From BlueObelisk

See also Blue Obelisk algorithm dictionary

Contents 1 Algorithm Dictionary 1.1 Chemical expert system kernel 1.2 General chemical expert system 1.3 Ring detection 1.4 Substructure search 1.5 Atom typing 1.6 Residue typing 1.7 Atom properties 1.8 Bond properties 1.9 Structural Feature Dictionary 1.9.1 Atom pair 1.9.2 Maximum Common Substructure 1.10 Vectorial Feature Dictionary 1.10.1 Complexity features 1.10.2 Counts 1.11 File formats 1.11.1 Structural 1.12 Image formats 1.12.1 Pixel based 1.12.2 Vector based 1.12.3 Others 1.12.4 Compressed 1.13 Similarity and Dissimilarity 1.13.1 Structual coding 1.14 Vectorial coding 1.15 Other Algorithms 1.15.1 Sorting

Algorithm Dictionary

JOELib algorithm dictionary

Chemical expert system kernel

Trace back mechanism for feature and expert system algorithms. This allows to see cumulative feature complexities and runtime bottlenecks.

Algorithm	API Link-Out	Source code Link-Out
Expert system identifier	IdentifierExpertSystem	IdentifierExpertSystem.java

General chemical expert system

Algorithm	API Link-Out	Source code Link-Out
(Topological) Distance matrix	DistanceMatrix	DistanceMatrix
Distance distance matrix	DistanceDistanceMatrix	DistanceDistanceMatrix.java
Geometrical distance matrix	GeomDistanceMatrix	GeomDistanceMatrix.java
Point group symmetry	Symmetry	Symmetry.java
Canonicalization (e.g. for unique SMILES)	Morgan	Morgan.java
Coordinate transformation	CoordinateTransformation	CoordinateTransformation.java
Crystal geometry tools	CrystalGeometryTools	CrystalGeometryTools.java
Internal coordinates	InternalCoordinates	InternalCoordinates.java
Spectras: Joint Commitee on Atomic and Molecular Physical Data (JCAMP)	JCAMPParser	JCAMPParser.java
Group contribution holder	BasicGroupContributionHolder	BasicGroupContributionHolder.java
Rotor rules holder	BasicRotorRulesHolder	BasicRotorRulesHolder.java
Transformation rules holder (e.g. reactions, tautomers)	BasicTransformationRulesHolder	BasicTransformationRulesHolder.java

Ring detection

Algorithm	API Link-Out	Source code Link-Out
Smallest Set of Smallest Rings (SSSR)	RingFinderSSSR	RingFinderSSSR.java

Substructure search

Algorithm	API Link-Out	Source code Link-Out
SMiles ARbitrary Target Specification (SMARTS) substructure search (subgraph isomorphism)	BasicSMARTSPatternMatcher	BasicSMARTSPatternMatcher.java
Programmable ATom TYper (PATTY)	ProgrammableAtomTyper	ProgrammableAtomTyper.java
Maximum common subgraph isomorphism	no open source code (clique problem)	no open source code (clique problem)

Atom typing

Algorithm	API Link-Out	Source code Link-Out
Aromaticity typer	BasicAromaticityTyper	BasicAromaticityTyper.java
Atom type conversion	BasicAtomTypeConversionHolder	BasicAtomTypeConversionHolder.java
Atom typer	BasicAtomTyper	BasicAtomTyper.java
Element table	BasicElementHolder	BasicElementHolder.java
Hybridisation typer	BasicHybridisationTyper	BasicHybridisationTyper.java
Implicit valence typer	BasicImplicitValenceTyper	BasicImplicitValenceTyper.java
Isotope holder	BasicIsotopeHolder	BasicIsotopeHolder.java
Protonation model	BasicProtonationModel	BasicProtonationModel.java

Residue typing

Algorithm	API Link-Out	Source code Link-Out
Residue data	BasicResidueData	BasicResidueData.java

Atom properties

Algorithm	API Link-Out	Source code Link-Out
Bond order sum	AtomBondOrderSum	AtomBondOrderSum.java
Electronegativity - Allred Rochow	AtomENAllredRochow	AtomENAllredRochow.java
Electronegativity - Pauling	AtomENPauling	AtomENPauling.java
Electronegativity - Sanderson	AtomENSanderson	AtomENSanderson.java
Electron affinity	AtomElectronAffinity	AtomElectronAffinity.java
Explicit hydrogen count	AtomExplicitHydrogenCount	AtomExplicitHydrogenCount.java
FreeElectronsCount	AtomFreeElectronsCount	AtomFreeElectronsCount.java
FreeOxygenCount	AtomFreeOxygenCount	AtomFreeOxygenCount.java
HeavyValence	AtomHeavyValence	AtomHeavyValence.java
HeteroValence	AtomHeteroValence	AtomHeteroValence.java
Hybridisation	AtomHybridisation	AtomHybridisation.java
Implicit hydrogen count	AtomImplicitHydrogenCount	AtomImplicitHydrogenCount.java
Implicit valence	AtomImplicitValence	AtomImplicitValence.java
In (hydrogen) acceptor	AtomInAcceptor	AtomInAcceptor.java
In aromatic system	AtomInAromaticSystem	AtomInAromaticSystem.java
In conjugated environment	AtomInConjEnvironment	AtomInConjEnvironment.java
In (hydrogen) donor or acceptor	AtomInDonAcc	AtomInDonAcc.java
In (hydrogen) donor	AtomInDonor	AtomInDonor.java
In ring	AtomInRing	AtomInRing.java
In rings count	AtomInRingsCount	AtomInRingsCount.java
In terminal carbon	AtomInTerminalCarbon	AtomInTerminalCarbon.java
Is alpha beta unsaturated	AtomIsAlphaBetaUnsaturated	AtomIsAlphaBetaUnsaturated.java
Is amide nitrogen	AtomIsAmideNitrogen	AtomIsAmideNitrogen.java
Is anti clockwise	AtomIsAntiClockwise	AtomIsAntiClockwise.java
Is aromatic NOxide	AtomIsAromaticNOxide	AtomIsAromaticNOxide.java
Is axial	AtomIsAxial	AtomIsAxial.java
Is carbon	AtomIsCarbon	AtomIsCarbon.java
Is carboxyl oxygen	AtomIsCarboxylOxygen	AtomIsCarboxylOxygen.java
Is chiral	AtomIsChiral	AtomIsChiral.java
Is clockwise	AtomIsClockwise	AtomIsClockwise.java
Is electronegative	AtomIsElectronegative	AtomIsElectronegative.java
Is halogen	AtomIsHalogen	AtomIsHalogen.java
Is heteroatom	AtomIsHeteroatom	AtomIsHeteroatom.java
Is hydrogen	AtomIsHydrogen	AtomIsHydrogen.java
Is negative	AtomIsNegative	AtomIsNegative.java
Is nitroOxygen	AtomIsNitroOxygen	AtomIsNitroOxygen.java
Is nitrogen	AtomIsNitrogen	AtomIsNitrogen.java
Is non polar hydrogen	AtomIsNonPolarHydrogen	AtomIsNonPolarHydrogen.java
Is oxygen	AtomIsOxygen	AtomIsOxygen.java
Is phosphate oxygen	AtomIsPhosphateOxygen	AtomIsPhosphateOxygen.java
Is phosphorus	AtomIsPhosphorus	AtomIsPhosphorus.java
Is polar hydrogen	AtomIsPolarHydrogen	AtomIsPolarHydrogen.java
Is positive	AtomIsPositive	AtomIsPositive.java
Is sulfate oxygen	AtomIsSulfateOxygen	AtomIsSulfateOxygen.java
Is sulfur	AtomIsSulfur	AtomIsSulfur.java
Is unsaturated	AtomIsUnsaturated	AtomIsUnsaturated.java
Kekule bond order sum	AtomKekuleBondOrderSum	AtomKekuleBondOrderSum.java
Mass	AtomMass	AtomMass.java
Partial charge (Gasteiger-Marsili)	AtomPartialCharge	AtomPartialCharge.java
Type	AtomType	AtomType.java
Valence	AtomValence	AtomValence.java
Valence sum	AtomValenceSum	AtomValenceSum.java
Van der Waals volume	AtomVanDerWaalsVolume	AtomVanDerWaalsVolume.java

Bond properties

Algorithm	API Link-Out	Source code Link-Out
In aromatic system	BondInAromaticSystem	BondInAromaticSystem.java
In ring	BondInRing	BondInRing.java
Is amide	BondIsAmide	BondIsAmide.java
Is carbonyl	BondIsCarbonyl	BondIsCarbonyl.java
Is closure	BondIsClosure	BondIsClosure.java
Is ester	BondIsEster	BondIsEster.java
Is primaryAmide	BondIsPrimaryAmide	BondIsPrimaryAmide.java
Is rotor	BondIsRotor	BondIsRotor.java
Kekule type	BondKekuleType	BondKekuleType.java

Structural Feature Dictionary

Atom pair

Algorithm	API Link-Out	Source code Link-Out
(Topological) Atom pair (CATS, ...)	TopologicalAtomPair	TopologicalAtomPair.java

Maximum Common Substructure

Algorithm	API Link-Out	Source code Link-Out
Maximum common subgraph isomorphism	no open source code (clique problem)	no open source code (clique problem)

Vectorial Feature Dictionary

Complexity features

Algorithm	API Link-Out	Source code Link-Out
APropertyDistanceMatrix	APropertyDistanceMatrix	APropertyDistanceMatrix.java
Autocorrelation	Autocorrelation	Autocorrelation.java
BCUT	BCUT	BCUT.java
BurdenEigenvalues	BurdenEigenvalues	BurdenEigenvalues.java
BurdenModifiedEigenvalues	BurdenModifiedEigenvalues	BurdenModifiedEigenvalues.java
CharacteristicPolynomial	CharacteristicPolynomial	CharacteristicPolynomial.java
CharacteristicPolynomialCoefficients	CharacteristicPolynomialCoefficients	CharacteristicPolynomialCoefficients.java
ConjElectroTopolState	ConjElectroTopolState	ConjElectroTopolState.java
ConjugatedTopologicalDistance	ConjugatedTopologicalDistance	ConjugatedTopologicalDistance.java
ElectrogeometricalState	ElectrogeometricalState	ElectrogeometricalState.java
ElectrotopologicalState	ElectrotopologicalState	ElectrotopologicalState.java
FractionRotatableBonds	FractionRotatableBonds	FractionRotatableBonds.java
GeometricalDiameter	GeometricalDiameter	GeometricalDiameter.java
GeometricalRadius	GeometricalRadius	GeometricalRadius.java
GeometricalShapeCoefficient	GeometricalShapeCoefficient	GeometricalShapeCoefficient.java
GlobalTopologicalChargeIndex	GlobalTopologicalChargeIndex	GlobalTopologicalChargeIndex.java
GraphPotentials	GraphPotentials	GraphPotentials.java
GraphShapeCoefficient	GraphShapeCoefficient	GraphShapeCoefficient.java
IntrinsicState	IntrinsicState	IntrinsicState.java
KierShape1	KierShape1	KierShape1.java
KierShape2	KierShape2	KierShape2.java
KierShape3	KierShape3	KierShape3.java
LogP	LogP	LogP.java
MolarRefractivity	MolarRefractivity	MolarRefractivity.java
MolecularWeight	MolecularWeight	MolecularWeight.java
MoleculeHashcode	MoleculeHashcode	MoleculeHashcode.java
PolarSurfaceArea	PolarSurfaceArea	PolarSurfaceArea.java
RadialDistributionFunction	RadialDistributionFunction	RadialDistributionFunction.java
RotatableBonds	RotatableBonds	RotatableBonds.java
SMILESMolecule	SMILESMolecule	SMILESMolecule.java
SSKey3DS	SSKey3DS	SSKey3DS.java
TopologicalDiameter	TopologicalDiameter	TopologicalDiameter.java
TopologicalRadius	TopologicalRadius	TopologicalRadius.java
WeightedBurdenEigenvalues	WeightedBurdenEigenvalues	WeightedBurdenEigenvalues.java
WeightedBurdenModifiedEigenvalues	WeightedBurdenModifiedEigenvalues	WeightedBurdenModifiedEigenvalues.java
ZagrebIndex1	ZagrebIndex1	ZagrebIndex1.java
ZagrebIndex2	ZagrebIndex2	ZagrebIndex2.java

Counts

Algorithm	API Link-Out	Source code Link-Out
AcidicGroups	AcidicGroups	AcidicGroups.java
AliphaticOHGroups	AliphaticOHGroups	AliphaticOHGroups.java
AromaticBonds	AromaticBonds	AromaticBonds.java
AromaticOHGroups	AromaticOHGroups	AromaticOHGroups.java
BasicGroups	BasicGroups	BasicGroups.java
HBA1	HBA1	HBA1.java
HBA2	HBA2	HBA2.java
HBD1	HBD1	HBD1.java
HBD2	HBD2	HBD2.java
HeavyBonds	HeavyBonds	HeavyBonds.java
HeteroCycles	HeteroCycles	HeteroCycles.java
HydrophobicGroups	HydrophobicGroups	HydrophobicGroups.java
NO2Groups	NO2Groups	NO2Groups.java
NumberOfAtoms	NumberOfAtoms	NumberOfAtoms.java
NumberOfB	NumberOfB	NumberOfB.java
NumberOfBonds	NumberOfBonds	NumberOfBonds.java
NumberOfBr	NumberOfBr	NumberOfBr.java
NumberOfC	NumberOfC	NumberOfC.java
NumberOfCl	NumberOfCl	NumberOfCl.java
NumberOfF	NumberOfF	NumberOfF.java
NumberOfHal	NumberOfHal	NumberOfHal.java
NumberOfI	NumberOfI	NumberOfI.java
NumberOfN	NumberOfN	NumberOfN.java
NumberOfO	NumberOfO	NumberOfO.java
NumberOfP	NumberOfP	NumberOfP.java
NumberOfS	NumberOfS	NumberOfS.java
OSOGroups	OSOGroups	OSOGroups.java
SO2Groups	SO2Groups	SO2Groups.java
SOGroups	SOGroups	SOGroups.java

File formats

Structural

Algorithm	API Link-Out	Source code Link-Out
Amber	Amber	Amber.java
ChemicalMarkupLanguage	ChemicalMarkupLanguage	ChemicalMarkupLanguage.java
ClearTextFormat	ClearTextFormat	ClearTextFormat.java
Flat	Flat	Flat.java
Gaussian	Gaussian	Gaussian.java
Ghemical	Ghemical	Ghemical.java
HIN	HIN	HIN.java
JCAMP	JCAMP	JCAMP.java
MDLSD	MDLSD	MDLSD.java
MolconnZ	MolconnZ	MolconnZ.java
Mopac	Mopac	Mopac.java
PDB	PDB	PDB.java
Smiles	Smiles	Smiles.java
SybylMol2	SybylMol2	SybylMol2.java
Tinker	Tinker	Tinker.java
XYZ	XYZ	XYZ.java

Image formats

Pixel based

Algorithm	API Link-Out	Source code Link-Out
Windows bitmap (BMP)	BMP	BMP.java
Joint Photographic Experts Group (JPEG)	JPEG	JPEG.java
Graphics Interchange Format (GIF)	GIF	GIF.java
Portable pixmap (PPM)	PPM	PPM.java
Portable Network Graphic (PNG)	PNG	PNG.java

Vector based

Algorithm	API Link-Out	Source code Link-Out
Portable Document Format	PDF	PDF.java

Others

Algorithm	API Link-Out	Source code Link-Out
POVRay	POVRay	POVRay.java
Matlab	Matlab	Matlab.java

Compressed

Algorithm	API Link-Out	Source code Link-Out
ZIP	ZIP	ZIP.java

Similarity and Dissimilarity

Structual coding

Algorithm	API Link-Out	Source code Link-Out
Atom pair metric (depends on 'atom type' coding)	BasicAPDistanceMetric	BasicAPDistanceMetric.java

Vectorial coding

Algorithm	API Link-Out	Source code Link-Out
Vector metric (depends on features used)	BasicFeatureMetrics	BasicFeatureMetrics.java

Other Algorithms

Sorting

Algorithm	API Link-Out	Source code Link-Out
Quick insert sort hybrid	QuickInsertSort	QuickInsertSort.java