egonw (Egon Willighagen)

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Name: Egon Willighagen

Website/Blog: http://chem-bla-ics.blogspot.com/

Location: Uppsala, Sweden

Member Since: Sep 29, 2008 (about 1 year)

33 public repos
11 followers

Following 6 githubbers and watching 52 repositories view all →

Public Repositories (33)

- 7
- 4
cdk

The Chemistry Development Kit

Last updated Wed Nov 18 07:41:57 -0800 2009
- 2
- 2
ojdcheck

OpenJavaDocCheck

Last updated Thu Nov 12 22:56:20 -0800 2009
- 5
- 5
bioclipse.cheminformatics

Bioclipse2 Cheminformatics.

Last updated Thu Nov 12 07:17:32 -0800 2009
- 2
- 2
bioclipse.social

Bioclipse Social - Linking Bioclipse to the Social Web.

Last updated Thu Nov 05 04:24:04 -0800 2009
- 5
- 4
bioclipse.rdf

Bioclipse2 RDF.

Last updated Thu Nov 05 04:22:51 -0800 2009
- 1
- 1
bioclipse.joelib

Bioclipse Git Repository for JOELib, http://joelib.sf.net/.

Last updated Thu Nov 05 04:22:26 -0800 2009
- 1
- 0
nmrshiftdb-rdf

RDF interface to the NMRShiftDB data.

Last updated Tue Nov 03 01:52:14 -0800 2009
- 3
- 2
blueobelisk.userscript

Blue Obelisk Userscripts

Last updated Sun Nov 01 01:49:07 -0800 2009
- 1
- 4
bioclipse.statistics

Bioclipse2 Statistics.

Forked from olas/bioclipse.statistics Wed Jul 15 02:54:25 -0700 2009

Last updated Mon Oct 26 08:58:25 -0700 2009
- 3
- 3
RobotDF

Google Wave robot for RDF functionality

Last updated Fri Oct 23 13:00:00 -0700 2009
- 1
- 0
egonw.github.com

Private Homepage

Last updated Sat Oct 17 11:41:02 -0700 2009
- 9
- 4
cheminfbenchmark

Cheminformatics Benchmark Toolkit

Last updated Tue Oct 13 08:10:10 -0700 2009
- 1
- 1
bioclipse.metabolomics

Metabolomics Feature

Last updated Thu Oct 08 02:23:18 -0700 2009
- 1
- 4
bioclipse.qsar

Bioclipse2 QSAR.

Forked from olas/bioclipse.qsar Mon Aug 24 09:07:16 -0700 2009

Last updated Wed Oct 07 06:20:31 -0700 2009
- 5
- 1
bioclipse.sdk

Bioclipse Software Development Toolkit

Last updated Wed Sep 23 23:46:08 -0700 2009
- 1
- 2
bioclipse.drprolog

Plugin for intregration of DR-PROLOG in Bioclipse

Forked from samuell/bioclipse.drprolog Wed Sep 09 11:51:18 -0700 2009

Last updated Thu Sep 10 15:35:19 -0700 2009
- 1
- 2
bioclipse.medea

MEDEA functionality in Bioclipse, for massspectroscopy-based structure elucidation.

Forked from miguelrojasch/bioclipse.medea Tue Jul 21 07:51:07 -0700 2009

Last updated Mon Sep 07 03:13:56 -0700 2009
- 4
- 1
CDKitty

The Chemistry Development Kit Google Wave Robot

Last updated Thu Sep 03 07:30:23 -0700 2009
- 1
- 3
java-rdfa

RDFa Parser for java

Forked from shellac/java-rdfa Thu Oct 01 06:56:16 -0700 2009

Last updated Mon Aug 24 15:13:14 -0700 2009
- 4
- 2
onssolubility

Open Notebook Science Solubility Project

Last updated Thu Aug 20 04:20:10 -0700 2009
- 1
- 1
bioclipse.ds

Bioclipe2 Decision Support.

Forked from olas/bioclipse.ds Wed Jul 15 07:06:58 -0700 2009

Last updated Wed Aug 19 06:38:59 -0700 2009
- 1
- 3
bioclipse.data

Bioclipse2 Data: including the Blue Obelisk Structure data set and and older DrugBank version.

Forked from olas/bioclipse.data Sat Jul 18 02:37:15 -0700 2009

Last updated Wed Aug 05 09:09:58 -0700 2009
- 1
- 2
medea_bmc_article

LaTeX sources for the J. Chem. Inf. article on Medea

Forked from steinbeck/medea_bmc_article Tue Jul 21 08:12:26 -0700 2009

Last updated Tue Jul 21 08:08:44 -0700 2009
- 1
- 2
bioclipse.experimental

Bioclipse2 Experimental features

Forked from olas/bioclipse.experimental Sat Jul 18 02:45:55 -0700 2009

Last updated Fri Jul 17 13:04:47 -0700 2009
- 1
- 2
biotools

Simple tools for teaching biology

Forked from cniehaus/biotools Thu Jul 09 23:46:35 -0700 2009

Last updated Sat Jul 04 01:38:48 -0700 2009
- 1
- 2
VFLib

CDK compatible VF library for substructure and MCS search

Forked from asad/VFLib Sat Jul 04 13:25:23 -0700 2009

Last updated Tue Jun 30 19:07:00 -0700 2009
- 1
- 0
rednael

IRC bot that propagates Git commit messages.

Last updated Mon May 25 03:36:57 -0700 2009
- 1
- 0
pubchem-cdk

PubChem from a CDK perspective.

Last updated Fri May 08 06:17:53 -0700 2009
- 1
- 0
ron

Tools for rdf.openmolecule.net

Last updated Fri May 08 01:50:14 -0700 2009
- 2
- 0
gtd

Git-based ToDo tool.

Last updated Wed Apr 08 01:12:06 -0700 2009
- 1
- 0
jnchem

Java library to extract data from the Nature Chemistry journal.

Last updated Sat Mar 21 01:17:27 -0700 2009
- 1
- 0
xws-taverna

XWS Plugin for Taverna

Last updated Tue Jan 20 01:58:59 -0800 2009
- 1
- 0
knime-chemspider

Source code for a ChemSpider query API plugin for KNIME.

Last updated Mon Dec 01 00:23:34 -0800 2008

Public Activity

egonw pushed to master at egonw/cdk Wed Nov 18 07:42:01 -0800 2009

HEAD is c31c297a592f8b68e7b7149ac46f814f620990df

8 commits »

egonw committed c31c297a:

Merged changes from the CDK 1.2.4 release
egonw committed 743bad34:

Fixed param name
egonw committed bbb78ee5:

Updated the makefp3d target to work with the current build system
egonw committed 4801d79b:

Set up a branch for the 1.2.4 release
rajarshi committed b67d76ac:

Fixes bug 2898399. Updates to the SMARTS parser to handle proper matching for explicit hydrogens (including H, 1H, 2H and 3H). SMARTSQueryVisitor updated to take into account different isotopes of H. Also updated unit tests to take into account proper H matching. Added a unit test to further check H matching.
mark_rynbeek committed 45a7f54c:

Added tests to match hydrogens
rajarshi committed 7f68b07a:

Reworked the tests for bug 2898032. Updated Javadocs for smiles generator
rajarshi committed 924b5639:

Added unit test to confirm and check for bug 2898032

egonw pushed to cdk-1.2.x at egonw/cdk Wed Nov 18 07:20:22 -0800 2009

HEAD is 553b54ab11c6ef6b4aeb57154238c00ceea6fd3b

egonw committed 553b54ab:

Bumped version number to distinguish from the 1.2.4 release

egonw deleted tag 1.2.3.0bioclipse1 at egonw/cdk Wed Nov 18 06:04:44 -0800 2009

Deleted tag was at egonw/cdk/tree/1.2.3.0bioclipse1

egonw created tag cdk-1.2.4 at egonw/cdk Wed Nov 18 06:04:10 -0800 2009

New tag is at egonw/cdk/tree/cdk-1.2.4

egonw created tag 1.2.3.0bioclipse1 at egonw/cdk Wed Nov 18 06:04:10 -0800 2009

New tag is at egonw/cdk/tree/1.2.3.0bioclipse1

egonw pushed to cdk-1.2.x at egonw/cdk Wed Nov 18 06:03:56 -0800 2009

HEAD is 743bad345e8b8570779d0b94689ff64aa8c67cb0

3 commits »

egonw deleted branch 62-1.2.4release at egonw/cdk Wed Nov 18 06:03:24 -0800 2009

Deleted branch was at egonw/cdk/tree/62-1.2.4release

egonw created branch 62-1.2.4release at egonw/cdk Wed Nov 18 06:03:13 -0800 2009

New branch is at egonw/cdk/tree/62-1.2.4release

egonw pushed to master at egonw/cdk Mon Nov 16 02:39:09 -0800 2009

HEAD is 484619e35da12a736ffbac9031656f7568831475

ulikoehler committed 484619e3:

Fixed junior issue 1816529: Missing Java5 generics for atomContainers() Iterator

egonw pushed to master at egonw/cdk Sun Nov 15 02:14:54 -0800 2009

HEAD is 12bec4f992ac8afb2aaaed70eae8885f74780aa2

ulikoehler committed 12bec4f9:

Fixed junior issue 1802586: Misuse of assertTrue for tested strings

egonw pushed to master at egonw/cdk Sat Nov 14 12:19:37 -0800 2009

HEAD is 8a95d93506b6e392b2b88fe0d238bc0c760ad42d

3 commits »

egonw pushed to cdk-1.2.x at egonw/cdk Sat Nov 14 12:04:31 -0800 2009

HEAD is dfb28054f2124655cfdff963c3fabc1905a763b9

rajarshi committed dfb28054:

Updated UIT to handle single atom queries and added a unit test for bug 2888845. Also updated Javadocs to specifically note behavior of single atom queries

egonw pushed to master at egonw/ojdcheck Thu Nov 12 22:56:21 -0800 2009

HEAD is 0086835bff41cde428e5c855c30dd10bb74f5577

2 commits »

egonw pushed to master at egonw/bioclipse.cheminformatics Thu Nov 12 07:17:33 -0800 2009

HEAD is 8c30dbd607dbdd8bcd25adab422f1e908f828957

11 commits »

Arvid Berg committed 8c30dbd6:

Changed add/remove explicit hydrogens to use IEdits
Arvid Berg committed 7e8ff0df:

Added class check in undo handler
Arvid Berg committed 333ad56b:

Added a selection sub-menu with 'Select All' and 'Sellect Part'
Arvid Berg committed 106c0946:

Added sellectAll and selectPart
Arvid Berg committed 26c596cc:

Added LinkedSelection
Arvid Berg committed 8cdda6bd:

Changed select(IncrementalSelection) to select(IChemObjectSelection)
Arvid Berg committed 5f0829f3:

Added parameter values to managerMethod command
Arvid Berg committed 65094838:

Removed extra bond generator
Arvid Berg committed 60726a10:

Added update of hydrogens after edit.
Arvid Berg committed b3f51393:

Only create atoms and bonds the first time redo is called.
Arvid Berg committed 57fc38fa:

Fixes dirty on Molecules editor

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 12 07:15:12 -0800 2009

HEAD is 8c30dbd607dbdd8bcd25adab422f1e908f828957

8 commits »

Arvid Berg committed 8c30dbd6:

Changed add/remove explicit hydrogens to use IEdits
Arvid Berg committed 7e8ff0df:

Added class check in undo handler
Arvid Berg committed 333ad56b:

Added a selection sub-menu with 'Select All' and 'Sellect Part'
Arvid Berg committed 106c0946:

Added sellectAll and selectPart
Arvid Berg committed 26c596cc:

Added LinkedSelection
Arvid Berg committed 8cdda6bd:

Changed select(IncrementalSelection) to select(IChemObjectSelection)
Arvid Berg committed 5f0829f3:

Added parameter values to managerMethod command
Arvid Berg committed 65094838:

Removed extra bond generator

egonw pushed to master at egonw/cdk Sat Nov 07 08:40:00 -0800 2009

HEAD is 9dc13e3c33fdc360b3cb61e06b074a64394d01a1

egonw committed 9dc13e3c:

Fixed the dist-large target: removed to no longer existing .libdepends after the log4j module patch

egonw pushed to 81-ojdcheck at egonw/cdk Sat Nov 07 08:37:13 -0800 2009

HEAD is f13147feea0bd0ed7cf301b979248a8c6946f291

2 commits »

egonw created branch 81-ojdcheck at egonw/cdk Sat Nov 07 07:41:16 -0800 2009

New branch is at egonw/cdk/tree/81-ojdcheck

egonw deleted branch 81-ojdcheck at egonw/cdk Sat Nov 07 07:41:07 -0800 2009

Deleted branch was at egonw/cdk/tree/81-ojdcheck

egonw created tag 0.1 at egonw/ojdcheck Sat Nov 07 02:12:31 -0800 2009

New tag is at egonw/ojdcheck/tree/0.1

egonw pushed to master at egonw/ojdcheck Sat Nov 07 01:41:19 -0800 2009

HEAD is a2223f79baaa50ce7b786a0b2b92358217b0a9fa

egonw committed a2223f79:

Added test for missing @param tags

egonw pushed to master at egonw/ojdcheck Sat Nov 07 01:18:04 -0800 2009

HEAD is 9f774377e105cc810311de4662d2b1880054c48f

egonw committed 9f774377:

Removed unused imports

egonw pushed to master at egonw/ojdcheck Sat Nov 07 01:15:45 -0800 2009

HEAD is 845b0b9f3899e69994579ff69f935df44e8c2494

egonw committed 845b0b9f:

Removed test classes

egonw pushed to master at egonw/ojdcheck Sat Nov 07 01:03:48 -0800 2009

HEAD is 2dd279c82850b31bccaa79885a3d41d84a5db26c

egonw committed 2dd279c8:

Moved tests into subfolders, to organize them a bit

egonw pushed to master at egonw/ojdcheck Fri Nov 06 15:21:41 -0800 2009

HEAD is 72244f4129871644fe19f44883619ff3a2976619

3 commits »

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Fri Nov 06 07:55:16 -0800 2009

HEAD is 60726a102a4400e2cddfae71c0eddb1af8f9822e

2 commits »

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Fri Nov 06 03:01:54 -0800 2009

HEAD is 57fc38faba605c6d0ef03e185d41fe5128e9cb8d

Arvid Berg committed 57fc38fa:

Fixes dirty on Molecules editor

egonw pushed to master at egonw/bioclipse.cheminformatics Thu Nov 05 10:29:53 -0800 2009

HEAD is fc08a407c8283f4bafacee6c7f279047a46e1da2

12 commits »

egonw committed fc08a407:

Trigger a refresh so that the new arrivals show up in the table (fixes #1718)
jonalv committed 562f0c95:

Only rebuild outline model on load append.
Ola Spjuth committed b87c984c:

Adapted menus for comparison and superimpose.
Ola Spjuth committed 300bca79:

Added a submenu "Compare" for cheminformatics.
jonalv committed 99f327ef:

added labels to calculateRMSD
jonalv committed 898967ff:

fixed generics
jonalv committed bcf93e6e:

layout
egonw committed 7b03ed5e:

Added labels to the tanimoto CSV output (addresses #1715)
egonw committed b081849e:

Force opening in the Jmol editor, which is currently part of the Bioclipse Platform feature anyway (fixes #1716)
egonw committed 1183a224:

Removed output to STDOUT (fixes #1712)
egonw committed 5cbbd2c4:

Restrict this handler to 2 resources, and remove the wizard for which we have the Tanimoto Matrix handler (fixes #1711)
egonw committed 98d74ca5:

PDB is not yet supported (fixes #1713)

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 05 08:56:09 -0800 2009

HEAD is fc08a407c8283f4bafacee6c7f279047a46e1da2

egonw committed fc08a407:

Trigger a refresh so that the new arrivals show up in the table (fixes #1718)

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 05 07:59:27 -0800 2009

HEAD is 562f0c953042270d89601da8a9c693ac0c440f39

jonalv committed 562f0c95:

Only rebuild outline model on load append.

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 05 07:51:23 -0800 2009

HEAD is b87c984cc4dcbd2fdad26b7b49f012f34fb425df

2 commits »

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 05 07:48:08 -0800 2009

HEAD is 99f327ef35046db56896e9e42bebb3790e2c1b28

3 commits »

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 05 06:08:37 -0800 2009

HEAD is 7b03ed5e9d883e3200d8af79ace70bcd861aece9

egonw committed 7b03ed5e:

Added labels to the tanimoto CSV output (addresses #1715)

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 05 05:40:25 -0800 2009

HEAD is b081849e809fcbff33a9dc8feed29790d90a3f3e

egonw committed b081849e:

Force opening in the Jmol editor, which is currently part of the Bioclipse Platform feature anyway (fixes #1716)

egonw pushed to 2.2.x at egonw/bioclipse.cheminformatics Thu Nov 05 05:37:27 -0800 2009

HEAD is 1183a224918299d6755bfc040ec18310b36405ea

egonw committed 1183a224:

Removed output to STDOUT (fixes #1712)