forked from jonalv/cdk
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathchangelog.txt
283 lines (280 loc) · 33.8 KB
/
changelog.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
CHANGELOG
---------
This changelog is automatically generated from the:
git log --pretty=format:"* %s (%aN <%ae>)" --no-merges <LAST-TAG>..HEAD >> changelog.txt
1.3.0
-----------
* Removed old changelog files (Egon Willighagen <[email protected]>)
* Capability to read and write reaction properties information. Added theirs corresponding tests (Miguel Rojas Cherto <[email protected]>)
* Fixed serialization of IAtom's with null formal charge to not cause NullPointerExceptions (Egon Willighagen <[email protected]>)
* Added unit test for serialization of null formal charges into the MDL molfile format (which currently fails) (Egon Willighagen <[email protected]>)
* Fixed a typo from the previous merge (Rajarshi Guha <[email protected]>)
* Updated Javadocs for SMARTS query tool to indicate unsupported features (Rajarshi Guha <[email protected]>)
* Cleaned up source file to remove spurious line endings (Rajarshi Guha <[email protected]>)
* Bumped version number (Egon Willighagen <[email protected]>)
* The formal charge of the IAtomcontainer is transfered to IMolecularFormula (Miguel Rojas Cherto <[email protected]>)
* Fixed bug 2787332 The old bond array in the gasteiger charge calculation was set to the wrong size (Rajarshi Guha <[email protected]>)
* Updated to fix bug 2788357 SMARTSQueryTool now catches TokenMgrError in the constructor and throws a CDKException. Also added unit test to check for this (Rajarshi Guha <[email protected]>)
* Added new taglet to process cdk.githash tag and link Javadocs to sources in Git repo (Rajarshi Guha <[email protected]>)
* Updated cdk.svnrev tags to cdk.githash tags (Rajarshi Guha <[email protected]>)
* Bug_2787332. Added test for the Triclosan molecule (InChI=1S/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,1 6H) the IPMolecularLearningDescriptor caluclation fails with java.lang.ArrayIndexOutOfBoundsException: 24. (Miguel Rojas Cherto <[email protected]>)
* Removed obsolete renderer code: either use cdk-1.0.x or jchempaint-primary (Egon Willighagen <[email protected]>)
* Added test for bug 2786624 in the parser test suite (Rajarshi Guha <[email protected]>)
* Added links to PMD pages (Egon Willighagen <[email protected]>)
* Added link to JUnit stats (Egon Willighagen <[email protected]>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* Fixed links. Suboptimal, as the path is still hardcoded to a single Nightly instance, but we do not have the XML framework yet to summarize things over all Nightlies (running different JDKs, OSs, etc) (Egon Willighagen <[email protected]>)
* Updated version number (Egon Willighagen <[email protected]>)
* Added test to ensure IAtomContainers are not sneaked in via IMoleculeSet.add(IAtomContainerSet) (Egon Willighagen <[email protected]>)
* Overwritten addAtomContainer(IAtomContainer, double) too, to throw an IllegalArgumentException when a non-IMolecule is passed (Egon Willighagen <[email protected]>)
* Now throws an IllegalArgumentException when it is tried to store an IAtomContainer which is not an IMolecule (Egon Willighagen <[email protected]>)
* Added unit test for #2784182 (Egon Willighagen <[email protected]>)
* new test with reserpine (Stefan Kuhn <[email protected]>)
* Added taglets for threading safety (Egon Willighagen <[email protected]>)
* With one atom or less, we define it to be connected, as there is no partitioning needed (fixes #2784209, NullPointerException on IAtomContainer with no atoms) (Egon Willighagen <[email protected]>)
* Added unit test for bug #2784209 which currently fails (Egon Willighagen <[email protected]>)
* More removal of explicit org.openscience.cdk package names: throws clauses (Egon Willighagen <[email protected]>)
* More removal of explicit org.openscience.cdk package names (Egon Willighagen <[email protected]>)
* More removal of explicit org.openscience.cdk package names: for new org.openscience.cdk.Foo() calls (Egon Willighagen <[email protected]>)
* Removed explicit org.openscience.cdk.interfaces packages names (fixes #2783549) (Egon Willighagen <[email protected]>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the datadebug module (fixes #2783549) (Egon Willighagen <[email protected]>)
* Removed explicit package names, in favor of imports, for org.openscience.cdk in the data module (fixes #2783549) (Egon Willighagen <[email protected]>)
* breakout of recursion option on AllRingsFinder (mark_rynbeek <[email protected]>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <[email protected]>)
* Extraction from the string elemental formula the charge. (Miguel Rojas Cherto <[email protected]>)
* Controller of the mass when it is out of the range (Miguel Rojas Cherto <[email protected]>)
* Updated source and test to address review issues. Updated typos in Javadocs and added link to AllRingFinder. Move instatiation of SMARTS matcher to constructor. The element count array is now of length 120. Updated JUnit test to remove superflous prints and updated copyright (Rajarshi Guha <[email protected]>)
* Moved the pubchem fingerprinter to the fingerprinter module, since it needs SMARTS which is not a dependency of the standard module (Rajarshi Guha <[email protected]>)
* Added more test cases comparing our FP's with those provided by Pubchem (Rajarshi Guha <[email protected]>)
* Updated Javadocs, cleaned up some tests (Rajarshi Guha <[email protected]>)
* Added test for benzene (Rajarshi Guha <[email protected]>)
* Updated SMARTS patterns to use H count specifications rather than explicit H matches (Rajarshi Guha <[email protected]>)
* Initial version of Pubchem fingerprints based on the public domain NCGC code. Includes unit tests (Rajarshi Guha <[email protected]>)
* Updated to intelligently add H's to a PLANAR3 N, fixes bug 2781199 (Rajarshi Guha <[email protected]>)
* Added test case for bug 2781199 (Rajarshi Guha <[email protected]>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now include the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* calls to CDKException constructor made within a catch block now includes the root exception to preserve stack trace (paulturner <paulturner@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated unit tests to employ equals tests. Fixed Javadocs. Address comments wrt the original patch (Rajarshi Guha <[email protected]>)
* removed needless white space (Rajarshi Guha <[email protected]>)
* Refactored to provide a query container specifically for pharmacophore queries. (Rajarshi Guha <[email protected]>)
* Updated the toString tests (Rajarshi Guha <[email protected]>)
* Added test methods for the new toString methods. Also added test method annotations (Rajarshi Guha <[email protected]>)
* provided toString methods for the pcore query classes (Rajarshi Guha <[email protected]>)
* Added a unit test to ensure SD fields are read for all molecules (Egon Willighagen <[email protected]>)
* Added unit test for bug 1579235, which checks for aromaticity in indolizine (Rajarshi Guha <[email protected]>)
* Updated code to use 1.5 idioms and remove use of Iterator (Rajarshi Guha <[email protected]>)
* Added links to PMD pages (Egon Willighagen <[email protected]>)
* Added link to JUnit stats (Egon Willighagen <[email protected]>)
* Added list of classes in the module, with links to Nightly@Pele (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* Added set up for creating module HTML pages (Egon Willighagen <[email protected]>)
* Updated build system to take into account non public classes as well. Also updated ChiIndexUtils to be package private (Rajarshi Guha <[email protected]>)
* split up test (Stefan Kuhn <[email protected]>)
* new files (Stefan Kuhn <[email protected]>)
* more tests for cml reading (Stefan Kuhn <[email protected]>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <[email protected]>)
* Fixed cast, remove redundant full package name (Egon Willighagen <[email protected]>)
* Added unit test for #2692107 (Egon Willighagen <[email protected]>)
* Fixed typo: missing 's' (Egon Willighagen <[email protected]>)
* Added unit test for #1848591: incorrect Murcko framework (Egon Willighagen <[email protected]>)
* Fixed cast, remove redundant full package name (Egon Willighagen <[email protected]>)
* Added unit test for #2692107 (Egon Willighagen <[email protected]>)
* Fixed typo: missing 's' (Egon Willighagen <[email protected]>)
* Use the proper folder name, including the CDK version (Egon Willighagen <[email protected]>)
* 1.2.1 release being prepared (Egon Willighagen <[email protected]>)
* Fixed bug 2714283, which properly throws an exception when rings are not closed properly. If a ring is not closed with the appropriate ring number, InvalidSmilesException is thrown. Matches Daylight behavior (Rajarshi Guha <[email protected]>)
* Fixed bug 2729120 and added unit test (Rajarshi Guha <[email protected]>)
* Updated comment to fix bug 2768643. (Rajarshi Guha <[email protected]>)
* Partial fix for bug 2719237. Made getBondOrderSum static, added unit test for it (Rajarshi Guha <[email protected]>)
* Typo: proteinl -> protein (Egon Willighagen <[email protected]>)
* Made class public, to unbreak adding it to the build/*.javafiles (Egon Willighagen <[email protected]>)
* Partially fixed SMARTS matching for R0. Updated target molecule initialization to explicitly (Rajarshi Guha <[email protected]>)
* Fixed dubious equality test. A private method was checking Double objects via reference. (Rajarshi Guha <[email protected]>)
* Added test method annotation. Completes coverage for data module (Rajarshi Guha <[email protected]>)
* Refactored ChiIndexUtils to make it package private. Cleans up public API, since it is only used by chi descriptor code. Updated all dependent classes. Moved test code (which needs to be filled in!) as well (Rajarshi Guha <[email protected]>)
* Code cleanup of ChiIndexUtils. Converted to 1.5 idioms (Rajarshi Guha <[email protected]>)
* Clean up of PathTools and added test method annotation, so that core is completely covered (Rajarshi Guha <[email protected]>)
* Fixed the previous commit to edit the cdk.keyword line, not the cdk.module line (Egon Willighagen <[email protected]>)
* More consistent keywords used (Egon Willighagen <[email protected]>)
* Added a test to ensure that Integer objects are compared by value rather than reference (Rajarshi Guha <[email protected]>)
* Added a test case to check that atom container diffs are correct when using deserialized objects (Rajarshi Guha <[email protected]>)
* Fixed IntegerDifference so that it actually checks the integer value rather than references of the Integer object. Fixes the problem whereby an object serialized to disk and then deserialized does not match the original object (i.e., non empty diff string) (Rajarshi Guha <[email protected]>)
* Applied patch #2675819 (Stefan Kuhn): Patch to add a removeReaction to reactionSet (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics, one last time... Leander should work by now... (Egon Willighagen <[email protected]>)
* Use interface instead of implementation (Egon Willighagen <[email protected]>)
* Some other code cleanup (Egon Willighagen <[email protected]>)
* Added generics, here too (Egon Willighagen <[email protected]>)
* Added generics, here too (Egon Willighagen <[email protected]>)
* Use interface instead of implementation (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Added generics (Egon Willighagen <[email protected]>)
* Removed an unused import (Egon Willighagen <[email protected]>)
* Use IAtomContainer instead of IMolecule, as the actual matching is using IAtomContainers already (fixes #2686249) (Egon Willighagen <[email protected]>)
* Fixed a ClassCastException (fixes #2685134) (Egon Willighagen <[email protected]>)
* Added source attrib to fix building the Ubuntu .deb (Egon Willighagen <[email protected]>)
* Fixed Help build system: use doclet jars in develjar/; updated for new src folder src/main; removed very outdated use of rt.jar (Egon Willighagen <[email protected]>)
* Removed libdepends include for test-ioformats, which does not actually have libdepends (Egon Willighagen <[email protected]>)
* Updated so that if a target atom has no symbol (such as pseudo atoms) the match returns false (rather than an NPE) (Rajarshi Guha <[email protected]>)
* Fixed proper handling of #n SMARTS querys (Rajarshi Guha <[email protected]>)
* Added test case for bug 2686473 (Rajarshi Guha <[email protected]>)
* Added note on Ant 1.7.1 required (Egon Willighagen <[email protected]>)
* Fixed a NPE source: 'null == 2' causes an exception, so first test for nullness (Egon Willighagen <[email protected]>)
* Added a missing dep (Egon Willighagen <[email protected]>)
* Correction of the solution (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* added method to calculate the Total Mass Number given a IMolecularFormula (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added copyright info (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added missing dep (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Rearranged the order of operations and provided a useful message. Added bug annotation (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated test to check that a aromatic molecle coming from two diferent sources (kekule and aromatic SMILES) gets represented internally as the same thing. Currently does not (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* removed "throws CDKException" from method StructureResonanceGenerator.setReactions(List<IReactionProcess> newReactionsList). And depending methods as StabilizationCharges.calculatePositive. It was producing some incoherences: org.openscience.cdk.charges.StabilizationCharges row 83: Unreachable catch block for CDKException. This exception is never thrown from the try statement body. (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Fixed a bunch of Javadoc errors (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added method to IAtomTypeMatcher to perceive types for all atoms in the container; allowing some removal of redundant calculations, and the addition of calculation of molecular properties, like aromaticity, as used in the Sybyl atom type matcher (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Updated tests: findType(IAC, IAtom) cannot detect aromaticity; but findType(IAtomContainer) does, but not tested yet (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* added a convenience constructor to smilesgenerator, improved a test to test the aromaticity behaviour (egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Fixed copyright notice for 2009 (Egon Willighagen <[email protected]>)
* Fixed duplicate storage of layout templates, which only belong in the sdg module, not extra module too (Egon Willighagen <[email protected]>)
* used interfaces where possible and updated to 1.5 idioms (Rajarshi Guha <[email protected]>)
* Updated to use interfaces where possible and cleaned up code to use 1.5 idioms (Rajarshi Guha <[email protected]>)
* Added unit test for a ONS Solubility solute, which fails to be parsed when RDF. But does not fail here. (egonw <[email protected]>)
* Export the jniinchi lib (Egon Willighagen <[email protected]>)
* Fixed a few test class instantiation problems (Egon Willighagen <[email protected]>)
* Fixed constructor: wrong file format; add getClassLoader() (Egon Willighagen <[email protected]>)
* Fixed for NewCDKTestCase -> CDKTestCase renaming (Egon Willighagen <[email protected]>)
* Added all existent reaction tests in MreactionTest (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added dictionary which reads from a reaction-process.owl the mechanism for specific type reaction. (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Invalid smiles string (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Set new methods to read new schemes of the reactions dictionary (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* Added testMethod value for Junit4 (miguelrojasch <miguelrojasch@eb4e18e3-b210-0410-a6ab-dec725e4b171>)
* For each data class, also test inherited methods for super classes implementing inherited superinterfaces (Egon Willighagen <[email protected]>)
1.3.1
-----------
* Bumped version for 1.3.1 release (Egon Willighagen <[email protected]>)
* Added some extra lines, hopefully fixing the conflicts all the time (Egon Willighagen <[email protected]>)
* Fixed param name (Egon Willighagen <[email protected]>)
* Updated the makefp3d target to work with the current build system (Egon Willighagen <[email protected]>)
* Set up a branch for the 1.2.4 release (Egon Willighagen <[email protected]>)
* 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. (Rajarshi Guha <[email protected]>)
* Added tests to match hydrogens (mark_rynbeek <[email protected]>)
* Fixed junior issue 1816529: Missing Java5 generics for atomContainers() Iterator (Uli Köhler <[email protected]>)
* Reworked the tests for bug 2898032. Updated Javadocs for smiles generator (Rajarshi Guha <[email protected]>)
* Added unit test to confirm and check for bug 2898032 (Rajarshi Guha <[email protected]>)
* Fixed junior issue 1802586: Misuse of assertTrue for tested strings (Uli Köhler <[email protected]>)
* Made the AtomContainerPermutors IAtomContainer implementation independent (Egon Willighagen <[email protected]>)
* 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 (Rajarshi Guha <[email protected]>)
* Fixed the dist-large target: removed to no longer existing .libdepends after the log4j module patch (Egon Willighagen <[email protected]>)
* Implemented instantiating custom loggers; example in the unit test class (Egon Willighagen <[email protected]>)
* Added the use of the SystemOutLoggingTool as back up (Egon Willighagen <[email protected]>)
* Added a ILoggerTool implementation for STDOUT (Egon Willighagen <[email protected]>)
* Dig up and updated the copyright history (Egon Willighagen <[email protected]>)
* Factored out initialization of the tool, to allow reusing the code for other logger class names (Egon Willighagen <[email protected]>)
* Moved the log4j.jar depending LoggingTool into a separate module (Egon Willighagen <[email protected]>)
* Introduces the ILoggingTool interface and a factory so that CDK code no longer needs to depend on LoggingTool which depends on Apache's Log4j library. (Egon Willighagen <[email protected]>)
* Added generation of java source jars (Peter Odéus <[email protected]>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <[email protected]>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <[email protected]>)
* Fixed matchers to allow XML without new lines (closes #2832835) (Egon Willighagen <[email protected]>)
* Added unit tests for detection of PubChem XML files. (Egon Willighagen <[email protected]>)
* Added reading of E/Z stereochemistry from double bonds in MDL V2000 molfiles. (Egon Willighagen <[email protected]>)
* A minor fix to clean up a PDMD warning (Rajarshi Guha <[email protected]>)
* Overwrite unit tests, because there are no change events passed around at all for the NoNotification interface implementations (Egon Willighagen <[email protected]>)
* Added missing unit tests for IChemModel event propagation for the ICrystal field (Egon Willighagen <[email protected]>)
* Fixed propagation of change events to IChemModel when modifications are made in child IChemObjects (Egon Willighagen <[email protected]>)
* Fixed unit tests: the IChemModel.setFoo(null) should actually give a change event on the listener of the IChemModel, and not after unregistering of the Foo object. (Egon Willighagen <[email protected]>)
* Synchronized with the Blue Obelisk version (Egon Willighagen <[email protected]>)
* Added unit test to the function of the new IO setting to force 2D coordinate output. (Egon Willighagen <[email protected]>)
* Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted. (Egon Willighagen <[email protected]>)
* Added unit test to verify that if 2D and 3D coordinates are available, the 3D coordinates are outputted. (Egon Willighagen <[email protected]>)
* Changed IBond.get/setStereo() to use a IBond.Stereo enumeration instead of an int (fixes #2855850): (Egon Willighagen <[email protected]>)
* Fixed Taglets: only return HTML if the Tag is really given; the toString() method is given for all cases, not just when the tag is found (Egon Willighagen <[email protected]>)
* Added the Mannhold LogP descriptor (Egon Willighagen <[email protected]>)
* Added the Mannhold LogP descriptor to the ontology (Egon Willighagen <[email protected]>)
* Fixeda bug which was causing various parts of the DescriptorEngine to fail - it was trying to instantiate a non-descriptor class which happens to reside in the descriptor package directory. This fix is a bit kludgy - ideally only descriptors should be in that directory (Rajarshi Guha <[email protected]>)
* Fixes ClassCastException when not IMolecule (Arvid Berg <[email protected]>)
* Upgraded to PMD 2.4.5 with many bug fixes, giving more accurate error reports (Egon Willighagen <[email protected]>)
* Added missing dependency on cdk-diff, being used in one of the unit tests (Egon Willighagen <[email protected]>)
* Fixed methods names to match those in the test class (Egon Willighagen <[email protected]>)
* Fixed test method name to match the expected patters, fixing a coverage test fail (Egon Willighagen <[email protected]>)
* Removed duplicate code: MolecularFormulaTest now extends AbstractMolecularFormulaTest (Egon Willighagen <[email protected]>)
* Fixed test method annotation to point to the right method (Egon Willighagen <[email protected]>)
* Added missing @TestMethod annotation (Egon Willighagen <[email protected]>)
* Added modules that were missing from the PMD testing (Egon Willighagen <[email protected]>)
* Added modules that were missing from the doccheck testing (Egon Willighagen <[email protected]>)
* Added reference to IUPAC documentation about stereochemistry visualization. (Stefan Kuhn <[email protected]>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <[email protected]>)
* Added missing dependency introduced by the use of AbstractFingerprinterTest in test-standard. (Egon Willighagen <[email protected]>)
* Updated the unit test classes for all IFingerprinter implementations to use the new AbstractFingerprinter class; a few unit tests actually fail (Egon Willighagen <[email protected]>)
* Extracted an AbstractFingerprinterTest with unit tests that should really apply to all IFingerprinter implementations (Egon Willighagen <[email protected]>)
* Clean up of layout. (Jonathan Alversson <[email protected]>)
* Fix the unit test to not give a 'input must support mark' exception on some platforms, by wrapping the InputStream in a BufferedInputStream. (Egon Willighagen <[email protected]>)
* Added missing dependencies (Egon Willighagen <[email protected]>)
* Added ioformats to modules to test (Egon Willighagen <[email protected]>)
* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where multiline field data is found. (Egon Willighagen <[email protected]>)
* Use StringBuilder to aggregate the field data, which gives an huge performance boost for SD file where very much field data, like the ChEBI_complete.sdf (Egon Willighagen <[email protected]>)
* Factored out steps in reading the SD file data block (Egon Willighagen <[email protected]>)
* Bumped version, to make it clear this is not the 1.2.3 release (Egon Willighagen <[email protected]>)
* Bumped version, to make it clear this is not the 1.3.0 release (Egon Willighagen <[email protected]>)
* Fixed registering on the cdk.threadnonsage tag (closes #2796362) (Egon Willighagen <[email protected]>)
* Removed obsolete pattern from old svnrev tag (Egon Willighagen <[email protected]>)
* Fixed JavaDoc to remove traces of the old svnrev Tag (Egon Willighagen <[email protected]>)
* Synchronized exception message with implementation (fixes #2844333) (Egon Willighagen <[email protected]>)
* Made class private again, per authors request (Egon Willighagen <[email protected]>)
* Any class will do, not just public, final and abstract (Egon Willighagen <[email protected]>)
* Two further compile fixes after the merge with CDK 1.2.x (Egon Willighagen <[email protected]>)
* Made the class public, to fix a compile problem introduced by the merge with CDK 1.2.x (Egon Willighagen <[email protected]>)
* Added ant task to calculate JavaNCSS code statistics (Egon Willighagen <[email protected]>)
* Added JavaNCSS 32.53 (LGPL 3.0) (Egon Willighagen <[email protected]>)
* The Pauling Electronegativity is copied in configure as well. I can't see why not copy everything we have. (Stefan Kuhn <[email protected]>)
* Revert "added a test for bug 2831420": (Egon Willighagen <[email protected]>)
* Patch for bug 2843445. Aims to fix generation of NaN coordinates by SDG (mark_rynbeek <[email protected]>)
* added a test for bug 2831420 (Stefan Kuhn <[email protected]>)
* added a test for bug #2831420 (Stefan Kuhn <[email protected]>)
* Made InChIGeneratorFactory a singleton. (jonalv <[email protected]>)
* Layout. (jonalv <[email protected]>)
* Added bug annotation (Rajarshi Guha <[email protected]>)
* test case for bug #2846213 (Stefan Kuhn <[email protected]>)
* Fixed perception of N.planar3 where N.sp2 was detected, by now taking into account the given hydrogen count. (Egon Willighagen <[email protected]>)
* Fixed perception of benzene with all single bond, but hydrogen count 1 and bonds flagged aromatic. In this case, the type is C.sp2 not C.sp3. (Egon Willighagen <[email protected]>)
* Added assertions to unit test for values being not null (Egon Willighagen <[email protected]>)
* Added two unit tests for the same problem: carbon atom types are not correctly perceived if bond order info is SINGLE only, and hydrogen count and aromaticity flag is set. (Egon Willighagen <[email protected]>)
* Moved class into a org.openscience.cdk package, which seems to work now. I'm puzzled why it did not before. Solved several unit test fails. (Egon Willighagen <[email protected]>)
* Unsealed the XOM jar to allow having the CustomSerializer (Egon Willighagen <[email protected]>)
* Fixed Javadocs error (Rajarshi Guha <[email protected]>)
* Fixed a wrong javadoc tag. Also removed svn tag in the SMARTS parser JJT file, replaced with git tag (Rajarshi Guha <[email protected]>)
* Added support for 'public enum's (Egon Willighagen <[email protected]>)
* corrected bug in bondtools.isStereo(IAtomContainer container, IAtom stereoAtom). A comparision of atom symbols in a nested loop was using the counter of the outer loop twice. Note it worked before, because there is a sort of fallback to Morgan numbers. fallback to morgan (fixes #2830287) (Stefan Kuhn <[email protected]>)
* added a new test for bondtools (Stefan Kuhn <[email protected]>)
* Fixed inconsistency between accepts() and write: also support writing of IAtomContainerSet and IAtomContainer as accepts() indicates (fixes #2827745) (Egon Willighagen <[email protected]>)
* General test for testing consistency between write() and accepts(), testing that all accepted IChemObject's can also be written (Egon Willighagen <[email protected]>)
* Added unit test for bug #2826961: inconsistent atom typing for two SMILES. Unit test does not show a fail, ruling out a CDK bug (Egon Willighagen <[email protected]>)
* Remove erroneous throws statement (Egon Willighagen <[email protected]>)
* Bug found calculating the exact mass given a molecular formula when it is negative charged. (Miguel Rojas Cherto <[email protected]>)
* Fixed reading of the cdk/dict/data/elements.owl database which is now in OWL (Egon Willighagen <[email protected]>)
* Fixed issue 2458210: use assertNotNull(foo) etc instead of assertTrue(foo != null). (Uli Köhler <[email protected]>)
* Added minimum equivalents for BondManipulator.getMaximumBondOrder() methods (Egon Willighagen <[email protected]>)
* Fixes asserts: after removal *no* change should be recorded (Egon Willighagen <[email protected]>)
* Added IO option to disable generator of XML declaration statements in the output CML. (Egon Willighagen <[email protected]>)
* Added generics, and consistified code by always returning a List<?> of the same '?'. (And some 80 chars fixes in the JavaDocs.) (Egon Willighagen <[email protected]>)
* Added unit tests to test that when a [Molecule|Reaction|Ring]Set has been removed from a ChemModel, the ChemModel should unregister as listener. (Egon Willighagen <[email protected]>)
* Added unit tests for event propagation from [Molecule|Reaction|Ring]Sets to ChemModel. (Egon Willighagen <[email protected]>)
* More testing of flags. (Egon Willighagen <[email protected]>)
* Fix for junior job id: [ 1837692 ] Test methods should throw only one Exception. (Paul Turner <[email protected]>)
* Fixed missing imports and wrapped to 80 chars (Egon Willighagen <[email protected]>)
* Better excpetion handling in builder3d: (Stefan Kuhn <[email protected]>)