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# Line 1 | Line 1
1 + 2011-09-14 16:49  thassine
2 +
3 +        * Makefile.in, autogen.sh, bin/Makefile.in, bin/amber/Makefile.in,
4 +          bin/builder/Makefile.in, bin/param_mm/Makefile.in,
5 +          bin/param_mm/default/Makefile.in,
6 +          bin/param_mm/prmfit/Makefile.in,
7 +          bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
8 +          bin/param_sf/default/Makefile.in, configure, po/LINGUAS,
9 +          po/Makefile.in, po/Makefile.in.in, po/de.po, src/Makefile.in,
10 +          src/libghemical-features.h, src/libghemicalconfig.h.in: add
11 +          german translation + configuration scripts updated.
12 +
13 + 2009-11-02 15:02  thassine
14 +
15 +        * po/LINGUAS, po/fi.po, po/ru.po: russian translation added.
16 +
17 + 2009-09-11 12:51  thassine
18 +
19 +        * configure, configure.ac, po/Makefile.in, src/Makefile.am,
20 +          src/Makefile.in, src/libghemical-features.h: version 2.99.1
21 +          released due to a missing file.
22 +
23 + 2009-09-04 12:41  thassine
24 +
25 +        * ChangeLog: ChangeLog update
26 +
27 + 2009-09-04 12:28  thassine
28 +
29 +        * configure, configure.ac, po/Makefile.in, src/Makefile.am,
30 +          src/Makefile.in, src/libghemical-features.h: release the version
31 +          2.99.1
32 +
33   2009-08-10 11:22  thassine
34  
35          * po/LINGUAS, po/pt_BR.po, src/libghemical-features.h: translation
# Line 26 | Line 58
58            src/engine.cpp, src/intcrd.cpp, src/mfinder.cpp, src/model.cpp,
59            src/pop_ana.cpp, src/sasaeval.cpp, src/sasaeval.h,
60            src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp,
61 <          src/typerule.cpp: added assertion_failed() method for fatal
62 <          error reporting.
61 >          src/typerule.cpp: added assertion_failed() method for fatal error
62 >          reporting.
63  
64   2008-12-09 10:41  thassine
65  
66          * INSTALL, po/Makefile.in, po/fi.po, src/atom.cpp, src/bond.cpp,
67            src/chn_info.cpp, src/conjgrad.cpp, src/eng1_mm.cpp,
68            src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
69 <          src/eng1_mm_tripos52.cpp, src/eng1_qm.cpp,
70 <          src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp,
71 <          src/engine.cpp, src/intcrd.cpp, src/libghemical-features.h,
72 <          src/mfinder.cpp, src/model.cpp, src/notice.cpp, src/notice.h,
73 <          src/pop_ana.cpp, src/sasaeval.cpp, src/sasaeval.h,
74 <          src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp,
75 <          src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp,
76 <          src/typerule.cpp, src/utility.cpp: translations added ; Vlado
45 <          Peshov.
69 >          src/eng1_mm_tripos52.cpp, src/eng1_qm.cpp, src/eng1_qm_mopac.cpp,
70 >          src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp, src/engine.cpp,
71 >          src/intcrd.cpp, src/libghemical-features.h, src/mfinder.cpp,
72 >          src/model.cpp, src/notice.cpp, src/notice.h, src/pop_ana.cpp,
73 >          src/sasaeval.cpp, src/sasaeval.h, src/search.cpp,
74 >          src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
75 >          src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp:
76 >          translations added ; Vlado Peshov.
77  
78   2008-11-26 11:03  thassine
79  
# Line 107 | Line 138
138   2008-07-31 10:06  thassine
139  
140          * configure, configure.ac, src/Makefile.am, src/Makefile.in,
141 <          src/libghemical-features.h, src/typedef.h: version number
142 <          changed to 2.98
141 >          src/libghemical-features.h, src/typedef.h: version number changed
142 >          to 2.98
143  
144   2008-07-31 07:59  thassine
145  
# Line 168 | Line 199
199          * src/atom.cpp, src/chn_info.cpp, src/eng1_mm.cpp,
200            src/eng1_qm_mopac.cpp, src/mfinder.cpp, src/model.cpp,
201            src/notice.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp,
202 <          src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp,
203 <          src/typerule.cpp, src/utility.cpp, src/win32_hacks.cpp: should
204 <          now compile with g++ v4.3
202 >          src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp,
203 >          src/utility.cpp, src/win32_hacks.cpp: should now compile with g++
204 >          v4.3
205  
206   2008-01-07 13:06  thassine
207  
# Line 181 | Line 212
212            src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp,
213            src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp,
214            src/eng1_mm_tripos52.h, src/eng1_qm.cpp, src/eng1_qm.h,
215 <          src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h,
216 <          src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp,
217 <          src/eng1_sf.h, src/eng1_sf_cg.cpp, src/eng1_sf_cg.h,
218 <          src/eng1_sf_ua.cpp, src/eng1_sf_ua.h, src/eng2_qm_mm.cpp,
219 <          src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/geomopt.cpp,
220 <          src/geomopt.h, src/intcrd.cpp, src/intcrd.h,
221 <          src/libghemicaldefine.h, src/mfinder.cpp, src/mfinder.h,
222 <          src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h,
223 <          src/notice.cpp, src/notice.h, src/pop_ana.cpp, src/pop_ana.h,
224 <          src/resonance.cpp, src/resonance.h, src/search.cpp,
225 <          src/search.h, src/seqbuild.cpp, src/seqbuild.h,
226 <          src/simple_test/example1.cpp, src/simple_test/example1.h,
227 <          src/simple_test/example2.cpp, src/simple_test/example2.h,
228 <          src/simple_test/example3.cpp, src/simple_test/example3.h,
229 <          src/simple_test/fileio.cpp, src/simple_test/streamio.cpp,
230 <          src/tab_mm_default.cpp, src/tab_mm_default.h,
200 <          src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h,
215 >          src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp,
216 >          src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h,
217 >          src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp,
218 >          src/eng1_sf_ua.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h,
219 >          src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h,
220 >          src/intcrd.cpp, src/intcrd.h, src/libghemicaldefine.h,
221 >          src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h,
222 >          src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h,
223 >          src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp,
224 >          src/resonance.h, src/search.cpp, src/search.h, src/seqbuild.cpp,
225 >          src/seqbuild.h, src/simple_test/example1.cpp,
226 >          src/simple_test/example1.h, src/simple_test/example2.cpp,
227 >          src/simple_test/example2.h, src/simple_test/example3.cpp,
228 >          src/simple_test/example3.h, src/simple_test/fileio.cpp,
229 >          src/simple_test/streamio.cpp, src/tab_mm_default.cpp,
230 >          src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h,
231            src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h,
232 <          src/typerule.cpp, src/typerule.h, src/utility.cpp,
233 <          src/utility.h, src/v3d.h, src/win32_hacks.cpp,
234 <          src/win32_hacks.h: copyright notice update
232 >          src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h,
233 >          src/v3d.h, src/win32_hacks.cpp, src/win32_hacks.h: copyright
234 >          notice update
235  
236   2008-01-07 11:28  thassine
237  
# Line 258 | Line 288
288   2007-02-13 08:22  thassine
289  
290          * bin/builder/amino.txt, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
291 <          src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp,
292 <          src/engine.cpp, src/engine.h, src/model.cpp, src/model.h,
293 <          src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp,
294 <          src/tab_mm_default.h, src/tab_mm_prmfit.cpp,
295 <          src/tab_mm_prmfit.h, src/tab_mm_tripos52.cpp,
296 <          src/tab_mm_tripos52.h: changes in seq-builder and in engine
267 <          classes.
291 >          src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/engine.cpp,
292 >          src/engine.h, src/model.cpp, src/model.h, src/search.cpp,
293 >          src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h,
294 >          src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h,
295 >          src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h: changes in
296 >          seq-builder and in engine classes.
297  
298   2007-02-01 13:16  thassine
299  
# Line 275 | Line 304
304   2007-01-30 09:12  thassine
305  
306          * src/atom.h, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
307 <          src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp,
308 <          src/intcrd.cpp, src/mfinder.cpp, src/model.cpp, src/model.h,
309 <          src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp,
310 <          src/typerule.cpp, src/utility.cpp: atom::cr_list is protected
311 <          now ; model::UpdateChains() may ask nucl-acid detection skipped.
307 >          src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/intcrd.cpp,
308 >          src/mfinder.cpp, src/model.cpp, src/model.h, src/seqbuild.cpp,
309 >          src/seqbuild.h, src/tab_mm_default.cpp, src/typerule.cpp,
310 >          src/utility.cpp: atom::cr_list is protected now ;
311 >          model::UpdateChains() may ask nucl-acid detection skipped.
312  
313   2007-01-25 10:17  thassine
314  
# Line 377 | Line 406
406            src/tab_mm_default.cpp, src/tab_mm_default.h,
407            src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h,
408            src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h,
409 <          src/typerule.cpp, src/typerule.h, src/utility.cpp,
410 <          src/utility.h: libghemical-features.h implemented (thanks to
382 <          Jean Brefort).
409 >          src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h:
410 >          libghemical-features.h implemented (thanks to Jean Brefort).
411  
412   2006-10-19 12:16  thassine
413  
# Line 512 | Line 540
540   2006-03-10 12:12  thassine
541  
542          * src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h,
543 <          src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.cpp,
544 <          src/model.h: added a mopac/mpqc patch (Jean Br�fort), and a new
545 <          Orient() method.
543 >          src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.cpp, src/model.h:
544 >          added a mopac/mpqc patch (Jean Br�fort), and a new Orient()
545 >          method.
546  
547   2006-03-08 10:33  thassine
548  
# Line 552 | Line 580
580  
581   2006-03-03 12:56  thassine
582  
583 <        * aclocal.m4, src/atom.cpp, src/atom.h: added Donald's freezed
584 <          atom changes.
583 >        * aclocal.m4, src/atom.cpp, src/atom.h: added Donald's freezed atom
584 >          changes.
585  
586   2006-03-03 12:24  thassine
587  
588          * ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, bin,
589 <          bin/.cvsignore, bin/Makefile.in, bin/amber,
590 <          bin/amber/.cvsignore, bin/amber/Makefile.in, bin/builder,
591 <          bin/builder/.cvsignore, bin/builder/Makefile.in, bin/param_mm,
592 <          bin/param_mm/.cvsignore, bin/param_mm/Makefile.in,
593 <          bin/param_mm/default, bin/param_mm/default/.cvsignore,
589 >          bin/.cvsignore, bin/Makefile.in, bin/amber, bin/amber/.cvsignore,
590 >          bin/amber/Makefile.in, bin/builder, bin/builder/.cvsignore,
591 >          bin/builder/Makefile.in, bin/param_mm, bin/param_mm/.cvsignore,
592 >          bin/param_mm/Makefile.in, bin/param_mm/default,
593 >          bin/param_mm/default/.cvsignore,
594            bin/param_mm/default/Makefile.in, bin/param_mm/prmfit,
595            bin/param_mm/prmfit/.cvsignore, bin/param_mm/prmfit/Makefile.in,
596            bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore,
597            bin/param_mm/tripos52/Makefile.in, bin/param_sf,
598            bin/param_sf/.cvsignore, bin/param_sf/Makefile.in,
599            bin/param_sf/default, bin/param_sf/default/.cvsignore,
600 <          bin/param_sf/default/Makefile.in, configure, src,
601 <          src/.cvsignore, src/Makefile.in, src/eng1_mm.cpp,
602 <          src/eng1_mm_default.cpp, src/engine.cpp, src/engine.h,
603 <          src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h: many
604 <          changes ; especially at mol.dyn. code ; autogen.sh added
600 >          bin/param_sf/default/Makefile.in, configure, src, src/.cvsignore,
601 >          src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
602 >          src/engine.cpp, src/engine.h, src/model.cpp, src/model.h,
603 >          src/moldyn.cpp, src/moldyn.h: many changes ; especially at
604 >          mol.dyn. code ; autogen.sh added
605  
606   2006-03-01 12:15  thassine
607  
# Line 595 | Line 623
623  
624   2006-02-27 11:25  thassine
625  
626 <        * aclocal.m4, src/eng1_mm.cpp, src/eng1_qm_mpqc.cpp,
627 <          src/model.cpp, src/search.cpp, src/tab_mm_prmfit.cpp: tried to
628 <          do a bit safer stringstream code ; only take the c_str out for
629 <          copying into a buffer or for passing as a parameter.
626 >        * aclocal.m4, src/eng1_mm.cpp, src/eng1_qm_mpqc.cpp, src/model.cpp,
627 >          src/search.cpp, src/tab_mm_prmfit.cpp: tried to do a bit safer
628 >          stringstream code ; only take the c_str out for copying into a
629 >          buffer or for passing as a parameter.
630  
631   2006-02-27 08:29  thassine
632  
# Line 630 | Line 658
658            src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
659            src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp,
660            src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/model.cpp,
661 <          src/moldyn.cpp, src/notice.cpp, src/search.cpp,
662 <          src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
663 <          src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp:
664 <          * src/*.cpp: Update to use stringstream and <sstream> headers
637 <          --
661 >          src/moldyn.cpp, src/notice.cpp, src/search.cpp, src/seqbuild.cpp,
662 >          src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
663 >          src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp: *
664 >          src/*.cpp: Update to use stringstream and <sstream> headers --
665            fixes backwards-compatibility warnings using GCC.
666  
667   2006-02-17 16:18  hutchisn
# Line 651 | Line 678
678            
679            * aclocal.m4, config.guess, config.sub, configure
680            depcomp, install-sh, ltmain.sh, missing, mkinstalldirs
681 <          */Makefile.in: Update with latest automake (1.9.6),
682 <          libtool (1.5.22).
681 >          */Makefile.in: Update with latest automake (1.9.6), libtool
682 >          (1.5.22).
683  
684   2006-02-16 09:20  thassine
685  
# Line 671 | Line 698
698            src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
699            src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp,
700            src/libghemicalconfig.h.in, src/model.cpp, src/pop_ana.cpp,
701 <          src/seqbuild.cpp, src/seqbuild.h, src/typedef.h,
702 <          src/utility.cpp, src/utility.h, src/v3d.h: many changes...
701 >          src/seqbuild.cpp, src/seqbuild.h, src/typedef.h, src/utility.cpp,
702 >          src/utility.h, src/v3d.h: many changes...
703  
704   2006-02-07 12:44  thassine
705  
# Line 707 | Line 734
734            src/libghemicaldefine.h, src/model.cpp, src/model.h,
735            src/notice.cpp, src/notice.h, src/seqbuild.cpp, src/seqbuild.h,
736            src/tab_mm_default.h, src/tab_mm_tripos52.h, src/typedef.h,
737 <          src/typerule.cpp, src/typerule.h, src/utility.cpp,
738 <          src/utility.h: libdefine.h was renamed to libghemicaldefine.h
737 >          src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h:
738 >          libdefine.h was renamed to libghemicaldefine.h
739  
740   2005-12-14 14:10  thassine
741  
# Line 722 | Line 749
749  
750          * src/atom.h, src/geomopt.cpp, src/model.cpp, src/moldyn.cpp,
751            src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
752 <          src/tab_mm_tripos52.cpp: some changes in the atom flags ; need
753 <          to separate the user/system level hidden atoms.
752 >          src/tab_mm_tripos52.cpp: some changes in the atom flags ; need to
753 >          separate the user/system level hidden atoms.
754  
755   2005-11-17 12:31  thassine
756  
# Line 757 | Line 784
784            bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
785            bin/param_sf/default/Makefile.in, config.guess, config.sub,
786            configure, configure.ac, ltmain.sh, src, src/.cvsignore,
787 <          src/Makefile.in: * configure.ac, configure: Update to
788 <          use openbabel-2.0 check,
787 >          src/Makefile.in: * configure.ac, configure: Update to use
788 >          openbabel-2.0 check,
789            rather than openbabel.
790            
791 <          * ltmain.sh, aclocal.m4, */Makefile.in: Update with
765 <          latest
791 >          * ltmain.sh, aclocal.m4, */Makefile.in: Update with latest
792            autoconf, libtool (1.5.20).
793  
794   2005-10-08 15:12  thassine
# Line 774 | Line 800
800            bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
801            bin/param_sf/default/Makefile.in, configure, configure.ac,
802            src/Makefile.in, src/atom.cpp, src/atom.h, src/libdefine.h,
803 <          src/libghemicalconfig.h.in: OpenGL bugfixes on 64-bit platforms
804 <          ; just a new value stored in atom objects
803 >          src/libghemicalconfig.h.in: OpenGL bugfixes on 64-bit platforms ;
804 >          just a new value stored in atom objects
805  
806   2005-09-26 08:46  thassine
807  
# Line 801 | Line 827
827            bin/param_mm/prmfit/Makefile.in,
828            bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
829            bin/param_sf/default/Makefile.in, configure, configure.ac,
830 <          depcomp, src/Makefile.am, src/Makefile.in,
831 <          src/eng1_qm_mopac.cpp, src/search.h, src/seqbuild.cpp,
832 <          src/seqbuild.h: now depends on mopac7-1.10 ; also other smaller
807 <          changes here and there.
830 >          depcomp, src/Makefile.am, src/Makefile.in, src/eng1_qm_mopac.cpp,
831 >          src/search.h, src/seqbuild.cpp, src/seqbuild.h: now depends on
832 >          mopac7-1.10 ; also other smaller changes here and there.
833  
834   2005-07-06 08:59  thassine
835  
# Line 843 | Line 868
868            src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/intcrd.h,
869            src/libdefine.h, src/model.h, src/moldyn.h, src/notice.h,
870            src/pop_ana.h, src/resonance.h, src/search.h, src/seqbuild.h,
871 <          src/tab_mm_default.h, src/tab_mm_prmfit.h,
872 <          src/tab_mm_tripos52.h, src/typedef.h, src/utility.cpp,
873 <          src/utility.h, src/v3d.h: some last-minute changes before
849 <          release.
871 >          src/tab_mm_default.h, src/tab_mm_prmfit.h, src/tab_mm_tripos52.h,
872 >          src/typedef.h, src/utility.cpp, src/utility.h, src/v3d.h: some
873 >          last-minute changes before release.
874  
875   2005-07-01 10:49  thassine
876  
# Line 934 | Line 958
958   2005-05-03 12:12  thassine
959  
960          * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp,
961 <          src/eng1_sf.cpp, src/model.cpp: some bugfixes added for
962 <          solvation functions.
961 >          src/eng1_sf.cpp, src/model.cpp: some bugfixes added for solvation
962 >          functions.
963  
964   2005-04-28 10:17  thassine
965  
# Line 952 | Line 976
976  
977   2005-04-22 13:41  thassine
978  
979 <        * Makefile.in, aclocal.m4, src/model.h: some class names changed
980 <          in the app ; sync here.
979 >        * Makefile.in, aclocal.m4, src/model.h: some class names changed in
980 >          the app ; sync here.
981  
982   2005-04-21 12:24  thassine
983  
# Line 1006 | Line 1030
1030            configure, configure.in, ltmain.sh, src/Makefile.am,
1031            src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm.h,
1032            src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/engine.h,
1033 <          src/libconfig.h.in, src/model.h: ported the tripos5.2 force
1034 <          field implementation from ghemical-1.01 into libghemical.
1033 >          src/libconfig.h.in, src/model.h: ported the tripos5.2 force field
1034 >          implementation from ghemical-1.01 into libghemical.
1035  
1036   2005-04-08 14:59  thassine
1037  
# Line 1034 | Line 1058
1058  
1059   2005-01-04 11:28  thassine
1060  
1061 <        * aclocal.m4, src/engine.cpp, src/engine.h, src/moldyn.cpp: added
1062 <          a new virtual method DoSHAKE() in engine class.
1061 >        * aclocal.m4, src/engine.cpp, src/engine.h, src/moldyn.cpp: added a
1062 >          new virtual method DoSHAKE() in engine class.
1063  
1064   2004-12-10 15:14  thassine
1065  
# Line 1046 | Line 1070
1070   2004-09-13 09:17  thassine
1071  
1072          * Makefile.in, src/atom.cpp, src/atom.h, src/eng1_sf.h,
1073 <          src/model.cpp: the atom objects now are aware of the model
1074 <          object ; added some stuff to make everything compile.
1073 >          src/model.cpp: the atom objects now are aware of the model object
1074 >          ; added some stuff to make everything compile.
1075  
1076   2004-08-30 09:28  thassine
1077  
# Line 1058 | Line 1082
1082   2004-08-27 12:07  thassine
1083  
1084          * Makefile.am, Makefile.in, aclocal.m4, libghemical.pc.in,
1085 <          src/Makefile.am, src/Makefile.in: changed includedir to
1086 <          /ghemical and some other changes ; .pc file not updated?
1085 >          src/Makefile.am, src/Makefile.in: changed includedir to /ghemical
1086 >          and some other changes ; .pc file not updated?
1087  
1088   2004-08-26 12:34  thassine
1089  
# Line 1128 | Line 1152
1152  
1153   2004-03-26 09:05  thassine
1154  
1155 <        * src/bond.cpp, src/bond.h, src/model.cpp, src/model.h: added a
1156 <          new GetRange() method for bonds in model class.
1155 >        * src/bond.cpp, src/bond.h, src/model.cpp, src/model.h: added a new
1156 >          GetRange() method for bonds in model class.
1157  
1158   2004-03-18 12:04  thassine
1159  
# Line 1177 | Line 1201
1201            bin/param_mm/prmfit/parameters2.txt,
1202            bin/param_mm/prmfit/parameters3.txt,
1203            bin/param_mm/prmfit/parameters4.txt, configure, configure.in,
1204 <          src/Makefile.in, src/atom.cpp, src/atom.h,
1205 <          src/eng1_qm_mopac.cpp, src/miniMOPAC, src/model.cpp,
1206 <          src/model.h: remove the mopac sources ; moved into a separate
1183 <          library.
1204 >          src/Makefile.in, src/atom.cpp, src/atom.h, src/eng1_qm_mopac.cpp,
1205 >          src/miniMOPAC, src/model.cpp, src/model.h: remove the mopac
1206 >          sources ; moved into a separate library.
1207  
1208   2003-11-06 11:59  thassine
1209  
# Line 1197 | Line 1220
1220  
1221   2003-09-01 09:25  thassine
1222  
1223 <        * src/engine.cpp, src/engine.h, src/model.cpp, src/search.cpp:
1224 <          some bugfixes added.
1223 >        * src/engine.cpp, src/engine.h, src/model.cpp, src/search.cpp: some
1224 >          bugfixes added.
1225  
1226   2003-08-29 07:39  thassine
1227  
# Line 1211 | Line 1234
1234            bin/param_mm/prmfit/parameters1.txt,
1235            bin/param_mm/prmfit/parameters2.txt,
1236            bin/param_mm/prmfit/parameters3.txt,
1237 <          bin/param_mm/prmfit/parameters4.txt: added a new set of
1238 <          mol.mech. parameters for testing ; less default force constants
1239 <          than in the prev. one.
1237 >          bin/param_mm/prmfit/parameters4.txt: added a new set of mol.mech.
1238 >          parameters for testing ; less default force constants than in the
1239 >          prev. one.
1240  
1241   2003-08-21 09:09  thassine
1242  
# Line 1306 | Line 1329
1329  
1330   2003-06-17 12:53  thassine
1331  
1332 <        * src/typerule.cpp: bugfixes added to the typerule class ; the
1333 <          next rule was not checked in many cases earlier.
1332 >        * src/typerule.cpp: bugfixes added to the typerule class ; the next
1333 >          rule was not checked in many cases earlier.
1334  
1335   2003-06-13 10:15  thassine
1336  
1337          * AUTHORS, acconfig.h, src/Doxyfile, src/eng1_sf.h, src/geomopt.h,
1338 <          src/model.cpp, src/model.h, src/moldyn.h, src/seqbuild.cpp:
1339 <          added more checks where/how the atom_list is sorted. that is
1340 <          important because sorting atom_list may change atom numbering
1341 <          (problem for example TSS).
1338 >          src/model.cpp, src/model.h, src/moldyn.h, src/seqbuild.cpp: added
1339 >          more checks where/how the atom_list is sorted. that is important
1340 >          because sorting atom_list may change atom numbering (problem for
1341 >          example TSS).
1342  
1343   2003-06-12 12:53  thassine
1344  
# Line 1325 | Line 1348
1348  
1349   2003-06-11 10:40  thassine
1350  
1351 <        * src/conjgrad.cpp, src/conjgrad.h, src/eng1_qm.cpp,
1352 <          src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/engine.h,
1353 <          src/geomopt.cpp, src/geomopt.h, src/model.cpp, src/search.cpp,
1354 <          src/search.h, src/utility.cpp: added transition_state_search and
1351 >        * src/conjgrad.cpp, src/conjgrad.h, src/eng1_qm.cpp, src/eng1_qm.h,
1352 >          src/eng1_qm_mopac.cpp, src/engine.h, src/geomopt.cpp,
1353 >          src/geomopt.h, src/model.cpp, src/search.cpp, src/search.h,
1354 >          src/utility.cpp: added transition_state_search and
1355            stationary_state_search + many related changes here and there.
1356            still need to do some testing, and after that add docs in
1357            user-docs and some example molecules.
# Line 1346 | Line 1369
1369   2003-06-02 15:20  thassine
1370  
1371          * src/eng1_mm.cpp, src/eng1_mm_prmfit.h, src/tab_mm_default.cpp,
1372 <          src/tab_mm_default.h, src/tab_mm_prmfit.cpp,
1373 <          src/tab_mm_prmfit.h: some changes in output at force fields and
1351 <          tabs.
1372 >          src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h:
1373 >          some changes in output at force fields and tabs.
1374  
1375   2003-06-02 14:29  thassine
1376  
# Line 1372 | Line 1394
1394  
1395   2003-05-16 10:20  thassine
1396  
1397 <        * bin/param_mm/default/parameters6.txt: changes to MM force field
1398 <          ; added one input file.
1397 >        * bin/param_mm/default/parameters6.txt: changes to MM force field ;
1398 >          added one input file.
1399  
1400   2003-05-16 10:19  thassine
1401  
# Line 1381 | Line 1403
1403            bin/param_mm/default/parameters5.txt, src/eng1_mm_default.cpp,
1404            src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp,
1405            src/eng1_mm_prmfit.h, src/model.cpp, src/tab_mm_default.cpp,
1406 <          src/tab_mm_default.h, src/tab_mm_prmfit.cpp,
1407 <          src/tab_mm_prmfit.h: changes to MM force field ; need to make it
1386 <          AMBER-compatible.
1406 >          src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h:
1407 >          changes to MM force field ; need to make it AMBER-compatible.
1408  
1409   2003-05-12 09:11  thassine
1410  
# Line 1400 | Line 1421
1421  
1422          * bin/param_mm/default/parameters5.txt, src/atom.cpp, src/atom.h,
1423            src/eng1_mm.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h:
1424 <          added an option to molecular mechanics, so that one can use
1425 <          AMBER forcefield charges/parameters for amino/nucleic acids.
1426 <          charges are OK now but other params not yet added. the option is
1427 <          very nifty about correctness of topology, but that will be fixed
1424 >          added an option to molecular mechanics, so that one can use AMBER
1425 >          forcefield charges/parameters for amino/nucleic acids. charges
1426 >          are OK now but other params not yet added. the option is very
1427 >          nifty about correctness of topology, but that will be fixed
1428            later.
1429  
1430   2003-04-17 07:34  thassine
1431  
1432          * src/model.cpp, src/seqbuild.cpp: setup objects were not deleted,
1433 <          causing MOPAC to leave some files around and also memory
1434 <          leaking; fixed now.
1433 >          causing MOPAC to leave some files around and also memory leaking;
1434 >          fixed now.
1435  
1436   2003-04-16 13:43  thassine
1437  
# Line 1441 | Line 1462
1462          * bin/amber, bin/amber/README, bin/amber/all_amino02.in,
1463            bin/amber/all_aminoct02.in, bin/amber/all_aminont02.in,
1464            bin/amber/all_nuc02.in, bin/amber/parm99.dat,
1465 <          bin/builder/amino.txt, bin/builder/nucleic.txt:
1466 <          changes/additions in data files.
1465 >          bin/builder/amino.txt, bin/builder/nucleic.txt: changes/additions
1466 >          in data files.
1467  
1468   2003-04-02 06:12  thassine
1469  
# Line 1460 | Line 1481
1481  
1482   2003-03-17 10:11  thassine
1483  
1484 <        * src/model.cpp, src/moldyn.cpp, src/moldyn.h: a bugfix for
1485 <          ribbons added, and some changes in moldyn.
1484 >        * src/model.cpp, src/moldyn.cpp, src/moldyn.h: a bugfix for ribbons
1485 >          added, and some changes in moldyn.
1486  
1487   2003-03-12 07:19  thassine
1488  
# Line 1505 | Line 1526
1526            src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h,
1527            src/eng1_mm_prmfit.h, src/eng1_sf.cpp, src/eng1_sf.h,
1528            src/eng2_mm_sf.cpp, src/eng2_qm_mm.cpp, src/engine.cpp,
1529 <          src/engine.h, src/model.cpp, src/model.h,
1530 <          src/tab_mm_default.cpp: make separate subclasses for
1531 <          boundary-potential and periodic-boundary eng-classes; also some
1511 <          comments added etc.
1529 >          src/engine.h, src/model.cpp, src/model.h, src/tab_mm_default.cpp:
1530 >          make separate subclasses for boundary-potential and
1531 >          periodic-boundary eng-classes; also some comments added etc.
1532  
1533   2003-02-06 14:50  thassine
1534  
# Line 1526 | Line 1546
1546          * bin/param_mm/default/parameters5.txt, src/eng1_mm.cpp,
1547            src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
1548            src/model.cpp, src/model.h, src/moldyn.cpp,
1549 <          src/tab_mm_default.cpp: some changes to MM force field
1550 <          parameters (for H2O) and some important bugfixes in MM
1551 <          connectivity records code; this will affect nonbonded
1532 <          interactions.
1549 >          src/tab_mm_default.cpp: some changes to MM force field parameters
1550 >          (for H2O) and some important bugfixes in MM connectivity records
1551 >          code; this will affect nonbonded interactions.
1552  
1553   2003-01-31 12:24  thassine
1554  
1555          * src/engine.cpp, src/geomopt.cpp, src/model.h, src/moldyn.cpp,
1556            src/utility.cpp, src/utility.h: many bugfixes added; it is
1557 <          important to note that model::GetAtomCount() may now be
1558 <          different from engine::GetAtomCount().
1557 >          important to note that model::GetAtomCount() may now be different
1558 >          from engine::GetAtomCount().
1559  
1560   2003-01-31 09:25  thassine
1561  
# Line 1562 | Line 1581
1581            src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp,
1582            src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp,
1583            src/model.h: many changes in the way how data is stored in
1584 <          different models; compiles but SF-stuff does not work yet; QM
1585 <          and MM should work.
1584 >          different models; compiles but SF-stuff does not work yet; QM and
1585 >          MM should work.
1586  
1587   2003-01-27 13:43  thassine
1588  
# Line 1694 | Line 1713
1713            src/miniMOPAC/dijkl1.c, src/miniMOPAC/dijkl2.c,
1714            src/miniMOPAC/dipind.c, src/miniMOPAC/dipole.c,
1715            src/miniMOPAC/dlaswp.c, src/miniMOPAC/dofs.c,
1716 <          src/miniMOPAC/dot.c, src/miniMOPAC/drc.c,
1717 <          src/miniMOPAC/drcout.c, src/miniMOPAC/dtrmm.c,
1718 <          src/miniMOPAC/dtrmv.c, src/miniMOPAC/dtrsm.c,
1719 <          src/miniMOPAC/dtrti2.c, src/miniMOPAC/dtrtri.c,
1720 <          src/miniMOPAC/dvfill.c, src/miniMOPAC/ef.c,
1702 <          src/miniMOPAC/enpart.c, src/miniMOPAC/esp.c,
1716 >          src/miniMOPAC/dot.c, src/miniMOPAC/drc.c, src/miniMOPAC/drcout.c,
1717 >          src/miniMOPAC/dtrmm.c, src/miniMOPAC/dtrmv.c,
1718 >          src/miniMOPAC/dtrsm.c, src/miniMOPAC/dtrti2.c,
1719 >          src/miniMOPAC/dtrtri.c, src/miniMOPAC/dvfill.c,
1720 >          src/miniMOPAC/ef.c, src/miniMOPAC/enpart.c, src/miniMOPAC/esp.c,
1721            src/miniMOPAC/etime.c, src/miniMOPAC/exchng.c,
1722            src/miniMOPAC/fdate.c, src/miniMOPAC/ffhpol.c,
1723            src/miniMOPAC/flepo.c, src/miniMOPAC/fmat.c,
# Line 1831 | Line 1849
1849            src/notice.h, src/search.cpp, src/search.h, src/seqbuild.cpp,
1850            src/seqbuild.h, src/tab_mm_default.cpp, src/tab_mm_default.h,
1851            src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typedef.h,
1852 <          src/typerule.cpp, src/typerule.h, src/utility.cpp,
1853 <          src/utility.h, src/v3d.h: Initial revision
1852 >          src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h,
1853 >          src/v3d.h: Initial revision
1854  
1855   2003-01-20 08:38  
1856  
1857 <        * branches, tags, .: New repository initialized by cvs2svn.
1857 >        * .: New repository initialized by cvs2svn.
1858  

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