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PerceiveMM2AtomTypes |
Perceive MM2 atom types |
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PerceiveMMFF94AtomTypes |
Perceive MMFF94 atom types |
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PerceiveAtomType |
Perceive atom types |
|
SubstructureFilter |
Substructure Filter |
|
DetectHueckelAromaticity |
Hueckel Aromaticity Detector |
|
StructureDiagramGenerator |
Structure Diagram Generator |
|
FingerprintCalculator |
Calculates Fingerprint for a given CML Chemfile |
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CreatePDFWith2DStructures |
Create PDF File with 2D Structures |
|
CreateJPGWith2DStructures |
Create JPG File with 2D Structures |
|
CreatePNGWith2DStructures |
Create PNG File with 2D Structures |
|
BioclipseResultViewer |
Start Bioclipse |
|
Model3DBuildersWithMM2ForceField |
Model 3D With MM2 ForceField |
|
ReactionEnumerator |
Reaction Enumerator |
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ART2AClassificatorWorker |
ART2A Classificator |
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GetART2AClassificationResultAsCSV |
Get classification result |
|
GetART2AClassificationResultAsPDF |
Get classification result as PDF |
|
GetInterAngleBetweenClassesAsCSV |
Get interangle between classes |
|
LeafOneOutIteratorInitializer |
Initialise leaf one out iterator |
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LeafOneOutIterator-GetNextFingerprintItemList |
Get next fingerprint item from leaf one out iterator |
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LeafOneOutIteratorHasNext |
Has next from the leaf one out iterator |
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CompareART2A-ClassificationResults |
CompareART2A classification results |
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GetMoleculeIDsForGivenClasses |
Get the molecule ids for a given class |
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GenerateRandomCentroidVectors |
Get random centroid vectors for testing |
|
GetART2AClassificationResultWithDifferentOriginsAsPDF |
Get classification result consider different origins as PDF |
|
GetART2AClassificationResultWithDifferentOriginsAsCSV |
Get classification result consider different origins as CSV |
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|
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InsertMoleculeIntoDB |
Insert Molecule into database |
|
GetMoleculesFromDB |
Get Molecules from database |
|
InsertQSARResultsIntoDB |
Insert QSAR Results into database |
|
UpdateQSARResultsIntoDB |
Update QSAR Results within the database |
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GetQSARVectorFromDB |
Get QSAR vector from database |
|
GetMolecularWeightFromDB |
Get Molecular Weight from database |
|
GetMoleculesFromDB |
Get molecules from database |
|
GetMoleculeIDsAndOriginFromDB |
Get molecule ID's and origin from database |
|
GetMoleculesFromDBForSubstructure |
Substructure Search of molecules on the database |
|
GetSelectedMoleculesFromDB |
Get selected molecules from database for given molecule ids |
|
|
|
IterativeGetMoleculeFromDB |
Get Molecule from database |
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IterativeHasNextMoleculeFromDB |
Has Next Molecule from database |
|
IterativeMoleculeFromDBReader |
Iterative Molecule from database reader |
|
|
|
ReadMDLSDFileAsDatabaseInput |
Read MDL SD File as DB input |
|
|
|
InChIParser |
Parse InChI |
|
InChIGeneratorWorker |
Generate InChI |
|
|
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ConvertToCMLString |
Convert to CML String |
|
WriteToCMLFile |
Write CMLChemFile to File |
|
WriteToMDLMolFile |
Write MDL Molfile to File |
|
ReadMDLMolFile |
Read MDL Molfile |
|
ReadMDLSDFile |
Read MDL SD File |
|
FileReader |
File Reader |
|
TextFileReader |
Text file 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 |
|
|
|
IteratingFileReader |
Iterating File Reader |
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IteratingFileReaderGetContent |
Get Content |
|
IteratingFileReaderHasNext |
Has Next |
|
IterativeFileWriter |
Iterative File Writer |
|
|
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QSARDescriptor |
QSAR worker |
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VectorGenerator |
Vector Generator |
|
CSVGenerator |
Generates a CSV (Comma Separated Value) |
|
VectorGeneratorForDBInput |
Vector Generator For Database Input |
|
|
|
AtomDegree |
Atom Degree Descriptor |
|
AtomHybridization |
Atom Hybridization Descriptor |
|
AtomHybridizationVSEPR |
Atom Hybridization VSEPR Descriptor |
|
AtomValence |
Atom Valence Descriptor |
|
BondsToAtom |
Bonds To Atom Descriptor |
|
CovalentRadius |
Covalent Radius Descriptor |
|
DistanceToAtom |
Distance To Atom Descriptor |
|
EffectiveAtomPolarizability |
Effective Atom Polarizability Descriptor |
|
InductiveAtomicHardness |
Inductive Atomic Hardness Descriptor |
|
InductiveAtomicSoftness |
Inductive Atomic Softness Descriptor |
|
IPAtomicHOSE |
IP Atomic HOSE Descriptor |
|
IPAtomicLearning |
IP Atomic Learning Descriptor |
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IsProtonInAromaticSystem |
Is Proton In Aromatic System Descriptor |
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IsProtonInConjugatedPiSystem |
Is Proton In Conjugated Pi System Descriptor |
|
PartialPiCharge |
Partial Pi Charge Descriptor |
|
PartialSigmaCharge |
Partial Sigma Charge Descriptor |
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PartialTChargeMMFF94 |
Partial T-Charge (MMFF94) Descriptor |
|
PartialTChargePEOE |
Partial T-Charge (PEOE) Descriptor |
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PeriodicTablePosition |
Periodic Table Position Descriptor |
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PiElectronegativity |
Pi Electronegativity-Descript |
|
ProtonTotalPartialCharge |
Proton Total Partial Charge Descriptor |
|
RDFProton_G3R |
RDF Proton_G3R Descriptor |
|
RDFProton_GDR |
RDF Proton_GDR Descriptor |
|
RDFProton_GHR_topol |
RDF Proton_GHR_topol Descriptor |
|
RDFProton_GHR |
RDF Proton_GHR Descriptor |
|
RDFProton_GSR |
RDF Proton_GSR Descriptor |
|
SigmaElectronegativity |
Sigma Electronegativity Descriptor |
|
VdWRadius |
VdW Radius Descriptor |
|
|
|
PiContactDetection |
Pi Contact Detection Descriptor |
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|
BondPartialPiCharge |
Bond Partial Pi Charge Descriptor |
|
BondPartialSigmaCharge |
Bond Partial Sigma Charge Descriptor |
|
BondPartialTCharge |
Bond Partial TCharge Descriptor |
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BondSigmaElectronegativity |
Bond Sigma Electronegativity Descriptor |
|
IPBondLearning |
IP Bond Descriptor |
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MassNumberDifference |
Mass Number Difference Descriptor |
|
|
|
SimpleKMeansWorker |
Simple KMeans Clusterer |
|
EMClusterWorker |
EM Clusterer |
|
ExtractClusterResultWorker |
Extract Cluster Result Worker |
|
|
|
AminoAcidCount |
Amino Acid Count Descriptor |
|
APol |
A-Pol Descriptor |
|
AromaticAtomsCount |
Aromatic Atoms Count Descriptor |
|
AromaticBondsCount |
Aromatic Bonds Count Descriptor |
|
AtomCount |
Atom Count Descriptor |
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Autocorrelation_Charge |
Autocorrelation (Charge) Descriptor |
|
Autocorrelation_Mass |
Autocorrelation (Mass) Descriptor |
|
Autocorrelation_Polarizability |
Autocorrelation (Polarizability) Descriptor |
|
BCUT |
BCUT Descriptor |
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BondCount |
Bond Count Descriptor |
|
BPol |
B-Pol Descriptor |
|
ChiChain |
Chi Chain Descriptor |
|
ChiCluster |
Chi Cluster Descriptor |
|
ChiPath |
Chi Path Descriptor |
|
ChiPathCluster |
Chi Path Cluster Descriptor |
|
CPSA |
CPSA Descriptor |
|
EccentricConnectivityIndex |
Eccentric Connectivity Index Descriptor |
|
FragmentComplexity |
Fragment Complexity Descriptor |
|
GravitationalIndex |
Gravitational Index Descriptor |
|
HBondAcceptorCount |
H-Bond Acceptor Count Descriptor |
|
HBondDonorCount |
H-Bond Donor Count Descriptor |
|
IPMolecularLearning |
IP Molecular Learning Descriptor |
|
KappaShapeIndices |
Kappa Shape Indices Descriptor |
|
LargestChain |
Largest Chain Descriptor |
|
LargestPiSystem |
Largest Pi System Descriptor |
|
LengthOverBreadth |
Length Over Breadth Descriptor |
|
LongestAliphaticChain |
Longest Aliphatic Chain Descriptor |
|
MDE |
MDE Descriptor |
|
MomentOfInertia |
Moment Of Inertia Descriptor |
|
PetitjeanNumber |
Calculate Petitjean Number Descriptor |
|
PetitjeanShapeIndex |
Petitjean Shape Index Descriptor |
|
RotatableBondsCount |
Rotatable Bonds Count Descriptor |
|
RuleOfFiveFilter |
Rule-of-Five Filter |
|
TPSA |
TPSA Descriptor |
|
VAdjMa |
VAdjMa Descriptor |
|
Weight |
Weight Descriptor |
|
WeightedPath |
Weighted Path Descriptor |
|
WHIM |
WHIM Descriptor |
|
WienerNumbers |
Wiener Numbers Descriptor |
|
XLogP |
XLogP Descriptor |
|
ZagrebIndex |
Zagreb Index Descriptor |
|
TaeAminoAcid |
Tae Amino Acid Descriptor |
|
SmilesTools |
|
|
SMILESGenerator |
Generates SMILES |
|
SMILESParser |
Parse SMILES |
|
|
|
RemoveMOLFilesWithoutStructureFromList |
Remove MOL Files without Structures from List |
|
ExtractIDFromMolFile |
Extract IDs from MOL File (EXNO) |
|
ExtractIntermedIDFromMolFile |
Extract 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 |
|
ConvertFingerprintItemListToMathematicaDataMatrix |
Convert Fingerprint item list to Mathematica data vector |
|
ScaleFingerprintItemArrayBetweenZeroAndOne |
Scale Fingerprint item list to values between 0 and 1 |
|
|
|
chebiExtractDataFromChebiStructureTSV |
Extract Data from ChEBI Structure TSV |
|
chebiRemoveAllNonMolFilesFromChebiStructureExtraction |
Remove all non MDL Mol entries from
list |