CDK-Taverna – List of workers

Workername / Group Description
Basics  
PerceiveMM2AtomTypes  Perceive
MM2 atom types
PerceiveMMFF94AtomTypes  Perceive
MMFF94 atom types
PerceiveAtomType  Perceive
atom types
SubstructureFilter  Substructure
Filter
DetectHueckelAromaticity  Hueckel
Aromaticity Detector
StructureDiagramGenerator  Structure
Diagram Generator
FingerprintCalculator  Calculates
Fingerprint for a given CMLChemfile
CreatePDFWith2DStructures  Create PDF
File with 2D Structures
CreateJPGWith2DStructures  Create JPG
File with 2D Structures
CreatePNGWith2DStructures  Create PNG
File with 2D Structures
BioclipseResultViewer  Start
Bioclipse
Model3DBuilders
WithMM2ForceField 
Model3DBuildersWithMM2ForceField
ReactionEnumerator  ReactionEnumerator
 Classificator  
ART2AClassificatorWorker  ART2A
Classificator
GetART2AClassification
ResultAsCSV 
Get classification result
GetART2AClassification
ResultAsPDF 
Get classification result as PDF
GetInterAngle
BetweenClassesAsCSV 
Get interangle between classes
LeafOneOutIteratorInitializer  Initialise
leaf one out iterator
LeafOneOutIterator-
GetNextFingerprintItemList 
Get next
fingerprint item from leaf one out iterator
LeafOneOutIteratorHasNext  Has next
from the leaf one out iterator
CompareART2A-
ClassificationResults 
Compare
ART2A classification results
GetMoleculeIDs
ForGivenClasses 
Get the
molecule ids for a given class
GenerateRandomCentroidVectors  Get random
centroid vectors for testing
GetART2AClassificationResult
WithDifferentOriginsAsPDF 
Get
classification result consider different origins as PDF
GetART2AClassificationResult
WithDifferentOriginsAsCSV 
Get
classification result consider different origins as CSV
 Database  
InsertMoleculeIntoDB  Insert
Molecule into database
GetMoleculesFromDB  Get
Molecules from database
InsertQSARResultsIntoDB  Insert
QSAR Results into database
UpdateQSARResultsIntoDB  Update
QSAR Results within the database
GetQSARVectorFromDB  Get QSAR
vector from database
GetMolecularWeightFromDB  Get
Molecular Weight from database
GetMoleculesFromDB  Get
molecules from database
GetMoleculeIDs
AndOriginFromDB 
Get
molecule ID’s and origin from database
GetMoleculesFrom
DBForSubstructure 
Substructure
Search of molecules on the database
GetSelectedMoleculesFromDB  Get
selected molecules from database for given molecule ids
 Database-Iterativ  
IterativeGetMoleculeFromDB  Get
Molecule from database
IterativeHasNext
MoleculeFromDB 
Has Next
Molecule from database
IterativeMoleculeFromDBReader  Iterative
Molecule from database reader
 Database-IO  
ReadMDLSDFileAs
DatabaseInput 
Read MDL
SD File as DB input
 InChITools  
InChIParser  Parse
InChI
InChIGeneratorWorker  Generate
InChI
 IO  
ConvertToCMLString  Convert to
CML String
WriteToCMLFile  Write
CMLChemFile to File
WriteToMDLMolFile  Write MDL
Mol File to File
ReadMDLMolFile  Read MDL
Mol File
ReadMDLSDFile  Read MDL
SD File
FileReader  File
Reader
TextFileReader  Textfile
Reader
ReadMDLRXNFile  Read MDL
RXN File
ReadMDLRXNV3000File  Read MDL
RXN V3000 File
ReadSMILESFromFile  Read
SMILES from File
ConvertGZFilesToXMLFiles  Converts
GZ files to XML files
ConvertXMLFilesToGZFiles  Converts
XML files to GZ files
FileWriter  Write CSV
/ TXT Files 
 IO-Iterative  
IteratingFileReader  IteratingFileReader
IteratingFileReaderGetContent  GetContent
IteratingFileReaderHasNext  HasNext
IterativeFileWriter  Iterative
File Writer
 QSAR  
QSARDescriptor  QSAR
worker
VectorGenerator  Vector
Generator
CSVGenerator  Generates
a CSV(Comma Separated Value)
VectorGeneratorForDBInput  Vector
Generator For Database Input
 QSAR_Atomic  
AtomDegree  AtomDegree-Descriptor
AtomHybridization  AtomHybridization-Descriptor
AtomHybridizationVSEPR  AtomHybridizationVSEPR-Descriptor
AtomValence  AtomValence-Descriptor
BondsToAtom  BondsToAtom-Descriptor
CovalentRadius  CovalentRadius-Descriptor
DistanceToAtom  DistanceToAtom-Descriptor
EffectiveAtomPolarizability  EffectiveAtomPolarizability-Descriptor
InductiveAtomicHardness  InductiveAtomicHardness-Descriptor
InductiveAtomicSoftness  InductiveAtomicSoftness-Descriptor
IPAtomicHOSE  IPAtomicHOSE-Descriptor
IPAtomicLearning  IPAtomicLearning-Descriptor
IsProtonInAromaticSystem  IsProtonInAromaticSystem-Descriptor
IsProtonInConjugatedPiSystem  IsProtonInConjugatedPiSystem-Descriptor
PartialPiCharge  PartialPiCharge-Descriptor
PartialSigmaCharge  PartialSigmaCharge-Descriptor
PartialTChargeMMFF94  PartialTChargeMMFF94-Descriptor
PartialTChargePEOE  PartialTChargePEOE-Descriptor
PeriodicTablePosition  PeriodicTablePosition-Descriptor
PiElectronegativity  PiElectronegativity-Descript
ProtonTotalPartialCharge  ProtonTotalPartialCharge-Descriptor
RDFProton_G3R  RDFProton_G3R-Descriptor
RDFProton_GDR  RDFProton_GDR-Descriptor
RDFProton_GHR_topol  RDFProton_GHR_topol-Descriptor
RDFProton_GHR  RDFProton_GHR-Descriptor
RDFProton_GSR  RDFProton_GSR-Descriptor
SigmaElectronegativity  SigmaElectronegativity-Descriptor
VdWRadius  VdWRadius-Descriptor
 QSAR_AtomPair  
PiContactDetection  PiContactDetection-Descriptor
 QSAR_Bond  
BondPartialPiCharge  BondPartialPiCharge-Descriptor
BondPartialSigmaCharge  BondPartialSigmaCharge-Descriptor
BondPartialTCharge  BondPartialTCharge-Descriptor
BondSigmaElectronegativity  BondSigmaElectronegativity-Descriptor
IPBondLearning  IPBond-Descriptor
MassNumberDifference  MassNumberDifference-Descriptor
 QSAR_Model_Weka  
SimpleKMeansWorker  Simple
KMeans Clusterer
EMClusterWorker  EM
Clusterer
ExtractClusterResultWorker  Extract
Cluster Result Worker
 QSAR_Molecular  
AminoAcidCount  AminoAcidCount-Descriptor
APol  APol-Descriptor
AromaticAtomsCount  AromaticAtomsCount-Descriptor
AromaticBondsCount  AromaticBondsCount-Descriptor
AtomCount  AtomCount-Descriptor
Autocorrelation_Charge  Autocorrelation_Charge-Descriptor
Autocorrelation_Mass  Autocorrelation_Mass-Descriptor
Autocorrelation_Polarizability  Autocorrelation_Polarizability-Descriptor
BCUT  BCUT-Descriptor
BondCount  BondCount-Descriptor
BPol  BPol-Descriptor
ChiChain  ChiChain-Descriptor
ChiCluster  ChiCluster-Descriptor
ChiPath  ChiPath-Descriptor
ChiPathCluster  ChiPathCluster-Descriptor
CPSA  CPSA-Descriptor
EccentricConnectivityIndex  EccentricConnectivityIndex-Descriptor
FragmentComplexity  FragmentComplexity-Descriptor
GravitationalIndex  GravitationalIndex-Descriptor
HBondAcceptorCount  HBondAcceptorCount-Descriptor
HBondDonorCount  HBondDonorCount-Descriptor
IPMolecularLearning  IPMolecularLearning-Descriptor
KappaShapeIndices  KappaShapeIndices-Descriptor
LargestChain  LargestChain-Descriptor
LargestPiSystem  LargestPiSystem-Descriptor
LengthOverBreadth  LengthOverBreadth-Descriptor
LongestAliphaticChain  LongestAliphaticChain-Descriptor
MDE  MDE-Descriptor
MomentOfInertia  MomentOfInertia-Descriptor
PetitjeanNumber  Calculate
PetitjeanNumber-Descriptor
PetitjeanShapeIndex  PetitjeanShapeIndex-Descriptor
RotatableBondsCount  RotatableBondsCount-Descriptor
RuleOfFiveFilter  Rule-of-Five
Filter
TPSA  TPSA-Descriptor
VAdjMa  VAdjMa-Descriptor
Weight  Weight-Descriptor
WeightedPath  WeightedPath-Descriptor
WHIM  WHIM-Descriptor
WienerNumbers  WienerNumbers-Descriptor
XLogP  XLogP-Descriptor
ZagrebIndex  ZagrebIndex-Descriptor
TaeAminoAcid  TaeAminoAcid-Descriptor
 SmilesTools  
SMILESGenerator  Generates
SMILES
SMILESParser  Parse
SMILES 
 Tools  
RemoveMOLFiles
WithoutStructureFromList 
Remove MOL
Files without Structures from List
ExtractIDFromMolFile  Extract
org IDs from MOL File (EXNO)
ExtractIntermedIDFromMolFile  Extract
org. IMD IDs from MOL File (IMD-No)
ImplicitHydrogenAdder  Add the
implicit hydrogens to each molecule
TagMolecules  Tag
molecules
ExtractDatabaseIDFromMolecule  Extract
the database ID from the molecule
GetMolecularWeightDistribution  Get a
molecular weight distribution
ConvertFingerprintItemListToCSV  Convert
Fingerprint item list to csv
ConvertFingerprintItemList
ToMathematicaDataMatrix 
Convert
Fingerprint item list to Mathematica data vector
ScaleFingerprintItemArray
BetweenZeroAndOne 
Scale
Fingerprint item list to values between 0 and 1
 Tools-Chebi  
chebiExtractDataFrom
ChebiStructureTSV 
Extract
Data from Chebi Structure TSV
chebiRemoveAllNonMolFiles
FromChebiStructureExtraction 
Remove all non MDL Mol entries from list

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