completed=current_timestamp"
public static final String	sql_current_user	"insert into sessions (idsessions,user_name,title,completed) values (?,SUBSTRING_INDEX(user(),\'@\',1),?,current_timestamp) on duplicate key update completed=current_timestamp"

ambit2.db.update.queryfolder.DeleteQueryFolder

Modifier and Type	Constant Field	Value
public static final String	sql	"delete from sessions where user_name=? and idsessions=?"
public static final String	sql_current_user	"delete from sessions where user_name=(SUBSTRING_INDEX(user(),\'@\',1)) and idsessions=?"

ambit2.db.update.queryfolder.UpdateQueryFolder

Modifier and Type	Constant Field	Value
public static final String	sql	"update sessions set title=? where idsessions=? and user_name=?"
public static final String	sql_current_user	"update sessions set title=? where idsessions=? and user_name=(SUBSTRING_INDEX(user(),\'@\',1))"

ambit2.db.update.storedquery.CreateStoredQuery

Modifier and Type	Constant Field	Value
public static final String	sql_byid	"insert ignore into query (idquery,idsessions,name,content) select ?,idsessions,?,? from sessions where idsessions=?"
public static final String	sql_byname	"insert ignore into query (idquery,idsessions,name,content) select ?,idsessions,?,? from sessions where title=?"

ambit2.db.update.storedquery.DeleteStoredQuery

Modifier and Type	Constant Field	Value
public static final String	delete_sql	"delete query FROM query, sessions where %s %s %s and query.idsessions=sessions.idsessions and user_name=SUBSTRING_INDEX(user(),\'@\',1)"

ambit2.db.update.storedquery.QueryAddTemplate

Modifier and Type	Constant Field	Value
public static final String	update_sql_id	"update query set idtemplate=? where idquery=?"
public static final String	update_sql_name	"insert query (idquery,idsessions,name,content,idtemplate)\nselect idquery,idsessions,query.name,content,template.idtemplate from template\njoin query\twhere template.name=? and idquery=?\non duplicate key update idtemplate=values(idtemplate)\n"

ambit2.db.update.storedquery.ReadStoredQuery

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select idquery,name,title,content from query join sessions using(idsessions)\n where %s order by name"

ambit2.db.update.storedquery.SearchStoredQueries

Modifier and Type	Constant Field	Value
public static final String	sqlField	"select idquery,count(idstructure) as `rows`,name,content from query_results join query using(idquery) join sessions using (idsessions) where user_name=SUBSTRING_INDEX(user(),\'@\',1) %s %s group by idquery order by idquery desc"
public static final String	where_query	"and name %s ?"
public static final String	where_session	"and idsessions = ?"

ambit2.db.update.structure.ChemicalByDataset

Modifier and Type	Constant Field	Value
public static final String	sql	"select idchemical from structure join struc_dataset using(idstructure) where id_srcdataset %s %s"

ambit2.db.update.structure.CreateStructure

Modifier and Type	Constant Field	Value
public static final String	create_sql	"INSERT INTO structure (idstructure,idchemical,structure,format,updated,user_name,type_structure,preference) values (null,?,compress(?),?,CURRENT_TIMESTAMP,SUBSTRING_INDEX(user(),\'@\',1),?,?)"

ambit2.db.update.value.UpdateCompoundPropertyValueNumber

Modifier and Type	Constant Field	Value
public static final String	select_number_compound	"select null,?,idchemical,idstructure,null,?,SUBSTRING_INDEX(user(),\'@\',1),null,?,\'NUMERIC\' from structure where idchemical=? order by idstructure limit 1"

ambit2.db.update.value.UpdateCompoundPropertyValueString

Modifier and Type	Constant Field	Value
public static final String	select_string_compound	"select null,?,idchemical,idstructure,idvalue_string,?,SUBSTRING_INDEX(user(),\'@\',1),?,null,\'STRING\' from property_string join structure where value=? and idchemical=? order by idstructure limit 1"

ambit2.db.update.value.UpdateStructurePropertyIDNumber

Modifier and Type	Constant Field	Value
public static final String	insert_descriptorvalue	"INSERT INTO property_values (id,idproperty,idchemical,idstructure,idvalue_string,status,user_name,text,value_num,idtype) "
public static final String	select_number	"values (null,?,?,?,null,?,SUBSTRING_INDEX(user(),\'@\',1),null,?,\'NUMERIC\')"

ambit2.db.update.value.UpdateStructurePropertyIDString

Modifier and Type	Constant Field	Value
public static final String	insert_string	"INSERT IGNORE INTO property_string (value) VALUES (?)"
public static final String	onduplicate_string	" on duplicate key update property_values.idvalue_string=property_string.idvalue_string, property_values.status=values(status), text=values(text),value_num=null,idtype=\'STRING\',user_name=values(user_name) "
public static final String	select_string	"select null,?,?,?,idvalue_string,?,SUBSTRING_INDEX(user(),\'@\',1),?,null,\'STRING\' from property_string where value=?"

ambit2.dbui.*

ambit2.dbui.QuerySmartsEditor

Modifier and Type	Constant Field	Value
protected static final String	t_family	"family"
protected static final String	t_group	"group"
protected static final String	t_hint	"hint"
protected static final String	t_name	"name"
protected static final String	t_smarts	"smarts"

ambit2.descriptors.*

ambit2.descriptors.AbstractKekulizationVerifier

Modifier and Type	Constant Field	Value
protected static final String	OK	"OK"
protected static final String	version	"1.4.9"

ambit2.descriptors.AtomTypeVerifierDescriptor

Modifier and Type	Constant Field	Value
protected static final String	OK	"OK"

ambit2.descriptors.CrossSectionalDiameterDescriptor

Modifier and Type	Constant Field	Value
public static final String	MAX_DIAMETER	"MAX_DIAMETER"
public static final String	MAX_LENGTH	"MAX_LENGTH"
public static final String	MIN_DIAMETER	"MIN_DIAMETER"

ambit2.descriptors.FunctionalGroup

Modifier and Type	Constant Field	Value
protected static final String	t_example	"example"
protected static final String	t_family	"family"
protected static final String	t_group	"group"
protected static final String	t_hint	"hint"
protected static final String	t_name	"name"
protected static final String	t_smarts	"smarts"

ambit2.descriptors.fingerprints.PubChemFingerprinter

Modifier and Type	Constant Field	Value
public static final int	FP_SIZE	881

ambit2.descriptors.fingerprints.PubChemFingerprinterAmbitSmarts

Modifier and Type	Constant Field	Value
public static final int	FP_SIZE	881

ambit2.descriptors.utils.RingInfo

Modifier and Type	Constant Field	Value
public static final String	moleculeProperty	"RingInfoMoleculeProperty"

ambit2.dragon.*

ambit2.dragon.DragonShell

Modifier and Type	Constant Field	Value
public static final String	DRAGON_EXE	"dragon6shell"
public static final String	DRAGON_HOME	"DRAGON_HOME"

ambit2.export.*

ambit2.export.isa.base.ExternalDataFileLocation

Modifier and Type	Constant Field	Value
public static final String	splitter	"/"

ambit2.export.isa.base.ISAConst

Modifier and Type	Constant Field	Value
public static final String	addSeparator	" "
public static final String	assayFilePrefix	"a_"
public static final String	investigationFilePrefix	"i_"
public static final String	studyFilePrefix	"s_"

ambit2.export.isa.base.ISALocation

Modifier and Type	Constant Field	Value
public static final String	splitter	"\\."

ambit2.export.isa.tab.ISATABConst

Modifier and Type	Constant Field	Value
public static final String	fieldSeparator	"\t"

ambit2.groupcontribution.*

ambit2.groupcontribution.nmr.nmr_1h.HNMRPredefinedKnowledgeBase

Modifier and Type	Constant Field	Value
public static final String	keyWordPrefix	"$$"
public static final String	keyWordSeparator	"="

ambit2.groupcontribution.transformations.TransformationComposition

Modifier and Type	Constant Field	Value
public static final String	composeSeparator	">>"

ambit2.model.*

ambit2.model.numeric.DataCoverageLeverage

Modifier and Type	Constant Field	Value
protected static final String	protocol	"WRITE_TRAINING_DATA"

ambit2.model.numeric.DataCoverageLeverageHatMatrix

Modifier and Type	Constant Field	Value
protected static final String	protocol	"WRITE_TRAINING_DATA"

ambit2.mopac.*

ambit2.mopac.DescriptorMopacShell

Modifier and Type	Constant Field	Value
public static final String	EHOMO	"EHOMO"
public static final String	ELUMO	"ELUMO"

ambit2.pubchem.*

ambit2.pubchem.EntrezESearchParser

Modifier and Type	Constant Field	Value
protected static final String	tag_ENTREZ_ErrorList	"ErrorList"
protected static final String	tag_ENTREZ_esearch	"eSearchResult"
protected static final String	tag_ENTREZ_Id	"Id"
protected static final String	tag_ENTREZ_IdList	"IdList"
protected static final String	tag_ENTREZ_PhraseNotFound	"PhraseNotFound"

ambit2.pubchem.PUGProcessor

Modifier and Type	Constant Field	Value
protected static final String	PCT_attribute_value	"value"
protected static final int	PCT_download_compression_bzip2	2
protected static final int	PCT_download_compression_gzip	1
protected static final int	PCT_download_compression_none	0
protected static final int	PCT_download_format_binary_asn	1
protected static final int	PCT_download_format_sdf	3
protected static final int	PCT_download_format_text_asn	0
protected static final int	PCT_download_format_xml	2
public static final String	PUBCHEM_CID	"CID"
protected static final String	tag_PCT_Data	"PCT-Data"
protected static final String	tag_PCT_Data_input	"PCT-Data_input"
protected static final String	tag_PCT_Data_output	"PCT-Data_output"
protected static final String	tag_PCT_Download	"PCT-Download"
protected static final String	tag_PCT_download_3D	"PCT-Download_use-3d"
protected static final String	tag_PCT_Download_compression	"PCT-Download_compression"
protected static final String	tag_PCT_Download_format	"PCT-Download_format"
protected static final String	tag_PCT_Download_uids	"PCT-Download_uids"
protected static final String	tag_PCT_Download_URL	"PCT-Download-URL"
protected static final String	tag_PCT_Download_URL_url	"PCT-Download-URL_url"
protected static final String	tag_PCT_ID_List	"PCT-ID-List"
protected static final String	tag_PCT_ID_List_db	"PCT-ID-List_db"
protected static final String	tag_PCT_ID_List_uids	"PCT-ID-List_uids"
protected static final String	tag_PCT_ID_List_uids_E	"PCT-ID-List_uids_E"
protected static final String	tag_PCT_InputData	"PCT-InputData"
protected static final String	tag_PCT_InputData_download	"PCT-InputData_download"
protected static final String	tag_PCT_OutputData	"PCT-OutputData"
protected static final String	tag_PCT_OutputData_output	"PCT-OutputData_output"
protected static final String	tag_PCT_OutputData_output_download_url	"PCT-OutputData_output_download-url"
protected static final String	tag_PCT_OutputData_output_waiting	"PCT-OutputData_output_waiting"
protected static final String	tag_PCT_OutputData_status	"PCT-OutputData_status"
protected static final String	tag_PCT_QueryUids	"PCT-QueryUids"
protected static final String	tag_PCT_QueryUids_ids	"PCT-QueryUids_ids"
protected static final String	tag_PCT_Waiting	"PCT-Waiting"
protected static final String	tag_PCT_Waiting_reqid	"PCT-Waiting_reqid"

ambit2.pubchem.rest.PUGRestRequest<R>

Modifier and Type	Constant Field	Value
public static final String	PUGREST_URL	"https://pubchem.ncbi.nlm.nih.gov/rest/pug/"

ambit2.reactions.*

ambit2.reactions.ReactionConst

Modifier and Type	Constant Field	Value
public static final String	KeyWordElementSeparator	","
public static final String	KeyWordPrefix	"$$"
public static final String	KeyWordSeparator	"="

ambit2.reactions.reactor.Reactor

Modifier and Type	Constant Field	Value
public static final String	PropertyInchiKey	"INCHI_KEY"
public static final String	PropertyReactionIds	"REACTION_IDS"

ambit2.reactions.retrosynth.ReactionSequence

Modifier and Type	Constant Field	Value
public static final String	MoleculeInChIKeyProperty	"MOLECULE_INCHI_KEY"
public static final String	MoleculeStatusProperty	"MOLECULE_STATUS"

ambit2.rendering.*

ambit2.rendering.CompoundImageTools

Modifier and Type	Constant Field	Value
public static final String	ATOM_ANNOTATION	"stdgen.annotation.label"
public static final String	SELECTED_ATOM_COLOR	"stdgen.highlight.color"
public static final String	SELECTED_ATOM_SIZE	"ambit2.size"

ambit2.rest.*

ambit2.rest.AbstractResource<Q,T extends Serializable,P extends net.idea.modbcum.i.processors.IProcessor<Q,org.restlet.representation.Representation>>

Modifier and Type	Constant Field	Value
public static final String	b64search_param	"b64search"
public static final String	caseSensitive	"casesens"
public static final String	condition	"condition"
public static final String	max_hits	"max"
public static final String	property	"property"
public static final String	returnProperties	"returnProperties"
public static final String	search_param	"search"

ambit2.rest.DataResources

Modifier and Type	Constant Field	Value
public static final String	conformerKey_resource	"/conformer"
public static final String	idconformer_resource	"idconformer"

ambit2.rest.SimpleTaskResource<USERID>

Modifier and Type	Constant Field	Value
public static final String	resource	"/task"
public static final String	resourceKey	"idtask"

ambit2.rest.config.AMBITAppConfigInternal

Modifier and Type	Constant Field	Value
protected static final String	adminAAEnabled	"aa.admin"
protected static final String	attachDepict	"attach.depict"
protected static final String	attachInvestigation	"attach.investigation"
protected static final String	attachSubstance	"attach.substance"
protected static final String	attachSubstanceOwner	"attach.substanceowner"
protected static final String	attachToxmatch	"attach.toxmatch"
protected static final String	compoundAAEnabled	"aa.compound"
public static final String	DB_AA_ENABLED	"aa.db.enabled"
protected static final String	featureAAEnabled	"aa.feature"
public static final String	LOCAL_AA_ENABLED	"aa.local.enabled"
protected static final String	modelAAEnabled	"aa.model"
public static final String	OPENTOX_AA_ENABLED	"aa.enabled"
public static final String	WARMUP_ENABLED	"warmup.enabled"

ambit2.rest.config.AMBITAppConfigProperties

Modifier and Type	Constant Field	Value
public static final String	AJAX_TIMEOUT	"ajax.timeout"
public static final String	ALLOWED_ORIGINS	"allowed.origins"
public static final String	BASEURL_DEPTH	"baseurl.depth"
protected static final String	config_changeLineSeparators	"changeLineSeparators"
protected static final String	custom_description	"custom.description"
protected static final String	custom_license	"custom.license"
protected static final String	custom_logo	"custom.logo"
protected static final String	custom_query	"custom.query"
protected static final String	custom_search	"custom.search"
protected static final String	custom_structurequery	"custom.structurequery"
protected static final String	custom_title	"custom.title"
protected static final String	database_create	"database.create"
protected static final String	dataset_members_prefix	"dataset.members.prefix"
protected static final String	googleAnalytics	"google.analytics"
public static final String	GUARD_ENABLED	"guard.enabled"
public static final String	GUARD_LIST	"guard.list"
protected static final String	identifierKey	"aa.local.admin.name"
protected static final String	identifierPass	"aa.local.admin.pass"
protected static final String	jsonp	"jsonp"
protected static final String	map_folder	"map.folder"
protected static final String	rdf_writer	"rdf.writer"
protected static final String	service_ontology	"service.ontology"
public static final String	SIMILARITY_ORDER	"similarity.order"
protected static final String	solr_basic_password	"solr.basic.password.%d"
protected static final String	solr_basic_user	"solr.basic.user.%d"
protected static final String	solr_filter	"solr.filter"
protected static final String	solr_service	"solr.service.%d"
protected static final String	solr_url	"solr.url.%d"
protected static final String	version	"ambit.version"
protected static final String	version_build	"ambit.build"
protected static final String	version_timestamp	"ambit.build.timestamp"

ambit2.rest.dataset.AbstractStaxRDFWriter<INPUT,OUTPUT>

Modifier and Type	Constant Field	Value
protected static final String	dc	"dc"
protected static final String	dcterms	"dcterms"
protected static final String	ot	"ot"
protected static final String	owl	"owl"
protected static final String	rdf	"rdf"

ambit2.rest.freemarker.FreeMarkerStatusService

Modifier and Type	Constant Field	Value
public static final String	report_level	"ambit.report.level"

ambit2.rest.legacy.RDFAbstractFeatureIterator<PROPERTY>

Modifier and Type	Constant Field	Value
protected static final String	sparql	"PREFIX ot:<http://www.opentox.org/api/1.1#>\nPREFIX ota:<http://www.opentox.org/algorithms.owl#>\nPREFIX owl:<http://www.w3.org/2002/07/owl#>\nPREFIX dc:<http://purl.org/dc/elements/1.1/>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>\nselect ?feature ?title ?units ?src ?sameas\nwhere {\n ?feature rdf:type ot:Feature.\n OPTIONAL {?feature dc:title ?title}.\n OPTIONAL {?feature ot:units ?units}.\n OPTIONAL {?feature ot:hasSource ?src}.\n OPTIONAL {?feature owl:sameAs ?sameas}.\n}\nORDER by ?feature ?title ?units ?src ?sameas\n"

ambit2.rest.rdf.Annotea

Modifier and Type	Constant Field	Value
protected static final String	_NS_ANNOTEA	"http://www.w3.org/2000/10/annotation-ns#"
protected static final String	_NS_BOOKMARK	"http://www.w3.org/2002/01/bookmark#%s"

ambit2.rest.rdf.BibTex

Modifier and Type	Constant Field	Value
protected static final String	_NS	"http://purl.org/net/nknouf/ns/bibtex#%s"

ambit2.rest.rdf.OTA

Modifier and Type	Constant Field	Value
protected static final String	_NS	"http://www.opentox.org/algorithmTypes.owl#%s"

ambit2.rest.rdf.OTEE

Modifier and Type	Constant Field	Value
protected static final String	_NS	"http://www.opentox.org/echaEndpoints.owl#%s"

ambit2.rest.rdf.RDFInstancesIterator

Modifier and Type	Constant Field	Value
public static final String	CompoundURI	"CompoundURI"

ambit2.rest.rdf.chembl.ChEMBLRawReader

Modifier and Type	Constant Field	Value
public final String	sparql	"PREFIX chembl:<http://pele.farmbio.uu.se/chembl/onto/#>\nPREFIX dc:<http://purl.org/dc/elements/1.1/>\nPREFIX bo:<http://www.blueobelisk.org/chemistryblogs/>\nselect ?forMolecule ?SMILES ?Activity ?Assay ?Target ?standardValue ?standardUnits ?activityType ?relation ?classL2 ?classL3 ?classL4 ?classL5 where\n{\n?forMolecule a chembl:SmallMolecule.\n?forMolecule bo:smiles ?SMILES.\n?Activity chembl:forMolecule ?forMolecule.\n?Activity a chembl:Activity.\n?Activity chembl:type ?activityType.\n?Activity chembl:relation ?relation.\n?Activity chembl:standardValue ?standardValue.\n?Activity chembl:standardUnits ?standardUnits.\n?Activity chembl:onAssay ?Assay.\n?Assay chembl:hasTarget ?Target.\n?Target chembl:classL2 ?classL2.\n?Target chembl:classL3 ?classL3.\n?Target chembl:classL4 ?classL4.\n?Target chembl:classL5 ?classL5.\nFILTER (?classL2 = \"P450\") .\nFILTER (?classL3 = \"3\") .\nFILTER (?classL4 = \"A\") .\nFILTER (?classL5 = \"4\") .\n}\nLIMIT 10\n"
public static final String	sparqlEndpoint	"http://rdf.farmbio.uu.se/chembl/sparql"

ambit2.rest.rdf.sparql.RDFAbstractCompoundIterator<COMPOUND,PROPERTY>

Modifier and Type	Constant Field	Value
protected static final String	sparql	"PREFIX ot:<http://www.opentox.org/api/1.1#>\nPREFIX ota:<http://www.opentox.org/algorithms.owl#>\nPREFIX owl:<http://www.w3.org/2002/07/owl#>\nPREFIX dc:<http://purl.org/dc/elements/1.1/#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>\nselect ?dataset ?dataEntry ?compound ?feature ?value\nwhere {\n ?dataset rdf:type ot:Dataset.\n ?dataset ot:dataEntry ?dataEntry.\n ?dataEntry ot:compound ?compound.\n OPTIONAL {\n ?dataEntry ot:values ?values.\n ?values rdf:type ot:FeatureValue.\n ?values ot:feature ?feature.\n ?values ot:value ?value.\n ?feature rdf:type ot:Feature.\n }.\n}\nORDER by ?dataset ?dataEntry ?compound ?feature ?value\n"

ambit2.rest.rdf.sparql.RDFAbstractFeatureIterator<PROPERTY>

Modifier and Type	Constant Field	Value
protected static final String	sparql	"PREFIX ot:<http://www.opentox.org/api/1.1#>\nPREFIX ota:<http://www.opentox.org/algorithms.owl#>\nPREFIX owl:<http://www.w3.org/2002/07/owl#>\nPREFIX dc:<http://purl.org/dc/elements/1.1/#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>\nselect ?feature ?title ?units ?src ?sameas\nwhere {\n ?feature rdf:type ot:Feature.\n OPTIONAL {?feature dc:title ?title}.\n OPTIONAL {?feature ot:units ?units}.\n OPTIONAL {?feature ot:hasSource ?src}.\n OPTIONAL {?feature owl:sameAs ?sameas}.\n}\nORDER by ?feature ?title ?units ?src ?sameas\n"

ambit2.rest.substance.SubstanceRecordStaxWriter

Modifier and Type	Constant Field	Value
protected static final String	obo_uri	"http://purl.obolibrary.org/obo/"
protected static final String	rdfs	"rdfs"
protected static final String	sio_uri	"http://semanticscience.org/resource/"

ambit2.search.*

ambit2.search.chemidplus.ChemIdPlusRequest

Modifier and Type	Constant Field	Value
public static final String	CHEMIDPLUS_URL	"https://chem.sis.nlm.nih.gov/chemidplus/mol3d/%s"

ambit2.search.csls.CSLSRequest<R>

Modifier and Type	Constant Field	Value
public static final String	CSLS_URL	"https://cactus.nci.nih.gov/chemical/structure"

ambit2.similarity.*

ambit2.similarity.stats.ClassificationModelStatistics<U extends Bin>

Modifier and Type	Constant Field	Value
protected static final int	ACCURACY	0
protected static final int	ALL	3
protected static final int	CORRECT	1
protected static final int	ERROR	2
protected static final int	LAST	4

ambit2.similarity.stats.PredictionModelStatistics<U extends Bin>

Modifier and Type	Constant Field	Value
protected static final int	ALL	2
protected static final int	IGNORED	3
protected static final int	LAST	4
protected static final int	MAE	0
protected static final int	RMSE	1

ambit2.sln.*

ambit2.sln.SLNConst

Modifier and Type	Constant Field	Value
public static final int	A_ATTR_charge	1
public static final int	A_ATTR_fcharge	3
public static final int	A_ATTR_I	2
public static final int	A_ATTR_s	4
public static final int	A_ATTR_spin	5
public static final int	A_ATTR_USER_DEFINED	500
public static final int	A_spin_d	1
public static final int	A_spin_s	0
public static final int	A_spin_t	2
public static final int	A_STEREO_D	4
public static final int	A_STEREO_D_	19
public static final int	A_STEREO_DE	12
public static final int	A_STEREO_DM	26
public static final int	A_STEREO_E	7
public static final int	A_STEREO_I	3
public static final int	A_STEREO_I_	22
public static final int	A_STEREO_IE	15
public static final int	A_STEREO_IM	29
public static final int	A_STEREO_L	5
public static final int	A_STEREO_L_	20
public static final int	A_STEREO_LE	13
public static final int	A_STEREO_LM	27
public static final int	A_STEREO_M	9
public static final int	A_STEREO_N	2
public static final int	A_STEREO_N_	21
public static final int	A_STEREO_NE	14
public static final int	A_STEREO_NM	28
public static final int	A_STEREO_R	0
public static final int	A_STEREO_R_	17
public static final int	A_STEREO_RE	10
public static final int	A_STEREO_Rel	8
public static final int	A_STEREO_RM	24
public static final int	A_STEREO_S	1
public static final int	A_STEREO_S_	18
public static final int	A_STEREO_SE	11
public static final int	A_STEREO_SM	25
public static final int	A_STEREO_U	6
public static final int	A_STEREO_U_	23
public static final int	A_STEREO_UE	16
public static final int	A_STEREO_UM	30
public static final int	B_ATTR_s	1
public static final int	B_ATTR_USER_DEFINED	500
public static final int	B_STEREO_C	0
public static final int	B_STEREO_E	2
public static final int	B_STEREO_I	5
public static final int	B_STEREO_N	4
public static final int	B_STEREO_T	1
public static final int	B_STEREO_U	6
public static final int	B_STEREO_U_	7
public static final int	B_STEREO_Z	3
public static final int	B_TYPE_1	1
public static final int	B_TYPE_2	2
public static final int	B_TYPE_3	3
public static final int	B_TYPE_ANY	0
public static final int	B_TYPE_aromatic	4
public static final int	B_TYPE_USER_DEFINED	100
public static final int	CO_DIFFERS	5
public static final int	CO_EQUALS	0
public static final int	CO_GREATER_OR_EQUALS	4
public static final int	CO_GREATER_THAN	3
public static final int	CO_LESS_OR_EQUALS	2
public static final int	CO_LESS_THAN	1
public static final int	CO_NO_COMPARISON	100
public static final String	CoveredAtomProperty	"SLN_COVERED"
public static final int	GlobDictOffseet	1000
public static final int	LO	1000
public static final int	LO_AND	1
public static final int	LO_ANDLO	3
public static final int	LO_NOT	0
public static final int	LO_OR	2
public static final int	LocalDictOffseet	1000000
public static final int	QA_ATTR_c	101
public static final int	QA_ATTR_f	102
public static final int	QA_ATTR_hac	108
public static final int	QA_ATTR_hc	109
public static final int	QA_ATTR_htc	110
public static final int	QA_ATTR_is	103
public static final int	QA_ATTR_mapNum	100
public static final int	QA_ATTR_mw	117
public static final int	QA_ATTR_n	104
public static final int	QA_ATTR_not	105
public static final int	QA_ATTR_ntc	111
public static final int	QA_ATTR_r	106
public static final int	QA_ATTR_rbc	115
public static final int	QA_ATTR_src	116
public static final int	QA_ATTR_tac	113
public static final int	QA_ATTR_tbo	114
public static final int	QA_ATTR_v	107
public static final int	QA_COVERED_n	0
public static final int	QA_COVERED_o	1
public static final int	QA_COVERED_y	2
public static final int	QB_ATTR_r	102
public static final int	QB_ATTR_rbc	103
public static final int	QB_ATTR_src	100
public static final int	QB_ATTR_type	101

ambit2.smarts.*

ambit2.smarts.AtomEquivalenceInfo

Modifier and Type	Constant Field	Value
public static final int	SHIFT_ATOM_ELEMENT	10000000
public static final int	SHIFT_BOND_TYPE	1000000
public static final int	SHIFT_INNER_BOND_TYPE	100
public static final int	SHIFT_ISOTOPE	100
public static final int	SHIFT_LAYER_AT1	100000
public static final int	SHIFT_LAYER_AT2	1000
public static final int	SHIFT_NEG_CHARGE	1000
public static final int	SHIFT_POS_CHARGE	10000
public static final int	SHIFT_TOP_DEGREE	100000
public static final int	SHIFT_TOP_LAYER	1

ambit2.smarts.CMLUtilities

Modifier and Type	Constant Field	Value
public static final String	ExplicitH	"ExplicitH"
public static final int	MAXRINGS	4
public static final String	RingData	"RingData"
public static final String	RingData2	"RingData2"
public static final String	SMARTSProp	"SMARTSProp"

ambit2.smarts.SmartsConst

Modifier and Type	Constant Field	Value
public static final int	ABSOLUTE_CIS	10
public static final int	ABSOLUTE_TRANS	11
public static final int	AP_a	1
public static final int	AP_A	2
public static final int	AP_ANY	0
public static final int	AP_AtNum	11
public static final int	AP_Charge	10
public static final int	AP_Chiral	12
public static final int	AP_D	3
public static final int	AP_GMOE	17
public static final int	AP_h	5
public static final int	AP_H	4
public static final int	AP_iMOE	16
public static final int	AP_Mass	13
public static final int	AP_NMOE	19
public static final int	AP_OB_Hybr	21
public static final int	AP_r	7
public static final int	AP_R	6
public static final int	AP_Recursive	14
public static final int	AP_v	8
public static final int	AP_vMOE	20
public static final int	AP_x	15
public static final int	AP_X	9
public static final int	AP_XMOE	18
public static final int	BT_ANY	0
public static final int	BT_AROMATIC	4
public static final int	BT_CIS	10
public static final int	BT_CISUNSPEC	11
public static final int	BT_DOUBLE	2
public static final int	BT_DOWN	7
public static final int	BT_DOWNUNSPEC	9
public static final int	BT_RING	5
public static final int	BT_SINGLE	1
public static final int	BT_TRANS	12
public static final int	BT_TRANSUNSPEC	13
public static final int	BT_TRIPLE	3
public static final int	BT_UNDEFINED	100
public static final int	BT_UP	6
public static final int	BT_UPUNSPEC	8
public static final int	ChC_AntiClock	1
public static final int	ChC_Clock	2
public static final int	ChC_R	1001
public static final int	ChC_S	1002
public static final int	ChC_Unspec	0
public static final int	LO	1000
public static final int	LO_AND	1
public static final int	LO_ANDLO	3
public static final int	LO_NOT	0
public static final int	LO_OR	2
public static final int	LO_UNDEFINED	100
public static final int	SMRK_UNSPEC_ATOM	-100000

ambit2.smarts.SmartsToChemObject

Modifier and Type	Constant Field	Value
public static final String	markProperty	"MARKED_AB"

ambit2.smarts.TopLayer

Modifier and Type	Constant Field	Value
public static final String	TLProp	"TL"

ambit2.some.*

ambit2.some.SOMEShell

Modifier and Type	Constant Field	Value
public static final String	SOME_HOME	"SOME_HOME"
public static final String	SOME_RESULT	"SOME_RESULT"

ambit2.tautomers.*

ambit2.tautomers.CACTVSRanking

Modifier and Type	Constant Field	Value
public static final double	score2eV	0.05

ambit2.tautomers.Filter

Modifier and Type	Constant Field	Value
public static final int	FT_EXCLUDE	2
public static final int	FT_WARNING	1

ambit2.tautomers.PredefinedKnowledgeBase

Modifier and Type	Constant Field	Value
public static final double	aromaticAtomEnergy	-0.1

ambit2.tautomers.TautomerConst

Modifier and Type	Constant Field	Value
public static final String	CACTVS_ENERGY_RANK	"CACTVS_ENERGY_RANK"
public static final int	ERM_NEW	1
public static final int	ERM_OLD	0
public static final int	HRM_Explicit	1
public static final int	HRM_Implicit	0
public static final int	HRM_Undefined	2
public static final int	IHA_INDEX	1000000
public static final String	KeyWordElementSeparator	","
public static final String	KeyWordPrefix	"$$"
public static final String	KeyWordSeparator	"="
public static final int	RT_MobileGroup	0
public static final int	RT_RingChain	1
public static final int	RULE_ORDER_BY_SIZE	1
public static final int	RULE_ORDER_NONE	0
public static final int	STATUS_FINISHED	10
public static final int	STATUS_NONE	0
public static final int	STATUS_SET_STRUCTURE	1
public static final int	STATUS_STARTED	2
public static final int	STATUS_STOPPED	5
public static final String	TAUTOMER_RANK	"TAUTOMER_RANK"

ambit2.tautomers.TautomerRanking

Modifier and Type	Constant Field	Value
public static final double	kB	1.3806488E-23
public static final double	KeVtoJ	1.602176565E-19

ambit2.tautomers.processor.StructureStandardizer

Modifier and Type	Constant Field	Value
public static final String	ERROR_TAG	"ERROR"

ambit2.ui.*

ambit2.ui.EditableHeader

Modifier and Type	Constant Field	Value
public final int	HEADER_ROW	-10

ambit2.ui.EditorPreferences

Modifier and Type	Constant Field	Value
protected static final String	filename	"ambit2.ui.pref"

ambit2.ui.WizardPanel

Modifier and Type	Constant Field	Value
protected final String	dlu	"12dlu"

ambit2.ui.table.IBrowserMode

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_MODE	"browserMode"
public static final String	PROPERTY_ZOOM	"zoom"

ambit2.ui.table.IFindNavigator<E>

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_VALUE	"value"

ambit2.ui.table.IPageNavigator

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_MAXPAGES	"maxPages"
public static final String	PROPERTY_PAGE	"page"
public static final String	PROPERTY_PAGERECORD	"pageRecord"
public static final String	PROPERTY_PAGESIZE	"pageSize"

ambit2.ui.table.IRecordNavigator

Modifier and Type	Constant Field	Value
public static final String	PROPERTY_MAXRECORDS	"maxRecords"
public static final String	PROPERTY_RECORD	"record"

ambit2.ui.table.StructureRecordsTableModel

Modifier and Type	Constant Field	Value
protected final int	offset	3

ambit2.vega.*

ambit2.vega.VegaShell

Modifier and Type	Constant Field	Value
public static final String	JAVA_BIN	"JAVA_BIN"
public static final String	JAVA_EXE	"java"
public static final String	JAVA_HOME	"JAVA_HOME"
public static final String	VEGA_HOME	"VEGA_HOME"