JOELib
Computational Chemistry Package

JOELib API Documentation


A Java based computational chemistry package - For additional informations a Tutorial is available.

See:
          Description

Packages
Acme  
Acme.JPM.Encoders  
cformat Provides classes allowing printf and scanf functionality for Java.
com.obrador  
joelib Provides classes for processing, converting molecular chemical data and calculate chemical properties (descriptors).
joelib.algo Provides classes for calculating Depth First Search (DFS) [clr98dfs] Breadth First Search (BFS) [clr98bfs] on molecular graphs.
joelib.algo.contribution Provides classes for value prediction based on group contribution models.
joelib.algo.datamining.weka Provides classes for an interface to the Weka Data Mining library.
joelib.algo.morgan Provides classes for Morgan number generation and unique molecule numbering.
joelib.algo.morgan.types  
joelib.data These classes are the chemical heart of JOELib.
joelib.desc Provides classes for defining molecular properties (descriptors).
joelib.desc.data Provides classes for building descriptor matrices.
joelib.desc.result Provides representating classes for molecular properties (descriptors).
joelib.desc.types Provides representating classes for the calculation of molecular properties (descriptors).
joelib.desc.types.atompair  
joelib.desc.util  
joelib.ext Provides classes for defining external molecular processing modules.
joelib.gui.molviewer.java3d Provides classes for a simple Java3D visualization of molecules.
joelib.gui.molviewer.java3d.graphics3D Provides core Java3D elements for the molecule visualization.
joelib.gui.molviewer.java3d.math.geometry Provides geometrical element classes for the Java3D visualization.
joelib.gui.molviewer.java3d.math.util Provides mathematical utilities for the Java3D visualization.
joelib.gui.molviewer.java3d.molecule Provides atoms, bonds and the molecule for the Java3D visualization.
joelib.gui.molviewer.java3d.util Provides event and adapter classes/patterns for the Java3D visualization.
joelib.gui.render  
joelib.gui.test  
joelib.gui.util  
joelib.io Provides classes for defining molecular import and export methods.
joelib.io.types Provides representating classes for the molecular import and export methods.
joelib.io.types.cml Provides helper classes for processing the Chemical Markup Language (CML) [rr99b, mr01, gmrw01, wil01, mr03, mrww04].
joelib.io.types.cml.elements  
joelib.jcamp Provides helper classes for processing spectroscopic data defined by the Joint Commitee on Atomic and Molecular Physical Data (JCAMP) [dl93, dw88, ghhjs91, lhdl94, dhl90].
joelib.math Provides mathematical oriented helper classes for molecular data processing.
joelib.math.similarity  
joelib.math.symmetry  
joelib.molecule Provides classes for molecular data structures.
joelib.molecule.charge Provides classes for the calculation of the partitial charge.
joelib.molecule.fragmentation Provides classes for fragmenting molecules.
joelib.molecule.generation Provides classes for generating molecules.
joelib.molecule.types Provides classes for atom and bond properties.
joelib.process Provides classes for defining molecular processing modules.
joelib.process.filter Provides representating classes for the specialized filter options for molecular processing methods.
joelib.process.types Provides representating classes for the molecular processing methods.
joelib.ring Provides classes for finding the Smallest Set of Smallest Rings (SSSR) [fig96].
joelib.smarts Provides classes for searching substructures in chemical structures based on the Smiles ARbitrary Target Specification (SMARTS) standard [smarts].
joelib.smarts.atomexpr Provides classes for SMARTS atom types.
joelib.smarts.bondexpr Provides classes for SMARTS bond types.
joelib.smarts.test  
joelib.smarts.types Provides classes for SMARTS special types.
joelib.smiles Provides classes for building molecules using the Simplified Molecular Input Line Entry System (SMILES) [smilesFormat, wei88, www89].
joelib.sort Provides classes for sorting data.
joelib.test Provides testing classes for processing molecular data.
joelib.util Provides all kind of additional technical/molecular helper classes.
joelib.util.cdk Provides classes for an interface to the Chemical Development Kit (CDK).
joelib.util.database  
joelib.util.ghemical Provides classes for an interface to the (Lib)Ghemical library.
joelib.util.iterator Provides iterator classes specialized for molecular operations.
joelib.util.types Provides special data types.
jtt.docbook  
jtt.util  
wsi.ra.database  
wsi.ra.image  
wsi.ra.io Provides simple helper classes for input/output routines.
wsi.ra.text  
wsi.ra.tool Provides some miscellaneous helper methods.

 


A Java based computational chemistry package - For additional informations a Tutorial is available.


JOELib
Computational Chemistry Package

Comments and Questions? mail to J.K.Wegner