forked from openbabel/openbabel
-
Notifications
You must be signed in to change notification settings - Fork 1
/
ChangeLog
10108 lines (6800 loc) · 354 KB
/
ChangeLog
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
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
2008-12-13 Geoffrey Hutchison <[email protected]>
* src/formats/outformat.cpp: New format to read files with
extensions .dat, .log, .out and try to guess the format based on
contents. Currently works with many GAMESS, Gaussian, MOPAC,
Q-Chem, Jaguar, and MPQC files.
2008-12-12 Geoffrey Hutchison <[email protected]>
* src/typer.cpp: Fix for PR#2017902 -- bug introduced by r2578 in
detecting guanidinium C atoms.
* data/element.txt, data/atomtyp.txt: Minor changes. Allow boron
to have 4 bonds and adjust implicit valence for several elements.
2008-12-02 Chris Morley
* src/tokenst.cpp, include/openbabel/tokenst.h: Add function
to ignore istream up to a specified string.
* src/formats/mdlformat.cppReadMolecule): give no warning if
there are blank lines at the end of the file.
(SkipObjects): rewrite to prevent confusion by $ chars in
properties. Should hve been done long ago.
* src/mcdlutil.cpp, include/openbabel/mcdlutil.h: more bug
fixes from Sergey Trepalin. Performs better, but still some
memory leaks.
2008-12-01 Geoffrey Hutchison <[email protected]>
* src/formats/pdbformat.cpp: Add support for reading CRYST1
records, contributed by Francois-Xavier Coudert. PR#2343128.
2008-11-22 Chris Morley
* src/mcdlutil.cpp: Small bug fixes from Sergei Trepalin
* windows-vc2005/babelconfig.h, windows-vc2005/OBDLL/OBDLL.vcproj,
windows-vc2005/OBMCDL/MCDL.vcproj,
windows-vc2005/OBUtilFormats/OBUtilFormats.vcproj: Windows
build updated to make groupRedraw() callable.
2008-11-22 Chris Morley
* src/ops/loader.cpp: do not remove comments after 4th line of
an entry in plugindefines.tx. SMARTS uses '#'!
* src/ops/optransform.cpp: revamp parsing.
* src/phmodel.cpp(OBChemTsfm::Init): correct bug in which some
kinds of transform were not taken into account when checking
whether there was anything to do.
2008-11-22 Chris Morley
* include/openbabel/text.h: NEW boring and trivial class OBText,
derived from OBBase. This was proposed last year for formats
which contained mixed content, like cdx, but has other uses.
* src/formats/xml/textformat.cpp: NEW input format for the above
* src/formats/xml/cmlreactformat.cpp: makes use of OBText class
to insert its output into boilerplate text provided in a file.
* include/openbabel/mol.h, src/mol.cpp(Has2D): add an extra
parameter to change from "has 2D or 3D" to "has 2D". Correct bug
which gave the wrong answer for some linear molecules.
* include/openbabel/obconversion.h, src/obconversion.cpp
(NumInputObjects): now adjusts for values of -f and -l options
* src/formats/xml/xml.cpp(GetDerived):correct bug which did not
update the XMLConversion object even when the base OBConversion
had changed (bug#2283422).
* src/formats/smilesformat.cpp*(SkipObjects): make work properly
for files without a new line at the end.
* src/ops/gen2D.cpp, src/ops/gen3d.cpp: set the molecule dimension.
2008-11-21 Geoff Hutchison <[email protected]>
* src/data.cpp (GetAtomicNum): Fix bug with patch supplied by
Wayne Volkmuth (PR#2289021). Crashes with 3-character element.
* include/openbabel/atom.h: Patch from Wayne Volkmuth to ensure
atomic numbers are unsigned (i.e., values above 127 are
OK). PR#2289628.
* src/formats/pdbformat.cpp: Patch from Francois-Xavier Coudert to
write CRYST1 records when unit cell data is present. PR#2023510.
* src/generic.cpp (OBUnitCell::GetLatticeType): Fix bug reported
(and patched) by Jonathan Coome. PR#2100535.
* configure.in, config.* ac*.m4, Makefile.am, Makefile.in: Remove
autotools build files. Use Cmake instead.
2008-11-21 Geoffrey Hutchison <[email protected]>
* src/Makefile.am, src/ops/Makefile.am: Build mcdlutil.cpp and
gen2D.cpp plugin.
* configure.in: Update to indicate that trunk is not 2.2.0
build. (May go into a 2.3 or 3.0 build.)
2008-11-12 Chris Morley
* src/mscdlutil.cpp, data/templates.sdf: revert to previous
version with templates internal, since external templates
did not seem to be always applied.
#define nRotBondsMax 20 (from 24) which should improve performance.
2008-11-05 Tim Vandermeersch <[email protected]>
* src/formats/pqrformat.cpp: Apply patch from Mikael Lund to read in
partial charges and radii. The radii are added to the atoms as
OBPairData with attribute "Radius".
2008-10-31 Chris Morley
* src/formats/getinchi.cpp: prevent failure when input contains
"InChI>InChI=...", which actually occurred in an SDF file.
2008-10-27 Chris Morley
* mcdlutil.cpp: Replace all calls to fabs with abs.
Remove internal templates and template molecule sorting; all
template molecules are now in templates.sdf which has to be sorted,
largest first.
* data/templates.sdf: 147 molecules, sorted
* obconversion.cpp(Convert): make OutputAtEnd option work with
multiple input files.
2008-10-23 Tim Vandermeersch <[email protected]>
* src/chains.cpp: Remove debug output.
* src/forcefields/forcefielduff.cpp: Check if parameters are found and
don't try to use a NULL pointer when there isn't a parameter. (Fixes:
#2187870)
2008-10-22 Tim Vandermeersch <[email protected]>
* src/forcefields/forcefield*.h: Fix MakeNewInstance().
2008-10-20 Tim Vandermeersch <[email protected]>
* src/CMakeLists.txt: Add gen2D.cpp and mcdlutil.cpp
* src/mcdlutil.cpp: Replace all calls to abs(double) with fabs(double)
* src/formats/MCDLformat.cpp: Replace string.npos with string::npos
2008-10-20 Chris Morley
* include/openbabel/mcdlutil.h, src/mcdlutil.cpp: New files
which use MCDL library to generate 2D coordinates
* src/formats/MCDLformat.cpp: some code moved to the above files.
* src/ops/gen2D.cpp: wrapper op for --gen2d
* data/templates.sdf: New file with example template
* src/transform.cpp: help on --sort and --revsort
2008-10-20 Chris Morley
* include/openbabel/obmolecformat.h, src/obmolecformat.cpp:
New functions to sort molecules, Sort(), OutputSortedMols()
and LessThan()
* include/openbabel/descriptor.h, src/descriptor.cpp: New
virtual function LessThan() and default implementation.
Make several error messages once only.
* src/descriptors/filters.cpp: Add LessThan functions for TitleFilter
and more complex one + GetCachedValue() + Init() for InChIFilter.
* include/openbabel/plugin.h: Add virtual funtion Init()
* include/openbabel/mol.h, src/mol.cpp: extra flag to indicate
is a pattern, not a complete molecule. SetIsPatternStructure()
Previously described, but somehow not committed.
2008-10-17 Tim Vandermeersch <[email protected]>
* src/forcefield.cpp: in OBForceField::GetGrid(), calculate grid size
before adding probe atom.
2008-10-17 Tim Vandermeersch <[email protected]>
* include/openbabel/chains.h, src/chains.cpp: some changes from
experimental branch, mainly documentation and some bug fixes.
* src/formats/atomrecord.cpp: Interpret HG11, HE11, ... as hydrogen
atoms at position gamma and epsilon. Previously these atom ids were
interpreted as Hg and He atoms. (Fixes: #2002557 & #2026265)
2008-10-16 Tim Vandermeersch <[email protected]>
* src/forcefields/forcefieldmmff94.cpp: Remove _logbuf[100] (Fixes
#2022120)
2008-10-16 Tim Vandermeersch <[email protected]>
* src/builder.cpp: fix bugs with linear molecules. (Fixes #2119034 & #2013814)
2008-10-15 Chris Morley
* src/fingerprint.cpp: correct yesterdays commit which used
the wrong size to reserve for the fingerprint vector.
2008-10-15 Chris Morley
* include/openbabel/obconversion.h, src/obconversion.cpp:
New function for counting the number of molecules in an input file.
Make option to force output at end more general (for sort).
* include/openbabel/fingerprint.h, src/fingerprint.cpp:
Add extra parameter to FastSearchIndexer constructor to
allow vectors to be pre-sized.
* src/formats/fastsearchformat.cpp(ReadChemObject): change the way
the last result molecule is flagged (for sort).
(WriteChemObject) Make index updating work with GUI by detecting
a ofstream object rather than cout.
Count number of molecules in input file, report it and use it
to pre-size the fingerprint and seekposition vectors.
* src/formats/smilesformat.cpp(SkipObjects): make compatible with
previous interpretation changes. (Lines which start with non-SMILES
character are ignored.)
2008-10-15 Tim Vandermeersch <[email protected]>
* src/forcefields/forcefieldmmff94.cpp: Accept both forms for sulfon
and nitro groups: N(=O)O, N(=O)=O, S(O)O, S(=O)(=O) are now all valid
and typed correctly.
2008-10-11 Tim Vandermeersch <[email protected]>
* src/forcefields/forcefielduff.cpp: Fix minor output bug reported by
Tapani Kinnunen (Fixes: #2144142)
2008-10-11 Tim Vandermeersch <[email protected]>
* src/forcefield.cpp, src/forcefields/forcefieldmmff94.cpp: Remove
redefinition of _logbuf[BUFF_SIZE+1] (This and Chris' previous commit
fixes: #2150390)
* src/forcefield.cpp: Fix OBForceField::GetAtomTypes() and
OBForceField::GetPartialCharges()
* src/forcefield.cpp: Check OBForceField::_validSetup flas before
doing anything that may cause a segfault. (Fixes: #2059299)
* src/forcefields/forcefield*.h: Set _validSetup to false in
constructor.
* CMakeLists.txt, src/config.h.cmake: apply patch from Christian
Ehrlicher to fix cmake MSVC compilation.
2008-10-10 Chris Morley
* src/fingerprints/finger3.cpp: rearrange
a) so that div and div-- do not appear in same statement, which
is illegal (Andrew Dalke).
b) replace ternary conditional, which did not compile in gcc
It's a pity the Microsoft compiler did not warn about either of these.
The preferred file format no longer needs a comment as first line.
* src/formats/chemkinformat.cpp(ReadReactionQualifierLines):
correct error similar to b) above flagged in bug #2150390
2008-09-26 Chris Morley
* src/formats/fastsearchformat.cpp: Improved error message when
target is SMARTS rather than SMILES. Bug #2129841
* src/formats/getinchi.cpp: small mod to avoid occasionally seeing
a "quoted" InChI when there isn't one. (There ARE none in the wild.)
2008-09-23 Chris Morley
* src/fingerprints/finger3.cpp: enhanced PatternFP which can take
extra parameters and file format.
* data/MACCS.txt; data for new MACCS fingerprint (from RDKit)
* data/plugindefines.txt; definition of MACCS fingerprint.
2008-07-19 Michael Banck <[email protected]>
* src/formats/opendxformat.cpp: Rename theGaussianCubeFormat global
variable to theOpenDXCubeFormat.
* src/formats/CMakeLists.txt: Added opendxformat to formats.
2008-07-11 Chris Morley
* windows-vc2005/Distribution/NSISScriptToCreateInstallerOBF.nsi
Set Env Var BABEL_DATADIR to installation directory. Safer than
relying on finding the data files in the current directory.
* include/openbabel/builder.h, src/builder.cpp: check whether
fragments.txt is loaded successfully and if not return false
from Build().
2008-07-09 Noel O'Boyle <[email protected]>
* scripts/python/pybel.py: Bug fix for make3D for linear molecules.
Fixes bug 2014055. Minor doc fixes. Remember to close output files
in Molecule.write().
2008-07-03 Noel O'Boyle <[email protected]>
* windows-vc2005/OBPythonOBF/setup.py: Update setup.py to include
forcefield files when installing
2008-07-03 Michael Banck <[email protected]>
* scripts/Makefile.am (dist-hook): Do not fail if make distclean does
not succeed in the perl and ruby directories.
* scripts/Makefile.in: Regenerated.
* data/Makefile.am (table_DATA): Added plugindefines.txt.
* data/Makefile.in: Regenerated.
* data/CMakelists.txt: Removed space-groups.xsl from to_install.
* test/cmlreadfile.cpp: Read files from TESTDATADIR, not relative to
current directory.
* test/wrapper.sh: Use ${srcdir}, not ${top_srcdir} to set
$BABEL_DATADIR.
* test/wrapper.sh: Run inchi tests from source directory if ${srcdir}
is non-empty. Set and export TESTDATADIR.
2008-07-03 Noel O'Boyle <[email protected]>
* scripts/ruby/README: Updated build instructions
2008-07-03 Michael Banck <[email protected]>
* src/CMakelists.txt (LIBRARY_VERSION): New variable.
* src/CMakelists.txt (BABEL_LIBRARY): Set VERSION property to
${LIBRARY_VERSION}.
2008-07-03 Geoffrey Hutchison <[email protected]>
* src/Makefile.am, src/CMakeLists.txt: Update SONAME to 3 for
version 2.2.0 release.
2008-07-03 Marcus D. Hanwell <[email protected]>
* CMakeLists.txt: Relaxed the CMake requirement to 2.4.7.
* include/openbabel/griddata.h, src/griddata.cpp: Added three new
getter functions to get the x, y and z axes.
* src/CMakeLists.txt: Updated to use SONAME 3.
* include/openbabel/mol.h, src/mol.cpp: Added extra arguments to
GetMolWt, GetExactMass and GetSpacedFormula to optionally disable
implicit hydrogens. Defaults to preserve existing behaviour.
* src/grid.cpp: Fixed the Init function to apply padding correctly.
2008-07-02 Marcus D. Hanwell <[email protected]>
* include/openbabel/grid.h, src/grid.cpp: Updated the documentation
and a few fixes to the function prototypes.
* include/openbabel/griddata.h, src/griddata.cpp: Updates to the
documentation, added a GetMaxVector function and made SetLimits const
fixes for the vector3 form.
* CMakeLists.txt, src/CMakeLists.txt, src/formats/CMakeLists.txt:
Reduce the number of version variables floating around to only those
that are used...
* CMakeLists.txt, src/formats/CMakeLists.txt: Use a versioned plugin
directory as autotools does.
2008-07-02 Geoffrey Hutchison <[email protected]>
* src/locale.cpp: Add string.h header, from patch by Marcus
Hufgard. Allows compilation with GCC 4.3.1 on Linux:
PR#2008642.
* src/formats/gausszmatformat.cpp: Add definition of
strcasestr if not defined. Solves compile problems on Cygwin.
* configure.in, src/config.h.in, configure: Check for
rpc/xdr.h needed for xtcformat.
* src/formats/xtcformat.cpp: Use new HAVE_RPC_XDR_H #define.
* src/formats/smilesformat.cpp: Bring back FIX format, killed
during merger of canonical and standard smiles.
* src/rotamer.cpp, src/locale.cpp, src/base.cpp,
include/openbabel/atom.h, include/openbabel/locale.h,
include/openbabel/forcefield.h,
include/openbabel/pointgroup.h,
include/openbabel/fingerprint.h: Doxygen updates for 2.2.0.
2008-07-02 Chris Morley
* src/descriptor.cpp(PredictandSave): don't duplicate an existing
OBPairData. Was crashing when adding a property that was already
present.
* src/formats/smilesformat.cpp(StandardLabels): A couple of vectors now
have 2147483647 pushed when the atom is H, to match the situation with
canonical ordering, rather than ending up with a size smaller than the
number of atoms. I assume 2147483647 = 2^31-1 is just a big number?
Fixes bug 1999348.
2008-07-01 Geoffrey Hutchison <[email protected]>
* src/kekulize.cpp (expandcycle): Add more flexible API for
expandcycle.
* scripts/perl/Makefile.PL: Update from Noel for PR#2007797.
* Makefile.*, configure.*: Update for 2.2.0 release.
2008-07-01 Tim Vandermeersch <[email protected]>
* src/formats/atomrecord.cpp: Fix bug where arginine hydrogen atoms
where read as dummy Xx atoms. (#2002557)
* src/formats/pdbformat.cpp: 1) Write the chain number. 2) Don't
rearrange atom ids when writing. (see chains item 2)
* src/chains.cpp: 1) Serine OG is now given the correct atom id.
2) produce correctly ordered atom ids (see pdbformat item 2)
3) fix for cyclic peptides (have no NTer)
4) water, ions and ligands are all placed in the ' ' chain now and get
unique residue numbers.
5) partially identified residues are merged with the atoms not used to
identify them and the resids is set to UNK (hetflags is also set to
true) (e.g. CSD in 1LWF = CYS with two O's on S )
2008-07-01 Noel O'Boyle <[email protected]>
* scripts/python/pybel.py: Make pybel use CloneData instead of SetData
2008-07-01 Noel O'Boyle <[email protected]>
* scripts/openbabel-python.i: Make the BFS Iterator return two values,
the Atom and the depth
2008-07-01 Chris Morley
* data/atomtyp.txt: remove IMPVAL entry for silicon to fix
bug #1911590. (I thought I had already done this.)
* windows-vc2005/babelconfig.h: add macro which apparently
disables native tr1 in recent VC++ 2008, so that boost version
will be used. Step towards getting tit to compile on this
platform but probably not there yet. Not critical for v2.2.0
release, since Windows compilation should be done from SVN.
2008-06-30 Geoffrey Hutchison <[email protected]>
* Makefile.am: Move cmake to EXTRA_DIST (4 Makefiles for one
file?)
* Makefile.in: Regenerated.
* include/openbabel/base.h, src/base.cpp: New CloneData()
method to solve PR#2004495 for scripting interfaces.
* src/Makefile.am, src/Makefile.in: Bump library version for
2.2 release.
* src/formats/smilesformat.cpp: Minor fix relating to
PR#1999348.
* src/patty.cpp, src/forcefield.cpp, src/oberror.cpp,
src/generic.cpp, src/canon.cpp, src/dlhandler_unix.cpp,
src/data.cpp, src/grid.cpp, src/mol.cpp: Minor fixes from
static code analysis. Test for empty() instead of size().
2008-06-30 Michael Banck <[email protected]>
* src/Makefile.am (EXTRA_DIST): Added config.h.cmake.
* src/Makefile.in: Regenerated.
* Makefile.am (SUBDIRS): Added cmake.
* Makefile.in: Regenerated.
* cmake/Makefile.am: New file.
* cmake/Makefile.in: New file.
* cmake/modules/Makefile.am: Likewise.
* cmake/modules/Makefile.in: Likewise.
* configure.in (AC_OUTPUT): Added cmake/Makefile and
cmake/modules/Makefile.
* configure: Regenerated.
* acinclude (AM_PATH_XML2): New macro, copied from aclocal.m4.
2008-06-29 Marcus D. Hanwell <[email protected]>
* include/openbabel/math/vector3.h,
include/openbabel/math/matrix3x3.h: Made the destructors non-virtual,
fixes Avogadro bug 2005984.
2008-06-27 Geoffrey Hutchison <[email protected]>
* include/openbabel/obiter.h, src/obiter.cpp: Fix
PR#1901348. Add support for BFS iteration from arbitrary
atoms.
* include/openbabel/math/*.h, src/math/*.cpp: Updates to fix
some GCC warnings.
* include/openbabel/bond.h, src/bond.cpp: Patch from Steven
Constable, PR#2004391. Adds SetLength() to move both atoms.
* include/openbabel/mol.h: Fix for ReserveAtoms() suggested by
Andrew Dalke.
* src/formats/mdlformat.cpp: Fix for SKP records, suggested by
Andrew.
* src/formats/pdbformat.cpp: Fix for CONECT records for atoms
with > 4 records (PR#1711154).
2008-06-26 Geoffrey Hutchison <[email protected]>
* src/parsmart.cpp: Add support for Isotopes in SMARTS. Fixes
PR#1987729.
* test/files/nci.smi: Add tests for matching isotopic
SMILES/SMARTS.
2008-06-23 Chris Morley
* test/inchiwrite.cpp: add -xn option so that the tests are done without
the 'recommended' InChI options. wInChI.exe is not yet available
for InChI 1.02. Needs revisting when it is.
* src/fingerprint.cpp(FastSearchIndexer): ensure fpid is terminated
when copied to guard against theoretical problem pointed out
by Andrew Dalke.
2008-06-21 Tim Vandermeersch <[email protected]>
* src/chains.cpp: Assign HOH and ligands to separate residues.
(#1774776)
2008-06-21 Tim Vandermeersch <[email protected]>
* src/formats/atomrecord.cpp: Keep original chain ID (#1760959).
2008-06-21 Carsten Niehaus <[email protected]>
* src/obutil.cpp: Typo fixes.
* src/forcefields/[forcefielduff.cpp,forcefieldmmff94.cpp]: Typo fixes
* src/formats/[mpdformat.cpp,xtcformat.cpp]: Typo fixes
* src/forcefields/*.h: Make ctor explicit.
2008-06-20 Geoffrey Hutchison <[email protected]>
* src/obutil.cpp (CartesianToInternal): Fix PR#1923896 for
Fenske-Hall z-matrix format. When looking for non-linear
atoms, don't pick non-bonded >10.0 Angstroms, which cause
problems with FH (and other) fixed format z-matrices.
* src/mol.cpp (ConnectTheDots): Fix for PR#1813502 for
existing bonds getting deleted by ConnectTheDots. Make sure to
preserve all original connections from PDB.
* src/formats/pdbformat.cpp (ReadMolecule): Fix for PR#1985681
with virtual bonds still built into a PDB file.
2008-06-20 Chris Morley
* include/openbabel/locale.h, src/locale.cpp: extra #includes
* windows-vc2005/babelconfig.h: define strdup. Version to 2.2.0
* include/openbabel/obiter.h: trivial change to avoid compiler warning
* src/fingerprints/finger3.cpp: do singel SMARTS match, as suggested by
Ernst-Georg Schmid
* windows-vc2005/OBError/OBError.vcproj: add locale.cpp
2008-06-20 Noel O'Boyle <[email protected]>
* Revert of r2347: I had set eol:native instead of eol-style native.
2008-06-19 Geoffrey Hutchison <[email protected]>
* src/fingerprint.cpp: Contribution from Andrew Dalke for
improved speed using GCC.
2008-06-18 Geoffrey Hutchison <[email protected]>
* include/openbabel/locale.h, src/locale.cpp: New OBLocale class
to centralize calls to setlocale/uselocale. Should solve strange
segfault on Linux with freelocale.
* include/openbabel/obiter.h, src/obiter.cpp: Add depth tracking
for DFS and BFS iterators. Addresses PR#1901348.
2008-06-18 Tim Vandermeersch <[email protected]>
* src/formats/*.cpp: Checked all files for their use of tokenize().
All added lines are like:
if (vs.size() < 1) return false; // timvdm 18/06/2008
* include/openbabel/obiter.h, src/obiter.cpp: Reimplement
FOR_PAIRS_OF_MOL. Do not build a list of all pairs in the constructor,
but find the pairs while iterating. This is faster and requires less
memory.
* include/openbabel/forcefield.cpp: Add SetParameterFile().
* src/forcefields/forcefieldmmff94.*: Use the new SetParameterFile().
Add a global definition for MMFF94s.
* data/*: Add MMFF94s parameters.
MMFF94s: Same functional form, only torsion and oop parameters are
different. To see the difference, you can try to minimize alanine with
both force fields, MMFF94s will give a planar nitrogen while MMFF94
will not.
2008-06-17 Noel O'Boyle <[email protected]>
* Reverted r2535 except for changes to scripts/perl/Makefile.PL
* scripts/openbabel-python.i: Updated SWIG interface file to ignore 21
methods of each std::vector created. This should substantially reduce
the size of the wrapper code.
2008-06-16 Tim Vandermeersch <[email protected]>
* src/formats/xtcformat.cpp: make confs a std::vector too. Was double
*confs = new double[natoms * 3].
2008-06-16 Chris Morley
* include/openbabel/oberror.h, src/oberror.cpp:
add a parameter to ThrowError to allow error messages to be
output only once (although they are all logged.). The default
behaviour is as at present.
* src/formats/inchiformat.cpp: default output uses the "recommended"
set of InChi options. -xn option uses no options as at present.
Add -xl option to output the InChI log - only once for multiple
molecules.
* include/openbabel/fingerprint.h, src/formats/fingerprintformat.cpp:
Make DescribeBits error message appear only once.
* src/mol.cpp(GetTitle): make variable title static to avoid returning
a pointer to a temporary variable. But this might cause problems with
multiple molecules unless the title is captured in the calling code
before getting the next. Until this is done properly, add a
test so that the problem can only occur with multi-line titles.
* src/formats/smilesformat.cpp: add option to output explicit hydrogen
form like [CH3][CH3].
**** The SMILES output currently crashes with Nc1nc(O)c2nc[nH]c2n1
but I haven't tracked this down.****
* src/ops/addpolarh.cpp: add simple op for Feature Request #1995162
* windows-vc2005/gen3D/gen3D.vcproj,
windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj: update
2008-06-15 Tim Vandermeersch <[email protected]>
* src/formats/cssrformat.cpp, src/formats/MCDLformat.cpp,
src/formats/mmcifformat.cpp, src/formats/balstformat.cpp,
src/formats/chemdrawcdx.cpp, src/formats/boxformat.cpp,
src/formats/unichemformat.cpp, src/formats/yasaraformat.cpp,
src/formats/zindoformat.cpp, src/formats/gromos96format.cpp,
src/formats/xedformat.cpp: sprintf --> snprintf
* src/chains.cpp, src/pointgroup.cpp, src/rotor.cpp: Some more sprintf
-> snprintf (I don't expect any problems here, but just in case...)
* include/openbabel/forcefield.cpp, src/forcefield.cpp,
src/forcefields/*: Replace sprintf(_logbuf, ...) with
snprintf(_logbuf, BUFF_SIZE).
2008-06-14 Tim Vandermeersch <[email protected]>
* include/openbabel/chain.h, src/chain.cpp: Replace:
1) malloc/free with new/delete
2) new T[n] with std::vector (where possible)
Original code still there as comments, can be removed once reviewed.
* src/parsmarts.cpp: Replace malloc/free with new/delete.
Replace realloc(array, size) with:
T *tmp = new T[size];
copy(array, array + old_size, tmp);
delete [] array;
array = tmp;
2005-06-14 Marcus D. Hanwell <[email protected]>
* src/formats/xtcformat.cpp: Some modifications to the xtc format to
use C++ structures.
* CMakeLists.txt, src/formats/CMakeLists.txt: Some build system
updates to build format plugins as modules.
* src/ops/loader.cpp: GCC 4.3 fix - cstdlib needed for free calls.
2008-06-14 Geoffrey Hutchison <[email protected]>
* include/openbabel/atom.h, src/atom.cpp: Add OBAtom::Duplcate()
which will copy everything except the internal index.
* include/openbabel/generic.h, src/generic.cpp: Add
OBUnitCell::FillUnitCell() method to create space-group-defined
atoms. Uses OBAtom::Duplicate.
2008-06-13 Tim Vandermeersch <[email protected]>
* include/openbabel/forcefield.cpp: Change GetGradient(..., int terms
= ...) to GetGradient(..., int /*terms*/ = ...). (comiler warning:
unused parameter).
* src/forcefields/*.cpp: Change i->Compute<gradients>() to i->template
Compute<gradients>().
* include/openbabel/builder.h, src/builder.cpp: Make most functions
static.
* src/mol.cpp: Use OBBuilder::GetNewBondVector() in AddHydrogens().
2005-06-13 Marcus D. Hanwell <[email protected]>
* src/formats/mdlformat.cpp: Use static_cast in the min function.
2008-06-13 Geoffrey Hutchison <[email protected]>
* src/typer.cpp: Add a special case for guanidinium carbon
atoms. (We may need additional special cases.)
* data/atomtyp.txt, data/atomtyp.h: Change pattern for N3+ to
match any 4-valent N, regardless of whether the formal charge has
been set.
* src/kekulize.cpp (NewPerceiveKekulizeBonds): Give up on
kekulization when we find "cycles" with < 3 atoms. Sybyl mol2
labels some atoms as aromatic that aren't in rings. Fixes
PR#1965566 and PR#1784204.
* include/openbabel/mol.h, src/mol.cpp (GetTitle): Add a parameter
to replace newlines with spaces. Fixes PR#1984742.
* configure.in: Check for xlocale.h, locale.h, and uselocale functions.
* src/data.cpp, src/ops/loader.cpp, src/ops/optransform.cpp,
src/descriptors/groupcontrib.cpp, src/builder.cpp,
src/forcefields/forcefieldmm2.cpp,
src/forcefields/forcefielduff.cpp,
src/forcefields/forcefieldmmff94.cpp,
src/forcefields/forcefieldghemical.cpp, src/obconversion.cpp:
Change locale using uselocale if available and reset it to the
afterwards. Update of previous change, suggested by Benoit.
* include/openbabel/bond.h, include/openbabel/atom.h,
src/bond.cpp: Fixes for "const" correctness. It's now possible to
get the bond length of a const OBBond.
2008-06-10 Geoffrey Hutchison <[email protected]>
* src/data.cpp, src/ops/loader.cpp, src/ops/optransform.cpp,
src/descriptors/groupcontrib.cpp, src/builder.cpp,
src/forcefields/forcefieldmm2.cpp,
src/forcefields/forcefielduff.cpp,
src/forcefields/forcefieldmmff94.cpp,
src/forcefields/forcefieldghemical.cpp, src/obconversion.cpp:
Change locale before parsing files to use "C" numeric locale and
reset it to the original state afterwards. Should solve PR#1785463.
* src/obiter.cpp: Fixes from Izhar for DFS and BFS iterators.
* src/mol.cpp, include/openbabel/mol.h: Added iterative
GetFragment method to augment Separate(), contributed by Izhar.
2008-06-07 Geoffrey Hutchison <[email protected]>
* src/phmodel.cpp (OBPhModel::CorrectForPH): Fix PR#1835204. Allow
SMILES to have pH-correction. (i.e., only check for automatic
formal charges for molecules with dimension > 0).
* src/formats/mdlformat.cpp: Add a check for EOF before reading,
as suggested by Izhar.
* src/formats/smilesformat.cpp: Add initial pass at "standard"
SMILES labels.
* Doxygen, include/*.h, src/*.cpp: Update doxygen documentation.
2008-06-07 Chris Morley
* src/formats/fingerprintformat.cpp: correct folding error message
and prevent description of bits when fingerprint is folded.
* src/formats/smilesformat.cpp: change -xc to -xa (for atomclass)
* windows-vc2005/OBFS/OBFS.vcproj,windows-vc2005/OpenBabelOBF.sln
add dependency of OBCommon to Fastsearch project
2008-06-06 Chris Morley
* src/formats/smilesformat.cpp: SMIFormat was being hidden because
its constructor was being called again when its derived class
CANSMIFormat was made. Now both derived from a base class with most
of the functionality.
Modified Description() and made same for both.
Removed DEFAULTFORMAT flag (MolFormat already is).
* include/openbabel/mol.h: add back #include <float.h> which was
somehow removed in the last commit and is need for Windows build.
* windows-vc2005/OBCommonFormats/OBCommonFormats.vcproj: remove
cansmilesformat.cpp
2008-06-06 Tim Vandermeersch <[email protected]>
* include/openbabel/phmodel.h, src/phmodel.cpp: Changes to OBPhModel,
use the Henderson-Hasselbalch formula to determine protonation states.
Updated doxygen documentation to give some info about the method.
* include/openbabel/mol.h, src/mol.cpp: Use it.
OBMol::AddHydrogens(bool polar=false, bool correctForPH=true, double
pH=7.4)
* data/phmodel.txt: Add extra column with pKa values.
* test/phmodel.cpp: Unit test for the new phmodel. The two errors are
Glutamate (4.0 used, should be 4.3) and Lysine (10.0 used, should be
10.1). I'll probably have to add a visited list so we can only
transform an atom once, transformations would then have to be ordered
by decreasing complexity. But the errors are very small and this is a
major improvement compared to what we had.
2008-06-05 Geoffrey Hutchison <[email protected]>
* scripts/openbabel-python*, scripts/python/*: Split the python
bindings into three pieces for improved compilation. Should solve
PR#1905826.
* src/obconversion.cpp: Add stdlib.h to hopefully solve
PR#1985717.
* configure.in, configure: Update to build libinchi by default.
* src/formats/smilesformat.cpp: Incorporate cansmilesformat
code. Now all SMILES export goes through Craig's cleaner,
less-buggy code. Currently all SMILES are canonically
ordered. Need to add code to provide non-canonical ordering for "regular."
* src/formats/Makefile.* src/formats/CMakeLists.txt: Update for above.
2008-06-05 Chris Morley
* src/obconversion.cpp(Convert): test for Cntl Z to terminate
commandline input rather than \n (a blank line).
Fixes bug 1984660: piping with titleless mol files.
Commandline data input always was clunky and is even clunkier now.
Being able to pipe is more important.
* src/forcefield.cpp:In line 2535 replace 'dafault:' by 'default:'
This may have a real effect and needs to be checked.
* include/openbabel/bitvec.h, src/canon.cpp,src/dlhandler_win32.cpp,
src/forcefield.cpp, src/formats/cansmilesformat.cpp,
src/formats/gamessformat.cpp, src/formats/gaussformat.cpp,
src/formats/KFReader.c,src/formats/mol2format.cpp,
src/formats/msmsformat.cpp, src/pointgroup.cpp,
src/tokenst.cpp:
Tidy to reduce compiler warnings: remove or comment out unreferenced
variables; size_t decalation replaces some int or unsigned;
!=NULL added to avoid implict const char* to bool conversion
* windows-vc2005/OBMoreFormats/OBMoreFormats.vcproj: change to
project build order as pointed out by peterennis bug #1985163
2008-06-04 Geoffrey Hutchison <[email protected]>
* src/formats/mopacformat.cpp: Fix for PR#1978982 with reading
Mopac 2007 force calculations.
* src/formats/atomrecord.cpp: Fix SetAtomID as reported in
PR#1838095. Thanks to Marc Lasson for bug report and fix.
* src/formats/adfformat.cpp, src/formats/Makefile.am: Add KFReader
and ArrayList code contributed under LGPL by SCM, Inc. for
improved ADF binary support.
2008-06-04 Chris Morley
* include/openbabel/mol.h: include float.h so that isinfinite
is handled properly in Windows
Deficiencies raised by Andrew Dalke
* src/fingerprint.cpp: Error message if attempting to fold to
less than size of unsigned int.
* src/formats/fingerprintformat.cpp(WriteMolecule) Error message
when parameter of -xN option (fold) is negative.
* src/formats/fastsearchformat.cpp(WriteChem Object):
Error message if more than one input file.
Delete the outputstream after deleting the index, which is when
it is written. Sometimes a fs file made without a specified name
was empty.
* tools/babel.cpp: change indentation on help text
* windows-vc2005/OpenBabelOBF.sln: another go at getting debug and
release configurations right. The scripting interfaces need to be
explicitly enabled before building if they are required. (I get
tired of waiting for them.)
2008-06-04 Geoffrey Hutchison <[email protected]>
* src/residue.cpp (GetResidueNumber): Fix bug reported by Izhar
Wallach.
* src/forcefields/forcefielduff.cpp: Fix error reported by Chris
Morley with Microsoft compiler -- don't duplicate loop variable names.
2008-06-03 Geoffrey Hutchison <[email protected]>
* data/atomtyp.txt, data/atomtyp.h: Add hybridization rules for
Si, Al, Ge, As, Se, and Te. (Atom typing and valence rules need to
be generalized.) Fixes problems with adding hydrogens to Si
uncovered in Avogadro.
2005-06-02 Marcus D. Hanwell <[email protected]>
* src/atom.cpp, src/mol.cpp: Added extra checks in AddHydrogens for
finite hydrogen coordinates. Also added some extra checks in the
GetNewBondVector function to check for sane numbers.
2008-06-02 Geoffrey Hutchison <[email protected]>
* Makefile.am, Makefile.in: Correct small automake typo with
"autoconf" libtool macro directory.
* configure: Regenerated using autogen.sh.
* include/openbabel/grid.h: Fix compiler warning -- make sure to
return values in all methods.
* src/forcefield.cpp: Fix compiler warning "default" not "dafault"
in switch statements.
* src/formats/qchemformat.cpp, src/formats/gamessformat.cpp,
src/formats/gaussformat.cpp, src/formats/fchkformat.cpp: Add
support for reading dipole moments using OBVectorData.
2008-06-01 Tim Vandermeersch <[email protected]>
* src/formats/atomrecord.cpp: Call OBAtom::ForceImplH() for all atoms.
Loading a pdb file and calling OBMol::AddHydrogens() added only on
hydrogen.
2005-05-31 Noel O'Boyle <[email protected]>
* scripts/openbabel-csharp.i: Fixed two of the three remaining
std::vectors based on examples found in Krugle code search
2005-05-30 Noel O'Boyle <[email protected]>
* scripts/openbabel-csharp.i: Fixed most of the std::vectors by using
weird macro described in std_vector.i in the SWIG distribution
2005-05-30 Marcus D. Hanwell <[email protected]>
* configure, configure.in: Stop the wx-config test being called when
the wx-gui is not enabled - bug 1979603.