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| • | joelib.algo.* (24) | • | joelib.data.* (18) | • | joelib.desc.* (99) |
| • | joelib.ext.* (7) | • | joelib.gui.* (61) | • | joelib.io.* (58) |
| • | joelib.jcamp.* (5) | • | joelib.math.* (17) | • | joelib.molecule.* (22) |
| • | joelib.process.* (29) | • | joelib.ring.* (4) | • | joelib.smarts.* (22) |
| • | joelib.smiles.* (4) | • | joelib.sort.* (8) | • | joelib.test.* (15) |
• joelib: Javadoc index of package joelib.
Package Samples:
• joelib.smarts.types: Provides classes for searching substructures in chemical structures based on the Smiles ARbitrary Target Specification (SMARTS) standard [].
• joelib.algo.morgan: Provides classes for calculating Depth First Search (DFS) [] Breadth First Search (BFS) [] on molecular graphs.
• joelib.io.types.cml.elements: Provides helper classes for processing the Chemical Markup Language (CML) [, , , ].
• joelib.algo.morgan.types: Provides classes for Morgan number generation and unique molecule numbering.
• joelib.io.types.cml: Provides representating classes for the molecular import and export methods.
• joelib.math.symmetry: Provides mathematical oriented helper classes for molecular data processing.
• joelib.io.types: Provides classes for defining molecular import and export methods.
• joelib.desc.types: Provides classes for defining molecular properties (descriptors).
• joelib.gui.molviewer.java3d.util: Provides classes for a simple Java3D visualization of molecules.
• joelib.process.types: Provides classes for defining molecular processing modules.
• joelib.molecule.types: Provides classes for molecular data structures.
• joelib.algo.contribution
• joelib.algo.datamining.weka
• joelib.algo
• joelib.data
• joelib.desc.data
• joelib.desc.result
• joelib.desc
• joelib.ext
• joelib.gui.molviewer.java3d.graphics3D
Classes:
• JOEDataType: Data type. There exists a lot of default data types which where defined in JOEDataType . These data types are used for caching ring searches and storing special data types like comments or virtual bonds. Furthermore there exist the most important data type JOEPairData for storing descriptor values. There exists an important difference between JOE_PAIR_DATA 55 and all other data types. Because there are many descriptor values possible for one molecule, they are hashed to enable a fast access to these values. This causes that every descriptor value must have a unique attribute name. It's not possible ...
• ConvertSkip: Example for converting/skipping molecules. Usage: java -cp . joelib.test.Convert [options] <input file> [<output file>] [<skip file>] Options: [-i<inputFormat>] - Format of the input file [-o<outputFormat>] - Format of the output file [-h] - Removes all hydrogens from molecule [+h] - Adds hydrogens to molecule [+p] - Adds only polar hydrogens (+h implicit) [-e] - Converts only non-empty molecules [-d] - Remove all descriptors from the molecule [+d|+d<descriptor name>]- Adds all (or defined) available descriptors to the molecule [+df<descFileName>] - Adds all descriptors defined ...
• Convert: Example for converting molecules and calculating descriptors. Usage: java -cp . joelib.test.Convert [options] <input file> [<output file>] Options: [-i<inputFormat>] - Format of the input file [-o<outputFormat>] - Format of the output file [-h] - Removes all hydrogens from molecule [+h] - Adds hydrogens to molecule [+p] - Adds only polar hydrogens (+h implicit) [-e] - Converts only non-empty molecules [-d] - Remove all descriptors from the molecule [+d] - Adds all available descriptors to the molecule [+v] - Switch verbosity ON [+snd] - Shows all available native value descriptors [+sad] ...
• ResultFactory: Factory class to get descriptor results and faciliate the parsing of descriptor entries. The definition file can be defined in the joelib.data.ResultFactory.resourceFile property in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. Let's have a look at a knownResults.txt example file: $JOELIB_RESULT$ joelib.desc.result.IntResult # # PETRA descriptors # E_CHARGE E_DELTAHF E_HASH E_POLARIZABILITY # # Molconn Z 350 # id nvx nrings ncirc nelem $REGEXP$ nas\p{Upper}\p{Lower}* $REGEXP$ nd\d $REGEXP$ ne\d+ This means all descriptors of the type ...
• JOE: Class for converting molecules and calculating descriptors. Usage: java -cp . joelib.JOE [options] <input file> [<output file>] Options: [-i<inputFormat>] - Format of the input file [-o<outputFormat>] - Format of the output file [-h] - Remove hydrogens from molecule [+h] - Add hydrogens to molecule [+p] - Add only polar hydrogens (+h implicit) [-e] - Converts only non-empty molecules [-d] - Remove all descriptors from the molecule [+d] - Add all available descriptors to the molecule [+v] - Switch verbosity ON [+snd] - Show all available native value descriptors [+sad] - Show all available ...
• JOECoordTrans: An object for storing, manipulating and applying coordinate transformations. The most basic way to setup a transformation is to use the member methodName setup(double []) 55 , which requires you to supply a specific set of 4 coordinates from the initial reference frame in the final reference frame. The methodName setup(double [], double [], int) 55 will set up a transformation given an arbitrary set of coordinates in the final and initial reference frame. A rotation/translation or a translation/rotation can also be supplied, see the various member functions begining with Setup. Applying the transformation ...
• Symmetry: Brute force symmetry analyzer. All specific structures should have corresponding elements in the same position generic structure does. Planes are characterized by the surface normal direction (taken in the direction from the coordinate origin) and distance from the coordinate origin to the plane in the direction of the surface normal. Inversion is characterized by location of the inversion center. Rotation is characterized by a vector (distance+direction) from the origin to the rotation axis, axis direction and rotation order. Rotations are in the clockwise direction looking opposite to the direction ...
• JOEMol: Molecule representation. There are different possibilities to build a molecule. Using SMILES notation to build a molecule. JOEMol mol=new JOEMol(); String smiles="c1cc(OH)cc1"; if (!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString())) { System.err.println("SMILES entry \"" + smiles + "\" could not be loaded."); } System.out.println(mol.toString()); Using plain atoms and bonds to build a molecule. JOEMol mol = new JOEMol(); // start molecule modification mol.beginModify(); mol.reserveAtoms(2); // build carbon atom JOEAtom C = new JOEAtom(); atomC.setAtomicNum(6); // build molecule for (int ...
• Smiles: Reader/Writer for Simplified Molecular Input Line Entry System (SMILES) files. The SMILES import/export has some additional parameters which were defined in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. Java property Description Default value joelib.io.types.Smiles.lineStructure Line structure of the SMILES in the file/inputstream. SMILES and TITLE are fixed code words, which represents the SMILES molecule and the molecule title. All other descriptor names, which represents native descriptor values, are allowed. SMILES|TITLE joelib.io.types.Smiles.lineStructure.delimiter ...
• BitSet14: This class implements a vector of bits that grows as needed. Each component of the bit set has a boolean value. The bits of a BitSet14 are indexed by nonnegative integers. Individual indexed bits can be examined, set, or cleared. One BitSet14 may be used to modify the contents of another BitSet14 through logical AND, logical inclusive OR, and logical exclusive OR operations. By default, all bits in the set initially have the value false . Every bit set has a current size, which is the number of bits of space currently in use by the bit set. Note that the size is related to the implementation of ...
• JCAMP: A class to interpret JCAMP-DX data (JCAMP-CS is not implemented yet). The supported data types are XYPAIRS, XYDATA=(X++(Y..Y)), PEAK TABLE and LINK. If you want load a file with multiple blocks or inner blocks you must use JCampMultipleFile . This class can only load separated single blocks with one TITLE and END label ! ... The International Union of Pure and Applied Chemistry (IUPAC) took over responsibility from the Joint Commitee on Atomic and Molecular Physical Data (JCAMP) in 1995 ... I U P A C Committee on Printed and Electronic Publications Working Party on Spectroscopic Data Standards ...
• JCAMPParser: A class to interpret JCAMP-DX data (JCAMP-CS is not implemented yet). The supported data types are XYPAIRS, XYDATA=(X++(Y..Y)), PEAK TABLE and LINK. If you want load a file with multiple blocks or inner blocks you must use JCampMultipleFile . This class can only load separated single blocks with one TITLE and END label ! ... The International Union of Pure and Applied Chemistry (IUPAC) took over responsibility from the Joint Commitee on Atomic and Molecular Physical Data (JCAMP) in 1995 ... I U P A C Committee on Printed and Electronic Publications Working Party on Spectroscopic Data Standards ...
• JOEAtomTyper: Atom typer based on structural expert rules. The definition file can be defined in the joelib.data.JOEAtomTyper.resourceFile property in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. For assigning atom types using a geometry-based algorithm have a look at and the dot connecting method JOEMol.connectTheDots() > JOEMol.connectTheDots() 55 . Default: joelib.data.JOEAtomTyper.resourceFile= joelib/data/plain/atomtype.txt
• IOTypeHolder: Holder for input/output types for molecules. Molecule import/export types are defined in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file. File types can be defined by using joelib.filetypes.NUMBER.name . The default representating class will be taken from the internal list. If you want another representating class use additional joelib.filetypes.NUMBER.representation . Example: joelib.filetypes.1.name = SDF joelib.filetypes.1.representation = joelib.io.types.MDLSD joelib.filetypes.2.name = SMILES joelib.filetypes.3.name = MOL2
• SMARTSFilter: Molecule process filter for SMARTS patterns. Example: // accept all molecules, where the molecule contains ONE NC=O group connected to an aromatic atom (aNC=O) SMARTSFilter filter =new SMARTSFilter( "aNC=O", NativeValueFilter.EQUAL, 1); // create molecule JOEMol mol=new JOEMol(); String smiles="c1cc(OH)cc1"; if (!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString())); // should we accept this molecule, what do you mean ? System.out.println("Accept: ("+filter.toString()+")="+filter.accept(mol));
• JOETypeTable: Type table to map internal atom types to atom types of other file formats. The definition file can be defined in the joelib.data.JOETypeTable.resourceFile property in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. Default: joelib.data.JOETypeTable.resourceFile= joelib/data/plain/types.txt
• NativeValueFilter: Molecule process filter for native value descriptor entries. Example: // accept all values with: Kier_shape_1
• JOEPhModel: Model for the protonation/deprotonation of molecules. The definition file can be defined in the joelib.data.JOEPhModel.resourceFile property in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. Default: joelib.data.JOEPhModel.resourceFile= joelib/data/plain/phmodel.txt
• JOEIsotopeTable: Isotope element table. The definition file can be defined in the joelib.data.JOEIsotopeTable.resourceFile property in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. Default: joelib.data.JOEIsotopeTable.resourceFile= joelib/data/plain/isotope.txt
• JOEAromaticTyper: Aromatic typer. The definition file can be defined in the joelib.data.JOEAromaticTyper.resourceFile property in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. Default: joelib.data.JOEAromaticTyper.resourceFile= joelib/data/plain/aromatic.txt
• JOEElementTable: Element table. The definition file can be defined in the joelib.data.JOEElementTable.resourceFile property in the wsi.ra.tool.PropertyHolder . The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default. Default: joelib.data.JOEElementTable.resourceFile= joelib/data/plain/element.txt
• MolFileFilter: A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about. Extensions are of the type ".foo", which is typically found on Windows and Unix boxes, but not on Macinthosh. Case is ignored. Example - create a new filter that filerts out all files but gif and jpg image files: JFileChooser chooser = new JFileChooser(); MolFileFilter filter = new MolFileFilter( new String{"sdf", "mol"}, "Structured Data File") chooser.addChoosableFileFilter(filter); chooser.showOpenDialog(this);
• JOESmartsPattern: Class to parse SMART pattern and store the search expressions. String smartsPattern = "c1ccccc1"; JOESmartsPattern smarts = new JOESmartsPattern(); // parse, initialize and generate SMARTS pattern // to allow fast pattern matching if(!smarts.init(smartsPattern) { System.err.println("Invalid SMARTS pattern."); } // find substructures smarts.match(mol); Vector matchList = smarts.getUMapList();
• Renderer2D: A Renderer class which draws 2D representations of molecules onto a given graphics objects using information from a Renderer2DModel. This renderer uses two coordinate systems. One that is a world coordinates system which is generated from the document coordinates. Additionally, the screen coordinates make up the second system, and are calculated by applying a zoom factor to the world coordinates.
• JOESmilesParser: Parser for Simplified Molecular Input Line Entry System (SMILES) strings. Example: JOEMol mol=new JOEMol(); String smiles="c1cc(OH)cc1"; if (!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString())) { System.err.println("SMILES entry \"" + smiles + "\" could not be loaded."); } System.out.println(mol.toString());
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