2006-08-28 12:26  thassine

	* configure.ac, src/project.cpp: changes at lib side

2006-08-07 12:33  thassine

	* ChangeLog: changelog updated using svn2cl v0.7

2006-08-07 12:22  thassine

	* .cvsignore, docs/.cvsignore, docs/user-docs/.cvsignore,
	  docs/user-docs/images/.cvsignore, examples/.cvsignore,
	  examples/TSS/E2-reaction/.cvsignore, examples/TSS/Makefile,
	  examples/TSS/Makefile.in, examples/TSS/SN2-reaction/.cvsignore,
	  examples/TSS/carbocation_rearrangement_hydride_shift/.cvsignore,
	  examples/TSS/carbocation_rearrangement_methide_shift/.cvsignore,
	  examples/TSS/cycloaddition_Diels-Alder/.cvsignore,
	  examples/TSS/sigmatropic_rearrangement_Cope/.cvsignore,
	  examples/TSS/tautomeric_shift_keto_enol/.cvsignore,
	  src/.cvsignore, src/res_gtk/Makefile.in: removed .cvsignore +
	  other old files.

2006-07-31 10:56  thassine

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

2006-07-24 11:45  thassine

	* configure.ac, examples/TSS/Makefile, src/gtk_app.cpp,
	  src/project.cpp: adapted to changes at lib side.

2006-07-12 09:42  thassine

	* examples/TSS/Makefile, examples/TSS/Makefile.in: added some
	  missing files.

2006-06-06 11:06  thassine

	* configure.ac, examples/Makefile.am, examples/TSS/Makefile.am:
	  subdirs examples/TSS and examples/tss were mixed up ; now only
	  TSS used (like in v2.00)

2006-04-11 09:39  thassine

	* INSTALL, configure.ac, src/gtk_app.cpp: updated INSTALL

2006-04-10 13:24  thassine

	* Makefile.am, configure.ac, docs, docs/.cvsignore,
	  docs/Makefile.am, src/gtk_app.cpp, src/pui_app.cpp,
	  src/pui_app.h, src/pui_main.cpp, src/pui_main.h,
	  src/pui_oglview_wnd.cpp, src/pui_oglview_wnd.h, src/pui_wnd.cpp,
	  src/pui_wnd.h: updated docs, docs viewed now using a browser.

2006-04-10 13:22  thassine

	* docs/user-docs, docs/user-docs/.cvsignore,
	  docs/user-docs/Makefile.am, 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,
	  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 docs.

2006-04-05 12:59  thassine

	* src/Makefile.am, src/custom_camera.cpp, src/custom_camera.h,
	  src/custom_lights.cpp, src/custom_lights.h, src/ogl_plane.cpp,
	  src/ogl_plane.h, src/ogl_surface.cpp, src/ogl_surface.h,
	  src/oglview_wcl.cpp, src/project.cpp, src/project.h: many
	  improvements + bugfixes ; the GL selection and zoom tool should
	  work now.

2006-03-28 12:25  thassine

	* configure.ac, examples/Makefile.am, examples/TSS,
	  examples/TSS/E2-reaction, examples/TSS/E2-reaction/.cvsignore,
	  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/README,
	  examples/TSS/SN2-reaction, examples/TSS/SN2-reaction/.cvsignore,
	  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/.cvsignore,
	  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/.cvsignore,
	  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/.cvsignore,
	  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/.cvsignore,
	  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/.cvsignore,
	  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: added
	  examples/tss

2006-03-28 12:08  thassine

	* configure.ac, examples/Makefile.am, src/gtk_app.cpp: renamed the
	  examples/transition_state_search to examples/TSS (make dist
	  limits filenames to 99 characters).

2006-03-28 12:01  thassine

	* examples/transition_state_search: removed the
	  transition_state_search directory.

2006-03-28 11:25  thassine

	* ., .cvsignore: removed some unnecessary files.

2006-03-28 10:38  thassine

	* config.guess, config.sub, ltmain.sh: removed some unnecessary
	  files.

2006-03-20 11:22  thassine

	* src/gtk_app.cpp, src/gtk_app.h: added optional long/short
	  toolbar labels.

2006-03-16 06:48  thassine

	* INSTALL, configure.ac: documentation updates.

2006-03-14 14:14  thassine

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

2006-03-10 12:23  thassine

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

2006-03-08 10:37  thassine

	* ., .cvsignore: cvsignore updated.

2006-03-08 08:58  thassine

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

2006-03-07 09:11  thassine

	* aclocal.m4, src/gtk_app.cpp, src/gtk_app.h,
	  src/gtk_setup_dialog.cpp, src/res_gtk/gtk_setup_dialog.glade:
	  synchronized with libghemical.

2006-03-03 13:41  thassine

	* aclocal.m4, src/gtk_app.cpp, src/gtk_app.h: ported Donald's
	  frozen atom improvements.

2006-03-03 12:37  thassine

	* ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, configure,
	  examples, examples/.cvsignore, examples/Makefile.in,
	  examples/transition_state_search,
	  examples/transition_state_search/.cvsignore,
	  examples/transition_state_search/E2-reaction,
	  examples/transition_state_search/E2-reaction/.cvsignore,
	  examples/transition_state_search/E2-reaction/Makefile.in,
	  examples/transition_state_search/Makefile.in,
	  examples/transition_state_search/SN2-reaction,
	  examples/transition_state_search/SN2-reaction/.cvsignore,
	  examples/transition_state_search/SN2-reaction/Makefile.in,
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/.cvsignore,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/.cvsignore,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/Makefile.in,
	  examples/transition_state_search/cycloaddition_Diels-Alder,
	  examples/transition_state_search/cycloaddition_Diels-Alder/.cvsignore,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope,
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/.cvsignore,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/Makefile.in,
	  examples/transition_state_search/tautomeric_shift_keto_enol,
	  examples/transition_state_search/tautomeric_shift_keto_enol/.cvsignore,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/Makefile.in,
	  src, src/.cvsignore, src/Makefile.in,
	  src/gtk_moldyn_dialog.cpp, src/gtk_trajview_dialog.cpp,
	  src/project.cpp, src/project.h,
	  src/res_gtk/gtk_moldyn_dialog.glade: many changes at the lib
	  side ; autogen.sh added

2006-03-01 12:31  thassine

	* Makefile.in, aclocal.m4, src/gtk_moldyn_dialog.cpp,
	  src/gtk_moldyn_dialog.h, src/project.cpp,
	  src/res_gtk/gtk_moldyn_dialog.glade: the mol.dyn. code was
	  changed at lib side.

2006-02-27 14:03  thassine

	* src/custom_camera.cpp, src/gtk_app.cpp,
	  src/gtk_glade_dialog.cpp, src/ogl_plane.cpp, src/ogl_ribbon.cpp,
	  src/ogl_surface.cpp, src/project.cpp: the stringstream code was
	  made safer ; avoid c_str() calls in which a reference to buffer
	  is stored (for possbile re-use).

2006-02-24 14:01  thassine

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

2006-02-23 12:29  thassine

	* src/gtk_trajview_dialog.cpp: a trajview dialog bug temporarily
	  fixed

2006-02-23 08:29  thassine

	* bin: remove the bin subdir.

2006-02-21 10:26  thassine

	* Makefile.in, src/fileio.cpp: file i/o cleanups added.

2006-02-21 08:00  thassine

	* aclocal.m4, src/custom_camera.cpp, src/fileio.cpp,
	  src/filetrans.cpp, src/gtk_app.cpp,
	  src/gtk_file_export_dialog.cpp, src/gtk_file_import_dialog.cpp,
	  src/gtk_geomopt_dialog.cpp, src/gtk_glade_dialog.cpp,
	  src/gtk_moldyn_dialog.cpp, src/gtk_progress_dialog.cpp,
	  src/gtk_project.cpp, src/gtk_setup_dialog.cpp,
	  src/gtk_trajview_dialog.cpp, src/ogl_plane.cpp,
	  src/ogl_ribbon.cpp, src/ogl_surface.cpp, src/project.cpp,
	  src/pui_app.cpp: changed strstream into stringstream.

2006-02-17 19:55  hutchisn

	* branches/VERSION_2_BRANCH/src,
	  branches/VERSION_2_BRANCH/src/.cvsignore, bin, bin/.cvsignore:
	  Update to remove spurious CVS warnings.

2006-02-17 11:31  thassine

	* Makefile.in, aclocal.m4, configure, configure.ac, ltmain.sh,
	  src/Makefile.am, src/Makefile.in, src/custom_app.cpp,
	  src/custom_app.h, src/custom_camera.cpp, src/custom_camera.h,
	  src/eldview_wcl.cpp, src/eldview_wcl.h, src/gtk_app.cpp,
	  src/gtk_app.h, src/gtk_eldview_wnd.cpp, src/gtk_eldview_wnd.h,
	  src/gtk_file_export_dialog.cpp, src/gtk_file_export_dialog.h,
	  src/gtk_file_import_dialog.cpp, src/gtk_file_import_dialog.h,
	  src/gtk_geomopt_dialog.cpp, src/gtk_geomopt_dialog.h,
	  src/gtk_glade_dialog.cpp, src/gtk_glade_dialog.h,
	  src/gtk_main.cpp, src/gtk_main.h, src/gtk_moldyn_dialog.cpp,
	  src/gtk_moldyn_dialog.h, src/gtk_oglview_wnd.cpp,
	  src/gtk_oglview_wnd.h, src/gtk_p1dview_wnd.cpp,
	  src/gtk_p1dview_wnd.h, src/gtk_p2dview_wnd.cpp,
	  src/gtk_p2dview_wnd.h, src/gtk_progress_dialog.cpp,
	  src/gtk_progress_dialog.h, src/gtk_rcpview_wnd.cpp,
	  src/gtk_rcpview_wnd.h, src/gtk_setup_dialog.cpp,
	  src/gtk_setup_dialog.h, src/gtk_sscview_wnd.cpp,
	  src/gtk_sscview_wnd.h, src/gtk_trajview_dialog.cpp,
	  src/gtk_trajview_dialog.h, src/gtk_wnd.cpp, src/gtk_wnd.h,
	  src/oglview_wcl.cpp, src/oglview_wcl.h, src/p1dview_wcl.cpp,
	  src/p1dview_wcl.h, src/p2dview_wcl.cpp, src/p2dview_wcl.h,
	  src/pui_app.cpp, src/pui_app.h, src/pui_main.cpp,
	  src/pui_main.h, src/pui_oglview_wnd.cpp, src/pui_oglview_wnd.h,
	  src/pui_wnd.cpp, src/pui_wnd.h, src/rcpview_wcl.cpp,
	  src/rcpview_wcl.h, src/res_gtk, src/res_gtk/Makefile.am,
	  src/res_gtk/Makefile.in, src/res_gtk/angle.xpm,
	  src/res_gtk/bond.xpm, src/res_gtk/bondtype.xpm,
	  src/res_gtk/chain.xpm, src/res_gtk/clipping.xpm,
	  src/res_gtk/dihedral.xpm, src/res_gtk/distance.xpm,
	  src/res_gtk/draw.xpm, src/res_gtk/element.xpm,
	  src/res_gtk/erase.xpm, src/res_gtk/gtk_file_export_dialog.glade,
	  src/res_gtk/gtk_file_export_dialog.gladep,
	  src/res_gtk/gtk_file_import_dialog.glade,
	  src/res_gtk/gtk_file_import_dialog.gladep,
	  src/res_gtk/gtk_geomopt_dialog.glade,
	  src/res_gtk/gtk_geomopt_dialog.gladep,
	  src/res_gtk/gtk_moldyn_dialog.glade,
	  src/res_gtk/gtk_moldyn_dialog.gladep,
	  src/res_gtk/gtk_progress_dialog.glade,
	  src/res_gtk/gtk_progress_dialog.gladep,
	  src/res_gtk/gtk_setup_dialog.glade,
	  src/res_gtk/gtk_setup_dialog.gladep,
	  src/res_gtk/gtk_trajview_dialog.glade,
	  src/res_gtk/gtk_trajview_dialog.gladep, src/res_gtk/invert.xpm,
	  src/res_gtk/measure.xpm, src/res_gtk/molecule.xpm,
	  src/res_gtk/orbit_xy.xpm, src/res_gtk/orbit_z.xpm,
	  src/res_gtk/residue.xpm, src/res_gtk/rotate_xy.xpm,
	  src/res_gtk/rotate_z.xpm, src/res_gtk/select.xpm,
	  src/res_gtk/setup.xpm, src/res_gtk/transl_xy.xpm,
	  src/res_gtk/transl_z.xpm, src/res_gtk/zoom.xpm,
	  src/sscview_wcl.cpp, src/sscview_wcl.h: added the new stuff ;
	  now most of the OpenGL-related code is in a separate libarary
	  called liboglappth.

2006-02-16 13:24  thassine

	* Makefile.in, aclocal.m4, configure, configure.ac,
	  examples/Makefile.in,
	  examples/transition_state_search/E2-reaction/Makefile.in,
	  examples/transition_state_search/Makefile.in,
	  examples/transition_state_search/SN2-reaction/Makefile.in,
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/Makefile.in,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/Makefile.in,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/Makefile.in,
	  src/Makefile.am, src/Makefile.in, src/base_app.cpp,
	  src/base_app.h, src/base_wnd.cpp, src/base_wnd.h,
	  src/fileio.cpp, src/ghemicalconfig.h.in, src/gtk_dialog.cpp,
	  src/gtk_dialog.h, src/gtk_project.cpp, src/gtk_project.h,
	  src/ogl_camera.cpp, src/ogl_camera.h, src/ogl_objects.cpp,
	  src/ogl_objects.h, src/ogl_plane.cpp, src/ogl_plane.h,
	  src/ogl_ribbon.cpp, src/ogl_ribbon.h, src/ogl_surface.cpp,
	  src/ogl_surface.h, src/pixmaps, src/project.cpp, src/project.h:
	  removed some old files ; does not compile right now...

2006-01-05 13:07  thassine

	* GNOME_Ghemical.server, configure, configure.ac, src/Makefile.am,
	  src/Makefile.in: removed the bonobo-related files ; there seems
	  to be no sufficient resources for bonobo stuff. :(

2006-01-05 11:08  thassine

	* Makefile.in, configure, configure.ac, examples/Makefile.in,
	  examples/transition_state_search/E2-reaction/Makefile.in,
	  examples/transition_state_search/Makefile.in,
	  examples/transition_state_search/SN2-reaction/Makefile.in,
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/Makefile.in,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/Makefile.in,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/Makefile.in:
	  minor changes.

2006-01-05 11:07  thassine

	* src/Makefile.am, src/Makefile.in, src/base_app.cpp,
	  src/base_app.h, src/base_wnd.cpp, src/base_wnd.h,
	  src/file_export_dialog.cpp, src/file_export_dialog.glade,
	  src/file_export_dialog.gladep, src/file_export_dialog.h,
	  src/file_import_dialog.cpp, src/file_import_dialog.glade,
	  src/file_import_dialog.gladep, src/file_import_dialog.h,
	  src/geomopt_dialog.cpp, src/geomopt_dialog.glade,
	  src/geomopt_dialog.gladep, src/geomopt_dialog.h,
	  src/ghemicalconfig.h.in, src/glade_dialog.cpp,
	  src/glade_dialog.h, src/gtk_app_main.cpp, src/gtk_app_main.h,
	  src/gtk_dialog.cpp, src/gtk_dialog.h, src/gtk_graphics_view.cpp,
	  src/gtk_graphics_view.h, src/gtk_plot_views.cpp,
	  src/gtk_plot_views.h, src/gtk_project.cpp, src/gtk_project.h,
	  src/gtk_project_view.cpp, src/gtk_project_view.h,
	  src/gtk_views.cpp, src/gtk_views.h, src/moldyn_dialog.cpp,
	  src/moldyn_dialog.glade, src/moldyn_dialog.gladep,
	  src/moldyn_dialog.h, src/mtools.cpp, src/mtools.h,
	  src/ogl_camera.cpp, src/ogl_camera.h, src/ogl_objects.cpp,
	  src/ogl_objects.h, src/ogl_plane.cpp, src/ogl_surface.h,
	  src/progress_dialog.cpp, src/progress_dialog.glade,
	  src/progress_dialog.gladep, src/progress_dialog.h,
	  src/project.cpp, src/project.h, src/setup_dialog.cpp,
	  src/setup_dialog.glade, src/setup_dialog.gladep,
	  src/setup_dialog.h, src/trajview_dialog.cpp,
	  src/trajview_dialog.glade, src/trajview_dialog.gladep,
	  src/trajview_dialog.h, src/views.cpp, src/views.h,
	  src/wnd_client.cpp, src/wnd_client.h: removed some obsolete
	  files ; NEW FILES NOT YET ADDED

2005-12-14 13:45  thassine

	* Makefile.in, aclocal.m4, configure, examples,
	  examples/.cvsignore, examples/Makefile.in,
	  examples/transition_state_search,
	  examples/transition_state_search/.cvsignore,
	  examples/transition_state_search/E2-reaction,
	  examples/transition_state_search/E2-reaction/.cvsignore,
	  examples/transition_state_search/E2-reaction/Makefile.in,
	  examples/transition_state_search/Makefile.in,
	  examples/transition_state_search/SN2-reaction,
	  examples/transition_state_search/SN2-reaction/.cvsignore,
	  examples/transition_state_search/SN2-reaction/Makefile.in,
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/.cvsignore,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/.cvsignore,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/Makefile.in,
	  examples/transition_state_search/cycloaddition_Diels-Alder,
	  examples/transition_state_search/cycloaddition_Diels-Alder/.cvsignore,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope,
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/.cvsignore,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/Makefile.in,
	  examples/transition_state_search/tautomeric_shift_keto_enol,
	  examples/transition_state_search/tautomeric_shift_keto_enol/.cvsignore,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/Makefile.in,
	  src, src/.cvsignore, src/Makefile.in: some makefile stuff
	  added/updated.

2005-12-14 13:30  thassine

	* Makefile.am, Makefile.in, NEWS, README, aclocal.m4,
	  config.guess, config.sub, configure, configure.ac, depcomp,
	  install-sh, missing, mkinstalldirs: added some missing/new files.

2005-12-14 13:26  thassine

	* src/Makefile.am, src/Makefile.in, src/base_app.cpp,
	  src/base_app.h, src/base_wnd.cpp, src/base_wnd.h,
	  src/file_export_dialog.cpp, src/file_export_dialog.glade,
	  src/file_export_dialog.gladep, src/file_export_dialog.h,
	  src/file_import_dialog.cpp, src/file_import_dialog.glade,
	  src/file_import_dialog.gladep, src/file_import_dialog.h,
	  src/fileio.cpp, src/geomopt_dialog.cpp,
	  src/geomopt_dialog.glade, src/geomopt_dialog.gladep,
	  src/geomopt_dialog.h, src/ghemicalconfig.h.in,
	  src/gtk_app_main.cpp, src/gtk_app_main.h, src/gtk_dialog.cpp,
	  src/gtk_dialog.h, src/gtk_project.cpp, src/gtk_project.h,
	  src/gtk_views.h, src/moldyn_dialog.cpp, src/moldyn_dialog.glade,
	  src/moldyn_dialog.gladep, src/moldyn_dialog.h, src/mtools.h,
	  src/ogl_camera.cpp, src/ogl_camera.h, src/ogl_objects.cpp,
	  src/ogl_objects.h, src/ogl_plane.cpp, src/ogl_plane.h,
	  src/ogl_ribbon.cpp, src/ogl_ribbon.h, src/ogl_surface.cpp,
	  src/ogl_surface.h, src/progress_dialog.cpp,
	  src/progress_dialog.glade, src/progress_dialog.gladep,
	  src/progress_dialog.h, src/project.cpp, src/project.h,
	  src/setup_dialog.cpp, src/setup_dialog.glade,
	  src/setup_dialog.gladep, src/setup_dialog.h,
	  src/trajview_dialog.cpp, src/trajview_dialog.glade,
	  src/trajview_dialog.gladep, src/trajview_dialog.h,
	  src/views.cpp, src/wnd_client.cpp, src/wnd_client.h: added the
	  renamed source files.

2005-12-14 13:17  thassine

	* src/camera.cpp, src/camera.h, src/main.cpp, src/main.h,
	  src/objects.cpp, src/objects.h, src/plane.cpp, src/plane.h,
	  src/ribbon.cpp, src/ribbon.h, src/surface.cpp, src/surface.h:
	  removed some renamed source files

2005-12-14 13:14  thassine

	* src/glade: removed the glade subdir from src

2005-12-14 13:11  thassine

	* docs, docs/user-docs, 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/images, 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/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:
	  re-added the user-docs directory, in a new docs directory

2005-12-14 13:09  thassine

	* examples, 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,
	  examples/transition_state_search,
	  examples/transition_state_search/E2-reaction,
	  examples/transition_state_search/E2-reaction/Makefile.am,
	  examples/transition_state_search/E2-reaction/Makefile.in,
	  examples/transition_state_search/E2-reaction/products.gpr,
	  examples/transition_state_search/E2-reaction/reactants.gpr,
	  examples/transition_state_search/E2-reaction/ts.gpr,
	  examples/transition_state_search/Makefile.am,
	  examples/transition_state_search/Makefile.in,
	  examples/transition_state_search/SN2-reaction,
	  examples/transition_state_search/SN2-reaction/Makefile.am,
	  examples/transition_state_search/SN2-reaction/Makefile.in,
	  examples/transition_state_search/SN2-reaction/products.gpr,
	  examples/transition_state_search/SN2-reaction/reactants.gpr,
	  examples/transition_state_search/SN2-reaction/ts.gpr,
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/Makefile.am,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/Makefile.in,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/products.gpr,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/reactants.gpr,
	  
	  examples/transition_state_search/carbocation_rearrangement_hydride_shift/ts.gpr,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/Makefile.am,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/Makefile.in,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/products.gpr,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/reactants.gpr,
	  
	  examples/transition_state_search/carbocation_rearrangement_methide_shift/ts.gpr,
	  examples/transition_state_search/cycloaddition_Diels-Alder,
	  examples/transition_state_search/cycloaddition_Diels-Alder/Makefile.am,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/Makefile.in,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/products.gpr,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/reactants.gpr,
	  
	  examples/transition_state_search/cycloaddition_Diels-Alder/ts.gpr,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope,
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/Makefile.am,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/Makefile.in,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/products.gpr,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/reactants.gpr,
	  
	  examples/transition_state_search/sigmatropic_rearrangement_Cope/ts.gpr,
	  examples/transition_state_search/tautomeric_shift_keto_enol,
	  examples/transition_state_search/tautomeric_shift_keto_enol/Makefile.am,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/Makefile.in,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/products.gpr,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/reactants.gpr,
	  
	  examples/transition_state_search/tautomeric_shift_keto_enol/ts.gpr:
	  re-added the examples directory

2005-12-14 13:01  thassine

	* bin: removed bin from CVS

2005-12-14 12:58  thassine

	* bin/examples: removed examples from CVS

2005-12-14 12:55  thassine

	* bin/examples/transition_state_search: removing tss examples form
	  CVS

2005-12-14 12:49  thassine

	* bin/user-docs: remove the user docs from CVS

2005-12-09 18:35  thassine

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

2005-11-29 12:42  thassine

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

2005-11-10 10:03  thassine

	* configure, configure.ac: changed the version number to 1.92
	  after a release.

2005-11-10 09:04  thassine

	* aclocal.m4, configure, configure.ac: changed the version numbmer
	  to 1.91 ; released.

2005-11-03 23:08  hutchisn

	* ., .cvsignore: Updated to make sure all configure / autoconf
	  temporary files are ignored.

2005-11-03 23:08  hutchisn

	* src, src/.cvsignore, src/filetrans.cpp, 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 12:29  thassine

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

2005-10-13 12:15  thassine

	* 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 10:36  thassine

	* 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 15:14  thassine

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

2005-09-28 00:32  hutchisn

	* TODO: Added request for polysaccharide builder

2005-09-27 09:37  thassine

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

2005-08-24 09:56  thassine

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

2005-08-23 11:30  thassine

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

2005-07-14 11:43  thassine

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

2005-07-06 09:04  thassine

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

2005-07-05 09:23  thassine

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

2005-07-01 13:00  thassine

	* CHANGES, ChangeLog, INSTALL, aclocal.m4, configure,
	  configure.ac, src/appdefine.h, src/camera.h, src/color.h,
	  src/filetrans.h, src/glade_dialog.h, src/gtk_dialog.h,
	  src/gtk_graphics_view.cpp, src/gtk_graphics_view.h,
	  src/gtk_plot_views.h, src/gtk_project.h, src/gtk_project_view.h,
	  src/gtk_views.h, src/main.h, src/mtools.h, src/objects.h,
	  src/plane.h, src/project.h, src/ribbon.h, src/spline.h,
	  src/surface.h, 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 13:04  thassine

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

2005-06-23 13:27  thassine

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

2005-06-20 09:34  thassine

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

2005-06-17 08:39  thassine

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

2005-06-14 10:28  thassine

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

2005-06-13 10:19  thassine

	* src/glade/Makefile.in, src/gtk_project.cpp, src/gtk_project.h,
	  src/project.cpp, src/project.h: the Random Search is now
	  completely multi-threaded.

2005-06-13 07:16  thassine

	* src/Makefile.in, src/gtk_graphics_view.cpp, src/gtk_views.cpp,
	  src/main.cpp, src/project.cpp, 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 15:33  thassine

	* src/gtk_project.cpp, src/gtk_project.h: now the text buffer
	  scrolling works and is smooth but does not update for example
	  when lengthy calculations ; add threading?

2005-06-09 12:47  thassine

	* src/gtk_dialog.cpp, src/gtk_dialog.h, src/gtk_project.cpp,
	  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.

2005-06-09 11:16  thassine

	* src/fileio.cpp, src/glade/file_export_dialog.cpp,
	  src/glade/file_export_dialog.glade,
	  src/glade/file_export_dialog.h,
	  src/glade/file_import_dialog.cpp,
	  src/glade/file_import_dialog.glade,
	  src/glade/file_import_dialog.h, src/glade/geomopt_dialog.cpp,
	  src/glade/geomopt_dialog.glade, src/glade/moldyn_dialog.cpp,
	  src/glade/moldyn_dialog.glade, src/glade/moldyn_dialog.h,
	  src/glade/setup_dialog.cpp, src/glade/setup_dialog.glade,
	  src/glade/trajview_dialog.cpp, src/project.cpp, src/project.h:
	  fixed the glade dialogs ; the file i/o should now work with
	  openbabel-1.100.2

2005-06-08 08:49  thassine

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

2005-05-24 12:00  thassine

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

2005-05-19 10:46  thassine

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

2005-05-17 09:11  thassine

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

2005-05-16 11:12  thassine

	* src/glade/file_export_dialog.cpp,
	  src/glade/file_export_dialog.h,
	  src/glade/file_import_dialog.cpp,
	  src/glade/file_import_dialog.h, src/glade/setup_dialog.cpp,
	  src/glade/setup_dialog.h, src/glade/trajview_dialog.cpp,
	  src/glade/trajview_dialog.h, src/gtk_graphics_view.cpp,
	  src/gtk_graphics_view.h, src/gtk_plot_views.cpp,
	  src/gtk_plot_views.h, src/gtk_project_view.cpp,
	  src/gtk_project_view.h, src/gtk_views.cpp, src/gtk_views.h,
	  src/main.cpp, src/main.h, src/project.h, src/views.h: class name
	  changes done ; gnome -> gtk

2005-05-16 09:30  thassine

	* src/Makefile.in, src/glade/file_export_dialog.h,
	  src/glade/file_import_dialog.h, src/glade/setup_dialog.h,
	  src/glade/trajview_dialog.h, src/gnome_dialog.cpp,
	  src/gnome_dialog.h, src/gnome_project.cpp, src/gnome_project.h,
	  src/gtk_project_view.h, src/gtk_views.cpp, src/gtk_views.h,
	  src/main.h: some changes in filenames ; converted gnome -> gtk

2005-05-13 12:49  thassine

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

2005-05-12 15:22  thassine

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

2005-05-11 15:16  thassine

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

2005-05-06 11:55  thassine

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

2005-05-03 12:57  thassine

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

2005-04-28 10:28  thassine

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

2005-04-26 08:26  thassine

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

2005-04-22 13:45  thassine

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

2005-04-21 12:46  thassine

	* aclocal.m4, configure, configure.in, src/Makefile.in,
	  src/appconfig.h.in, src/appdefine.h, src/gnome_project.cpp,
	  src/gtk_views.cpp, src/main.cpp, src/notice.cpp, src/notice.h:
	  some new stuff added ; the main menu now works except Help/Help
	  item.

2005-04-21 08:57  thassine

	* aclocal.m4, configure, configure.in, src/Makefile.in,
	  src/glade/Makefile.in, src/glade/file_export_dialog.cpp,
	  src/glade/file_export_dialog.glade,
	  src/glade/file_import_dialog.cpp,
	  src/glade/file_import_dialog.glade,
	  src/glade/geomopt_dialog.cpp, src/glade/moldyn_dialog.cpp,
	  src/glade/moldyn_dialog.glade, src/glade/setup_druid.cpp,
	  src/glade/setup_druid.h, src/gnome_project.cpp,
	  src/gnome_project.h, src/gtk_graphics_view.cpp,
	  src/gtk_graphics_view.h, src/gtk_plot_views.cpp,
	  src/gtk_plot_views.h, src/gtk_project_view.cpp,
	  src/gtk_project_view.h, src/gtk_views.cpp, src/gtk_views.h,
	  src/main.cpp, src/main.h, src/project.cpp, src/project.h,
	  src/surface.h, src/views.cpp, src/views.h: added the next round
	  of changes ; compiles and works but the menus are still
	  incomplete.

2005-04-15 13:51  thassine

	* src/Makefile.in, src/appconfig.h.in, src/fileio.cpp,
	  src/gnome_dialog.h, src/gnome_project.cpp, src/gnome_views.cpp,
	  src/gnome_views.h, src/main.cpp, src/main.h, src/notice.cpp:
	  started adding the popup menu for gtk_graphics_view.

2005-04-15 11:36  thassine

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

2005-03-23 14:06  thassine

	* src/gnome_dialog.cpp, src/gnome_dialog.h, src/gnome_project.cpp,
	  src/gnome_views.cpp, src/main.cpp, 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 09:37  thassine

	* Makefile.in, configure, configure.in, src/Makefile.in,
	  src/appconfig.h.in, src/glade_dialog.cpp, src/gnome_dialog.cpp,
	  src/gnome_dialog.h, src/gnome_project.cpp, src/main.cpp,
	  src/main.h, 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 12:16  thassine

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

2004-12-23 14:12  thassine

	* bin/ghemical-ui.xml, configure, configure.in,
	  src/appconfig.h.in, src/ghemical-server.cpp,
	  src/ghemical-server.h, src/ghemical.cpp, src/ghemical.h,
	  src/gnome_project.cpp, src/gnome_project.h, src/main.cpp,
	  src/main.h, src/simple_test/container-ui.xml,
	  src/simple_test/container.cpp: continued to implement separate
	  gtk+/bonobo modes.

2004-12-23 11:33  thassine

	* GNOME_Ghemical.server, Makefile.in, src/Makefile.in,
	  src/gnome_project.cpp, src/gnome_project.h,
	  src/simple_test/Makefile, src/simple_test/README,
	  src/simple_test/container-ui.xml, src/simple_test/container.c,
	  src/simple_test/container.cpp, src/simple_test/container.h:
	  started creating a single ghemical/ghemical-server executable
	  that uses either gtk+ or bonobo.

2004-12-21 14:46  thassine

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

2004-12-10 15:22  thassine

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

2004-09-06 10:51  thassine

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

2004-08-30 09:36  thassine

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

2004-08-25 11:28  thassine

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

2004-05-13 11:51  thassine

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

2004-03-17 14:26  thassine

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

2004-02-18 11:54  thassine

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

2004-02-17 14:49  thassine

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

2004-02-11 09:40  thassine

	* src/fileio.cpp, src/project.h: added setlocale() calls into
	  fileio.cpp ; also added formal charges into the file format
	  (version string now 111)

2004-02-11 09:06  thassine

	* src/Makefile.in, src/gnome_project.cpp, src/gnome_project.h,
	  src/project.cpp: added -lmopac7 into src/Makefile.in
	  (temporarily) and other minor changes.

2003-11-06 12:22  thassine

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

2003-10-10 08:53  thassine

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

2003-10-03 13:29  thassine

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

2003-09-12 10:34  thassine

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

2003-09-10 12:04  thassine

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

2003-09-01 09:43  thassine

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

2003-08-08 06:55  thassine

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

2003-08-01 11:05  thassine

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

2003-07-30 10:11  thassine

	* src/camera.cpp, src/gnome_dialog.cpp, src/gnome_project.cpp,
	  src/gnome_project.h, src/project.cpp, 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 13:48  thassine

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

2003-07-24 10:12  thassine

	* src/gnome_project.cpp, src/gnome_project.h, src/gnome_views.cpp,
	  src/gnome_views.h, src/project.cpp, src/project.h, 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 12:18  thassine

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

2003-07-14 09:20  thassine

	* src/glade/file_export_dialog.glade,
	  src/glade/file_import_dialog.glade,
	  src/glade/geomopt_dialog.glade, src/glade/moldyn_dialog.glade,
	  src/glade/setup_druid.glade, src/glade/trajview_dialog.glade,
	  src/gnome_dialog.cpp, src/gnome_project.cpp,
	  src/gnome_project.h, src/gnome_views.cpp, 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 09:28  thassine

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

2003-07-11 13:01  thassine

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

2003-06-13 10:18  thassine

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

2003-06-12 13:12  thassine

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

2003-06-11 11:06  thassine

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

2003-05-19 07:09  thassine

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

2003-05-13 13:44  thassine

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

2003-05-12 09:13  thassine

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

2003-04-29 10:22  thassine

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

2003-04-17 07:37  thassine

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

2003-04-16 13:46  thassine

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

2003-04-10 14:02  thassine

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

2003-04-02 06:14  thassine

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

2003-03-07 11:37  thassine

	* src/fileio.cpp: a minor addition to fileio.cpp

2003-03-07 09:11  thassine

	* 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 12:20  thassine

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

2003-02-14 14:51  thassine

	* src/fileio.cpp: just cleanups, no real changes.

2003-02-14 08:02  thassine

	* src/project.cpp: sf virtual bonds now rendered also using
	  wireframes.

2003-02-06 14:53  thassine

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

2003-02-03 09:54  thassine

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

2003-01-31 12:06  thassine

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

2003-01-30 08:31  thassine

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

2003-01-27 13:45  thassine

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

2003-01-23 13:02  thassine

	* src/camera.cpp, src/camera.h, src/gnome_project.cpp,
	  src/gnome_views.cpp, src/gnome_views.h, src/main.cpp,
	  src/main.h, src/mtools.cpp, src/mtools.h,
	  src/pixmaps/clipping.xpm, src/project.cpp, src/project.h,
	  src/views.cpp, 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 11:25  thassine

	* Makefile.in: make install also works now.

2003-01-22 11:11  thassine

	* src, src/.cvsignore: minor cleanups added.

2003-01-22 11:06  thassine

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

2003-01-21 10:05  thassine

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

2003-01-20 14:08  thassine

	* configure, configure.in: many changes all over the tree; does
	  not compile yet...

2003-01-20 09:22  thassine

	* src/graphics, src/target3: moved the contents of src/graphics
	  and src/target3 to src/.

2003-01-20 09:17  thassine

	* src/target3/pixmaps: moved the src/target3/pixmaps to
	  src/pixmaps.

2003-01-20 09:13  thassine

	* Makefile.in, src/target3/glade: moved the /src/target3/glade to
	  /src/glade.

2003-01-20 09:05  thassine

	* src/common: removed the common-directory (now in libghemical).

2003-01-20 08:50  thassine

	* BUGLIST, Makefile.in, PROJECT, configure.in, miniMOPAC,
	  src/Makefile.OLD, src/common/Makefile.in,
	  src/graphics/Makefile.in, src/some-extra-files, src/target1,
	  src/target2, src/target3/Makefile.in,
	  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 15:35  thassine

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

2003-01-03 11:11  thassine

	* src/common/utility.cpp, 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 13:55  thassine

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

2002-12-12 07:34  thassine

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

2002-12-11 13:12  thassine

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

2002-12-09 09:01  thassine

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

2002-12-05 11:44  thassine

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

2002-12-04 07:47  thassine

	* CHANGES: updated the changelog

2002-12-04 07:45  thassine

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

2002-12-03 07:50  thassine

	* Makefile.in: minor fixes to make install.

2002-12-03 07:42  thassine

	* bin/user-docs/geometry_optimization.html,
	  bin/user-docs/images/geometry_opimization_console.png,
	  bin/user-docs/images/sequence_builder_console.png,
	  bin/user-docs/index.html, bin/user-docs/introduction.html,
	  bin/user-docs/measure.html, bin/user-docs/references.html,
	  bin/user-docs/sequence_builder.html,
	  bin/user-docs/using_mm.html, bin/user-docs/using_qm.html,
	  bin/user-docs/using_sf.html, bin/user-docs/visualization.html:
	  added the improved docs from Christopher also here.

2002-11-22 09:02  thassine

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

2002-11-20 15:54  thassine

	* bin/examples, bin/examples/2-chlorobutane.gpr,
	  bin/examples/3-phenylpropanal.gpr,
	  bin/examples/PeriodicTable.gpr,
	  bin/examples/acetylsalicylic_acid.gpr,
	  bin/examples/alpha-pinene.gpr, bin/examples/bromobenzene.gpr,
	  bin/examples/camphor.gpr, bin/examples/cinnamaldehyde.gpr,
	  bin/examples/cis-2-pentene.gpr, bin/examples/cyclohexane.gpr,
	  bin/examples/naphtalene.gpr: added also the new example files.

2002-11-20 15:53  thassine

	* bin/examples, openbabel/extable.h, openbabel/extable.txt,
	  openbabel/ghemical.cpp, src/common/model.cpp,
	  src/common/model.h, src/common/oldfiles.cpp,
	  src/common/tab_mm_prmfit.cpp, src/graphics/project.cpp,
	  src/target1/t1m_param_mm_cpp.h, src/target1/t1main.cpp,
	  src/target3/t3dialog.cpp, src/target3/t3main.cpp,
	  src/target3/t3project.cpp, src/target3/t3project.h: the file
	  format detection is now fixed; now can read the current (.gpr)
	  and old (.mm1gp) v1.0 files.

2002-11-20 10:38  thassine

	* Makefile.in: make install now installs the docs correctly.

2002-11-14 13:00  thassine

	* bin/user-docs/MD.html, bin/user-docs/MD_viewer.html,
	  bin/user-docs/aa_table.html, bin/user-docs/add_hydrogens.html,
	  bin/user-docs/basic_mm.html,
	  bin/user-docs/conf_search_tools.html,
	  bin/user-docs/energy_vs_torsion.html,
	  bin/user-docs/enlevdiag.jpg, bin/user-docs/filetypes.html,
	  bin/user-docs/formula.html,
	  bin/user-docs/geometry_optimization.html,
	  bin/user-docs/images/energy_vs_torsion1.png,
	  bin/user-docs/images/energy_vs_torsion2.png,
	  bin/user-docs/images/energy_vs_torsion3.png,
	  bin/user-docs/images/energy_vs_torsion4.png,
	  bin/user-docs/images/enlevdiag.png,
	  bin/user-docs/images/esp-plane_mm.png,
	  bin/user-docs/images/esp-plane_qm.png,
	  bin/user-docs/images/esp-plane_select.png,
	  bin/user-docs/images/esp-plane_select_obj.png,
	  bin/user-docs/index.html, bin/user-docs/labels.html,
	  bin/user-docs/mdi_mode.html, bin/user-docs/measure.html,
	  bin/user-docs/perspective.html, bin/user-docs/references.html,
	  bin/user-docs/sequence_builder.html,
	  bin/user-docs/using_cs_tools.html,
	  bin/user-docs/using_cs_tools01.jpg,
	  bin/user-docs/using_cs_tools02.jpg,
	  bin/user-docs/using_cs_tools03.jpg,
	  bin/user-docs/using_cs_tools04.jpg,
	  bin/user-docs/using_cs_tools05.jpg, bin/user-docs/using_mm.html,
	  bin/user-docs/using_qm.html, bin/user-docs/using_sf.html,
	  bin/user-docs/visualization.html: updated the documentation.

2002-11-14 09:16  thassine

	* bin/user-docs/basic_mm.html, bin/user-docs/images/mainmenu.png,
	  bin/user-docs/images/maintools.png, bin/user-docs/index.html,
	  bin/user-docs/introduction.html, bin/user-docs/maintools.jpg:
	  the chapter 1. introduction seems to be ok now.

2002-11-14 07:59  thassine

	* bin/user-docs/index.html: oops! fixed the absolute links from
	  index.html

2002-11-13 08:32  thassine

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

2002-11-11 09:22  thassine

	* src/Doxyfile, src/graphics/views.cpp: changed doxygen settings,
	  and added some fixes for gcc-3.2

2002-11-11 09:21  thassine

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

2002-11-06 10:29  thassine

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

2002-11-05 08:48  thassine

	* AUTHORS, src/target2/Makefile.OLD, src/target3/Makefile.OLD,
	  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 14:09  thassine

	* src/graphics/project.cpp, src/graphics/surface.cpp,
	  src/graphics/surface.h, src/target2/t2project.cpp: various small
	  fixes added to plane/surface/etc objects.

2002-10-31 10:27  thassine

	* 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,
	  bin/user-docs/index.html, src/common/eng1_sf.h,
	  src/target1/t1m_param_sf_h.h: just terminology changes: reduced
	  now changed to simplified in strings.

2002-10-29 10:11  thassine

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

2002-10-28 13:38  thassine

	* src/common/model.cpp, src/target3/glade/trajview_dialog.cpp,
	  src/target3/t3dialog.cpp: moldyn now also uses logbox.

2002-10-28 12:45  thassine

	* src/common/eng1_mm.cpp, src/common/eng1_qm.cpp,
	  src/common/eng1_sf.cpp, src/graphics/project.cpp: bugfixes added.

2002-10-25 13:02  thassine

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

2002-10-24 13:02  thassine

	* src/graphics/project.cpp, src/target3/t3project.cpp,
	  src/target3/t3project.h: seq-builder now has a command string.

2002-10-24 12:01  thassine

	* src/graphics/project.cpp, src/graphics/project.h,
	  src/graphics/views.cpp, src/target3/t3project.cpp: the 1d and 2d
	  plots now have command strings.

2002-10-23 14:38  thassine

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

2002-10-22 15:40  thassine

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

2002-10-21 10:43  thassine

	* src/common/model.cpp, src/common/model.h, src/common/search.cpp,
	  src/graphics/project.cpp, src/target2/t2project.cpp,
	  src/target3/t3project.cpp: added the
	  random/systematic/montecarlo conformational search commands.

2002-10-21 07:53  thassine

	* src/graphics/project.cpp, src/target3/t3project.cpp,
	  src/target3/t3views.cpp: the add light-operation is a bit
	  improved.

2002-10-17 14:17  thassine

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

2002-10-16 08:08  thassine

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

2002-10-15 08:46  thassine

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

2002-10-14 12:55  thassine

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

2002-10-05 08:31  thassine

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

2002-10-04 12:18  thassine

	* src/common/eng1_sf.cpp, src/common/model.cpp: the values of
	  model::sf_types array are now the same as those in the
	  atom::sf_atmtp records.

2002-10-04 10:52  thassine

	* src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/typedef.h, src/graphics/plane.cpp,
	  src/graphics/plane.h, src/graphics/project.cpp,
	  src/graphics/project.h, src/graphics/ribbon.cpp,
	  src/graphics/ribbon.h, src/graphics/spline.cpp,
	  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).

2002-10-04 08:10  thassine

	* src/common/model.cpp: more fixes to aa2sf conversion (temporary
	  coordinate handling).

2002-10-04 07:20  thassine

	* src/common/model.cpp, src/common/model.h: a potential bug
	  related to aa2sf conversion is fixed.

2002-10-03 12:12  thassine

	* src/common/model.cpp, src/common/utility.cpp: a few changes here
	  and there...

2002-10-03 09:09  thassine

	* src/common/oldfiles.cpp: the oldfiles.cpp file was added.

2002-10-03 08:27  thassine

	* src/common/Makefile.OLD, src/common/Makefile.in,
	  src/common/eng1_mm.cpp, src/common/eng1_mm.h,
	  src/common/eng1_qm.cpp, src/common/eng1_qm.h,
	  src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/eng2_mm_sf.cpp, src/common/eng2_mm_sf.h,
	  src/common/eng2_qm_mm.cpp, src/common/eng2_qm_mm.h,
	  src/common/engine.h, src/common/model.cpp, src/common/model.h,
	  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 10:50  thassine

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

2002-09-11 14:35  thassine

	* src/graphics/ribbon.cpp, src/target3/t3dialog.cpp,
	  src/target3/t3project.cpp, 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 14:36  thassine

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

2002-09-10 08:47  thassine

	* src/common/model.cpp, src/common/seqbuild.cpp,
	  src/common/seqbuild.h: the seqbuilder::Identify() now handles
	  correctly also the simplified chains.

2002-09-08 10:05  thassine

	* src/Doxyfile, src/Makefile.OLD, src/common/atom.h,
	  src/common/bond.h, src/common/conjgrad.h, src/common/eng1_sf.h,
	  src/common/engine.h, 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 08:25  thassine

	* src/target1/t1m_mm2param_cpp.h, src/target1/t1m_mm2param_h.h:
	  removed some old files from the console target.

2002-09-07 08:24  thassine

	* src/target1/t1m_mm1param_cpp.h, src/target1/t1m_mm1param_h.h,
	  src/target1/t1m_param_mm_cpp.h, src/target1/t1m_param_mm_h.h,
	  src/target1/t1m_param_sf_cpp.h, src/target1/t1m_param_sf_h.h,
	  src/target1/t1main.cpp, src/target1/t1main.h: some filenames
	  changed at the console target...

2002-09-06 09:07  thassine

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

2002-09-05 13:47  thassine

	* src/common/eng1_sf.cpp, src/common/eng1_sf.h: in sf, all terms
	  except the solvation one works like before.

2002-09-05 10:18  thassine

	* src/common/eng1_sf.cpp, src/common/eng1_sf.h: the nbt1 terms
	  work now in sf.

2002-09-05 07:26  thassine

	* src/common/eng1_sf.cpp: minor bugs fixed in bonded-term creation
	  in the sf.

2002-09-04 13:56  thassine

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

2002-09-03 10:45  thassine

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

2002-09-03 09:39  thassine

	* src/common/atom.h, src/common/bond.cpp, src/common/bond.h,
	  src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/engine.cpp, src/common/model.cpp,
	  src/graphics/project.cpp: some improvements added to sf.

2002-09-02 13:28  thassine

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

2002-08-31 09:57  thassine

	* src/common/eng1_qm_mpqc.cpp, src/common/eng2_qm_mm.cpp,
	  src/common/eng2_qm_mm.h, src/target3/glade/setup_druid.cpp,
	  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.

2002-08-31 08:39  thassine

	* src/common/eng1_mm.cpp, src/common/eng1_mm.h,
	  src/common/eng1_mm_default.cpp, 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 15:33  thassine

	* src/common/eng1_mm.cpp, src/common/eng1_mm.h,
	  src/common/eng1_mm_default.cpp, src/common/eng1_mm_prmfit.cpp,
	  src/common/eng1_qm.cpp, src/common/eng1_qm.h,
	  src/common/eng1_qm_mopac.cpp, src/common/eng1_qm_mopac.h,
	  src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/eng2_qm_mm.cpp, src/common/engine.cpp,
	  src/common/engine.h, src/common/model.h,
	  src/common/tab_mm_default.cpp, src/common/tab_mm_prmfit.cpp,
	  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.

2002-08-30 10:54  thassine

	* src/common/eng1_mm.cpp, src/common/eng1_mm.h,
	  src/common/eng1_qm.cpp, src/common/eng1_qm.h,
	  src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/eng2_mm_sf.cpp, src/common/eng2_mm_sf.h,
	  src/common/eng2_qm_mm.cpp, src/common/eng2_qm_mm.h,
	  src/common/engine.cpp, src/common/engine.h,
	  src/target2/t2project.cpp, src/target2/t2project.h,
	  src/target3/glade/setup_druid.cpp: the setup classes are now
	  initialized correctly. setup::GetMaxEngineIndex() renamed to
	  setup::GetEngineCount().

2002-08-30 09:36  thassine

	* src/common/Makefile.OLD, src/common/Makefile.in,
	  src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/eng2_mm_sf.cpp, src/common/eng2_mm_sf.h,
	  src/target3/glade/setup_druid.cpp: ok, everything compiles now,
	  including the simplified forcefield stuff.

2002-08-30 06:27  thassine

	* src/common/atom.cpp, src/common/atom.h, src/common/eng1_sf.cpp,
	  src/common/eng1_sf.h, src/common/engine.cpp,
	  src/common/model.cpp, src/common/model.h,
	  src/common/seqbuild.cpp, src/common/tab_mm_default.cpp,
	  src/common/tab_mm_prmfit.cpp, src/graphics/project.cpp,
	  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 06:30  thassine

	* src/common/model.cpp, src/common/seqbuild.cpp,
	  src/target1/Makefile.OLD, src/target1/t1m_mm1param_cpp.h,
	  src/target1/t1m_mm1param_h.h, src/target1/t1main.cpp,
	  src/target2/t2project.cpp, 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 14:40  thassine

	* src/common/atom.cpp, src/common/atom.h, src/common/eng1_mm.cpp,
	  src/common/model.cpp, src/common/model.h, src/common/search.cpp,
	  src/common/seqbuild.cpp, src/graphics/project.cpp,
	  src/target2/t2project.cpp, 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.

2002-08-28 09:59  thassine

	* src/common/eng1_mm.cpp, src/common/eng1_mm.h,
	  src/common/eng1_qm.cpp, src/common/eng1_qm.h,
	  src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/eng2_qm_mm.cpp, src/common/eng2_qm_mm.h,
	  src/common/engine.h, src/common/model.h,
	  src/target3/glade/setup_druid.cpp,
	  src/target3/glade/setup_druid.glade,
	  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 14:54  thassine

	* src/common/atom.cpp, src/common/eng1_sf.h,
	  src/common/intcrd.cpp, src/common/model.cpp: some bugfixes
	  added; the conformational search tools should work now.

2002-08-27 11:41  thassine

	* src/target3/glade/file_import_dialog.cpp,
	  src/target3/t3dialog.cpp, src/target3/t3dialog.h,
	  src/target3/t3project.cpp, src/target3/t3project.h: added the
	  File/ExtraTools also here.

2002-08-21 07:32  thassine

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

2002-08-01 07:31  thassine

	* src/common/engine.cpp, src/common/intcrd.cpp,
	  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 10:09  thassine

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

2002-07-30 07:07  thassine

	* src/common/atom.cpp, src/common/atom.h, src/common/eng1_mm.cpp,
	  src/common/eng1_qm.cpp, src/common/eng1_qm_mopac.cpp,
	  src/common/engine.cpp, src/common/filetrans.cpp,
	  src/common/intcrd.cpp, src/common/intcrd.h,
	  src/common/model.cpp, src/common/model.h,
	  src/common/seqbuild.cpp, src/common/tab_mm_prmfit.cpp,
	  src/common/utility.cpp, src/graphics/project.cpp,
	  src/graphics/ribbon.cpp, 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 12:27  thassine

	* src/common/model.cpp, src/common/model.h,
	  src/graphics/project.cpp, src/target2/t2project.cpp: the memory
	  management scheme of crd_set objects is now simpler.

2002-07-23 09:34  thassine

	* src/common/engine.h, src/common/model.cpp, src/common/model.h,
	  src/common/search.cpp, src/common/search.h,
	  src/target2/t2project.cpp, src/target3/t3project.cpp,
	  src/target3/t3project.h: the search tool improvements ported
	  also here.

2002-07-23 09:04  thassine

	* src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  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 13:48  thassine

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

2002-06-19 12:56  thassine

	* src/common/Makefile.OLD, src/common/Makefile.in,
	  src/common/atom.cpp, src/common/atom.h, src/common/eng1_mm.h,
	  src/common/eng1_sf.cpp, src/common/eng1_sf.h,
	  src/common/engine.h, src/common/model.cpp,
	  src/common/moldyn.cpp, src/common/seqbuild.h,
	  src/graphics/project.cpp, src/target1/config.h.OLD,
	  src/target2/config.h.OLD, src/target2/t2project.cpp,
	  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 10:40  thassine

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

2002-06-14 11:47  thassine

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

2002-06-13 13:09  thassine

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

2002-06-08 09:01  thassine

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

2002-06-07 12:49  thassine

	* src/target3/glade/Makefile.OLD, src/target3/glade/Makefile.in,
	  src/target3/glade/setup_druid.cpp,
	  src/target3/glade/setup_druid.glade,
	  src/target3/glade/setup_druid.h, src/target3/t3project.cpp:
	  added an initial version of the setup druid (nothing except
	  cancel works).

2002-06-07 08:26  thassine

	* src/target3/glade/Makefile.OLD, src/target3/glade/Makefile.in,
	  src/target3/glade/file_export_dialog.cpp,
	  src/target3/glade/file_export_dialog.glade,
	  src/target3/glade/file_export_dialog.h,
	  src/target3/glade/file_import_dialog.cpp,
	  src/target3/glade/file_import_dialog.glade,
	  src/target3/glade/file_import_dialog.h,
	  src/target3/t3project.cpp: added the file import/export dialogs.

2002-06-07 06:38  thassine

	* src/target3/glade/Makefile.OLD, src/target3/glade/Makefile.in,
	  src/target3/glade/geomopt_dialog.cpp,
	  src/target3/glade/geomopt_dialog.glade,
	  src/target3/glade/geomopt_dialog.h,
	  src/target3/glade/moldyn_dialog.cpp,
	  src/target3/glade/moldyn_dialog.glade,
	  src/target3/glade/moldyn_dialog.h,
	  src/target3/glade/trajview_dialog.cpp,
	  src/target3/glade/trajview_dialog.glade,
	  src/target3/glade/trajview_dialog.h, src/target3/t3dialog.cpp,
	  src/target3/t3dialog.h, src/target3/t3main.cpp,
	  src/target3/t3project.cpp, 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 11:39  thassine

	* src/Makefile.OLD: added some Makefile tweaks.

2002-06-05 10:25  thassine

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

2002-06-03 10:23  thassine

	* 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.

2002-06-03 09:50  thassine

	* 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 16:34  hutchisn

	* configure, configure.in, miniMOPAC/Makefile.in,
	  src/common/Makefile.in, src/graphics/Makefile.in,
	  src/target3/Makefile.in, src/target3/glade/Makefile.in,
	  src/target3/glade/geomopt_dialog.h: Updated makefiles for
	  libglade, etc.

2002-05-31 16:31  hutchisn

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

2002-05-31 08:12  thassine

	* src/common/Makefile.in, src/graphics/Makefile.in,
	  src/target3/Makefile.in, 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 12:43  thassine

	* configure, configure.in, src/common/define.h: promoted the
	  version number to 0.85 in the HEAD branch.

2002-05-30 11:07  thassine

	* Makefile.in, configure, configure.in, src/common/Makefile.in,
	  src/common/eng1_sf.cpp, src/common/tab_mm_default.cpp,
	  src/graphics/Makefile.in, src/target3/Makefile.in,
	  src/target3/glade/Makefile.in: minor fixes like changed
	  directories etc added.

2002-05-30 09:39  thassine

	* bin/parameters/param_mm, bin/parameters/param_mm/default,
	  bin/parameters/param_mm/default/atomtypes.txt,
	  bin/parameters/param_mm/default/parameters1.txt,
	  bin/parameters/param_mm/default/parameters2.txt,
	  bin/parameters/param_mm/default/parameters3.txt,
	  bin/parameters/param_mm/default/parameters4.txt,
	  bin/parameters/param_mm/default/parameters5.txt,
	  bin/parameters/param_sf, bin/parameters/param_sf/default,
	  bin/parameters/param_sf/default/loopdip.txt,
	  bin/parameters/param_sf/default/looptor.txt,
	  bin/parameters/param_sf/default/nonbonded.txt,
	  src/some-extra-files/newfile.cpp,
	  src/some-extra-files/newfile.h: added new files to
	  bin/parameters and some minor stuff.

2002-05-30 09:34  thassine

	* bin/parameters/mm1param, bin/parameters/mm2param: removed old
	  files under bin/parameters.

2002-05-30 09:29  thassine

	* src/common/atom.cpp, src/common/atom.h, src/common/bond.cpp,
	  src/common/bond.h, src/common/define.h, src/common/eng1_mm.cpp,
	  src/common/eng1_mm.h, src/common/eng1_mm_default.cpp,
	  src/common/eng1_mm_default.h, src/common/eng1_mm_prmfit.cpp,
	  src/common/eng1_mm_prmfit.h, src/common/eng1_qm.cpp,
	  src/common/eng1_qm.h, src/common/eng1_qm_mopac.cpp,
	  src/common/eng1_qm_mopac.h, src/common/eng1_qm_mpqc.cpp,
	  src/common/eng1_qm_mpqc.h, src/common/eng1_sf.cpp,
	  src/common/eng1_sf.h, src/common/eng2_qm_mm.cpp,
	  src/common/eng2_qm_mm.h, src/common/engine.cpp,
	  src/common/engine.h, src/common/filetrans.cpp,
	  src/common/filetrans.h, src/common/geomopt.cpp,
	  src/common/geomopt.h, src/common/intcrd.cpp,
	  src/common/intcrd.h, src/common/model.cpp, src/common/model.h,
	  src/common/moldyn.cpp, src/common/moldyn.h,
	  src/common/search.cpp, src/common/search.h,
	  src/common/seqbuild.cpp, src/common/seqbuild.h,
	  src/common/tab_mm_default.cpp, src/common/tab_mm_default.h,
	  src/common/tab_mm_prmfit.cpp, src/common/tab_mm_prmfit.h,
	  src/common/typedef.h, src/common/typerule.cpp,
	  src/common/typerule.h, src/common/utility.cpp,
	  src/common/utility.h, src/graphics/camera.cpp,
	  src/graphics/camera.h, src/graphics/color.h,
	  src/graphics/mtools.cpp, src/graphics/plane.cpp,
	  src/graphics/plane.h, src/graphics/project.cpp,
	  src/graphics/project.h, src/graphics/ribbon.cpp,
	  src/graphics/ribbon.h, src/graphics/surface.cpp,
	  src/graphics/surface.h, src/graphics/views.cpp,
	  src/graphics/views.h, src/target1/t1main.cpp,
	  src/target2/t2main.cpp, src/target2/t2main.h,
	  src/target2/t2project.cpp, src/target2/t2project.h,
	  src/target2/t2views.cpp, src/target2/t2views.h,
	  src/target3/glade_dialog.cpp, src/target3/glade_dialog.h,
	  src/target3/t3dialog.cpp, src/target3/t3dialog.h,
	  src/target3/t3main.cpp, src/target3/t3main.h,
	  src/target3/t3project.cpp, src/target3/t3project.h,
	  src/target3/t3views.cpp, src/target3/t3views.h: added the new
	  files.

2002-05-30 09:18  thassine

	* src/common/interface.cpp, src/common/interface.h,
	  src/common/matrix.h, src/common/mm1alg.cpp, src/common/mm1alg.h,
	  src/common/mm1eng.cpp, src/common/mm1eng.h,
	  src/common/mm1eng1.cpp, src/common/mm1eng1.h,
	  src/common/mm1eng9.cpp, src/common/mm1eng9.h,
	  src/common/mm1ic.cpp, src/common/mm1ic.h, src/common/mm1mdl.cpp,
	  src/common/mm1mdl.h, src/common/mm1tab1.cpp,
	  src/common/mm1tab1.h, src/common/mm1tab9.cpp,
	  src/common/mm1tab9.h, src/common/mm1util.cpp,
	  src/common/mm1util.h, src/common/mm2alg.cpp,
	  src/common/mm2alg.h, src/common/mm2eng.cpp, src/common/mm2eng.h,
	  src/common/mm2mdl.cpp, src/common/mm2mdl.h,
	  src/common/mm2util.cpp, src/common/mm2util.h,
	  src/common/mm3mdl.cpp, src/common/mm3mdl.h,
	  src/common/qm1alg.cpp, src/common/qm1alg.h,
	  src/common/qm1e_mopac.cpp, src/common/qm1e_mopac.h,
	  src/common/qm1e_mpqc.cpp, src/common/qm1e_mpqc.h,
	  src/common/qm1eng.cpp, src/common/qm1eng.h,
	  src/common/qm1mdl.cpp, src/common/qm1mdl.h,
	  src/common/qm2eng.cpp, src/common/qm2eng.h,
	  src/common/qm2mdl.cpp, src/common/qm2mdl.h,
	  src/graphics/docview.cpp, src/graphics/docview.h,
	  src/graphics/io-jpg.cpp, src/graphics/io-jpg.h,
	  src/graphics/io-png.cpp, src/graphics/io-png.h,
	  src/graphics/mm1docv.cpp, src/graphics/mm1docv.h,
	  src/graphics/mm1rbn.cpp, src/graphics/mm1rbn.h,
	  src/graphics/mm2docv.cpp, src/graphics/mm2docv.h,
	  src/graphics/mm2rbn.cpp, src/graphics/mm2rbn.h,
	  src/graphics/mm3docv.cpp, src/graphics/mm3docv.h,
	  src/graphics/qm1docv.cpp, src/graphics/qm1docv.h,
	  src/graphics/qm2docv.cpp, src/graphics/qm2docv.h,
	  src/target2/t2docv.cpp, src/target2/t2docv.h,
	  src/target2/t2mm1docv.cpp, src/target2/t2mm1docv.h,
	  src/target2/t2mm2docv.cpp, src/target2/t2mm2docv.h,
	  src/target2/t2mm3docv.cpp, src/target2/t2mm3docv.h,
	  src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h,
	  src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h,
	  src/target3/glade_callbacks.cpp, src/target3/glade_callbacks.h,
	  src/target3/glade_interface.cpp, src/target3/glade_interface.h,
	  src/target3/glade_support.cpp, src/target3/glade_support.h,
	  src/target3/t3docv.cpp, src/target3/t3docv.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3mm2docv.cpp, src/target3/t3mm2docv.h,
	  src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h,
	  src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h: the
	  old/renamed files are removed.

2002-05-30 08:29  thassine

	* src/target3/glade/README: update the glade README

2002-05-30 08:27  thassine

	* src/target1/config.h.OLD, src/target2/config.h.OLD,
	  src/target3/config.h.OLD, src/target3/glade/Makefile.OLD,
	  src/target3/glade/Makefile.in,
	  src/target3/glade/geomopt_dialog.cpp,
	  src/target3/glade/geomopt_dialog.glade,
	  src/target3/glade/geomopt_dialog.h,
	  src/target3/glade/ghemical.glade, src/target3/glade/src: added
	  changes to config.h.OLD files and src/target3/glade dir.

2002-05-30 08:17  thassine

	* src/Makefile.OLD, src/common/Makefile.OLD,
	  src/common/Makefile.in, src/graphics/Makefile.OLD,
	  src/graphics/Makefile.in, src/target2/Makefile.OLD,
	  src/target3/Makefile.OLD, src/target3/Makefile.in: the makefiles
	  are updated.

2002-05-30 07:40  thassine

	* CHANGES: the changelog is updated.

2002-05-30 07:35  thassine

	* src/Makefile.OLD: test; this goes to HEAD branch...

2002-05-29 08:11  thassine

	* 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 09:03  thassine

	* CHANGES: updated the changelog (using cvs2cl again).

2002-05-28 07:57  thassine

	* src/common/define.h: ooop, reverted the previous.

2002-05-28 07:55  thassine

	* src/common/define.h: just testing how the branches work.

2002-05-27 13:36  thassine

	* bin/parameters/mm2param/loopdip.txt,
	  bin/parameters/mm2param/looptor.txt,
	  bin/parameters/mm2param/nonbonded.txt,
	  small-utilities/getpdb_cd.cpp, small-utilities/getpdb_ftp.cpp,
	  src/common/Makefile.OLD, src/common/Makefile.in,
	  src/common/mm1mdl.h, src/common/mm1util.h, src/common/mm2alg.h,
	  src/common/mm2eng.cpp, src/common/mm2eng.h,
	  src/common/mm2mdl.cpp, src/common/mm2mdl.h,
	  src/common/mm2util.cpp, src/common/mm2util.h,
	  src/common/mm3mdl.cpp, src/common/mm3mdl.h,
	  src/graphics/Makefile.OLD, src/graphics/Makefile.in,
	  src/graphics/mm2docv.cpp, src/graphics/mm3docv.cpp,
	  src/graphics/mm3docv.h, src/graphics/views.h,
	  src/target1/Makefile.OLD, src/target1/t1m_mm2param_cpp.h,
	  src/target2/Makefile.OLD, src/target2/t2main.cpp,
	  src/target2/t2main.h, src/target2/t2mm2docv.cpp,
	  src/target2/t2mm3docv.cpp, src/target2/t2mm3docv.h,
	  src/target3/Makefile.OLD, 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 07:23  thassine

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

2002-05-21 11:06  thassine

	* aclocal.m4, configure.in, src/common/Makefile.OLD,
	  src/common/qm1e_mpqc.cpp, src/common/qm1e_mpqc.h,
	  src/config.h.in, src/graphics/Makefile.OLD,
	  src/graphics/Makefile.in, src/target1/Makefile.OLD,
	  src/target1/config.h.OLD, src/target2/Makefile.OLD,
	  src/target2/config.h.OLD, src/target3/Makefile.OLD,
	  src/target3/Makefile.in, 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 07:45  thassine

	* src/common/Makefile.OLD, src/common/qm1e_mpqc.cpp,
	  src/common/qm1e_mpqc.h, src/graphics/Makefile.OLD,
	  src/target1/Makefile.OLD, src/target2/Makefile.OLD,
	  src/target3/Makefile.OLD: support for MPQC v2 was added (but
	  ./configure still needs update).

2002-05-20 06:17  thassine

	* src/target1/t1m_mm1param_cpp.h, src/target1/t1m_mm1param_h.h:
	  oops, forgot to add some files last time.

2002-05-17 07:30  thassine

	* src/common/mm1eng9.cpp, src/common/mm1eng9.h,
	  src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/mm1tab9.cpp, src/common/mm1tab9.h,
	  src/target1/t1main.cpp, src/target1/t1main.h,
	  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 14:03  thassine

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

2002-04-17 10:24  thassine

	* src/common/mm2util.cpp, 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 06:56  thassine

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

2002-04-09 10:18  thassine

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

2002-04-08 14:32  thassine

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

2002-04-04 12:18  thassine

	* BUGLIST, 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.

2002-04-04 08:43  thassine

	* src/graphics/camera.cpp: some cleanups done for the stereo
	  modes; now the effect seems to be independent of orientation.

2002-03-26 18:27  hutchisn

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

2002-02-28 11:43  thassine

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

2002-02-27 09:26  thassine

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

2002-02-26 08:28  thassine

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

2002-02-25 11:29  thassine

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

2002-02-22 14:09  thassine

	* configure, configure.in, src/common/define.h,
	  src/common/notice.cpp: switch back to development settings.

2002-02-22 10:36  thassine

	* CHANGES, INSTALL, src/common/define.h: changelog updated and all
	  settings are now ready for release as v0.82

2002-02-22 08:29  thassine

	* src/target3/t3mm1docv.cpp: a small fix added to the library
	  widget generation code.

2002-02-21 14:26  thassine

	* bin/user-docs/index.html, bin/user-docs/using_cs_tools.html,
	  bin/user-docs/using_cs_tools01.jpg,
	  bin/user-docs/using_cs_tools02.jpg,
	  bin/user-docs/using_cs_tools03.jpg,
	  bin/user-docs/using_cs_tools04.jpg,
	  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 10:34  thassine

	* INSTALL, src/common/mm1alg.h, src/common/mm1mdl.cpp,
	  src/common/mm2alg.h, src/common/mm2mdl.cpp, src/common/qm1alg.h,
	  src/common/qm1mdl.cpp, src/target1/Makefile.OLD,
	  src/target2/Makefile.OLD, src/target2/t2mm1docv.cpp,
	  src/target2/t2mm2docv.cpp, src/target2/t2qm1docv.cpp,
	  src/target3/Makefile.OLD, src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm2docv.cpp, 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 17:06  hutchisn

	* openbabel/pdb.cpp: Don't try to run PerceiveBondOrders yet...
	  this seems to be very buggy.

2002-02-18 16:53  hutchisn

	* openbabel/Makefile.in, openbabel/alchemy.cpp,
	  openbabel/amber.cpp, openbabel/aromatic.txt, openbabel/atom.cpp,
	  openbabel/balst.cpp, openbabel/box.cpp, openbabel/c3d.cpp,
	  openbabel/cacao.cpp, openbabel/car.cpp, openbabel/ccc.cpp,
	  openbabel/commandline.h, openbabel/ctransform.h,
	  openbabel/data.cpp, openbabel/data.h, openbabel/dmol.cpp,
	  openbabel/element.h, openbabel/element.txt, openbabel/extable.h,
	  openbabel/extable.txt, openbabel/feat.cpp, openbabel/gamess.cpp,
	  openbabel/gaussian.cpp, openbabel/ghemical.cpp,
	  openbabel/grid.h, openbabel/hin.cpp, openbabel/jaguar.cpp,
	  openbabel/main.cpp, openbabel/mol.cpp, openbabel/mol.h,
	  openbabel/mopac.cpp, openbabel/mpqc.cpp, openbabel/nwchem.cpp,
	  openbabel/obutil.cpp, openbabel/obutil.h, openbabel/patty.cpp,
	  openbabel/pdb.cpp, openbabel/phmodel.cpp, openbabel/qchem.cpp,
	  openbabel/report.cpp, openbabel/rotor.cpp, openbabel/smarts.h,
	  openbabel/typer.cpp, openbabel/unichem.cpp,
	  openbabel/version.h.in, openbabel/xyz.cpp: Updated Open Babel
	  code, including preliminary bond-order perception.

2002-01-31 13:50  thassine

	* miniMOPAC/README: some documentation fixes for miniMOPAC.

2002-01-31 12:25  thassine

	* src/target3/glade/ghemical.glade,
	  src/target3/glade/src/glade_interface.cpp,
	  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 16:09  hutchisn

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

2002-01-25 13:42  thassine

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

2002-01-25 04:39  hutchisn

	* src/target3/glade_callbacks.cpp, src/target3/t3mm1docv.cpp: Make
	  sure we actually set the optimization limits after the dialog
	  completes...

2002-01-25 04:35  hutchisn

	* openbabel/unichem.cpp: Fix unichem XYZ support (read should
	  expect atomic numbers in Unichem files).

2002-01-22 15:27  thassine

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

2002-01-21 22:23  hutchisn

	* src/common/mm1alg.h, src/common/mm1mdl.cpp, src/common/mm2alg.h,
	  src/common/qm1alg.h, src/common/qm1mdl.cpp,
	  src/target3/glade/ghemical.glade,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade/src/glade_support.cpp,
	  src/target3/glade_interface.cpp, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm2docv.cpp, 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 11:45  thassine

	* src/common/mm1mdl.cpp, src/common/qm1mdl.cpp: the geomopt output
	  now displays accurate gradient vector lengths.

2002-01-21 07:44  thassine

	* INSTALL, oelib: removed .cvsignore from the oelib directory.

2002-01-18 19:59  hutchisn

	* src/common/mm1mdl.cpp, 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 09:12  thassine

	* 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 19:10  thassine

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

2002-01-14 18:12  hutchisn

	* src/common/filetrans.cpp: Delete filename at appropriate
	  time--Babel uses it for a Title when exporting.

2002-01-14 03:57  hutchisn

	* configure, 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 15:20  hutchisn

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

2002-01-10 23:04  hutchisn

	* configure, configure.in, src/common/Makefile.in,
	  src/target3/Makefile.in: Added support for Michael Banck's SC
	  autoconf macros to simplify building MPQC.

2002-01-10 22:45  hutchisn

	* Makefile.in, PROJECT, config.guess, config.sub, configure,
	  configure.in, oelib/GNULICENSE.txt, oelib/Makefile.in,
	  oelib/OELibPrimer.html, oelib/StdAfx.cpp, oelib/StdAfx.h,
	  oelib/Vector.cpp, oelib/Vector.h, oelib/alchemy.cpp,
	  oelib/amber.cpp, oelib/aromatic.h, oelib/aromatic.txt,
	  oelib/atom.cpp, oelib/atomtyp.h, oelib/atomtyp.txt,
	  oelib/balst.cpp, oelib/base.cpp, oelib/base.h, oelib/bgf.cpp,
	  oelib/bin2hex.pl, oelib/binary.cpp, oelib/binary.h,
	  oelib/binary_io.cpp, oelib/binary_io.h, oelib/bitgrid.cpp,
	  oelib/bitgrid.h, oelib/bitvec.cpp, oelib/bitvec.h,
	  oelib/bond.cpp, oelib/box.cpp, oelib/c3d.cpp, oelib/cacao.cpp,
	  oelib/cache.cpp, oelib/car.cpp, oelib/ccc.cpp, oelib/chains.cpp,
	  oelib/chains.h, oelib/chdrw.cpp, oelib/chiral.cpp,
	  oelib/chiral.h, oelib/commandline.cpp, oelib/commandline.h,
	  oelib/configure, oelib/csr.cpp, oelib/cssr.cpp,
	  oelib/ctransform.cpp, oelib/ctransform.h, oelib/cwrap.cpp,
	  oelib/cwrap.h, oelib/data.cpp, oelib/data.h, oelib/dmol.cpp,
	  oelib/element.h, oelib/element.txt, oelib/extable.h,
	  oelib/extable.txt, oelib/feat.cpp, oelib/fh.cpp,
	  oelib/fileformat.cpp, oelib/fileformat.h, oelib/gamess.cpp,
	  oelib/gaussian.cpp, oelib/generic.cpp, oelib/generic.h,
	  oelib/ghemical.cpp, oelib/globals.cpp, oelib/grid.cpp,
	  oelib/grid.h, oelib/gromos96.cpp, oelib/hin.cpp,
	  oelib/jaguar.cpp, oelib/main.cpp, oelib/matrix.cpp,
	  oelib/matrix.h, oelib/mdl.cpp, oelib/mmod.cpp, oelib/mol.cpp,
	  oelib/mol.h, oelib/mol2.cpp, oelib/molchrg.cpp, oelib/molchrg.h,
	  oelib/molvector.cpp, oelib/molvector.h, oelib/mopac.cpp,
	  oelib/mpqc.cpp, oelib/nwchem.cpp, oelib/oeifstream.h,
	  oelib/oelib.dsp, oelib/oelib.dsw, oelib/oeutil.cpp,
	  oelib/oeutil.h, oelib/parsmart.cpp, oelib/parsmart.h,
	  oelib/parsmi.cpp, oelib/patty.cpp, oelib/patty.h, oelib/pdb.cpp,
	  oelib/phmodel.cpp, oelib/phmodel.h, oelib/phmodel.txt,
	  oelib/phmodeldata.h, oelib/qchem.cpp, oelib/quat.c,
	  oelib/rand.cpp, oelib/report.cpp, oelib/resdata.h,
	  oelib/resdata.txt, oelib/ring.cpp, oelib/ring.h,
	  oelib/rotor.cpp, oelib/rotor.h, oelib/smarts.cpp,
	  oelib/smarts.h, oelib/smi.cpp, oelib/smi.h, oelib/tinker.cpp,
	  oelib/tokenst.cpp, oelib/typer.cpp, oelib/typer.h,
	  oelib/types.h, oelib/types.txt, oelib/unichem.cpp,
	  oelib/version.h, oelib/xed.cpp, oelib/xyz.cpp, openbabel,
	  openbabel/Makefile.in, openbabel/StdAfx.cpp, openbabel/StdAfx.h,
	  openbabel/Vector.cpp, openbabel/Vector.h, openbabel/alchemy.cpp,
	  openbabel/amber.cpp, openbabel/aromatic.h,
	  openbabel/aromatic.txt, openbabel/atom.cpp, openbabel/atomtyp.h,
	  openbabel/atomtyp.txt, openbabel/balst.cpp, openbabel/base.cpp,
	  openbabel/base.h, openbabel/bgf.cpp, openbabel/bin2hex.pl,
	  openbabel/binary.cpp, openbabel/binary.h,
	  openbabel/binary_io.cpp, openbabel/binary_io.h,
	  openbabel/bitgrid.cpp, openbabel/bitgrid.h,
	  openbabel/bitvec.cpp, openbabel/bitvec.h, openbabel/bond.cpp,
	  openbabel/box.cpp, openbabel/c3d.cpp, openbabel/cacao.cpp,
	  openbabel/cache.cpp, openbabel/car.cpp, openbabel/ccc.cpp,
	  openbabel/chains.cpp, openbabel/chains.h, openbabel/chdrw.cpp,
	  openbabel/chiral.cpp, openbabel/chiral.h,
	  openbabel/commandline.cpp, openbabel/commandline.h,
	  openbabel/csr.cpp, openbabel/cssr.cpp, openbabel/ctransform.cpp,
	  openbabel/ctransform.h, openbabel/cwrap.cpp, openbabel/cwrap.h,
	  openbabel/data.cpp, openbabel/data.h, openbabel/dmol.cpp,
	  openbabel/element.h, openbabel/element.txt, openbabel/extable.h,
	  openbabel/extable.txt, openbabel/feat.cpp, openbabel/fh.cpp,
	  openbabel/fileformat.cpp, openbabel/fileformat.h,
	  openbabel/gamess.cpp, openbabel/gaussian.cpp,
	  openbabel/generic.cpp, openbabel/generic.h,
	  openbabel/ghemical.cpp, openbabel/grid.cpp, openbabel/grid.h,
	  openbabel/gromos96.cpp, openbabel/hin.cpp, openbabel/jaguar.cpp,
	  openbabel/main.cpp, openbabel/matrix.cpp, openbabel/matrix.h,
	  openbabel/mdl.cpp, openbabel/mmod.cpp, openbabel/mol.cpp,
	  openbabel/mol.h, openbabel/mol2.cpp, openbabel/molchrg.cpp,
	  openbabel/molchrg.h, openbabel/molvector.cpp,
	  openbabel/molvector.h, openbabel/mopac.cpp, openbabel/mpqc.cpp,
	  openbabel/nwchem.cpp, openbabel/obifstream.h,
	  openbabel/oblib.dsp, openbabel/oblib.dsw, openbabel/obutil.cpp,
	  openbabel/obutil.h, openbabel/parsmart.cpp,
	  openbabel/parsmart.h, openbabel/parsmi.cpp, openbabel/patty.cpp,
	  openbabel/patty.h, openbabel/pdb.cpp, openbabel/phmodel.cpp,
	  openbabel/phmodel.h, openbabel/phmodel.txt,
	  openbabel/phmodeldata.h, openbabel/qchem.cpp, openbabel/quat.c,
	  openbabel/rand.cpp, openbabel/report.cpp, openbabel/resdata.h,
	  openbabel/resdata.txt, openbabel/ring.cpp, openbabel/ring.h,
	  openbabel/rotor.cpp, openbabel/rotor.h, openbabel/smarts.cpp,
	  openbabel/smarts.h, openbabel/smi.cpp, openbabel/smi.h,
	  openbabel/tinker.cpp, openbabel/tokenst.cpp,
	  openbabel/typer.cpp, openbabel/typer.h, openbabel/types.h,
	  openbabel/types.txt, openbabel/unichem.cpp, openbabel/version.h,
	  openbabel/xed.cpp, openbabel/xyz.cpp, src/common/Makefile.in,
	  src/common/filetrans.cpp, src/common/filetrans.h,
	  src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/notice.cpp, src/common/utility.cpp,
	  src/graphics/Makefile.in, src/graphics/docview.cpp,
	  src/target3/Makefile.in: Updated with OpenBabel replacing OELib.

2002-01-10 18:28  hutchisn

	* src/graphics/mtools.h, src/graphics/views.cpp,
	  src/graphics/views.h: Add data types for select modes and
	  measure modes.

2002-01-10 18:20  hutchisn

	* 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 13:51  thassine

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

2002-01-05 23:00  hutchisn

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

2002-01-02 14:40  thassine

	* INSTALL, src/common/Makefile.OLD, src/graphics/Makefile.OLD,
	  src/target1/Makefile.OLD, src/target2/Makefile.OLD,
	  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 13:19  thassine

	* src/common/interface.cpp, src/common/interface.h,
	  src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/qm1mdl.cpp, src/common/qm1mdl.h,
	  src/target3/t3mm1docv.cpp, 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 14:56  thassine

	* src/graphics/camera.cpp, src/graphics/camera.h,
	  src/graphics/docview.cpp, src/graphics/objects.cpp,
	  src/graphics/objects.h, src/graphics/views.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3qm1docv.cpp,
	  src/target3/t3views.cpp: the convert-project-to-QM/MM and
	  attach/detach-this-view operations now retain the graphics
	  settings.

2001-12-29 11:51  thassine

	* 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 13:43  thassine

	* src/graphics/camera.cpp, src/graphics/mm1docv.cpp,
	  src/graphics/mm2docv.cpp, src/graphics/qm1docv.cpp,
	  src/graphics/views.cpp, 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 11:11  thassine

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

2001-12-19 14:47  thassine

	* src/graphics/mm1docv.cpp, src/graphics/mtools.cpp,
	  src/graphics/views.cpp, 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.

2001-12-19 11:45  thassine

	* src/graphics/docview.cpp, src/graphics/docview.h,
	  src/graphics/mtools.cpp, src/graphics/qm1docv.cpp,
	  src/graphics/qm1docv.h, src/graphics/views.cpp,
	  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 15:20  thassine

	* src/common/mm1eng1.cpp, src/common/mm1eng9.cpp: just docs
	  clarified a bit...

2001-12-18 12:43  thassine

	* src/common/mm1eng1.cpp, src/common/mm1eng9.cpp,
	  src/common/mm1mdl.cpp, src/graphics/mm1docv.cpp: a better
	  tor-constraints added to mm1_eng classes for the 1d and 2d plots.

2001-12-18 07:53  thassine

	* INSTALL: updated the installation docs.

2001-12-17 15:17  thassine

	* src/common/intcrd.cpp, src/common/intcrd.h,
	  src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/graphics/docview.h, src/graphics/mm1docv.cpp,
	  src/graphics/mm1docv.h, src/graphics/views.cpp,
	  src/graphics/views.h, src/target2/t2mm1docv.cpp,
	  src/target2/t2views.cpp, src/target2/t2views.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3views.cpp, 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 12:35  thassine

	* bin/user-docs/index.html, src/graphics/docview.cpp,
	  src/graphics/docview.h, src/graphics/views.cpp,
	  src/graphics/views.h, src/target2/t2qm1docv.cpp,
	  src/target2/t2views.cpp, src/target2/t2views.h,
	  src/target3/t3docv.cpp, src/target3/t3docv.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp,
	  src/target3/t3qm1docv.cpp, src/target3/t3views.cpp,
	  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 13:27  thassine

	* src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/model.cpp, src/common/model.h, src/common/qm1alg.cpp,
	  src/common/qm1alg.h, src/common/qm1e_mopac.cpp,
	  src/common/qm1eng.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h,
	  src/target2/t2mm1docv.cpp, 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 13:56  thassine

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

2001-12-05 16:11  thassine

	* src/common/mm1eng.h, src/common/mm1eng1.cpp,
	  src/common/mm1eng1.h, src/common/mm1eng9.cpp,
	  src/common/mm1eng9.h: added an initial framework for adding
	  torsional constraints in molecular mechanics force fields; the
	  old stuff should work as usual.

2001-12-05 14:53  thassine

	* src/common/errutil.cpp, src/common/notice.h,
	  src/common/typedef.h, src/graphics/mm2rbn.cpp: added some Alpha
	  platform fixes from Bob Williams.

2001-11-27 05:35  hutchisn

	* Makefile.in: Added distclean target and changed help destination
	  to smooth with Debian package.

2001-11-27 05:32  hutchisn

	* src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3prefs.cpp: Added Selection Mode submenu (w/radio
	  items) and fixed library error message.

2001-11-26 23:31  hutchisn

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

2001-11-26 09:05  thassine

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

2001-11-21 05:28  hutchisn

	* src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  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 12:27  thassine

	* INSTALL, src/common/mm1mdl.h, src/common/mm2mdl.h,
	  src/common/qm1mdl.h, src/common/qm2mdl.h,
	  src/graphics/docview.h, src/graphics/mm1docv.cpp,
	  src/graphics/mm1docv.h, src/graphics/mm2docv.cpp,
	  src/graphics/mm2docv.h, src/graphics/qm1docv.cpp,
	  src/graphics/qm1docv.h, src/target3/t3main.cpp,
	  src/target3/t3mm1docv.cpp, src/target3/t3qm1docv.cpp,
	  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 16:20  hutchisn

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

2001-11-09 18:32  hutchisn

	* oelib/mol.cpp, 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 10:19  thassine

	* configure, configure.in, src/common/define.h: back to devel
	  settings, version number changed to 0.82.

2001-11-08 07:51  thassine

	* CHANGES, src/common/define.h: some final changes for the new
	  release; this is released as 0.81.

2001-11-07 09:43  thassine

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

2001-10-29 15:48  thassine

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

2001-10-23 13:10  thassine

	* src/common/mm1eng.cpp, src/common/mm1eng.h,
	  src/common/mm1eng1.cpp, src/common/mm1eng1.h,
	  src/common/mm1eng9.cpp, src/common/mm1eng9.h,
	  src/common/mm1mdl.cpp, src/common/mm1tab1.cpp,
	  src/common/mm1tab1.h, src/common/mm1tab9.cpp,
	  src/common/mm1tab9.h, src/common/mm1util.cpp,
	  src/common/mm2eng.cpp, src/common/mm2eng.h,
	  src/common/mm2mdl.cpp, src/common/model.cpp,
	  src/graphics/mm2docv.cpp, src/graphics/plane.cpp,
	  src/graphics/surface.cpp, src/target1/t1m_mm2param_cpp.h,
	  src/target1/t1main.cpp, src/target3/t3mm1docv.cpp,
	  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 15:01  thassine

	* src/common/mm1eng.cpp, src/common/mm1eng.h,
	  src/common/mm1eng1.cpp, src/common/mm1eng1.h,
	  src/common/mm1eng9.cpp, 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 14:39  thassine

	* bin/parameters/mm1param/stable/atomtypes.txt,
	  bin/parameters/mm1param/stable/parameters1.txt,
	  bin/parameters/mm1param/stable/parameters2.txt,
	  bin/parameters/mm1param/stable/parameters3.txt,
	  bin/parameters/mm1param/stable/parameters4.txt,
	  bin/parameters/mm1param/stable/parameters5.txt,
	  bin/parameters/mm1param/unstable/atomtypes.txt,
	  bin/parameters/mm1param/unstable/parameters1.txt,
	  bin/parameters/mm1param/unstable/parameters2.txt,
	  bin/parameters/mm1param/unstable/parameters3.txt,
	  bin/parameters/mm1param/unstable/parameters4.txt,
	  bin/parameters/mm1param/unstable/parameters5.txt,
	  src/common/mm1eng1.h, src/common/mm1eng9.h,
	  src/common/mm1mdl.cpp, src/common/mm1tab1.cpp,
	  src/common/mm1tab1.h, src/common/mm1tab9.cpp,
	  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 10:56  thassine

	* CHANGES, 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/

2001-10-03 10:47  thassine

	* src/common/mm2mdl.h, src/common/qm2mdl.h,
	  src/target3/t3main.cpp, 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 03:50  hutchisn

	* src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm2mdl.h,
	  src/common/model.h, src/common/qm1mdl.h,
	  src/target3/glade_callbacks.cpp, 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.

2001-10-01 03:42  hutchisn

	* oelib/data.cpp: Fix bugs with extension handling--make sure to
	  lowercase before comparisons.
	  Fixes problems, e.g. .PDB = .pdb

2001-10-01 03:39  hutchisn

	* oelib/element.txt: Fix max valence on P to allow PF6, etc.

2001-09-27 12:57  thassine

	* src/common/define.h: changed the main web address to
	  www.bioinformatics.org

2001-09-27 12:14  thassine

	* CHANGES, miniMOPAC/README, miniMOPAC/fortran/iter.f,
	  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 14:35  thassine

	* CHANGES, INSTALL, miniMOPAC/README, miniMOPAC/esp.c,
	  miniMOPAC/fortran/esp.f, miniMOPAC/fortran/iter.f,
	  miniMOPAC/fortran/minimopac.f, miniMOPAC/fortran/mopac.f,
	  miniMOPAC/iter.c, miniMOPAC/minimopac.c,
	  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 14:21  thassine

	* src/graphics/docview.cpp, src/graphics/docview.h,
	  src/graphics/mm1docv.cpp, src/graphics/qm1docv.cpp: added to
	  measure tool a set if model-independent measurement functions in
	  an effort to make it simpler.

2001-09-24 13:10  thassine

	* BUGLIST, src/target2/t2qm1docv.cpp,
	  src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/t3qm1docv.cpp,
	  src/target3/t3qm1docv.h: a new known bug was added; qm1 geomopt
	  dialog was added for gnome version.

2001-09-14 21:17  hutchisn

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

2001-09-14 13:08  thassine

	* 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.

2001-09-14 10:44  thassine

	* src/graphics/docview.cpp, src/graphics/mm1docv.cpp: completed
	  the fixes for known mem leaks at docview.cpp

2001-09-07 23:20  hutchisn

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

2001-09-07 13:22  thassine

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

2001-09-06 07:21  thassine

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

2001-09-05 13:37  thassine

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

2001-09-04 09:38  thassine

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

2001-09-04 08:07  thassine

	* src/common/mm1eng.h, src/common/mm1tab1.cpp,
	  src/common/mm1tab9.cpp: minor changes and cleanups.

2001-09-03 10:01  thassine

	* src/common/mm1tab1.cpp, src/common/mm1tab9.cpp,
	  src/common/mm1util.cpp, src/common/mm1util.h: a minor cleanup
	  for mm1_typerule.

2001-09-03 07:06  thassine

	* miniMOPAC/README, src/common/mm1mdl.h: minor additions to
	  mm1_mdl and MOPAC docs.

2001-08-30 04:22  hutchisn

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

2001-08-29 13:21  thassine

	* AUTHORS, src/graphics/camera.cpp, src/graphics/camera.h,
	  src/target3/t3main.cpp, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp,
	  src/target3/t3views.cpp, src/target3/t3views.h: added an
	  alternative way for camera setup in stereo viewing modes;
	  copyright notices etc updated.

2001-08-29 10:18  thassine

	* src/target3/t3mm1docv.cpp, src/target3/t3views.cpp,
	  src/target3/t3views.h: added Mike's stereo code (under target3).

2001-08-29 10:18  thassine

	* src/graphics/camera.cpp, src/graphics/camera.h: added Mike's
	  stereo code (under graphics).

2001-08-29 07:08  thassine

	* configure, configure.in, src/common/define.h,
	  src/common/qm1e_mopac.cpp, src/common/qm1e_mopac.h,
	  src/common/qm1mdl.cpp: a safer mopac locking mechanism added,
	  version number promoted to 0.80.

2001-08-28 07:04  thassine

	* INSTALL, miniMOPAC/README, miniMOPAC/fortran/minimopac.f,
	  miniMOPAC/minimopac.c, 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 12:35  thassine

	* bin/user-docs/enlevdiag.jpg, bin/user-docs/index.html,
	  bin/user-docs/maintools.jpg: user's manual quickly updated.

2001-08-27 09:26  thassine

	* src/common/qm1e_mopac.cpp: added comments about a specifig bug
	  in mopac.

2001-08-27 08:13  thassine

	* src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/mm2mdl.cpp, src/common/qm1e_mopac.cpp,
	  src/common/qm1e_mopac.h, src/common/qm1e_mpqc.cpp,
	  src/common/qm1e_mpqc.h, src/common/qm1mdl.cpp,
	  src/common/qm1mdl.h: hamiltonian/basis set selection added for
	  QM engs.

2001-08-26 09:45  thassine

	* src/common/mm1alg.cpp, src/common/mm2alg.cpp,
	  src/common/qm1alg.cpp, src/common/qm1e_mopac.cpp,
	  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 14:48  thassine

	* src/common/qm1e_mopac.cpp, src/common/qm1e_mpqc.cpp,
	  src/common/qm1mdl.cpp, src/common/qm1mdl.h,
	  src/target3/glade/ghemical.glade,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp: now the total charge can be
	  specified in QM models; also checking added for QM setup.

2001-08-25 11:50  thassine

	* src/common/qm1e_mpqc.cpp: energy level diagram now works for ab
	  initio as well.

2001-08-24 13:12  thassine

	* src/common/qm1e_mopac.cpp, src/common/qm1e_mpqc.cpp,
	  src/common/qm1e_mpqc.h: force calculations + algorithms added
	  for MPQC.

2001-08-24 08:34  thassine

	* src/common/qm1e_mopac.cpp, src/common/qm1mdl.cpp: fixed a
	  gradient scaling bug in MOPAC engine; the geometry optimization
	  is much more robust now.

2001-08-23 18:06  hutchisn

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

2001-08-23 12:38  thassine

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

2001-08-22 22:21  hutchisn

	* src/graphics/mm1docv.cpp, src/graphics/qm1docv.cpp: add QM
	  measure functionality

2001-08-22 22:20  hutchisn

	* src/common/mm1mdl.cpp, src/common/mm2mdl.cpp,
	  src/common/qm1mdl.cpp: Use sprintf to give a standardized output
	  to the geometry opt. output.

2001-08-22 16:31  hutchisn

	* src/common/qm1mdl.cpp, src/target3/t3qm1docv.cpp: Use the same
	  methods for ImportMM command as "convert" routines--and make
	  sure we update the title!

2001-08-22 13:27  thassine

	* src/common/mm1mdl.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h,
	  src/graphics/docview.cpp, src/graphics/docview.h,
	  src/graphics/mm1docv.cpp, src/graphics/qm1docv.cpp,
	  src/target3/t3docv.cpp, src/target3/t3mm1docv.cpp,
	  src/target3/t3qm1docv.cpp: various smaller changes...

2001-08-22 11:18  thassine

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

2001-08-21 15:07  hutchisn

	* src/graphics/mm2docv.cpp, src/target3/t3qm1docv.cpp: Add more
	  config use in QM and MM2 modes.

2001-08-21 15:07  hutchisn

	* 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 11:03  thassine

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

2001-08-18 09:45  thassine

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

2001-08-18 07:01  thassine

	* miniMOPAC/fortran/SIZES: ooops, forgot to add the SIZES file.

2001-08-17 17:17  thassine

	* miniMOPAC/fortran/esp.f, miniMOPAC/fortran/minimopac.f: added
	  all changes to mopac fortran source before 2001-08-17.

2001-08-17 17:12  thassine

	* miniMOPAC/fortran, miniMOPAC/fortran/aababc.f,
	  miniMOPAC/fortran/addfck.f, miniMOPAC/fortran/addhcr.f,
	  miniMOPAC/fortran/addnuc.f, miniMOPAC/fortran/analyt.f,
	  miniMOPAC/fortran/anavib.f, miniMOPAC/fortran/axis.f,
	  miniMOPAC/fortran/block.f, miniMOPAC/fortran/bonds.f,
	  miniMOPAC/fortran/brlzon.f, miniMOPAC/fortran/btoc.f,
	  miniMOPAC/fortran/calpar.f, miniMOPAC/fortran/capcor.f,
	  miniMOPAC/fortran/cdiag.f, miniMOPAC/fortran/chrge.f,
	  miniMOPAC/fortran/cnvg.f, miniMOPAC/fortran/compfg.f,
	  miniMOPAC/fortran/consts.f, miniMOPAC/fortran/cqden.f,
	  miniMOPAC/fortran/datin.f, miniMOPAC/fortran/dcart.f,
	  miniMOPAC/fortran/delmol.f, miniMOPAC/fortran/delri.f,
	  miniMOPAC/fortran/denrot.f, miniMOPAC/fortran/densit.f,
	  miniMOPAC/fortran/depvar.f, miniMOPAC/fortran/deri0.f,
	  miniMOPAC/fortran/deri1.f, miniMOPAC/fortran/deri2.f,
	  miniMOPAC/fortran/deri21.f, miniMOPAC/fortran/deri22.f,
	  miniMOPAC/fortran/deri23.f, miniMOPAC/fortran/deritr.f,
	  miniMOPAC/fortran/deriv.f, miniMOPAC/fortran/dernvo.f,
	  miniMOPAC/fortran/ders.f, miniMOPAC/fortran/dfock2.f,
	  miniMOPAC/fortran/dfpsav.f, miniMOPAC/fortran/dgemm.f,
	  miniMOPAC/fortran/dgemv.f, miniMOPAC/fortran/dger.f,
	  miniMOPAC/fortran/dgetf2.f, miniMOPAC/fortran/dgetrf.f,
	  miniMOPAC/fortran/dgetri.f, miniMOPAC/fortran/diag.f,
	  miniMOPAC/fortran/diat.f, miniMOPAC/fortran/diat2.f,
	  miniMOPAC/fortran/diegrd.f, miniMOPAC/fortran/dielen.f,
	  miniMOPAC/fortran/diis.f, miniMOPAC/fortran/dijkl1.f,
	  miniMOPAC/fortran/dijkl2.f, miniMOPAC/fortran/dipind.f,
	  miniMOPAC/fortran/dipole.f, miniMOPAC/fortran/dlaswp.f,
	  miniMOPAC/fortran/dofs.f, miniMOPAC/fortran/dot.f,
	  miniMOPAC/fortran/drc.f, miniMOPAC/fortran/drcout.f,
	  miniMOPAC/fortran/dtrmm.f, miniMOPAC/fortran/dtrmv.f,
	  miniMOPAC/fortran/dtrsm.f, miniMOPAC/fortran/dtrti2.f,
	  miniMOPAC/fortran/dtrtri.f, miniMOPAC/fortran/dvfill.f,
	  miniMOPAC/fortran/ef.f, miniMOPAC/fortran/enpart.f,
	  miniMOPAC/fortran/esp.f, miniMOPAC/fortran/etime.c,
	  miniMOPAC/fortran/exchng.f, miniMOPAC/fortran/fdate.c,
	  miniMOPAC/fortran/ffhpol.f, miniMOPAC/fortran/flepo.f,
	  miniMOPAC/fortran/fmat.f, miniMOPAC/fortran/fock1.f,
	  miniMOPAC/fortran/fock2.f, miniMOPAC/fortran/force.f,
	  miniMOPAC/fortran/formxy.f, miniMOPAC/fortran/forsav.f,
	  miniMOPAC/fortran/frame.f, miniMOPAC/fortran/freqcy.f,
	  miniMOPAC/fortran/geout.f, miniMOPAC/fortran/geoutg.f,
	  miniMOPAC/fortran/getgeg.f, miniMOPAC/fortran/getgeo.f,
	  miniMOPAC/fortran/getsym.f, miniMOPAC/fortran/gettxt.f,
	  miniMOPAC/fortran/gmetry.f, miniMOPAC/fortran/gover.f,
	  miniMOPAC/fortran/greenf.f, miniMOPAC/fortran/grid.f,
	  miniMOPAC/fortran/h1elec.f, miniMOPAC/fortran/haddon.f,
	  miniMOPAC/fortran/hcore.f, miniMOPAC/fortran/helect.f,
	  miniMOPAC/fortran/hqrii.f, miniMOPAC/fortran/ijkl.f,
	  miniMOPAC/fortran/ilaenv.f, miniMOPAC/fortran/initsv.f,
	  miniMOPAC/fortran/interp.f, miniMOPAC/fortran/iter.f,
	  miniMOPAC/fortran/jcarin.f, miniMOPAC/fortran/linmin.f,
	  miniMOPAC/fortran/local.f, miniMOPAC/fortran/locmin.f,
	  miniMOPAC/fortran/lsame.f, miniMOPAC/fortran/makpol.f,
	  miniMOPAC/fortran/mamult.f, miniMOPAC/fortran/matou1.f,
	  miniMOPAC/fortran/matout.f, miniMOPAC/fortran/matpak.f,
	  miniMOPAC/fortran/meci.f, miniMOPAC/fortran/mecid.f,
	  miniMOPAC/fortran/mecih.f, miniMOPAC/fortran/mecip.f,
	  miniMOPAC/fortran/moldat.f, miniMOPAC/fortran/molval.f,
	  miniMOPAC/fortran/mopac.f, miniMOPAC/fortran/mullik.f,
	  miniMOPAC/fortran/mult.f, miniMOPAC/fortran/nllsq.f,
	  miniMOPAC/fortran/nuchar.f, miniMOPAC/fortran/parsav.f,
	  miniMOPAC/fortran/partxy.f, miniMOPAC/fortran/pathk.f,
	  miniMOPAC/fortran/paths.f, miniMOPAC/fortran/perm.f,
	  miniMOPAC/fortran/polar.f, miniMOPAC/fortran/powsav.f,
	  miniMOPAC/fortran/powsq.f, miniMOPAC/fortran/prtdrc.f,
	  miniMOPAC/fortran/quadr.f, miniMOPAC/fortran/react1.f,
	  miniMOPAC/fortran/reada.f, miniMOPAC/fortran/readmo.f,
	  miniMOPAC/fortran/refer.f, miniMOPAC/fortran/repp.f,
	  miniMOPAC/fortran/rotat.f, miniMOPAC/fortran/rotate.f,
	  miniMOPAC/fortran/rsp.f, miniMOPAC/fortran/search.f,
	  miniMOPAC/fortran/second.f, miniMOPAC/fortran/setupg.f,
	  miniMOPAC/fortran/solrot.f, miniMOPAC/fortran/swap.f,
	  miniMOPAC/fortran/sympro.f, miniMOPAC/fortran/symtry.f,
	  miniMOPAC/fortran/symtrz.f, miniMOPAC/fortran/thermo.f,
	  miniMOPAC/fortran/timer.f, miniMOPAC/fortran/timout.f,
	  miniMOPAC/fortran/update.f, miniMOPAC/fortran/upsurf.f,
	  miniMOPAC/fortran/vecprt.f, miniMOPAC/fortran/writmo.f,
	  miniMOPAC/fortran/wrtkey.f, miniMOPAC/fortran/wrttxt.f,
	  miniMOPAC/fortran/xerbla.f, 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.

2001-08-17 13:44  thassine

	* miniMOPAC/esp.c, src/common/qm1e_mopac.cpp: miniMOPAC tweaks;
	  ESP plot drawing is now faster, plus MO plotting added.

2001-08-16 10:40  thassine

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

2001-08-15 13:04  thassine

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

2001-08-13 13:14  thassine

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

2001-08-09 08:30  thassine

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

2001-08-08 13:29  thassine

	* CHANGES, src/common/mm2mdl.cpp, src/target2/t2mm1docv.cpp,
	  src/target2/t2mm1docv.h, src/target2/t2mm2docv.cpp,
	  src/target2/t2mm2docv.h, src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm1docv.h, src/target3/t3mm2docv.cpp,
	  src/target3/t3mm2docv.h: algorithms for mm2_mdl are added.

2001-08-08 10:36  thassine

	* src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/t3docv.cpp,
	  src/target3/t3docv.h, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm1docv.h, src/target3/t3qm1docv.cpp,
	  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 21:04  hutchisn

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

2001-08-03 13:09  thassine

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

2001-08-02 11:36  thassine

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

2001-08-01 13:46  thassine

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

2001-07-30 12:07  thassine

	* src/graphics/mm1docv.cpp, src/graphics/mm2docv.cpp,
	  src/graphics/qm1docv.cpp, src/target3/t3main.cpp,
	  src/target3/t3main.h, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm1docv.h, src/target3/t3qm1docv.cpp,
	  src/target3/t3qm1docv.h: the 4 first shortcut buttons work now.

2001-07-30 08:14  thassine

	* src/graphics/mm1docv.cpp, src/graphics/mm2docv.cpp,
	  src/graphics/qm2docv.cpp, src/graphics/qm2docv.h: added
	  MeasureEvent() also to (obsolete) qm2_mdl.

2001-07-28 18:46  hutchisn

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

2001-07-24 17:04  hutchisn

	* src/graphics/docview.h, src/graphics/mm1docv.cpp,
	  src/graphics/mm1docv.h, src/graphics/mtools.cpp: Change
	  rendering to support more prefs--including passing prefs for
	  element colors.

2001-07-24 17:00  hutchisn

	* src/graphics/camera.cpp, src/graphics/camera.h: Improve
	  selection with wireframe slightly and add Measure enum.

2001-07-24 16:56  hutchisn

	* src/common/utility.cpp, src/common/utility.h: Change elements to
	  allow prefs class to override colors and VdW radii.

2001-07-24 16:55  hutchisn

	* src/common/prefs.cpp, src/common/prefs.h,
	  src/target3/t3prefs.cpp, src/target3/t3prefs.h: Add Color methods

2001-07-24 16:55  hutchisn

	* src/common/filetrans.cpp, src/common/mm1mdl.cpp: Fix OELib bond
	  synchronization and switch hydrogens to use OELib method.

2001-07-23 23:10  hutchisn

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

2001-07-22 14:28  thassine

	* src/target1/t1m_mm2param_cpp.h, src/target1/t1m_mm2param_h.h:
	  added some files for mm2_mdl.

2001-07-22 13:37  thassine

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

2001-07-20 19:30  hutchisn

	* src/common/factory.h, src/common/model.cpp, src/common/model.h,
	  src/graphics/mm1docv.cpp, src/target3/t3prefs.cpp,
	  src/target3/t3prefs.h, src/target3/t3views.cpp,
	  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 13:07  thassine

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

2001-06-29 12:15  thassine

	* src/common/intcrd.cpp, src/common/intcrd.h,
	  src/common/mm1ic.cpp, src/common/mm1ic.h: ooops, forgot to add
	  some files in the last commit.

2001-06-29 12:12  thassine

	* src/common/Makefile.OLD, src/common/Makefile.in,
	  src/common/mm1alg.cpp, src/common/mm1alg.h,
	  src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/mm2mdl.cpp, src/common/model.cpp, src/common/model.h,
	  src/common/qm1mdl.cpp, src/target2/t2mm1docv.cpp: some
	  groundwork added for mm1_mdl multiple crd_sets and
	  conformational search tools.

2001-06-25 11:21  thassine

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

2001-06-21 08:49  thassine

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

2001-06-19 13:15  thassine

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

2001-06-13 13:30  thassine

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

2001-05-28 12:47  thassine

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

2001-05-23 13:28  thassine

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

2001-05-21 14:45  thassine

	* src/common/mm1mdl.cpp: again some readpdb tweaks.

2001-05-21 10:39  thassine

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

2001-05-18 13:09  thassine

	* src/common/factory.cpp, src/common/factory.h: ooops, forgot to
	  add the class_factory files...

2001-05-18 13:07  thassine

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

2001-05-16 11:30  thassine

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

2001-05-16 03:56  hutchisn

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

2001-05-15 11:57  thassine

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

2001-05-15 08:49  thassine

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

2001-05-14 09:10  thassine

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

2001-05-11 15:18  hutchisn

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

2001-05-11 12:10  thassine

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

2001-05-08 11:25  thassine

	* miniMOPAC/Makefile: miniMOPAC/Makefile removed; configure will
	  update it.

2001-05-08 11:22  thassine

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

2001-05-07 14:33  hutchisn

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

2001-05-04 20:32  hutchisn

	* src/target3/t3main.cpp, src/target3/t3main.h: Add buttons for
	  measure tools.

2001-05-04 20:31  hutchisn

	* src/graphics/mtools.cpp, src/graphics/mtools.h,
	  src/graphics/views.cpp, src/graphics/views.h: Add tools for
	  measurements.

2001-05-04 20:30  hutchisn

	* src/target3/pixmaps, src/target3/pixmaps/.cvsignore,
	  src/target3/pixmaps/angle.xpm, src/target3/pixmaps/dihedral.xpm,
	  src/target3/pixmaps/distance.xpm, src/target3/pixmaps/draw.xpm,
	  src/target3/pixmaps/erase.xpm, src/target3/pixmaps/orb_xy.xpm,
	  src/target3/pixmaps/orb_z.xpm, src/target3/pixmaps/rot_xy.xpm,
	  src/target3/pixmaps/rot_z.xpm, src/target3/pixmaps/select.xpm,
	  src/target3/pixmaps/trans_xy.xpm,
	  src/target3/pixmaps/trans_z.xpm, src/target3/pixmaps/zoom.xpm:
	  Add transparency to button pics and buttons for measure tools.

2001-05-04 18:28  hutchisn

	* src/graphics/docview.cpp, src/graphics/docview.h,
	  src/target3/t3docv.cpp, src/target3/t3docv.h: Changes to make
	  sure window titles update when importing.

2001-05-04 18:27  hutchisn

	* src/target3/Makefile.in: Make sure miniMOPAC is compiled in.

2001-05-04 18:26  hutchisn

	* src/graphics/Makefile.in: Compile io-* for exporting.

2001-05-04 16:39  hutchisn

	* src/common/mm1mdl.cpp, src/common/mm1mdl.h: Added CLear and
	  DoFormula methods.

2001-05-04 16:38  hutchisn

	* src/common/Makefile.in: Remove EXTERN_GLOBALS -- not needed

2001-05-04 16:37  hutchisn

	* src/graphics/io-jpg.cpp, src/graphics/io-jpg.h,
	  src/graphics/io-png.cpp, src/graphics/io-png.h: Add GNOME code
	  for exporting GdkPixbuf -> PNG or JPEG files.

2001-05-04 15:51  hutchisn

	* oelib/aromatic.h, oelib/atom.cpp, oelib/atomtyp.h,
	  oelib/bin2hex.pl, oelib/binary.cpp, oelib/binary.h,
	  oelib/binary_io.cpp, oelib/binary_io.h, oelib/chains.cpp,
	  oelib/chains.h, oelib/configure, oelib/ctransform.cpp,
	  oelib/ctransform.h, oelib/data.cpp, oelib/data.h,
	  oelib/dmol.cpp, oelib/element.h, oelib/extable.h,
	  oelib/extable.txt, oelib/fileformat.cpp, oelib/fileformat.h,
	  oelib/gaussian.cpp, oelib/generic.cpp, oelib/generic.h,
	  oelib/ghemical.cpp, oelib/jaguar.cpp, oelib/main.cpp,
	  oelib/matrix.cpp, oelib/matrix.h, oelib/mdl.cpp, oelib/mol.cpp,
	  oelib/mol.h, oelib/mol2.cpp, oelib/mopac.cpp, oelib/nwchem.cpp,
	  oelib/oelib.dsp, oelib/oeutil.cpp, oelib/oeutil.h,
	  oelib/parsmart.cpp, oelib/parsmi.cpp, oelib/phmodel.cpp,
	  oelib/phmodeldata.h, oelib/report.cpp, oelib/resdata.h,
	  oelib/rotor.cpp, oelib/smi.cpp, oelib/typer.cpp, oelib/types.h:
	  Update with current OELib version.

2001-05-03 16:52  hutchisn

	* Makefile.in, configure, configure.in, miniMOPAC/Makefile.in,
	  oelib/Makefile.in: Update for miniMOPAC, test for g2c/f2c
	  library (hopefully).

2001-05-03 16:50  hutchisn

	* src/target3/glade/ghemical.glade,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade/src/glade_interface.h,
	  src/target3/glade/src/glade_support.cpp: Add Element options
	  dialog to glade.

2001-05-02 09:31  thassine

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

2001-04-30 10:58  thassine

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

2001-04-27 12:40  thassine

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

2001-04-24 11:10  thassine

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

2001-04-20 10:11  thassine

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

2001-04-19 10:16  thassine

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

2001-04-18 11:04  thassine

	* CHANGES, bin/parameters/mm2param,
	  bin/parameters/mm2param/loopdip.txt,
	  bin/parameters/mm2param/looptor.txt, src/common/Makefile.OLD,
	  src/common/Makefile.in, src/common/mm1mdl.h,
	  src/common/mm1util.h, src/common/mm2eng.cpp,
	  src/common/mm2eng.h, src/common/mm2mdl.cpp, src/common/mm2mdl.h,
	  src/graphics/mm2docv.cpp, src/graphics/mm2docv.h,
	  src/target2/t2mm1docv.cpp, src/target2/t2mm2docv.cpp,
	  src/target2/t2mm2docv.h, src/target3/t3mm2docv.cpp,
	  src/target3/t3mm2docv.h: started merging the mm2_mdl code
	  (accepted for publication :)

2001-04-18 08:22  thassine

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

2001-03-30 10:21  thassine

	* configure, configure.in, src/common/define.h: switched back to
	  devel settings; the version number is now 0.43

2001-03-30 08:30  thassine

	* CHANGES, src/common/define.h, src/common/notice.cpp,
	  src/target3/t3main.cpp, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp: minor
	  cleanups; this is released as 0.42

2001-03-28 11:08  thassine

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

2001-03-23 22:33  hutchisn

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

2001-03-22 16:43  hutchisn

	* src/graphics/mm1docv.cpp: Add new multiple-bond rendering. Now
	  uses line stipple to render conjugated bonds fairly well.

2001-03-22 16:42  hutchisn

	* oelib/Makefile, oelib/Makefile.in, oelib/data.cpp, oelib/data.h,
	  oelib/dmol.cpp, oelib/extable.txt, oelib/fileformat.cpp,
	  oelib/fileformat.h, oelib/gamess.cpp, oelib/ghemical.cpp: Added
	  Dmol format and cleanups.

2001-03-22 15:51  thassine

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

2001-03-19 11:46  thassine

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

2001-03-16 12:17  thassine

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

2001-03-15 19:53  hutchisn

	* oelib/ghemical.cpp, oelib/xyz.cpp: Fix minor bugs in file
	  translators.

2001-03-15 18:50  hutchisn

	* src/common/filetrans.cpp: Fix "the bug" with calling extab
	  before it was properly set.

2001-03-15 18:49  hutchisn

	* oelib/alchemy.cpp, oelib/amber.cpp, oelib/atomtyp.h,
	  oelib/atomtyp.txt, oelib/element.h, oelib/element.txt,
	  oelib/extable.h, oelib/ghemical.cpp, oelib/hin.cpp,
	  oelib/jaguar.cpp, oelib/mpqc.cpp, oelib/oelib.dsp,
	  oelib/phmodeldata.h, oelib/qchem.cpp, oelib/tinker.cpp,
	  oelib/types.h, oelib/types.txt, oelib/unichem.cpp,
	  oelib/xyz.cpp: Added fixes to the translators--now much better
	  about getting elements correct for rare atoms (e.g. Pb).

2001-03-15 11:15  thassine

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

2001-03-14 16:40  hutchisn

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

2001-03-14 13:00  thassine

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

2001-03-12 12:00  thassine

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

2001-03-08 22:54  hutchisn

	* src/common/define.h, src/graphics/mm1docv.cpp,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h: Add support
	  for label Atom IDs

2001-03-08 22:53  hutchisn

	* src/common/mm1mdl.cpp: ReadStream changes to support reading
	  charges

2001-03-08 22:53  hutchisn

	* src/common/notice.cpp: Update copyright with OELib info.

2001-03-08 22:51  hutchisn

	* src/common/filetrans.cpp: Update for new OELib changes.

2001-03-08 22:49  hutchisn

	* Makefile.in: Add target for help files.

2001-03-08 22:47  hutchisn

	* oelib/Makefile.in, oelib/Vector.cpp, oelib/Vector.h,
	  oelib/alchemy.cpp, oelib/amber.cpp, oelib/aromatic.h,
	  oelib/aromatic.txt, oelib/atom.cpp, oelib/atomtyp.h,
	  oelib/atomtyp.txt, oelib/balst.cpp, oelib/bgf.cpp,
	  oelib/bin2hex.pl, oelib/binary.cpp, oelib/binary.h,
	  oelib/bitgrid.cpp, oelib/bitgrid.h, oelib/bitvec.cpp,
	  oelib/bitvec.h, oelib/bond.cpp, oelib/box.cpp, oelib/c3d.cpp,
	  oelib/cacao.cpp, oelib/cache.cpp, oelib/car.cpp, oelib/ccc.cpp,
	  oelib/chdrw.cpp, oelib/chiral.cpp, oelib/chiral.h,
	  oelib/commandline.cpp, oelib/commandline.h, oelib/configure,
	  oelib/csr.cpp, oelib/cssr.cpp, oelib/cwrap.cpp, oelib/cwrap.h,
	  oelib/data.cpp, oelib/data.h, oelib/element.h, oelib/extable.h,
	  oelib/extable.txt, oelib/feat.cpp, oelib/fh.cpp,
	  oelib/fileformat.cpp, oelib/fileformat.h, oelib/gamess.cpp,
	  oelib/ghemical.cpp, oelib/grid.cpp, oelib/grid.h,
	  oelib/gromos96.cpp, oelib/hin.cpp, oelib/jaguar.cpp,
	  oelib/main.cpp, oelib/matrix.cpp, oelib/matrix.h, oelib/mdl.cpp,
	  oelib/mmod.cpp, oelib/mol.cpp, oelib/mol.h, oelib/mol2.cpp,
	  oelib/molchrg.cpp, oelib/molchrg.h, oelib/molvector.cpp,
	  oelib/molvector.h, oelib/mpqc.cpp, oelib/oeifstream.h,
	  oelib/oelib.dsp, oelib/oeutil.cpp, oelib/oeutil.h,
	  oelib/parsmart.cpp, oelib/parsmart.h, oelib/parsmi.cpp,
	  oelib/patty.cpp, oelib/patty.h, oelib/pdb.cpp,
	  oelib/phmodel.cpp, oelib/phmodel.h, oelib/phmodel.txt,
	  oelib/phmodeldata.h, oelib/qchem.cpp, oelib/rand.cpp,
	  oelib/resdata.h, oelib/ring.cpp, oelib/ring.h, oelib/rotor.cpp,
	  oelib/rotor.h, oelib/smi.cpp, oelib/smi.h, oelib/tokenst.cpp,
	  oelib/typer.cpp, oelib/typer.h, oelib/types.h, oelib/version.h,
	  oelib/xed.cpp: Updates to oelib files.

2001-03-08 14:59  thassine

	* CHANGES, src/common/notice.cpp, src/common/notice.h,
	  src/target3/t3main.cpp, src/target3/t3main.h: added the
	  Help/Help item to the main menu, copyright notices updated to
	  include OELib

2001-03-08 13:51  thassine

	* bin/user-docs/index.html, bin/user-docs/maintools.jpg: updated
	  the user's manual

2001-02-16 15:14  thassine

	* src/Makefile.OLD: this will make quick test builds easier.

2001-02-16 14:29  thassine

	* bin/user-docs, bin/user-docs/index.html: added some framework
	  for the user manual

2001-02-13 14:32  thassine

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

2001-02-12 17:07  hutchisn

	* configure, configure.in: Solved configure problems with MPQC and
	  oelib.

2001-02-12 16:25  hutchisn

	* configure, configure.in: Fix problem with configure in srcdir.

2001-02-12 09:41  thassine

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

2001-02-11 14:36  thassine

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

2001-02-10 15:09  thassine

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

2001-02-07 09:24  thassine

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

2001-02-06 18:24  hutchisn

	* oelib/extable.txt: Add sorted extable to make menus more
	  user-friendly.

2001-02-06 18:24  hutchisn

	* src/common/filetrans.cpp: Fix bug with GetImportDescription.

2001-02-06 18:05  hutchisn

	* oelib/data.cpp: Fix problem with GetType from an integer--table
	  lookup was in the wrong place!

2001-02-06 13:10  thassine

	* src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/graphics/docview.h, src/graphics/mm1docv.cpp,
	  src/graphics/mm1docv.h, src/target2/t2docv.h,
	  src/target3/t3docv.h, src/target3/t3errutil.h,
	  src/target3/t3main.h, src/target3/t3mm1docv.h,
	  src/target3/t3qm1docv.h, src/target3/t3views.h: added some more
	  DOC++ style documentation.

2001-02-06 09:21  thassine

	* AUTHORS, CHANGES, INSTALL, PROJECT: revised/updated some
	  documentation.

2001-02-06 08:44  thassine

	* configure, configure.in, oelib/Makefile, src/common/define.h,
	  src/common/notice.cpp, src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/glade_interface.h:
	  some cleanups at glade optionmenus; the version number promoted
	  to 0.40

2001-02-06 06:17  hutchisn

	* 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.

2001-02-06 06:16  hutchisn

	* src/common/filetrans.cpp, src/common/filetrans.h: Add support
	  for specifically requesting an import or export type (by index
	  #).

2001-02-06 06:16  hutchisn

	* oelib/Makefile.in: Add target to rebuild Makefile if Makefile.in
	  or configure script changes.

2001-02-05 15:26  thassine

	* src/target3/glade_callbacks.cpp: the file import/export dialogs
	  seem to work now...

2001-02-05 14:48  thassine

	* oelib/data.cpp, oelib/extable.txt, oelib/ghemical.cpp,
	  oelib/mol.cpp, src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/glade_interface.h:
	  the filename change is done also in oelib; the file
	  import/export dialogs almost work now.

2001-02-05 13:55  thassine

	* src/target3/glade/ghemical.glade,
	  src/target3/glade/src/glade_callbacks.cpp,
	  src/target3/glade/src/glade_callbacks.h,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade/src/glade_interface.h,
	  src/target3/glade/src/main.cpp, src/target3/glade_callbacks.cpp,
	  src/target3/glade_callbacks.h, src/target3/glade_interface.cpp,
	  src/target3/glade_interface.h, src/target3/t3mm1docv.cpp,
	  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 18:30  thassine

	* src/common/qm1eng.cpp, src/common/qm1eng.h,
	  src/common/qm1mdl.cpp, src/common/qm1mdl.h,
	  src/common/qm2eng.cpp, src/common/qm2eng.h,
	  src/common/qm2mdl.cpp, src/common/qm2mdl.h,
	  src/graphics/qm1docv.cpp, src/graphics/qm1docv.h,
	  src/graphics/qm2docv.cpp, src/graphics/qm2docv.h,
	  src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h,
	  src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h,
	  src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h,
	  src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h: some files
	  were lost in the last commit; added them back...

2001-02-04 18:11  thassine

	* CHANGES, INSTALL, bin/examples/2-chlorobutane.gpMM,
	  bin/examples/2-chlorobutane.mm1gp,
	  bin/examples/3-phenylpropanal.gpMM,
	  bin/examples/3-phenylpropanal.mm1gp,
	  bin/examples/acetylsalicylic_acid.gpMM,
	  bin/examples/acetylsalicylic_acid.mm1gp,
	  bin/examples/alpha-pinene.gpMM, bin/examples/alpha-pinene.mm1gp,
	  bin/examples/bromobenzene.gpMM, bin/examples/bromobenzene.mm1gp,
	  bin/examples/camphor.gpMM, bin/examples/camphor.mm1gp,
	  bin/examples/cinnamaldehyde.gpMM,
	  bin/examples/cinnamaldehyde.mm1gp,
	  bin/examples/cis-2-pentene.gpMM,
	  bin/examples/cis-2-pentene.mm1gp, bin/examples/cyclohexane.gpMM,
	  bin/examples/cyclohexane.mm1gp, bin/examples/naphtalene.gpMM,
	  bin/examples/naphtalene.mm1gp, src/common/Makefile.OLD,
	  src/common/Makefile.in, src/common/mm1mdl.cpp,
	  src/common/mm1mdl.h, src/common/model.h, src/common/qm1eng.cpp,
	  src/common/qm1eng.h, src/common/qm1eng1.cpp,
	  src/common/qm1eng1.h, src/common/qm1eng9.cpp,
	  src/common/qm1eng9.h, src/common/qm1mdl.cpp,
	  src/common/qm1mdl.h, src/common/qm2eng.cpp, src/common/qm2eng.h,
	  src/common/qm2eng1.cpp, src/common/qm2eng1.h,
	  src/common/qm2eng9.cpp, src/common/qm2eng9.h,
	  src/common/qm2mdl.cpp, src/common/qm2mdl.h,
	  src/graphics/qm1docv.cpp, src/graphics/qm1docv.h,
	  src/graphics/qm2docv.cpp, src/graphics/qm2docv.h,
	  src/target1/t1main.cpp, src/target2/t2main.cpp,
	  src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h,
	  src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h,
	  src/target3/glade/ghemical.glade,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade/src/glade_interface.h,
	  src/target3/glade/src/main.cpp, src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/glade_interface.h,
	  src/target3/t3docv.h, src/target3/t3main.cpp,
	  src/target3/t3main.h, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm1docv.h, src/target3/t3qm1docv.cpp,
	  src/target3/t3qm1docv.h, src/target3/t3qm2docv.cpp,
	  src/target3/t3qm2docv.h, 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 16:27  thassine

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

2001-01-31 17:32  thassine

	* CHANGES, src/common/errutil.cpp, src/common/errutil.h,
	  src/common/mm1alg.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/model.h, src/common/qm2mdl.cpp, src/common/qm2mdl.h,
	  src/graphics/docview.h, src/graphics/mm1docv.cpp,
	  src/graphics/mm1docv.h, src/graphics/qm2docv.cpp,
	  src/graphics/qm2docv.h, src/target2/t2mm1docv.cpp,
	  src/target2/t2mm1docv.h, src/target2/t2qm2docv.cpp,
	  src/target2/t2qm2docv.h, src/target3/t3errutil.cpp,
	  src/target3/t3errutil.h, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm1docv.h, src/target3/t3qm2docv.cpp,
	  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 19:44  hutchisn

	* src/common/filetrans.cpp, src/common/filetrans.h,
	  src/common/utility.cpp, src/target3/glade_interface.cpp,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h: Switch to
	  new GLADE-designed import/export boxes.

2001-01-30 19:41  hutchisn

	* oelib/aromatic.txt, oelib/atom.cpp, oelib/atomtyp.txt,
	  oelib/binary.cpp, oelib/bond.cpp, oelib/csr.cpp, oelib/data.cpp,
	  oelib/data.h, oelib/extable.txt, oelib/fileformat.cpp,
	  oelib/fileformat.h, oelib/gamess.cpp, oelib/ghemical.cpp,
	  oelib/hin.cpp, oelib/main.cpp, oelib/mdl.cpp, oelib/mol.cpp,
	  oelib/mol.h, oelib/mpqc.cpp, oelib/oeutil.cpp,
	  oelib/parsmart.cpp, oelib/patty.cpp, oelib/patty.h,
	  oelib/pdb.cpp, oelib/quat.c, oelib/ring.cpp, oelib/ring.h,
	  oelib/rotor.cpp, oelib/smi.cpp, oelib/typer.cpp, oelib/typer.h,
	  oelib/types.txt: Synch with current OELib code.

2001-01-30 15:21  thassine

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

2001-01-29 15:54  thassine

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

2001-01-25 13:45  thassine

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

2001-01-24 14:08  thassine

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

2001-01-22 18:43  hutchisn

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

2001-01-22 07:52  thassine

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

2001-01-20 06:19  hutchisn

	* PROJECT, oelib/Makefile.in, oelib/data.cpp, oelib/tinker.cpp,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h: *** empty
	  log message ***

2001-01-20 06:19  hutchisn

	* src/target3/glade/ghemical.glade,
	  src/target3/glade/src/glade_callbacks.cpp,
	  src/target3/glade/src/glade_callbacks.h,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade/src/glade_interface.h,
	  src/target3/glade/src/glade_support.cpp,
	  src/target3/glade/src/main.cpp, src/target3/glade_callbacks.cpp,
	  src/target3/glade_callbacks.h, src/target3/glade_interface.cpp,
	  src/target3/glade_interface.h, src/target3/glade_support.cpp:
	  Added new import/export dialogues using Glade.
	  (Still need to figure out how to update the option menu
	  appropriately.)

2001-01-20 06:18  hutchisn

	* oelib/data.h, oelib/extable.txt: Added all options from Babel 1.6

2001-01-19 04:22  hutchisn

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

2001-01-16 17:51  hutchisn

	* oelib/data.cpp, oelib/data.h, oelib/extable.txt,
	  oelib/fileformat.cpp, oelib/fileformat.h, oelib/qchem.cpp: Added
	  a QChem file export translator.

2001-01-16 16:24  hutchisn

	* oelib/data.cpp, oelib/data.h, oelib/extable.txt,
	  oelib/fileformat.cpp, oelib/fileformat.h: More OELib
	  updates--removing incomplete formats for now.

2001-01-16 16:00  hutchisn

	* oelib/extable.txt, oelib/fileformat.cpp, oelib/gamess.cpp,
	  oelib/hin.cpp: More OELib cleanups.

2001-01-13 21:31  hutchisn

	* oelib/Makefile.in, oelib/data.cpp, oelib/data.h,
	  oelib/extable.txt, oelib/fileformat.cpp, oelib/fileformat.h,
	  oelib/gamess.cpp, oelib/ghemical.cpp, oelib/hin.cpp,
	  oelib/main.cpp, oelib/mol.h, oelib/mpqc.cpp, oelib/oelib.dsp,
	  oelib/oelib.dsw, oelib/pdb.cpp, oelib/quat.c, oelib/rotor.cpp,
	  oelib/typer.cpp, oelib/xyz.cpp: Added new translators, updated
	  to be in sync with OpenEyes code.

2001-01-13 21:29  hutchisn

	* src/common/utility.cpp: Small modifications to vdW radii to be
	  closer to literature (Bondi) values

2001-01-13 21:28  hutchisn

	* src/common/filetrans.cpp: Use filename for molecule title -- we
	  don't currently have another way of titling.

2001-01-05 22:38  hutchisn

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

2001-01-05 15:34  thassine

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

2001-01-03 17:09  thassine

	* src/common/mm1mdl.cpp, src/graphics/mm1docv.cpp,
	  src/graphics/mm1docv.h, src/graphics/qm2docv.cpp,
	  src/graphics/qm2docv.h, src/target3/glade/ghemical.glade,
	  src/target3/glade/src/Makefile,
	  src/target3/glade/src/glade_callbacks.cpp,
	  src/target3/glade/src/glade_callbacks.h,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade_callbacks.cpp, src/target3/glade_callbacks.h,
	  src/target3/glade_interface.cpp, src/target3/glade_interface.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h: the setup
	  dialog should now work for MM.

2001-01-03 10:03  thassine

	* CHANGES, src/target3/glade/ghemical.glade,
	  src/target3/glade/src/Makefile,
	  src/target3/glade/src/glade_callbacks.cpp,
	  src/target3/glade/src/glade_callbacks.h,
	  src/target3/glade/src/glade_interface.cpp,
	  src/target3/glade/src/glade_interface.h,
	  src/target3/glade/src/glade_support.cpp,
	  src/target3/glade/src/glade_support.h,
	  src/target3/glade/src/main.cpp, src/target3/glade_callbacks.cpp,
	  src/target3/glade_interface.cpp, src/target3/glade_interface.h:
	  dialogs; read from glade/src/Makefile how to retain your changes
	  in GLADE code.

2001-01-02 16:00  thassine

	* src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/qm2mdl.cpp, src/common/qm2mdl.h,
	  src/graphics/mm1docv.cpp, src/graphics/mm1docv.h: some
	  preliminary stuff for the setup dialogs

2001-01-02 12:42  thassine

	* INSTALL, PROJECT, src/target3/Makefile.OLD, src/target3/glade,
	  src/target3/glade/ghemical.glade, src/target3/glade/src,
	  src/target3/glade/src/Makefile, src/target3/glade_callbacks.cpp,
	  src/target3/glade_callbacks.h, src/target3/glade_interface.cpp,
	  src/target3/glade_interface.h, src/target3/glade_support.cpp,
	  src/target3/glade_support.h, src/target3/t3dialog.cpp: started
	  making some dialogs using GLADE...

2001-01-01 13:53  thassine

	* AUTHORS, INSTALL, PROJECT, src/common/Makefile.OLD,
	  src/common/mm1mdl.h, src/common/qm1eng.cpp, src/common/qm1eng.h,
	  src/common/qm2eng.h, src/common/qm2eng1.h, src/common/qm2mdl.h,
	  src/graphics/Makefile.OLD, src/target1/Makefile.OLD,
	  src/target2/Makefile.OLD, src/target3/Makefile.OLD: just some
	  cleanups and some improvements to documentation

2001-01-01 11:30  thassine

	* small-utilities, small-utilities/Makefile,
	  small-utilities/getpdb_cd.cpp, small-utilities/getpdb_ftp.cpp,
	  small-utilities/gp2mpqc.cpp: HAPPY NEW YEAR; some
	  small-utilities added...

2000-12-27 13:59  thassine

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

2000-12-22 15:09  thassine

	* src/target3/t3docv.cpp, src/target3/t3docv.h: added some missing
	  files...

2000-12-22 14:47  thassine

	* CHANGES, src/graphics/camera.cpp, src/graphics/docview.cpp,
	  src/graphics/docview.h, src/graphics/mm1docv.cpp,
	  src/graphics/mm1docv.h, src/graphics/mtools.cpp,
	  src/graphics/qm1docv.h, src/graphics/qm2docv.h,
	  src/graphics/views.cpp, src/graphics/views.h,
	  src/target2/Makefile.OLD, src/target2/t2docv.cpp,
	  src/target2/t2docv.h, src/target2/t2mm1docv.cpp,
	  src/target2/t2mm1docv.h, src/target2/t2qm1docv.cpp,
	  src/target2/t2qm1docv.h, src/target2/t2qm2docv.cpp,
	  src/target2/t2qm2docv.h, src/target2/t2views.cpp,
	  src/target2/t2views.h, src/target3/Makefile.OLD,
	  src/target3/t3main.cpp, src/target3/t3main.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h,
	  src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h,
	  src/target3/t3views.cpp, src/target3/t3views.h: added
	  target-dependent middle classes for docviews and views;
	  simplifies the base-classes a bit

2000-12-22 11:34  thassine

	* BUGLIST, src/graphics/docview.cpp, src/target3/t3main.cpp,
	  src/target3/t3main.h, src/target3/t3mm1docv.cpp,
	  src/target3/t3qm2docv.cpp, src/target3/t3views.cpp: treelist
	  works now pretty well (see BUGLIST for some details)

2000-12-21 17:16  thassine

	* src/graphics/docview.cpp, src/graphics/docview.h,
	  src/target3/t3main.cpp, src/target3/t3main.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3qm2docv.cpp,
	  src/target3/t3views.cpp, src/target3/t3views.h: improved proper
	  model closing/cleanup in GNOME version, but still problems (try
	  File/Close and File/Exit)

2000-12-21 13:19  thassine

	* src/graphics/docview.cpp, src/graphics/docview.h,
	  src/graphics/views.h, src/target3/t3views.cpp,
	  src/target3/t3views.h: treelist (now actually works) - added
	  subtrees and lights

2000-12-20 15:01  thassine

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

2000-12-19 16:57  thassine

	* CHANGES, src/graphics/docview.cpp, src/graphics/docview.h,
	  src/graphics/views.cpp, src/graphics/views.h,
	  src/target2/t2main.cpp, src/target2/t2views.cpp,
	  src/target2/t2views.h, src/target3/t3main.cpp,
	  src/target3/t3main.h, src/target3/t3mm1docv.cpp,
	  src/target3/t3mm1docv.h, src/target3/t3qm2docv.cpp,
	  src/target3/t3views.cpp, src/target3/t3views.h: added framework
	  for tree/list views, and smaller changes

2000-12-19 12:45  thassine

	* src/common/notice.cpp, src/graphics/docview.h,
	  src/target3/t3main.cpp, src/target3/t3main.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3qm2docv.cpp,
	  src/target3/t3views.cpp: the toolbar buttons work again as
	  toggle buttons

2000-12-18 15:24  thassine

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

2000-12-08 17:22  hutchisn

	* src/common/filetrans.cpp, src/common/filetrans.h,
	  src/target3/t3mm1docv.cpp: Use new OEFileFormat code to check if
	  formats are valid.

2000-12-08 17:21  hutchisn

	* oelib/Makefile, oelib/Makefile.in, oelib/aromatic.txt,
	  oelib/binary.cpp, oelib/data.cpp, oelib/data.h,
	  oelib/extable.txt, oelib/fileformat.cpp, oelib/fileformat.h,
	  oelib/globals.cpp, oelib/main.cpp, oelib/mol.cpp, oelib/mol.h,
	  oelib/molvector.cpp, oelib/oeutil.h, oelib/rotor.cpp,
	  oelib/rotor.h, oelib/typer.cpp, oelib/xyz.cpp: Synched with
	  current oelib version--fixed bugs finding data files.

2000-12-08 16:41  thassine

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

2000-12-02 00:29  hutchisn

	* src/target3/t3mm1docv.cpp: OKEvent should return true for now.

2000-12-02 00:28  hutchisn

	* src/target3/t3dialog.cpp, src/target3/t3dialog.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3qm2docv.cpp, 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.)

2000-12-02 00:27  hutchisn

	* oelib/data.cpp, oelib/mol.h, oelib/pdb.cpp, oelib/rotor.cpp,
	  oelib/typer.cpp, src/common/Makefile.in: One more bug
	  fix--really get the logic in initialization correct!

2000-12-01 22:38  hutchisn

	* oelib/data.cpp, oelib/pdb.cpp, oelib/rotor.cpp, oelib/typer.cpp:
	  Ensure that the directory is checked AND the environment
	  variable is checked
	  when initializing.

2000-12-01 21:49  hutchisn

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

2000-12-01 13:27  thassine

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

2000-12-01 00:13  hutchisn

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

2000-11-30 12:18  thassine

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

2000-11-29 17:18  thassine

	* src/graphics/docview.h, src/graphics/views.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h,
	  src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h,
	  src/target3/t3views.cpp, src/target3/t3views.h: GNOME popup menu
	  callbacks finished - but some items are still disabled

2000-11-29 14:43  thassine

	* src/target3/t3mm1docv.cpp, src/target3/t3qm2docv.cpp,
	  src/target3/t3views.cpp, src/target3/t3views.h: popup-menu
	  callbacks changed (for model-independent items)

2000-11-29 13:10  thassine

	* src/common/model.cpp, src/common/model.h,
	  src/graphics/views.cpp, src/graphics/views.h,
	  src/target2/t2views.cpp, src/target2/t2views.h,
	  src/target3/t3main.cpp, src/target3/t3views.cpp,
	  src/target3/t3views.h: OpenGL initialization in GNOME fixed (so
	  that we have colors back).

2000-11-28 17:43  hutchisn

	* src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h,
	  src/target3/t3views.cpp: Add import/export menu items, center
	  command and move things to "build" submenu.

2000-11-28 17:42  hutchisn

	* src/target3/t3main.cpp: Can't pass VERSION since it's a double.
	  Run it through sprintf first.

2000-11-28 17:40  hutchisn

	* acconfig.h, configure, configure.in, src/config.h.in,
	  src/graphics/Makefile.in: Fix build environment to define
	  appropriate flags, etc.

2000-11-28 17:39  hutchisn

	* oelib/quat.c: fixed problem with undeclared memset

2000-11-28 15:41  thassine

	* CHANGES, src/common/conjgrad.h, src/common/errutil.h,
	  src/common/mm1alg.h, src/common/mm1eng.h, src/common/mm1eng1.h,
	  src/common/mm1mdl.h, src/common/mm1util.h, src/common/model.h,
	  src/common/qm2eng.h, src/common/qm2eng9.h, src/common/qm2mdl.h,
	  src/common/v3d.h, src/graphics/mtools.h, src/graphics/views.h,
	  src/target2/t2mm1docv.cpp, src/target2/t2views.cpp,
	  src/target2/t2views.h, src/target3/t3main.h,
	  src/target3/t3qm2docv.cpp, src/target3/t3views.cpp,
	  src/target3/t3views.h: some cleanups : public data changed
	  protected in many classes

2000-11-28 12:18  thassine

	* CHANGES, src/common/define.h, src/graphics/Makefile.OLD,
	  src/graphics/docview.cpp, src/graphics/docview.h,
	  src/graphics/views.h, src/target2/t2views.cpp,
	  src/target3/t3main.cpp, src/target3/t3main.h,
	  src/target3/t3mm1docv.cpp, src/target3/t3views.cpp,
	  src/target3/t3views.h: any things broken/mixed up, but we have a
	  standard GNOME MDI app now

2000-11-27 16:50  hutchisn

	* src/target3/t3dialog.cpp, src/target3/t3dialog.h: Modify dialog
	  to show which element is currently selected.

2000-11-27 16:48  hutchisn

	* src/common/filetrans.cpp, src/common/filetrans.h,
	  src/common/mm1mdl.cpp, src/common/mm1mdl.h: Remove import
	  functions from mm1mdl and use new filetrans code through OELib.

2000-11-27 16:47  hutchisn

	* Makefile.in, acconfig.h, configure, configure.in,
	  oelib/Makefile.in, oelib/configure, src/common/Makefile.in,
	  src/config.h.in, src/graphics/Makefile.in,
	  src/target3/Makefile.in: Add changes to support linking in OELib
	  and slightly cleaned up build system.

2000-11-27 08:51  thassine

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

2000-11-26 13:05  thassine

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

2000-11-24 13:36  thassine

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

2000-11-23 15:07  thassine

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

2000-11-20 10:18  thassine

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

2000-11-16 15:06  hutchisn

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

2000-11-16 11:55  thassine

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

2000-11-15 15:01  hutchisn

	* src/common/Makefile.in, src/common/errorutil.cpp,
	  src/common/errorutil.h, src/target3/Makefile.in,
	  src/target3/t3errorutil.cpp, src/target3/t3errorutil.h: Add
	  error-handling classes with support for GNOME.

2000-11-15 15:00  hutchisn

	* oelib/Makefile, oelib/Makefile.in, oelib/data.cpp, oelib/data.h,
	  oelib/extable.txt, oelib/ghemical.cpp, oelib/mol.cpp,
	  oelib/mol.h: Add read/write for ghemical file format.

2000-11-14 21:52  hutchisn

	* oelib, oelib/.cvsignore, oelib/GNULICENSE.txt, oelib/Makefile,
	  oelib/Makefile.in, oelib/OELibPrimer.html, oelib/StdAfx.cpp,
	  oelib/StdAfx.h, oelib/Vector.cpp, oelib/Vector.h,
	  oelib/alchemy.cpp, oelib/aromatic.txt, oelib/atom.cpp,
	  oelib/atomtyp.txt, oelib/balst.cpp, oelib/bgf.cpp,
	  oelib/binary.cpp, oelib/binary.h, oelib/bitgrid.cpp,
	  oelib/bitgrid.h, oelib/bitvec.cpp, oelib/bitvec.h,
	  oelib/bond.cpp, oelib/box.cpp, oelib/c3d.cpp, oelib/cacao.cpp,
	  oelib/cache.cpp, oelib/ccc.cpp, oelib/chdrw.cpp,
	  oelib/chiral.cpp, oelib/chiral.h, oelib/commandline.cpp,
	  oelib/commandline.h, oelib/configure, oelib/csr.cpp,
	  oelib/cssr.cpp, oelib/cwrap.cpp, oelib/cwrap.h, oelib/data.cpp,
	  oelib/data.h, oelib/element.txt, oelib/extable.txt,
	  oelib/feat.cpp, oelib/fh.cpp, oelib/grid.cpp, oelib/grid.h,
	  oelib/gromos96.cpp, oelib/main.cpp, oelib/matrix.cpp,
	  oelib/matrix.h, oelib/mdl.cpp, oelib/mmod.cpp, oelib/mol.cpp,
	  oelib/mol.h, oelib/mol2.cpp, oelib/molchrg.cpp, oelib/molchrg.h,
	  oelib/molvector.cpp, oelib/molvector.h, oelib/oeutil.cpp,
	  oelib/oeutil.h, oelib/parsmart.cpp, oelib/parsmart.h,
	  oelib/parsmi.cpp, oelib/patty.cpp, oelib/patty.h, oelib/pdb.cpp,
	  oelib/quat.c, oelib/rand.cpp, oelib/resdata.txt, oelib/ring.cpp,
	  oelib/ring.h, oelib/rotor.cpp, oelib/rotor.h, oelib/smi.cpp,
	  oelib/smi.h, oelib/tokenst.cpp, oelib/typer.cpp, oelib/typer.h,
	  oelib/types.txt, oelib/version.h: Initial revision

2000-11-14 21:32  hutchisn

	* src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h,
	  src/target3/t3window.cpp: Added menu items and user-visible
	  feedback for menu choices.

2000-11-14 21:23  hutchisn

	* Makefile.in, 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 19:56  hutchisn

	* src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h,
	  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.

2000-11-10 16:48  hutchisn

	* bin/examples/2-chlorobutane.gpMM,
	  bin/examples/3-phenylpropanal.gpMM,
	  bin/examples/acetylsalicylic_acid.gpMM,
	  bin/examples/alpha-pinene.gpMM, bin/examples/bromobenzene.gpMM,
	  bin/examples/camphor.gpMM, bin/examples/cinnamaldehyde.gpMM,
	  bin/examples/cis-2-pentene.gpMM, bin/examples/cyclohexane.gpMM,
	  bin/examples/naphtalene.gpMM: Update examples to new file format
	  (read in and re-saved).

2000-11-10 12:46  thassine

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

2000-11-09 12:42  thassine

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

2000-11-08 21:30  hutchisn

	* src/common/utility.cpp, 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 20:00  hutchisn

	* src/target3/t3dialog.cpp: Add feedback for currently selected
	  bondtype and element in dialogues.

2000-11-07 19:59  hutchisn

	* src/target3/t3mm1gui.cpp, src/target3/t3qm2gui.cpp: Temporarily
	  fix bug for open file filters--don't supply a filter until GTK is
	  fixed.

2000-11-02 14:34  thassine

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

2000-11-01 12:43  thassine

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

2000-10-31 22:37  hutchisn

	* src/common/utility.cpp, src/graphics/mm1gui.cpp: Enter real vdW
	  radii from several sources and update GUI to draw accordingly

2000-10-31 22:34  hutchisn

	* src/target3/t3dialog.cpp: Fixed bug with elements beyond #105.

2000-10-31 17:55  hutchisn

	* configure, configure.in: Another attempt to pick up Xmu and glut
	  appropirately.

2000-10-31 08:17  thassine

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

2000-10-30 16:41  hutchisn

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

2000-10-30 15:10  thassine

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

2000-10-30 13:50  hutchisn

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

2000-10-25 09:06  thassine

	* src/common/conjgrad.cpp, src/common/utility.cpp: added some
	  missing header files

2000-10-25 08:45  thassine

	* CHANGES, src/common/conjgrad.cpp, src/common/utility.cpp,
	  src/target3/t3main.cpp, src/target3/t3mm1gui.cpp,
	  src/target3/t3qm2gui.cpp: better GnomeUIInfo initialization (the
	  RH7-patch from GH)

2000-10-25 07:47  thassine

	* CHANGES, src/graphics/guibase.cpp, src/graphics/mm1gui.cpp: the
	  multiple view management bug fixed (at last)

2000-10-25 00:03  hutchisn

	* src/common/conjgrad.cpp, src/common/utility.cpp,
	  src/target3/t3main.cpp, src/target3/t3mm1gui.cpp,
	  src/target3/t3qm2gui.cpp: Minor changes to allow compilation on
	  RH7.

2000-10-25 00:02  hutchisn

	* bin, bin/.cvsignore, src, src/.cvsignore, src/common,
	  src/common/.cvsignore, src/graphics, src/graphics/.cvsignore,
	  src/target2, src/target2/.cvsignore, src/target3,
	  src/target3/.cvsignore: CVS ignore files to remove common build
	  objects, etc.

2000-10-24 09:28  thassine

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

2000-10-23 14:20  thassine

	* src/new.cpp, src/new.h, src/some-extra-files,
	  src/some-extra-files/newfile.cpp,
	  src/some-extra-files/newfile.h: moved some conflicting files to
	  some-extra-files

2000-10-23 08:59  thassine

	* CHANGES, src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/mm1util.cpp, src/common/mm1util.h,
	  src/graphics/mm1rbn.cpp: improved mm1_chn_info

2000-10-21 10:14  thassine

	* src/common/Makefile, src/common/color.h, src/common/config.h,
	  src/common/guibase.cpp, src/common/guibase.h,
	  src/common/mm1gui.cpp, src/common/mm1gui.h,
	  src/common/mm1rbn.cpp, src/common/mm1rbn.h,
	  src/common/mtools.cpp, src/common/mtools.h,
	  src/common/objects.cpp, src/common/objects.h,
	  src/common/plane.cpp, src/common/plane.h, src/common/qm1gui.cpp,
	  src/common/qm1gui.h, src/common/qm2gui.cpp, src/common/qm2gui.h,
	  src/common/spline.cpp, src/common/spline.h,
	  src/common/surface.cpp, src/common/surface.h,
	  src/common/viewing.cpp, src/common/viewing.h,
	  src/common/window.cpp, src/common/window.h: removed some
	  duplicate files

2000-10-21 10:02  thassine

	* src/common/library: removed library-dir

2000-10-21 09:42  thassine

	* CHANGES, src/Makefile, src/common/Makefile.OLD,
	  src/common/conjgrad.cpp, src/common/conjgrad.h,
	  src/common/define.h, src/common/engbase.cpp,
	  src/common/engbase.h, src/common/mdlbase.cpp,
	  src/common/mdlbase.h, src/common/mm1alg.cpp,
	  src/common/mm1alg.h, src/common/mm1eng.cpp, src/common/mm1eng.h,
	  src/common/mm1eng1.cpp, src/common/mm1eng1.h,
	  src/common/mm1eng9.cpp, src/common/mm1eng9.h,
	  src/common/mm1mdl.cpp, src/common/mm1mdl.h,
	  src/common/mm1tab1.cpp, src/common/mm1tab1.h,
	  src/common/mm1tab9.cpp, src/common/mm1tab9.h,
	  src/common/mm1util.cpp, src/common/mm1util.h,
	  src/common/qm1eng.cpp, src/common/qm1eng.h,
	  src/common/qm1mdl.cpp, src/common/qm1mdl.h,
	  src/common/qm2eng.cpp, src/common/qm2eng.h,
	  src/common/qm2eng1.cpp, src/common/qm2eng1.h,
	  src/common/qm2eng9.cpp, src/common/qm2eng9.h,
	  src/common/qm2mdl.cpp, src/common/qm2mdl.h,
	  src/common/typedef.h, src/common/utility.cpp,
	  src/common/utility.h, src/common/v3d.h, src/graphics,
	  src/graphics/Makefile.OLD, src/graphics/color.h,
	  src/graphics/guibase.cpp, src/graphics/guibase.h,
	  src/graphics/mm1gui.cpp, src/graphics/mm1gui.h,
	  src/graphics/mm1rbn.cpp, src/graphics/mm1rbn.h,
	  src/graphics/mtools.cpp, src/graphics/mtools.h,
	  src/graphics/objects.cpp, src/graphics/objects.h,
	  src/graphics/plane.cpp, src/graphics/plane.h,
	  src/graphics/qm1gui.cpp, src/graphics/qm1gui.h,
	  src/graphics/qm2gui.cpp, src/graphics/qm2gui.h,
	  src/graphics/spline.cpp, src/graphics/spline.h,
	  src/graphics/surface.cpp, src/graphics/surface.h,
	  src/graphics/viewing.cpp, src/graphics/viewing.h,
	  src/graphics/window.cpp, src/graphics/window.h,
	  src/target1/Makefile, src/target1/Makefile.OLD,
	  src/target1/config.h, src/target1/config.h.OLD,
	  src/target2/Makefile, src/target2/Makefile.OLD,
	  src/target2/config.h, src/target2/config.h.OLD,
	  src/target3/Makefile, src/target3/Makefile.OLD,
	  src/target3/config.h, src/target3/config.h.OLD: new source tree
	  with old makefiles

2000-10-21 08:16  thassine

	* CHANGES, src/common/guibase.cpp, src/common/guibase.h,
	  src/common/library/define.h, src/common/library/mdlbase.cpp,
	  src/common/library/mdlbase.h, src/common/viewing.cpp,
	  src/target3/t3dialog.cpp, src/target3/t3dialog.h,
	  src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h,
	  src/target3/t3qm2gui.cpp, src/target3/t3qm2gui.h,
	  src/target3/t3window.cpp: file save dialogs added, selection bug
	  fixed

2000-10-18 14:13  thassine

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

2000-10-16 07:07  thassine

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

2000-09-09 14:49  thassine

	* CHANGES, src/common/config.h, src/common/library/config.h,
	  src/common/library/define.h, src/target1/Makefile: just a few
	  minor changes

2000-09-09 12:17  thassine

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

2000-09-06 09:02  thassine

	* src/Makefile: made some changes in makefiles

2000-09-06 08:38  thassine

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

2000-09-06 08:38  

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