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r8425 | egonw | 2007-06-26 15:39:30 +0200 (Tue, 26 Jun 2007) | 1 line
4
Created a new changelog with 'svn log' which makes more sense than an outdated, unmaintained XML
5
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6
r8426 | egonw | 2007-06-26 15:40:13 +0200 (Tue, 26 Jun 2007) | 1 line
8
Bumped version: about to make a release
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r8455 | shk3 | 2007-06-29 14:15:27 +0200 (Fri, 29 Jun 2007) | 1 line
12
the viewer can now resize the molecule instead of adding scrollbars (requested by a user).
13
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14
r8510 | shk3 | 2007-07-05 11:08:25 +0200 (Thu, 05 Jul 2007) | 1 line
16
the hydrogen count of an atom in the cml convertor included the atom itself in the count
17
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r8512 | shk3 | 2007-07-05 11:21:45 +0200 (Thu, 05 Jul 2007) | 1 line
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r8529 | shk3 | 2007-07-10 10:41:20 +0200 (Tue, 10 Jul 2007) | 1 line
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added a new test (not sure about the correct results, but the actual ones are strange).
25
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r8530 | shk3 | 2007-07-10 10:42:32 +0200 (Tue, 10 Jul 2007) | 2 lines
28
the test file for the test just added
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r8531 | shk3 | 2007-07-10 10:43:38 +0200 (Tue, 10 Jul 2007) | 1 line
33
changed name of test file
34
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r8583 | shk3 | 2007-07-25 14:02:46 +0200 (Wed, 25 Jul 2007) | 1 line
37
a new test file for a descriptor
38
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39
r8584 | shk3 | 2007-07-25 14:03:49 +0200 (Wed, 25 Jul 2007) | 1 line
41
there was a really stupid bug in this
42
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43
r8585 | shk3 | 2007-07-25 14:04:28 +0200 (Wed, 25 Jul 2007) | 1 line
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47
r8587 | shk3 | 2007-07-25 21:17:13 +0200 (Wed, 25 Jul 2007) | 1 line
49
slight performance increase
50
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r8588 | shk3 | 2007-07-25 22:36:23 +0200 (Wed, 25 Jul 2007) | 1 line
53
the extra bits of the extended fingerprinter need to be relativ to the size of the extended fingerprint, not to the size of the normal part.
54
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r8589 | shk3 | 2007-07-26 10:04:35 +0200 (Thu, 26 Jul 2007) | 1 line
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removed some system.outs
58
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r8590 | shk3 | 2007-07-26 10:13:28 +0200 (Thu, 26 Jul 2007) | 1 line
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removed some system.outs
62
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r8591 | shk3 | 2007-07-26 10:14:52 +0200 (Thu, 26 Jul 2007) | 2 lines
65
this should not have been committed
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68
r8624 | egonw | 2007-07-27 16:23:27 +0200 (Fri, 27 Jul 2007) | 1 line
70
Removed work in progress; does not belong in CDK 1.0
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r8625 | egonw | 2007-07-27 16:28:25 +0200 (Fri, 27 Jul 2007) | 1 line
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Added list of possible patches to incorporate for release 1.0.2 (cd trunk; svn log -r 8426:HEAD > patches.txt)
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r8677 | shk3 | 2007-08-11 23:55:05 +0200 (Sat, 11 Aug 2007) | 1 line
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added a trigger to user aromaticity for smiles. Note this is important since without this the smiles generator will generate different smiles for identical molecules.
79
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80
r8690 | egonw | 2007-08-15 07:40:24 +0200 (Wed, 15 Aug 2007) | 1 line
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Added more recent candidate patches
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84
r8703 | shk3 | 2007-08-23 00:55:40 +0200 (Thu, 23 Aug 2007) | 1 line
86
added rajarshis changes to 1.0 branch
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88
r8707 | egonw | 2007-08-28 09:41:36 +0200 (Tue, 28 Aug 2007) | 1 line
90
Applied patch 8439 from trunk/: 'Updated entry for Arsenic which is trivalent so maxBondOrderSum should be 3'
91
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92
r8708 | egonw | 2007-08-28 09:43:54 +0200 (Tue, 28 Aug 2007) | 1 line
94
Applied patch 8466 from trunk/: 'Fixed title of atom type list'
95
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96
r8709 | egonw | 2007-08-28 09:48:38 +0200 (Tue, 28 Aug 2007) | 1 line
98
Applied patch 8483 and 8486 from trunk/: 'Updated to include hyb state labels for some of the missing entries' and 'Fixed some more entries'
99
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100
r8710 | egonw | 2007-08-28 09:51:32 +0200 (Tue, 28 Aug 2007) | 1 line
102
Applied patch 8501 and 8502 from trunk/: 'Updated to throw an exception if 3D coordinates are not available'
103
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104
r8711 | egonw | 2007-08-28 10:10:54 +0200 (Tue, 28 Aug 2007) | 1 line
106
Applied patch 8517 from trunk/: 'getDescriptorResultType() did return DoubleResult instead of DoubleArrayResult'
107
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108
r8712 | egonw | 2007-08-28 10:12:57 +0200 (Tue, 28 Aug 2007) | 1 line
110
Applied patch 8518 (and test in 8519) from trunk/: 'pending fix for z-coordinate sign. Besides the normalization of axes is dispensable'
111
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112
r8713 | egonw | 2007-08-28 10:14:27 +0200 (Tue, 28 Aug 2007) | 1 line
114
Applied patch 8520 from trunk/: 'fix rotation angle in testRotate_IAtomContainer_Point2d_double'
115
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116
r8714 | egonw | 2007-08-28 10:15:53 +0200 (Tue, 28 Aug 2007) | 1 line
118
Applied patch 8521 from trunk/: 'Updated entry for Arsenic which is trivalent so maxBondOrderSum should be 3 (copied from r8439)'
119
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120
r8715 | egonw | 2007-08-28 10:17:20 +0200 (Tue, 28 Aug 2007) | 1 line
122
Applied patch 8525 from trunk/: 'Fixed element symbols'
123
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124
r8716 | egonw | 2007-08-28 10:18:50 +0200 (Tue, 28 Aug 2007) | 1 line
126
Applied patch 8535 from trunk/: 'Removed a line which originally for debug purposes and causes the RingPartioner to run twice during each call.'
127
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128
r8717 | egonw | 2007-08-28 10:19:38 +0200 (Tue, 28 Aug 2007) | 1 line
130
Applied patch 8537 from trunk/: 'Fixed correct reader to use'
131
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132
r8718 | egonw | 2007-08-28 10:22:35 +0200 (Tue, 28 Aug 2007) | 1 line
134
Applied patches 8552 and 8553: 'Linker includes ring atoms, SMILES could be converted to UpperCase' and 'Add test for linkers'
135
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136
r8719 | egonw | 2007-08-28 10:29:51 +0200 (Tue, 28 Aug 2007) | 1 line
138
Applied patch 8576: 'Fixed writers: the BufferedReader must not be static; that messes up threaded writing'
139
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140
r8721 | egonw | 2007-08-28 10:32:51 +0200 (Tue, 28 Aug 2007) | 1 line
142
Applied patch 8577-8586: adding cdk.conformer by Rajarshi
143
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144
r8722 | egonw | 2007-08-28 10:42:00 +0200 (Tue, 28 Aug 2007) | 1 line
146
Applied patch 8596-8612: adding cdk.pcore by Rajarshi
147
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148
r8723 | egonw | 2007-08-28 10:46:55 +0200 (Tue, 28 Aug 2007) | 1 line
150
Updated: backlog is up to r8623 now
151
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152
r8724 | egonw | 2007-08-28 10:47:32 +0200 (Tue, 28 Aug 2007) | 1 line
154
Applied patch 8623: 'Updated scripts so that testing is performed on the pcore module'
155
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156
r8725 | egonw | 2007-08-28 10:50:37 +0200 (Tue, 28 Aug 2007) | 1 line
158
Added patches 8626-8229: deal with zero atom MDL molfiles
159
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160
r8726 | egonw | 2007-08-28 10:52:34 +0200 (Tue, 28 Aug 2007) | 1 line
162
Added patches 8630-8632: Added a test case for honoring of IOSettings, Updated the test to honor IOSettings for zero Z-coordinates
163
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164
r8727 | egonw | 2007-08-28 10:54:38 +0200 (Tue, 28 Aug 2007) | 1 line
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Added patches 8633-8634: 'Added a convenience method to get the sum of implicit and explicit hydrogens on an IAtom in an IAtomContainer.'
167
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168
r8728 | egonw | 2007-08-28 10:56:02 +0200 (Tue, 28 Aug 2007) | 1 line
170
Applied patch 8638: 'Some possible documentation is added.'
171
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172
r8729 | egonw | 2007-08-28 10:58:31 +0200 (Tue, 28 Aug 2007) | 1 line
174
Applied patch 8663: 'Fixed SMARTS to parse (closes #1760968).'
175
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176
r8730 | egonw | 2007-08-28 11:05:57 +0200 (Tue, 28 Aug 2007) | 1 line
178
Reverted the pcore patch applied earlier (patches 8722 and 8724): I did not realize it used J5-isms
179
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180
r8731 | egonw | 2007-08-28 11:07:59 +0200 (Tue, 28 Aug 2007) | 1 line
182
Applied patch 8648: 'Updated Javadocs'
183
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184
r8732 | egonw | 2007-08-28 11:11:10 +0200 (Tue, 28 Aug 2007) | 1 line
186
Applied patches 8673-8676: the SDG improvements by steinbeck
187
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188
r8733 | egonw | 2007-08-28 11:16:54 +0200 (Tue, 28 Aug 2007) | 1 line
190
Applied patches 8678 and 8681: 'Applied pathes by Andreas Schueller. Fixes bug #1772609 "NPE with bridged rings in SDG/RingPlacer"'
191
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192
r8734 | egonw | 2007-08-28 11:18:32 +0200 (Tue, 28 Aug 2007) | 1 line
194
Applied patch 8679: 'getMorganNumbes may fail due to an overflow of an int. Deprecated old method and added a new one returning a long[] array'
195
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196
r8735 | egonw | 2007-08-28 11:20:11 +0200 (Tue, 28 Aug 2007) | 1 line
198
Applied patch 8680: 'Fixed bug #1773119 "SDG wrongly folds short chains connecting two rings". We now calculate the degreeSum of atoms in chains and thereby find the one without terminal atoms. This one is then layed out first.'
199
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200
r8736 | egonw | 2007-08-28 11:21:42 +0200 (Tue, 28 Aug 2007) | 1 line
202
Applied patch 8682 from trunk/: 'Applied patch for bug #1772613 (RingSet.getConnectedRings() returns duplicate rings) and added a test case. Also had to correct test case testGetConnectedRings_IRing() in RingSetTest.java.'
203
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204
r8737 | egonw | 2007-08-28 11:23:21 +0200 (Tue, 28 Aug 2007) | 1 line
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Applied patches 8683-8687: more SDG patches from steinbeck
207
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208
r8738 | egonw | 2007-08-28 11:25:37 +0200 (Tue, 28 Aug 2007) | 1 line
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OK, new state of cdk-1.0.x/: back in synch with trunk up to 8690
211
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212
r8739 | egonw | 2007-08-28 11:31:14 +0200 (Tue, 28 Aug 2007) | 1 line
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216
r8740 | egonw | 2007-08-28 11:33:28 +0200 (Tue, 28 Aug 2007) | 1 line
218
Reverted conformer patch: also uses J5 stuff
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220
r8741 | egonw | 2007-08-28 11:38:40 +0200 (Tue, 28 Aug 2007) | 1 line
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Fixed project name to not conflict with trunk/cdk
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224
r8742 | egonw | 2007-08-28 11:46:31 +0200 (Tue, 28 Aug 2007) | 1 line
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Last few compile fixes
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r8743 | egonw | 2007-08-28 16:00:07 +0200 (Tue, 28 Aug 2007) | 1 line
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Rather dirty patch to get it compile with Java1.4: need FIXING
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r8744 | egonw | 2007-08-28 16:02:55 +0200 (Tue, 28 Aug 2007) | 1 line
234
Reverted patch 8743: was only meant to commit a change to one file
235
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r8745 | egonw | 2007-08-28 16:05:30 +0200 (Tue, 28 Aug 2007) | 1 line
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Rather dirty patch to get it compile with Java1.4: needs FIXING
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r8746 | egonw | 2007-08-28 16:05:48 +0200 (Tue, 28 Aug 2007) | 1 line
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Removed a test which requires J5
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r8747 | egonw | 2007-08-28 16:06:20 +0200 (Tue, 28 Aug 2007) | 1 line
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Removed a test which requires J5
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r8748 | egonw | 2007-08-28 16:07:16 +0200 (Tue, 28 Aug 2007) | 1 line
250
Do some magic to load J5-depending classes
251
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r8749 | egonw | 2007-08-28 16:08:43 +0200 (Tue, 28 Aug 2007) | 1 line
254
Marked classes as requiring Java5
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r8750 | egonw | 2007-08-28 16:09:19 +0200 (Tue, 28 Aug 2007) | 1 line
258
Fixed detection of what to compile with J5
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260
r8753 | shk3 | 2007-08-28 23:40:30 +0200 (Tue, 28 Aug 2007) | 1 line
262
the enter element stuff had some flaws
263
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r8756 | egonw | 2007-08-29 07:30:10 +0200 (Wed, 29 Aug 2007) | 1 line
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Added missing file :(
267
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r8772 | egonw | 2007-08-29 14:31:15 +0200 (Wed, 29 Aug 2007) | 1 line
270
Should fix creating HTML with J1.4
271
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272
r8789 | shk3 | 2007-08-31 00:44:30 +0200 (Fri, 31 Aug 2007) | 2 lines
274
the image export automatically adds a file extension
276
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277
r8812 | shk3 | 2007-09-01 21:14:42 +0200 (Sat, 01 Sep 2007) | 1 line
279
export does not change screen
280
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r8815 | shk3 | 2007-09-01 21:39:38 +0200 (Sat, 01 Sep 2007) | 1 line
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export warns if file already exists
284
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285
r8822 | shk3 | 2007-09-01 22:04:09 +0200 (Sat, 01 Sep 2007) | 1 line
287
the image is not set off the border 40 px (til now, labels at the border were cut off)
288
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r8838 | rajarshi | 2007-09-02 16:22:15 +0200 (Sun, 02 Sep 2007) | 1 line
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Added latest version of nightly to this branch
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r8845 | shk3 | 2007-09-02 18:43:36 +0200 (Sun, 02 Sep 2007) | 1 line
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image no longer upside down
296
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297
r8887 | shk3 | 2007-09-05 19:45:31 +0200 (Wed, 05 Sep 2007) | 2 lines
299
better comment for canonlabeler
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r9042 | egonw | 2007-10-14 20:01:54 +0200 (Sun, 14 Oct 2007) | 1 line
304
Updated; going to try to get a 1.0.2 released
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306
r9043 | egonw | 2007-10-14 20:05:38 +0200 (Sun, 14 Oct 2007) | 1 line
308
Merged r8691: Added test case for bug #1772609 'NPE with bridged rings in SDG/RingPlacer'.
309
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310
r9044 | egonw | 2007-10-14 20:07:41 +0200 (Sun, 14 Oct 2007) | 1 line
312
Merged r8697: Add a method to the query atom container creator which creates an queryatomcontainer. This replaces each pseudoatom to an anyatom.
313
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r9045 | egonw | 2007-10-14 20:09:30 +0200 (Sun, 14 Oct 2007) | 1 line
316
Merged r8699 and r8700: Added test file by Volker (see cdk-user) for the shortest path problem; JUnit test provided by Volker Haehnke (haehnke - bioinformatik uni-frankfurt de), somewhat rewritten.
317
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r9046 | egonw | 2007-10-14 20:11:06 +0200 (Sun, 14 Oct 2007) | 1 line
320
Merged r8701: Renamed a variable to comply with http://en.wikipedia.org/wiki/Dijkstra's_algorithm
321
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r9047 | egonw | 2007-10-14 20:13:30 +0200 (Sun, 14 Oct 2007) | 1 line
324
Merged r8751: Bug fixes for bugs #1783367 'SmilesParser incorrectly assigns double bonds' and #1783381 'SmilesParser uses Molecule instead of IMolecule'. Test case for bug #1783367.
325
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r9048 | egonw | 2007-10-14 20:15:39 +0200 (Sun, 14 Oct 2007) | 1 line
328
Merged r8754 and r8773: Fix and test case for bug #1783547 and #1783546 'Lost aromaticity in SmilesParser with Biphenyl and Benzene'
329
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r9049 | egonw | 2007-10-14 20:16:50 +0200 (Sun, 14 Oct 2007) | 1 line
332
Merged r8774: Add a MDL RXN reader which uses the MDLV2000Reader instead of the MDLReader
333
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r9050 | egonw | 2007-10-14 20:23:40 +0200 (Sun, 14 Oct 2007) | 1 line
336
Merged r8775, r8776, r8777: bug fixes for #150354 #1783774 #1778479 in the SmilesParser, SmilesGenerator and MDLWriter/PseudoAtom.
337
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338
r9051 | egonw | 2007-10-14 20:25:40 +0200 (Sun, 14 Oct 2007) | 1 line
340
Merged r8791: Code for v,mass atom two digits mass atom and exception handeling
341
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342
r9052 | egonw | 2007-10-14 20:26:33 +0200 (Sun, 14 Oct 2007) | 1 line
344
Merged r8800: Fixed reading of MDL molfiles with exactly 12 columns (==valid) in the bond block
345
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346
r9053 | egonw | 2007-10-14 20:28:59 +0200 (Sun, 14 Oct 2007) | 1 line
348
Merged r8802: Made a little more memory efficient by removing unnesscary cloning operations
349
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350
r9054 | egonw | 2007-10-14 20:29:40 +0200 (Sun, 14 Oct 2007) | 1 line
352
Merged r8803: Fixed it so that we make a deep copy of the input molecule
353
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354
r9055 | egonw | 2007-10-14 20:30:46 +0200 (Sun, 14 Oct 2007) | 1 line
356
Merged r8809: Added code to work on a local copy of theinput molecule
357
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358
r9056 | egonw | 2007-10-14 20:32:26 +0200 (Sun, 14 Oct 2007) | 1 line
360
Merged r8811: Updated Javadocs
361
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362
r9057 | egonw | 2007-10-14 20:35:55 +0200 (Sun, 14 Oct 2007) | 1 line
364
Merged 8824 8821 8820 8819 8817 8816: Added code to properly work on a local copy
365
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r9058 | egonw | 2007-10-14 21:39:12 +0200 (Sun, 14 Oct 2007) | 1 line
369
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r9059 | egonw | 2007-10-14 21:39:50 +0200 (Sun, 14 Oct 2007) | 1 line
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r9060 | egonw | 2007-10-14 21:44:41 +0200 (Sun, 14 Oct 2007) | 1 line
376
Merged 8848: Fixed an ArrayIndexOutOfBoundsException
377
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r9061 | egonw | 2007-10-14 21:46:19 +0200 (Sun, 14 Oct 2007) | 1 line
380
Merged r8850: Removed tainted code (unclear license, no statement) and classes depending on it (closes #1701312)
381
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382
r9062 | egonw | 2007-10-14 21:47:32 +0200 (Sun, 14 Oct 2007) | 1 line
384
Merged r8881: The cause for hard to reproduce StructureDiagramGenerator bugs was the undeterministic order of the rings returned by SSSRFinder.findSSSR(). The rings are now sorted by a new method AtomContainerSetManipulator.sort() which uses the new class AtomContainerComparator. Also the safetyCounters in the SDG were made effective. This should prevent all hangs of the SDG in future.
385
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r9063 | egonw | 2007-10-14 21:50:06 +0200 (Sun, 14 Oct 2007) | 1 line
388
Merged r8883: Added SVN keywords to the copyright comment.
389
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390
r9064 | egonw | 2007-10-14 21:51:01 +0200 (Sun, 14 Oct 2007) | 1 line
392
Merged r8884: The molecule ID of diamantane.cml incorrectly was 'cubane'
393
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r9065 | egonw | 2007-10-14 22:04:57 +0200 (Sun, 14 Oct 2007) | 1 line
396
Merged r8885 and r8886: This commit fixes bugs #1784850, #1677912 and #1714794
397
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398
r9066 | egonw | 2007-10-14 22:11:39 +0200 (Sun, 14 Oct 2007) | 1 line
400
Merged r8901: Added a statement to say that the current PDBWriter does not write protein structures
401
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402
r9067 | egonw | 2007-10-14 22:12:33 +0200 (Sun, 14 Oct 2007) | 1 line
404
Merged 8903: Applied patch by Bala <bkbsub@gmail.com>: more integers
405
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406
r9068 | egonw | 2007-10-14 22:14:39 +0200 (Sun, 14 Oct 2007) | 1 line
408
Merged r8911: Added correct bibliography into javaDoc
409
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410
r9069 | egonw | 2007-10-14 22:54:58 +0200 (Sun, 14 Oct 2007) | 1 line
412
Merged 8924-8927: SMARTS updates
413
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414
r9070 | egonw | 2007-10-14 22:57:14 +0200 (Sun, 14 Oct 2007) | 1 line
416
Merged r8940: Fixed a recursive smarts matching bug found by Rajarshi
417
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418
r9071 | egonw | 2007-10-14 23:00:16 +0200 (Sun, 14 Oct 2007) | 1 line
420
Merged 8942: Updated to take into accout the pathological case of a single atom
421
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422
r9072 | egonw | 2007-10-14 23:02:38 +0200 (Sun, 14 Oct 2007) | 1 line
424
Merged 8960 and 8961: Updated the JavaDoc for the recently added primes. Fixed the test for the recently added primes, and split up two situations into separate tests.
425
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r9073 | egonw | 2007-10-14 23:14:23 +0200 (Sun, 14 Oct 2007) | 1 line
428
Missing ref: merged from trunk, unknown commit
429
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430
r9074 | egonw | 2007-10-14 23:14:48 +0200 (Sun, 14 Oct 2007) | 1 line
432
Merged 9041: Fixed bug when reuse the same QueryAtomContainer with RecursiveSmarts
433
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r9075 | egonw | 2007-10-14 23:22:14 +0200 (Sun, 14 Oct 2007) | 1 line
437
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added
removed
changelog.txt
