2006-07-31  thassine

	* src/project.cpp: seqbuild code changed at libghemical

2006-07-24  thassine

	* configure.ac, src/gtk_project_view.cpp, src/project.cpp: adapted
	  to changes at libghemical side.

2006-07-21  dcurtis3

	* src/main.cpp: Moved the #include for ghemicalconfig.h so that it
	  is before the #define tests. More "proper" than assuming it
	  gets included by other headers.
	* src/gamess_dialog.cpp, src/gamess_dialog.h: Previous update was
	  ignoring all code because there was no #import of the
	  ghemicalconfig2.h file so as far as these source files were
	  concerned there was never any definition.

2006-07-12  thassine

	* src/gamess_dialog.cpp, src/gamess_dialog.h: added some missing
	  ENABLE_GAMESS macros

2006-07-11  dcurtis3

	* src/efp_dialog.cpp, src/efp_dialog.h, src/gamess.cpp,
	  src/gamess.h, src/gamess_dialog.cpp, src/gamess_dialog.h,
	  src/gtk_project.cpp, src/gtk_project_view.cpp,
	  src/gtk_project_view.h: EFP Changes to GAMESS Extension!

2006-06-13  dcurtis3

	* src/gamess_dialog.cpp:

2006-06-06  dcurtis3

	* src/gamess.cpp, src/gamess.h, src/gamess_dialog.cpp,
	  src/gamess_dialog.h: Added EFP Input Deck Generation!

2006-06-06  thassine

	* src/views.cpp: added a fix for 64-bit compilers.

2006-06-05  hutchisn

	* examples/TSS, examples/TSS/E2-reaction,
	  examples/TSS/SN2-reaction,
	  examples/TSS/carbocation_rearrangement_hydride_shift,
	  examples/TSS/carbocation_rearrangement_methide_shift,
	  examples/TSS/cycloaddition_Diels-Alder,
	  examples/TSS/sigmatropic_rearrangement_Cope,
	  examples/TSS/tautomeric_shift_keto_enol, src/pixmaps: Added
	  Makefiles to svn:ignore properties
	* examples/TSS, examples/TSS/E2-reaction,
	  examples/TSS/E2-reaction/Makefile.am,
	  examples/TSS/E2-reaction/products.gpr,
	  examples/TSS/E2-reaction/reactants.gpr,
	  examples/TSS/E2-reaction/ts.gpr, examples/TSS/Makefile.am,
	  examples/TSS/README, examples/TSS/SN2-reaction,
	  examples/TSS/SN2-reaction/Makefile.am,
	  examples/TSS/SN2-reaction/products.gpr,
	  examples/TSS/SN2-reaction/reactants.gpr,
	  examples/TSS/SN2-reaction/ts.gpr,
	  examples/TSS/carbocation_rearrangement_hydride_shift,
	  examples/TSS/carbocation_rearrangement_hydride_shift/Makefile.am,
	  
	  examples/TSS/carbocation_rearrangement_hydride_shift/products.gpr,
	  
	  examples/TSS/carbocation_rearrangement_hydride_shift/reactants.gpr,
	  examples/TSS/carbocation_rearrangement_hydride_shift/ts.gpr,
	  examples/TSS/carbocation_rearrangement_methide_shift,
	  examples/TSS/carbocation_rearrangement_methide_shift/Makefile.am,
	  
	  examples/TSS/carbocation_rearrangement_methide_shift/products.gpr,
	  
	  examples/TSS/carbocation_rearrangement_methide_shift/reactants.gpr,
	  examples/TSS/carbocation_rearrangement_methide_shift/ts.gpr,
	  examples/TSS/cycloaddition_Diels-Alder,
	  examples/TSS/cycloaddition_Diels-Alder/Makefile.am,
	  examples/TSS/cycloaddition_Diels-Alder/products.gpr,
	  examples/TSS/cycloaddition_Diels-Alder/reactants.gpr,
	  examples/TSS/cycloaddition_Diels-Alder/ts.gpr,
	  examples/TSS/sigmatropic_rearrangement_Cope,
	  examples/TSS/sigmatropic_rearrangement_Cope/Makefile.am,
	  examples/TSS/sigmatropic_rearrangement_Cope/products.gpr,
	  examples/TSS/sigmatropic_rearrangement_Cope/reactants.gpr,
	  examples/TSS/sigmatropic_rearrangement_Cope/ts.gpr,
	  examples/TSS/tautomeric_shift_keto_enol,
	  examples/TSS/tautomeric_shift_keto_enol/Makefile.am,
	  examples/TSS/tautomeric_shift_keto_enol/products.gpr,
	  examples/TSS/tautomeric_shift_keto_enol/reactants.gpr,
	  examples/TSS/tautomeric_shift_keto_enol/ts.gpr: Add back missing
	  example files, accidentally deleted in SVN->CVS migration.

2006-06-01  dcurtis3

	* Makefile.am, src/Makefile.am, src/efp_dialog.cpp,
	  src/efp_dialog.glade, src/efp_dialog.h, src/gamess.cpp,
	  src/gamess.h, src/gtk_graphics_view.cpp, src/gtk_project.cpp,
	  src/gtk_project.h, src/gtk_project_view.cpp,
	  src/gtk_project_view.h, src/main.cpp, src/project.cpp,
	  src/project.h, src/views.h: Added ability to define GAMESS EFP
	  information.
	  TODO: Need to fix the compilation without gamess enabled.

2006-05-27  dcurtis3

	* Makefile.am, configure.ac, src/Makefile.am,
	  src/pixmaps/Makefile.am: Added/Modified logo install
	* configure.ac: updated ghemical version 2.02

2006-05-23  dcurtis3

	* src/Makefile.am, src/main.cpp, src/pixmaps/ghemical.png: Added
	  Ghemical Logo

2006-05-04  dcurtis3

	* src/gamess_dialog.cpp: *** empty log message ***

2006-04-24  thassine

	* configure.ac: version number changed after a release
	* ChangeLog, configure.ac: this is v2.00

2006-04-23  dcurtis3

	* configure.ac: PKGCONFIG env variable definition was stuck in a
	  autoconf test for threads. needed moving.

2006-04-11  thassine

	* ChangeLog, INSTALL, configure.ac, src/gamess_dialog.glade,
	  src/gtk_project_view.cpp, src/main.cpp: this is v2.00rc1

2006-04-10  thassine

	* Makefile.am, configure.ac, docs, docs/.cvsignore,
	  docs/Makefile.am, src, src/.cvsignore, src/main.cpp: the user's
	  manual is installed and viewed using a browser.
	* docs/user-docs, docs/user-docs/.cvsignore,
	  docs/user-docs/Makefile.am, docs/user-docs/index.html,
	  docs/user-docs/introduction.html, docs/user-docs/mdi_mode.html,
	  docs/user-docs/perspective.html, docs/user-docs/ribbon.html,
	  docs/user-docs/setup_dialog.html, docs/user-docs/using_mm.html,
	  docs/user-docs/visualization.html: updated the user-docs
	* docs/user-docs/images, docs/user-docs/images/.cvsignore,
	  docs/user-docs/images/2atoms_bond.png,
	  docs/user-docs/images/Makefile.am,
	  docs/user-docs/images/change_bond_select.png,
	  docs/user-docs/images/clipping1.png,
	  docs/user-docs/images/clipping2.png,
	  docs/user-docs/images/draw_button.png,
	  docs/user-docs/images/draw_hydrogens.png,
	  docs/user-docs/images/first_atom.png,
	  docs/user-docs/images/new_mm.png,
	  docs/user-docs/images/periodic_button.png,
	  docs/user-docs/images/periodic_table.png,
	  docs/user-docs/images/setup1.png,
	  docs/user-docs/images/setup2.png,
	  docs/user-docs/images/setup_select.png,
	  docs/user-docs/images/using_mm_01.png,
	  docs/user-docs/images/using_mm_02.png,
	  docs/user-docs/images/using_mm_03.png,
	  docs/user-docs/images/using_mm_04.png,
	  docs/user-docs/images/using_mm_05.png,
	  docs/user-docs/images/using_mm_06.png,
	  docs/user-docs/images/using_mm_07.png,
	  docs/user-docs/images/using_mm_08.png,
	  docs/user-docs/images/using_mm_09.png,
	  docs/user-docs/images/using_mm_10.png,
	  docs/user-docs/images/using_mm_11.png: updated the user-docs

2006-04-05  thassine

	* src/camera.cpp, src/camera.h: fixed yet another OpenGL
	  names-related bug.

2006-04-03  thassine

	* configure.ac, src/Makefile.am, src/gamess_dialog.cpp,
	  src/gamess_dialog.glade, src/ghemicalconfig.h.in,
	  src/gtk_graphics_view.cpp, src/gtk_project.cpp,
	  src/gtk_project.h, src/main.cpp, src/main.h,
	  src/pixmaps/addh.xpm, src/pixmaps/constrain.xpm,
	  src/pixmaps/gamess.xpm, src/pixmaps/geomopt.xpm,
	  src/pixmaps/import.xpm, src/pixmaps/lock.xpm,
	  src/pixmaps/none.xpm, src/pixmaps/removeh.xpm,
	  src/pixmaps/unlock.xpm, src/project.cpp: added optional shortcut
	  toolbar + other fixes (Donald Curtis).

2006-03-29  thassine

	* INSTALL, src/file_export_dialog.cpp, src/fileio.cpp,
	  src/filetrans.cpp, src/gtk_graphics_view.cpp,
	  src/gtk_project.cpp, src/main.cpp, src/project.cpp,
	  src/project.h: minor changes ; a lock patch (DEC).

2006-03-28  hutchisn

	* src/gtk_graphics_view.cpp, src/gtk_project.cpp,
	  src/gtk_project.h, src/project.cpp, src/project.h: Add H->Methyl
	  builder feature to convert selected hydrogens to methyls
	  (or methylate the whole molecule).
	* src/main.cpp: Make sure to set the project filename when
	  importing or reading a file from
	  the commandline.
	* src/fileio.cpp: Remove warning for WriteGPR -- Ghemical now
	  depends on OB-2.0, which can read
	  these gpr files with no problems.
	* src/file_export_dialog.cpp: Add filename to default text for
	  export.
	* src, src/.cvsignore: Add built ghemical file to ignore list

2006-03-28  thassine

	* configure.ac, examples/Makefile.am: examples/TSS fix
	* examples/transition_state_search2: renamed
	  transition_state_search -> TSS
	* ., .cvsignore: removed some unnecessary files.
	* config.guess, config.sub, ltmain.sh: removed some unnecessary
	  files.

2006-03-27  hutchisn

	* src/main.cpp: Set default window size to 830x640 to show all the
	  toolbar buttons by default

2006-03-27  thassine

	* src/constraint_dialog.cpp, src/constraint_dialog.glade,
	  src/gtk_project_view.cpp, src/gtk_project_view.h, src/main.cpp:
	  added constraint_dst/project view improvements (by Donald
	  Curtis).

2006-03-22  thassine

	* src/Makefile.am, src/constraint_dialog.cpp,
	  src/constraint_dialog.glade, src/constraint_dialog.h,
	  src/gtk_graphics_view.cpp, src/gtk_project.cpp,
	  src/gtk_project.h, src/gtk_project_view.cpp,
	  src/gtk_project_view.h, src/project.cpp, src/project.h,
	  src/views.h: added (distance)constraints ; by Donald Curtis.

2006-03-20  thassine

	* src/main.cpp, src/main.h: made the short toolbar labels optional.

2006-03-16  thassine

	* INSTALL, configure.ac: documentation updates.

2006-03-16  hutchisn

	* src/main.cpp: Adding text labels to identify toolbar icons

2006-03-14  thassine

	* src/moldyn_dialog.cpp, src/moldyn_dialog.glade,
	  src/moldyn_dialog.h: updated the mol.dyn. dialog.

2006-03-10  thassine

	* src/project.cpp: added a new orient-command.

2006-03-08  thassine

	* ., .cvsignore: cvsignore updated.
	* aclocal.m4, autogen.sh: removed acloca.m4 and updated autogen.sh

2006-03-07  thassine

	* aclocal.m4, src/gtk_project_view.cpp, src/gtk_project_view.h,
	  src/setup_dialog.cpp, src/setup_dialog.glade: synchronized with
	  libghemical.

2006-03-03  thassine

	* aclocal.m4, src/gtk_project.cpp, src/gtk_project_view.cpp,
	  src/gtk_project_view.h, src/project.h: added Donald's frozed
	  atom improvements.
	* ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, configure,
	  examples, examples/.cvsignore, examples/Makefile.in,
	  examples/transition_state_search2,
	  examples/transition_state_search2/.cvsignore,
	  examples/transition_state_search2/E2-reaction,
	  examples/transition_state_search2/E2-reaction/.cvsignore,
	  examples/transition_state_search2/E2-reaction/Makefile.in,
	  examples/transition_state_search2/Makefile.in,
	  examples/transition_state_search2/SN2-reaction,
	  examples/transition_state_search2/SN2-reaction/.cvsignore,
	  examples/transition_state_search2/SN2-reaction/Makefile.in,
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/.cvsignore,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/.cvsignore,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
	  examples/transition_state_search2/cycloaddition_Diels-Alder,
	  examples/transition_state_search2/cycloaddition_Diels-Alder/.cvsignore,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/.cvsignore,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
	  examples/transition_state_search2/tautomeric_shift_keto_enol,
	  examples/transition_state_search2/tautomeric_shift_keto_enol/.cvsignore,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
	  src, src/.cvsignore, src/Makefile.in, src/moldyn_dialog.cpp,
	  src/moldyn_dialog.glade, src/project.cpp, src/project.h,
	  src/trajview_dialog.cpp: many changes in lib side.

2006-03-01  thassine

	* Makefile.in, aclocal.m4, src/moldyn_dialog.cpp,
	  src/moldyn_dialog.glade, src/moldyn_dialog.h, src/project.cpp:
	  mol.dyn. changes on lib side.

2006-02-27  thassine

	* src/camera.cpp, src/glade_dialog.cpp, src/gtk_project.cpp,
	  src/gtk_project_view.cpp, src/gtk_views.cpp, src/main.cpp,
	  src/plane.cpp, src/project.cpp, src/surface.cpp, src/views.cpp:
	  the stringstream code was made safer ; avoid c_str() calls in
	  which a reference to buffer is stored for re-use.

2006-02-24  thassine

	* src/project.cpp: fixed a bug in box solvation.

2006-02-23  thassine

	* src/project.cpp, src/trajview_dialog.cpp: trajview dialog bug
	  temporarily fixed ; something wrong with the PrintToLog() method?

2006-02-21  thassine

	* src/fileio.cpp: fileio cleanups.

2006-02-20  thassine

	* src/camera.cpp, src/geomopt_dialog.cpp, src/glade_dialog.cpp,
	  src/gtk_project_view.cpp, src/gtk_views.cpp, src/main.cpp,
	  src/moldyn_dialog.cpp, src/plane.cpp, src/project.cpp,
	  src/ribbon.cpp, src/setup_dialog.cpp, src/surface.cpp,
	  src/trajview_dialog.cpp, src/views.cpp: output-stringstream code
	  changed.
	* Makefile.in, src/glade_dialog.cpp: glade filename fix (initial)
	  added.

2006-02-17  hutchisn

	* src/camera.cpp, src/file_export_dialog.cpp,
	  src/file_import_dialog.cpp, src/fileio.cpp, src/filetrans.h,
	  src/gamess_dialog.cpp, src/geomopt_dialog.cpp,
	  src/glade_dialog.cpp, src/gtk_project.cpp,
	  src/gtk_project_view.cpp, src/gtk_views.cpp, src/main.cpp,
	  src/moldyn_dialog.cpp, src/plane.cpp, src/progress_dialog.cpp,
	  src/project.cpp, src/ribbon.cpp, src/setup_dialog.cpp,
	  src/surface.cpp, src/trajview_dialog.cpp, src/views.cpp: Update
	  to change strstream to modern versions to remove compiler
	  warnings with GCC.
	* src/filetrans.cpp: Update to include a molecule title (from the
	  filename) for Open Babel export.
	* src, src/.cvsignore, trunk/bin, trunk/bin/.cvsignore: Update to
	  remove spurious CVS warnings.

2006-02-16  thassine

	* AUTHORS, aclocal.m4, src/Makefile.am, src/Makefile.in,
	  src/gamess_dialog.cpp, src/gamess_dialog.glade,
	  src/gamess_dialog.h, src/gtk_graphics_view.cpp,
	  src/gtk_project.cpp, src/gtk_project.h, src/main.cpp: added the
	  gamess-interface contributed by Donald Curtis.
	* ., .cvsignore, BRANCHNAME, Makefile.in, aclocal.m4,
	  config.guess, config.sub, configure, configure.ac,
	  examples/Makefile.in,
	  examples/transition_state_search2/E2-reaction/Makefile.in,
	  examples/transition_state_search2/Makefile.in,
	  examples/transition_state_search2/SN2-reaction/Makefile.in,
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
	  ltmain.sh, src/Makefile.in, src/ghemicalconfig.h.in: updated
	  the build scripts.

2006-02-10  thassine

	* Makefile.in, aclocal.m4, configure, configure.ac,
	  examples/Makefile.in,
	  examples/transition_state_search2/E2-reaction/Makefile.in,
	  examples/transition_state_search2/Makefile.in,
	  examples/transition_state_search2/SN2-reaction/Makefile.in,
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
	  src/Makefile.in, src/ghemicalconfig.h.in, src/objects.h: many
	  changes...

2006-02-07  thassine

	* src/fileio.cpp, src/geomopt_dialog.cpp, src/moldyn_dialog.cpp,
	  src/project.cpp, src/ribbon.cpp, src/setup_dialog.cpp,
	  src/views.cpp: the data hiding fixes of libghemical added.

2006-01-19  thassine

	* src/objects.h: fixed an include file name.

2006-01-05  thassine

	* Makefile.am, Makefile.in, NEWS, README, depcomp, src,
	  src/.cvsignore, src/Makefile.am, src/Makefile.in,
	  src/gtk_project.h, src/main.cpp: some missing files added ; now
	  automake based.
	* missing, src/Makefile.am, src/file_export_dialog.cpp,
	  src/file_export_dialog.glade, src/file_export_dialog.h,
	  src/file_import_dialog.cpp, src/file_import_dialog.glade,
	  src/file_import_dialog.h, src/geomopt_dialog.cpp,
	  src/geomopt_dialog.glade, src/geomopt_dialog.h,
	  src/moldyn_dialog.cpp, src/moldyn_dialog.glade,
	  src/moldyn_dialog.h, src/progress_dialog.cpp,
	  src/progress_dialog.glade, src/progress_dialog.h,
	  src/setup_dialog.cpp, src/setup_dialog.glade,
	  src/setup_dialog.h, src/trajview_dialog.cpp,
	  src/trajview_dialog.glade, src/trajview_dialog.h: added the
	  relocated files.
	* aclocal.m4, configure, configure.ac, examples/Makefile.am,
	  examples/Makefile.in,
	  examples/transition_state_search2/E2-reaction/Makefile.in,
	  examples/transition_state_search2/Makefile.in,
	  examples/transition_state_search2/SN2-reaction/Makefile.in,
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
	  src/ghemicalconfig.h.in, src/glade: the src/glade directory is
	  removed.

2006-01-05  

	* src/Makefile.am: This commit was manufactured by cvs2svn to
	  create branch
	  'VERSION_2_BRANCH'.

2006-01-05  thassine

	* examples/transition_state_search2/E2-reaction/products.gpr,
	  examples/transition_state_search2/E2-reaction/reactants.gpr,
	  examples/transition_state_search2/E2-reaction/ts.gpr,
	  examples/transition_state_search2/SN2-reaction,
	  examples/transition_state_search2/SN2-reaction/.cvsignore,
	  examples/transition_state_search2/SN2-reaction/Makefile.am,
	  examples/transition_state_search2/SN2-reaction/Makefile.in,
	  examples/transition_state_search2/SN2-reaction/products.gpr,
	  examples/transition_state_search2/SN2-reaction/reactants.gpr,
	  examples/transition_state_search2/SN2-reaction/ts.gpr,
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/.cvsignore,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.am,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/products.gpr,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/reactants.gpr,
	  
	  examples/transition_state_search2/carbocation_rearrangement_hydride_shift/ts.gpr,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/.cvsignore,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.am,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/products.gpr,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/reactants.gpr,
	  
	  examples/transition_state_search2/carbocation_rearrangement_methide_shift/ts.gpr,
	  examples/transition_state_search2/cycloaddition_Diels-Alder,
	  examples/transition_state_search2/cycloaddition_Diels-Alder/.cvsignore,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.am,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/products.gpr,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/reactants.gpr,
	  
	  examples/transition_state_search2/cycloaddition_Diels-Alder/ts.gpr,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/.cvsignore,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.am,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/products.gpr,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/reactants.gpr,
	  
	  examples/transition_state_search2/sigmatropic_rearrangement_Cope/ts.gpr,
	  examples/transition_state_search2/tautomeric_shift_keto_enol,
	  examples/transition_state_search2/tautomeric_shift_keto_enol/.cvsignore,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.am,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/products.gpr,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/reactants.gpr,
	  
	  examples/transition_state_search2/tautomeric_shift_keto_enol/ts.gpr:
	  added the rest of example files.
	* examples/transition_state_search2,
	  examples/transition_state_search2/.cvsignore,
	  examples/transition_state_search2/E2-reaction,
	  examples/transition_state_search2/E2-reaction/.cvsignore,
	  examples/transition_state_search2/E2-reaction/Makefile.am,
	  examples/transition_state_search2/E2-reaction/Makefile.in,
	  examples/transition_state_search2/Makefile.am,
	  examples/transition_state_search2/Makefile.in: added the rest of
	  example files.
	* examples, examples/.cvsignore, examples/2-chlorobutane.gpr,
	  examples/3-phenylpropanal.gpr, examples/Makefile.am,
	  examples/Makefile.in, examples/PeriodicTable.gpr,
	  examples/acetylsalicylic_acid.gpr, examples/alpha-pinene.gpr,
	  examples/bromobenzene.gpr, examples/camphor.gpr,
	  examples/cinnamaldehyde.gpr, examples/cis-2-pentene.gpr,
	  examples/cyclohexane.gpr, examples/dna_AGTC.gpr,
	  examples/naphtalene.gpr, examples/rna_aguc.gpr: added examples
	* docs/user-docs/images/2atoms_bond.png,
	  docs/user-docs/images/2atoms_unbonded.png,
	  docs/user-docs/images/aa_builder_ci.png,
	  docs/user-docs/images/aa_builder_menu.png,
	  docs/user-docs/images/aa_builder_note.png,
	  docs/user-docs/images/aa_builder_w_h.png,
	  docs/user-docs/images/aa_builder_wo_h.png,
	  docs/user-docs/images/add_hydrogens.png,
	  docs/user-docs/images/add_hydrogens_select.png,
	  docs/user-docs/images/change_bond_dialog.png,
	  docs/user-docs/images/change_bond_select.png,
	  docs/user-docs/images/ci_plane.png,
	  docs/user-docs/images/cyclohexane1.png,
	  docs/user-docs/images/cyclohexane2.png,
	  docs/user-docs/images/cyclohexane_optimized.png,
	  docs/user-docs/images/cyclohexane_unoptimized.png,
	  docs/user-docs/images/draw_button.png,
	  docs/user-docs/images/draw_hydrogens.png,
	  docs/user-docs/images/energy_vs_torsion1.png,
	  docs/user-docs/images/energy_vs_torsion2.png,
	  docs/user-docs/images/energy_vs_torsion3.png,
	  docs/user-docs/images/energy_vs_torsion4.png,
	  docs/user-docs/images/enlevdiag.png,
	  docs/user-docs/images/esp-plane_mm.png,
	  docs/user-docs/images/esp-plane_qm.png,
	  docs/user-docs/images/esp-plane_select.png,
	  docs/user-docs/images/esp-plane_select_obj.png,
	  docs/user-docs/images/first_atom.png,
	  docs/user-docs/images/formula.png,
	  docs/user-docs/images/formula_select.png,
	  docs/user-docs/images/geometry_op_dialog.png,
	  docs/user-docs/images/geometry_optimization_select.png,
	  docs/user-docs/images/labels_menu.png,
	  docs/user-docs/images/mainmenu.png,
	  docs/user-docs/images/maintools.png,
	  docs/user-docs/images/md_dialog.png,
	  docs/user-docs/images/modal.png,
	  docs/user-docs/images/new_mm.png,
	  docs/user-docs/images/notebook.png,
	  docs/user-docs/images/optimized_ethane.png,
	  docs/user-docs/images/periodic_button.png,
	  docs/user-docs/images/periodic_table.png,
	  docs/user-docs/images/remove_hydrogens.png,
	  docs/user-docs/images/ribbon.png,
	  docs/user-docs/images/sequence_builder.png,
	  docs/user-docs/images/toplevel.png,
	  docs/user-docs/images/traj_dialog.png,
	  docs/user-docs/images/window.png: docs/user-docs/images added.
	* docs/user-docs/MD.html, docs/user-docs/MD_viewer.html,
	  docs/user-docs/aa_table.html, docs/user-docs/add_hydrogens.html,
	  docs/user-docs/conf_search_tools.html,
	  docs/user-docs/documentation.css,
	  docs/user-docs/energy_vs_torsion.html,
	  docs/user-docs/filetypes.html, docs/user-docs/formula.html,
	  docs/user-docs/geometry_optimization.html,
	  docs/user-docs/import_types.html, docs/user-docs/index.html,
	  docs/user-docs/introduction.html, docs/user-docs/labels.html,
	  docs/user-docs/mdi_mode.html, docs/user-docs/measure.html,
	  docs/user-docs/perspective.html, docs/user-docs/references.html,
	  docs/user-docs/ribbon.html,
	  docs/user-docs/sequence_builder.html,
	  docs/user-docs/using_mm.html, docs/user-docs/using_qm.html,
	  docs/user-docs/using_sf.html, docs/user-docs/visualization.html:
	  more files added.
	* configure.ac: removed the old bin directory, added docs and
	  examples directories.

2006-01-05  

	* ., COPYING, Makefile.am, NEWS, README, depcomp, docs, examples,
	  examples/transition_state_search, missing: This commit was
	  manufactured by cvs2svn to create branch
	  'VERSION_2_BRANCH'.

2005-12-09  thassine

	* trunk/src/main.cpp: added a missing glutInit() call.

2005-11-29  thassine

	* trunk/src/fileio.cpp, trunk/src/gtk_graphics_view.cpp,
	  trunk/src/gtk_project.cpp, trunk/src/gtk_project.h,
	  trunk/src/gtk_project_view.cpp, trunk/src/project.cpp,
	  trunk/src/project.h: some new selection-based features were
	  added.

2005-11-10  thassine

	* trunk/configure, trunk/configure.ac: changed the version number
	  to 1.92 after a release.
	* trunk/aclocal.m4, trunk/configure, trunk/configure.ac: changed
	  the version numbmer to 1.91 ; released.

2005-11-03  hutchisn

	* trunk, trunk/.cvsignore: Updated to make sure all configure /
	  autoconf temporary files are ignored.
	* trunk/src, trunk/src/.cvsignore, trunk/src/filetrans.cpp,
	  trunk/src/filetrans.h: Changes to use Open Babel 2.0 for import
	  / export.
	  (May have memory leaks -- haven't checked thoroughly yet.)

2005-11-02  thassine

	* trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_plot_views.cpp,
	  trunk/src/gtk_plot_views.h, trunk/src/gtk_project.cpp,
	  trunk/src/gtk_project.h, trunk/src/gtk_views.cpp,
	  trunk/src/gtk_views.h, trunk/src/project.cpp,
	  trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
	  started adding a secondary structure constraints view.

2005-10-13  thassine

	* trunk/src/project.cpp: bugfix : plotting views are closed when a
	  project is closed. earlier this was forgotten, which easily lead
	  to program crashes. still not OK yet since the view windows are
	  not closed ; no way to close them from project view either.
	  leaves orphaned windows behind now but should not crash anymore.

2005-10-11  thassine

	* trunk/src/main.cpp: minor changes in main.cpp ; do not allow the
	  menubar and toolbar to expand when the main window is resized.

2005-10-08  thassine

	* trunk/configure, trunk/configure.ac, trunk/src/camera.cpp,
	  trunk/src/plane.cpp, trunk/src/plane.h, trunk/src/project.cpp,
	  trunk/src/project.h, trunk/src/surface.cpp, trunk/src/surface.h:
	  OpenGL bugfixes on 64-bit platforms

2005-09-28  hutchisn

	* trunk/TODO: Added request for polysaccharide builder

2005-09-27  thassine

	* trunk/src/objects.h: just some minor changes to adapt for
	  different compilers.

2005-08-24  thassine

	* trunk/src/fileio.cpp, trunk/src/glade/setup_dialog.cpp,
	  trunk/src/project.cpp: the mm_sf model type was removed from lib.

2005-08-23  thassine

	* trunk/aclocal.m4, trunk/configure, trunk/src/gtk_project.h:
	  small fixes added (should work with gcc-4 now.)

2005-07-14  thassine

	* trunk/src/main.cpp, trunk/src/main.h, trunk/src/project.cpp:
	  added the -f and -i command line options for opening a file and
	  importing a file.

2005-07-06  thassine

	* trunk/aclocal.m4, trunk/configure, trunk/configure.ac,
	  trunk/src/appconfig.h.in, trunk/src/appdefine.h,
	  trunk/src/camera.cpp, trunk/src/camera.h, trunk/src/color.h,
	  trunk/src/filetrans.h, trunk/src/ghemicalconfig.h.in,
	  trunk/src/glade/file_export_dialog.h,
	  trunk/src/glade/file_import_dialog.h,
	  trunk/src/glade/geomopt_dialog.h,
	  trunk/src/glade/moldyn_dialog.h,
	  trunk/src/glade/progress_dialog.h,
	  trunk/src/glade/setup_dialog.h,
	  trunk/src/glade/trajview_dialog.h, trunk/src/glade_dialog.h,
	  trunk/src/gtk_dialog.h, trunk/src/gtk_graphics_view.cpp,
	  trunk/src/gtk_graphics_view.h, trunk/src/gtk_plot_views.cpp,
	  trunk/src/gtk_plot_views.h, trunk/src/gtk_project.h,
	  trunk/src/gtk_project_view.h, trunk/src/gtk_views.h,
	  trunk/src/main.h, trunk/src/mtools.h, trunk/src/objects.cpp,
	  trunk/src/objects.h, trunk/src/plane.cpp, trunk/src/plane.h,
	  trunk/src/project.h, trunk/src/ribbon.h, trunk/src/spline.h,
	  trunk/src/surface.h, trunk/src/views.cpp, trunk/src/views.h:
	  config headers changed to avoid multiple PACKAGE definitions.

2005-07-05  thassine

	* trunk/INSTALL, trunk/aclocal.m4, trunk/configure,
	  trunk/src/Doxyfile, trunk/src/fileio.cpp, trunk/src/objects.h:
	  now compiles with g++-3.4

2005-07-01  thassine

	* trunk/CHANGES, trunk/ChangeLog, trunk/INSTALL, trunk/aclocal.m4,
	  trunk/configure, trunk/configure.ac, trunk/src/appdefine.h,
	  trunk/src/camera.h, trunk/src/color.h, trunk/src/filetrans.h,
	  trunk/src/glade_dialog.h, trunk/src/gtk_dialog.h,
	  trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_graphics_view.h,
	  trunk/src/gtk_plot_views.h, trunk/src/gtk_project.h,
	  trunk/src/gtk_project_view.h, trunk/src/gtk_views.h,
	  trunk/src/main.h, trunk/src/mtools.h, trunk/src/objects.h,
	  trunk/src/plane.h, trunk/src/project.h, trunk/src/ribbon.h,
	  trunk/src/spline.h, trunk/src/surface.h, trunk/src/views.h:
	  changes for a release 1.90 ; there remains an unsolved conflict
	  with OpenBabel since superimpose class is perhaps mixed with a
	  superimpose() function in OB ; but this needs to be studied
	  later.

2005-06-30  thassine

	* trunk/Makefile.in, trunk/acconfig.h, trunk/acinclude.m4,
	  trunk/aclocal.m4, trunk/configure, trunk/configure.ac,
	  trunk/configure.in, trunk/src/Makefile.in,
	  trunk/src/appconfig.h.in, trunk/src/filetrans.cpp,
	  trunk/src/filetrans.h, trunk/src/glade/Makefile.in,
	  trunk/src/glade/file_export_dialog.cpp,
	  trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/gtk_graphics_view.cpp, trunk/src/project.cpp,
	  trunk/src/project.h: a lot of changes in configuration scripts.

2005-06-23  thassine

	* trunk/src/glade/setup_dialog.cpp,
	  trunk/src/glade/setup_dialog.glade, trunk/src/project.cpp,
	  trunk/src/ribbon.cpp: the lib/app interface has changed somewhat.

2005-06-20  thassine

	* trunk/src/glade/geomopt_dialog.glade,
	  trunk/src/glade/progress_dialog.cpp,
	  trunk/src/glade/progress_dialog.h, trunk/src/gtk_project.cpp,
	  trunk/src/gtk_project.h, trunk/src/project.cpp: added progress
	  dialogs for GO, MD, random search.

2005-06-17  thassine

	* trunk/src/gtk_project.cpp, trunk/src/project.cpp,
	  trunk/src/project.h: bugfix added to GO/MD initialization code.

2005-06-14  thassine

	* trunk/src/glade/file_export_dialog.cpp,
	  trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/glade/geomopt_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.cpp,
	  trunk/src/glade/progress_dialog.cpp,
	  trunk/src/glade/progress_dialog.glade,
	  trunk/src/glade/progress_dialog.h,
	  trunk/src/glade/setup_dialog.cpp,
	  trunk/src/glade/trajview_dialog.cpp, trunk/src/gtk_dialog.cpp,
	  trunk/src/gtk_project.cpp, trunk/src/gtk_project.h,
	  trunk/src/project.cpp, trunk/src/project.h: started converting
	  GO and MD into multithreaded versions ; added the files that
	  left out yesterday.

2005-06-13  thassine

	* trunk/src/glade/Makefile.in, trunk/src/gtk_project.cpp,
	  trunk/src/gtk_project.h, trunk/src/project.cpp,
	  trunk/src/project.h: the Random Search is now completely
	  multi-threaded.
	* trunk/src/Makefile.in, trunk/src/gtk_graphics_view.cpp,
	  trunk/src/gtk_views.cpp, trunk/src/main.cpp,
	  trunk/src/project.cpp, trunk/src/project.h: added an initial
	  framework for multithreading ; switch off from the beginning of
	  project.h if needed (the ENABLE_THREADS macro).

2005-06-09  thassine

	* trunk/src/gtk_project.cpp, trunk/src/gtk_project.h: now the text
	  buffer scrolling works and is smooth but does not update for
	  example when lengthy calculations ; add threading?
	* trunk/src/gtk_dialog.cpp, trunk/src/gtk_dialog.h,
	  trunk/src/gtk_project.cpp, trunk/src/gtk_project.h: some missing
	  files added ; the text widget scrolling problems have now a
	  partial solution that works in most cases but flickers and is
	  slow.
	* trunk/src/fileio.cpp, trunk/src/glade/file_export_dialog.cpp,
	  trunk/src/glade/file_export_dialog.glade,
	  trunk/src/glade/file_export_dialog.h,
	  trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/glade/file_import_dialog.glade,
	  trunk/src/glade/file_import_dialog.h,
	  trunk/src/glade/geomopt_dialog.cpp,
	  trunk/src/glade/geomopt_dialog.glade,
	  trunk/src/glade/moldyn_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.glade,
	  trunk/src/glade/moldyn_dialog.h,
	  trunk/src/glade/setup_dialog.cpp,
	  trunk/src/glade/setup_dialog.glade,
	  trunk/src/glade/trajview_dialog.cpp, trunk/src/project.cpp,
	  trunk/src/project.h: fixed the glade dialogs ; the file i/o
	  should now work with openbabel-1.100.2

2005-06-08  thassine

	* trunk/src/main.cpp, trunk/src/project.cpp, trunk/src/ribbon.cpp,
	  trunk/src/views.cpp: minor fixes added, now in sync with the lib.

2005-05-24  thassine

	* trunk/src/gtk_plot_views.cpp, trunk/src/gtk_plot_views.h,
	  trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h,
	  trunk/src/gtk_views.h, trunk/src/project.cpp,
	  trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
	  plotting view popup menus should work now ; TSS broken?

2005-05-19  thassine

	* trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_project_view.cpp,
	  trunk/src/gtk_project_view.h: the project view popup menus
	  should work now.

2005-05-17  thassine

	* trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h:
	  did the project view a bit further.

2005-05-16  thassine

	* trunk/src/glade/file_export_dialog.cpp,
	  trunk/src/glade/file_export_dialog.h,
	  trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/glade/file_import_dialog.h,
	  trunk/src/glade/setup_dialog.cpp,
	  trunk/src/glade/setup_dialog.h,
	  trunk/src/glade/trajview_dialog.cpp,
	  trunk/src/glade/trajview_dialog.h,
	  trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_graphics_view.h,
	  trunk/src/gtk_plot_views.cpp, trunk/src/gtk_plot_views.h,
	  trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h,
	  trunk/src/gtk_views.cpp, trunk/src/gtk_views.h,
	  trunk/src/main.cpp, trunk/src/main.h, trunk/src/project.h,
	  trunk/src/views.h: class name changes done ; gnome -> gtk
	* trunk/src/Makefile.in, trunk/src/glade/file_export_dialog.h,
	  trunk/src/glade/file_import_dialog.h,
	  trunk/src/glade/setup_dialog.h,
	  trunk/src/glade/trajview_dialog.h, trunk/src/gnome_dialog.cpp,
	  trunk/src/gnome_dialog.h, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/gtk_project_view.h,
	  trunk/src/gtk_views.cpp, trunk/src/gtk_views.h,
	  trunk/src/main.h: some changes in filenames ; converted gnome ->
	  gtk

2005-05-13  thassine

	* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
	  trunk/src/gtk_graphics_view.cpp, trunk/src/project.cpp:
	  continued porting the popup menus in GTK2 ; the graphics view
	  menu now complete.

2005-05-12  thassine

	* trunk/src/glade/setup_dialog.cpp,
	  trunk/src/glade/setup_dialog.glade: the new setup dialog should
	  more or less work now.

2005-05-11  thassine

	* trunk/src/glade/setup_dialog.cpp,
	  trunk/src/glade/setup_dialog.glade,
	  trunk/src/glade/setup_dialog.h: added some improvements to the
	  setup dialog ; now works initially.

2005-05-06  thassine

	* trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/gnome_project.cpp, trunk/src/project.cpp: now in synch
	  with the library.

2005-05-03  thassine

	* trunk/src/glade/Makefile.in, trunk/src/glade/setup_dialog.cpp,
	  trunk/src/glade/setup_dialog.glade,
	  trunk/src/glade/setup_dialog.h, trunk/src/glade/setup_druid.cpp,
	  trunk/src/glade/setup_druid.glade,
	  trunk/src/glade/setup_druid.h, trunk/src/gnome_project.cpp,
	  trunk/src/main.cpp: removed the setup druid (gnome-1 based) and
	  started adding a setup dialog.

2005-04-28  thassine

	* trunk/src/project.cpp: just adapt in slight changes in the lib
	  side.

2005-04-26  thassine

	* trunk/src/gnome_project.cpp, trunk/src/project.cpp: some changes
	  in libghemical ; sync.

2005-04-22  thassine

	* trunk/src/appdefine.h, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/gtk_graphics_view.cpp,
	  trunk/src/gtk_graphics_view.h, trunk/src/main.cpp,
	  trunk/src/main.h, trunk/src/project.cpp, trunk/src/project.h:
	  added new popup menu items ; tweaked the stereo adjustment box ;
	  bugfixes.

2005-04-21  thassine

	* trunk/aclocal.m4, trunk/configure, trunk/configure.in,
	  trunk/src/Makefile.in, trunk/src/appconfig.h.in,
	  trunk/src/appdefine.h, trunk/src/gnome_project.cpp,
	  trunk/src/gtk_views.cpp, trunk/src/main.cpp,
	  trunk/src/notice.cpp, trunk/src/notice.h: some new stuff added ;
	  the main menu now works except Help/Help item.
	* trunk/aclocal.m4, trunk/configure, trunk/configure.in,
	  trunk/src/Makefile.in, trunk/src/glade/Makefile.in,
	  trunk/src/glade/file_export_dialog.cpp,
	  trunk/src/glade/file_export_dialog.glade,
	  trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/glade/file_import_dialog.glade,
	  trunk/src/glade/geomopt_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.glade,
	  trunk/src/glade/setup_druid.cpp, trunk/src/glade/setup_druid.h,
	  trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
	  trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_graphics_view.h,
	  trunk/src/gtk_plot_views.cpp, trunk/src/gtk_plot_views.h,
	  trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h,
	  trunk/src/gtk_views.cpp, trunk/src/gtk_views.h,
	  trunk/src/main.cpp, trunk/src/main.h, trunk/src/project.cpp,
	  trunk/src/project.h, trunk/src/surface.h, trunk/src/views.cpp,
	  trunk/src/views.h: added the next round of changes ; compiles
	  and works but the menus are still incomplete.

2005-04-15  thassine

	* trunk/src/Makefile.in, trunk/src/appconfig.h.in,
	  trunk/src/fileio.cpp, trunk/src/gnome_dialog.h,
	  trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
	  trunk/src/notice.cpp: started adding the popup menu for
	  gtk_graphics_view.
	* trunk/src/gnome_dialog.cpp, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
	  trunk/src/pixmaps/bondtype.xpm, trunk/src/pixmaps/measure.xpm,
	  trunk/src/pixmaps/orb_xy.xpm, trunk/src/pixmaps/orb_z.xpm,
	  trunk/src/pixmaps/orbit_xy.xpm, trunk/src/pixmaps/orbit_z.xpm,
	  trunk/src/pixmaps/rot_xy.xpm, trunk/src/pixmaps/rot_z.xpm,
	  trunk/src/pixmaps/rotate_xy.xpm, trunk/src/pixmaps/rotate_z.xpm,
	  trunk/src/pixmaps/setup.xpm, trunk/src/pixmaps/trans_xy.xpm,
	  trunk/src/pixmaps/trans_z.xpm, trunk/src/pixmaps/transl_xy.xpm,
	  trunk/src/pixmaps/transl_z.xpm: major changes in GUI code ; uses
	  GtkUIManager now (GTK+-2.4) ; menus still not ready yet.

2005-03-23  thassine

	* trunk/src/gnome_dialog.cpp, trunk/src/gnome_dialog.h,
	  trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
	  trunk/src/main.cpp, trunk/src/main.h: bad problems because the
	  popup menus still are generated using gnome-1 code in a gtk2 app
	  ; crashes but started to add fixes ; still not OK.

2005-03-21  thassine

	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/src/Makefile.in, trunk/src/appconfig.h.in,
	  trunk/src/glade_dialog.cpp, trunk/src/gnome_dialog.cpp,
	  trunk/src/gnome_dialog.h, trunk/src/gnome_project.cpp,
	  trunk/src/main.cpp, trunk/src/main.h, trunk/src/views.h: added
	  many improvements ; the GTK2 version is now built by default
	  (--enable-bonobo changes this) and it's quite usable now...

2005-02-03  thassine

	* trunk/src/spline.cpp: minor changes to make it compile in FC3.

2004-12-23  thassine

	* trunk/bin/ghemical-ui.xml, trunk/configure, trunk/configure.in,
	  trunk/src/appconfig.h.in, trunk/src/ghemical-server.cpp,
	  trunk/src/ghemical-server.h, trunk/src/ghemical.cpp,
	  trunk/src/ghemical.h, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/main.cpp, trunk/src/main.h,
	  trunk/src/simple_test/container-ui.xml,
	  trunk/src/simple_test/container.cpp: continued to implement
	  separate gtk+/bonobo modes.
	* trunk/GNOME_Ghemical.server, trunk/Makefile.in,
	  trunk/src/Makefile.in, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/simple_test/Makefile,
	  trunk/src/simple_test/README,
	  trunk/src/simple_test/container-ui.xml,
	  trunk/src/simple_test/container.c,
	  trunk/src/simple_test/container.cpp,
	  trunk/src/simple_test/container.h: started creating a single
	  ghemical/ghemical-server executable that uses either gtk+ or
	  bonobo.

2004-12-21  thassine

	* trunk/src/camera.cpp, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
	  trunk/src/project.cpp, trunk/src/project.h: fixes added for
	  stereo display modes (especially red/blue mode).

2004-12-10  thassine

	* branches/MANY_PROJECTS_BRANCH/aclocal.m4, trunk/configure,
	  trunk/configure.in, trunk/src/gnome_views.cpp,
	  trunk/src/mtools.cpp, trunk/src/project.cpp,
	  trunk/src/project.h: many small fixes added.

2004-09-06  thassine

	* trunk/configure, trunk/configure.in: configure.in updated (still
	  needs similar fixes ; see also Makefiles.

2004-08-30  thassine

	* trunk/src/color.h, trunk/src/fileio.cpp,
	  trunk/src/filetrans.cpp, trunk/src/glade/geomopt_dialog.h,
	  trunk/src/glade/moldyn_dialog.h,
	  trunk/src/glade/setup_druid.cpp, trunk/src/gnome_dialog.cpp,
	  trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
	  trunk/src/gnome_views.cpp, trunk/src/notice.cpp,
	  trunk/src/objects.cpp, trunk/src/objects.h,
	  trunk/src/project.cpp, trunk/src/project.h,
	  trunk/src/ribbon.cpp, trunk/src/spline.h, trunk/src/views.cpp:
	  changed the include directory of libghemical.

2004-08-25  thassine

	* trunk/src/appdefine.h, trunk/src/project.cpp,
	  trunk/src/project.h: minor changes in labels etc (not yet same
	  as in BBB).

2004-05-13  thassine

	* trunk/acinclude.m4, trunk/aclocal.m4, trunk/configure,
	  trunk/configure.in, trunk/src/glade/setup_druid.cpp: libmopac7,
	  OpenBabel and libghemical now properly detected in configure.in

2004-03-17  thassine

	* trunk/Makefile.in: changed VERSION into APPVERSION in Makefile.in

2004-02-18  thassine

	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/src/Makefile.in, trunk/src/appconfig.h.in,
	  trunk/src/glade/Makefile.in: now properly reads settings from
	  libghemical.pc using pkg-config.

2004-02-17  thassine

	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/openbabel, trunk/src/Makefile.in,
	  trunk/src/glade/Makefile.in, trunk/src/project.cpp: now uses an
	  external OpenBabel library ; make install should now properly
	  install both executables and files.

2004-02-11  thassine

	* trunk/src/fileio.cpp, trunk/src/project.h: added setlocale()
	  calls into fileio.cpp ; also added formal charges into the file
	  format (version string now 111)
	* trunk/src/Makefile.in, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/project.cpp: added -lmopac7
	  into src/Makefile.in (temporarily) and other minor changes.

2003-11-06  thassine

	* trunk/src/fileio.cpp: a minor fix in file-IO; still need to save
	  secondary structures for SF?

2003-10-10  thassine

	* trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h: added a new (experimental) menu item.

2003-10-03  thassine

	* trunk/src/project.cpp: fixed a drawing tool bug.

2003-09-12  thassine

	* trunk/src/gnome_project.cpp, trunk/src/plane.cpp,
	  trunk/src/plane.h, trunk/src/project.cpp, trunk/src/surface.cpp,
	  trunk/src/surface.h: improved planes/surfaces ; now adapt better
	  for charged molecules.

2003-09-10  thassine

	* trunk/src/appdefine.h, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/project.cpp: a rendering
	  bug was fixed, and LABEL_RESIDUE was implemented.

2003-09-01  thassine

	* trunk/src/project.cpp: added some bugfixes/comments

2003-08-08  thassine

	* trunk/src/fileio.cpp, trunk/src/gnome_project.cpp,
	  trunk/src/project.cpp, trunk/src/project.h: the Solvate??()
	  functions have changed.

2003-08-01  thassine

	* trunk/src/glade/file_export_dialog.cpp,
	  trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/glade/geomopt_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.cpp: fixed the dialogs by changing
	  gnome_dialog -> gtk_dialog.

2003-07-30  thassine

	* trunk/src/camera.cpp, trunk/src/gnome_dialog.cpp,
	  trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
	  trunk/src/project.cpp, trunk/src/project.h: a few more changes
	  added ; now the bonobo-component seems to work pretty well and
	  is usable, but the toolbar buttons (mouse tool, element,
	  bondtype) are still missing.

2003-07-29  thassine

	* trunk/src/camera.cpp, trunk/src/camera.h,
	  trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
	  trunk/src/objects.cpp, trunk/src/objects.h, trunk/src/plane.cpp,
	  trunk/src/plane.h, trunk/src/project.cpp, trunk/src/project.h,
	  trunk/src/ribbon.cpp, trunk/src/ribbon.h, trunk/src/surface.cpp,
	  trunk/src/surface.h, trunk/src/views.cpp, trunk/src/views.h: the
	  project_view now works reasonably well ; also popup-menus added
	  to project_view pages.

2003-07-24  thassine

	* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
	  trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
	  trunk/src/project.cpp, trunk/src/project.h, trunk/src/views.h:
	  the popup-menu, text buffer, and the project view seems to work
	  quite reasonably now ; in project view only atoms and bonds
	  pages are ok, others still have many problems.

2003-07-15  thassine

	* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
	  trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
	  trunk/src/project.cpp, trunk/src/project.h, trunk/src/views.cpp,
	  trunk/src/views.h: the message log now works (more or less) and
	  project_view work started.

2003-07-14  thassine

	* trunk/src/glade/file_export_dialog.glade,
	  trunk/src/glade/file_import_dialog.glade,
	  trunk/src/glade/geomopt_dialog.glade,
	  trunk/src/glade/moldyn_dialog.glade,
	  trunk/src/glade/setup_druid.glade,
	  trunk/src/glade/trajview_dialog.glade,
	  trunk/src/gnome_dialog.cpp, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h: the .glade files are updated for
	  libglade-2 (using libglade-convert) glade-dialogs are displayed
	  correctly but handlers still not updated ; the gnome-dialogs
	  should work also now ; added (temporary) CURRENT submenu into
	  ppoup-menu for accesssing mouse tool and other settings.

2003-07-12  thassine

	* trunk/GNOME_Ghemical.server: added the .server file
	  (bonobo-activation).

2003-07-11  thassine

	* trunk/bin/ghemical-ui.xml, trunk/configure, trunk/configure.in,
	  trunk/src/Makefile.in, trunk/src/fileio.cpp,
	  trunk/src/filetrans.cpp, trunk/src/filetrans.h,
	  trunk/src/ghemical-server.cpp, trunk/src/ghemical-server.h,
	  trunk/src/ghemical.cpp, trunk/src/ghemical.h,
	  trunk/src/glade/Makefile.in, trunk/src/glade/geomopt_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.cpp,
	  trunk/src/glade/setup_druid.cpp, trunk/src/glade_dialog.cpp,
	  trunk/src/gnome_dialog.cpp, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
	  trunk/src/notice.cpp, trunk/src/notice.h, trunk/src/plane.h,
	  trunk/src/project.cpp, trunk/src/project.h,
	  trunk/src/ribbon.cpp, trunk/src/ribbon.h, trunk/src/simple_test,
	  trunk/src/simple_test/Makefile,
	  trunk/src/simple_test/container-ui.xml,
	  trunk/src/simple_test/container.c, trunk/src/surface.h,
	  trunk/src/views.cpp, trunk/src/views.h: started porting to
	  gnome2 and converting into bonobo.

2003-06-13  thassine

	* trunk/AUTHORS, trunk/acconfig.h, trunk/src/Doxyfile,
	  trunk/src/camera.cpp, trunk/src/gnome_project.cpp,
	  trunk/src/project.cpp: more checks added for atom_list sorting.
	  also misc cleanups.

2003-06-12  thassine

	* trunk/bin/examples/transition_state_search,
	  trunk/bin/examples/transition_state_search/E2-reaction,
	  trunk/bin/examples/transition_state_search/E2-reaction/products.gpr,
	  
	  trunk/bin/examples/transition_state_search/E2-reaction/reactants.gpr,
	  trunk/bin/examples/transition_state_search/E2-reaction/ts.gpr,
	  trunk/bin/examples/transition_state_search/SN2-reaction,
	  trunk/bin/examples/transition_state_search/SN2-reaction/products.gpr,
	  
	  trunk/bin/examples/transition_state_search/SN2-reaction/reactants.gpr,
	  trunk/bin/examples/transition_state_search/SN2-reaction/ts.gpr,
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift,
	  
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift/products.gpr,
	  
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift/reactants.gpr,
	  
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift/ts.gpr,
	  
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift,
	  
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift/products.gpr,
	  
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift/reactants.gpr,
	  
	  trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift/ts.gpr,
	  
	  trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder,
	  
	  trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder/products.gpr,
	  
	  trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder/reactants.gpr,
	  
	  trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder/ts.gpr,
	  
	  trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope,
	  
	  trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope/products.gpr,
	  
	  trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope/reactants.gpr,
	  
	  trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope/ts.gpr,
	  
	  trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol,
	  
	  trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol/products.gpr,
	  
	  trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol/reactants.gpr,
	  
	  trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol/ts.gpr,
	  trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
	  trunk/src/project.cpp, trunk/src/views.cpp, trunk/src/views.h:
	  added imrovements to transition_state_search + other search
	  tools, and added examples for TSS.

2003-06-11  thassine

	* trunk/src/glade/setup_druid.cpp, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h, trunk/src/project.cpp,
	  trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
	  added transition_state_search and stationary_state_search ;
	  user-docs and examples will follow in a few days.

2003-05-19  thassine

	* trunk/src/project.cpp: some debugging-label options added.

2003-05-13  thassine

	* trunk/src/gnome_project.cpp: removed some redundant
	  DefineSecondaryStructure() runs.

2003-05-12  thassine

	* trunk/src/project.cpp, trunk/src/ribbon.cpp, trunk/src/ribbon.h:
	  minor changes in ribbon object.

2003-04-29  thassine

	* trunk/src/gnome_project.cpp, trunk/src/project.cpp,
	  trunk/src/project.h, trunk/src/ribbon.cpp: many changes in lib,
	  adaptaptations to those added.

2003-04-17  thassine

	* trunk/src/gnome_project.cpp: added better defaults for glade
	  dialogs.

2003-04-16  thassine

	* trunk/src/glade/moldyn_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.glade,
	  trunk/src/glade/moldyn_dialog.h,
	  trunk/src/glade/setup_druid.cpp,
	  trunk/src/glade/setup_druid.glade, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
	  trunk/src/project.cpp: many small changes (including trajectory
	  reading).

2003-04-10  thassine

	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/src/appconfig.h.in, trunk/src/appdefine.h,
	  trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
	  trunk/src/project.cpp: changes in configure script (now tested
	  to work with --enable-mpqc).

2003-04-02  thassine

	* trunk/src/ribbon.cpp: changes in ribbon due to changes in atom
	  class.

2003-03-07  thassine

	* trunk/src/fileio.cpp: a minor addition to fileio.cpp
	* trunk/src/fileio.cpp: the functions in fileio.cpp now handle
	  data using member functions, not direclty (so that they now are
	  more portable).

2003-03-05  thassine

	* trunk/src/gnome_project.cpp, trunk/src/main.cpp: added some
	  changes related to gcc-3.2

2003-02-14  thassine

	* trunk/src/fileio.cpp: just cleanups, no real changes.
	* trunk/src/project.cpp: sf virtual bonds now rendered also using
	  wireframes.

2003-02-06  thassine

	* trunk/src/gnome_project.cpp, trunk/src/main.cpp,
	  trunk/src/notice.cpp, trunk/src/project.cpp: many changes; for
	  example added tool for adding solvent (not ready yet).

2003-02-03  thassine

	* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h: added
	  tools for solvation (using H2O).

2003-01-31  thassine

	* trunk/src/filetrans.cpp, trunk/src/project.cpp,
	  trunk/src/project.h: some bugfixes were added; mostly because of
	  changes in model::GetAtomCount() and engine::GetAtomCount().

2003-01-30  thassine

	* trunk/src/Makefile.in, trunk/src/fileio.cpp,
	  trunk/src/glade/Makefile.in, trunk/src/gnome_project.cpp,
	  trunk/src/project.cpp, trunk/src/project.h: changes in SF-stuff
	  rendering and file operations.

2003-01-27  thassine

	* trunk/src/fileio.cpp, trunk/src/glade/setup_druid.cpp,
	  trunk/src/project.cpp, trunk/src/project.h,
	  trunk/src/ribbon.cpp: some additions to graphics code (how the
	  new flags work).

2003-01-23  thassine

	* trunk/src/camera.cpp, trunk/src/camera.h,
	  trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
	  trunk/src/mtools.cpp, trunk/src/mtools.h,
	  trunk/src/pixmaps/clipping.xpm, trunk/src/project.cpp,
	  trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
	  added a new clipping mtool, the selections by atm/res/chn/mol is
	  added, and a new tool delete selected atoms is added.

2003-01-22  thassine

	* trunk/Makefile.in: make install also works now.
	* trunk/src, trunk/src/.cvsignore: minor cleanups added.
	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/src/Makefile.in, trunk/src/appconfig.h.in,
	  trunk/src/appdefine.h, trunk/src/camera.cpp, trunk/src/camera.h,
	  trunk/src/color.h, trunk/src/config.h.in, trunk/src/fileio.cpp,
	  trunk/src/filetrans.cpp, trunk/src/filetrans.h, trunk/src/glade,
	  trunk/src/glade/.cvsignore, trunk/src/glade/Makefile.in,
	  trunk/src/glade/README, trunk/src/glade/file_export_dialog.cpp,
	  trunk/src/glade/file_export_dialog.glade,
	  trunk/src/glade/file_export_dialog.h,
	  trunk/src/glade/file_import_dialog.cpp,
	  trunk/src/glade/file_import_dialog.glade,
	  trunk/src/glade/file_import_dialog.h,
	  trunk/src/glade/geomopt_dialog.cpp,
	  trunk/src/glade/geomopt_dialog.glade,
	  trunk/src/glade/geomopt_dialog.h,
	  trunk/src/glade/moldyn_dialog.cpp,
	  trunk/src/glade/moldyn_dialog.glade,
	  trunk/src/glade/moldyn_dialog.h,
	  trunk/src/glade/setup_druid.cpp,
	  trunk/src/glade/setup_druid.glade,
	  trunk/src/glade/setup_druid.h,
	  trunk/src/glade/trajview_dialog.cpp,
	  trunk/src/glade/trajview_dialog.glade,
	  trunk/src/glade/trajview_dialog.h, trunk/src/glade_dialog.cpp,
	  trunk/src/glade_dialog.h, trunk/src/gnome_dialog.cpp,
	  trunk/src/gnome_dialog.h, trunk/src/gnome_project.cpp,
	  trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
	  trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
	  trunk/src/mtools.cpp, trunk/src/mtools.h, trunk/src/notice.cpp,
	  trunk/src/notice.h, trunk/src/objects.cpp, trunk/src/objects.h,
	  trunk/src/pixmaps, trunk/src/pixmaps/.cvsignore,
	  trunk/src/pixmaps/angle.xpm, trunk/src/pixmaps/bond.xpm,
	  trunk/src/pixmaps/chain.xpm, trunk/src/pixmaps/dihedral.xpm,
	  trunk/src/pixmaps/distance.xpm, trunk/src/pixmaps/draw.xpm,
	  trunk/src/pixmaps/element.xpm, trunk/src/pixmaps/erase.xpm,
	  trunk/src/pixmaps/invert.xpm, trunk/src/pixmaps/molecule.xpm,
	  trunk/src/pixmaps/orb_xy.xpm, trunk/src/pixmaps/orb_z.xpm,
	  trunk/src/pixmaps/residue.xpm, trunk/src/pixmaps/rot_xy.xpm,
	  trunk/src/pixmaps/rot_z.xpm, trunk/src/pixmaps/select.xpm,
	  trunk/src/pixmaps/trans_xy.xpm, trunk/src/pixmaps/trans_z.xpm,
	  trunk/src/pixmaps/zoom.xpm, trunk/src/plane.cpp,
	  trunk/src/plane.h, trunk/src/project.cpp, trunk/src/project.h,
	  trunk/src/ribbon.cpp, trunk/src/ribbon.h, trunk/src/spline.cpp,
	  trunk/src/spline.h, trunk/src/surface.cpp, trunk/src/surface.h,
	  trunk/src/views.cpp, trunk/src/views.h: added the missing files;
	  some changes have happened in the filenames.

2003-01-21  thassine

	* trunk/bin/parameters: removed bin/prameters since it is now
	  contained in libghemical.

2003-01-20  thassine

	* trunk/configure, trunk/configure.in: many changes all over the
	  tree; does not compile yet...
	* trunk/src/graphics, trunk/src/target3: moved the contents of
	  src/graphics and src/target3 to src/.
	* trunk/src/target3/pixmaps: moved the src/target3/pixmaps to
	  src/pixmaps.
	* trunk/Makefile.in, trunk/src/target3/glade: moved the
	  /src/target3/glade to /src/glade.
	* trunk/src/common: removed the common-directory (now in
	  libghemical).
	* trunk/BUGLIST, trunk/Makefile.in, trunk/PROJECT,
	  trunk/configure.in, trunk/miniMOPAC, trunk/src/Makefile.OLD,
	  trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
	  trunk/src/some-extra-files, trunk/src/target1,
	  trunk/src/target2, trunk/src/target3/Makefile.in,
	  trunk/src/target3/glade/Makefile.in: some directories removed;
	  this stuff is either moved into the new libghemical library, or
	  (target1/target2) is discarded.

2003-01-15  thassine

	* trunk/src/common/matrix.h: added matrix.h back (from v1.0 source
	  tree).

2003-01-03  thassine

	* trunk/src/common/utility.cpp, trunk/src/common/utility.h:
	  superimpose is no longer a virtual class; only one class needed
	  since there's only one model class.

2003-01-02  thassine

	* trunk/src/common/moldyn.h: minor improvements to MD.

2002-12-12  thassine

	* trunk/src/common/model.cpp: some extra checks were added (for
	  simplified force field, does not affect all-atom stuff).

2002-12-11  thassine

	* trunk/src/common/model.cpp, trunk/src/common/seqbuild.cpp:
	  bugfix; adding ribbons re-ordered the atoms (via
	  seqbuild::Identify()) but this is now fixed.

2002-12-09  thassine

	* trunk/src/common/eng1_qm_mopac.cpp,
	  trunk/src/common/eng1_qm_mpqc.cpp,
	  trunk/src/target3/glade/Makefile.in: added a bugfix (now builds
	  with --enable-mpqc) and added some comments about MPQC/MOPAC
	  output.

2002-12-05  thassine

	* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
	  changed the version number to 1.51

2002-12-04  thassine

	* trunk/CHANGES: updated the changelog
	* trunk/INSTALL, trunk/bin/user-docs/images/aa_builder_ci.png,
	  trunk/bin/user-docs/images/aa_builder_menu.png,
	  trunk/bin/user-docs/images/aa_builder_note.png,
	  trunk/bin/user-docs/images/aa_builder_w_h.png,
	  trunk/bin/user-docs/images/aa_builder_wo_h.png,
	  trunk/bin/user-docs/images/ci_plane.png,
	  trunk/bin/user-docs/images/ribbon.png,
	  trunk/bin/user-docs/ribbon.html, trunk/ghemical.spec: final
	  fixes before release as v1.50

2002-12-03  thassine

	* trunk/Makefile.in: minor fixes to make install.
	* trunk/bin/user-docs/geometry_optimization.html,
	  trunk/bin/user-docs/images/geometry_opimization_console.png,
	  trunk/bin/user-docs/images/sequence_builder_console.png,
	  trunk/bin/user-docs/index.html,
	  trunk/bin/user-docs/introduction.html,
	  trunk/bin/user-docs/measure.html,
	  trunk/bin/user-docs/references.html,
	  trunk/bin/user-docs/sequence_builder.html,
	  trunk/bin/user-docs/using_mm.html,
	  trunk/bin/user-docs/using_qm.html,
	  trunk/bin/user-docs/using_sf.html,
	  trunk/bin/user-docs/visualization.html: added the improved docs
	  from Christopher also here.

2002-11-22  thassine

	* trunk, trunk/.cvsignore, trunk/miniMOPAC,
	  trunk/miniMOPAC/.cvsignore, trunk/openbabel,
	  trunk/openbabel/.cvsignore, trunk/openbabel/aromatic.h,
	  trunk/openbabel/aromatic.txt, trunk/openbabel/extable.h,
	  trunk/openbabel/extable.txt, trunk/src/common/model.cpp,
	  trunk/src/target3/glade, trunk/src/target3/glade/.cvsignore:
	  synchronized openbabel with the v1.0 tree, and added a notice
	  about incompleteness of the file format.

2002-11-20  thassine

	* trunk/bin/examples, trunk/bin/examples/2-chlorobutane.gpr,
	  trunk/bin/examples/3-phenylpropanal.gpr,
	  trunk/bin/examples/PeriodicTable.gpr,
	  trunk/bin/examples/acetylsalicylic_acid.gpr,
	  trunk/bin/examples/alpha-pinene.gpr,
	  trunk/bin/examples/bromobenzene.gpr,
	  trunk/bin/examples/camphor.gpr,
	  trunk/bin/examples/cinnamaldehyde.gpr,
	  trunk/bin/examples/cis-2-pentene.gpr,
	  trunk/bin/examples/cyclohexane.gpr,
	  trunk/bin/examples/naphtalene.gpr: added also the new example
	  files.
	* trunk/bin/examples, trunk/openbabel/extable.h,
	  trunk/openbabel/extable.txt, trunk/openbabel/ghemical.cpp,
	  trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/common/oldfiles.cpp,
	  trunk/src/common/tab_mm_prmfit.cpp,
	  trunk/src/graphics/project.cpp,
	  trunk/src/target1/t1m_param_mm_cpp.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target3/t3dialog.cpp,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3project.cpp,
	  trunk/src/target3/t3project.h: the file format detection is now
	  fixed; now can read the current (.gpr) and old (.mm1gp) v1.0
	  files.
	* trunk/Makefile.in: make install now installs the docs correctly.

2002-11-14  thassine

	* trunk/bin/user-docs/MD.html, trunk/bin/user-docs/MD_viewer.html,
	  trunk/bin/user-docs/aa_table.html,
	  trunk/bin/user-docs/add_hydrogens.html,
	  trunk/bin/user-docs/basic_mm.html,
	  trunk/bin/user-docs/conf_search_tools.html,
	  trunk/bin/user-docs/energy_vs_torsion.html,
	  trunk/bin/user-docs/enlevdiag.jpg,
	  trunk/bin/user-docs/filetypes.html,
	  trunk/bin/user-docs/formula.html,
	  trunk/bin/user-docs/geometry_optimization.html,
	  trunk/bin/user-docs/images/energy_vs_torsion1.png,
	  trunk/bin/user-docs/images/energy_vs_torsion2.png,
	  trunk/bin/user-docs/images/energy_vs_torsion3.png,
	  trunk/bin/user-docs/images/energy_vs_torsion4.png,
	  trunk/bin/user-docs/images/enlevdiag.png,
	  trunk/bin/user-docs/images/esp-plane_mm.png,
	  trunk/bin/user-docs/images/esp-plane_qm.png,
	  trunk/bin/user-docs/images/esp-plane_select.png,
	  trunk/bin/user-docs/images/esp-plane_select_obj.png,
	  trunk/bin/user-docs/index.html, trunk/bin/user-docs/labels.html,
	  trunk/bin/user-docs/mdi_mode.html,
	  trunk/bin/user-docs/measure.html,
	  trunk/bin/user-docs/perspective.html,
	  trunk/bin/user-docs/references.html,
	  trunk/bin/user-docs/sequence_builder.html,
	  trunk/bin/user-docs/using_cs_tools.html,
	  trunk/bin/user-docs/using_cs_tools01.jpg,
	  trunk/bin/user-docs/using_cs_tools02.jpg,
	  trunk/bin/user-docs/using_cs_tools03.jpg,
	  trunk/bin/user-docs/using_cs_tools04.jpg,
	  trunk/bin/user-docs/using_cs_tools05.jpg,
	  trunk/bin/user-docs/using_mm.html,
	  trunk/bin/user-docs/using_qm.html,
	  trunk/bin/user-docs/using_sf.html,
	  trunk/bin/user-docs/visualization.html: updated the
	  documentation.
	* trunk/bin/user-docs/basic_mm.html,
	  trunk/bin/user-docs/images/mainmenu.png,
	  trunk/bin/user-docs/images/maintools.png,
	  trunk/bin/user-docs/index.html,
	  trunk/bin/user-docs/introduction.html,
	  trunk/bin/user-docs/maintools.jpg: the chapter 1. introduction
	  seems to be ok now.
	* trunk/bin/user-docs/index.html: oops! fixed the absolute links
	  from index.html

2002-11-13  thassine

	* trunk/bin/parameters/param_mm/default/parameters1.txt,
	  trunk/bin/parameters/param_mm/default/parameters2.txt,
	  trunk/configure, trunk/configure.in, trunk/src/common/define.h:
	  added some halogen MM parameters, and changed the version number.

2002-11-11  thassine

	* trunk/src/Doxyfile, trunk/src/graphics/views.cpp: changed
	  doxygen settings, and added some fixes for gcc-3.2
	* trunk/openbabel/Makefile.in, trunk/openbabel/Vector.cpp,
	  trunk/openbabel/Vector.h, trunk/openbabel/alchemy.cpp,
	  trunk/openbabel/aromatic.h, trunk/openbabel/atom.cpp,
	  trunk/openbabel/atomtyp.h, trunk/openbabel/atomtyp.txt,
	  trunk/openbabel/balst.cpp, trunk/openbabel/base.h,
	  trunk/openbabel/bin2hex.pl, trunk/openbabel/binary.h,
	  trunk/openbabel/binary_io.h, trunk/openbabel/bitgrid.h,
	  trunk/openbabel/bitvec.h, trunk/openbabel/bond.txt,
	  trunk/openbabel/c3d.cpp, trunk/openbabel/cacao.cpp,
	  trunk/openbabel/chains.cpp, trunk/openbabel/chains.h,
	  trunk/openbabel/chiral.h, trunk/openbabel/commandline.h,
	  trunk/openbabel/ctransform.h, trunk/openbabel/cwrap.cpp,
	  trunk/openbabel/cwrap.h, trunk/openbabel/data.cpp,
	  trunk/openbabel/data.h, trunk/openbabel/element.h,
	  trunk/openbabel/element.txt, trunk/openbabel/extable.h,
	  trunk/openbabel/extable.txt, trunk/openbabel/fileformat.cpp,
	  trunk/openbabel/fileformat.h, trunk/openbabel/generic.cpp,
	  trunk/openbabel/generic.h, trunk/openbabel/grid.h,
	  trunk/openbabel/main.cpp, trunk/openbabel/matrix.h,
	  trunk/openbabel/mol.cpp, trunk/openbabel/mol.h,
	  trunk/openbabel/mol2.cpp, trunk/openbabel/molchrg.h,
	  trunk/openbabel/molvector.cpp, trunk/openbabel/molvector.h,
	  trunk/openbabel/obifstream.h, trunk/openbabel/obutil.cpp,
	  trunk/openbabel/obutil.h, trunk/openbabel/parsmart.cpp,
	  trunk/openbabel/parsmart.h, trunk/openbabel/patty.h,
	  trunk/openbabel/pdb.cpp, trunk/openbabel/phmodel.cpp,
	  trunk/openbabel/phmodel.h, trunk/openbabel/phmodeldata.h,
	  trunk/openbabel/resdata.h, trunk/openbabel/ring.h,
	  trunk/openbabel/rotor.h, trunk/openbabel/smarts.cpp,
	  trunk/openbabel/smarts.h, trunk/openbabel/smi.h,
	  trunk/openbabel/typer.cpp, trunk/openbabel/typer.h,
	  trunk/openbabel/types.h, trunk/openbabel/types.txt: the
	  openbabel tree is now in sync with v1.00

2002-11-06  thassine

	* trunk/bin/user-docs/MD.html, trunk/bin/user-docs/MD_viewer.html,
	  trunk/bin/user-docs/aa_table.html,
	  trunk/bin/user-docs/add_hydrogens.html,
	  trunk/bin/user-docs/basic_mm.html,
	  trunk/bin/user-docs/documentation.css,
	  trunk/bin/user-docs/filetypes.html,
	  trunk/bin/user-docs/formula.html,
	  trunk/bin/user-docs/geometry_optimization.html,
	  trunk/bin/user-docs/images,
	  trunk/bin/user-docs/images/2atoms_bond.png,
	  trunk/bin/user-docs/images/2atoms_unbonded.png,
	  trunk/bin/user-docs/images/add_hydrogens.png,
	  trunk/bin/user-docs/images/add_hydrogens_select.png,
	  trunk/bin/user-docs/images/change_bond_dialog.png,
	  trunk/bin/user-docs/images/change_bond_select.png,
	  trunk/bin/user-docs/images/cyclohexane1.png,
	  trunk/bin/user-docs/images/cyclohexane2.png,
	  trunk/bin/user-docs/images/cyclohexane_optimized.png,
	  trunk/bin/user-docs/images/cyclohexane_unoptimized.png,
	  trunk/bin/user-docs/images/draw_button.png,
	  trunk/bin/user-docs/images/draw_hydrogens.png,
	  trunk/bin/user-docs/images/first_atom.png,
	  trunk/bin/user-docs/images/formula.png,
	  trunk/bin/user-docs/images/formula_select.png,
	  trunk/bin/user-docs/images/geometry_op_dialog.png,
	  trunk/bin/user-docs/images/geometry_opimization_console.png,
	  trunk/bin/user-docs/images/geometry_optimization_select.png,
	  trunk/bin/user-docs/images/labels_menu.png,
	  trunk/bin/user-docs/images/md_dialog.png,
	  trunk/bin/user-docs/images/modal.png,
	  trunk/bin/user-docs/images/new_mm.png,
	  trunk/bin/user-docs/images/notebook.png,
	  trunk/bin/user-docs/images/optimized_ethane.png,
	  trunk/bin/user-docs/images/periodic_button.png,
	  trunk/bin/user-docs/images/periodic_table.png,
	  trunk/bin/user-docs/images/remove_hydrogens.png,
	  trunk/bin/user-docs/images/sequence_builder.png,
	  trunk/bin/user-docs/images/sequence_builder_console.png,
	  trunk/bin/user-docs/images/toplevel.png,
	  trunk/bin/user-docs/images/traj_dialog.png,
	  trunk/bin/user-docs/images/window.png,
	  trunk/bin/user-docs/import_types.html,
	  trunk/bin/user-docs/index.html,
	  trunk/bin/user-docs/introduction.html,
	  trunk/bin/user-docs/labels.html,
	  trunk/bin/user-docs/mdi_mode.html,
	  trunk/bin/user-docs/measure.html,
	  trunk/bin/user-docs/perspective.html,
	  trunk/bin/user-docs/references.html,
	  trunk/bin/user-docs/sequence_builder.html: added the
	  Christopher's new docs.

2002-11-05  thassine

	* trunk/AUTHORS, trunk/src/target2/Makefile.OLD,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/t3main.cpp:
	  added some new libs (reported that a modified RedHat7.3 needed
	  these; should be added to configure system as well) : -lXt -lSM
	  -lICE

2002-10-31  thassine

	* trunk/src/graphics/project.cpp, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/surface.h, trunk/src/target2/t2project.cpp:
	  various small fixes added to plane/surface/etc objects.
	* branches/MANY_PROJECTS_BRANCH/src/common/engine.h,
	  branches/MANY_PROJECTS_BRANCH/src/common/mm2eng.h,
	  branches/MANY_PROJECTS_BRANCH/src/common/mm2mdl.h,
	  branches/MANY_PROJECTS_BRANCH/src/common/mm2util.h,
	  branches/MANY_PROJECTS_BRANCH/src/graphics/mm2docv.cpp,
	  branches/MANY_PROJECTS_BRANCH/src/target1/t1m_mm2param_h.h,
	  branches/MANY_PROJECTS_BRANCH/src/target2/t2main.cpp,
	  branches/MANY_PROJECTS_BRANCH/src/target3/t3main.cpp,
	  trunk/bin/user-docs/index.html, trunk/src/common/eng1_sf.h,
	  trunk/src/target1/t1m_param_sf_h.h: just terminology changes:
	  reduced now changed to simplified in strings.

2002-10-29  thassine

	* trunk/src/common/model.cpp: a bugfix added that makes model.cpp
	  compile with the configure script.

2002-10-28  thassine

	* trunk/src/common/model.cpp,
	  trunk/src/target3/glade/trajview_dialog.cpp,
	  trunk/src/target3/t3dialog.cpp: moldyn now also uses logbox.
	* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_qm.cpp,
	  trunk/src/common/eng1_sf.cpp, trunk/src/graphics/project.cpp:
	  bugfixes added.

2002-10-25  thassine

	* trunk/src/target3/t3project.cpp: optimized the default settings
	  for planes/surfaces etc.

2002-10-24  thassine

	* trunk/src/graphics/project.cpp, trunk/src/target3/t3project.cpp,
	  trunk/src/target3/t3project.h: seq-builder now has a command
	  string.
	* trunk/src/graphics/project.cpp, trunk/src/graphics/project.h,
	  trunk/src/graphics/views.cpp, trunk/src/target3/t3project.cpp:
	  the 1d and 2d plots now have command strings.

2002-10-23  thassine

	* trunk/src/common/model.cpp, trunk/src/graphics/project.cpp,
	  trunk/src/graphics/project.h, trunk/src/target3/t3project.cpp,
	  trunk/src/target3/t3project.h, trunk/src/target3/t3views.cpp:
	  qm-related planes/surfaces added, enlev-diagram addded.

2002-10-22  thassine

	* trunk/src/graphics/project.cpp, trunk/src/target3/t3project.cpp:
	  plane/volrend/surface command strings added.

2002-10-21  thassine

	* trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/common/search.cpp, trunk/src/graphics/project.cpp,
	  trunk/src/target2/t2project.cpp,
	  trunk/src/target3/t3project.cpp: added the
	  random/systematic/montecarlo conformational search commands.
	* trunk/src/graphics/project.cpp, trunk/src/target3/t3project.cpp,
	  trunk/src/target3/t3views.cpp: the add light-operation is a bit
	  improved.

2002-10-17  thassine

	* trunk/src/graphics/project.cpp, trunk/src/graphics/project.h,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
	  trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h,
	  trunk/src/target3/t3views.cpp: the command interpreter added;
	  now initially only commands help and add light works.

2002-10-16  thassine

	* trunk/src/common/eng1_mm_default.cpp,
	  trunk/src/common/eng1_mm_prmfit.cpp,
	  trunk/src/common/tab_mm_default.cpp,
	  trunk/src/common/tab_mm_prmfit.cpp,
	  trunk/src/target3/glade/setup_druid.cpp,
	  trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
	  setup changes and possible mol.mech. error messages are now
	  displayed in the new logbox.

2002-10-15  thassine

	* trunk/src/common/model.cpp, trunk/src/target3/t3project.cpp:
	  moved output from console to output box; CalcEnergy and GeomOpt.

2002-10-14  thassine

	* trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h,
	  trunk/src/target3/t3views.cpp: a text log box was added to the
	  GUI. works now for CalcEnergy and GeomOpt operations.

2002-10-05  thassine

	* trunk/src/common/model.cpp, trunk/src/target3/t3dialog.cpp:
	  after the aa2sf conversion, the setup is automatically set
	  suitable for doing calculations with the simplified model.

2002-10-04  thassine

	* trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp: the
	  values of model::sf_types array are now the same as those in the
	  atom::sf_atmtp records.
	* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/typedef.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/plane.h, trunk/src/graphics/project.cpp,
	  trunk/src/graphics/project.h, trunk/src/graphics/ribbon.cpp,
	  trunk/src/graphics/ribbon.h, trunk/src/graphics/spline.cpp,
	  trunk/src/graphics/spline.h: the use of typedef- or
	  template-based arrays (see typedef.h) seems to be a continuous
	  source of memory-handling bugs. therefore removed all such
	  constructs and banned their future use as well (removed from
	  typedef.h).
	* trunk/src/common/model.cpp: more fixes to aa2sf conversion
	  (temporary coordinate handling).
	* trunk/src/common/model.cpp, trunk/src/common/model.h: a
	  potential bug related to aa2sf conversion is fixed.

2002-10-03  thassine

	* trunk/src/common/model.cpp, trunk/src/common/utility.cpp: a few
	  changes here and there...
	* trunk/src/common/oldfiles.cpp: the oldfiles.cpp file was added.
	* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
	  trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/eng2_mm_sf.cpp, trunk/src/common/eng2_mm_sf.h,
	  trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
	  trunk/src/common/engine.h, trunk/src/common/model.cpp,
	  trunk/src/common/model.h,
	  trunk/src/target3/glade/setup_druid.cpp: an initial version of
	  the new file format is now added; needs some futher testing
	  however.

2002-09-12  thassine

	* trunk/src/target3/t3dialog.cpp: a warning message was added
	  (readpdb).

2002-09-11  thassine

	* trunk/src/graphics/ribbon.cpp, trunk/src/target3/t3dialog.cpp,
	  trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
	  the ribbon object now can handle both all-atom and simplified
	  peptides/proteins. set #define ENABLE_SIMPLIFIED in config.h
	  before compiling. how to use/try: first use
	  File/ExtraTools/ImportPDB to read the file in and then
	  File/ExtraTools/Convert_aa2sf for getting the simplified
	  presentation (you can't save it yet). then Objects/Ribbon.

2002-09-10  thassine

	* trunk/bin/parameters/builder/amino.txt,
	  trunk/src/common/seqbuild.cpp, trunk/src/common/utility.cpp: the
	  DefineSecondaryStructure() function now works with simplified
	  residues as well; also a ribbon bug is fixed.
	* trunk/src/common/model.cpp, trunk/src/common/seqbuild.cpp,
	  trunk/src/common/seqbuild.h: the seqbuilder::Identify() now
	  handles correctly also the simplified chains.

2002-09-08  thassine

	* trunk/src/Doxyfile, trunk/src/Makefile.OLD,
	  trunk/src/common/atom.h, trunk/src/common/bond.h,
	  trunk/src/common/conjgrad.h, trunk/src/common/eng1_sf.h,
	  trunk/src/common/engine.h, trunk/src/common/model.h: changed the
	  docs system into a doxygen-based one. now using /// as a brief
	  comment /** and this as a detailed comment. */ int example;
	  ///< this is for comments at end of statements.

2002-09-07  thassine

	* trunk/src/target1/t1m_mm2param_cpp.h,
	  trunk/src/target1/t1m_mm2param_h.h: removed some old files from
	  the console target.
	* trunk/src/target1/t1m_mm1param_cpp.h,
	  trunk/src/target1/t1m_mm1param_h.h,
	  trunk/src/target1/t1m_param_mm_cpp.h,
	  trunk/src/target1/t1m_param_mm_h.h,
	  trunk/src/target1/t1m_param_sf_cpp.h,
	  trunk/src/target1/t1m_param_sf_h.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h: some
	  filenames changed at the console target...

2002-09-06  thassine

	* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp: the sf
	  is now in sync with the version in MANY_PROJECTS_BRANCH.

2002-09-05  thassine

	* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h: in sf,
	  all terms except the solvation one works like before.
	* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h: the
	  nbt1 terms work now in sf.
	* trunk/src/common/eng1_sf.cpp: minor bugs fixed in bonded-term
	  creation in the sf.

2002-09-04  thassine

	* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h:
	  continued to port the sf stuff.

2002-09-03  thassine

	* trunk/src/common/atom.cpp, trunk/src/common/eng1_mm.cpp,
	  trunk/src/common/eng1_mm_default.cpp,
	  trunk/src/common/eng1_mm_prmfit.cpp,
	  trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
	  trunk/src/common/eng1_qm_mopac.cpp,
	  trunk/src/common/eng1_qm_mpqc.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/eng2_mm_sf.h, trunk/src/common/eng2_qm_mm.h,
	  trunk/src/common/engine.cpp, trunk/src/common/filetrans.cpp,
	  trunk/src/common/intcrd.cpp, trunk/src/common/model.cpp,
	  trunk/src/common/seqbuild.cpp,
	  trunk/src/common/tab_mm_prmfit.cpp,
	  trunk/src/graphics/project.cpp, trunk/src/graphics/ribbon.cpp,
	  trunk/src/target1/t1m_mm1param_cpp.h,
	  trunk/src/target1/t1m_mm2param_cpp.h,
	  trunk/src/target3/glade/setup_druid.cpp,
	  trunk/src/target3/glade_dialog.cpp,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3project.cpp: checked the bug report messages
	  in various little run-time tests; they now all carry a BUG: tag.
	* trunk/src/common/atom.h, trunk/src/common/bond.cpp,
	  trunk/src/common/bond.h, trunk/src/common/eng1_sf.cpp,
	  trunk/src/common/eng1_sf.h, trunk/src/common/engine.cpp,
	  trunk/src/common/model.cpp, trunk/src/graphics/project.cpp: some
	  improvements added to sf.

2002-09-02  thassine

	* trunk/src/common/bond.cpp, trunk/src/common/bond.h,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/model.cpp, trunk/src/graphics/project.cpp: the
	  all-atoms -> simplified conversion seems to work now.

2002-08-31  thassine

	* trunk/src/common/eng1_qm_mpqc.cpp,
	  trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
	  trunk/src/target3/glade/setup_druid.cpp,
	  trunk/src/target3/glade/setup_druid.glade: updated the
	  mpqc-related stuff; now there are qm/mm engine classes for both
	  mopac and mpqc. they seem to work technically fine, but without
	  any glue code the qm and mm parts are not interacting at all.
	  yet.
	* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
	  trunk/src/common/eng1_mm_default.cpp,
	  trunk/src/common/eng1_mm_prmfit.cpp: the qm_mm bug was because
	  connectivity records used (global) indices. now the connectivity
	  records use pointers instead of indices and now eng2_qm_mm works
	  like expected (when there is no glue code between the mm and qm
	  parts).

2002-08-30  thassine

	* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
	  trunk/src/common/eng1_mm_default.cpp,
	  trunk/src/common/eng1_mm_prmfit.cpp,
	  trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
	  trunk/src/common/eng1_qm_mopac.cpp,
	  trunk/src/common/eng1_qm_mopac.h, trunk/src/common/eng1_sf.cpp,
	  trunk/src/common/eng1_sf.h, trunk/src/common/eng2_qm_mm.cpp,
	  trunk/src/common/engine.cpp, trunk/src/common/engine.h,
	  trunk/src/common/model.h, trunk/src/common/tab_mm_default.cpp,
	  trunk/src/common/tab_mm_prmfit.cpp,
	  trunk/src/target2/t2project.cpp: the eng classes now use local
	  instead of global atom numbering (more like the old system).
	  there is a nonbonded-term bug in qmmm but otherwise it looks
	  good. sf only compiles.
	* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
	  trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/eng2_mm_sf.cpp, trunk/src/common/eng2_mm_sf.h,
	  trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
	  trunk/src/common/engine.cpp, trunk/src/common/engine.h,
	  trunk/src/target2/t2project.cpp, trunk/src/target2/t2project.h,
	  trunk/src/target3/glade/setup_druid.cpp: the setup classes are
	  now initialized correctly. setup::GetMaxEngineIndex() renamed to
	  setup::GetEngineCount().
	* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/eng2_mm_sf.cpp, trunk/src/common/eng2_mm_sf.h,
	  trunk/src/target3/glade/setup_druid.cpp: ok, everything compiles
	  now, including the simplified forcefield stuff.
	* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/engine.cpp, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/seqbuild.cpp,
	  trunk/src/common/tab_mm_default.cpp,
	  trunk/src/common/tab_mm_prmfit.cpp,
	  trunk/src/graphics/project.cpp,
	  trunk/src/target1/t1m_mm2param_cpp.h: continued porting the
	  simplified forcefield here (not ready yet, doesn't compile, and
	  needs file format changes). modified seqbuider::Indentify() so
	  that it would also detect simplified protein/peptide chains (not
	  ready yet). converted the bool atom::selected flag into i32u
	  atom::flags that can carry more information.

2002-08-29  thassine

	* trunk/src/common/model.cpp, trunk/src/common/seqbuild.cpp,
	  trunk/src/target1/Makefile.OLD,
	  trunk/src/target1/t1m_mm1param_cpp.h,
	  trunk/src/target1/t1m_mm1param_h.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target2/t2project.cpp,
	  trunk/src/target3/t3project.cpp: the new model::UpdateChains()
	  function now updates the chain/residue information. all targets
	  brought up-to-date again.

2002-08-28  thassine

	* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
	  trunk/src/common/eng1_mm.cpp, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/search.cpp,
	  trunk/src/common/seqbuild.cpp, trunk/src/graphics/project.cpp,
	  trunk/src/target2/t2project.cpp,
	  trunk/src/target3/glade/setup_druid.glade: many changes added.
	  GatherGroups() renamed to UpdateGroups(). is_index_clean and
	  is_groups_clean flags are added so that it would be better
	  defined whether groups/chains/etc information is up-to-date or
	  not.
	* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
	  trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
	  trunk/src/common/engine.h, trunk/src/common/model.h,
	  trunk/src/target3/glade/setup_druid.cpp,
	  trunk/src/target3/glade/setup_druid.glade,
	  trunk/src/target3/glade/setup_druid.h: the setup_druid now
	  works, with minimal functionality so that one can select between
	  an MM and QM model.

2002-08-27  thassine

	* trunk/src/common/atom.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/intcrd.cpp, trunk/src/common/model.cpp: some
	  bugfixes added; the conformational search tools should work now.
	* trunk/src/target3/glade/file_import_dialog.cpp,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
	  trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
	  added the File/ExtraTools also here.

2002-08-21  thassine

	* trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/seqbuild.cpp,
	  trunk/src/common/seqbuild.h, trunk/src/graphics/ribbon.cpp,
	  trunk/src/target2/t2project.cpp,
	  trunk/src/target3/t3project.cpp: improvements added to the
	  seqbuilder and chn_info classes.

2002-08-01  thassine

	* trunk/src/common/engine.cpp, trunk/src/common/intcrd.cpp,
	  trunk/src/common/model.cpp: bounds checking added to CopyCRD()
	  functions; bugs fixed from the new crd_set data storage system;
	  WARNING there still is something wrong with the intcrd class
	  (geometries get distorted).

2002-07-31  thassine

	* trunk/src/graphics/camera.cpp: the fps counter added also to
	  HEAD.

2002-07-30  thassine

	* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
	  trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_qm.cpp,
	  trunk/src/common/eng1_qm_mopac.cpp, trunk/src/common/engine.cpp,
	  trunk/src/common/filetrans.cpp, trunk/src/common/intcrd.cpp,
	  trunk/src/common/intcrd.h, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/seqbuild.cpp,
	  trunk/src/common/tab_mm_prmfit.cpp,
	  trunk/src/common/utility.cpp, trunk/src/graphics/project.cpp,
	  trunk/src/graphics/ribbon.cpp, trunk/src/graphics/views.cpp: the
	  coordinate data storage at atom class is converted into a less
	  error-prone system. it's no more possible to access the data
	  directly, but only using the atom::GetCRD() and atom::SetCRD()
	  member functions.

2002-07-23  thassine

	* trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/graphics/project.cpp, trunk/src/target2/t2project.cpp:
	  the memory management scheme of crd_set objects is now simpler.
	* trunk/src/common/engine.h, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/search.cpp,
	  trunk/src/common/search.h, trunk/src/target2/t2project.cpp,
	  trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
	  the search tool improvements ported also here.
	* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
	  trunk/src/common/engine.h: added some fixes to SF, althought it
	  does not even compile yet; therefore the ENABLE_SIMPLIFIED macro
	  is disabled at config.h

2002-06-20  thassine

	* trunk/src/common/prefs.h, trunk/src/target3/t3prefs.cpp,
	  trunk/src/target3/t3prefs.h, trunk/src/target3/t3project.cpp:
	  added the v0.90 bugfixes also to HEAD.

2002-06-19  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/atom.cpp, trunk/src/common/atom.h,
	  trunk/src/common/eng1_mm.h, trunk/src/common/eng1_sf.cpp,
	  trunk/src/common/eng1_sf.h, trunk/src/common/engine.h,
	  trunk/src/common/model.cpp, trunk/src/common/moldyn.cpp,
	  trunk/src/common/seqbuild.h, trunk/src/graphics/project.cpp,
	  trunk/src/target1/config.h.OLD, trunk/src/target2/config.h.OLD,
	  trunk/src/target2/t2project.cpp, trunk/src/target3/config.h.OLD:
	  added some changes that were needed to port the simplified
	  forcefield of mine to HEAD. it's not working yet and not even
	  compile yet, but it doesn't matter since one have to set the
	  ENABLE_SIMPLIFIED macro to compile that stuff in...

2002-06-17  thassine

	* trunk/Makefile.in, trunk/src/common/define.h,
	  trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/tab_mm_default.cpp,
	  trunk/src/target3/glade/file_export_dialog.cpp,
	  trunk/src/target3/glade/file_export_dialog.h,
	  trunk/src/target3/glade/file_import_dialog.cpp,
	  trunk/src/target3/glade/file_import_dialog.h,
	  trunk/src/target3/glade/geomopt_dialog.cpp,
	  trunk/src/target3/glade/geomopt_dialog.h,
	  trunk/src/target3/glade/moldyn_dialog.cpp,
	  trunk/src/target3/glade/moldyn_dialog.h,
	  trunk/src/target3/glade/setup_druid.cpp,
	  trunk/src/target3/glade/setup_druid.h,
	  trunk/src/target3/glade/trajview_dialog.cpp,
	  trunk/src/target3/glade/trajview_dialog.h,
	  trunk/src/target3/glade_dialog.cpp,
	  trunk/src/target3/glade_dialog.h,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3project.cpp:
	  the glade files are now installed correctly by make install.

2002-06-14  thassine

	* trunk/src/Makefile.OLD: fixed src/Makefile.OLD clean: also in
	  HEAD.

2002-06-13  thassine

	* trunk/src/common/conjgrad.cpp, trunk/src/common/conjgrad.h: also
	  copied conjgrad changes to HEAD.

2002-06-08  thassine

	* trunk/src/target3/glade/setup_druid.cpp,
	  trunk/src/target3/glade/setup_druid.glade,
	  trunk/src/target3/glade/setup_druid.h,
	  trunk/src/target3/t3main.cpp: the setup_druid can now correctly
	  change the pages with prev/next buttons.

2002-06-07  thassine

	* trunk/src/target3/glade/Makefile.OLD,
	  trunk/src/target3/glade/Makefile.in,
	  trunk/src/target3/glade/setup_druid.cpp,
	  trunk/src/target3/glade/setup_druid.glade,
	  trunk/src/target3/glade/setup_druid.h,
	  trunk/src/target3/t3project.cpp: added an initial version of the
	  setup druid (nothing except cancel works).
	* trunk/src/target3/glade/Makefile.OLD,
	  trunk/src/target3/glade/Makefile.in,
	  trunk/src/target3/glade/file_export_dialog.cpp,
	  trunk/src/target3/glade/file_export_dialog.glade,
	  trunk/src/target3/glade/file_export_dialog.h,
	  trunk/src/target3/glade/file_import_dialog.cpp,
	  trunk/src/target3/glade/file_import_dialog.glade,
	  trunk/src/target3/glade/file_import_dialog.h,
	  trunk/src/target3/t3project.cpp: added the file import/export
	  dialogs.
	* trunk/src/target3/glade/Makefile.OLD,
	  trunk/src/target3/glade/Makefile.in,
	  trunk/src/target3/glade/geomopt_dialog.cpp,
	  trunk/src/target3/glade/geomopt_dialog.glade,
	  trunk/src/target3/glade/geomopt_dialog.h,
	  trunk/src/target3/glade/moldyn_dialog.cpp,
	  trunk/src/target3/glade/moldyn_dialog.glade,
	  trunk/src/target3/glade/moldyn_dialog.h,
	  trunk/src/target3/glade/trajview_dialog.cpp,
	  trunk/src/target3/glade/trajview_dialog.glade,
	  trunk/src/target3/glade/trajview_dialog.h,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3project.cpp,
	  trunk/src/target3/t3project.h: new dialogs added, and dialog
	  memory leaks fixed (hopefully). the dialogs are now always
	  created with new, and delete is always called at destroy signal
	  handler of the dialog.

2002-06-05  thassine

	* trunk/src/Makefile.OLD: added some Makefile tweaks.
	* trunk/src/target3/glade/Makefile.OLD,
	  trunk/src/target3/glade/geomopt_dialog.cpp,
	  trunk/src/target3/glade/geomopt_dialog.glade,
	  trunk/src/target3/glade/geomopt_dialog.h,
	  trunk/src/target3/glade_dialog.h,
	  trunk/src/target3/t3project.cpp: the geomopt dialog now works
	  using libglade.

2002-06-03  thassine

	* trunk/openbabel/fileformat.h: oops, my mistake. of course there
	  were nothing wrong with fileformat.h but I had an obsolete
	  Makefile. the changes are reverted.
	* trunk/openbabel/fileformat.h: there were some undefined
	  functions at fileformat.cpp; just made some dummy functions in
	  fileformat.h so that OB can be compiled...

2002-05-31  hutchisn

	* trunk/configure, trunk/configure.in,
	  trunk/miniMOPAC/Makefile.in, trunk/src/common/Makefile.in,
	  trunk/src/graphics/Makefile.in, trunk/src/target3/Makefile.in,
	  trunk/src/target3/glade/Makefile.in,
	  trunk/src/target3/glade/geomopt_dialog.h: Updated makefiles for
	  libglade, etc.
	* trunk/openbabel/Makefile.in, trunk/openbabel/Vector.cpp,
	  trunk/openbabel/Vector.h, trunk/openbabel/alchemy.cpp,
	  trunk/openbabel/amber.cpp, trunk/openbabel/aromatic.h,
	  trunk/openbabel/aromatic.txt, trunk/openbabel/atom.cpp,
	  trunk/openbabel/atomtyp.h, trunk/openbabel/atomtyp.txt,
	  trunk/openbabel/balst.cpp, trunk/openbabel/base.cpp,
	  trunk/openbabel/base.h, trunk/openbabel/bgf.cpp,
	  trunk/openbabel/bin2hex.pl, trunk/openbabel/binary.cpp,
	  trunk/openbabel/binary.h, trunk/openbabel/binary_io.cpp,
	  trunk/openbabel/binary_io.h, trunk/openbabel/bitgrid.cpp,
	  trunk/openbabel/bitgrid.h, trunk/openbabel/bitvec.h,
	  trunk/openbabel/bond.cpp, trunk/openbabel/bond.txt,
	  trunk/openbabel/box.cpp, trunk/openbabel/c3d.cpp,
	  trunk/openbabel/cacao.cpp, trunk/openbabel/cache.cpp,
	  trunk/openbabel/car.cpp, trunk/openbabel/chains.cpp,
	  trunk/openbabel/chdrw.cpp, trunk/openbabel/chiral.cpp,
	  trunk/openbabel/chiral.h, trunk/openbabel/cml.cpp,
	  trunk/openbabel/commandline.h, trunk/openbabel/csr.cpp,
	  trunk/openbabel/cssr.cpp, trunk/openbabel/ctransform.cpp,
	  trunk/openbabel/ctransform.h, trunk/openbabel/data.cpp,
	  trunk/openbabel/data.h, trunk/openbabel/dmol.cpp,
	  trunk/openbabel/element.h, trunk/openbabel/extable.h,
	  trunk/openbabel/extable.txt, trunk/openbabel/feat.cpp,
	  trunk/openbabel/fh.cpp, trunk/openbabel/fileformat.cpp,
	  trunk/openbabel/fileformat.h, trunk/openbabel/gamess.cpp,
	  trunk/openbabel/gaussian.cpp, trunk/openbabel/generic.cpp,
	  trunk/openbabel/generic.h, trunk/openbabel/ghemical.cpp,
	  trunk/openbabel/grid.h, trunk/openbabel/gromos96.cpp,
	  trunk/openbabel/hin.cpp, trunk/openbabel/jaguar.cpp,
	  trunk/openbabel/main.cpp, trunk/openbabel/matrix.cpp,
	  trunk/openbabel/matrix.h, trunk/openbabel/mmod.cpp,
	  trunk/openbabel/mol.cpp, trunk/openbabel/mol.h,
	  trunk/openbabel/molchrg.cpp, trunk/openbabel/molchrg.h,
	  trunk/openbabel/molvector.cpp, trunk/openbabel/molvector.h,
	  trunk/openbabel/mopac.cpp, trunk/openbabel/mpqc.cpp,
	  trunk/openbabel/nwchem.cpp, trunk/openbabel/obifstream.h,
	  trunk/openbabel/oblib.dsp, trunk/openbabel/obutil.cpp,
	  trunk/openbabel/obutil.h, trunk/openbabel/parsmart.cpp,
	  trunk/openbabel/parsmart.h, trunk/openbabel/parsmi.cpp,
	  trunk/openbabel/patty.cpp, trunk/openbabel/patty.h,
	  trunk/openbabel/pdb.cpp, trunk/openbabel/phmodel.cpp,
	  trunk/openbabel/phmodel.h, trunk/openbabel/phmodel.txt,
	  trunk/openbabel/phmodeldata.h, trunk/openbabel/qchem.cpp,
	  trunk/openbabel/report.cpp, trunk/openbabel/resdata.h,
	  trunk/openbabel/ring.cpp, trunk/openbabel/ring.h,
	  trunk/openbabel/rotor.cpp, trunk/openbabel/rotor.h,
	  trunk/openbabel/smarts.cpp, trunk/openbabel/smarts.h,
	  trunk/openbabel/smi.cpp, trunk/openbabel/smi.h,
	  trunk/openbabel/tinker.cpp, trunk/openbabel/tokenst.cpp,
	  trunk/openbabel/typer.cpp, trunk/openbabel/typer.h,
	  trunk/openbabel/types.h, trunk/openbabel/unichem.cpp,
	  trunk/openbabel/viewmol.cpp, trunk/openbabel/xed.cpp,
	  trunk/openbabel/xyz.cpp: Merge in current Open Babel (w/ CML and
	  proper namespace support).

2002-05-31  thassine

	* trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
	  trunk/src/target3/Makefile.in,
	  trunk/src/target3/glade/Makefile.in: fixes added to makefiles;
	  now the configuration works otherwise except that libglade incs
	  and libs are missing.

2002-05-30  thassine

	* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
	  promoted the version number to 0.85 in the HEAD branch.
	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/src/common/Makefile.in, trunk/src/common/eng1_sf.cpp,
	  trunk/src/common/tab_mm_default.cpp,
	  trunk/src/graphics/Makefile.in, trunk/src/target3/Makefile.in,
	  trunk/src/target3/glade/Makefile.in: minor fixes like changed
	  directories etc added.
	* trunk/bin/parameters/param_mm,
	  trunk/bin/parameters/param_mm/default,
	  trunk/bin/parameters/param_mm/default/atomtypes.txt,
	  trunk/bin/parameters/param_mm/default/parameters1.txt,
	  trunk/bin/parameters/param_mm/default/parameters2.txt,
	  trunk/bin/parameters/param_mm/default/parameters3.txt,
	  trunk/bin/parameters/param_mm/default/parameters4.txt,
	  trunk/bin/parameters/param_mm/default/parameters5.txt,
	  trunk/bin/parameters/param_sf,
	  trunk/bin/parameters/param_sf/default,
	  trunk/bin/parameters/param_sf/default/loopdip.txt,
	  trunk/bin/parameters/param_sf/default/looptor.txt,
	  trunk/bin/parameters/param_sf/default/nonbonded.txt,
	  trunk/src/some-extra-files/newfile.cpp,
	  trunk/src/some-extra-files/newfile.h: added new files to
	  bin/parameters and some minor stuff.
	* trunk/bin/parameters/mm1param, trunk/bin/parameters/mm2param:
	  removed old files under bin/parameters.
	* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
	  trunk/src/common/bond.cpp, trunk/src/common/bond.h,
	  trunk/src/common/define.h, trunk/src/common/eng1_mm.cpp,
	  trunk/src/common/eng1_mm.h,
	  trunk/src/common/eng1_mm_default.cpp,
	  trunk/src/common/eng1_mm_default.h,
	  trunk/src/common/eng1_mm_prmfit.cpp,
	  trunk/src/common/eng1_mm_prmfit.h, trunk/src/common/eng1_qm.cpp,
	  trunk/src/common/eng1_qm.h, trunk/src/common/eng1_qm_mopac.cpp,
	  trunk/src/common/eng1_qm_mopac.h,
	  trunk/src/common/eng1_qm_mpqc.cpp,
	  trunk/src/common/eng1_qm_mpqc.h, trunk/src/common/eng1_sf.cpp,
	  trunk/src/common/eng1_sf.h, trunk/src/common/eng2_qm_mm.cpp,
	  trunk/src/common/eng2_qm_mm.h, trunk/src/common/engine.cpp,
	  trunk/src/common/engine.h, trunk/src/common/filetrans.cpp,
	  trunk/src/common/filetrans.h, trunk/src/common/geomopt.cpp,
	  trunk/src/common/geomopt.h, trunk/src/common/intcrd.cpp,
	  trunk/src/common/intcrd.h, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/moldyn.cpp,
	  trunk/src/common/moldyn.h, trunk/src/common/search.cpp,
	  trunk/src/common/search.h, trunk/src/common/seqbuild.cpp,
	  trunk/src/common/seqbuild.h,
	  trunk/src/common/tab_mm_default.cpp,
	  trunk/src/common/tab_mm_default.h,
	  trunk/src/common/tab_mm_prmfit.cpp,
	  trunk/src/common/tab_mm_prmfit.h, trunk/src/common/typedef.h,
	  trunk/src/common/typerule.cpp, trunk/src/common/typerule.h,
	  trunk/src/common/utility.cpp, trunk/src/common/utility.h,
	  trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h,
	  trunk/src/graphics/color.h, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/plane.cpp, trunk/src/graphics/plane.h,
	  trunk/src/graphics/project.cpp, trunk/src/graphics/project.h,
	  trunk/src/graphics/ribbon.cpp, trunk/src/graphics/ribbon.h,
	  trunk/src/graphics/surface.cpp, trunk/src/graphics/surface.h,
	  trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2main.h, trunk/src/target2/t2project.cpp,
	  trunk/src/target2/t2project.h, trunk/src/target2/t2views.cpp,
	  trunk/src/target2/t2views.h, trunk/src/target3/glade_dialog.cpp,
	  trunk/src/target3/glade_dialog.h,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
	  added the new files.
	* trunk/src/common/interface.cpp, trunk/src/common/interface.h,
	  trunk/src/common/matrix.h, trunk/src/common/mm1alg.cpp,
	  trunk/src/common/mm1alg.h, trunk/src/common/mm1eng.cpp,
	  trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.cpp,
	  trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.cpp,
	  trunk/src/common/mm1eng9.h, trunk/src/common/mm1ic.cpp,
	  trunk/src/common/mm1ic.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
	  trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.cpp,
	  trunk/src/common/mm1util.h, trunk/src/common/mm2alg.cpp,
	  trunk/src/common/mm2alg.h, trunk/src/common/mm2eng.cpp,
	  trunk/src/common/mm2eng.h, trunk/src/common/mm2mdl.cpp,
	  trunk/src/common/mm2mdl.h, trunk/src/common/mm2util.cpp,
	  trunk/src/common/mm2util.h, trunk/src/common/mm3mdl.cpp,
	  trunk/src/common/mm3mdl.h, trunk/src/common/qm1alg.cpp,
	  trunk/src/common/qm1alg.h, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1eng.cpp,
	  trunk/src/common/qm1eng.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.cpp,
	  trunk/src/common/qm2eng.h, trunk/src/common/qm2mdl.cpp,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/io-jpg.cpp,
	  trunk/src/graphics/io-jpg.h, trunk/src/graphics/io-png.cpp,
	  trunk/src/graphics/io-png.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm2docv.h, trunk/src/graphics/mm2rbn.cpp,
	  trunk/src/graphics/mm2rbn.h, trunk/src/graphics/mm3docv.cpp,
	  trunk/src/graphics/mm3docv.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h, trunk/src/target2/t2docv.cpp,
	  trunk/src/target2/t2docv.h, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2mm2docv.h, trunk/src/target2/t2mm3docv.cpp,
	  trunk/src/target2/t2mm3docv.h, trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.cpp,
	  trunk/src/target2/t2qm2docv.h,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_callbacks.h,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/glade_support.cpp,
	  trunk/src/target3/glade_support.h, trunk/src/target3/t3docv.cpp,
	  trunk/src/target3/t3docv.h, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3mm2docv.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3qm2docv.cpp,
	  trunk/src/target3/t3qm2docv.h: the old/renamed files are removed.
	* trunk/src/target3/glade/README: update the glade README
	* trunk/src/target1/config.h.OLD, trunk/src/target2/config.h.OLD,
	  trunk/src/target3/config.h.OLD,
	  trunk/src/target3/glade/Makefile.OLD,
	  trunk/src/target3/glade/Makefile.in,
	  trunk/src/target3/glade/geomopt_dialog.cpp,
	  trunk/src/target3/glade/geomopt_dialog.glade,
	  trunk/src/target3/glade/geomopt_dialog.h,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src: added changes to config.h.OLD files
	  and src/target3/glade dir.
	* trunk/src/Makefile.OLD, trunk/src/common/Makefile.OLD,
	  trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.OLD,
	  trunk/src/graphics/Makefile.in, trunk/src/target2/Makefile.OLD,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in:
	  the makefiles are updated.
	* trunk/CHANGES: the changelog is updated.
	* trunk/src/Makefile.OLD: test; this goes to HEAD branch...

2002-05-29  thassine

	* trunk/CHANGES: again testing that the OSP_BRANCH is separate;
	  seems to be but cvs2cl picks all commits to the log; I'll start
	  using OSP: identifier when working with the branch in the future.

2002-05-28  thassine

	* trunk/CHANGES: updated the changelog (using cvs2cl again).
	* trunk/src/common/define.h: ooop, reverted the previous.
	* trunk/src/common/define.h: just testing how the branches work.

2002-05-27  thassine

	* trunk/bin/parameters/mm2param/loopdip.txt,
	  trunk/bin/parameters/mm2param/looptor.txt,
	  trunk/bin/parameters/mm2param/nonbonded.txt,
	  trunk/small-utilities/getpdb_cd.cpp,
	  trunk/small-utilities/getpdb_ftp.cpp,
	  trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.h,
	  trunk/src/common/mm2alg.h, trunk/src/common/mm2eng.cpp,
	  trunk/src/common/mm2eng.h, trunk/src/common/mm2mdl.cpp,
	  trunk/src/common/mm2mdl.h, trunk/src/common/mm2util.cpp,
	  trunk/src/common/mm2util.h, trunk/src/common/mm3mdl.cpp,
	  trunk/src/common/mm3mdl.h, trunk/src/graphics/Makefile.OLD,
	  trunk/src/graphics/Makefile.in, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm3docv.cpp, trunk/src/graphics/mm3docv.h,
	  trunk/src/graphics/views.h, trunk/src/target1/Makefile.OLD,
	  trunk/src/target1/t1m_mm2param_cpp.h,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2main.h, trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2mm3docv.cpp, trunk/src/target2/t2mm3docv.h,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in:
	  added some of my own works; not all of this stuff is ready, but
	  I need to start converting them to fit into single-project
	  environment.

2002-05-22  thassine

	* trunk/Makefile.in, trunk/configure, trunk/configure.in:
	  configure script now updated, scripts now compatible with
	  autoconf 2.53

2002-05-21  thassine

	* trunk/aclocal.m4, trunk/configure.in,
	  trunk/src/common/Makefile.OLD, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1e_mpqc.h, trunk/src/config.h.in,
	  trunk/src/graphics/Makefile.OLD, trunk/src/graphics/Makefile.in,
	  trunk/src/target1/Makefile.OLD, trunk/src/target1/config.h.OLD,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/config.h.OLD,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in,
	  trunk/src/target3/config.h.OLD: added the configuration system
	  for MPQC v1/v2 (thanks to Michael); BTW you still have to run
	  autoconf to update the configure script.

2002-05-20  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1e_mpqc.h, trunk/src/graphics/Makefile.OLD,
	  trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
	  trunk/src/target3/Makefile.OLD: support for MPQC v2 was added
	  (but ./configure still needs update).
	* trunk/src/target1/t1m_mm1param_cpp.h,
	  trunk/src/target1/t1m_mm1param_h.h: oops, forgot to add some
	  files last time.

2002-05-17  thassine

	* trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1tab9.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h,
	  trunk/src/target2/t2mm1docv.cpp: added my (so far incomplete)
	  system for fitting MM force field parameters; this stuff is not
	  really working yet.

2002-04-29  thassine

	* trunk/src/common/define.h, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
	  added LABEL_RESIDUE for mm2_docv.

2002-04-17  thassine

	* trunk/src/common/mm2util.cpp, trunk/src/common/model.cpp: a few
	  bugs that freed memory multiple times were fixed. there still
	  remains maaany memory leaks, but they are less dangerous than
	  these.

2002-04-16  thassine

	* trunk/src/common/mm2mdl.cpp, trunk/src/graphics/mm2docv.cpp:
	  some comments and minor fixes added to mm2_mdl.

2002-04-09  thassine

	* trunk/src/graphics/mm2docv.cpp, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3mm2docv.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.h: some colour/label mode
	  improvements added.

2002-04-08  thassine

	* trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
	  trunk/src/graphics/mm2rbn.cpp: some cleanups added to the
	  mm2_docv rendering code - should not change the looks/anything.

2002-04-04  thassine

	* trunk/BUGLIST, trunk/TODO: the BUGLIST and TODO files are now
	  CSV text files - use a spreadsheet program like Gnumeric or
	  StarOffice/Calc to read and/or modify them.
	* trunk/src/graphics/camera.cpp: some cleanups done for the stereo
	  modes; now the effect seems to be independent of orientation.

2002-03-26  hutchisn

	* trunk/openbabel/mol.cpp, trunk/openbabel/pdb.cpp: Fixes
	  OpenBabel PDB import problems (PR #529744 for OpenBabel).

2002-02-28  thassine

	* trunk/ghemical.spec: the .spec file updated; the RPM now does
	  the installation with prefix /usr instead of /usr/local.

2002-02-27  thassine

	* trunk/miniMOPAC/Makefile.in: modified miniMOPAC/Makefile.in so
	  that -O optimization is forced in the miniMOPAC directory.

2002-02-26  thassine

	* trunk/ghemical.spec: some updates added to .spec file.

2002-02-25  thassine

	* trunk/AUTHORS, trunk/bin/ghemical.xpm, trunk/ghemical.spec:
	  added the files for building RedHat binary packages, contributed
	  by Radek Liboska.

2002-02-22  thassine

	* trunk/configure, trunk/configure.in, trunk/src/common/define.h,
	  trunk/src/common/notice.cpp: switch back to development settings.
	* trunk/CHANGES, trunk/INSTALL, trunk/src/common/define.h:
	  changelog updated and all settings are now ready for release as
	  v0.82
	* trunk/src/target3/t3mm1docv.cpp: a small fix added to the
	  library widget generation code.

2002-02-21  thassine

	* trunk/bin/user-docs/index.html,
	  trunk/bin/user-docs/using_cs_tools.html,
	  trunk/bin/user-docs/using_cs_tools01.jpg,
	  trunk/bin/user-docs/using_cs_tools02.jpg,
	  trunk/bin/user-docs/using_cs_tools03.jpg,
	  trunk/bin/user-docs/using_cs_tools04.jpg,
	  trunk/bin/user-docs/using_cs_tools05.jpg: user's manual is
	  enhanced; it now contains a section about 1D and 2D energy plots.

2002-02-20  thassine

	* trunk/INSTALL, trunk/src/common/mm1alg.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm2alg.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/qm1alg.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/target1/Makefile.OLD,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target3/Makefile.OLD,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp: old makefiles updated, and the
	  code added for geomopt dialogs + calculations that separates the
	  different termination criteria and makes them optional. it also
	  prints out which criteria was used to terminate the optimization.

2002-02-18  hutchisn

	* trunk/openbabel/pdb.cpp: Don't try to run PerceiveBondOrders
	  yet... this seems to be very buggy.
	* trunk/openbabel/Makefile.in, trunk/openbabel/alchemy.cpp,
	  trunk/openbabel/amber.cpp, trunk/openbabel/aromatic.txt,
	  trunk/openbabel/atom.cpp, trunk/openbabel/balst.cpp,
	  trunk/openbabel/box.cpp, trunk/openbabel/c3d.cpp,
	  trunk/openbabel/cacao.cpp, trunk/openbabel/car.cpp,
	  trunk/openbabel/ccc.cpp, trunk/openbabel/commandline.h,
	  trunk/openbabel/ctransform.h, trunk/openbabel/data.cpp,
	  trunk/openbabel/data.h, trunk/openbabel/dmol.cpp,
	  trunk/openbabel/element.h, trunk/openbabel/element.txt,
	  trunk/openbabel/extable.h, trunk/openbabel/extable.txt,
	  trunk/openbabel/feat.cpp, trunk/openbabel/gamess.cpp,
	  trunk/openbabel/gaussian.cpp, trunk/openbabel/ghemical.cpp,
	  trunk/openbabel/grid.h, trunk/openbabel/hin.cpp,
	  trunk/openbabel/jaguar.cpp, trunk/openbabel/main.cpp,
	  trunk/openbabel/mol.cpp, trunk/openbabel/mol.h,
	  trunk/openbabel/mopac.cpp, trunk/openbabel/mpqc.cpp,
	  trunk/openbabel/nwchem.cpp, trunk/openbabel/obutil.cpp,
	  trunk/openbabel/obutil.h, trunk/openbabel/patty.cpp,
	  trunk/openbabel/pdb.cpp, trunk/openbabel/phmodel.cpp,
	  trunk/openbabel/qchem.cpp, trunk/openbabel/report.cpp,
	  trunk/openbabel/rotor.cpp, trunk/openbabel/smarts.h,
	  trunk/openbabel/typer.cpp, trunk/openbabel/unichem.cpp,
	  trunk/openbabel/version.h.in, trunk/openbabel/xyz.cpp: Updated
	  Open Babel code, including preliminary bond-order perception.

2002-01-31  thassine

	* trunk/miniMOPAC/README: some documentation fixes for miniMOPAC.
	* trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade_interface.cpp: the check boxes for
	  different termination criteria were added to the geomopt GLADE
	  dialog; their states are not yet checked however.

2002-01-25  hutchisn

	* trunk/small-utilities/Makefile, trunk/small-utilities/README,
	  trunk/small-utilities/symmetry.c: Add Symmetry program (from
	  Sergei Pachkovsky, who gave OK to use in Ghemical)

2002-01-25  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/define.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/graphics/Makefile.OLD,
	  trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
	  trunk/src/target3/Makefile.OLD: some comments added, and old
	  makefiles are fixed/updated.

2002-01-25  hutchisn

	* trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/t3mm1docv.cpp: Make sure we actually set the
	  optimization limits after the dialog completes...
	* trunk/openbabel/unichem.cpp: Fix unichem XYZ support (read
	  should expect atomic numbers in Unichem files).

2002-01-22  thassine

	* trunk/src/target3/glade_interface.h,
	  trunk/src/target3/glade_support.cpp: verified that /target3 and
	  /target3/glade/src keep in sync...

2002-01-21  hutchisn

	* trunk/src/common/mm1alg.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm2alg.h, trunk/src/common/qm1alg.h,
	  trunk/src/common/qm1mdl.cpp,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_support.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp: Add support for terminating
	  geometry optimizations "early" based on delta E or
	  small gradient. Currently does not have a UI for termination
	  based on small
	  step, and this is set to 1.0e-12 so this should never happen.

2002-01-21  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/qm1mdl.cpp: the
	  geomopt output now displays accurate gradient vector lengths.
	* trunk/INSTALL, trunk/oelib: removed .cvsignore from the oelib
	  directory.

2002-01-18  hutchisn

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/qm1mdl.cpp: Added
	  user-friendly display of the step-size, displacement and delta E
	  in geom opt.
	  Seems to indicate that most geom opt can quit early with tests
	  for displ. and/or delta E.

2002-01-15  thassine

	* trunk/src/graphics/mm1docv.cpp: in the 1D and 2D energy plotting
	  tools of mm1_docv it is now possible to select a smaller range
	  of angles if needed, and the final energy can be calculated also
	  using QM methods (so now it's possible to compare MM results
	  against QM results as well as compare different QM results).

2002-01-14  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/graphics/Makefile.OLD,
	  trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
	  trunk/src/target3/Makefile.OLD: converted the old makefiles to
	  use the new openbabel-paths.

2002-01-14  hutchisn

	* trunk/src/common/filetrans.cpp: Delete filename at appropriate
	  time--Babel uses it for a Title when exporting.
	* trunk/configure, trunk/configure.in: Add almost-forgotten
	  configure tests contributed by Michael Banck--check for f2c if
	  g2c is not found (and give an error if neither is found).

2002-01-11  hutchisn

	* trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
	  trunk/src/target3/Makefile.in: Makefile fixes.

2002-01-10  hutchisn

	* trunk/configure, trunk/configure.in,
	  trunk/src/common/Makefile.in, trunk/src/target3/Makefile.in:
	  Added support for Michael Banck's SC autoconf macros to simplify
	  building MPQC.
	* trunk/Makefile.in, trunk/PROJECT, trunk/config.guess,
	  trunk/config.sub, trunk/configure, trunk/configure.in,
	  trunk/oelib/GNULICENSE.txt, trunk/oelib/Makefile.in,
	  trunk/oelib/OELibPrimer.html, trunk/oelib/StdAfx.cpp,
	  trunk/oelib/StdAfx.h, trunk/oelib/Vector.cpp,
	  trunk/oelib/Vector.h, trunk/oelib/alchemy.cpp,
	  trunk/oelib/amber.cpp, trunk/oelib/aromatic.h,
	  trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
	  trunk/oelib/atomtyp.h, trunk/oelib/atomtyp.txt,
	  trunk/oelib/balst.cpp, trunk/oelib/base.cpp, trunk/oelib/base.h,
	  trunk/oelib/bgf.cpp, trunk/oelib/bin2hex.pl,
	  trunk/oelib/binary.cpp, trunk/oelib/binary.h,
	  trunk/oelib/binary_io.cpp, trunk/oelib/binary_io.h,
	  trunk/oelib/bitgrid.cpp, trunk/oelib/bitgrid.h,
	  trunk/oelib/bitvec.cpp, trunk/oelib/bitvec.h,
	  trunk/oelib/bond.cpp, trunk/oelib/box.cpp, trunk/oelib/c3d.cpp,
	  trunk/oelib/cacao.cpp, trunk/oelib/cache.cpp,
	  trunk/oelib/car.cpp, trunk/oelib/ccc.cpp,
	  trunk/oelib/chains.cpp, trunk/oelib/chains.h,
	  trunk/oelib/chdrw.cpp, trunk/oelib/chiral.cpp,
	  trunk/oelib/chiral.h, trunk/oelib/commandline.cpp,
	  trunk/oelib/commandline.h, trunk/oelib/configure,
	  trunk/oelib/csr.cpp, trunk/oelib/cssr.cpp,
	  trunk/oelib/ctransform.cpp, trunk/oelib/ctransform.h,
	  trunk/oelib/cwrap.cpp, trunk/oelib/cwrap.h,
	  trunk/oelib/data.cpp, trunk/oelib/data.h, trunk/oelib/dmol.cpp,
	  trunk/oelib/element.h, trunk/oelib/element.txt,
	  trunk/oelib/extable.h, trunk/oelib/extable.txt,
	  trunk/oelib/feat.cpp, trunk/oelib/fh.cpp,
	  trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
	  trunk/oelib/gamess.cpp, trunk/oelib/gaussian.cpp,
	  trunk/oelib/generic.cpp, trunk/oelib/generic.h,
	  trunk/oelib/ghemical.cpp, trunk/oelib/globals.cpp,
	  trunk/oelib/grid.cpp, trunk/oelib/grid.h,
	  trunk/oelib/gromos96.cpp, trunk/oelib/hin.cpp,
	  trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
	  trunk/oelib/matrix.cpp, trunk/oelib/matrix.h,
	  trunk/oelib/mdl.cpp, trunk/oelib/mmod.cpp, trunk/oelib/mol.cpp,
	  trunk/oelib/mol.h, trunk/oelib/mol2.cpp,
	  trunk/oelib/molchrg.cpp, trunk/oelib/molchrg.h,
	  trunk/oelib/molvector.cpp, trunk/oelib/molvector.h,
	  trunk/oelib/mopac.cpp, trunk/oelib/mpqc.cpp,
	  trunk/oelib/nwchem.cpp, trunk/oelib/oeifstream.h,
	  trunk/oelib/oelib.dsp, trunk/oelib/oelib.dsw,
	  trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
	  trunk/oelib/parsmart.cpp, trunk/oelib/parsmart.h,
	  trunk/oelib/parsmi.cpp, trunk/oelib/patty.cpp,
	  trunk/oelib/patty.h, trunk/oelib/pdb.cpp,
	  trunk/oelib/phmodel.cpp, trunk/oelib/phmodel.h,
	  trunk/oelib/phmodel.txt, trunk/oelib/phmodeldata.h,
	  trunk/oelib/qchem.cpp, trunk/oelib/quat.c, trunk/oelib/rand.cpp,
	  trunk/oelib/report.cpp, trunk/oelib/resdata.h,
	  trunk/oelib/resdata.txt, trunk/oelib/ring.cpp,
	  trunk/oelib/ring.h, trunk/oelib/rotor.cpp, trunk/oelib/rotor.h,
	  trunk/oelib/smarts.cpp, trunk/oelib/smarts.h,
	  trunk/oelib/smi.cpp, trunk/oelib/smi.h, trunk/oelib/tinker.cpp,
	  trunk/oelib/tokenst.cpp, trunk/oelib/typer.cpp,
	  trunk/oelib/typer.h, trunk/oelib/types.h, trunk/oelib/types.txt,
	  trunk/oelib/unichem.cpp, trunk/oelib/version.h,
	  trunk/oelib/xed.cpp, trunk/oelib/xyz.cpp, trunk/openbabel,
	  trunk/openbabel/Makefile.in, trunk/openbabel/StdAfx.cpp,
	  trunk/openbabel/StdAfx.h, trunk/openbabel/Vector.cpp,
	  trunk/openbabel/Vector.h, trunk/openbabel/alchemy.cpp,
	  trunk/openbabel/amber.cpp, trunk/openbabel/aromatic.h,
	  trunk/openbabel/aromatic.txt, trunk/openbabel/atom.cpp,
	  trunk/openbabel/atomtyp.h, trunk/openbabel/atomtyp.txt,
	  trunk/openbabel/balst.cpp, trunk/openbabel/base.cpp,
	  trunk/openbabel/base.h, trunk/openbabel/bgf.cpp,
	  trunk/openbabel/bin2hex.pl, trunk/openbabel/binary.cpp,
	  trunk/openbabel/binary.h, trunk/openbabel/binary_io.cpp,
	  trunk/openbabel/binary_io.h, trunk/openbabel/bitgrid.cpp,
	  trunk/openbabel/bitgrid.h, trunk/openbabel/bitvec.cpp,
	  trunk/openbabel/bitvec.h, trunk/openbabel/bond.cpp,
	  trunk/openbabel/box.cpp, trunk/openbabel/c3d.cpp,
	  trunk/openbabel/cacao.cpp, trunk/openbabel/cache.cpp,
	  trunk/openbabel/car.cpp, trunk/openbabel/ccc.cpp,
	  trunk/openbabel/chains.cpp, trunk/openbabel/chains.h,
	  trunk/openbabel/chdrw.cpp, trunk/openbabel/chiral.cpp,
	  trunk/openbabel/chiral.h, trunk/openbabel/commandline.cpp,
	  trunk/openbabel/commandline.h, trunk/openbabel/csr.cpp,
	  trunk/openbabel/cssr.cpp, trunk/openbabel/ctransform.cpp,
	  trunk/openbabel/ctransform.h, trunk/openbabel/cwrap.cpp,
	  trunk/openbabel/cwrap.h, trunk/openbabel/data.cpp,
	  trunk/openbabel/data.h, trunk/openbabel/dmol.cpp,
	  trunk/openbabel/element.h, trunk/openbabel/element.txt,
	  trunk/openbabel/extable.h, trunk/openbabel/extable.txt,
	  trunk/openbabel/feat.cpp, trunk/openbabel/fh.cpp,
	  trunk/openbabel/fileformat.cpp, trunk/openbabel/fileformat.h,
	  trunk/openbabel/gamess.cpp, trunk/openbabel/gaussian.cpp,
	  trunk/openbabel/generic.cpp, trunk/openbabel/generic.h,
	  trunk/openbabel/ghemical.cpp, trunk/openbabel/grid.cpp,
	  trunk/openbabel/grid.h, trunk/openbabel/gromos96.cpp,
	  trunk/openbabel/hin.cpp, trunk/openbabel/jaguar.cpp,
	  trunk/openbabel/main.cpp, trunk/openbabel/matrix.cpp,
	  trunk/openbabel/matrix.h, trunk/openbabel/mdl.cpp,
	  trunk/openbabel/mmod.cpp, trunk/openbabel/mol.cpp,
	  trunk/openbabel/mol.h, trunk/openbabel/mol2.cpp,
	  trunk/openbabel/molchrg.cpp, trunk/openbabel/molchrg.h,
	  trunk/openbabel/molvector.cpp, trunk/openbabel/molvector.h,
	  trunk/openbabel/mopac.cpp, trunk/openbabel/mpqc.cpp,
	  trunk/openbabel/nwchem.cpp, trunk/openbabel/obifstream.h,
	  trunk/openbabel/oblib.dsp, trunk/openbabel/oblib.dsw,
	  trunk/openbabel/obutil.cpp, trunk/openbabel/obutil.h,
	  trunk/openbabel/parsmart.cpp, trunk/openbabel/parsmart.h,
	  trunk/openbabel/parsmi.cpp, trunk/openbabel/patty.cpp,
	  trunk/openbabel/patty.h, trunk/openbabel/pdb.cpp,
	  trunk/openbabel/phmodel.cpp, trunk/openbabel/phmodel.h,
	  trunk/openbabel/phmodel.txt, trunk/openbabel/phmodeldata.h,
	  trunk/openbabel/qchem.cpp, trunk/openbabel/quat.c,
	  trunk/openbabel/rand.cpp, trunk/openbabel/report.cpp,
	  trunk/openbabel/resdata.h, trunk/openbabel/resdata.txt,
	  trunk/openbabel/ring.cpp, trunk/openbabel/ring.h,
	  trunk/openbabel/rotor.cpp, trunk/openbabel/rotor.h,
	  trunk/openbabel/smarts.cpp, trunk/openbabel/smarts.h,
	  trunk/openbabel/smi.cpp, trunk/openbabel/smi.h,
	  trunk/openbabel/tinker.cpp, trunk/openbabel/tokenst.cpp,
	  trunk/openbabel/typer.cpp, trunk/openbabel/typer.h,
	  trunk/openbabel/types.h, trunk/openbabel/types.txt,
	  trunk/openbabel/unichem.cpp, trunk/openbabel/version.h,
	  trunk/openbabel/xed.cpp, trunk/openbabel/xyz.cpp,
	  trunk/src/common/Makefile.in, trunk/src/common/filetrans.cpp,
	  trunk/src/common/filetrans.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/notice.cpp,
	  trunk/src/common/utility.cpp, trunk/src/graphics/Makefile.in,
	  trunk/src/graphics/docview.cpp, trunk/src/target3/Makefile.in:
	  Updated with OpenBabel replacing OELib.
	* trunk/src/graphics/mtools.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h: Add data types for select modes and
	  measure modes.
	* trunk/oelib/gamess.cpp: Small fix for GAMESS file format.
	  (this is a temporary issue until OpenBabel is imported in a day
	  or so.)

2002-01-07  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h: some
	  cleanups for the model classes, plus some documentation updates.

2002-01-05  hutchisn

	* trunk/aclocal.m4: Added Michael Banck's contributed SC tests.
	  These have not yet been implemented into configure.in yet.

2002-01-02  thassine

	* trunk/INSTALL, trunk/src/common/Makefile.OLD,
	  trunk/src/graphics/Makefile.OLD, trunk/src/target1/Makefile.OLD,
	  trunk/src/target2/Makefile.OLD, trunk/src/target3/Makefile.OLD:
	  converted the old makefiles to use the Scientific Computation
	  toolkit (SC toolkit) of MPQC, instead of the MPQC object files
	  and headers directly.

2001-12-31  thassine

	* trunk/src/common/interface.cpp, trunk/src/common/interface.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp: the all_atoms_interface is now
	  implemented. it works as a bridge between MM and QM models, and
	  offers a stadard set of functions to access atoms and bonds in
	  them. the convert-to-MM/QM feature is now implemented using
	  all_atoms_interface, and also the OELib/OpenBabel complatibility
	  methods might fit into it.

2001-12-29  thassine

	* trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h,
	  trunk/src/graphics/docview.cpp, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/graphics/views.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp:
	  the convert-project-to-QM/MM and attach/detach-this-view
	  operations now retain the graphics settings.
	* trunk/src/graphics/views.cpp: the GLUT stroke fonts now make
	  readable text in all cases, but 3D text (as in labels) is still
	  misaligned.

2001-12-28  thassine

	* trunk/src/graphics/camera.cpp, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/views.cpp, trunk/src/graphics/views.h: tried
	  to simplify the text rendering functions; also an initial
	  support for line-based font rendering (using glutStrokeBitmap())
	  but it's still quite broken.

2001-12-20  thassine

	* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h: the plots are now checked and
	  commented; should work but UI is still console-based.

2001-12-19  thassine

	* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/views.cpp, trunk/src/graphics/views.h: now
	  it's possible to scale colors of plot2d_view (using zoom
	  mousetool), and the plot views now store and display the
	  strcutures (using select/orbit/rotate tools); still need to do
	  some testing for the plots but they look good for symmterical
	  molecules.
	* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mtools.cpp, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h: moved the enlevdiag_view class to
	  the newly created plotting_view class family; now there is a
	  consistent way to handle non-graphics (energy-level diagram,
	  plot1d, plot2d) views.

2001-12-18  thassine

	* trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng9.cpp: just
	  docs clarified a bit...
	* trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng9.cpp,
	  trunk/src/common/mm1mdl.cpp, trunk/src/graphics/mm1docv.cpp: a
	  better tor-constraints added to mm1_eng classes for the 1d and
	  2d plots.
	* trunk/INSTALL: updated the installation docs.

2001-12-17  thassine

	* trunk/src/common/intcrd.cpp, trunk/src/common/intcrd.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
	  added 1D and 2D energy vs. torsion angles-plotting feature; it
	  compiles and even more or less works, but it still needs a lot
	  of finishing.

2001-12-12  thassine

	* trunk/bin/user-docs/index.html, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: added attach/detach feature for
	  gnome_graphics_views. earlier it was somewhat difficult to use
	  multiple views, because only one at a time could be looked at
	  the GtkNotebook. now the views can be detached from the notebook
	  to separate windows, and attached back to notebook as well. also
	  some GLUT and plotting improvements are added.

2001-12-10  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/common/qm1alg.cpp, trunk/src/common/qm1alg.h,
	  trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp: a simple transition state
	  search tool added for qm1_mdl; at the moment it's badly
	  documented and only works in the GLUT user interface (target2).

2001-12-07  thassine

	* trunk/src/common/model.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp: some t2 cleanups added, and
	  improved qm1_mdl support for multiple crd-sets.

2001-12-05  thassine

	* trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.cpp,
	  trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.cpp,
	  trunk/src/common/mm1eng9.h: added an initial framework for
	  adding torsional constraints in molecular mechanics force
	  fields; the old stuff should work as usual.
	* trunk/src/common/errutil.cpp, trunk/src/common/notice.h,
	  trunk/src/common/typedef.h, trunk/src/graphics/mm2rbn.cpp: added
	  some Alpha platform fixes from Bob Williams.

2001-11-27  hutchisn

	* trunk/Makefile.in: Added distclean target and changed help
	  destination to smooth with Debian package.
	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3prefs.cpp: Added Selection Mode submenu
	  (w/radio items) and fixed library error message.

2001-11-26  hutchisn

	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
	  Updated library feature to be fully user-configurable (# levels,
	  directory path)
	  Now also add submenus for subdirectories!

2001-11-26  thassine

	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3views.h:
	  minor fixes for 'Library', and some cleanups.

2001-11-21  hutchisn

	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3views.h: Add "library submenu" as a first
	  draft--still needs to be user-configurable
	  (recursive function to establish the menu) and still buggy.

2001-11-13  thassine

	* trunk/INSTALL, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.h, trunk/src/common/qm1mdl.h,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
	  trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp:
	  made the SelectNone feature as a combination of SelectAll and
	  InvertSelection (less code this way), and added some
	  enhancements to FileOpen (graphics update forced, and possibly
	  selected new atoms now replace the old selection).

2001-11-12  hutchisn

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/common/model.h, trunk/src/common/qm1mdl.h,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
	  Added SelectNone() and support for "inserting" files (open with
	  molecules selected).

2001-11-09  hutchisn

	* trunk/oelib/mol.cpp, trunk/src/common/filetrans.cpp: Fix bug
	  with OELib making Kekule structures. OELib now no longer clears
	  flags
	  for perceived Aromatic bonds and atoms. Our code makes bonds
	  conjugated if
	  OE has marked the bond as aromatic.

2001-11-08  thassine

	* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
	  back to devel settings, version number changed to 0.82.
	* trunk/CHANGES, trunk/src/common/define.h: some final changes for
	  the new release; this is released as 0.81.

2001-11-07  thassine

	* trunk/CHANGES, trunk/INSTALL, trunk/bin/user-docs/index.html:
	  some documentation updates added.

2001-10-29  thassine

	* trunk/src/common/define.h, trunk/src/common/mm2mdl.cpp,
	  trunk/src/common/mm2mdl.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
	  trunk/src/target3/t3qm1docv.cpp: some generic improvements
	  added: some t3 file operations added and mm1_mdl labels feature
	  improved.

2001-10-23  thassine

	* trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
	  trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
	  trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
	  trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.cpp,
	  trunk/src/common/mm2eng.cpp, trunk/src/common/mm2eng.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/model.cpp,
	  trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/surface.cpp,
	  trunk/src/target1/t1m_mm2param_cpp.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h: did some cleanups for eng-classes
	  (removed some old unnecessary parts); nothing should have
	  changed in how the classes actually work. also tried to improve
	  code readability generally. in summary: everything should still
	  work as it used to...

2001-10-18  thassine

	* trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
	  trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
	  trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h: a new
	  energy term for out of plane bending must be added soon to
	  forcefield; added an empty framework for the new term.

2001-10-08  thassine

	* trunk/bin/parameters/mm1param/stable/atomtypes.txt,
	  trunk/bin/parameters/mm1param/stable/parameters1.txt,
	  trunk/bin/parameters/mm1param/stable/parameters2.txt,
	  trunk/bin/parameters/mm1param/stable/parameters3.txt,
	  trunk/bin/parameters/mm1param/stable/parameters4.txt,
	  trunk/bin/parameters/mm1param/stable/parameters5.txt,
	  trunk/bin/parameters/mm1param/unstable/atomtypes.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters1.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters2.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters3.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters4.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters5.txt,
	  trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
	  trunk/src/common/mm1tab9.h: made some rearrangements at mm1_eng
	  classes that make expermimentation with the classes easier; also
	  the parameter files have been changed so you should do the #make
	  install# for this version.

2001-10-03  thassine

	* trunk/CHANGES, trunk/PROJECT: changed the old manually
	  maintained changes-file to a newer log that is maintained using
	  a cvs2cl.pl utility; it makes a logfile using cvs log
	  information; see http://www.red-bean.com/cvs2cl/
	* trunk/src/common/mm2mdl.h, trunk/src/common/qm2mdl.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3prefs.cpp: a
	  temporary modification done for colour prefs at t3prefs.cpp
	  where the default values are just quickly returned (a quick fix
	  to improve graphics performance of 0.80 compared to 0.42).

2001-10-01  hutchisn

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.h, trunk/src/common/model.h,
	  trunk/src/common/qm1mdl.h,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/t3main.cpp: Moved import code into mm1model so
	  it can be called from other parts of the code.
	  Added support for command-line flags, e.g. -f opens a ghemical
	  file, -i imports a file.
	  And any remaining arguments are assumed to be filenames to
	  import.
	  (Keep in mind that we can import a .mm1gp or .qm1gp anyway.)
	  
	  Allows $PATH/ghemical to be used as a web helper application.
	* trunk/oelib/data.cpp: Fix bugs with extension handling--make
	  sure to lowercase before comparisons.
	  Fixes problems, e.g. .PDB = .pdb
	* trunk/oelib/element.txt: Fix max valence on P to allow PF6, etc.

2001-09-27  thassine

	* trunk/src/common/define.h: changed the main web address to
	  www.bioinformatics.org
	* trunk/CHANGES, trunk/miniMOPAC/README,
	  trunk/miniMOPAC/fortran/iter.f, trunk/miniMOPAC/iter.c: mopac
	  iter.f changed so that the program is not closed even if SCF
	  convergence problems; the mopac geometry optimization is now
	  much more resistant to crashes.

2001-09-26  thassine

	* trunk/CHANGES, trunk/INSTALL, trunk/miniMOPAC/README,
	  trunk/miniMOPAC/esp.c, trunk/miniMOPAC/fortran/esp.f,
	  trunk/miniMOPAC/fortran/iter.f,
	  trunk/miniMOPAC/fortran/minimopac.f,
	  trunk/miniMOPAC/fortran/mopac.f, trunk/miniMOPAC/iter.c,
	  trunk/miniMOPAC/minimopac.c, trunk/src/common/qm1e_mopac.cpp:
	  some MOPAC fortran code cleanups; unnecessary file operations
	  removed, and output is now directed to console. now works also
	  with redhat 7.1???

2001-09-24  thassine

	* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/qm1docv.cpp:
	  added to measure tool a set if model-independent measurement
	  functions in an effort to make it simpler.
	* trunk/BUGLIST, trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
	  a new known bug was added; qm1 geomopt dialog was added for
	  gnome version.

2001-09-14  hutchisn

	* trunk/Makefile.in, trunk/bin/ghemical.png,
	  trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
	  trunk/src/target3/Makefile.in: Add distclean targets to Makefiles

2001-09-14  thassine

	* trunk/src/graphics/views.cpp: the energy level diagram now tries
	  to detect degenerate energy levels (like in N2 or F2) and draw
	  them side by side rather than overlapped.
	* trunk/src/graphics/docview.cpp, trunk/src/graphics/mm1docv.cpp:
	  completed the fixes for known mem leaks at docview.cpp

2001-09-07  hutchisn

	* trunk/oelib, trunk/oelib/.cvsignore, trunk/oelib/configure,
	  trunk/oelib/dmol.cpp, trunk/src/common/filetrans.cpp,
	  trunk/src/graphics/docview.cpp, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/views.cpp, trunk/src/target3/t3prefs.cpp: Fix
	  a few memory leaks and bugs.

2001-09-07  thassine

	* trunk/CHANGES, trunk/configure, trunk/configure.in,
	  trunk/src/common/define.h: development starts again, promoted
	  version number to 0.81

2001-09-06  thassine

	* trunk/CHANGES, trunk/INSTALL, trunk/bin/user-docs/index.html,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
	  did a last-minute addition of random conformational search; this
	  is released as version 0.80

2001-09-05  thassine

	* trunk/CHANGES, trunk/INSTALL, trunk/bin/user-docs/index.html:
	  final fixes to documentation etc...

2001-09-04  thassine

	* trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng9.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab9.cpp: some cleanups at MM eng/tab
	  classes.
	* trunk/src/common/mm1eng.h, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab9.cpp: minor changes and cleanups.

2001-09-03  thassine

	* trunk/src/common/mm1tab1.cpp, trunk/src/common/mm1tab9.cpp,
	  trunk/src/common/mm1util.cpp, trunk/src/common/mm1util.h: a
	  minor cleanup for mm1_typerule.
	* trunk/miniMOPAC/README, trunk/src/common/mm1mdl.h: minor
	  additions to mm1_mdl and MOPAC docs.

2001-08-30  hutchisn

	* trunk/oelib/Makefile.in, trunk/oelib/atom.cpp,
	  trunk/oelib/base.cpp, trunk/oelib/base.h,
	  trunk/oelib/binary.cpp, trunk/oelib/binary_io.cpp,
	  trunk/oelib/binary_io.h, trunk/oelib/bitgrid.cpp,
	  trunk/oelib/bond.cpp, trunk/oelib/chains.cpp,
	  trunk/oelib/chiral.cpp, trunk/oelib/ctransform.cpp,
	  trunk/oelib/ctransform.h, trunk/oelib/data.cpp,
	  trunk/oelib/data.h, trunk/oelib/element.h,
	  trunk/oelib/element.txt, trunk/oelib/gamess.cpp,
	  trunk/oelib/generic.cpp, trunk/oelib/generic.h,
	  trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
	  trunk/oelib/mdl.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
	  trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
	  trunk/oelib/parsmart.cpp, trunk/oelib/parsmart.h,
	  trunk/oelib/parsmi.cpp, trunk/oelib/patty.cpp,
	  trunk/oelib/patty.h, trunk/oelib/phmodel.cpp,
	  trunk/oelib/phmodel.txt, trunk/oelib/ring.cpp,
	  trunk/oelib/ring.h, trunk/oelib/smarts.cpp,
	  trunk/oelib/smarts.h, trunk/oelib/smi.cpp,
	  trunk/oelib/tokenst.cpp, trunk/oelib/typer.cpp,
	  trunk/src/common/filetrans.cpp: Update with new OELib code -- a
	  few new filetypes, cleanups and better bonding
	  for QM files.

2001-08-29  thassine

	* trunk/AUTHORS, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/camera.h, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: added an alternative way for camera
	  setup in stereo viewing modes; copyright notices etc updated.
	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: added Mike's stereo code (under
	  target3).
	* trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h:
	  added Mike's stereo code (under graphics).
	* trunk/configure, trunk/configure.in, trunk/src/common/define.h,
	  trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mopac.h,
	  trunk/src/common/qm1mdl.cpp: a safer mopac locking mechanism
	  added, version number promoted to 0.80.

2001-08-28  thassine

	* trunk/INSTALL, trunk/miniMOPAC/README,
	  trunk/miniMOPAC/fortran/minimopac.f,
	  trunk/miniMOPAC/minimopac.c, trunk/src/common/qm1e_mopac.cpp:
	  mopac engine now survives from change of molecule (the fortran
	  variables NUMCAL and ISOK were handled wrong), and some docs
	  updated.

2001-08-27  thassine

	* trunk/bin/user-docs/enlevdiag.jpg,
	  trunk/bin/user-docs/index.html,
	  trunk/bin/user-docs/maintools.jpg: user's manual quickly updated.
	* trunk/src/common/qm1e_mopac.cpp: added comments about a specifig
	  bug in mopac.
	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h: hamiltonian/basis set selection added
	  for QM engs.

2001-08-26  thassine

	* trunk/src/common/mm1alg.cpp, trunk/src/common/mm2alg.cpp,
	  trunk/src/common/qm1alg.cpp, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1mdl.cpp: minor bugs fixed in
	  mm1/qm1_geomopt::GetValue() where it calculated gradient when
	  only energy was needed. also qm1_eng_mopac and qm1_geomopt
	  settings are optimized for speed/stability (now simple molecules
	  with good starting geometries are quite safe).

2001-08-25  thassine

	* trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp: now the total charge can
	  be specified in QM models; also checking added for QM setup.
	* trunk/src/common/qm1e_mpqc.cpp: energy level diagram now works
	  for ab initio as well.

2001-08-24  thassine

	* trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1e_mpqc.h: force calculations + algorithms
	  added for MPQC.
	* trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1mdl.cpp:
	  fixed a gradient scaling bug in MOPAC engine; the geometry
	  optimization is much more robust now.

2001-08-23  hutchisn

	* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/views.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp: Migrate general "Graphics"
	  prefs section to MM1Graphics, etc.

2001-08-23  thassine

	* trunk/src/common/engine.h, trunk/src/common/mm1eng.cpp,
	  trunk/src/common/mm1eng.h, trunk/src/common/mm2eng.cpp,
	  trunk/src/common/mm2eng.h, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1eng.cpp,
	  trunk/src/common/qm1eng.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/graphics/views.cpp, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp: many smaller cleanups/fixes...

2001-08-22  hutchisn

	* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/qm1docv.cpp:
	  add QM measure functionality
	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm2mdl.cpp,
	  trunk/src/common/qm1mdl.cpp: Use sprintf to give a standardized
	  output to the geometry opt. output.
	* trunk/src/common/qm1mdl.cpp, trunk/src/target3/t3qm1docv.cpp:
	  Use the same methods for ImportMM command as "convert"
	  routines--and make sure we update the title!

2001-08-22  thassine

	* trunk/src/common/mm1mdl.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/target3/t3docv.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp: various smaller changes...
	* trunk/CHANGES, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/graphics/mtools.cpp, trunk/src/graphics/mtools.h,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
	  trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2views.cpp,
	  trunk/src/target2/t2views.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: an initial version of energy-level
	  diagrams for QM models added (now works for mopac only).

2001-08-21  hutchisn

	* trunk/src/graphics/mm2docv.cpp, trunk/src/target3/t3qm1docv.cpp:
	  Add more config use in QM and MM2 modes.
	* trunk/src/target3/t3mm1docv.cpp: Add minimal MM -> QM conversion
	  code. Doesn't quite set the filename correctly
	  but otherwise pretty much correct.

2001-08-20  thassine

	* trunk/CHANGES, trunk/miniMOPAC/esp.c,
	  trunk/miniMOPAC/fortran/esp.f, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1e_mpqc.cpp, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
	  the rest of qm1_eng_mopac plots added, and a scaling bug in MO
	  plots fixed.

2001-08-18  thassine

	* trunk/CHANGES, trunk/miniMOPAC/README,
	  trunk/miniMOPAC/fortran/minimopac.f,
	  trunk/miniMOPAC/minimopac.c, trunk/src/common/qm1e_mopac.cpp:
	  some cleanups done in qm1_eng_mopac (the fortran and C code are
	  now better separated, easier to maintain).
	* trunk/miniMOPAC/fortran/SIZES: ooops, forgot to add the SIZES
	  file.

2001-08-17  thassine

	* trunk/miniMOPAC/fortran/esp.f,
	  trunk/miniMOPAC/fortran/minimopac.f: added all changes to mopac
	  fortran source before 2001-08-17.
	* trunk/miniMOPAC/fortran, trunk/miniMOPAC/fortran/aababc.f,
	  trunk/miniMOPAC/fortran/addfck.f,
	  trunk/miniMOPAC/fortran/addhcr.f,
	  trunk/miniMOPAC/fortran/addnuc.f,
	  trunk/miniMOPAC/fortran/analyt.f,
	  trunk/miniMOPAC/fortran/anavib.f,
	  trunk/miniMOPAC/fortran/axis.f, trunk/miniMOPAC/fortran/block.f,
	  trunk/miniMOPAC/fortran/bonds.f,
	  trunk/miniMOPAC/fortran/brlzon.f,
	  trunk/miniMOPAC/fortran/btoc.f,
	  trunk/miniMOPAC/fortran/calpar.f,
	  trunk/miniMOPAC/fortran/capcor.f,
	  trunk/miniMOPAC/fortran/cdiag.f,
	  trunk/miniMOPAC/fortran/chrge.f, trunk/miniMOPAC/fortran/cnvg.f,
	  trunk/miniMOPAC/fortran/compfg.f,
	  trunk/miniMOPAC/fortran/consts.f,
	  trunk/miniMOPAC/fortran/cqden.f,
	  trunk/miniMOPAC/fortran/datin.f,
	  trunk/miniMOPAC/fortran/dcart.f,
	  trunk/miniMOPAC/fortran/delmol.f,
	  trunk/miniMOPAC/fortran/delri.f,
	  trunk/miniMOPAC/fortran/denrot.f,
	  trunk/miniMOPAC/fortran/densit.f,
	  trunk/miniMOPAC/fortran/depvar.f,
	  trunk/miniMOPAC/fortran/deri0.f,
	  trunk/miniMOPAC/fortran/deri1.f,
	  trunk/miniMOPAC/fortran/deri2.f,
	  trunk/miniMOPAC/fortran/deri21.f,
	  trunk/miniMOPAC/fortran/deri22.f,
	  trunk/miniMOPAC/fortran/deri23.f,
	  trunk/miniMOPAC/fortran/deritr.f,
	  trunk/miniMOPAC/fortran/deriv.f,
	  trunk/miniMOPAC/fortran/dernvo.f,
	  trunk/miniMOPAC/fortran/ders.f,
	  trunk/miniMOPAC/fortran/dfock2.f,
	  trunk/miniMOPAC/fortran/dfpsav.f,
	  trunk/miniMOPAC/fortran/dgemm.f,
	  trunk/miniMOPAC/fortran/dgemv.f, trunk/miniMOPAC/fortran/dger.f,
	  trunk/miniMOPAC/fortran/dgetf2.f,
	  trunk/miniMOPAC/fortran/dgetrf.f,
	  trunk/miniMOPAC/fortran/dgetri.f,
	  trunk/miniMOPAC/fortran/diag.f, trunk/miniMOPAC/fortran/diat.f,
	  trunk/miniMOPAC/fortran/diat2.f,
	  trunk/miniMOPAC/fortran/diegrd.f,
	  trunk/miniMOPAC/fortran/dielen.f,
	  trunk/miniMOPAC/fortran/diis.f,
	  trunk/miniMOPAC/fortran/dijkl1.f,
	  trunk/miniMOPAC/fortran/dijkl2.f,
	  trunk/miniMOPAC/fortran/dipind.f,
	  trunk/miniMOPAC/fortran/dipole.f,
	  trunk/miniMOPAC/fortran/dlaswp.f,
	  trunk/miniMOPAC/fortran/dofs.f, trunk/miniMOPAC/fortran/dot.f,
	  trunk/miniMOPAC/fortran/drc.f, trunk/miniMOPAC/fortran/drcout.f,
	  trunk/miniMOPAC/fortran/dtrmm.f,
	  trunk/miniMOPAC/fortran/dtrmv.f,
	  trunk/miniMOPAC/fortran/dtrsm.f,
	  trunk/miniMOPAC/fortran/dtrti2.f,
	  trunk/miniMOPAC/fortran/dtrtri.f,
	  trunk/miniMOPAC/fortran/dvfill.f, trunk/miniMOPAC/fortran/ef.f,
	  trunk/miniMOPAC/fortran/enpart.f, trunk/miniMOPAC/fortran/esp.f,
	  trunk/miniMOPAC/fortran/etime.c,
	  trunk/miniMOPAC/fortran/exchng.f,
	  trunk/miniMOPAC/fortran/fdate.c,
	  trunk/miniMOPAC/fortran/ffhpol.f,
	  trunk/miniMOPAC/fortran/flepo.f, trunk/miniMOPAC/fortran/fmat.f,
	  trunk/miniMOPAC/fortran/fock1.f,
	  trunk/miniMOPAC/fortran/fock2.f,
	  trunk/miniMOPAC/fortran/force.f,
	  trunk/miniMOPAC/fortran/formxy.f,
	  trunk/miniMOPAC/fortran/forsav.f,
	  trunk/miniMOPAC/fortran/frame.f,
	  trunk/miniMOPAC/fortran/freqcy.f,
	  trunk/miniMOPAC/fortran/geout.f,
	  trunk/miniMOPAC/fortran/geoutg.f,
	  trunk/miniMOPAC/fortran/getgeg.f,
	  trunk/miniMOPAC/fortran/getgeo.f,
	  trunk/miniMOPAC/fortran/getsym.f,
	  trunk/miniMOPAC/fortran/gettxt.f,
	  trunk/miniMOPAC/fortran/gmetry.f,
	  trunk/miniMOPAC/fortran/gover.f,
	  trunk/miniMOPAC/fortran/greenf.f,
	  trunk/miniMOPAC/fortran/grid.f,
	  trunk/miniMOPAC/fortran/h1elec.f,
	  trunk/miniMOPAC/fortran/haddon.f,
	  trunk/miniMOPAC/fortran/hcore.f,
	  trunk/miniMOPAC/fortran/helect.f,
	  trunk/miniMOPAC/fortran/hqrii.f, trunk/miniMOPAC/fortran/ijkl.f,
	  trunk/miniMOPAC/fortran/ilaenv.f,
	  trunk/miniMOPAC/fortran/initsv.f,
	  trunk/miniMOPAC/fortran/interp.f,
	  trunk/miniMOPAC/fortran/iter.f,
	  trunk/miniMOPAC/fortran/jcarin.f,
	  trunk/miniMOPAC/fortran/linmin.f,
	  trunk/miniMOPAC/fortran/local.f,
	  trunk/miniMOPAC/fortran/locmin.f,
	  trunk/miniMOPAC/fortran/lsame.f,
	  trunk/miniMOPAC/fortran/makpol.f,
	  trunk/miniMOPAC/fortran/mamult.f,
	  trunk/miniMOPAC/fortran/matou1.f,
	  trunk/miniMOPAC/fortran/matout.f,
	  trunk/miniMOPAC/fortran/matpak.f,
	  trunk/miniMOPAC/fortran/meci.f, trunk/miniMOPAC/fortran/mecid.f,
	  trunk/miniMOPAC/fortran/mecih.f,
	  trunk/miniMOPAC/fortran/mecip.f,
	  trunk/miniMOPAC/fortran/moldat.f,
	  trunk/miniMOPAC/fortran/molval.f,
	  trunk/miniMOPAC/fortran/mopac.f,
	  trunk/miniMOPAC/fortran/mullik.f,
	  trunk/miniMOPAC/fortran/mult.f, trunk/miniMOPAC/fortran/nllsq.f,
	  trunk/miniMOPAC/fortran/nuchar.f,
	  trunk/miniMOPAC/fortran/parsav.f,
	  trunk/miniMOPAC/fortran/partxy.f,
	  trunk/miniMOPAC/fortran/pathk.f,
	  trunk/miniMOPAC/fortran/paths.f, trunk/miniMOPAC/fortran/perm.f,
	  trunk/miniMOPAC/fortran/polar.f,
	  trunk/miniMOPAC/fortran/powsav.f,
	  trunk/miniMOPAC/fortran/powsq.f,
	  trunk/miniMOPAC/fortran/prtdrc.f,
	  trunk/miniMOPAC/fortran/quadr.f,
	  trunk/miniMOPAC/fortran/react1.f,
	  trunk/miniMOPAC/fortran/reada.f,
	  trunk/miniMOPAC/fortran/readmo.f,
	  trunk/miniMOPAC/fortran/refer.f, trunk/miniMOPAC/fortran/repp.f,
	  trunk/miniMOPAC/fortran/rotat.f,
	  trunk/miniMOPAC/fortran/rotate.f, trunk/miniMOPAC/fortran/rsp.f,
	  trunk/miniMOPAC/fortran/search.f,
	  trunk/miniMOPAC/fortran/second.f,
	  trunk/miniMOPAC/fortran/setupg.f,
	  trunk/miniMOPAC/fortran/solrot.f,
	  trunk/miniMOPAC/fortran/swap.f,
	  trunk/miniMOPAC/fortran/sympro.f,
	  trunk/miniMOPAC/fortran/symtry.f,
	  trunk/miniMOPAC/fortran/symtrz.f,
	  trunk/miniMOPAC/fortran/thermo.f,
	  trunk/miniMOPAC/fortran/timer.f,
	  trunk/miniMOPAC/fortran/timout.f,
	  trunk/miniMOPAC/fortran/update.f,
	  trunk/miniMOPAC/fortran/upsurf.f,
	  trunk/miniMOPAC/fortran/vecprt.f,
	  trunk/miniMOPAC/fortran/writmo.f,
	  trunk/miniMOPAC/fortran/wrtkey.f,
	  trunk/miniMOPAC/fortran/wrttxt.f,
	  trunk/miniMOPAC/fortran/xerbla.f,
	  trunk/miniMOPAC/fortran/xyzint.f: added the original
	  mopac-7.01-4 fortran source, since it seems to be impossible to
	  maintain this stuff from f2c'd source.
	* trunk/miniMOPAC/esp.c, trunk/src/common/qm1e_mopac.cpp:
	  miniMOPAC tweaks; ESP plot drawing is now faster, plus MO
	  plotting added.

2001-08-16  thassine

	* trunk/CHANGES, trunk/miniMOPAC/README: added some documentation
	  about the mopac ESP plots.

2001-08-15  thassine

	* trunk/miniMOPAC/esp.c, trunk/src/common/qm1e_mopac.cpp: ESP
	  plotting added to MOPAC-engine (1st working version).

2001-08-13  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/interface.cpp, trunk/src/common/interface.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
	  trajectory viewer for mm2_mdl added (and fixed the timestep of
	  MD).

2001-08-09  thassine

	* trunk/CHANGES, trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3mm2docv.h: the plotting stuff for mm2_mdl is
	  now also added.

2001-08-08  thassine

	* trunk/CHANGES, trunk/src/common/mm2mdl.cpp,
	  trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
	  trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2mm2docv.h,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
	  algorithms for mm2_mdl are added.
	* trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
	  glade_modal_dialog_owner moved into glade_docv class, in order
	  to make the dialogs work with multiple mdl-classes.

2001-08-03  hutchisn

	* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h: Moved InitGL() to parent
	  DocumentView class--allows all classes to inherit config code
	  easily.

2001-08-03  thassine

	* trunk/src/target3/glade/README,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/Makefile,
	  trunk/src/target3/glade/src/glade_callbacks.cpp,
	  trunk/src/target3/glade/src/glade_callbacks.h,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_interface.h,
	  trunk/src/target3/glade/src/glade_support.cpp,
	  trunk/src/target3/glade/src/main.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_callbacks.h,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/t3mm1docv.cpp: rebuilt the glade code; some
	  docs added for the glade stuff.

2001-08-02  thassine

	* trunk/src/common/qm1e_mpqc.cpp, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
	  ESP plotting added to qm1_eng_mpqc.

2001-08-01  thassine

	* trunk/CHANGES, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm2alg.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/common/qm1e_mpqc.cpp, trunk/src/common/qm1eng.cpp,
	  trunk/src/common/qm1eng.h, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp: small improvements for mm2_mdl
	  and qm1_eng_mpqc but nothing ready yet.

2001-07-30  thassine

	* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.h: the 4 first shortcut buttons work
	  now.
	* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h:
	  added MeasureEvent() also to (obsolete) qm2_mdl.

2001-07-28  hutchisn

	* trunk/src/graphics/camera.cpp, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
	  trunk/src/graphics/mm1rbn.cpp, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/target3/t3mm1docv.cpp:
	  Add preliminary measure tool code. Works well--need to add
	  "modes"

2001-07-24  hutchisn

	* trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mtools.cpp:
	  Change rendering to support more prefs--including passing prefs
	  for element colors.
	* trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h:
	  Improve selection with wireframe slightly and add Measure enum.
	* trunk/src/common/utility.cpp, trunk/src/common/utility.h: Change
	  elements to allow prefs class to override colors and VdW radii.
	* trunk/src/common/prefs.cpp, trunk/src/common/prefs.h,
	  trunk/src/target3/t3prefs.cpp, trunk/src/target3/t3prefs.h: Add
	  Color methods
	* trunk/src/common/filetrans.cpp, trunk/src/common/mm1mdl.cpp: Fix
	  OELib bond synchronization and switch hydrogens to use OELib
	  method.

2001-07-23  hutchisn

	* trunk/src/target3/pixmaps/bond.xpm,
	  trunk/src/target3/pixmaps/chain.xpm,
	  trunk/src/target3/pixmaps/element.xpm,
	  trunk/src/target3/pixmaps/invert.xpm,
	  trunk/src/target3/pixmaps/molecule.xpm,
	  trunk/src/target3/pixmaps/residue.xpm,
	  trunk/src/target3/t3main.cpp: Added sample pixmaps for shortcut
	  bar.

2001-07-22  thassine

	* trunk/src/target1/t1m_mm2param_cpp.h,
	  trunk/src/target1/t1m_mm2param_h.h: added some files for mm2_mdl.
	* trunk/miniMOPAC/README, trunk/miniMOPAC/dgetf2.c,
	  trunk/miniMOPAC/dgetri.c, trunk/miniMOPAC/dlaswp.c,
	  trunk/miniMOPAC/dtrti2.c, trunk/miniMOPAC/ef.c,
	  trunk/src/common/Makefile.OLD, trunk/src/common/factory.cpp,
	  trunk/src/common/factory.h, trunk/src/common/prefs.cpp,
	  trunk/src/common/prefs.h, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
	  trunk/src/graphics/Makefile.OLD, trunk/src/target1/Makefile.OLD,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/t2views.cpp,
	  trunk/src/target2/t2views.h, trunk/src/target3/Makefile.OLD,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3prefs.cpp,
	  trunk/src/target3/t3prefs.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3views.h: some mopac/mpqc conflicts fixed,
	  and mopac intermediate files FOR005 FOR006 SHUTDOWN cleaned.

2001-07-20  hutchisn

	* trunk/src/common/factory.h, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/target3/t3prefs.cpp, trunk/src/target3/t3prefs.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
	  Finished implementation of prefs class through GNOME config
	  classes. Currently nothing sets prefs from the code, and
	  rendering is an example of accessing pref values.

2001-07-09  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
	  trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/views.cpp,
	  trunk/src/target2/t2mm1docv.cpp: some comments added and
	  arrangements done for stereo image viewing.

2001-06-29  thassine

	* trunk/src/common/intcrd.cpp, trunk/src/common/intcrd.h,
	  trunk/src/common/mm1ic.cpp, trunk/src/common/mm1ic.h: ooops,
	  forgot to add some files in the last commit.
	* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/mm1alg.cpp, trunk/src/common/mm1alg.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/target2/t2mm1docv.cpp: some groundwork added for
	  mm1_mdl multiple crd_sets and conformational search tools.

2001-06-25  thassine

	* trunk/bin/user-docs/index.html, trunk/src/common/notice.cpp,
	  trunk/src/common/notice.h, trunk/src/target3/t3main.cpp: minor
	  updates in user's manual and copyright notices (MOPAC included).

2001-06-21  thassine

	* trunk/CHANGES, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3mm2docv.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: gnome MDI system revised; one
	  view/child (GtkNotebook container), project views now grouped
	  together.

2001-06-19  thassine

	* trunk/miniMOPAC/etime.c, trunk/src/common/conjgrad.h,
	  trunk/src/common/errutil.cpp, trunk/src/common/factory.cpp,
	  trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
	  trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
	  trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
	  trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm1tab1.cpp, trunk/src/common/mm1tab1.h,
	  trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1tab9.h,
	  trunk/src/common/mm1util.cpp, trunk/src/common/mm1util.h,
	  trunk/src/common/mm2eng.cpp, trunk/src/common/mm2eng.h,
	  trunk/src/common/mm2mdl.h, trunk/src/common/mm2util.h,
	  trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/common/notice.cpp, trunk/src/common/notice.h,
	  trunk/src/common/prefs.cpp, trunk/src/common/qm1e_mopac.cpp,
	  trunk/src/common/qm1e_mpqc.cpp, trunk/src/common/qm1e_mpqc.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/common/typedef.h, trunk/src/common/utility.cpp,
	  trunk/src/common/v3d.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/surface.cpp, trunk/src/graphics/surface.h,
	  trunk/src/target2/t2main.h, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2views.cpp,
	  trunk/src/target2/t2views.h,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3docv.cpp,
	  trunk/src/target3/t3docv.h, trunk/src/target3/t3errutil.cpp,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3prefs.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: some cleanups done for redhat7.1
	  (seems to work) and gcc3.0 (still some stl/namespace problems?).

2001-06-13  thassine

	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
	  some menuitems added, and an initial mm1gp <-> qm1gp conversion
	  feature

2001-05-28  thassine

	* trunk/src/common/filetrans.cpp: some comments added

2001-05-23  thassine

	* trunk/src/common/factory.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm2mdl.cpp,
	  trunk/src/target2/t2views.h, trunk/src/target3/t3views.h: just
	  some cleanups here and there

2001-05-21  thassine

	* trunk/src/common/mm1mdl.cpp: again some readpdb tweaks.
	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: some
	  readpdb changes again

2001-05-18  thassine

	* trunk/src/common/factory.cpp, trunk/src/common/factory.h: ooops,
	  forgot to add the class_factory files...
	* trunk/CHANGES, trunk/src/common/Makefile.OLD,
	  trunk/src/common/Makefile.in, trunk/src/common/errutil.cpp,
	  trunk/src/common/errutil.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm2mdl.cpp,
	  trunk/src/common/mm2mdl.h, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h, trunk/src/common/qm2mdl.cpp,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h, trunk/src/graphics/views.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target2/t2docv.cpp,
	  trunk/src/target2/t2docv.h, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
	  trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2mm2docv.h,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: many
	  factory classes combined to class_factory.

2001-05-16  thassine

	* trunk/src/target3/t3main.cpp: just added some buttons, to see
	  what it looks like...

2001-05-16  hutchisn

	* trunk/src/common/Makefile.in, trunk/src/common/prefs.cpp,
	  trunk/src/common/prefs.h, trunk/src/target3/Makefile.in,
	  trunk/src/target3/t3prefs.cpp, trunk/src/target3/t3prefs.h: Add
	  new "prefs" class to interface with gnome-config
	  to allow user-config for various things.

2001-05-15  thassine

	* trunk/src/common/mm1mdl.cpp: again some fixes to readpdb
	* trunk/src/common/mm1mdl.cpp: just some fixes added to readpdb

2001-05-14  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/target3/t3mm1docv.cpp:
	  organized menus a bit, some changes to readpdb

2001-05-11  hutchisn

	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
	  Add stubs for export graphics, as well as "zap all" and "compute
	  formula"

2001-05-11  thassine

	* trunk/src/graphics/mtools.cpp, trunk/src/graphics/mtools.h,
	  trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h:
	  switched to a single measure tool, multiple toolbars added.

2001-05-08  thassine

	* trunk/miniMOPAC/Makefile: miniMOPAC/Makefile removed; configure
	  will update it.
	* trunk/miniMOPAC/Makefile, trunk/miniMOPAC/Makefile.OLD,
	  trunk/src/Makefile.OLD, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm2mdl.cpp,
	  trunk/src/common/mm2mdl.h, trunk/src/common/model.h,
	  trunk/src/target2/t2mm2docv.cpp: some improvements to readpdb;
	  it now reads multiple crd-sets present in NMR entries

2001-05-07  hutchisn

	* trunk/src/graphics/Makefile.in: Remove io-* from build list
	  until GNOME catches up (!)

2001-05-04  hutchisn

	* trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h: Add
	  buttons for measure tools.
	* trunk/src/graphics/mtools.cpp, trunk/src/graphics/mtools.h,
	  trunk/src/graphics/views.cpp, trunk/src/graphics/views.h: Add
	  tools for measurements.
	* trunk/src/target3/pixmaps, trunk/src/target3/pixmaps/.cvsignore,
	  trunk/src/target3/pixmaps/angle.xpm,
	  trunk/src/target3/pixmaps/dihedral.xpm,
	  trunk/src/target3/pixmaps/distance.xpm,
	  trunk/src/target3/pixmaps/draw.xpm,
	  trunk/src/target3/pixmaps/erase.xpm,
	  trunk/src/target3/pixmaps/orb_xy.xpm,
	  trunk/src/target3/pixmaps/orb_z.xpm,
	  trunk/src/target3/pixmaps/rot_xy.xpm,
	  trunk/src/target3/pixmaps/rot_z.xpm,
	  trunk/src/target3/pixmaps/select.xpm,
	  trunk/src/target3/pixmaps/trans_xy.xpm,
	  trunk/src/target3/pixmaps/trans_z.xpm,
	  trunk/src/target3/pixmaps/zoom.xpm: Add transparency to button
	  pics and buttons for measure tools.
	* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h:
	  Changes to make sure window titles update when importing.
	* trunk/src/target3/Makefile.in: Make sure miniMOPAC is compiled
	  in.
	* trunk/src/graphics/Makefile.in: Compile io-* for exporting.
	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: Added
	  CLear and DoFormula methods.
	* trunk/src/common/Makefile.in: Remove EXTERN_GLOBALS -- not needed
	* trunk/src/graphics/io-jpg.cpp, trunk/src/graphics/io-jpg.h,
	  trunk/src/graphics/io-png.cpp, trunk/src/graphics/io-png.h: Add
	  GNOME code for exporting GdkPixbuf -> PNG or JPEG files.
	* trunk/oelib/aromatic.h, trunk/oelib/atom.cpp,
	  trunk/oelib/atomtyp.h, trunk/oelib/bin2hex.pl,
	  trunk/oelib/binary.cpp, trunk/oelib/binary.h,
	  trunk/oelib/binary_io.cpp, trunk/oelib/binary_io.h,
	  trunk/oelib/chains.cpp, trunk/oelib/chains.h,
	  trunk/oelib/configure, trunk/oelib/ctransform.cpp,
	  trunk/oelib/ctransform.h, trunk/oelib/data.cpp,
	  trunk/oelib/data.h, trunk/oelib/dmol.cpp, trunk/oelib/element.h,
	  trunk/oelib/extable.h, trunk/oelib/extable.txt,
	  trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
	  trunk/oelib/gaussian.cpp, trunk/oelib/generic.cpp,
	  trunk/oelib/generic.h, trunk/oelib/ghemical.cpp,
	  trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
	  trunk/oelib/matrix.cpp, trunk/oelib/matrix.h,
	  trunk/oelib/mdl.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
	  trunk/oelib/mol2.cpp, trunk/oelib/mopac.cpp,
	  trunk/oelib/nwchem.cpp, trunk/oelib/oelib.dsp,
	  trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
	  trunk/oelib/parsmart.cpp, trunk/oelib/parsmi.cpp,
	  trunk/oelib/phmodel.cpp, trunk/oelib/phmodeldata.h,
	  trunk/oelib/report.cpp, trunk/oelib/resdata.h,
	  trunk/oelib/rotor.cpp, trunk/oelib/smi.cpp,
	  trunk/oelib/typer.cpp, trunk/oelib/types.h: Update with current
	  OELib version.

2001-05-03  hutchisn

	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/miniMOPAC/Makefile.in, trunk/oelib/Makefile.in: Update for
	  miniMOPAC, test for g2c/f2c library (hopefully).
	* trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_interface.h,
	  trunk/src/target3/glade/src/glade_support.cpp: Add Element
	  options dialog to glade.

2001-05-02  thassine

	* trunk/src/common/mm1mdl.cpp: added a small fix to readpdb so
	  that it can read also NMR entries.

2001-04-30  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: some
	  improvements to readpdb-functions.

2001-04-27  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp: revived ImportENT_OLD and
	  changed them to readpdb-functions (for advanced PDB file imports)

2001-04-24  thassine

	* trunk/INSTALL, trunk/src/common/Makefile.OLD,
	  trunk/src/target3/t3dialog.cpp: documentation, old makefile, t3
	  bondtype dialog fixed a bit.

2001-04-20  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm2alg.cpp, trunk/src/common/mm2alg.h,
	  trunk/src/common/mm2mdl.h, trunk/src/common/model.h,
	  trunk/src/target2/t2mm2docv.cpp: continued merging the mm2_mdl.

2001-04-19  thassine

	* trunk/src/common/mm1mdl.h, trunk/src/common/mm2eng.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/common/mm2util.cpp, trunk/src/common/mm2util.h,
	  trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/common/qm1mdl.h, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm2docv.h,
	  trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.h:
	  continued merging the mm2_mdl, plus some cleanups.

2001-04-18  thassine

	* trunk/CHANGES, trunk/bin/parameters/mm2param,
	  trunk/bin/parameters/mm2param/loopdip.txt,
	  trunk/bin/parameters/mm2param/looptor.txt,
	  trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.h,
	  trunk/src/common/mm2eng.cpp, trunk/src/common/mm2eng.h,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2mm2docv.h,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
	  started merging the mm2_mdl code (accepted for publication :)
	* trunk/CHANGES, trunk/miniMOPAC, trunk/miniMOPAC/Makefile,
	  trunk/miniMOPAC/Makefile.OLD, trunk/miniMOPAC/README,
	  trunk/miniMOPAC/aababc.c, trunk/miniMOPAC/addfck.c,
	  trunk/miniMOPAC/addhcr.c, trunk/miniMOPAC/addnuc.c,
	  trunk/miniMOPAC/analyt.c, trunk/miniMOPAC/anavib.c,
	  trunk/miniMOPAC/axis.c, trunk/miniMOPAC/block.c,
	  trunk/miniMOPAC/bonds.c, trunk/miniMOPAC/brlzon.c,
	  trunk/miniMOPAC/btoc.c, trunk/miniMOPAC/calpar.c,
	  trunk/miniMOPAC/capcor.c, trunk/miniMOPAC/cdiag.c,
	  trunk/miniMOPAC/chrge.c, trunk/miniMOPAC/cnvg.c,
	  trunk/miniMOPAC/compfg.c, trunk/miniMOPAC/consts.c,
	  trunk/miniMOPAC/cqden.c, trunk/miniMOPAC/datin.c,
	  trunk/miniMOPAC/dcart.c, trunk/miniMOPAC/delmol.c,
	  trunk/miniMOPAC/delri.c, trunk/miniMOPAC/denrot.c,
	  trunk/miniMOPAC/densit.c, trunk/miniMOPAC/depvar.c,
	  trunk/miniMOPAC/deri0.c, trunk/miniMOPAC/deri1.c,
	  trunk/miniMOPAC/deri2.c, trunk/miniMOPAC/deri21.c,
	  trunk/miniMOPAC/deri22.c, trunk/miniMOPAC/deri23.c,
	  trunk/miniMOPAC/deritr.c, trunk/miniMOPAC/deriv.c,
	  trunk/miniMOPAC/dernvo.c, trunk/miniMOPAC/ders.c,
	  trunk/miniMOPAC/dfock2.c, trunk/miniMOPAC/dfpsav.c,
	  trunk/miniMOPAC/dgemm.c, trunk/miniMOPAC/dgemv.c,
	  trunk/miniMOPAC/dger.c, trunk/miniMOPAC/dgetf2.c,
	  trunk/miniMOPAC/dgetrf.c, trunk/miniMOPAC/dgetri.c,
	  trunk/miniMOPAC/diag.c, trunk/miniMOPAC/diat.c,
	  trunk/miniMOPAC/diat2.c, trunk/miniMOPAC/diegrd.c,
	  trunk/miniMOPAC/dielen.c, trunk/miniMOPAC/diis.c,
	  trunk/miniMOPAC/dijkl1.c, trunk/miniMOPAC/dijkl2.c,
	  trunk/miniMOPAC/dipind.c, trunk/miniMOPAC/dipole.c,
	  trunk/miniMOPAC/dlaswp.c, trunk/miniMOPAC/dofs.c,
	  trunk/miniMOPAC/dot.c, trunk/miniMOPAC/drc.c,
	  trunk/miniMOPAC/drcout.c, trunk/miniMOPAC/dtrmm.c,
	  trunk/miniMOPAC/dtrmv.c, trunk/miniMOPAC/dtrsm.c,
	  trunk/miniMOPAC/dtrti2.c, trunk/miniMOPAC/dtrtri.c,
	  trunk/miniMOPAC/dvfill.c, trunk/miniMOPAC/ef.c,
	  trunk/miniMOPAC/enpart.c, trunk/miniMOPAC/esp.c,
	  trunk/miniMOPAC/etime.c, trunk/miniMOPAC/exchng.c,
	  trunk/miniMOPAC/fdate.c, trunk/miniMOPAC/ffhpol.c,
	  trunk/miniMOPAC/flepo.c, trunk/miniMOPAC/fmat.c,
	  trunk/miniMOPAC/fock1.c, trunk/miniMOPAC/fock2.c,
	  trunk/miniMOPAC/force.c, trunk/miniMOPAC/formxy.c,
	  trunk/miniMOPAC/forsav.c, trunk/miniMOPAC/frame.c,
	  trunk/miniMOPAC/freqcy.c, trunk/miniMOPAC/geout.c,
	  trunk/miniMOPAC/geoutg.c, trunk/miniMOPAC/getgeg.c,
	  trunk/miniMOPAC/getgeo.c, trunk/miniMOPAC/getsym.c,
	  trunk/miniMOPAC/gettxt.c, trunk/miniMOPAC/gmetry.c,
	  trunk/miniMOPAC/gover.c, trunk/miniMOPAC/greenf.c,
	  trunk/miniMOPAC/grid.c, trunk/miniMOPAC/h1elec.c,
	  trunk/miniMOPAC/haddon.c, trunk/miniMOPAC/hcore.c,
	  trunk/miniMOPAC/helect.c, trunk/miniMOPAC/hqrii.c,
	  trunk/miniMOPAC/ijkl.c, trunk/miniMOPAC/ilaenv.c,
	  trunk/miniMOPAC/initsv.c, trunk/miniMOPAC/interp.c,
	  trunk/miniMOPAC/iter.c, trunk/miniMOPAC/jcarin.c,
	  trunk/miniMOPAC/linmin.c, trunk/miniMOPAC/local.c,
	  trunk/miniMOPAC/locmin.c, trunk/miniMOPAC/lsame.c,
	  trunk/miniMOPAC/makpol.c, trunk/miniMOPAC/mamult.c,
	  trunk/miniMOPAC/matou1.c, trunk/miniMOPAC/matout.c,
	  trunk/miniMOPAC/matpak.c, trunk/miniMOPAC/meci.c,
	  trunk/miniMOPAC/mecid.c, trunk/miniMOPAC/mecih.c,
	  trunk/miniMOPAC/mecip.c, trunk/miniMOPAC/minimopac.c,
	  trunk/miniMOPAC/moldat.c, trunk/miniMOPAC/molval.c,
	  trunk/miniMOPAC/mullik.c, trunk/miniMOPAC/mult.c,
	  trunk/miniMOPAC/nllsq.c, trunk/miniMOPAC/nuchar.c,
	  trunk/miniMOPAC/parsav.c, trunk/miniMOPAC/partxy.c,
	  trunk/miniMOPAC/pathk.c, trunk/miniMOPAC/paths.c,
	  trunk/miniMOPAC/perm.c, trunk/miniMOPAC/polar.c,
	  trunk/miniMOPAC/powsav.c, trunk/miniMOPAC/powsq.c,
	  trunk/miniMOPAC/prtdrc.c, trunk/miniMOPAC/quadr.c,
	  trunk/miniMOPAC/react1.c, trunk/miniMOPAC/reada.c,
	  trunk/miniMOPAC/readmo.c, trunk/miniMOPAC/refer.c,
	  trunk/miniMOPAC/repp.c, trunk/miniMOPAC/rotat.c,
	  trunk/miniMOPAC/rotate.c, trunk/miniMOPAC/rsp.c,
	  trunk/miniMOPAC/search.c, trunk/miniMOPAC/second.c,
	  trunk/miniMOPAC/setupg.c, trunk/miniMOPAC/solrot.c,
	  trunk/miniMOPAC/swap.c, trunk/miniMOPAC/sympro.c,
	  trunk/miniMOPAC/symtry.c, trunk/miniMOPAC/symtrz.c,
	  trunk/miniMOPAC/thermo.c, trunk/miniMOPAC/timer.c,
	  trunk/miniMOPAC/timout.c, trunk/miniMOPAC/update.c,
	  trunk/miniMOPAC/upsurf.c, trunk/miniMOPAC/vecprt.c,
	  trunk/miniMOPAC/writmo.c, trunk/miniMOPAC/wrtkey.c,
	  trunk/miniMOPAC/wrttxt.c, trunk/miniMOPAC/xerbla.c,
	  trunk/miniMOPAC/xyzint.c, trunk/src/common/Makefile.OLD,
	  trunk/src/common/Makefile.in, trunk/src/common/errutil.cpp,
	  trunk/src/common/qm1alg.cpp, trunk/src/common/qm1alg.h,
	  trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mopac.h,
	  trunk/src/common/qm1e_mpqc.cpp, trunk/src/common/qm1e_mpqc.h,
	  trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm1eng1.cpp, trunk/src/common/qm1eng1.h,
	  trunk/src/common/qm1eng9.cpp, trunk/src/common/qm1eng9.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/graphics/camera.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
	  trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
	  trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target2/t2qm1docv.h, trunk/src/target3/Makefile.OLD,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
	  added miniMOPAC and QM geometry optimization.

2001-03-30  thassine

	* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
	  switched back to devel settings; the version number is now 0.43
	* trunk/CHANGES, trunk/src/common/define.h,
	  trunk/src/common/notice.cpp, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm2docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp: minor cleanups; this is
	  released as 0.42

2001-03-28  thassine

	* trunk/src/common/model.cpp, trunk/src/common/typedef.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/target1/Makefile.OLD,
	  trunk/src/target2/Makefile.OLD, trunk/src/target3/Makefile.OLD:
	  some comments added, X11/ogl headers and libs removed from
	  TARGET1.

2001-03-23  hutchisn

	* trunk/oelib/jaguar.cpp: Fix problems with Jaguar translator.

2001-03-22  hutchisn

	* trunk/src/graphics/mm1docv.cpp: Add new multiple-bond rendering.
	  Now uses line stipple to render conjugated bonds fairly well.
	* trunk/oelib/Makefile, trunk/oelib/Makefile.in,
	  trunk/oelib/data.cpp, trunk/oelib/data.h, trunk/oelib/dmol.cpp,
	  trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
	  trunk/oelib/fileformat.h, trunk/oelib/gamess.cpp,
	  trunk/oelib/ghemical.cpp: Added Dmol format and cleanups.

2001-03-22  thassine

	* trunk/src/common/mm1util.h, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.cpp: the bug with ribbon objects
	  should now be fixed.

2001-03-19  thassine

	* trunk/oelib/Makefile, trunk/src/common/filetrans.cpp,
	  trunk/src/common/filetrans.h: added syncronization for bonds
	  into file_trans::Synchronize().

2001-03-16  thassine

	* trunk/oelib/Makefile, trunk/src/common/filetrans.cpp,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/utility.cpp,
	  trunk/src/common/utility.h, trunk/src/target2/t2mm1docv.cpp:
	  oelib syncronization and other small improvements.

2001-03-15  hutchisn

	* trunk/oelib/ghemical.cpp, trunk/oelib/xyz.cpp: Fix minor bugs in
	  file translators.
	* trunk/src/common/filetrans.cpp: Fix "the bug" with calling extab
	  before it was properly set.
	* trunk/oelib/alchemy.cpp, trunk/oelib/amber.cpp,
	  trunk/oelib/atomtyp.h, trunk/oelib/atomtyp.txt,
	  trunk/oelib/element.h, trunk/oelib/element.txt,
	  trunk/oelib/extable.h, trunk/oelib/ghemical.cpp,
	  trunk/oelib/hin.cpp, trunk/oelib/jaguar.cpp,
	  trunk/oelib/mpqc.cpp, trunk/oelib/oelib.dsp,
	  trunk/oelib/phmodeldata.h, trunk/oelib/qchem.cpp,
	  trunk/oelib/tinker.cpp, trunk/oelib/types.h,
	  trunk/oelib/types.txt, trunk/oelib/unichem.cpp,
	  trunk/oelib/xyz.cpp: Added fixes to the translators--now much
	  better about getting elements correct for rare atoms (e.g. Pb).

2001-03-15  thassine

	* trunk/oelib/Makefile, trunk/oelib/atom.cpp, trunk/oelib/mol.h,
	  trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h:
	  switched to a less complicated way to do oelib compatibility

2001-03-14  hutchisn

	* trunk/bin/examples/PeriodicTable.mm1gp,
	  trunk/src/common/utility.cpp, trunk/src/common/utility.h: Fixed
	  atom colors and add example Periodic Table.

2001-03-14  thassine

	* trunk/CHANGES, trunk/configure, trunk/configure.in,
	  trunk/oelib/atom.cpp, trunk/oelib/mol.h,
	  trunk/src/common/define.h, trunk/src/common/filetrans.cpp,
	  trunk/src/common/filetrans.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/utility.cpp,
	  trunk/src/common/utility.h, trunk/src/graphics/Makefile.OLD,
	  trunk/src/graphics/Makefile.in, trunk/src/target1/Makefile.OLD,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in:
	  some mm1_mdl <=> oelib compatibility features started.

2001-03-12  thassine

	* trunk/BUGLIST, trunk/CHANGES, trunk/INSTALL, trunk/PROJECT,
	  trunk/bin/examples/2-chlorobutane.mm1gp,
	  trunk/bin/examples/3-phenylpropanal.mm1gp,
	  trunk/bin/examples/acetylsalicylic_acid.mm1gp,
	  trunk/bin/examples/alpha-pinene.mm1gp,
	  trunk/bin/examples/bromobenzene.mm1gp,
	  trunk/bin/examples/camphor.mm1gp,
	  trunk/bin/examples/cinnamaldehyde.mm1gp,
	  trunk/bin/examples/cis-2-pentene.mm1gp,
	  trunk/bin/examples/cyclohexane.mm1gp,
	  trunk/bin/examples/naphtalene.mm1gp, trunk/oelib/Makefile,
	  trunk/src/common/mm1mdl.cpp, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3views.cpp: this is released as version 0.41

2001-03-08  hutchisn

	* trunk/src/common/define.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
	  Add support for label Atom IDs
	* trunk/src/common/mm1mdl.cpp: ReadStream changes to support
	  reading charges
	* trunk/src/common/notice.cpp: Update copyright with OELib info.
	* trunk/src/common/filetrans.cpp: Update for new OELib changes.
	* trunk/Makefile.in: Add target for help files.
	* trunk/oelib/Makefile.in, trunk/oelib/Vector.cpp,
	  trunk/oelib/Vector.h, trunk/oelib/alchemy.cpp,
	  trunk/oelib/amber.cpp, trunk/oelib/aromatic.h,
	  trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
	  trunk/oelib/atomtyp.h, trunk/oelib/atomtyp.txt,
	  trunk/oelib/balst.cpp, trunk/oelib/bgf.cpp,
	  trunk/oelib/bin2hex.pl, trunk/oelib/binary.cpp,
	  trunk/oelib/binary.h, trunk/oelib/bitgrid.cpp,
	  trunk/oelib/bitgrid.h, trunk/oelib/bitvec.cpp,
	  trunk/oelib/bitvec.h, trunk/oelib/bond.cpp, trunk/oelib/box.cpp,
	  trunk/oelib/c3d.cpp, trunk/oelib/cacao.cpp,
	  trunk/oelib/cache.cpp, trunk/oelib/car.cpp, trunk/oelib/ccc.cpp,
	  trunk/oelib/chdrw.cpp, trunk/oelib/chiral.cpp,
	  trunk/oelib/chiral.h, trunk/oelib/commandline.cpp,
	  trunk/oelib/commandline.h, trunk/oelib/configure,
	  trunk/oelib/csr.cpp, trunk/oelib/cssr.cpp,
	  trunk/oelib/cwrap.cpp, trunk/oelib/cwrap.h,
	  trunk/oelib/data.cpp, trunk/oelib/data.h, trunk/oelib/element.h,
	  trunk/oelib/extable.h, trunk/oelib/extable.txt,
	  trunk/oelib/feat.cpp, trunk/oelib/fh.cpp,
	  trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
	  trunk/oelib/gamess.cpp, trunk/oelib/ghemical.cpp,
	  trunk/oelib/grid.cpp, trunk/oelib/grid.h,
	  trunk/oelib/gromos96.cpp, trunk/oelib/hin.cpp,
	  trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
	  trunk/oelib/matrix.cpp, trunk/oelib/matrix.h,
	  trunk/oelib/mdl.cpp, trunk/oelib/mmod.cpp, trunk/oelib/mol.cpp,
	  trunk/oelib/mol.h, trunk/oelib/mol2.cpp,
	  trunk/oelib/molchrg.cpp, trunk/oelib/molchrg.h,
	  trunk/oelib/molvector.cpp, trunk/oelib/molvector.h,
	  trunk/oelib/mpqc.cpp, trunk/oelib/oeifstream.h,
	  trunk/oelib/oelib.dsp, trunk/oelib/oeutil.cpp,
	  trunk/oelib/oeutil.h, trunk/oelib/parsmart.cpp,
	  trunk/oelib/parsmart.h, trunk/oelib/parsmi.cpp,
	  trunk/oelib/patty.cpp, trunk/oelib/patty.h, trunk/oelib/pdb.cpp,
	  trunk/oelib/phmodel.cpp, trunk/oelib/phmodel.h,
	  trunk/oelib/phmodel.txt, trunk/oelib/phmodeldata.h,
	  trunk/oelib/qchem.cpp, trunk/oelib/rand.cpp,
	  trunk/oelib/resdata.h, trunk/oelib/ring.cpp, trunk/oelib/ring.h,
	  trunk/oelib/rotor.cpp, trunk/oelib/rotor.h, trunk/oelib/smi.cpp,
	  trunk/oelib/smi.h, trunk/oelib/tokenst.cpp,
	  trunk/oelib/typer.cpp, trunk/oelib/typer.h, trunk/oelib/types.h,
	  trunk/oelib/version.h, trunk/oelib/xed.cpp: Updates to oelib
	  files.

2001-03-08  thassine

	* trunk/CHANGES, trunk/src/common/notice.cpp,
	  trunk/src/common/notice.h, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3main.h: added the Help/Help item to the main
	  menu, copyright notices updated to include OELib
	* trunk/bin/user-docs/index.html,
	  trunk/bin/user-docs/maintools.jpg: updated the user's manual

2001-02-16  thassine

	* trunk/src/Makefile.OLD: this will make quick test builds easier.
	* trunk/bin/user-docs, trunk/bin/user-docs/index.html: added some
	  framework for the user manual

2001-02-13  thassine

	* trunk/INSTALL, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
	  added some quick improvements to qm1-model to boost its ease of
	  use.

2001-02-12  hutchisn

	* trunk/configure, trunk/configure.in: Solved configure problems
	  with MPQC and oelib.
	* trunk/configure, trunk/configure.in: Fix problem with configure
	  in srcdir.

2001-02-12  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/qm1eng1.cpp,
	  trunk/src/common/qm1mdl.cpp, trunk/src/graphics/Makefile.OLD,
	  trunk/src/graphics/camera.cpp, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2rbn.cpp,
	  trunk/src/graphics/mtools.cpp, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/plane.cpp, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/views.cpp, trunk/src/target1/Makefile.OLD,
	  trunk/src/target1/config.h.OLD, trunk/src/target2/Makefile.OLD,
	  trunk/src/target2/config.h.OLD, trunk/src/target3/Makefile.OLD,
	  trunk/src/target3/config.h.OLD: a bug that affected MPQC front
	  end compilation is now fixed (thanks Mark).

2001-02-11  thassine

	* trunk/CHANGES, trunk/bin/examples/1gar.mm2gp,
	  trunk/bin/examples/1hcl.mm2gp, trunk/bin/examples/4rhn.mm2gp,
	  trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
	  trunk/src/common/mm2util.cpp, trunk/src/common/mm2util.h,
	  trunk/src/common/model.h, trunk/src/graphics/Makefile.OLD,
	  trunk/src/graphics/Makefile.in, trunk/src/graphics/mm2docv.cpp,
	  trunk/src/graphics/mm2docv.h, trunk/src/graphics/mm2rbn.cpp,
	  trunk/src/graphics/mm2rbn.h, trunk/src/graphics/views.h,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2main.h, trunk/src/target2/t2mm2docv.cpp,
	  trunk/src/target2/t2mm2docv.h, trunk/src/target3/Makefile.OLD,
	  trunk/src/target3/Makefile.in, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
	  trunk/src/target3/t3views.h: tadaall added a preview version of
	  the reduced protein modelling thing.

2001-02-10  thassine

	* trunk/INSTALL, trunk/configure, trunk/configure.in,
	  trunk/src/common/define.h, trunk/src/common/engine.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/qm1mdl.cpp,
	  trunk/src/target3/t3views.cpp: changed back to devel settings
	  (version number, releasedate); small fixes appled here and there.

2001-02-07  thassine

	* trunk/small-utilities/README, trunk/small-utilities/gp2mpqc.cpp,
	  trunk/src/graphics/spline.h, trunk/src/graphics/views.h: added
	  some final fixes to documentation; this is released as 0.40

2001-02-06  hutchisn

	* trunk/oelib/extable.txt: Add sorted extable to make menus more
	  user-friendly.
	* trunk/src/common/filetrans.cpp: Fix bug with
	  GetImportDescription.
	* trunk/oelib/data.cpp: Fix problem with GetType from an
	  integer--table lookup was in the wrong place!

2001-02-06  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/target2/t2docv.h,
	  trunk/src/target3/t3docv.h, trunk/src/target3/t3errutil.h,
	  trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3views.h:
	  added some more DOC++ style documentation.
	* trunk/AUTHORS, trunk/CHANGES, trunk/INSTALL, trunk/PROJECT:
	  revised/updated some documentation.
	* trunk/configure, trunk/configure.in, trunk/oelib/Makefile,
	  trunk/src/common/define.h, trunk/src/common/notice.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h: some cleanups at glade
	  optionmenus; the version number promoted to 0.40

2001-02-06  hutchisn

	* trunk/src/target3/glade_callbacks.cpp: Use file_trans methods to
	  specifically request a file type when the user picks it or
	  "Automatic" based on the file name.
	* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h:
	  Add support for specifically requesting an import or export type
	  (by index #).
	* trunk/oelib/Makefile.in: Add target to rebuild Makefile if
	  Makefile.in or configure script changes.

2001-02-05  thassine

	* trunk/src/target3/glade_callbacks.cpp: the file import/export
	  dialogs seem to work now...
	* trunk/oelib/data.cpp, trunk/oelib/extable.txt,
	  trunk/oelib/ghemical.cpp, trunk/oelib/mol.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h: the filename change is done
	  also in oelib; the file import/export dialogs almost work now.
	* trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_callbacks.cpp,
	  trunk/src/target3/glade/src/glade_callbacks.h,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_interface.h,
	  trunk/src/target3/glade/src/main.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_callbacks.h,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp: changed the glade project and
	  code so that each dialog (and most important widgets) have their
	  own simple namespace.

2001-02-04  thassine

	* trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/common/qm2eng.cpp, trunk/src/common/qm2eng.h,
	  trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
	  trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
	  trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
	  some files were lost in the last commit; added them back...
	* trunk/CHANGES, trunk/INSTALL,
	  trunk/bin/examples/2-chlorobutane.gpMM,
	  trunk/bin/examples/2-chlorobutane.mm1gp,
	  trunk/bin/examples/3-phenylpropanal.gpMM,
	  trunk/bin/examples/3-phenylpropanal.mm1gp,
	  trunk/bin/examples/acetylsalicylic_acid.gpMM,
	  trunk/bin/examples/acetylsalicylic_acid.mm1gp,
	  trunk/bin/examples/alpha-pinene.gpMM,
	  trunk/bin/examples/alpha-pinene.mm1gp,
	  trunk/bin/examples/bromobenzene.gpMM,
	  trunk/bin/examples/bromobenzene.mm1gp,
	  trunk/bin/examples/camphor.gpMM,
	  trunk/bin/examples/camphor.mm1gp,
	  trunk/bin/examples/cinnamaldehyde.gpMM,
	  trunk/bin/examples/cinnamaldehyde.mm1gp,
	  trunk/bin/examples/cis-2-pentene.gpMM,
	  trunk/bin/examples/cis-2-pentene.mm1gp,
	  trunk/bin/examples/cyclohexane.gpMM,
	  trunk/bin/examples/cyclohexane.mm1gp,
	  trunk/bin/examples/naphtalene.gpMM,
	  trunk/bin/examples/naphtalene.mm1gp,
	  trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/model.h, trunk/src/common/qm1eng.cpp,
	  trunk/src/common/qm1eng.h, trunk/src/common/qm1eng1.cpp,
	  trunk/src/common/qm1eng1.h, trunk/src/common/qm1eng9.cpp,
	  trunk/src/common/qm1eng9.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.cpp,
	  trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.cpp,
	  trunk/src/common/qm2eng1.h, trunk/src/common/qm2eng9.cpp,
	  trunk/src/common/qm2eng9.h, trunk/src/common/qm2mdl.cpp,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h, trunk/src/target1/t1main.cpp,
	  trunk/src/target2/t2main.cpp, trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.cpp,
	  trunk/src/target2/t2qm2docv.h,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_interface.h,
	  trunk/src/target3/glade/src/main.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
	  trunk/src/target3/t3views.h: swapped the classnames qm1* and qm2
	  (as well as filenames) in an effort to make the class naming
	  scheme more reasonnable (now we have a clear division in mm/qm,
	  and the all-atoms classes (most used) have numbers 1); also
	  changed nicer filename extensions.

2001-02-02  thassine

	* trunk/src/common/mm1alg.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3dialog.h, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h: the trajectory viewer works now
	  (as a modal dialog, but anyway).

2001-01-31  thassine

	* trunk/CHANGES, trunk/src/common/errutil.cpp,
	  trunk/src/common/errutil.h, trunk/src/common/mm1alg.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/model.h, trunk/src/common/qm2mdl.cpp,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
	  trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h,
	  trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
	  trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
	  changed MM trajectory file format; some Do???-functions moved to
	  model (and are now accessible in TARGET1 also).

2001-01-30  hutchisn

	* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
	  trunk/src/common/utility.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
	  Switch to new GLADE-designed import/export boxes.
	* trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
	  trunk/oelib/atomtyp.txt, trunk/oelib/binary.cpp,
	  trunk/oelib/bond.cpp, trunk/oelib/csr.cpp, trunk/oelib/data.cpp,
	  trunk/oelib/data.h, trunk/oelib/extable.txt,
	  trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
	  trunk/oelib/gamess.cpp, trunk/oelib/ghemical.cpp,
	  trunk/oelib/hin.cpp, trunk/oelib/main.cpp, trunk/oelib/mdl.cpp,
	  trunk/oelib/mol.cpp, trunk/oelib/mol.h, trunk/oelib/mpqc.cpp,
	  trunk/oelib/oeutil.cpp, trunk/oelib/parsmart.cpp,
	  trunk/oelib/patty.cpp, trunk/oelib/patty.h, trunk/oelib/pdb.cpp,
	  trunk/oelib/quat.c, trunk/oelib/ring.cpp, trunk/oelib/ring.h,
	  trunk/oelib/rotor.cpp, trunk/oelib/smi.cpp,
	  trunk/oelib/typer.cpp, trunk/oelib/typer.h,
	  trunk/oelib/types.txt: Synch with current OELib code.

2001-01-30  thassine

	* trunk/src/common/mm1alg.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm1docv.h,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/Makefile,
	  trunk/src/target3/glade/src/glade_callbacks.cpp,
	  trunk/src/target3/glade/src/glade_callbacks.h,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_callbacks.h,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/glade_support.cpp,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
	  the geomopt/moldyn dialogs should now mostly work (except the
	  traj filename).

2001-01-29  thassine

	* trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_interface.h,
	  trunk/src/target3/glade/src/glade_support.cpp,
	  trunk/src/target3/glade/src/main.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/t3mm1docv.cpp: added geomopt and moldyn
	  dialogs, but wont work yet (just press cancel)

2001-01-25  thassine

	* trunk/src/common/conjgrad.h, trunk/src/common/define.h,
	  trunk/src/common/engine.h, trunk/src/common/errutil.h,
	  trunk/src/common/mm1alg.h, trunk/src/common/mm1eng.h,
	  trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
	  trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
	  trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.h,
	  trunk/src/common/model.h, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.h,
	  trunk/src/common/qm2eng1.h, trunk/src/common/qm2mdl.h,
	  trunk/src/common/typedef.h, trunk/src/common/utility.h,
	  trunk/src/common/v3d.h, trunk/src/graphics/camera.h,
	  trunk/src/graphics/color.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h, trunk/src/graphics/spline.cpp,
	  trunk/src/graphics/spline.h, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/surface.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/target1/config.h.OLD,
	  trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h,
	  trunk/src/target2/config.h.OLD, trunk/src/target2/t2docv.cpp,
	  trunk/src/target2/t2docv.h, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2main.h, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.cpp,
	  trunk/src/target2/t2qm2docv.h, trunk/src/target2/t2views.cpp,
	  trunk/src/target2/t2views.h, trunk/src/target3/config.h.OLD,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
	  trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: all
	  documentation is now in DOC++ form, it's a bit sparse, but
	  usable.

2001-01-24  thassine

	* trunk/oelib/Makefile, trunk/oelib/data.cpp,
	  trunk/oelib/mpqc.cpp, trunk/src/common/qm1eng.cpp,
	  trunk/src/common/qm1eng.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.cpp,
	  trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.cpp,
	  trunk/src/common/qm2eng1.h, trunk/src/common/qm2eng9.cpp,
	  trunk/src/common/qm2eng9.h, trunk/src/common/qm2mdl.cpp,
	  trunk/src/common/qm2mdl.h, trunk/src/common/typedef.h,
	  trunk/src/common/utility.cpp, trunk/src/common/utility.h,
	  trunk/src/common/v3d.h, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/camera.h, trunk/src/graphics/color.h: some
	  more documentation converted into DOC++ form

2001-01-22  hutchisn

	* trunk/oelib/Makefile.in, trunk/oelib/data.cpp,
	  trunk/oelib/data.h, trunk/oelib/extable.txt,
	  trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
	  trunk/oelib/mpqc.cpp, trunk/oelib/tinker.cpp,
	  trunk/oelib/unichem.cpp: Added unichem and mpqc formats.

2001-01-22  thassine

	* trunk/oelib/Makefile, trunk/oelib/tinker.cpp,
	  trunk/src/Makefile.OLD, trunk/src/common/conjgrad.cpp,
	  trunk/src/common/conjgrad.h, trunk/src/common/define.h,
	  trunk/src/common/engine.cpp, trunk/src/common/engine.h,
	  trunk/src/common/errutil.cpp, trunk/src/common/errutil.h,
	  trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
	  trunk/src/common/matrix.h, trunk/src/common/mm1alg.cpp,
	  trunk/src/common/mm1alg.h, trunk/src/common/mm1eng.cpp,
	  trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.cpp,
	  trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.cpp,
	  trunk/src/common/mm1eng9.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
	  trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.cpp,
	  trunk/src/common/mm1util.h, trunk/src/common/model.cpp,
	  trunk/src/common/model.h, trunk/src/common/notice.cpp,
	  trunk/src/common/notice.h, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/target3/t3mm1docv.cpp:
	  started to convert comments into a form suitable to DOC++

2001-01-20  hutchisn

	* trunk/PROJECT, trunk/oelib/Makefile.in, trunk/oelib/data.cpp,
	  trunk/oelib/tinker.cpp, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h: *** empty log message ***
	* trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/glade_callbacks.cpp,
	  trunk/src/target3/glade/src/glade_callbacks.h,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_interface.h,
	  trunk/src/target3/glade/src/glade_support.cpp,
	  trunk/src/target3/glade/src/main.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_callbacks.h,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/glade_support.cpp: Added new import/export
	  dialogues using Glade.
	  (Still need to figure out how to update the option menu
	  appropriately.)
	* trunk/oelib/data.h, trunk/oelib/extable.txt: Added all options
	  from Babel 1.6

2001-01-19  hutchisn

	* trunk/oelib/Makefile.in, trunk/oelib/fileformat.cpp,
	  trunk/oelib/qchem.cpp: Added export to QChem input files.

2001-01-16  hutchisn

	* trunk/oelib/data.cpp, trunk/oelib/data.h,
	  trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
	  trunk/oelib/fileformat.h, trunk/oelib/qchem.cpp: Added a QChem
	  file export translator.
	* trunk/oelib/data.cpp, trunk/oelib/data.h,
	  trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
	  trunk/oelib/fileformat.h: More OELib updates--removing
	  incomplete formats for now.
	* trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
	  trunk/oelib/gamess.cpp, trunk/oelib/hin.cpp: More OELib cleanups.

2001-01-13  hutchisn

	* trunk/oelib/Makefile.in, trunk/oelib/data.cpp,
	  trunk/oelib/data.h, trunk/oelib/extable.txt,
	  trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
	  trunk/oelib/gamess.cpp, trunk/oelib/ghemical.cpp,
	  trunk/oelib/hin.cpp, trunk/oelib/main.cpp, trunk/oelib/mol.h,
	  trunk/oelib/mpqc.cpp, trunk/oelib/oelib.dsp,
	  trunk/oelib/oelib.dsw, trunk/oelib/pdb.cpp, trunk/oelib/quat.c,
	  trunk/oelib/rotor.cpp, trunk/oelib/typer.cpp,
	  trunk/oelib/xyz.cpp: Added new translators, updated to be in
	  sync with OpenEyes code.
	* trunk/src/common/utility.cpp: Small modifications to vdW radii
	  to be closer to literature (Bondi) values
	* trunk/src/common/filetrans.cpp: Use filename for molecule title
	  -- we don't currently have another way of titling.

2001-01-05  hutchisn

	* trunk/acconfig.h, trunk/configure, trunk/configure.in,
	  trunk/src/config.h.in, trunk/src/target3/Makefile.in: Fix build
	  environment

2001-01-05  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.h,
	  trunk/src/common/qm2eng9.cpp, trunk/src/common/qm2mdl.cpp,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
	  trunk/src/graphics/plane.cpp, trunk/src/graphics/plane.h,
	  trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h,
	  trunk/src/graphics/surface.cpp, trunk/src/graphics/surface.h,
	  trunk/src/target1/Makefile.OLD, trunk/src/target1/t1main.cpp,
	  trunk/src/target2/t2qm2docv.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/t3qm2docv.cpp: added a simple TARGET1 example,
	  the QM setup dialog should also now work.

2001-01-03  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h,
	  trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/Makefile,
	  trunk/src/target3/glade/src/glade_callbacks.cpp,
	  trunk/src/target3/glade/src/glade_callbacks.h,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_callbacks.h,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
	  the setup dialog should now work for MM.
	* trunk/CHANGES, trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src/Makefile,
	  trunk/src/target3/glade/src/glade_callbacks.cpp,
	  trunk/src/target3/glade/src/glade_callbacks.h,
	  trunk/src/target3/glade/src/glade_interface.cpp,
	  trunk/src/target3/glade/src/glade_interface.h,
	  trunk/src/target3/glade/src/glade_support.cpp,
	  trunk/src/target3/glade/src/glade_support.h,
	  trunk/src/target3/glade/src/main.cpp,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h: dialogs; read from
	  glade/src/Makefile how to retain your changes in GLADE code.

2001-01-02  thassine

	* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h:
	  some preliminary stuff for the setup dialogs
	* trunk/INSTALL, trunk/PROJECT, trunk/src/target3/Makefile.OLD,
	  trunk/src/target3/glade, trunk/src/target3/glade/ghemical.glade,
	  trunk/src/target3/glade/src,
	  trunk/src/target3/glade/src/Makefile,
	  trunk/src/target3/glade_callbacks.cpp,
	  trunk/src/target3/glade_callbacks.h,
	  trunk/src/target3/glade_interface.cpp,
	  trunk/src/target3/glade_interface.h,
	  trunk/src/target3/glade_support.cpp,
	  trunk/src/target3/glade_support.h,
	  trunk/src/target3/t3dialog.cpp: started making some dialogs
	  using GLADE...

2001-01-01  thassine

	* trunk/AUTHORS, trunk/INSTALL, trunk/PROJECT,
	  trunk/src/common/Makefile.OLD, trunk/src/common/mm1mdl.h,
	  trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.h,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/Makefile.OLD,
	  trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
	  trunk/src/target3/Makefile.OLD: just some cleanups and some
	  improvements to documentation
	* trunk/small-utilities, trunk/small-utilities/Makefile,
	  trunk/small-utilities/getpdb_cd.cpp,
	  trunk/small-utilities/getpdb_ftp.cpp,
	  trunk/small-utilities/gp2mpqc.cpp: HAPPY NEW YEAR; some
	  small-utilities added...

2000-12-27  thassine

	* trunk/src/graphics/camera.cpp, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/views.h, trunk/src/target2/t2docv.cpp,
	  trunk/src/target2/t2docv.h, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: some
	  cleanups; status bars now work in the GNOME version

2000-12-22  thassine

	* trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h: added
	  some missing files...
	* trunk/CHANGES, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
	  trunk/src/graphics/mtools.cpp, trunk/src/graphics/qm1docv.h,
	  trunk/src/graphics/qm2docv.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/target2/Makefile.OLD,
	  trunk/src/target2/t2docv.cpp, trunk/src/target2/t2docv.h,
	  trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3qm2docv.cpp,
	  trunk/src/target3/t3qm2docv.h, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: added target-dependent middle
	  classes for docviews and views; simplifies the base-classes a bit
	* trunk/BUGLIST, trunk/src/graphics/docview.cpp,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
	  treelist works now pretty well (see BUGLIST for some details)

2000-12-21  thassine

	* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: improved proper model
	  closing/cleanup in GNOME version, but still problems (try
	  File/Close and File/Exit)
	* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/graphics/views.h, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: treelist (now actually works) -
	  added subtrees and lights

2000-12-20  thassine

	* trunk/src/graphics/docview.cpp, trunk/src/graphics/views.h,
	  trunk/src/target3/t3main.h, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: treelist - now shows objects
	  (planes etc), and selection is possible

2000-12-19  thassine

	* trunk/CHANGES, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: added framework for tree/list
	  views, and smaller changes
	* trunk/src/common/notice.cpp, trunk/src/graphics/docview.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
	  the toolbar buttons work again as toggle buttons

2000-12-18  thassine

	* trunk/oelib/Makefile, trunk/src/common/filetrans.cpp,
	  trunk/src/target3/t3main.cpp: changes for old makefiles, and a
	  statusbar added (which is empty so far)

2000-12-08  hutchisn

	* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
	  trunk/src/target3/t3mm1docv.cpp: Use new OEFileFormat code to
	  check if formats are valid.
	* trunk/oelib/Makefile, trunk/oelib/Makefile.in,
	  trunk/oelib/aromatic.txt, trunk/oelib/binary.cpp,
	  trunk/oelib/data.cpp, trunk/oelib/data.h,
	  trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
	  trunk/oelib/fileformat.h, trunk/oelib/globals.cpp,
	  trunk/oelib/main.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
	  trunk/oelib/molvector.cpp, trunk/oelib/oeutil.h,
	  trunk/oelib/rotor.cpp, trunk/oelib/rotor.h,
	  trunk/oelib/typer.cpp, trunk/oelib/xyz.cpp: Synched with current
	  oelib version--fixed bugs finding data files.

2000-12-08  thassine

	* trunk/oelib/Makefile, trunk/oelib/mol.h,
	  trunk/src/common/filetrans.cpp, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
	  trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/qm2docv.cpp, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2views.cpp,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
	  various fixes (like exit-command) - oelib?

2000-12-02  hutchisn

	* trunk/src/target3/t3mm1docv.cpp: OKEvent should return true for
	  now.
	* trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
	  OKEvent should return bool in case there's a problem
	  (e.g. file doesn't exist, save might overwrite a file, format is
	  not supported, etc.)
	* trunk/oelib/data.cpp, trunk/oelib/mol.h, trunk/oelib/pdb.cpp,
	  trunk/oelib/rotor.cpp, trunk/oelib/typer.cpp,
	  trunk/src/common/Makefile.in: One more bug fix--really get the
	  logic in initialization correct!

2000-12-01  hutchisn

	* trunk/oelib/data.cpp, trunk/oelib/pdb.cpp,
	  trunk/oelib/rotor.cpp, trunk/oelib/typer.cpp: Ensure that the
	  directory is checked AND the environment variable is checked
	  when initializing.
	* trunk/Makefile.in, trunk/configure, trunk/configure.in,
	  trunk/oelib/Makefile, trunk/oelib/Vector.cpp,
	  trunk/oelib/configure, trunk/oelib/data.cpp, trunk/oelib/data.h,
	  trunk/oelib/extable.txt, trunk/oelib/gromos96.cpp,
	  trunk/oelib/main.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
	  trunk/oelib/oeutil.cpp, trunk/oelib/pdb.cpp,
	  trunk/oelib/rotor.cpp, trunk/oelib/rotor.h,
	  trunk/oelib/typer.cpp, trunk/oelib/typer.h,
	  trunk/src/common/Makefile.in, trunk/src/common/filetrans.cpp:
	  Update OELib to use GHEMICAL_DIR environment variable or
	  specified directories
	  installed by "make install" target.

2000-12-01  thassine

	* trunk/oelib/Makefile, trunk/src/common/Makefile.OLD,
	  trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
	  trunk/src/target3/Makefile.OLD: updated the old makefiles...

2000-12-01  hutchisn

	* trunk/src/common/Makefile.in, trunk/src/common/define.h,
	  trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
	  trunk/src/common/model.cpp, trunk/src/graphics/Makefile.in,
	  trunk/src/target3/Makefile.in, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3mm1docv.cpp: add support for import/export
	  methods using oelib

2000-11-30  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/qm2mdl.h,
	  trunk/src/graphics/Makefile.OLD, trunk/src/graphics/mm1docv.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
	  GNOME erase-tool fixed, STATICpopupmenu removed, all popup-items
	  enabled again

2000-11-29  thassine

	* trunk/src/graphics/docview.h, trunk/src/graphics/views.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
	  GNOME popup menu callbacks finished - but some items are still
	  disabled
	* trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: popup-menu callbacks changed (for
	  model-independent items)
	* trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: OpenGL initialization in GNOME
	  fixed (so that we have colors back).

2000-11-28  hutchisn

	* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3views.cpp: Add import/export menu items,
	  center command and move things to "build" submenu.
	* trunk/src/target3/t3main.cpp: Can't pass VERSION since it's a
	  double. Run it through sprintf first.
	* trunk/acconfig.h, trunk/configure, trunk/configure.in,
	  trunk/src/config.h.in, trunk/src/graphics/Makefile.in: Fix build
	  environment to define appropriate flags, etc.
	* trunk/oelib/quat.c: fixed problem with undeclared memset

2000-11-28  thassine

	* trunk/CHANGES, trunk/src/common/conjgrad.h,
	  trunk/src/common/errutil.h, trunk/src/common/mm1alg.h,
	  trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.h,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.h,
	  trunk/src/common/model.h, trunk/src/common/qm2eng.h,
	  trunk/src/common/qm2eng9.h, trunk/src/common/qm2mdl.h,
	  trunk/src/common/v3d.h, trunk/src/graphics/mtools.h,
	  trunk/src/graphics/views.h, trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3main.h, trunk/src/target3/t3qm2docv.cpp,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: some
	  cleanups : public data changed protected in many classes
	* trunk/CHANGES, trunk/src/common/define.h,
	  trunk/src/graphics/Makefile.OLD, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/views.h,
	  trunk/src/target2/t2views.cpp, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: any
	  things broken/mixed up, but we have a standard GNOME MDI app now

2000-11-27  hutchisn

	* trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h:
	  Modify dialog to show which element is currently selected.
	* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: Remove
	  import functions from mm1mdl and use new filetrans code through
	  OELib.
	* trunk/Makefile.in, trunk/acconfig.h, trunk/configure,
	  trunk/configure.in, trunk/oelib/Makefile.in,
	  trunk/oelib/configure, trunk/src/common/Makefile.in,
	  trunk/src/config.h.in, trunk/src/graphics/Makefile.in,
	  trunk/src/target3/Makefile.in: Add changes to support linking in
	  OELib and slightly cleaned up build system.

2000-11-27  thassine

	* trunk/configure, trunk/configure.in,
	  trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
	  trunk/src/target3/Makefile.in: Makefile.in -files updated
	  (configure still broken)

2000-11-26  thassine

	* trunk/CHANGES, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/camera.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/surface.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/target2/config.h.OLD,
	  trunk/src/target2/t2mm1docv.cpp,
	  trunk/src/target2/t2qm1docv.cpp,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2views.cpp,
	  trunk/src/target3/config.h.OLD, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
	  3rd stage of doc/view changes

2000-11-24  thassine

	* trunk/CHANGES, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/camera.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/mtools.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/surface.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
	  trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
	  trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3qm2docv.cpp,
	  trunk/src/target3/t3qm2docv.h, trunk/src/target3/t3views.cpp,
	  trunk/src/target3/t3views.h: 2nd stage of doc/view reorganization

2000-11-23  thassine

	* trunk/CHANGES, trunk/src/common/Makefile.OLD,
	  trunk/src/common/conjgrad.h, trunk/src/common/engbase.cpp,
	  trunk/src/common/engbase.h, trunk/src/common/engine.cpp,
	  trunk/src/common/engine.h, trunk/src/common/mdlbase.cpp,
	  trunk/src/common/mdlbase.h, trunk/src/common/mm1eng.cpp,
	  trunk/src/common/mm1eng.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1util.cpp,
	  trunk/src/common/model.cpp, trunk/src/common/model.h,
	  trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/common/qm2eng.cpp, trunk/src/common/qm2eng.h,
	  trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
	  trunk/src/graphics/Makefile.OLD, trunk/src/graphics/camera.cpp,
	  trunk/src/graphics/camera.h, trunk/src/graphics/docview.cpp,
	  trunk/src/graphics/docview.h, trunk/src/graphics/guibase.cpp,
	  trunk/src/graphics/guibase.h, trunk/src/graphics/mm1docv.cpp,
	  trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1gui.cpp,
	  trunk/src/graphics/mm1gui.h, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
	  trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm1gui.cpp,
	  trunk/src/graphics/qm1gui.h, trunk/src/graphics/qm2docv.cpp,
	  trunk/src/graphics/qm2docv.h, trunk/src/graphics/qm2gui.cpp,
	  trunk/src/graphics/qm2gui.h, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/surface.h, trunk/src/graphics/viewing.cpp,
	  trunk/src/graphics/viewing.h, trunk/src/graphics/views.cpp,
	  trunk/src/graphics/views.h, trunk/src/graphics/window.cpp,
	  trunk/src/graphics/window.h, trunk/src/target1/Makefile.OLD,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.h,
	  trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
	  trunk/src/target2/t2mm1gui.cpp, trunk/src/target2/t2mm1gui.h,
	  trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
	  trunk/src/target2/t2qm1gui.cpp, trunk/src/target2/t2qm1gui.h,
	  trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
	  trunk/src/target2/t2qm2gui.cpp, trunk/src/target2/t2qm2gui.h,
	  trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
	  trunk/src/target2/t2window.cpp, trunk/src/target2/t2window.h,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
	  trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
	  trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
	  trunk/src/target3/t3qm1gui.cpp, trunk/src/target3/t3qm1gui.h,
	  trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
	  trunk/src/target3/t3qm2gui.cpp, trunk/src/target3/t3qm2gui.h,
	  trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h,
	  trunk/src/target3/t3window.cpp, trunk/src/target3/t3window.h:
	  1st round of doc/view changes (will break the configure-script)

2000-11-20  thassine

	* trunk/src/common/qm2mdl.cpp, trunk/src/graphics/guibase.h,
	  trunk/src/graphics/mm1gui.cpp, trunk/src/graphics/mm1gui.h,
	  trunk/src/graphics/mm1rbn.cpp, trunk/src/graphics/qm2gui.cpp,
	  trunk/src/graphics/qm2gui.h: fixed QM import bug + some
	  potential graphics bugs

2000-11-16  hutchisn

	* trunk/Makefile.in: Removed configure target--something is
	  strange with the timestamps.

2000-11-16  thassine

	* trunk/src/common/Makefile.OLD, trunk/src/common/errorutil.cpp,
	  trunk/src/common/errorutil.h, trunk/src/common/errutil.cpp,
	  trunk/src/common/errutil.h, trunk/src/common/mdlbase.cpp,
	  trunk/src/common/mdlbase.h, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/qm1mdl.cpp,
	  trunk/src/common/qm1mdl.h, trunk/src/common/qm2mdl.cpp,
	  trunk/src/common/qm2mdl.h, trunk/src/graphics/Makefile.OLD,
	  trunk/src/graphics/guibase.cpp, trunk/src/graphics/guibase.h,
	  trunk/src/graphics/mm1gui.cpp, trunk/src/graphics/mm1gui.h,
	  trunk/src/graphics/qm1gui.cpp, trunk/src/graphics/qm1gui.h,
	  trunk/src/graphics/qm2gui.cpp, trunk/src/graphics/qm2gui.h,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2mm1gui.cpp, trunk/src/target2/t2mm1gui.h,
	  trunk/src/target2/t2qm1gui.cpp, trunk/src/target2/t2qm1gui.h,
	  trunk/src/target2/t2qm2gui.cpp, trunk/src/target2/t2qm2gui.h,
	  trunk/src/target2/t2window.cpp, trunk/src/target3/Makefile.OLD,
	  trunk/src/target3/t3errorutil.cpp,
	  trunk/src/target3/t3errorutil.h,
	  trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1gui.cpp,
	  trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm1gui.cpp,
	  trunk/src/target3/t3qm1gui.h, trunk/src/target3/t3qm2gui.cpp,
	  trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp:
	  added err_util for all models

2000-11-15  hutchisn

	* trunk/src/common/Makefile.in, trunk/src/common/errorutil.cpp,
	  trunk/src/common/errorutil.h, trunk/src/target3/Makefile.in,
	  trunk/src/target3/t3errorutil.cpp,
	  trunk/src/target3/t3errorutil.h: Add error-handling classes with
	  support for GNOME.
	* trunk/oelib/Makefile, trunk/oelib/Makefile.in,
	  trunk/oelib/data.cpp, trunk/oelib/data.h,
	  trunk/oelib/extable.txt, trunk/oelib/ghemical.cpp,
	  trunk/oelib/mol.cpp, trunk/oelib/mol.h: Add read/write for
	  ghemical file format.

2000-11-14  hutchisn

	* trunk/oelib, trunk/oelib/.cvsignore, trunk/oelib/GNULICENSE.txt,
	  trunk/oelib/Makefile, trunk/oelib/Makefile.in,
	  trunk/oelib/OELibPrimer.html, trunk/oelib/StdAfx.cpp,
	  trunk/oelib/StdAfx.h, trunk/oelib/Vector.cpp,
	  trunk/oelib/Vector.h, trunk/oelib/alchemy.cpp,
	  trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
	  trunk/oelib/atomtyp.txt, trunk/oelib/balst.cpp,
	  trunk/oelib/bgf.cpp, trunk/oelib/binary.cpp,
	  trunk/oelib/binary.h, trunk/oelib/bitgrid.cpp,
	  trunk/oelib/bitgrid.h, trunk/oelib/bitvec.cpp,
	  trunk/oelib/bitvec.h, trunk/oelib/bond.cpp, trunk/oelib/box.cpp,
	  trunk/oelib/c3d.cpp, trunk/oelib/cacao.cpp,
	  trunk/oelib/cache.cpp, trunk/oelib/ccc.cpp,
	  trunk/oelib/chdrw.cpp, trunk/oelib/chiral.cpp,
	  trunk/oelib/chiral.h, trunk/oelib/commandline.cpp,
	  trunk/oelib/commandline.h, trunk/oelib/configure,
	  trunk/oelib/csr.cpp, trunk/oelib/cssr.cpp,
	  trunk/oelib/cwrap.cpp, trunk/oelib/cwrap.h,
	  trunk/oelib/data.cpp, trunk/oelib/data.h,
	  trunk/oelib/element.txt, trunk/oelib/extable.txt,
	  trunk/oelib/feat.cpp, trunk/oelib/fh.cpp, trunk/oelib/grid.cpp,
	  trunk/oelib/grid.h, trunk/oelib/gromos96.cpp,
	  trunk/oelib/main.cpp, trunk/oelib/matrix.cpp,
	  trunk/oelib/matrix.h, trunk/oelib/mdl.cpp, trunk/oelib/mmod.cpp,
	  trunk/oelib/mol.cpp, trunk/oelib/mol.h, trunk/oelib/mol2.cpp,
	  trunk/oelib/molchrg.cpp, trunk/oelib/molchrg.h,
	  trunk/oelib/molvector.cpp, trunk/oelib/molvector.h,
	  trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
	  trunk/oelib/parsmart.cpp, trunk/oelib/parsmart.h,
	  trunk/oelib/parsmi.cpp, trunk/oelib/patty.cpp,
	  trunk/oelib/patty.h, trunk/oelib/pdb.cpp, trunk/oelib/quat.c,
	  trunk/oelib/rand.cpp, trunk/oelib/resdata.txt,
	  trunk/oelib/ring.cpp, trunk/oelib/ring.h, trunk/oelib/rotor.cpp,
	  trunk/oelib/rotor.h, trunk/oelib/smi.cpp, trunk/oelib/smi.h,
	  trunk/oelib/tokenst.cpp, trunk/oelib/typer.cpp,
	  trunk/oelib/typer.h, trunk/oelib/types.txt,
	  trunk/oelib/version.h: Initial revision
	* trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
	  trunk/src/target3/t3window.cpp: Added menu items and
	  user-visible feedback for menu choices.
	* trunk/Makefile.in, trunk/configure.in: Add makefile targets to
	  ensure configure script and Makefiles are updated properly.
	  Also add AC_PREREQ to configure.in to ensure configure script
	  isn't updated by
	  an old version of autoconf.

2000-11-10  hutchisn

	* trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
	  trunk/src/target3/t3window.cpp: Remove menu items for import HIN
	  and PDB files (soon to be done through OELib)
	  Add menu items and support for render labels and coloring and
	  quick update mode.
	* trunk/bin/examples/2-chlorobutane.gpMM,
	  trunk/bin/examples/3-phenylpropanal.gpMM,
	  trunk/bin/examples/acetylsalicylic_acid.gpMM,
	  trunk/bin/examples/alpha-pinene.gpMM,
	  trunk/bin/examples/bromobenzene.gpMM,
	  trunk/bin/examples/camphor.gpMM,
	  trunk/bin/examples/cinnamaldehyde.gpMM,
	  trunk/bin/examples/cis-2-pentene.gpMM,
	  trunk/bin/examples/cyclohexane.gpMM,
	  trunk/bin/examples/naphtalene.gpMM: Update examples to new file
	  format (read in and re-saved).

2000-11-10  thassine

	* trunk/CHANGES, trunk/src/common/mdlbase.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm1util.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/common/qm2mdl.h: 1st round of mm1_mdl file format
	  revision

2000-11-09  thassine

	* trunk/BUGLIST, trunk/CHANGES, trunk/src/Makefile.OLD,
	  trunk/src/common/typedef.h, trunk/src/common/utility.cpp,
	  trunk/src/graphics/color.h, trunk/src/graphics/guibase.cpp,
	  trunk/src/graphics/guibase.h, trunk/src/graphics/mm1gui.cpp,
	  trunk/src/graphics/mm1rbn.h, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/plane.h, trunk/src/graphics/qm1gui.cpp,
	  trunk/src/graphics/qm2gui.cpp, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/surface.h, trunk/src/graphics/viewing.cpp,
	  trunk/src/graphics/viewing.h, trunk/src/target2/t2mm1gui.cpp,
	  trunk/src/target2/t2qm2gui.cpp, trunk/src/target3/t3mm1gui.cpp,
	  trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm2gui.cpp,
	  trunk/src/target3/t3window.cpp: graphics improvements, volume
	  rendering added

2000-11-08  hutchisn

	* trunk/src/common/utility.cpp, trunk/src/common/utility.h: Add
	  back correct symbol for element 110. This may cause problems
	  with atom
	  type rules, but how many rules involve element 110 anyway?

2000-11-07  hutchisn

	* trunk/src/target3/t3dialog.cpp: Add feedback for currently
	  selected bondtype and element in dialogues.
	* trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3qm2gui.cpp:
	  Temporarily fix bug for open file filters--don't supply a filter
	  until GTK is
	  fixed.

2000-11-02  thassine

	* trunk/src/common/define.h, trunk/src/target3/t3main.cpp: fixed
	  those about-dialog crashes...

2000-11-01  thassine

	* trunk/CHANGES, trunk/src/common/define.h,
	  trunk/src/common/mdlbase.cpp, trunk/src/common/mdlbase.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1tab1.cpp,
	  trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1util.cpp,
	  trunk/src/target3/Makefile.OLD: added primary/secondary paths
	  for parameter files

2000-10-31  hutchisn

	* trunk/src/common/utility.cpp, trunk/src/graphics/mm1gui.cpp:
	  Enter real vdW radii from several sources and update GUI to draw
	  accordingly
	* trunk/src/target3/t3dialog.cpp: Fixed bug with elements beyond
	  #105.
	* trunk/configure, trunk/configure.in: Another attempt to pick up
	  Xmu and glut appropirately.

2000-10-31  thassine

	* trunk/src/Makefile.OLD: revieved the /src/Makefile.OLD

2000-10-30  hutchisn

	* trunk/configure, trunk/configure.in, trunk/src/Makefile.OLD,
	  trunk/src/target3/Makefile.in: Bugfixes for the autoconf
	  changes--should now work on systems needing -Xmu.

2000-10-30  thassine

	* trunk/src/Makefile.OLD: added yet another Makefile.OLD

2000-10-30  hutchisn

	* trunk/INSTALL, trunk/Makefile.in, trunk/acconfig.h,
	  trunk/aclocal.m4, trunk/configure, trunk/configure.in,
	  trunk/install-sh, trunk/mkinstalldirs, trunk/src/Makefile,
	  trunk/src/common/Makefile.in, trunk/src/common/define.h,
	  trunk/src/config.h.in, trunk/src/graphics/Makefile.in,
	  trunk/src/target3/Makefile.in, trunk/src/target3/t3main.cpp:
	  Changes to move to an autoconf-derived configure script.

2000-10-25  thassine

	* trunk/src/common/conjgrad.cpp, trunk/src/common/utility.cpp:
	  added some missing header files
	* trunk/CHANGES, trunk/src/common/conjgrad.cpp,
	  trunk/src/common/utility.cpp, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3qm2gui.cpp:
	  better GnomeUIInfo initialization (the RH7-patch from GH)
	* trunk/CHANGES, trunk/src/graphics/guibase.cpp,
	  trunk/src/graphics/mm1gui.cpp: the multiple view management bug
	  fixed (at last)

2000-10-25  hutchisn

	* trunk/src/common/conjgrad.cpp, trunk/src/common/utility.cpp,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1gui.cpp,
	  trunk/src/target3/t3qm2gui.cpp: Minor changes to allow
	  compilation on RH7.
	* trunk/bin, trunk/bin/.cvsignore, trunk/src,
	  trunk/src/.cvsignore, trunk/src/common,
	  trunk/src/common/.cvsignore, trunk/src/graphics,
	  trunk/src/graphics/.cvsignore, trunk/src/target2,
	  trunk/src/target2/.cvsignore, trunk/src/target3,
	  trunk/src/target3/.cvsignore: CVS ignore files to remove common
	  build objects, etc.

2000-10-24  thassine

	* trunk/src/graphics/mm1gui.cpp, trunk/src/graphics/mm1gui.h,
	  trunk/src/target2/t2mm1gui.cpp, trunk/src/target3/t3mm1gui.cpp:
	  cleaned some graphics code

2000-10-23  thassine

	* trunk/src/new.cpp, trunk/src/new.h, trunk/src/some-extra-files,
	  trunk/src/some-extra-files/newfile.cpp,
	  trunk/src/some-extra-files/newfile.h: moved some conflicting
	  files to some-extra-files
	* trunk/CHANGES, trunk/src/common/mm1mdl.cpp,
	  trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.cpp,
	  trunk/src/common/mm1util.h, trunk/src/graphics/mm1rbn.cpp:
	  improved mm1_chn_info

2000-10-21  thassine

	* trunk/src/common/Makefile, trunk/src/common/color.h,
	  trunk/src/common/config.h, trunk/src/common/guibase.cpp,
	  trunk/src/common/guibase.h, trunk/src/common/mm1gui.cpp,
	  trunk/src/common/mm1gui.h, trunk/src/common/mm1rbn.cpp,
	  trunk/src/common/mm1rbn.h, trunk/src/common/mtools.cpp,
	  trunk/src/common/mtools.h, trunk/src/common/objects.cpp,
	  trunk/src/common/objects.h, trunk/src/common/plane.cpp,
	  trunk/src/common/plane.h, trunk/src/common/qm1gui.cpp,
	  trunk/src/common/qm1gui.h, trunk/src/common/qm2gui.cpp,
	  trunk/src/common/qm2gui.h, trunk/src/common/spline.cpp,
	  trunk/src/common/spline.h, trunk/src/common/surface.cpp,
	  trunk/src/common/surface.h, trunk/src/common/viewing.cpp,
	  trunk/src/common/viewing.h, trunk/src/common/window.cpp,
	  trunk/src/common/window.h: removed some duplicate files
	* trunk/src/common/library: removed library-dir
	* trunk/CHANGES, trunk/src/Makefile,
	  trunk/src/common/Makefile.OLD, trunk/src/common/conjgrad.cpp,
	  trunk/src/common/conjgrad.h, trunk/src/common/define.h,
	  trunk/src/common/engbase.cpp, trunk/src/common/engbase.h,
	  trunk/src/common/mdlbase.cpp, trunk/src/common/mdlbase.h,
	  trunk/src/common/mm1alg.cpp, trunk/src/common/mm1alg.h,
	  trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
	  trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
	  trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
	  trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
	  trunk/src/common/mm1tab1.cpp, trunk/src/common/mm1tab1.h,
	  trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1tab9.h,
	  trunk/src/common/mm1util.cpp, trunk/src/common/mm1util.h,
	  trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
	  trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
	  trunk/src/common/qm2eng.cpp, trunk/src/common/qm2eng.h,
	  trunk/src/common/qm2eng1.cpp, trunk/src/common/qm2eng1.h,
	  trunk/src/common/qm2eng9.cpp, trunk/src/common/qm2eng9.h,
	  trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
	  trunk/src/common/typedef.h, trunk/src/common/utility.cpp,
	  trunk/src/common/utility.h, trunk/src/common/v3d.h,
	  trunk/src/graphics, trunk/src/graphics/Makefile.OLD,
	  trunk/src/graphics/color.h, trunk/src/graphics/guibase.cpp,
	  trunk/src/graphics/guibase.h, trunk/src/graphics/mm1gui.cpp,
	  trunk/src/graphics/mm1gui.h, trunk/src/graphics/mm1rbn.cpp,
	  trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
	  trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
	  trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
	  trunk/src/graphics/plane.h, trunk/src/graphics/qm1gui.cpp,
	  trunk/src/graphics/qm1gui.h, trunk/src/graphics/qm2gui.cpp,
	  trunk/src/graphics/qm2gui.h, trunk/src/graphics/spline.cpp,
	  trunk/src/graphics/spline.h, trunk/src/graphics/surface.cpp,
	  trunk/src/graphics/surface.h, trunk/src/graphics/viewing.cpp,
	  trunk/src/graphics/viewing.h, trunk/src/graphics/window.cpp,
	  trunk/src/graphics/window.h, trunk/src/target1/Makefile,
	  trunk/src/target1/Makefile.OLD, trunk/src/target1/config.h,
	  trunk/src/target1/config.h.OLD, trunk/src/target2/Makefile,
	  trunk/src/target2/Makefile.OLD, trunk/src/target2/config.h,
	  trunk/src/target2/config.h.OLD, trunk/src/target3/Makefile,
	  trunk/src/target3/Makefile.OLD, trunk/src/target3/config.h,
	  trunk/src/target3/config.h.OLD: new source tree with old
	  makefiles
	* trunk/CHANGES, trunk/src/common/guibase.cpp,
	  trunk/src/common/guibase.h, trunk/src/common/library/define.h,
	  trunk/src/common/library/mdlbase.cpp,
	  trunk/src/common/library/mdlbase.h,
	  trunk/src/common/viewing.cpp, trunk/src/target3/t3dialog.cpp,
	  trunk/src/target3/t3dialog.h, trunk/src/target3/t3mm1gui.cpp,
	  trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm2gui.cpp,
	  trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp:
	  file save dialogs added, selection bug fixed

2000-10-18  thassine

	* trunk/CHANGES, trunk/bin/examples/2-chlorobutane.gpMM,
	  trunk/bin/examples/2-chlorobutane.mm1gp,
	  trunk/bin/examples/3-phenylpropanal.gpMM,
	  trunk/bin/examples/3-phenylpropanal.mm1gp,
	  trunk/bin/examples/acetylsalicylic_acid.gpMM,
	  trunk/bin/examples/acetylsalicylic_acid.mm1gp,
	  trunk/bin/examples/alpha-pinene.gpMM,
	  trunk/bin/examples/alpha-pinene.mm1gp,
	  trunk/bin/examples/bromobenzene.gpMM,
	  trunk/bin/examples/bromobenzene.mm1gp,
	  trunk/bin/examples/camphor.gpMM,
	  trunk/bin/examples/camphor.mm1gp,
	  trunk/bin/examples/cinnamaldehyde.gpMM,
	  trunk/bin/examples/cinnamaldehyde.mm1gp,
	  trunk/bin/examples/cis-2-pentene.gpMM,
	  trunk/bin/examples/cis-2-pentene.mm1gp,
	  trunk/bin/examples/cyclohexane.gpMM,
	  trunk/bin/examples/cyclohexane.mm1gp,
	  trunk/bin/examples/naphtalene.gpMM,
	  trunk/bin/examples/naphtalene.mm1gp,
	  trunk/src/common/guibase.cpp, trunk/src/common/guibase.h,
	  trunk/src/common/library/mm1mdl.cpp,
	  trunk/src/common/library/qm1mdl.cpp,
	  trunk/src/common/library/qm2mdl.cpp,
	  trunk/src/common/mm1gui.cpp, trunk/src/common/mm1gui.h,
	  trunk/src/common/qm1gui.cpp, trunk/src/common/qm1gui.h,
	  trunk/src/common/qm2gui.cpp, trunk/src/common/qm2gui.h,
	  trunk/src/target2/t2main.cpp, trunk/src/target3/t3dialog.cpp,
	  trunk/src/target3/t3dialog.h, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3main.h, trunk/src/target3/t3mm1gui.cpp,
	  trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm2gui.cpp,
	  trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp,
	  trunk/src/target3/t3window.h: added file dialogs for GNOME
	  version, changed examples

2000-10-16  thassine

	* trunk/src/common/config.h, trunk/src/common/library/config.h,
	  trunk/src/common/library/mm1mdl.cpp,
	  trunk/src/common/library/mm1util.cpp,
	  trunk/src/common/library/utility.cpp,
	  trunk/src/common/library/utility.h: merged the patches from GH

2000-09-09  thassine

	* trunk/CHANGES, trunk/src/common/config.h,
	  trunk/src/common/library/config.h,
	  trunk/src/common/library/define.h, trunk/src/target1/Makefile:
	  just a few minor changes
	* trunk/BUGLIST, trunk/CHANGES, trunk/INSTALL, trunk/PROJECT,
	  trunk/src/common/Makefile, trunk/src/common/library/Makefile,
	  trunk/src/common/library/define.h, trunk/src/common/qm2gui.cpp,
	  trunk/src/new.h, trunk/src/target2/Makefile,
	  trunk/src/target3/Makefile, trunk/src/target3/t3main.cpp,
	  trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3qm2gui.cpp,
	  trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp:
	  improvements in gt3. this is released as 0.2.2

2000-09-06  thassine

	* trunk/src/Makefile: made some changes in makefiles
	* trunk/AUTHORS, trunk/BUGLIST, trunk/CHANGES, trunk/COPYING,
	  trunk/INSTALL, trunk/PROJECT, trunk/bin, trunk/bin/examples,
	  trunk/bin/examples/2-chlorobutane.mm1gp,
	  trunk/bin/examples/3-phenylpropanal.mm1gp,
	  trunk/bin/examples/acetylsalicylic_acid.mm1gp,
	  trunk/bin/examples/alpha-pinene.mm1gp,
	  trunk/bin/examples/bromobenzene.mm1gp,
	  trunk/bin/examples/camphor.mm1gp,
	  trunk/bin/examples/cinnamaldehyde.mm1gp,
	  trunk/bin/examples/cis-2-pentene.mm1gp,
	  trunk/bin/examples/cyclohexane.mm1gp,
	  trunk/bin/examples/naphtalene.mm1gp, trunk/bin/parameters,
	  trunk/bin/parameters/builder,
	  trunk/bin/parameters/builder/amino.txt,
	  trunk/bin/parameters/builder/nucleic.txt,
	  trunk/bin/parameters/mm1param,
	  trunk/bin/parameters/mm1param/stable,
	  trunk/bin/parameters/mm1param/stable/atomtypes.txt,
	  trunk/bin/parameters/mm1param/stable/parameters1.txt,
	  trunk/bin/parameters/mm1param/stable/parameters2.txt,
	  trunk/bin/parameters/mm1param/stable/parameters3.txt,
	  trunk/bin/parameters/mm1param/stable/parameters4.txt,
	  trunk/bin/parameters/mm1param/stable/parameters5.txt,
	  trunk/bin/parameters/mm1param/unstable,
	  trunk/bin/parameters/mm1param/unstable/atomtypes.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters1.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters2.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters3.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters4.txt,
	  trunk/bin/parameters/mm1param/unstable/parameters5.txt,
	  trunk/src, trunk/src/Makefile, trunk/src/common,
	  trunk/src/common/Makefile, trunk/src/common/color.h,
	  trunk/src/common/config.h, trunk/src/common/guibase.cpp,
	  trunk/src/common/guibase.h, trunk/src/common/library,
	  trunk/src/common/library/Makefile,
	  trunk/src/common/library/config.h,
	  trunk/src/common/library/conjgrad.cpp,
	  trunk/src/common/library/conjgrad.h,
	  trunk/src/common/library/define.h,
	  trunk/src/common/library/engbase.cpp,
	  trunk/src/common/library/engbase.h,
	  trunk/src/common/library/mdlbase.cpp,
	  trunk/src/common/library/mdlbase.h,
	  trunk/src/common/library/mm1alg.cpp,
	  trunk/src/common/library/mm1alg.h,
	  trunk/src/common/library/mm1eng.cpp,
	  trunk/src/common/library/mm1eng.h,
	  trunk/src/common/library/mm1eng1.cpp,
	  trunk/src/common/library/mm1eng1.h,
	  trunk/src/common/library/mm1eng9.cpp,
	  trunk/src/common/library/mm1eng9.h,
	  trunk/src/common/library/mm1mdl.cpp,
	  trunk/src/common/library/mm1mdl.h,
	  trunk/src/common/library/mm1tab1.cpp,
	  trunk/src/common/library/mm1tab1.h,
	  trunk/src/common/library/mm1tab9.cpp,
	  trunk/src/common/library/mm1tab9.h,
	  trunk/src/common/library/mm1util.cpp,
	  trunk/src/common/library/mm1util.h,
	  trunk/src/common/library/qm1eng.cpp,
	  trunk/src/common/library/qm1eng.h,
	  trunk/src/common/library/qm1mdl.cpp,
	  trunk/src/common/library/qm1mdl.h,
	  trunk/src/common/library/qm2eng.cpp,
	  trunk/src/common/library/qm2eng.h,
	  trunk/src/common/library/qm2eng1.cpp,
	  trunk/src/common/library/qm2eng1.h,
	  trunk/src/common/library/qm2eng9.cpp,
	  trunk/src/common/library/qm2eng9.h,
	  trunk/src/common/library/qm2mdl.cpp,
	  trunk/src/common/library/qm2mdl.h,
	  trunk/src/common/library/typedef.h,
	  trunk/src/common/library/utility.cpp,
	  trunk/src/common/library/utility.h,
	  trunk/src/common/library/v3d.h, trunk/src/common/matrix.h,
	  trunk/src/common/mm1gui.cpp, trunk/src/common/mm1gui.h,
	  trunk/src/common/mm1rbn.cpp, trunk/src/common/mm1rbn.h,
	  trunk/src/common/mtools.cpp, trunk/src/common/mtools.h,
	  trunk/src/common/notice.cpp, trunk/src/common/notice.h,
	  trunk/src/common/objects.cpp, trunk/src/common/objects.h,
	  trunk/src/common/plane.cpp, trunk/src/common/plane.h,
	  trunk/src/common/qm1gui.cpp, trunk/src/common/qm1gui.h,
	  trunk/src/common/qm2gui.cpp, trunk/src/common/qm2gui.h,
	  trunk/src/common/spline.cpp, trunk/src/common/spline.h,
	  trunk/src/common/surface.cpp, trunk/src/common/surface.h,
	  trunk/src/common/viewing.cpp, trunk/src/common/viewing.h,
	  trunk/src/common/window.cpp, trunk/src/common/window.h,
	  trunk/src/new.cpp, trunk/src/new.h, trunk/src/target1,
	  trunk/src/target1/Makefile, trunk/src/target1/config.h,
	  trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h,
	  trunk/src/target2, trunk/src/target2/Makefile,
	  trunk/src/target2/config.h, trunk/src/target2/t2main.cpp,
	  trunk/src/target2/t2main.h, trunk/src/target2/t2mm1gui.cpp,
	  trunk/src/target2/t2mm1gui.h, trunk/src/target2/t2qm1gui.cpp,
	  trunk/src/target2/t2qm1gui.h, trunk/src/target2/t2qm2gui.cpp,
	  trunk/src/target2/t2qm2gui.h, trunk/src/target2/t2window.cpp,
	  trunk/src/target2/t2window.h, trunk/src/target3,
	  trunk/src/target3/Makefile, trunk/src/target3/config.h,
	  trunk/src/target3/pixmaps, trunk/src/target3/pixmaps/draw.xpm,
	  trunk/src/target3/pixmaps/erase.xpm,
	  trunk/src/target3/pixmaps/orb_xy.xpm,
	  trunk/src/target3/pixmaps/orb_z.xpm,
	  trunk/src/target3/pixmaps/rot_xy.xpm,
	  trunk/src/target3/pixmaps/rot_z.xpm,
	  trunk/src/target3/pixmaps/select.xpm,
	  trunk/src/target3/pixmaps/trans_xy.xpm,
	  trunk/src/target3/pixmaps/trans_z.xpm,
	  trunk/src/target3/pixmaps/zoom.xpm,
	  trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
	  trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
	  trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
	  trunk/src/target3/t3qm1gui.cpp, trunk/src/target3/t3qm1gui.h,
	  trunk/src/target3/t3qm2gui.cpp, trunk/src/target3/t3qm2gui.h,
	  trunk/src/target3/t3window.cpp, trunk/src/target3/t3window.h:
	  Initial revision

2000-09-06  

	* branches, tags, trunk: New repository initialized by cvs2svn.

