File Release Notes and Changelog
Release Name: 2007-03-03
Notes: ######################################################################## # Version: $Revision: 1.1 $ # $Date: 2005/01/09 13:50:34 $ ######################################################################## # Copyright OELIB: OpenEye Scientific Software, Santa Fe, # U.S.A., 1999,2000,2001 # Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of # Tuebingen, Germany, 2001,2002,2003,2004,2005 # Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, # 2003,2004,2005 # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation version 2 of the License. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. ######################################################################## ======================================================================== JOELib 2 Release Log : ======================================================================== General: ------------------------------------------------------------------------ We recommend ALWAYS the source code release, because you can simply build your own binary release with: joelib2/ant> ant dist or joelib2> sh build.sh dist Furthermore you can have a look at the source code and improve/change things. We mention this to remind you to share your experience. Additionally we want to initialize the open-source mind for your special requirements without loosing generalization ability for other users! ------------------------------------------------------------------------ Features: ------------------------------------------------------------------------ - chemical expert systems: -- ring detection and ring set finder using the Smallest Set of Smallest Ring (SSSR) algorithm with the Figueras extension -- kekule bond order detection algorithm -- hybridisation detection -- implicit valence detection algorithm -- aromaticity detection algorithm -- implicit hydrogen calculation -- automatic detection of chemical atom types -- over 50 different chemical atom labels -- over 5 differet chemical bond labels - query search algorithm, based on SMARTS -- Programmable Atom Typer based on SMARTS - A huge number of chemical export/import formats -- automatic detection of atom types and atom type conversion -- Structuread Data Files (SDF) + feature import/export -- Chemical Markup Language (CML1 and CML2) + feature import/export -- CACTVS + feature import -- Flat file + feature import/export -- Molecular mechanics formats: Tinker, Ghemical, ... -- SMILES line notation export (no 2D layout generation for import, use CDK interface) -- ZIP import/export which can contain multiple files (no need to waste space :-) - Image, Document and Rendering export -- Image file formats: BMP, GIF, JPEG, PDF, PPM, PBM -- PovRay export with three different rendering modes -- Portable Document File (PDF) export - JCAMP Spectra import/export -- Uncompressed JCAMP-DX import/export - Protonation/Deprotonation -- Protonation model for protonating molecular structures -- Deprotonation of molecular structures - Feature calculation -- Radial Distribution Function (RDF), e.g. (100 values) * (50 atom labels)=5000 features -- Burden Modified Eigenvalues (BCUT, if one uses several atom labels) -- Complexity features, like kier and zagreb index -- Atom and group count features -- Pharmacophore fingerprint SSKey3D -- Group Contribution (GC) prediction of LogP, molar refractivity (MR) and polar surface area (PSA) -- Some more ... - Process and Filter functionality -- Each available feature can be used to build filter and processing pipes -- Internal (only Java) processing pipes -- External (external libray, e.g. JNI, shared library, executable, ...) processing pipes - Algorithms -- Query substructure search with SMARTS -- Morgan molecule canonization with tie resolvers - Hashcode calculation for molecules - Unique/Canonical SMILES - Unique renumbering of atoms -- Symmetry detection facility of rotation axes, mirror planes and resulting point groups. -- Molecule fragmentation and RGroup based generation algorithm - Interfaces -- Default database interface (e.g. MySQL) with automatic identifier (ID) calculation -- DataMining: Interface to Weka, Yale, and Matlab - http://www.cs.waikato.ac.nz/ml/weka/ -- Cheminformatics: Interface to the Chemical Development Kit (CDK), e.g. for 2D layout -- Interface to the computationl library Ghemical (molecular mechanics and more) - http://bioinformatics.org/project/?group_id=41 - Visualization -- 2D rendering (no 2D layout), but interface to the Chemical Development Kit (CDK) -- 3D rendering (no 3D generation), but interface to Ghemical -- Primitive GUI for file conversion and feature calculation (use command line) - Examples -- A huge number of practical examples for calculating features, selecting features, ... - Documentation -- Programming interface: API documentation -- Tutorial: XML based DocBook tutorial
Changes: ######################################################################## # Version: $Revision: 1.16 $ # $Date: 2007/03/03 00:22:39 $ ######################################################################## # Copyright OELIB: OpenEye Scientific Software, Santa Fe, # U.S.A., 1999,2000,2001 # Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of # Tuebingen, Germany, 2001,2002,2003,2004,2005 # Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, # 2003,2004,2005 # Copyright JOELIB/JOELib2: J. K. Wegner, Mechelen, Belgium # 2001,2002,2003,2004,2005,2006,2007 # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation version 2 of the License. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. ######################################################################## Change Log : ----------------------------------------------------------------------------- - JOELib2:2007-03-03 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/molecule/BasicConformerMolecule.java Bugfix for non-defined stereochemistry, which will now be retrieved from 2D/3D conformations. - JOELib2:2006-07-24 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/smiles/SMILESParser.java Bugfix for problems with aromatic systems (bond order forwarding). - JOELib2:2006-02-22 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Some minor but nasty bugs are fixed. Especially the default feature calculation should now work for non-experts, also. IF NOT, just let me know. Test this: >export JOELIB2=`pwd` >sh featureCalculation.sh +ap +countSMARTS +binarySMARTS +jcc +SSKey src/resources/multiple.mol multiple_features.sdf yourSMARTSpattern.txt > logging.txt >sh featureStatistic.sh multiple_features.sdf > logging-stat.txt The two generated files - yourSMARTSPattern.txt file might contain: [CX4H3][#6] [CX4H2]([#6])[#6] [CX4H1]([#6])([#6])[#6] [CX4]([#6])([#6])([#6])[#6] [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] [CX2]#[CX2] [CX3]=[CX2]=[CX3] [ClX1][CX4] [FX1][CX4] - JOELib2:2005-03-03 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/data/BasicAromaticityTyper.java joelib2/src/joelib2/molecule/KekuleHelper.java joelib2/src/joelib2/io/types/MDLSD.java Allow users to switch off the automatic aromaticity check and assignment. This will enable query input graphs, which must not have a valid aromatic system. - Some minor bug fixes. - JOELib2:2005-02-12 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/molecule/Molecule.java joelib2/src/joelib2/molecule/BasicConformerMolecule.java Bug fix: Consolidated caller pipe for protonation model. Now it is allways called in the endModify method of the molecule. This fixes several 'now we miss a hydrogen atom'-bugs, e.g. in the SMARTS matching, SDF export. - joelib2/src/joelib2/molecule/IsomerismHelper.java Bug fix: Resolving dependency on neighborhood occurence and ignore double bonds in rings. - JOELib2:2005-02-08 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/molecule/BasicConformerAtom.java joelib2/src/joelib2/molecule/BasicConformerMolecule.java joelib2/src/joelib2/molecule/BasicBond.java Added consistency check for atom and bond access. Ensure that the developer uses always the same parent molecule, otherwise the debugging will get hard. - JOELib2:2005-02-06 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/types/atomlabel/*.java Bug fix: Use also the atom with the largest index. - joelib2/src/joelib2/types/CharacteristicPolynomial*.java Le Verrier-Faddeev-Frame method to calculate the characteristic polynomial of general weighted graphs allowing atom and bond labels. - JOELib2:2005-01-26 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/data/BasicAtomTyper.java Bug fix: ensure applied protonation model and assigned aromaticity flags for query matching. - JOELib2:2005-01-20 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/molecule/Molecule.java joelib2/src/joelib2/molecule/BasicConformerMolecule.java Hardened policy: Never delete atoms without calling endModify, which causes RuntimeException. - JOELib2:2005-01-20 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/molecule/KekuleHelper.java Bug fix for returning not successfull flag for cases in which the kekulization is estimating the first round. Added debug messages. - joelib2/src/joelib2/data/BasicImplicitValenceTyper.java Calling pH model correction before calculating implicite valence - JOELib2:2005-01-16 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Code cleanup: Heavily refactored classes and interfaces, especially for joelib2.util, joelib2.molecule.types, joelib2.smarts, joelib2.data. - JOELib2:2005-01-14 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Code cleanup: Trying to reduce the distance to the optimal Instability/Abstractness line. See Code Analysis Plugin for Eclipse for details: http://sourceforge.net/projects/cap4e/ - JOELib2:2005-01-09 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib2/src/joelib2/feature/result/DynamicArrayResult.java Bug fix: Corrected fromString method, which affects also all atom and bond labels. - JOELib2:2005-01-08 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Bug fix: Fixing the recursive atom label assignment dependencies previously hidden in the method calling hierarchy. - JOELib2:2005-01-07 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Bug fix: Avoid the replacement of valid bond orders with invalid kekule bond orders, if the kekulization algorithm is unable to find a solution. - JOELib2:2004-12-29 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Added dependency identifiers for all feature calculators and an hashed identifier for each class, which includes also the chemistry kernel identifier. This is based on a Java hack to obtain all loaded classes by tracing back the caller hierarchy and reflection call for the public static dependency and CVS-tag methods. - JOELib2:2004-12-06 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Complete redesign and refactoring. Now we are back in pre-alpha mode. - JOELib2:2004-11-04 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/molecule/JOEAtom.java 0. PMD convention refactoring 1. Externalized feature functionality for JOEAtom see joelib.desc.types.AtomIs... 2. TODO: Replace atom flags with feature caching - joelib/src/joelib/molecule/JOEBond.java PMD convention refactoring - joelib/src/joelib/desc/types/AtomIs....java Classes for atom properties externalized from JOEAtom - 2004-09-24 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Renamed abstract helper classes for descriptor calculation AtomsCounter.java --> AbstractAtomsCounter.java SMARTSCounter.java --> AbstractSMARTSCounter.java BooleanDesc.java --> AbstractBooleanDesc.java DoubleDesc.java --> AbstractDoubleDesc.java IntDesc.java --> AbstractIntDesc.java StringAtomProperty.java --> AbstractStringAtomProperty.java DynamicAtomProperty.java --> AbstractDynamicAtomProperty.java DoubleAtomProperty.java --> AbstractDoubleAtomProperty.java - 2004-09-22 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/math/distance/AtomDistanceHelper.java Added helper class for easier access to the atom-atom distances. So you do not need to access the distance descriptors directly. - 2004-08-30 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/*.java Reduced number for some of the PMD metrics for different classes. But for some metrics i've furthermore reduced the number of warnings for more than a half since the last release version. - 2004-08-30 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/io/types/MDLSD.java PMD 'codesize': Reduced cyclomatic complexity (from 42 to <10) - Code cleanup warning: Dear developer and user. I've started with refactoring the sources following the PMD rules. Until now i've corrected the 'basic', 'coupling' and 'import' rules. Two of them causes no problems. But the 'coupling' rule has forced me to change 'Vector-->List', 'HashMap-->Map'. So, this affects method calls and forces you to change these things also, if you are using the JOELib library for your own implementations. This causes three main changes for you: 0. joelibMethod(myVector); Nothing to do here, because List is an interface for the Vector class 1. Vector myVector=joelibMethod(); Must be changed to: List myList=joelibMethod(); or you should use casting from Vector to List and vice versa. Depends on your implementation. 2. Vector myVector=joelibMethod(); Enumeration enum=myVector.enumeration(); enum.hasNextElement(); enum.nextElement(); Must be changed to: Iteration iter=myVector.iterator(); iter.hasNext(); iter.next(); 3. All users which have used the 'addElement', 'getElementAt' should use the access method, which are recommended from the interface: 'add' and 'get' And 'setElementAt(object, index)' should be replaced by 'set(index, object)' interchanging the order of the arguments. - 2004-08-27 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/desc/SimpleStringAtomProperty.java Added calculations class for String based atom properties - joelib/src/joelib/desc/result/StringArrayResult.java Added result class for String based arrays - joelib/src/joelib/desc/result/AtomStringResult.java Added result class for String based atom properties - joelib/src/joelib/desc/types/AtomType.java Added JOELib internal atom type as String based atom property descriptor - joelib/src/joelib/desc/types/AtomInAromaticSystem.java Added atom property descriptor for aromatic status of atoms - joelib/src/joelib/util/JOEPropertyHelper.java Bug fix: Fixed null pointer exception - joelib/src/joelib/desc/types/atompair/TopologicalAtomPair.java Bug fix: Fixed null pointer exception for parameter initalization - joelib/src/joelib/util/LineArrayHelper.java joelib/src/joelib/util/ArrayHelper.java Added String based storing and loading methods for String arrays - 2004-07-29 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/smarts/ParseSmart.java Bug fix: AGAIN! SMARTS encoder writes Stereo-Up as '\' and Stereo-Down as '/' but the specification says it vise versa. And added unspecific matching using '\?' and '/?', please remember that the implementation in JOELib requires C/?C=C/?C to match CC=CC sucessfully - 2004-07-25 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - Partial code cleanup. - Added formal definition of a molecular graph to the DocBook-Tutorial. - 2004-07-07 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/io/MDLSD.java Added dummy atom support for 'Du' entries. - joelib/src/joelib/data/plain/types.txt Internal representation of dummy atoms changed from 'X' to 'Xx'. Now we are conform with joelib/src/joelib/data/plain/element.txt - 2004-07-02 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/smarts/ParseSmart.java Cis/trans detection was replaced by IsomerismDetection.isCisTransBond. - joelib/src/joelib/util/IsomerismDetection.java Cis/trans detection from 2D/3D contains now up/up flags for cis and up/down flags for trans bonds. - 2004-07-02 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/smarts/ParseSmart.java Added cis/trans support or more correctly up/down detection ability. - joelib/src/joelib/smiles/JOEMol2Smi.java Bug fix: Wrong detection of the 'a' atom in a 'abcd' cis/trans pattern corrected. - joelib/src/resources/smartsEvaluation/cis_ and trans_butene.mol joelib/src/resources/smartsEvaluation/evaluation.txt Added testing methods for MDL SDF import with cis/trans autodetection and then SMARTS matching. - 2004-06-29 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/desc/DescriptorHelper.java Bug fix for handling empty DescResult and avoiding to calculate it twice. - joelib/src/joelib/smarts/ParseSmart.java Bug fix: SMARTS encoder writes Stereo-Up as '\' and Stereo-Down as '/' but the specification says it vise versa. - 2004-06-21 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/io/types/MDLSD.java Stabelized kekule-writting mode. Uses now directly isKSingle/isKDouble/ isKTriple instead of mol.kekulize(). - wsi/ra/PropertyHolder.java Allow additional joelib.properties in user.home/.joelib-directory. If found, this will used, otherwise the one in the classpath/jar-file. - 2004-06-15 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/src/joelib/smarts/test/SMARTSEvaluation.java SMARTS matching test class to check cross-dependencies for the atom typer or simple testing purpose. So, this is the first step to be able to formulate a classification problem for the atom type assignment process. So let me know if you are interested to discuss the details for this idea. I think this can be published, also. Data files are located in: joelib/src/resource/smartsEvaluation/evaluation.txt joelib/src/resource/smartsEvaluation/*.mol - joelib/src/wsi/ra/io/RegExpFilenameFilter.java Regular expression filter for files. - 2004-05-28 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - viewer*.sh New shell scripts to allow easier access to the 'primitive' viewers. Especially the 2D visualisation has not a good user interface at the moment (only one molecule allowed). But SMARTS highlighting and retro-synthetical cutting visualisation is still possible. - 2004-04-20 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.algo.datamining.weka.* Weka specific Instances with molecular data. The first step to general similarity/dissimilarity metrics for the already introduced joelib.math.similarity interfaces. - joelib.desc.data.* Introduced MoleculeCache interface to store data. - joelib.util.MDMatrixCache renamed to joelib.util.MoleculeDataCacheHolder Molecule data holder for matrices AND Weka-Molecule-instances. - Corrected usage of kekulization for MDL SD export and visualization using JOEMol.kekulize() - Slightly updated DocBook-tutorial. - 2004-03-20 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.io.types.cml.* Bug fixes for complex descriptor entries. - joelib.io.types.Amber joelib.io.types.Mopac Added support for 'Amber PREP' and 'Mopac Out' format. - joelib.io.Sybyl Corrected reading of partial charges from Sybyl format. Now the readed partial charges will not be overwritten by JOELib's Gasteiger-Marsili partial charges. - joelib.molecule.JOEMol Added partial charge vendor to allow to store this information in CML2. - 2004-03-18 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.io.MoleculeCallback joelib.io.types.cml.CMLSequentialSAXReader Support for reading sequentially huge uncompressed CML files using a molecule callback method. - joelib.io.types.ChemicalMarkupLanguage Added molecule string reader and support for using this facility e.g. for loading huge CML files in compressed ZIP files (workaround to avoid using the SAX parser directly) - joelib.io.types.cml.MoleculeAttributeArray Added for allowing CML in RSS feeds by avoiding showing single entries (attributes are not shown, e.g. in Mozilla). - joelib.io.types.cml.MoleculeArray Added missing stereochemistry 'bondStereo'. - joelib.test.GhemicalTest Added geometry optimization test using Ghemical. This can be only used under Linux or from the Cygwin shell ! - 2004-03-16 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.data.* Added hashed chemistry kernel identifier, which is always used by descriptor calculation and file format conversion. Now you know which version was used. This kernel ID is written to SDF as comment and CML as metadata ! - joelib.io.types.MDLSD Added missing stereochemistry informations to MDL SD writer. - joelib.gui.render.Renderer2D Corrected bond visualization for stereochemistry (cis/trans should not be drawn as hash/wedge!:-) - joelib.io.types.cml.* Updated to CML2 support with namespace and CML2 tags ! - joelib.io.types.ZIP Added compressed file reader/writer. Can read multiple files in one ZIP file, except CML entries, because the SAX parser closes after the first readed entry. Please send me a workaround if you find one. - joelib.gui.test.ConvertPanel Added '+split' option to panel. - joelib.gui.test.InfoPanel Added chemistry kernel (used expert systems) informations to panel. - 2004-01-24 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.desc.types.* Added a hug amount of descriptor calculation methods. - 2003-12-09 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.molecule.JOEMol Fixed 'dead loop' in deleteAtom(JOEAtom) for heavy weight atoms. Concerns also stripSalts(). - 2003-12-09 Gerd Mueller (gerd@smb-tec.com) - wsi.ra.tool.ResourceLoader Fixed resource locations for paths with white spaces. - 2003-12-03 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.desc.data.MoleculesDescriptorMatrix The generated 'yourMoleculeFile.matrix'-files contains now also informations if the descriptor is a binary-descriptor. So if you have already such files, please delete them and let JOELib them create again. - joelib.desc.result.IntResult The descriptor class can now also read double values and stores also double values set by setDoubleNV(double). This is important if you plan to normalize your data. - joelib/molecule/JOEMol Dead-loop-bug was fixed in deleteHydrogen(JOEAtom) - 2003-11-01 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/test/Convert.java Added 'split' option to generate splitted files - joelib/data/JOEAromaticTyper.java Avoiding two root atoms in one ring ! - 2003-10-20 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/io/types/PDF.java Improved layout and storage of descriptor values - joelib/lib/vecmath.jar Added, because the 2D renderer requires some classes. This is not really necessary for Java3D users, but for the others we will obtain some errors without it. - 2003-10-13 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/gui/render 2D molecule rendering facility using AWT - joelib/io/SimpleImageWriter joelib/io/types/BMP, GIF, JPEG, PDF, PPM 2D molecule rendering image writting classes - 2003-10-01 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/molecule/JOEMol assigning stereo flags for tempoary JOEVirtualBond when adding bonds to an molecule where an atom is missing - 2003-09-15 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib/docs/docbook: Changing .xml to .sgml for avoiding misunderstanding of the SGML-DocBook-Files ! Index and Glossary was added when changing from DocBook 4.1 to 4.2 ! Java based equation generation jtt/docbook/* without shell scripts and changed docbook generation shell script joelib/docs/docbook/generate.sh - 2003-08-26 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.test.Convert: joelib.test.ConvertSkip: Recognize file output type correctly (and do not use the input file name !;-) - joelib.molecule.JOEBond: Calculate correct bond length. - 2003-08-19 Gert Sclep (http://sourceforge.net/users/gsclep/) - joelib.gui.molviewer.java3d.Viewer: joelib.gui.molviewer.java3d.util.Java3DHelper: When molecules couldn't be drawn due to a buggy Java3D, the ViewerFrame was still shown when executing the Viewer class. - 2003-08-19 Joerg Kurt Wegner (http://sourceforge.net/users/wegner/) - joelib.molecule.GenericDataHolder: Return null for emtpy descriptor names. - joelib.data.JOEAromaticTyper: Find new root ring atoms, if more than 2 other neighbour ring atoms (ignore non-heavy weight atoms). - 2003-08-19 Gert Sclep (http://sourceforge.net/users/gsclep/) - joelib.io.types.ClearTextFormat: Comment of a CTX-file was added to the JOEMol object as an empty JOECommentData-object. - 2003-08-12 Gert Sclep (http://sourceforge.net/users/gsclep/) -joelib.io.types.ClearTextFormat: Code for parsing /2DCOORD section of CTX-format wasn't compliant with CTX-format produced by CACTVS program (version 2.95).
About SourceForge
Develop Software
Community
Copyright © 2009 Geeknet, Inc. All rights reserved. Terms of Use
