Algorithm dictionary - JOELib (original) (raw)
From JOELib
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
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Algorithm Dictionary
JOELib algorithm dictionary
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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 |
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General chemical expert system
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Ring detection
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| Smallest Set of Smallest Rings (SSSR) | RingFinderSSSR | RingFinderSSSR.java |
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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) |
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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 |
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Residue typing
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| Residue data | BasicResidueData | BasicResidueData.java |
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Atom properties
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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 |
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Structural Feature Dictionary
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Atom pair
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| (Topological) Atom pair (CATS, ...) | TopologicalAtomPair | TopologicalAtomPair.java |
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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) |
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Vectorial Feature Dictionary
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Complexity features
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Counts
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File formats
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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 |
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Image formats
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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 |
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Vector based
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| Portable Document Format | PDF.java |
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Others
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| POVRay | POVRay | POVRay.java |
| Matlab | Matlab | Matlab.java |
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Compressed
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| ZIP | ZIP | ZIP.java |
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Similarity and Dissimilarity
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Structual coding
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| Atom pair metric (depends on 'atom type' coding) | BasicAPDistanceMetric | BasicAPDistanceMetric.java |
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Vectorial coding
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| Vector metric (depends on features used) | BasicFeatureMetrics | BasicFeatureMetrics.java |
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Other Algorithms
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Sorting
| Algorithm | API Link-Out | Source code Link-Out |
|---|---|---|
| Quick insert sort hybrid | QuickInsertSort | QuickInsertSort.java |
Retrieved from "http://joelib.sourceforge.net/wiki/index.php/Algorithm_dictionary"