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|
2006-07-31 thassine
* src/project.cpp: seqbuild code changed at libghemical
2006-07-24 thassine
* configure.ac, src/gtk_project_view.cpp, src/project.cpp: adapted
to changes at libghemical side.
2006-07-21 dcurtis3
* src/main.cpp: Moved the #include for ghemicalconfig.h so that it
is before the #define tests. More "proper" than assuming it
gets included by other headers.
* src/gamess_dialog.cpp, src/gamess_dialog.h: Previous update was
ignoring all code because there was no #import of the
ghemicalconfig2.h file so as far as these source files were
concerned there was never any definition.
2006-07-12 thassine
* src/gamess_dialog.cpp, src/gamess_dialog.h: added some missing
ENABLE_GAMESS macros
2006-07-11 dcurtis3
* src/efp_dialog.cpp, src/efp_dialog.h, src/gamess.cpp,
src/gamess.h, src/gamess_dialog.cpp, src/gamess_dialog.h,
src/gtk_project.cpp, src/gtk_project_view.cpp,
src/gtk_project_view.h: EFP Changes to GAMESS Extension!
2006-06-13 dcurtis3
* src/gamess_dialog.cpp:
2006-06-06 dcurtis3
* src/gamess.cpp, src/gamess.h, src/gamess_dialog.cpp,
src/gamess_dialog.h: Added EFP Input Deck Generation!
2006-06-06 thassine
* src/views.cpp: added a fix for 64-bit compilers.
2006-06-05 hutchisn
* examples/TSS, examples/TSS/E2-reaction,
examples/TSS/SN2-reaction,
examples/TSS/carbocation_rearrangement_hydride_shift,
examples/TSS/carbocation_rearrangement_methide_shift,
examples/TSS/cycloaddition_Diels-Alder,
examples/TSS/sigmatropic_rearrangement_Cope,
examples/TSS/tautomeric_shift_keto_enol, src/pixmaps: Added
Makefiles to svn:ignore properties
* examples/TSS, examples/TSS/E2-reaction,
examples/TSS/E2-reaction/Makefile.am,
examples/TSS/E2-reaction/products.gpr,
examples/TSS/E2-reaction/reactants.gpr,
examples/TSS/E2-reaction/ts.gpr, examples/TSS/Makefile.am,
examples/TSS/README, examples/TSS/SN2-reaction,
examples/TSS/SN2-reaction/Makefile.am,
examples/TSS/SN2-reaction/products.gpr,
examples/TSS/SN2-reaction/reactants.gpr,
examples/TSS/SN2-reaction/ts.gpr,
examples/TSS/carbocation_rearrangement_hydride_shift,
examples/TSS/carbocation_rearrangement_hydride_shift/Makefile.am,
examples/TSS/carbocation_rearrangement_hydride_shift/products.gpr,
examples/TSS/carbocation_rearrangement_hydride_shift/reactants.gpr,
examples/TSS/carbocation_rearrangement_hydride_shift/ts.gpr,
examples/TSS/carbocation_rearrangement_methide_shift,
examples/TSS/carbocation_rearrangement_methide_shift/Makefile.am,
examples/TSS/carbocation_rearrangement_methide_shift/products.gpr,
examples/TSS/carbocation_rearrangement_methide_shift/reactants.gpr,
examples/TSS/carbocation_rearrangement_methide_shift/ts.gpr,
examples/TSS/cycloaddition_Diels-Alder,
examples/TSS/cycloaddition_Diels-Alder/Makefile.am,
examples/TSS/cycloaddition_Diels-Alder/products.gpr,
examples/TSS/cycloaddition_Diels-Alder/reactants.gpr,
examples/TSS/cycloaddition_Diels-Alder/ts.gpr,
examples/TSS/sigmatropic_rearrangement_Cope,
examples/TSS/sigmatropic_rearrangement_Cope/Makefile.am,
examples/TSS/sigmatropic_rearrangement_Cope/products.gpr,
examples/TSS/sigmatropic_rearrangement_Cope/reactants.gpr,
examples/TSS/sigmatropic_rearrangement_Cope/ts.gpr,
examples/TSS/tautomeric_shift_keto_enol,
examples/TSS/tautomeric_shift_keto_enol/Makefile.am,
examples/TSS/tautomeric_shift_keto_enol/products.gpr,
examples/TSS/tautomeric_shift_keto_enol/reactants.gpr,
examples/TSS/tautomeric_shift_keto_enol/ts.gpr: Add back missing
example files, accidentally deleted in SVN->CVS migration.
2006-06-01 dcurtis3
* Makefile.am, src/Makefile.am, src/efp_dialog.cpp,
src/efp_dialog.glade, src/efp_dialog.h, src/gamess.cpp,
src/gamess.h, src/gtk_graphics_view.cpp, src/gtk_project.cpp,
src/gtk_project.h, src/gtk_project_view.cpp,
src/gtk_project_view.h, src/main.cpp, src/project.cpp,
src/project.h, src/views.h: Added ability to define GAMESS EFP
information.
TODO: Need to fix the compilation without gamess enabled.
2006-05-27 dcurtis3
* Makefile.am, configure.ac, src/Makefile.am,
src/pixmaps/Makefile.am: Added/Modified logo install
* configure.ac: updated ghemical version 2.02
2006-05-23 dcurtis3
* src/Makefile.am, src/main.cpp, src/pixmaps/ghemical.png: Added
Ghemical Logo
2006-05-04 dcurtis3
* src/gamess_dialog.cpp: *** empty log message ***
2006-04-24 thassine
* configure.ac: version number changed after a release
* ChangeLog, configure.ac: this is v2.00
2006-04-23 dcurtis3
* configure.ac: PKGCONFIG env variable definition was stuck in a
autoconf test for threads. needed moving.
2006-04-11 thassine
* ChangeLog, INSTALL, configure.ac, src/gamess_dialog.glade,
src/gtk_project_view.cpp, src/main.cpp: this is v2.00rc1
2006-04-10 thassine
* Makefile.am, configure.ac, docs, docs/.cvsignore,
docs/Makefile.am, src, src/.cvsignore, src/main.cpp: the user's
manual is installed and viewed using a browser.
* docs/user-docs, docs/user-docs/.cvsignore,
docs/user-docs/Makefile.am, docs/user-docs/index.html,
docs/user-docs/introduction.html, docs/user-docs/mdi_mode.html,
docs/user-docs/perspective.html, docs/user-docs/ribbon.html,
docs/user-docs/setup_dialog.html, docs/user-docs/using_mm.html,
docs/user-docs/visualization.html: updated the user-docs
* docs/user-docs/images, docs/user-docs/images/.cvsignore,
docs/user-docs/images/2atoms_bond.png,
docs/user-docs/images/Makefile.am,
docs/user-docs/images/change_bond_select.png,
docs/user-docs/images/clipping1.png,
docs/user-docs/images/clipping2.png,
docs/user-docs/images/draw_button.png,
docs/user-docs/images/draw_hydrogens.png,
docs/user-docs/images/first_atom.png,
docs/user-docs/images/new_mm.png,
docs/user-docs/images/periodic_button.png,
docs/user-docs/images/periodic_table.png,
docs/user-docs/images/setup1.png,
docs/user-docs/images/setup2.png,
docs/user-docs/images/setup_select.png,
docs/user-docs/images/using_mm_01.png,
docs/user-docs/images/using_mm_02.png,
docs/user-docs/images/using_mm_03.png,
docs/user-docs/images/using_mm_04.png,
docs/user-docs/images/using_mm_05.png,
docs/user-docs/images/using_mm_06.png,
docs/user-docs/images/using_mm_07.png,
docs/user-docs/images/using_mm_08.png,
docs/user-docs/images/using_mm_09.png,
docs/user-docs/images/using_mm_10.png,
docs/user-docs/images/using_mm_11.png: updated the user-docs
2006-04-05 thassine
* src/camera.cpp, src/camera.h: fixed yet another OpenGL
names-related bug.
2006-04-03 thassine
* configure.ac, src/Makefile.am, src/gamess_dialog.cpp,
src/gamess_dialog.glade, src/ghemicalconfig.h.in,
src/gtk_graphics_view.cpp, src/gtk_project.cpp,
src/gtk_project.h, src/main.cpp, src/main.h,
src/pixmaps/addh.xpm, src/pixmaps/constrain.xpm,
src/pixmaps/gamess.xpm, src/pixmaps/geomopt.xpm,
src/pixmaps/import.xpm, src/pixmaps/lock.xpm,
src/pixmaps/none.xpm, src/pixmaps/removeh.xpm,
src/pixmaps/unlock.xpm, src/project.cpp: added optional shortcut
toolbar + other fixes (Donald Curtis).
2006-03-29 thassine
* INSTALL, src/file_export_dialog.cpp, src/fileio.cpp,
src/filetrans.cpp, src/gtk_graphics_view.cpp,
src/gtk_project.cpp, src/main.cpp, src/project.cpp,
src/project.h: minor changes ; a lock patch (DEC).
2006-03-28 hutchisn
* src/gtk_graphics_view.cpp, src/gtk_project.cpp,
src/gtk_project.h, src/project.cpp, src/project.h: Add H->Methyl
builder feature to convert selected hydrogens to methyls
(or methylate the whole molecule).
* src/main.cpp: Make sure to set the project filename when
importing or reading a file from
the commandline.
* src/fileio.cpp: Remove warning for WriteGPR -- Ghemical now
depends on OB-2.0, which can read
these gpr files with no problems.
* src/file_export_dialog.cpp: Add filename to default text for
export.
* src, src/.cvsignore: Add built ghemical file to ignore list
2006-03-28 thassine
* configure.ac, examples/Makefile.am: examples/TSS fix
* examples/transition_state_search2: renamed
transition_state_search -> TSS
* ., .cvsignore: removed some unnecessary files.
* config.guess, config.sub, ltmain.sh: removed some unnecessary
files.
2006-03-27 hutchisn
* src/main.cpp: Set default window size to 830x640 to show all the
toolbar buttons by default
2006-03-27 thassine
* src/constraint_dialog.cpp, src/constraint_dialog.glade,
src/gtk_project_view.cpp, src/gtk_project_view.h, src/main.cpp:
added constraint_dst/project view improvements (by Donald
Curtis).
2006-03-22 thassine
* src/Makefile.am, src/constraint_dialog.cpp,
src/constraint_dialog.glade, src/constraint_dialog.h,
src/gtk_graphics_view.cpp, src/gtk_project.cpp,
src/gtk_project.h, src/gtk_project_view.cpp,
src/gtk_project_view.h, src/project.cpp, src/project.h,
src/views.h: added (distance)constraints ; by Donald Curtis.
2006-03-20 thassine
* src/main.cpp, src/main.h: made the short toolbar labels optional.
2006-03-16 thassine
* INSTALL, configure.ac: documentation updates.
2006-03-16 hutchisn
* src/main.cpp: Adding text labels to identify toolbar icons
2006-03-14 thassine
* src/moldyn_dialog.cpp, src/moldyn_dialog.glade,
src/moldyn_dialog.h: updated the mol.dyn. dialog.
2006-03-10 thassine
* src/project.cpp: added a new orient-command.
2006-03-08 thassine
* ., .cvsignore: cvsignore updated.
* aclocal.m4, autogen.sh: removed acloca.m4 and updated autogen.sh
2006-03-07 thassine
* aclocal.m4, src/gtk_project_view.cpp, src/gtk_project_view.h,
src/setup_dialog.cpp, src/setup_dialog.glade: synchronized with
libghemical.
2006-03-03 thassine
* aclocal.m4, src/gtk_project.cpp, src/gtk_project_view.cpp,
src/gtk_project_view.h, src/project.h: added Donald's frozed
atom improvements.
* ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, configure,
examples, examples/.cvsignore, examples/Makefile.in,
examples/transition_state_search2,
examples/transition_state_search2/.cvsignore,
examples/transition_state_search2/E2-reaction,
examples/transition_state_search2/E2-reaction/.cvsignore,
examples/transition_state_search2/E2-reaction/Makefile.in,
examples/transition_state_search2/Makefile.in,
examples/transition_state_search2/SN2-reaction,
examples/transition_state_search2/SN2-reaction/.cvsignore,
examples/transition_state_search2/SN2-reaction/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/.cvsignore,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_methide_shift,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/.cvsignore,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
examples/transition_state_search2/cycloaddition_Diels-Alder,
examples/transition_state_search2/cycloaddition_Diels-Alder/.cvsignore,
examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
examples/transition_state_search2/sigmatropic_rearrangement_Cope,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/.cvsignore,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
examples/transition_state_search2/tautomeric_shift_keto_enol,
examples/transition_state_search2/tautomeric_shift_keto_enol/.cvsignore,
examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
src, src/.cvsignore, src/Makefile.in, src/moldyn_dialog.cpp,
src/moldyn_dialog.glade, src/project.cpp, src/project.h,
src/trajview_dialog.cpp: many changes in lib side.
2006-03-01 thassine
* Makefile.in, aclocal.m4, src/moldyn_dialog.cpp,
src/moldyn_dialog.glade, src/moldyn_dialog.h, src/project.cpp:
mol.dyn. changes on lib side.
2006-02-27 thassine
* src/camera.cpp, src/glade_dialog.cpp, src/gtk_project.cpp,
src/gtk_project_view.cpp, src/gtk_views.cpp, src/main.cpp,
src/plane.cpp, src/project.cpp, src/surface.cpp, src/views.cpp:
the stringstream code was made safer ; avoid c_str() calls in
which a reference to buffer is stored for re-use.
2006-02-24 thassine
* src/project.cpp: fixed a bug in box solvation.
2006-02-23 thassine
* src/project.cpp, src/trajview_dialog.cpp: trajview dialog bug
temporarily fixed ; something wrong with the PrintToLog() method?
2006-02-21 thassine
* src/fileio.cpp: fileio cleanups.
2006-02-20 thassine
* src/camera.cpp, src/geomopt_dialog.cpp, src/glade_dialog.cpp,
src/gtk_project_view.cpp, src/gtk_views.cpp, src/main.cpp,
src/moldyn_dialog.cpp, src/plane.cpp, src/project.cpp,
src/ribbon.cpp, src/setup_dialog.cpp, src/surface.cpp,
src/trajview_dialog.cpp, src/views.cpp: output-stringstream code
changed.
* Makefile.in, src/glade_dialog.cpp: glade filename fix (initial)
added.
2006-02-17 hutchisn
* src/camera.cpp, src/file_export_dialog.cpp,
src/file_import_dialog.cpp, src/fileio.cpp, src/filetrans.h,
src/gamess_dialog.cpp, src/geomopt_dialog.cpp,
src/glade_dialog.cpp, src/gtk_project.cpp,
src/gtk_project_view.cpp, src/gtk_views.cpp, src/main.cpp,
src/moldyn_dialog.cpp, src/plane.cpp, src/progress_dialog.cpp,
src/project.cpp, src/ribbon.cpp, src/setup_dialog.cpp,
src/surface.cpp, src/trajview_dialog.cpp, src/views.cpp: Update
to change strstream to modern versions to remove compiler
warnings with GCC.
* src/filetrans.cpp: Update to include a molecule title (from the
filename) for Open Babel export.
* src, src/.cvsignore, trunk/bin, trunk/bin/.cvsignore: Update to
remove spurious CVS warnings.
2006-02-16 thassine
* AUTHORS, aclocal.m4, src/Makefile.am, src/Makefile.in,
src/gamess_dialog.cpp, src/gamess_dialog.glade,
src/gamess_dialog.h, src/gtk_graphics_view.cpp,
src/gtk_project.cpp, src/gtk_project.h, src/main.cpp: added the
gamess-interface contributed by Donald Curtis.
* ., .cvsignore, BRANCHNAME, Makefile.in, aclocal.m4,
config.guess, config.sub, configure, configure.ac,
examples/Makefile.in,
examples/transition_state_search2/E2-reaction/Makefile.in,
examples/transition_state_search2/Makefile.in,
examples/transition_state_search2/SN2-reaction/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
ltmain.sh, src/Makefile.in, src/ghemicalconfig.h.in: updated
the build scripts.
2006-02-10 thassine
* Makefile.in, aclocal.m4, configure, configure.ac,
examples/Makefile.in,
examples/transition_state_search2/E2-reaction/Makefile.in,
examples/transition_state_search2/Makefile.in,
examples/transition_state_search2/SN2-reaction/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
src/Makefile.in, src/ghemicalconfig.h.in, src/objects.h: many
changes...
2006-02-07 thassine
* src/fileio.cpp, src/geomopt_dialog.cpp, src/moldyn_dialog.cpp,
src/project.cpp, src/ribbon.cpp, src/setup_dialog.cpp,
src/views.cpp: the data hiding fixes of libghemical added.
2006-01-19 thassine
* src/objects.h: fixed an include file name.
2006-01-05 thassine
* Makefile.am, Makefile.in, NEWS, README, depcomp, src,
src/.cvsignore, src/Makefile.am, src/Makefile.in,
src/gtk_project.h, src/main.cpp: some missing files added ; now
automake based.
* missing, src/Makefile.am, src/file_export_dialog.cpp,
src/file_export_dialog.glade, src/file_export_dialog.h,
src/file_import_dialog.cpp, src/file_import_dialog.glade,
src/file_import_dialog.h, src/geomopt_dialog.cpp,
src/geomopt_dialog.glade, src/geomopt_dialog.h,
src/moldyn_dialog.cpp, src/moldyn_dialog.glade,
src/moldyn_dialog.h, src/progress_dialog.cpp,
src/progress_dialog.glade, src/progress_dialog.h,
src/setup_dialog.cpp, src/setup_dialog.glade,
src/setup_dialog.h, src/trajview_dialog.cpp,
src/trajview_dialog.glade, src/trajview_dialog.h: added the
relocated files.
* aclocal.m4, configure, configure.ac, examples/Makefile.am,
examples/Makefile.in,
examples/transition_state_search2/E2-reaction/Makefile.in,
examples/transition_state_search2/Makefile.in,
examples/transition_state_search2/SN2-reaction/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
src/ghemicalconfig.h.in, src/glade: the src/glade directory is
removed.
2006-01-05
* src/Makefile.am: This commit was manufactured by cvs2svn to
create branch
'VERSION_2_BRANCH'.
2006-01-05 thassine
* examples/transition_state_search2/E2-reaction/products.gpr,
examples/transition_state_search2/E2-reaction/reactants.gpr,
examples/transition_state_search2/E2-reaction/ts.gpr,
examples/transition_state_search2/SN2-reaction,
examples/transition_state_search2/SN2-reaction/.cvsignore,
examples/transition_state_search2/SN2-reaction/Makefile.am,
examples/transition_state_search2/SN2-reaction/Makefile.in,
examples/transition_state_search2/SN2-reaction/products.gpr,
examples/transition_state_search2/SN2-reaction/reactants.gpr,
examples/transition_state_search2/SN2-reaction/ts.gpr,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/.cvsignore,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.am,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/products.gpr,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/reactants.gpr,
examples/transition_state_search2/carbocation_rearrangement_hydride_shift/ts.gpr,
examples/transition_state_search2/carbocation_rearrangement_methide_shift,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/.cvsignore,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.am,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/Makefile.in,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/products.gpr,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/reactants.gpr,
examples/transition_state_search2/carbocation_rearrangement_methide_shift/ts.gpr,
examples/transition_state_search2/cycloaddition_Diels-Alder,
examples/transition_state_search2/cycloaddition_Diels-Alder/.cvsignore,
examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.am,
examples/transition_state_search2/cycloaddition_Diels-Alder/Makefile.in,
examples/transition_state_search2/cycloaddition_Diels-Alder/products.gpr,
examples/transition_state_search2/cycloaddition_Diels-Alder/reactants.gpr,
examples/transition_state_search2/cycloaddition_Diels-Alder/ts.gpr,
examples/transition_state_search2/sigmatropic_rearrangement_Cope,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/.cvsignore,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.am,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/Makefile.in,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/products.gpr,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/reactants.gpr,
examples/transition_state_search2/sigmatropic_rearrangement_Cope/ts.gpr,
examples/transition_state_search2/tautomeric_shift_keto_enol,
examples/transition_state_search2/tautomeric_shift_keto_enol/.cvsignore,
examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.am,
examples/transition_state_search2/tautomeric_shift_keto_enol/Makefile.in,
examples/transition_state_search2/tautomeric_shift_keto_enol/products.gpr,
examples/transition_state_search2/tautomeric_shift_keto_enol/reactants.gpr,
examples/transition_state_search2/tautomeric_shift_keto_enol/ts.gpr:
added the rest of example files.
* examples/transition_state_search2,
examples/transition_state_search2/.cvsignore,
examples/transition_state_search2/E2-reaction,
examples/transition_state_search2/E2-reaction/.cvsignore,
examples/transition_state_search2/E2-reaction/Makefile.am,
examples/transition_state_search2/E2-reaction/Makefile.in,
examples/transition_state_search2/Makefile.am,
examples/transition_state_search2/Makefile.in: added the rest of
example files.
* examples, examples/.cvsignore, examples/2-chlorobutane.gpr,
examples/3-phenylpropanal.gpr, examples/Makefile.am,
examples/Makefile.in, examples/PeriodicTable.gpr,
examples/acetylsalicylic_acid.gpr, examples/alpha-pinene.gpr,
examples/bromobenzene.gpr, examples/camphor.gpr,
examples/cinnamaldehyde.gpr, examples/cis-2-pentene.gpr,
examples/cyclohexane.gpr, examples/dna_AGTC.gpr,
examples/naphtalene.gpr, examples/rna_aguc.gpr: added examples
* docs/user-docs/images/2atoms_bond.png,
docs/user-docs/images/2atoms_unbonded.png,
docs/user-docs/images/aa_builder_ci.png,
docs/user-docs/images/aa_builder_menu.png,
docs/user-docs/images/aa_builder_note.png,
docs/user-docs/images/aa_builder_w_h.png,
docs/user-docs/images/aa_builder_wo_h.png,
docs/user-docs/images/add_hydrogens.png,
docs/user-docs/images/add_hydrogens_select.png,
docs/user-docs/images/change_bond_dialog.png,
docs/user-docs/images/change_bond_select.png,
docs/user-docs/images/ci_plane.png,
docs/user-docs/images/cyclohexane1.png,
docs/user-docs/images/cyclohexane2.png,
docs/user-docs/images/cyclohexane_optimized.png,
docs/user-docs/images/cyclohexane_unoptimized.png,
docs/user-docs/images/draw_button.png,
docs/user-docs/images/draw_hydrogens.png,
docs/user-docs/images/energy_vs_torsion1.png,
docs/user-docs/images/energy_vs_torsion2.png,
docs/user-docs/images/energy_vs_torsion3.png,
docs/user-docs/images/energy_vs_torsion4.png,
docs/user-docs/images/enlevdiag.png,
docs/user-docs/images/esp-plane_mm.png,
docs/user-docs/images/esp-plane_qm.png,
docs/user-docs/images/esp-plane_select.png,
docs/user-docs/images/esp-plane_select_obj.png,
docs/user-docs/images/first_atom.png,
docs/user-docs/images/formula.png,
docs/user-docs/images/formula_select.png,
docs/user-docs/images/geometry_op_dialog.png,
docs/user-docs/images/geometry_optimization_select.png,
docs/user-docs/images/labels_menu.png,
docs/user-docs/images/mainmenu.png,
docs/user-docs/images/maintools.png,
docs/user-docs/images/md_dialog.png,
docs/user-docs/images/modal.png,
docs/user-docs/images/new_mm.png,
docs/user-docs/images/notebook.png,
docs/user-docs/images/optimized_ethane.png,
docs/user-docs/images/periodic_button.png,
docs/user-docs/images/periodic_table.png,
docs/user-docs/images/remove_hydrogens.png,
docs/user-docs/images/ribbon.png,
docs/user-docs/images/sequence_builder.png,
docs/user-docs/images/toplevel.png,
docs/user-docs/images/traj_dialog.png,
docs/user-docs/images/window.png: docs/user-docs/images added.
* docs/user-docs/MD.html, docs/user-docs/MD_viewer.html,
docs/user-docs/aa_table.html, docs/user-docs/add_hydrogens.html,
docs/user-docs/conf_search_tools.html,
docs/user-docs/documentation.css,
docs/user-docs/energy_vs_torsion.html,
docs/user-docs/filetypes.html, docs/user-docs/formula.html,
docs/user-docs/geometry_optimization.html,
docs/user-docs/import_types.html, docs/user-docs/index.html,
docs/user-docs/introduction.html, docs/user-docs/labels.html,
docs/user-docs/mdi_mode.html, docs/user-docs/measure.html,
docs/user-docs/perspective.html, docs/user-docs/references.html,
docs/user-docs/ribbon.html,
docs/user-docs/sequence_builder.html,
docs/user-docs/using_mm.html, docs/user-docs/using_qm.html,
docs/user-docs/using_sf.html, docs/user-docs/visualization.html:
more files added.
* configure.ac: removed the old bin directory, added docs and
examples directories.
2006-01-05
* ., COPYING, Makefile.am, NEWS, README, depcomp, docs, examples,
examples/transition_state_search, missing: This commit was
manufactured by cvs2svn to create branch
'VERSION_2_BRANCH'.
2005-12-09 thassine
* trunk/src/main.cpp: added a missing glutInit() call.
2005-11-29 thassine
* trunk/src/fileio.cpp, trunk/src/gtk_graphics_view.cpp,
trunk/src/gtk_project.cpp, trunk/src/gtk_project.h,
trunk/src/gtk_project_view.cpp, trunk/src/project.cpp,
trunk/src/project.h: some new selection-based features were
added.
2005-11-10 thassine
* trunk/configure, trunk/configure.ac: changed the version number
to 1.92 after a release.
* trunk/aclocal.m4, trunk/configure, trunk/configure.ac: changed
the version numbmer to 1.91 ; released.
2005-11-03 hutchisn
* trunk, trunk/.cvsignore: Updated to make sure all configure /
autoconf temporary files are ignored.
* trunk/src, trunk/src/.cvsignore, trunk/src/filetrans.cpp,
trunk/src/filetrans.h: Changes to use Open Babel 2.0 for import
/ export.
(May have memory leaks -- haven't checked thoroughly yet.)
2005-11-02 thassine
* trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_plot_views.cpp,
trunk/src/gtk_plot_views.h, trunk/src/gtk_project.cpp,
trunk/src/gtk_project.h, trunk/src/gtk_views.cpp,
trunk/src/gtk_views.h, trunk/src/project.cpp,
trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
started adding a secondary structure constraints view.
2005-10-13 thassine
* trunk/src/project.cpp: bugfix : plotting views are closed when a
project is closed. earlier this was forgotten, which easily lead
to program crashes. still not OK yet since the view windows are
not closed ; no way to close them from project view either.
leaves orphaned windows behind now but should not crash anymore.
2005-10-11 thassine
* trunk/src/main.cpp: minor changes in main.cpp ; do not allow the
menubar and toolbar to expand when the main window is resized.
2005-10-08 thassine
* trunk/configure, trunk/configure.ac, trunk/src/camera.cpp,
trunk/src/plane.cpp, trunk/src/plane.h, trunk/src/project.cpp,
trunk/src/project.h, trunk/src/surface.cpp, trunk/src/surface.h:
OpenGL bugfixes on 64-bit platforms
2005-09-28 hutchisn
* trunk/TODO: Added request for polysaccharide builder
2005-09-27 thassine
* trunk/src/objects.h: just some minor changes to adapt for
different compilers.
2005-08-24 thassine
* trunk/src/fileio.cpp, trunk/src/glade/setup_dialog.cpp,
trunk/src/project.cpp: the mm_sf model type was removed from lib.
2005-08-23 thassine
* trunk/aclocal.m4, trunk/configure, trunk/src/gtk_project.h:
small fixes added (should work with gcc-4 now.)
2005-07-14 thassine
* trunk/src/main.cpp, trunk/src/main.h, trunk/src/project.cpp:
added the -f and -i command line options for opening a file and
importing a file.
2005-07-06 thassine
* trunk/aclocal.m4, trunk/configure, trunk/configure.ac,
trunk/src/appconfig.h.in, trunk/src/appdefine.h,
trunk/src/camera.cpp, trunk/src/camera.h, trunk/src/color.h,
trunk/src/filetrans.h, trunk/src/ghemicalconfig.h.in,
trunk/src/glade/file_export_dialog.h,
trunk/src/glade/file_import_dialog.h,
trunk/src/glade/geomopt_dialog.h,
trunk/src/glade/moldyn_dialog.h,
trunk/src/glade/progress_dialog.h,
trunk/src/glade/setup_dialog.h,
trunk/src/glade/trajview_dialog.h, trunk/src/glade_dialog.h,
trunk/src/gtk_dialog.h, trunk/src/gtk_graphics_view.cpp,
trunk/src/gtk_graphics_view.h, trunk/src/gtk_plot_views.cpp,
trunk/src/gtk_plot_views.h, trunk/src/gtk_project.h,
trunk/src/gtk_project_view.h, trunk/src/gtk_views.h,
trunk/src/main.h, trunk/src/mtools.h, trunk/src/objects.cpp,
trunk/src/objects.h, trunk/src/plane.cpp, trunk/src/plane.h,
trunk/src/project.h, trunk/src/ribbon.h, trunk/src/spline.h,
trunk/src/surface.h, trunk/src/views.cpp, trunk/src/views.h:
config headers changed to avoid multiple PACKAGE definitions.
2005-07-05 thassine
* trunk/INSTALL, trunk/aclocal.m4, trunk/configure,
trunk/src/Doxyfile, trunk/src/fileio.cpp, trunk/src/objects.h:
now compiles with g++-3.4
2005-07-01 thassine
* trunk/CHANGES, trunk/ChangeLog, trunk/INSTALL, trunk/aclocal.m4,
trunk/configure, trunk/configure.ac, trunk/src/appdefine.h,
trunk/src/camera.h, trunk/src/color.h, trunk/src/filetrans.h,
trunk/src/glade_dialog.h, trunk/src/gtk_dialog.h,
trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_graphics_view.h,
trunk/src/gtk_plot_views.h, trunk/src/gtk_project.h,
trunk/src/gtk_project_view.h, trunk/src/gtk_views.h,
trunk/src/main.h, trunk/src/mtools.h, trunk/src/objects.h,
trunk/src/plane.h, trunk/src/project.h, trunk/src/ribbon.h,
trunk/src/spline.h, trunk/src/surface.h, trunk/src/views.h:
changes for a release 1.90 ; there remains an unsolved conflict
with OpenBabel since superimpose class is perhaps mixed with a
superimpose() function in OB ; but this needs to be studied
later.
2005-06-30 thassine
* trunk/Makefile.in, trunk/acconfig.h, trunk/acinclude.m4,
trunk/aclocal.m4, trunk/configure, trunk/configure.ac,
trunk/configure.in, trunk/src/Makefile.in,
trunk/src/appconfig.h.in, trunk/src/filetrans.cpp,
trunk/src/filetrans.h, trunk/src/glade/Makefile.in,
trunk/src/glade/file_export_dialog.cpp,
trunk/src/glade/file_import_dialog.cpp,
trunk/src/gtk_graphics_view.cpp, trunk/src/project.cpp,
trunk/src/project.h: a lot of changes in configuration scripts.
2005-06-23 thassine
* trunk/src/glade/setup_dialog.cpp,
trunk/src/glade/setup_dialog.glade, trunk/src/project.cpp,
trunk/src/ribbon.cpp: the lib/app interface has changed somewhat.
2005-06-20 thassine
* trunk/src/glade/geomopt_dialog.glade,
trunk/src/glade/progress_dialog.cpp,
trunk/src/glade/progress_dialog.h, trunk/src/gtk_project.cpp,
trunk/src/gtk_project.h, trunk/src/project.cpp: added progress
dialogs for GO, MD, random search.
2005-06-17 thassine
* trunk/src/gtk_project.cpp, trunk/src/project.cpp,
trunk/src/project.h: bugfix added to GO/MD initialization code.
2005-06-14 thassine
* trunk/src/glade/file_export_dialog.cpp,
trunk/src/glade/file_import_dialog.cpp,
trunk/src/glade/geomopt_dialog.cpp,
trunk/src/glade/moldyn_dialog.cpp,
trunk/src/glade/progress_dialog.cpp,
trunk/src/glade/progress_dialog.glade,
trunk/src/glade/progress_dialog.h,
trunk/src/glade/setup_dialog.cpp,
trunk/src/glade/trajview_dialog.cpp, trunk/src/gtk_dialog.cpp,
trunk/src/gtk_project.cpp, trunk/src/gtk_project.h,
trunk/src/project.cpp, trunk/src/project.h: started converting
GO and MD into multithreaded versions ; added the files that
left out yesterday.
2005-06-13 thassine
* trunk/src/glade/Makefile.in, trunk/src/gtk_project.cpp,
trunk/src/gtk_project.h, trunk/src/project.cpp,
trunk/src/project.h: the Random Search is now completely
multi-threaded.
* trunk/src/Makefile.in, trunk/src/gtk_graphics_view.cpp,
trunk/src/gtk_views.cpp, trunk/src/main.cpp,
trunk/src/project.cpp, trunk/src/project.h: added an initial
framework for multithreading ; switch off from the beginning of
project.h if needed (the ENABLE_THREADS macro).
2005-06-09 thassine
* trunk/src/gtk_project.cpp, trunk/src/gtk_project.h: now the text
buffer scrolling works and is smooth but does not update for
example when lengthy calculations ; add threading?
* trunk/src/gtk_dialog.cpp, trunk/src/gtk_dialog.h,
trunk/src/gtk_project.cpp, trunk/src/gtk_project.h: some missing
files added ; the text widget scrolling problems have now a
partial solution that works in most cases but flickers and is
slow.
* trunk/src/fileio.cpp, trunk/src/glade/file_export_dialog.cpp,
trunk/src/glade/file_export_dialog.glade,
trunk/src/glade/file_export_dialog.h,
trunk/src/glade/file_import_dialog.cpp,
trunk/src/glade/file_import_dialog.glade,
trunk/src/glade/file_import_dialog.h,
trunk/src/glade/geomopt_dialog.cpp,
trunk/src/glade/geomopt_dialog.glade,
trunk/src/glade/moldyn_dialog.cpp,
trunk/src/glade/moldyn_dialog.glade,
trunk/src/glade/moldyn_dialog.h,
trunk/src/glade/setup_dialog.cpp,
trunk/src/glade/setup_dialog.glade,
trunk/src/glade/trajview_dialog.cpp, trunk/src/project.cpp,
trunk/src/project.h: fixed the glade dialogs ; the file i/o
should now work with openbabel-1.100.2
2005-06-08 thassine
* trunk/src/main.cpp, trunk/src/project.cpp, trunk/src/ribbon.cpp,
trunk/src/views.cpp: minor fixes added, now in sync with the lib.
2005-05-24 thassine
* trunk/src/gtk_plot_views.cpp, trunk/src/gtk_plot_views.h,
trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h,
trunk/src/gtk_views.h, trunk/src/project.cpp,
trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
plotting view popup menus should work now ; TSS broken?
2005-05-19 thassine
* trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_project_view.cpp,
trunk/src/gtk_project_view.h: the project view popup menus
should work now.
2005-05-17 thassine
* trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h:
did the project view a bit further.
2005-05-16 thassine
* trunk/src/glade/file_export_dialog.cpp,
trunk/src/glade/file_export_dialog.h,
trunk/src/glade/file_import_dialog.cpp,
trunk/src/glade/file_import_dialog.h,
trunk/src/glade/setup_dialog.cpp,
trunk/src/glade/setup_dialog.h,
trunk/src/glade/trajview_dialog.cpp,
trunk/src/glade/trajview_dialog.h,
trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_graphics_view.h,
trunk/src/gtk_plot_views.cpp, trunk/src/gtk_plot_views.h,
trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h,
trunk/src/gtk_views.cpp, trunk/src/gtk_views.h,
trunk/src/main.cpp, trunk/src/main.h, trunk/src/project.h,
trunk/src/views.h: class name changes done ; gnome -> gtk
* trunk/src/Makefile.in, trunk/src/glade/file_export_dialog.h,
trunk/src/glade/file_import_dialog.h,
trunk/src/glade/setup_dialog.h,
trunk/src/glade/trajview_dialog.h, trunk/src/gnome_dialog.cpp,
trunk/src/gnome_dialog.h, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/gtk_project_view.h,
trunk/src/gtk_views.cpp, trunk/src/gtk_views.h,
trunk/src/main.h: some changes in filenames ; converted gnome ->
gtk
2005-05-13 thassine
* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
trunk/src/gtk_graphics_view.cpp, trunk/src/project.cpp:
continued porting the popup menus in GTK2 ; the graphics view
menu now complete.
2005-05-12 thassine
* trunk/src/glade/setup_dialog.cpp,
trunk/src/glade/setup_dialog.glade: the new setup dialog should
more or less work now.
2005-05-11 thassine
* trunk/src/glade/setup_dialog.cpp,
trunk/src/glade/setup_dialog.glade,
trunk/src/glade/setup_dialog.h: added some improvements to the
setup dialog ; now works initially.
2005-05-06 thassine
* trunk/src/glade/file_import_dialog.cpp,
trunk/src/gnome_project.cpp, trunk/src/project.cpp: now in synch
with the library.
2005-05-03 thassine
* trunk/src/glade/Makefile.in, trunk/src/glade/setup_dialog.cpp,
trunk/src/glade/setup_dialog.glade,
trunk/src/glade/setup_dialog.h, trunk/src/glade/setup_druid.cpp,
trunk/src/glade/setup_druid.glade,
trunk/src/glade/setup_druid.h, trunk/src/gnome_project.cpp,
trunk/src/main.cpp: removed the setup druid (gnome-1 based) and
started adding a setup dialog.
2005-04-28 thassine
* trunk/src/project.cpp: just adapt in slight changes in the lib
side.
2005-04-26 thassine
* trunk/src/gnome_project.cpp, trunk/src/project.cpp: some changes
in libghemical ; sync.
2005-04-22 thassine
* trunk/src/appdefine.h, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/gtk_graphics_view.cpp,
trunk/src/gtk_graphics_view.h, trunk/src/main.cpp,
trunk/src/main.h, trunk/src/project.cpp, trunk/src/project.h:
added new popup menu items ; tweaked the stereo adjustment box ;
bugfixes.
2005-04-21 thassine
* trunk/aclocal.m4, trunk/configure, trunk/configure.in,
trunk/src/Makefile.in, trunk/src/appconfig.h.in,
trunk/src/appdefine.h, trunk/src/gnome_project.cpp,
trunk/src/gtk_views.cpp, trunk/src/main.cpp,
trunk/src/notice.cpp, trunk/src/notice.h: some new stuff added ;
the main menu now works except Help/Help item.
* trunk/aclocal.m4, trunk/configure, trunk/configure.in,
trunk/src/Makefile.in, trunk/src/glade/Makefile.in,
trunk/src/glade/file_export_dialog.cpp,
trunk/src/glade/file_export_dialog.glade,
trunk/src/glade/file_import_dialog.cpp,
trunk/src/glade/file_import_dialog.glade,
trunk/src/glade/geomopt_dialog.cpp,
trunk/src/glade/moldyn_dialog.cpp,
trunk/src/glade/moldyn_dialog.glade,
trunk/src/glade/setup_druid.cpp, trunk/src/glade/setup_druid.h,
trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
trunk/src/gtk_graphics_view.cpp, trunk/src/gtk_graphics_view.h,
trunk/src/gtk_plot_views.cpp, trunk/src/gtk_plot_views.h,
trunk/src/gtk_project_view.cpp, trunk/src/gtk_project_view.h,
trunk/src/gtk_views.cpp, trunk/src/gtk_views.h,
trunk/src/main.cpp, trunk/src/main.h, trunk/src/project.cpp,
trunk/src/project.h, trunk/src/surface.h, trunk/src/views.cpp,
trunk/src/views.h: added the next round of changes ; compiles
and works but the menus are still incomplete.
2005-04-15 thassine
* trunk/src/Makefile.in, trunk/src/appconfig.h.in,
trunk/src/fileio.cpp, trunk/src/gnome_dialog.h,
trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
trunk/src/notice.cpp: started adding the popup menu for
gtk_graphics_view.
* trunk/src/gnome_dialog.cpp, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
trunk/src/pixmaps/bondtype.xpm, trunk/src/pixmaps/measure.xpm,
trunk/src/pixmaps/orb_xy.xpm, trunk/src/pixmaps/orb_z.xpm,
trunk/src/pixmaps/orbit_xy.xpm, trunk/src/pixmaps/orbit_z.xpm,
trunk/src/pixmaps/rot_xy.xpm, trunk/src/pixmaps/rot_z.xpm,
trunk/src/pixmaps/rotate_xy.xpm, trunk/src/pixmaps/rotate_z.xpm,
trunk/src/pixmaps/setup.xpm, trunk/src/pixmaps/trans_xy.xpm,
trunk/src/pixmaps/trans_z.xpm, trunk/src/pixmaps/transl_xy.xpm,
trunk/src/pixmaps/transl_z.xpm: major changes in GUI code ; uses
GtkUIManager now (GTK+-2.4) ; menus still not ready yet.
2005-03-23 thassine
* trunk/src/gnome_dialog.cpp, trunk/src/gnome_dialog.h,
trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
trunk/src/main.cpp, trunk/src/main.h: bad problems because the
popup menus still are generated using gnome-1 code in a gtk2 app
; crashes but started to add fixes ; still not OK.
2005-03-21 thassine
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/src/Makefile.in, trunk/src/appconfig.h.in,
trunk/src/glade_dialog.cpp, trunk/src/gnome_dialog.cpp,
trunk/src/gnome_dialog.h, trunk/src/gnome_project.cpp,
trunk/src/main.cpp, trunk/src/main.h, trunk/src/views.h: added
many improvements ; the GTK2 version is now built by default
(--enable-bonobo changes this) and it's quite usable now...
2005-02-03 thassine
* trunk/src/spline.cpp: minor changes to make it compile in FC3.
2004-12-23 thassine
* trunk/bin/ghemical-ui.xml, trunk/configure, trunk/configure.in,
trunk/src/appconfig.h.in, trunk/src/ghemical-server.cpp,
trunk/src/ghemical-server.h, trunk/src/ghemical.cpp,
trunk/src/ghemical.h, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/main.cpp, trunk/src/main.h,
trunk/src/simple_test/container-ui.xml,
trunk/src/simple_test/container.cpp: continued to implement
separate gtk+/bonobo modes.
* trunk/GNOME_Ghemical.server, trunk/Makefile.in,
trunk/src/Makefile.in, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/simple_test/Makefile,
trunk/src/simple_test/README,
trunk/src/simple_test/container-ui.xml,
trunk/src/simple_test/container.c,
trunk/src/simple_test/container.cpp,
trunk/src/simple_test/container.h: started creating a single
ghemical/ghemical-server executable that uses either gtk+ or
bonobo.
2004-12-21 thassine
* trunk/src/camera.cpp, trunk/src/gnome_project.cpp,
trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
trunk/src/project.cpp, trunk/src/project.h: fixes added for
stereo display modes (especially red/blue mode).
2004-12-10 thassine
* branches/MANY_PROJECTS_BRANCH/aclocal.m4, trunk/configure,
trunk/configure.in, trunk/src/gnome_views.cpp,
trunk/src/mtools.cpp, trunk/src/project.cpp,
trunk/src/project.h: many small fixes added.
2004-09-06 thassine
* trunk/configure, trunk/configure.in: configure.in updated (still
needs similar fixes ; see also Makefiles.
2004-08-30 thassine
* trunk/src/color.h, trunk/src/fileio.cpp,
trunk/src/filetrans.cpp, trunk/src/glade/geomopt_dialog.h,
trunk/src/glade/moldyn_dialog.h,
trunk/src/glade/setup_druid.cpp, trunk/src/gnome_dialog.cpp,
trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
trunk/src/gnome_views.cpp, trunk/src/notice.cpp,
trunk/src/objects.cpp, trunk/src/objects.h,
trunk/src/project.cpp, trunk/src/project.h,
trunk/src/ribbon.cpp, trunk/src/spline.h, trunk/src/views.cpp:
changed the include directory of libghemical.
2004-08-25 thassine
* trunk/src/appdefine.h, trunk/src/project.cpp,
trunk/src/project.h: minor changes in labels etc (not yet same
as in BBB).
2004-05-13 thassine
* trunk/acinclude.m4, trunk/aclocal.m4, trunk/configure,
trunk/configure.in, trunk/src/glade/setup_druid.cpp: libmopac7,
OpenBabel and libghemical now properly detected in configure.in
2004-03-17 thassine
* trunk/Makefile.in: changed VERSION into APPVERSION in Makefile.in
2004-02-18 thassine
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/src/Makefile.in, trunk/src/appconfig.h.in,
trunk/src/glade/Makefile.in: now properly reads settings from
libghemical.pc using pkg-config.
2004-02-17 thassine
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/openbabel, trunk/src/Makefile.in,
trunk/src/glade/Makefile.in, trunk/src/project.cpp: now uses an
external OpenBabel library ; make install should now properly
install both executables and files.
2004-02-11 thassine
* trunk/src/fileio.cpp, trunk/src/project.h: added setlocale()
calls into fileio.cpp ; also added formal charges into the file
format (version string now 111)
* trunk/src/Makefile.in, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/project.cpp: added -lmopac7
into src/Makefile.in (temporarily) and other minor changes.
2003-11-06 thassine
* trunk/src/fileio.cpp: a minor fix in file-IO; still need to save
secondary structures for SF?
2003-10-10 thassine
* trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h: added a new (experimental) menu item.
2003-10-03 thassine
* trunk/src/project.cpp: fixed a drawing tool bug.
2003-09-12 thassine
* trunk/src/gnome_project.cpp, trunk/src/plane.cpp,
trunk/src/plane.h, trunk/src/project.cpp, trunk/src/surface.cpp,
trunk/src/surface.h: improved planes/surfaces ; now adapt better
for charged molecules.
2003-09-10 thassine
* trunk/src/appdefine.h, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/project.cpp: a rendering
bug was fixed, and LABEL_RESIDUE was implemented.
2003-09-01 thassine
* trunk/src/project.cpp: added some bugfixes/comments
2003-08-08 thassine
* trunk/src/fileio.cpp, trunk/src/gnome_project.cpp,
trunk/src/project.cpp, trunk/src/project.h: the Solvate??()
functions have changed.
2003-08-01 thassine
* trunk/src/glade/file_export_dialog.cpp,
trunk/src/glade/file_import_dialog.cpp,
trunk/src/glade/geomopt_dialog.cpp,
trunk/src/glade/moldyn_dialog.cpp: fixed the dialogs by changing
gnome_dialog -> gtk_dialog.
2003-07-30 thassine
* trunk/src/camera.cpp, trunk/src/gnome_dialog.cpp,
trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
trunk/src/project.cpp, trunk/src/project.h: a few more changes
added ; now the bonobo-component seems to work pretty well and
is usable, but the toolbar buttons (mouse tool, element,
bondtype) are still missing.
2003-07-29 thassine
* trunk/src/camera.cpp, trunk/src/camera.h,
trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
trunk/src/objects.cpp, trunk/src/objects.h, trunk/src/plane.cpp,
trunk/src/plane.h, trunk/src/project.cpp, trunk/src/project.h,
trunk/src/ribbon.cpp, trunk/src/ribbon.h, trunk/src/surface.cpp,
trunk/src/surface.h, trunk/src/views.cpp, trunk/src/views.h: the
project_view now works reasonably well ; also popup-menus added
to project_view pages.
2003-07-24 thassine
* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
trunk/src/project.cpp, trunk/src/project.h, trunk/src/views.h:
the popup-menu, text buffer, and the project view seems to work
quite reasonably now ; in project view only atoms and bonds
pages are ok, others still have many problems.
2003-07-15 thassine
* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
trunk/src/project.cpp, trunk/src/project.h, trunk/src/views.cpp,
trunk/src/views.h: the message log now works (more or less) and
project_view work started.
2003-07-14 thassine
* trunk/src/glade/file_export_dialog.glade,
trunk/src/glade/file_import_dialog.glade,
trunk/src/glade/geomopt_dialog.glade,
trunk/src/glade/moldyn_dialog.glade,
trunk/src/glade/setup_druid.glade,
trunk/src/glade/trajview_dialog.glade,
trunk/src/gnome_dialog.cpp, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h: the .glade files are updated for
libglade-2 (using libglade-convert) glade-dialogs are displayed
correctly but handlers still not updated ; the gnome-dialogs
should work also now ; added (temporary) CURRENT submenu into
ppoup-menu for accesssing mouse tool and other settings.
2003-07-12 thassine
* trunk/GNOME_Ghemical.server: added the .server file
(bonobo-activation).
2003-07-11 thassine
* trunk/bin/ghemical-ui.xml, trunk/configure, trunk/configure.in,
trunk/src/Makefile.in, trunk/src/fileio.cpp,
trunk/src/filetrans.cpp, trunk/src/filetrans.h,
trunk/src/ghemical-server.cpp, trunk/src/ghemical-server.h,
trunk/src/ghemical.cpp, trunk/src/ghemical.h,
trunk/src/glade/Makefile.in, trunk/src/glade/geomopt_dialog.cpp,
trunk/src/glade/moldyn_dialog.cpp,
trunk/src/glade/setup_druid.cpp, trunk/src/glade_dialog.cpp,
trunk/src/gnome_dialog.cpp, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
trunk/src/notice.cpp, trunk/src/notice.h, trunk/src/plane.h,
trunk/src/project.cpp, trunk/src/project.h,
trunk/src/ribbon.cpp, trunk/src/ribbon.h, trunk/src/simple_test,
trunk/src/simple_test/Makefile,
trunk/src/simple_test/container-ui.xml,
trunk/src/simple_test/container.c, trunk/src/surface.h,
trunk/src/views.cpp, trunk/src/views.h: started porting to
gnome2 and converting into bonobo.
2003-06-13 thassine
* trunk/AUTHORS, trunk/acconfig.h, trunk/src/Doxyfile,
trunk/src/camera.cpp, trunk/src/gnome_project.cpp,
trunk/src/project.cpp: more checks added for atom_list sorting.
also misc cleanups.
2003-06-12 thassine
* trunk/bin/examples/transition_state_search,
trunk/bin/examples/transition_state_search/E2-reaction,
trunk/bin/examples/transition_state_search/E2-reaction/products.gpr,
trunk/bin/examples/transition_state_search/E2-reaction/reactants.gpr,
trunk/bin/examples/transition_state_search/E2-reaction/ts.gpr,
trunk/bin/examples/transition_state_search/SN2-reaction,
trunk/bin/examples/transition_state_search/SN2-reaction/products.gpr,
trunk/bin/examples/transition_state_search/SN2-reaction/reactants.gpr,
trunk/bin/examples/transition_state_search/SN2-reaction/ts.gpr,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift/products.gpr,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift/reactants.gpr,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_hydride_shift/ts.gpr,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift/products.gpr,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift/reactants.gpr,
trunk/bin/examples/transition_state_search/carbocation_rearrangement_methide_shift/ts.gpr,
trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder,
trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder/products.gpr,
trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder/reactants.gpr,
trunk/bin/examples/transition_state_search/cycloaddition_Diels-Alder/ts.gpr,
trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope,
trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope/products.gpr,
trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope/reactants.gpr,
trunk/bin/examples/transition_state_search/sigmatropic_rearrangement_Cope/ts.gpr,
trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol,
trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol/products.gpr,
trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol/reactants.gpr,
trunk/bin/examples/transition_state_search/tautomeric_shift_keto_enol/ts.gpr,
trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
trunk/src/project.cpp, trunk/src/views.cpp, trunk/src/views.h:
added imrovements to transition_state_search + other search
tools, and added examples for TSS.
2003-06-11 thassine
* trunk/src/glade/setup_druid.cpp, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h, trunk/src/project.cpp,
trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
added transition_state_search and stationary_state_search ;
user-docs and examples will follow in a few days.
2003-05-19 thassine
* trunk/src/project.cpp: some debugging-label options added.
2003-05-13 thassine
* trunk/src/gnome_project.cpp: removed some redundant
DefineSecondaryStructure() runs.
2003-05-12 thassine
* trunk/src/project.cpp, trunk/src/ribbon.cpp, trunk/src/ribbon.h:
minor changes in ribbon object.
2003-04-29 thassine
* trunk/src/gnome_project.cpp, trunk/src/project.cpp,
trunk/src/project.h, trunk/src/ribbon.cpp: many changes in lib,
adaptaptations to those added.
2003-04-17 thassine
* trunk/src/gnome_project.cpp: added better defaults for glade
dialogs.
2003-04-16 thassine
* trunk/src/glade/moldyn_dialog.cpp,
trunk/src/glade/moldyn_dialog.glade,
trunk/src/glade/moldyn_dialog.h,
trunk/src/glade/setup_druid.cpp,
trunk/src/glade/setup_druid.glade, trunk/src/gnome_project.cpp,
trunk/src/gnome_views.cpp, trunk/src/gnome_views.h,
trunk/src/project.cpp: many small changes (including trajectory
reading).
2003-04-10 thassine
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/src/appconfig.h.in, trunk/src/appdefine.h,
trunk/src/gnome_project.cpp, trunk/src/gnome_project.h,
trunk/src/project.cpp: changes in configure script (now tested
to work with --enable-mpqc).
2003-04-02 thassine
* trunk/src/ribbon.cpp: changes in ribbon due to changes in atom
class.
2003-03-07 thassine
* trunk/src/fileio.cpp: a minor addition to fileio.cpp
* trunk/src/fileio.cpp: the functions in fileio.cpp now handle
data using member functions, not direclty (so that they now are
more portable).
2003-03-05 thassine
* trunk/src/gnome_project.cpp, trunk/src/main.cpp: added some
changes related to gcc-3.2
2003-02-14 thassine
* trunk/src/fileio.cpp: just cleanups, no real changes.
* trunk/src/project.cpp: sf virtual bonds now rendered also using
wireframes.
2003-02-06 thassine
* trunk/src/gnome_project.cpp, trunk/src/main.cpp,
trunk/src/notice.cpp, trunk/src/project.cpp: many changes; for
example added tool for adding solvent (not ready yet).
2003-02-03 thassine
* trunk/src/gnome_project.cpp, trunk/src/gnome_project.h: added
tools for solvation (using H2O).
2003-01-31 thassine
* trunk/src/filetrans.cpp, trunk/src/project.cpp,
trunk/src/project.h: some bugfixes were added; mostly because of
changes in model::GetAtomCount() and engine::GetAtomCount().
2003-01-30 thassine
* trunk/src/Makefile.in, trunk/src/fileio.cpp,
trunk/src/glade/Makefile.in, trunk/src/gnome_project.cpp,
trunk/src/project.cpp, trunk/src/project.h: changes in SF-stuff
rendering and file operations.
2003-01-27 thassine
* trunk/src/fileio.cpp, trunk/src/glade/setup_druid.cpp,
trunk/src/project.cpp, trunk/src/project.h,
trunk/src/ribbon.cpp: some additions to graphics code (how the
new flags work).
2003-01-23 thassine
* trunk/src/camera.cpp, trunk/src/camera.h,
trunk/src/gnome_project.cpp, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
trunk/src/mtools.cpp, trunk/src/mtools.h,
trunk/src/pixmaps/clipping.xpm, trunk/src/project.cpp,
trunk/src/project.h, trunk/src/views.cpp, trunk/src/views.h:
added a new clipping mtool, the selections by atm/res/chn/mol is
added, and a new tool delete selected atoms is added.
2003-01-22 thassine
* trunk/Makefile.in: make install also works now.
* trunk/src, trunk/src/.cvsignore: minor cleanups added.
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/src/Makefile.in, trunk/src/appconfig.h.in,
trunk/src/appdefine.h, trunk/src/camera.cpp, trunk/src/camera.h,
trunk/src/color.h, trunk/src/config.h.in, trunk/src/fileio.cpp,
trunk/src/filetrans.cpp, trunk/src/filetrans.h, trunk/src/glade,
trunk/src/glade/.cvsignore, trunk/src/glade/Makefile.in,
trunk/src/glade/README, trunk/src/glade/file_export_dialog.cpp,
trunk/src/glade/file_export_dialog.glade,
trunk/src/glade/file_export_dialog.h,
trunk/src/glade/file_import_dialog.cpp,
trunk/src/glade/file_import_dialog.glade,
trunk/src/glade/file_import_dialog.h,
trunk/src/glade/geomopt_dialog.cpp,
trunk/src/glade/geomopt_dialog.glade,
trunk/src/glade/geomopt_dialog.h,
trunk/src/glade/moldyn_dialog.cpp,
trunk/src/glade/moldyn_dialog.glade,
trunk/src/glade/moldyn_dialog.h,
trunk/src/glade/setup_druid.cpp,
trunk/src/glade/setup_druid.glade,
trunk/src/glade/setup_druid.h,
trunk/src/glade/trajview_dialog.cpp,
trunk/src/glade/trajview_dialog.glade,
trunk/src/glade/trajview_dialog.h, trunk/src/glade_dialog.cpp,
trunk/src/glade_dialog.h, trunk/src/gnome_dialog.cpp,
trunk/src/gnome_dialog.h, trunk/src/gnome_project.cpp,
trunk/src/gnome_project.h, trunk/src/gnome_views.cpp,
trunk/src/gnome_views.h, trunk/src/main.cpp, trunk/src/main.h,
trunk/src/mtools.cpp, trunk/src/mtools.h, trunk/src/notice.cpp,
trunk/src/notice.h, trunk/src/objects.cpp, trunk/src/objects.h,
trunk/src/pixmaps, trunk/src/pixmaps/.cvsignore,
trunk/src/pixmaps/angle.xpm, trunk/src/pixmaps/bond.xpm,
trunk/src/pixmaps/chain.xpm, trunk/src/pixmaps/dihedral.xpm,
trunk/src/pixmaps/distance.xpm, trunk/src/pixmaps/draw.xpm,
trunk/src/pixmaps/element.xpm, trunk/src/pixmaps/erase.xpm,
trunk/src/pixmaps/invert.xpm, trunk/src/pixmaps/molecule.xpm,
trunk/src/pixmaps/orb_xy.xpm, trunk/src/pixmaps/orb_z.xpm,
trunk/src/pixmaps/residue.xpm, trunk/src/pixmaps/rot_xy.xpm,
trunk/src/pixmaps/rot_z.xpm, trunk/src/pixmaps/select.xpm,
trunk/src/pixmaps/trans_xy.xpm, trunk/src/pixmaps/trans_z.xpm,
trunk/src/pixmaps/zoom.xpm, trunk/src/plane.cpp,
trunk/src/plane.h, trunk/src/project.cpp, trunk/src/project.h,
trunk/src/ribbon.cpp, trunk/src/ribbon.h, trunk/src/spline.cpp,
trunk/src/spline.h, trunk/src/surface.cpp, trunk/src/surface.h,
trunk/src/views.cpp, trunk/src/views.h: added the missing files;
some changes have happened in the filenames.
2003-01-21 thassine
* trunk/bin/parameters: removed bin/prameters since it is now
contained in libghemical.
2003-01-20 thassine
* trunk/configure, trunk/configure.in: many changes all over the
tree; does not compile yet...
* trunk/src/graphics, trunk/src/target3: moved the contents of
src/graphics and src/target3 to src/.
* trunk/src/target3/pixmaps: moved the src/target3/pixmaps to
src/pixmaps.
* trunk/Makefile.in, trunk/src/target3/glade: moved the
/src/target3/glade to /src/glade.
* trunk/src/common: removed the common-directory (now in
libghemical).
* trunk/BUGLIST, trunk/Makefile.in, trunk/PROJECT,
trunk/configure.in, trunk/miniMOPAC, trunk/src/Makefile.OLD,
trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
trunk/src/some-extra-files, trunk/src/target1,
trunk/src/target2, trunk/src/target3/Makefile.in,
trunk/src/target3/glade/Makefile.in: some directories removed;
this stuff is either moved into the new libghemical library, or
(target1/target2) is discarded.
2003-01-15 thassine
* trunk/src/common/matrix.h: added matrix.h back (from v1.0 source
tree).
2003-01-03 thassine
* trunk/src/common/utility.cpp, trunk/src/common/utility.h:
superimpose is no longer a virtual class; only one class needed
since there's only one model class.
2003-01-02 thassine
* trunk/src/common/moldyn.h: minor improvements to MD.
2002-12-12 thassine
* trunk/src/common/model.cpp: some extra checks were added (for
simplified force field, does not affect all-atom stuff).
2002-12-11 thassine
* trunk/src/common/model.cpp, trunk/src/common/seqbuild.cpp:
bugfix; adding ribbons re-ordered the atoms (via
seqbuild::Identify()) but this is now fixed.
2002-12-09 thassine
* trunk/src/common/eng1_qm_mopac.cpp,
trunk/src/common/eng1_qm_mpqc.cpp,
trunk/src/target3/glade/Makefile.in: added a bugfix (now builds
with --enable-mpqc) and added some comments about MPQC/MOPAC
output.
2002-12-05 thassine
* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
changed the version number to 1.51
2002-12-04 thassine
* trunk/CHANGES: updated the changelog
* trunk/INSTALL, trunk/bin/user-docs/images/aa_builder_ci.png,
trunk/bin/user-docs/images/aa_builder_menu.png,
trunk/bin/user-docs/images/aa_builder_note.png,
trunk/bin/user-docs/images/aa_builder_w_h.png,
trunk/bin/user-docs/images/aa_builder_wo_h.png,
trunk/bin/user-docs/images/ci_plane.png,
trunk/bin/user-docs/images/ribbon.png,
trunk/bin/user-docs/ribbon.html, trunk/ghemical.spec: final
fixes before release as v1.50
2002-12-03 thassine
* trunk/Makefile.in: minor fixes to make install.
* trunk/bin/user-docs/geometry_optimization.html,
trunk/bin/user-docs/images/geometry_opimization_console.png,
trunk/bin/user-docs/images/sequence_builder_console.png,
trunk/bin/user-docs/index.html,
trunk/bin/user-docs/introduction.html,
trunk/bin/user-docs/measure.html,
trunk/bin/user-docs/references.html,
trunk/bin/user-docs/sequence_builder.html,
trunk/bin/user-docs/using_mm.html,
trunk/bin/user-docs/using_qm.html,
trunk/bin/user-docs/using_sf.html,
trunk/bin/user-docs/visualization.html: added the improved docs
from Christopher also here.
2002-11-22 thassine
* trunk, trunk/.cvsignore, trunk/miniMOPAC,
trunk/miniMOPAC/.cvsignore, trunk/openbabel,
trunk/openbabel/.cvsignore, trunk/openbabel/aromatic.h,
trunk/openbabel/aromatic.txt, trunk/openbabel/extable.h,
trunk/openbabel/extable.txt, trunk/src/common/model.cpp,
trunk/src/target3/glade, trunk/src/target3/glade/.cvsignore:
synchronized openbabel with the v1.0 tree, and added a notice
about incompleteness of the file format.
2002-11-20 thassine
* trunk/bin/examples, trunk/bin/examples/2-chlorobutane.gpr,
trunk/bin/examples/3-phenylpropanal.gpr,
trunk/bin/examples/PeriodicTable.gpr,
trunk/bin/examples/acetylsalicylic_acid.gpr,
trunk/bin/examples/alpha-pinene.gpr,
trunk/bin/examples/bromobenzene.gpr,
trunk/bin/examples/camphor.gpr,
trunk/bin/examples/cinnamaldehyde.gpr,
trunk/bin/examples/cis-2-pentene.gpr,
trunk/bin/examples/cyclohexane.gpr,
trunk/bin/examples/naphtalene.gpr: added also the new example
files.
* trunk/bin/examples, trunk/openbabel/extable.h,
trunk/openbabel/extable.txt, trunk/openbabel/ghemical.cpp,
trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/common/oldfiles.cpp,
trunk/src/common/tab_mm_prmfit.cpp,
trunk/src/graphics/project.cpp,
trunk/src/target1/t1m_param_mm_cpp.h,
trunk/src/target1/t1main.cpp, trunk/src/target3/t3dialog.cpp,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3project.cpp,
trunk/src/target3/t3project.h: the file format detection is now
fixed; now can read the current (.gpr) and old (.mm1gp) v1.0
files.
* trunk/Makefile.in: make install now installs the docs correctly.
2002-11-14 thassine
* trunk/bin/user-docs/MD.html, trunk/bin/user-docs/MD_viewer.html,
trunk/bin/user-docs/aa_table.html,
trunk/bin/user-docs/add_hydrogens.html,
trunk/bin/user-docs/basic_mm.html,
trunk/bin/user-docs/conf_search_tools.html,
trunk/bin/user-docs/energy_vs_torsion.html,
trunk/bin/user-docs/enlevdiag.jpg,
trunk/bin/user-docs/filetypes.html,
trunk/bin/user-docs/formula.html,
trunk/bin/user-docs/geometry_optimization.html,
trunk/bin/user-docs/images/energy_vs_torsion1.png,
trunk/bin/user-docs/images/energy_vs_torsion2.png,
trunk/bin/user-docs/images/energy_vs_torsion3.png,
trunk/bin/user-docs/images/energy_vs_torsion4.png,
trunk/bin/user-docs/images/enlevdiag.png,
trunk/bin/user-docs/images/esp-plane_mm.png,
trunk/bin/user-docs/images/esp-plane_qm.png,
trunk/bin/user-docs/images/esp-plane_select.png,
trunk/bin/user-docs/images/esp-plane_select_obj.png,
trunk/bin/user-docs/index.html, trunk/bin/user-docs/labels.html,
trunk/bin/user-docs/mdi_mode.html,
trunk/bin/user-docs/measure.html,
trunk/bin/user-docs/perspective.html,
trunk/bin/user-docs/references.html,
trunk/bin/user-docs/sequence_builder.html,
trunk/bin/user-docs/using_cs_tools.html,
trunk/bin/user-docs/using_cs_tools01.jpg,
trunk/bin/user-docs/using_cs_tools02.jpg,
trunk/bin/user-docs/using_cs_tools03.jpg,
trunk/bin/user-docs/using_cs_tools04.jpg,
trunk/bin/user-docs/using_cs_tools05.jpg,
trunk/bin/user-docs/using_mm.html,
trunk/bin/user-docs/using_qm.html,
trunk/bin/user-docs/using_sf.html,
trunk/bin/user-docs/visualization.html: updated the
documentation.
* trunk/bin/user-docs/basic_mm.html,
trunk/bin/user-docs/images/mainmenu.png,
trunk/bin/user-docs/images/maintools.png,
trunk/bin/user-docs/index.html,
trunk/bin/user-docs/introduction.html,
trunk/bin/user-docs/maintools.jpg: the chapter 1. introduction
seems to be ok now.
* trunk/bin/user-docs/index.html: oops! fixed the absolute links
from index.html
2002-11-13 thassine
* trunk/bin/parameters/param_mm/default/parameters1.txt,
trunk/bin/parameters/param_mm/default/parameters2.txt,
trunk/configure, trunk/configure.in, trunk/src/common/define.h:
added some halogen MM parameters, and changed the version number.
2002-11-11 thassine
* trunk/src/Doxyfile, trunk/src/graphics/views.cpp: changed
doxygen settings, and added some fixes for gcc-3.2
* trunk/openbabel/Makefile.in, trunk/openbabel/Vector.cpp,
trunk/openbabel/Vector.h, trunk/openbabel/alchemy.cpp,
trunk/openbabel/aromatic.h, trunk/openbabel/atom.cpp,
trunk/openbabel/atomtyp.h, trunk/openbabel/atomtyp.txt,
trunk/openbabel/balst.cpp, trunk/openbabel/base.h,
trunk/openbabel/bin2hex.pl, trunk/openbabel/binary.h,
trunk/openbabel/binary_io.h, trunk/openbabel/bitgrid.h,
trunk/openbabel/bitvec.h, trunk/openbabel/bond.txt,
trunk/openbabel/c3d.cpp, trunk/openbabel/cacao.cpp,
trunk/openbabel/chains.cpp, trunk/openbabel/chains.h,
trunk/openbabel/chiral.h, trunk/openbabel/commandline.h,
trunk/openbabel/ctransform.h, trunk/openbabel/cwrap.cpp,
trunk/openbabel/cwrap.h, trunk/openbabel/data.cpp,
trunk/openbabel/data.h, trunk/openbabel/element.h,
trunk/openbabel/element.txt, trunk/openbabel/extable.h,
trunk/openbabel/extable.txt, trunk/openbabel/fileformat.cpp,
trunk/openbabel/fileformat.h, trunk/openbabel/generic.cpp,
trunk/openbabel/generic.h, trunk/openbabel/grid.h,
trunk/openbabel/main.cpp, trunk/openbabel/matrix.h,
trunk/openbabel/mol.cpp, trunk/openbabel/mol.h,
trunk/openbabel/mol2.cpp, trunk/openbabel/molchrg.h,
trunk/openbabel/molvector.cpp, trunk/openbabel/molvector.h,
trunk/openbabel/obifstream.h, trunk/openbabel/obutil.cpp,
trunk/openbabel/obutil.h, trunk/openbabel/parsmart.cpp,
trunk/openbabel/parsmart.h, trunk/openbabel/patty.h,
trunk/openbabel/pdb.cpp, trunk/openbabel/phmodel.cpp,
trunk/openbabel/phmodel.h, trunk/openbabel/phmodeldata.h,
trunk/openbabel/resdata.h, trunk/openbabel/ring.h,
trunk/openbabel/rotor.h, trunk/openbabel/smarts.cpp,
trunk/openbabel/smarts.h, trunk/openbabel/smi.h,
trunk/openbabel/typer.cpp, trunk/openbabel/typer.h,
trunk/openbabel/types.h, trunk/openbabel/types.txt: the
openbabel tree is now in sync with v1.00
2002-11-06 thassine
* trunk/bin/user-docs/MD.html, trunk/bin/user-docs/MD_viewer.html,
trunk/bin/user-docs/aa_table.html,
trunk/bin/user-docs/add_hydrogens.html,
trunk/bin/user-docs/basic_mm.html,
trunk/bin/user-docs/documentation.css,
trunk/bin/user-docs/filetypes.html,
trunk/bin/user-docs/formula.html,
trunk/bin/user-docs/geometry_optimization.html,
trunk/bin/user-docs/images,
trunk/bin/user-docs/images/2atoms_bond.png,
trunk/bin/user-docs/images/2atoms_unbonded.png,
trunk/bin/user-docs/images/add_hydrogens.png,
trunk/bin/user-docs/images/add_hydrogens_select.png,
trunk/bin/user-docs/images/change_bond_dialog.png,
trunk/bin/user-docs/images/change_bond_select.png,
trunk/bin/user-docs/images/cyclohexane1.png,
trunk/bin/user-docs/images/cyclohexane2.png,
trunk/bin/user-docs/images/cyclohexane_optimized.png,
trunk/bin/user-docs/images/cyclohexane_unoptimized.png,
trunk/bin/user-docs/images/draw_button.png,
trunk/bin/user-docs/images/draw_hydrogens.png,
trunk/bin/user-docs/images/first_atom.png,
trunk/bin/user-docs/images/formula.png,
trunk/bin/user-docs/images/formula_select.png,
trunk/bin/user-docs/images/geometry_op_dialog.png,
trunk/bin/user-docs/images/geometry_opimization_console.png,
trunk/bin/user-docs/images/geometry_optimization_select.png,
trunk/bin/user-docs/images/labels_menu.png,
trunk/bin/user-docs/images/md_dialog.png,
trunk/bin/user-docs/images/modal.png,
trunk/bin/user-docs/images/new_mm.png,
trunk/bin/user-docs/images/notebook.png,
trunk/bin/user-docs/images/optimized_ethane.png,
trunk/bin/user-docs/images/periodic_button.png,
trunk/bin/user-docs/images/periodic_table.png,
trunk/bin/user-docs/images/remove_hydrogens.png,
trunk/bin/user-docs/images/sequence_builder.png,
trunk/bin/user-docs/images/sequence_builder_console.png,
trunk/bin/user-docs/images/toplevel.png,
trunk/bin/user-docs/images/traj_dialog.png,
trunk/bin/user-docs/images/window.png,
trunk/bin/user-docs/import_types.html,
trunk/bin/user-docs/index.html,
trunk/bin/user-docs/introduction.html,
trunk/bin/user-docs/labels.html,
trunk/bin/user-docs/mdi_mode.html,
trunk/bin/user-docs/measure.html,
trunk/bin/user-docs/perspective.html,
trunk/bin/user-docs/references.html,
trunk/bin/user-docs/sequence_builder.html: added the
Christopher's new docs.
2002-11-05 thassine
* trunk/AUTHORS, trunk/src/target2/Makefile.OLD,
trunk/src/target3/Makefile.OLD, trunk/src/target3/t3main.cpp:
added some new libs (reported that a modified RedHat7.3 needed
these; should be added to configure system as well) : -lXt -lSM
-lICE
2002-10-31 thassine
* trunk/src/graphics/project.cpp, trunk/src/graphics/surface.cpp,
trunk/src/graphics/surface.h, trunk/src/target2/t2project.cpp:
various small fixes added to plane/surface/etc objects.
* branches/MANY_PROJECTS_BRANCH/src/common/engine.h,
branches/MANY_PROJECTS_BRANCH/src/common/mm2eng.h,
branches/MANY_PROJECTS_BRANCH/src/common/mm2mdl.h,
branches/MANY_PROJECTS_BRANCH/src/common/mm2util.h,
branches/MANY_PROJECTS_BRANCH/src/graphics/mm2docv.cpp,
branches/MANY_PROJECTS_BRANCH/src/target1/t1m_mm2param_h.h,
branches/MANY_PROJECTS_BRANCH/src/target2/t2main.cpp,
branches/MANY_PROJECTS_BRANCH/src/target3/t3main.cpp,
trunk/bin/user-docs/index.html, trunk/src/common/eng1_sf.h,
trunk/src/target1/t1m_param_sf_h.h: just terminology changes:
reduced now changed to simplified in strings.
2002-10-29 thassine
* trunk/src/common/model.cpp: a bugfix added that makes model.cpp
compile with the configure script.
2002-10-28 thassine
* trunk/src/common/model.cpp,
trunk/src/target3/glade/trajview_dialog.cpp,
trunk/src/target3/t3dialog.cpp: moldyn now also uses logbox.
* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_qm.cpp,
trunk/src/common/eng1_sf.cpp, trunk/src/graphics/project.cpp:
bugfixes added.
2002-10-25 thassine
* trunk/src/target3/t3project.cpp: optimized the default settings
for planes/surfaces etc.
2002-10-24 thassine
* trunk/src/graphics/project.cpp, trunk/src/target3/t3project.cpp,
trunk/src/target3/t3project.h: seq-builder now has a command
string.
* trunk/src/graphics/project.cpp, trunk/src/graphics/project.h,
trunk/src/graphics/views.cpp, trunk/src/target3/t3project.cpp:
the 1d and 2d plots now have command strings.
2002-10-23 thassine
* trunk/src/common/model.cpp, trunk/src/graphics/project.cpp,
trunk/src/graphics/project.h, trunk/src/target3/t3project.cpp,
trunk/src/target3/t3project.h, trunk/src/target3/t3views.cpp:
qm-related planes/surfaces added, enlev-diagram addded.
2002-10-22 thassine
* trunk/src/graphics/project.cpp, trunk/src/target3/t3project.cpp:
plane/volrend/surface command strings added.
2002-10-21 thassine
* trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/common/search.cpp, trunk/src/graphics/project.cpp,
trunk/src/target2/t2project.cpp,
trunk/src/target3/t3project.cpp: added the
random/systematic/montecarlo conformational search commands.
* trunk/src/graphics/project.cpp, trunk/src/target3/t3project.cpp,
trunk/src/target3/t3views.cpp: the add light-operation is a bit
improved.
2002-10-17 thassine
* trunk/src/graphics/project.cpp, trunk/src/graphics/project.h,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h,
trunk/src/target3/t3views.cpp: the command interpreter added;
now initially only commands help and add light works.
2002-10-16 thassine
* trunk/src/common/eng1_mm_default.cpp,
trunk/src/common/eng1_mm_prmfit.cpp,
trunk/src/common/tab_mm_default.cpp,
trunk/src/common/tab_mm_prmfit.cpp,
trunk/src/target3/glade/setup_druid.cpp,
trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
setup changes and possible mol.mech. error messages are now
displayed in the new logbox.
2002-10-15 thassine
* trunk/src/common/model.cpp, trunk/src/target3/t3project.cpp:
moved output from console to output box; CalcEnergy and GeomOpt.
2002-10-14 thassine
* trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h,
trunk/src/target3/t3views.cpp: a text log box was added to the
GUI. works now for CalcEnergy and GeomOpt operations.
2002-10-05 thassine
* trunk/src/common/model.cpp, trunk/src/target3/t3dialog.cpp:
after the aa2sf conversion, the setup is automatically set
suitable for doing calculations with the simplified model.
2002-10-04 thassine
* trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp: the
values of model::sf_types array are now the same as those in the
atom::sf_atmtp records.
* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/typedef.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/plane.h, trunk/src/graphics/project.cpp,
trunk/src/graphics/project.h, trunk/src/graphics/ribbon.cpp,
trunk/src/graphics/ribbon.h, trunk/src/graphics/spline.cpp,
trunk/src/graphics/spline.h: the use of typedef- or
template-based arrays (see typedef.h) seems to be a continuous
source of memory-handling bugs. therefore removed all such
constructs and banned their future use as well (removed from
typedef.h).
* trunk/src/common/model.cpp: more fixes to aa2sf conversion
(temporary coordinate handling).
* trunk/src/common/model.cpp, trunk/src/common/model.h: a
potential bug related to aa2sf conversion is fixed.
2002-10-03 thassine
* trunk/src/common/model.cpp, trunk/src/common/utility.cpp: a few
changes here and there...
* trunk/src/common/oldfiles.cpp: the oldfiles.cpp file was added.
* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/eng2_mm_sf.cpp, trunk/src/common/eng2_mm_sf.h,
trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
trunk/src/common/engine.h, trunk/src/common/model.cpp,
trunk/src/common/model.h,
trunk/src/target3/glade/setup_druid.cpp: an initial version of
the new file format is now added; needs some futher testing
however.
2002-09-12 thassine
* trunk/src/target3/t3dialog.cpp: a warning message was added
(readpdb).
2002-09-11 thassine
* trunk/src/graphics/ribbon.cpp, trunk/src/target3/t3dialog.cpp,
trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
the ribbon object now can handle both all-atom and simplified
peptides/proteins. set #define ENABLE_SIMPLIFIED in config.h
before compiling. how to use/try: first use
File/ExtraTools/ImportPDB to read the file in and then
File/ExtraTools/Convert_aa2sf for getting the simplified
presentation (you can't save it yet). then Objects/Ribbon.
2002-09-10 thassine
* trunk/bin/parameters/builder/amino.txt,
trunk/src/common/seqbuild.cpp, trunk/src/common/utility.cpp: the
DefineSecondaryStructure() function now works with simplified
residues as well; also a ribbon bug is fixed.
* trunk/src/common/model.cpp, trunk/src/common/seqbuild.cpp,
trunk/src/common/seqbuild.h: the seqbuilder::Identify() now
handles correctly also the simplified chains.
2002-09-08 thassine
* trunk/src/Doxyfile, trunk/src/Makefile.OLD,
trunk/src/common/atom.h, trunk/src/common/bond.h,
trunk/src/common/conjgrad.h, trunk/src/common/eng1_sf.h,
trunk/src/common/engine.h, trunk/src/common/model.h: changed the
docs system into a doxygen-based one. now using /// as a brief
comment /** and this as a detailed comment. */ int example;
///< this is for comments at end of statements.
2002-09-07 thassine
* trunk/src/target1/t1m_mm2param_cpp.h,
trunk/src/target1/t1m_mm2param_h.h: removed some old files from
the console target.
* trunk/src/target1/t1m_mm1param_cpp.h,
trunk/src/target1/t1m_mm1param_h.h,
trunk/src/target1/t1m_param_mm_cpp.h,
trunk/src/target1/t1m_param_mm_h.h,
trunk/src/target1/t1m_param_sf_cpp.h,
trunk/src/target1/t1m_param_sf_h.h,
trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h: some
filenames changed at the console target...
2002-09-06 thassine
* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp: the sf
is now in sync with the version in MANY_PROJECTS_BRANCH.
2002-09-05 thassine
* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h: in sf,
all terms except the solvation one works like before.
* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h: the
nbt1 terms work now in sf.
* trunk/src/common/eng1_sf.cpp: minor bugs fixed in bonded-term
creation in the sf.
2002-09-04 thassine
* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h:
continued to port the sf stuff.
2002-09-03 thassine
* trunk/src/common/atom.cpp, trunk/src/common/eng1_mm.cpp,
trunk/src/common/eng1_mm_default.cpp,
trunk/src/common/eng1_mm_prmfit.cpp,
trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
trunk/src/common/eng1_qm_mopac.cpp,
trunk/src/common/eng1_qm_mpqc.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/eng2_mm_sf.h, trunk/src/common/eng2_qm_mm.h,
trunk/src/common/engine.cpp, trunk/src/common/filetrans.cpp,
trunk/src/common/intcrd.cpp, trunk/src/common/model.cpp,
trunk/src/common/seqbuild.cpp,
trunk/src/common/tab_mm_prmfit.cpp,
trunk/src/graphics/project.cpp, trunk/src/graphics/ribbon.cpp,
trunk/src/target1/t1m_mm1param_cpp.h,
trunk/src/target1/t1m_mm2param_cpp.h,
trunk/src/target3/glade/setup_druid.cpp,
trunk/src/target3/glade_dialog.cpp,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3project.cpp: checked the bug report messages
in various little run-time tests; they now all carry a BUG: tag.
* trunk/src/common/atom.h, trunk/src/common/bond.cpp,
trunk/src/common/bond.h, trunk/src/common/eng1_sf.cpp,
trunk/src/common/eng1_sf.h, trunk/src/common/engine.cpp,
trunk/src/common/model.cpp, trunk/src/graphics/project.cpp: some
improvements added to sf.
2002-09-02 thassine
* trunk/src/common/bond.cpp, trunk/src/common/bond.h,
trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/model.cpp, trunk/src/graphics/project.cpp: the
all-atoms -> simplified conversion seems to work now.
2002-08-31 thassine
* trunk/src/common/eng1_qm_mpqc.cpp,
trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
trunk/src/target3/glade/setup_druid.cpp,
trunk/src/target3/glade/setup_druid.glade: updated the
mpqc-related stuff; now there are qm/mm engine classes for both
mopac and mpqc. they seem to work technically fine, but without
any glue code the qm and mm parts are not interacting at all.
yet.
* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
trunk/src/common/eng1_mm_default.cpp,
trunk/src/common/eng1_mm_prmfit.cpp: the qm_mm bug was because
connectivity records used (global) indices. now the connectivity
records use pointers instead of indices and now eng2_qm_mm works
like expected (when there is no glue code between the mm and qm
parts).
2002-08-30 thassine
* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
trunk/src/common/eng1_mm_default.cpp,
trunk/src/common/eng1_mm_prmfit.cpp,
trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
trunk/src/common/eng1_qm_mopac.cpp,
trunk/src/common/eng1_qm_mopac.h, trunk/src/common/eng1_sf.cpp,
trunk/src/common/eng1_sf.h, trunk/src/common/eng2_qm_mm.cpp,
trunk/src/common/engine.cpp, trunk/src/common/engine.h,
trunk/src/common/model.h, trunk/src/common/tab_mm_default.cpp,
trunk/src/common/tab_mm_prmfit.cpp,
trunk/src/target2/t2project.cpp: the eng classes now use local
instead of global atom numbering (more like the old system).
there is a nonbonded-term bug in qmmm but otherwise it looks
good. sf only compiles.
* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/eng2_mm_sf.cpp, trunk/src/common/eng2_mm_sf.h,
trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
trunk/src/common/engine.cpp, trunk/src/common/engine.h,
trunk/src/target2/t2project.cpp, trunk/src/target2/t2project.h,
trunk/src/target3/glade/setup_druid.cpp: the setup classes are
now initialized correctly. setup::GetMaxEngineIndex() renamed to
setup::GetEngineCount().
* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/eng2_mm_sf.cpp, trunk/src/common/eng2_mm_sf.h,
trunk/src/target3/glade/setup_druid.cpp: ok, everything compiles
now, including the simplified forcefield stuff.
* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/engine.cpp, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/seqbuild.cpp,
trunk/src/common/tab_mm_default.cpp,
trunk/src/common/tab_mm_prmfit.cpp,
trunk/src/graphics/project.cpp,
trunk/src/target1/t1m_mm2param_cpp.h: continued porting the
simplified forcefield here (not ready yet, doesn't compile, and
needs file format changes). modified seqbuider::Indentify() so
that it would also detect simplified protein/peptide chains (not
ready yet). converted the bool atom::selected flag into i32u
atom::flags that can carry more information.
2002-08-29 thassine
* trunk/src/common/model.cpp, trunk/src/common/seqbuild.cpp,
trunk/src/target1/Makefile.OLD,
trunk/src/target1/t1m_mm1param_cpp.h,
trunk/src/target1/t1m_mm1param_h.h,
trunk/src/target1/t1main.cpp, trunk/src/target2/t2project.cpp,
trunk/src/target3/t3project.cpp: the new model::UpdateChains()
function now updates the chain/residue information. all targets
brought up-to-date again.
2002-08-28 thassine
* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
trunk/src/common/eng1_mm.cpp, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/search.cpp,
trunk/src/common/seqbuild.cpp, trunk/src/graphics/project.cpp,
trunk/src/target2/t2project.cpp,
trunk/src/target3/glade/setup_druid.glade: many changes added.
GatherGroups() renamed to UpdateGroups(). is_index_clean and
is_groups_clean flags are added so that it would be better
defined whether groups/chains/etc information is up-to-date or
not.
* trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_mm.h,
trunk/src/common/eng1_qm.cpp, trunk/src/common/eng1_qm.h,
trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/eng2_qm_mm.cpp, trunk/src/common/eng2_qm_mm.h,
trunk/src/common/engine.h, trunk/src/common/model.h,
trunk/src/target3/glade/setup_druid.cpp,
trunk/src/target3/glade/setup_druid.glade,
trunk/src/target3/glade/setup_druid.h: the setup_druid now
works, with minimal functionality so that one can select between
an MM and QM model.
2002-08-27 thassine
* trunk/src/common/atom.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/intcrd.cpp, trunk/src/common/model.cpp: some
bugfixes added; the conformational search tools should work now.
* trunk/src/target3/glade/file_import_dialog.cpp,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
added the File/ExtraTools also here.
2002-08-21 thassine
* trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/seqbuild.cpp,
trunk/src/common/seqbuild.h, trunk/src/graphics/ribbon.cpp,
trunk/src/target2/t2project.cpp,
trunk/src/target3/t3project.cpp: improvements added to the
seqbuilder and chn_info classes.
2002-08-01 thassine
* trunk/src/common/engine.cpp, trunk/src/common/intcrd.cpp,
trunk/src/common/model.cpp: bounds checking added to CopyCRD()
functions; bugs fixed from the new crd_set data storage system;
WARNING there still is something wrong with the intcrd class
(geometries get distorted).
2002-07-31 thassine
* trunk/src/graphics/camera.cpp: the fps counter added also to
HEAD.
2002-07-30 thassine
* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
trunk/src/common/eng1_mm.cpp, trunk/src/common/eng1_qm.cpp,
trunk/src/common/eng1_qm_mopac.cpp, trunk/src/common/engine.cpp,
trunk/src/common/filetrans.cpp, trunk/src/common/intcrd.cpp,
trunk/src/common/intcrd.h, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/seqbuild.cpp,
trunk/src/common/tab_mm_prmfit.cpp,
trunk/src/common/utility.cpp, trunk/src/graphics/project.cpp,
trunk/src/graphics/ribbon.cpp, trunk/src/graphics/views.cpp: the
coordinate data storage at atom class is converted into a less
error-prone system. it's no more possible to access the data
directly, but only using the atom::GetCRD() and atom::SetCRD()
member functions.
2002-07-23 thassine
* trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/graphics/project.cpp, trunk/src/target2/t2project.cpp:
the memory management scheme of crd_set objects is now simpler.
* trunk/src/common/engine.h, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/search.cpp,
trunk/src/common/search.h, trunk/src/target2/t2project.cpp,
trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h:
the search tool improvements ported also here.
* trunk/src/common/eng1_sf.cpp, trunk/src/common/eng1_sf.h,
trunk/src/common/engine.h: added some fixes to SF, althought it
does not even compile yet; therefore the ENABLE_SIMPLIFIED macro
is disabled at config.h
2002-06-20 thassine
* trunk/src/common/prefs.h, trunk/src/target3/t3prefs.cpp,
trunk/src/target3/t3prefs.h, trunk/src/target3/t3project.cpp:
added the v0.90 bugfixes also to HEAD.
2002-06-19 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/atom.cpp, trunk/src/common/atom.h,
trunk/src/common/eng1_mm.h, trunk/src/common/eng1_sf.cpp,
trunk/src/common/eng1_sf.h, trunk/src/common/engine.h,
trunk/src/common/model.cpp, trunk/src/common/moldyn.cpp,
trunk/src/common/seqbuild.h, trunk/src/graphics/project.cpp,
trunk/src/target1/config.h.OLD, trunk/src/target2/config.h.OLD,
trunk/src/target2/t2project.cpp, trunk/src/target3/config.h.OLD:
added some changes that were needed to port the simplified
forcefield of mine to HEAD. it's not working yet and not even
compile yet, but it doesn't matter since one have to set the
ENABLE_SIMPLIFIED macro to compile that stuff in...
2002-06-17 thassine
* trunk/Makefile.in, trunk/src/common/define.h,
trunk/src/common/eng1_sf.cpp, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/tab_mm_default.cpp,
trunk/src/target3/glade/file_export_dialog.cpp,
trunk/src/target3/glade/file_export_dialog.h,
trunk/src/target3/glade/file_import_dialog.cpp,
trunk/src/target3/glade/file_import_dialog.h,
trunk/src/target3/glade/geomopt_dialog.cpp,
trunk/src/target3/glade/geomopt_dialog.h,
trunk/src/target3/glade/moldyn_dialog.cpp,
trunk/src/target3/glade/moldyn_dialog.h,
trunk/src/target3/glade/setup_druid.cpp,
trunk/src/target3/glade/setup_druid.h,
trunk/src/target3/glade/trajview_dialog.cpp,
trunk/src/target3/glade/trajview_dialog.h,
trunk/src/target3/glade_dialog.cpp,
trunk/src/target3/glade_dialog.h,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3project.cpp:
the glade files are now installed correctly by make install.
2002-06-14 thassine
* trunk/src/Makefile.OLD: fixed src/Makefile.OLD clean: also in
HEAD.
2002-06-13 thassine
* trunk/src/common/conjgrad.cpp, trunk/src/common/conjgrad.h: also
copied conjgrad changes to HEAD.
2002-06-08 thassine
* trunk/src/target3/glade/setup_druid.cpp,
trunk/src/target3/glade/setup_druid.glade,
trunk/src/target3/glade/setup_druid.h,
trunk/src/target3/t3main.cpp: the setup_druid can now correctly
change the pages with prev/next buttons.
2002-06-07 thassine
* trunk/src/target3/glade/Makefile.OLD,
trunk/src/target3/glade/Makefile.in,
trunk/src/target3/glade/setup_druid.cpp,
trunk/src/target3/glade/setup_druid.glade,
trunk/src/target3/glade/setup_druid.h,
trunk/src/target3/t3project.cpp: added an initial version of the
setup druid (nothing except cancel works).
* trunk/src/target3/glade/Makefile.OLD,
trunk/src/target3/glade/Makefile.in,
trunk/src/target3/glade/file_export_dialog.cpp,
trunk/src/target3/glade/file_export_dialog.glade,
trunk/src/target3/glade/file_export_dialog.h,
trunk/src/target3/glade/file_import_dialog.cpp,
trunk/src/target3/glade/file_import_dialog.glade,
trunk/src/target3/glade/file_import_dialog.h,
trunk/src/target3/t3project.cpp: added the file import/export
dialogs.
* trunk/src/target3/glade/Makefile.OLD,
trunk/src/target3/glade/Makefile.in,
trunk/src/target3/glade/geomopt_dialog.cpp,
trunk/src/target3/glade/geomopt_dialog.glade,
trunk/src/target3/glade/geomopt_dialog.h,
trunk/src/target3/glade/moldyn_dialog.cpp,
trunk/src/target3/glade/moldyn_dialog.glade,
trunk/src/target3/glade/moldyn_dialog.h,
trunk/src/target3/glade/trajview_dialog.cpp,
trunk/src/target3/glade/trajview_dialog.glade,
trunk/src/target3/glade/trajview_dialog.h,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3project.cpp,
trunk/src/target3/t3project.h: new dialogs added, and dialog
memory leaks fixed (hopefully). the dialogs are now always
created with new, and delete is always called at destroy signal
handler of the dialog.
2002-06-05 thassine
* trunk/src/Makefile.OLD: added some Makefile tweaks.
* trunk/src/target3/glade/Makefile.OLD,
trunk/src/target3/glade/geomopt_dialog.cpp,
trunk/src/target3/glade/geomopt_dialog.glade,
trunk/src/target3/glade/geomopt_dialog.h,
trunk/src/target3/glade_dialog.h,
trunk/src/target3/t3project.cpp: the geomopt dialog now works
using libglade.
2002-06-03 thassine
* trunk/openbabel/fileformat.h: oops, my mistake. of course there
were nothing wrong with fileformat.h but I had an obsolete
Makefile. the changes are reverted.
* trunk/openbabel/fileformat.h: there were some undefined
functions at fileformat.cpp; just made some dummy functions in
fileformat.h so that OB can be compiled...
2002-05-31 hutchisn
* trunk/configure, trunk/configure.in,
trunk/miniMOPAC/Makefile.in, trunk/src/common/Makefile.in,
trunk/src/graphics/Makefile.in, trunk/src/target3/Makefile.in,
trunk/src/target3/glade/Makefile.in,
trunk/src/target3/glade/geomopt_dialog.h: Updated makefiles for
libglade, etc.
* trunk/openbabel/Makefile.in, trunk/openbabel/Vector.cpp,
trunk/openbabel/Vector.h, trunk/openbabel/alchemy.cpp,
trunk/openbabel/amber.cpp, trunk/openbabel/aromatic.h,
trunk/openbabel/aromatic.txt, trunk/openbabel/atom.cpp,
trunk/openbabel/atomtyp.h, trunk/openbabel/atomtyp.txt,
trunk/openbabel/balst.cpp, trunk/openbabel/base.cpp,
trunk/openbabel/base.h, trunk/openbabel/bgf.cpp,
trunk/openbabel/bin2hex.pl, trunk/openbabel/binary.cpp,
trunk/openbabel/binary.h, trunk/openbabel/binary_io.cpp,
trunk/openbabel/binary_io.h, trunk/openbabel/bitgrid.cpp,
trunk/openbabel/bitgrid.h, trunk/openbabel/bitvec.h,
trunk/openbabel/bond.cpp, trunk/openbabel/bond.txt,
trunk/openbabel/box.cpp, trunk/openbabel/c3d.cpp,
trunk/openbabel/cacao.cpp, trunk/openbabel/cache.cpp,
trunk/openbabel/car.cpp, trunk/openbabel/chains.cpp,
trunk/openbabel/chdrw.cpp, trunk/openbabel/chiral.cpp,
trunk/openbabel/chiral.h, trunk/openbabel/cml.cpp,
trunk/openbabel/commandline.h, trunk/openbabel/csr.cpp,
trunk/openbabel/cssr.cpp, trunk/openbabel/ctransform.cpp,
trunk/openbabel/ctransform.h, trunk/openbabel/data.cpp,
trunk/openbabel/data.h, trunk/openbabel/dmol.cpp,
trunk/openbabel/element.h, trunk/openbabel/extable.h,
trunk/openbabel/extable.txt, trunk/openbabel/feat.cpp,
trunk/openbabel/fh.cpp, trunk/openbabel/fileformat.cpp,
trunk/openbabel/fileformat.h, trunk/openbabel/gamess.cpp,
trunk/openbabel/gaussian.cpp, trunk/openbabel/generic.cpp,
trunk/openbabel/generic.h, trunk/openbabel/ghemical.cpp,
trunk/openbabel/grid.h, trunk/openbabel/gromos96.cpp,
trunk/openbabel/hin.cpp, trunk/openbabel/jaguar.cpp,
trunk/openbabel/main.cpp, trunk/openbabel/matrix.cpp,
trunk/openbabel/matrix.h, trunk/openbabel/mmod.cpp,
trunk/openbabel/mol.cpp, trunk/openbabel/mol.h,
trunk/openbabel/molchrg.cpp, trunk/openbabel/molchrg.h,
trunk/openbabel/molvector.cpp, trunk/openbabel/molvector.h,
trunk/openbabel/mopac.cpp, trunk/openbabel/mpqc.cpp,
trunk/openbabel/nwchem.cpp, trunk/openbabel/obifstream.h,
trunk/openbabel/oblib.dsp, trunk/openbabel/obutil.cpp,
trunk/openbabel/obutil.h, trunk/openbabel/parsmart.cpp,
trunk/openbabel/parsmart.h, trunk/openbabel/parsmi.cpp,
trunk/openbabel/patty.cpp, trunk/openbabel/patty.h,
trunk/openbabel/pdb.cpp, trunk/openbabel/phmodel.cpp,
trunk/openbabel/phmodel.h, trunk/openbabel/phmodel.txt,
trunk/openbabel/phmodeldata.h, trunk/openbabel/qchem.cpp,
trunk/openbabel/report.cpp, trunk/openbabel/resdata.h,
trunk/openbabel/ring.cpp, trunk/openbabel/ring.h,
trunk/openbabel/rotor.cpp, trunk/openbabel/rotor.h,
trunk/openbabel/smarts.cpp, trunk/openbabel/smarts.h,
trunk/openbabel/smi.cpp, trunk/openbabel/smi.h,
trunk/openbabel/tinker.cpp, trunk/openbabel/tokenst.cpp,
trunk/openbabel/typer.cpp, trunk/openbabel/typer.h,
trunk/openbabel/types.h, trunk/openbabel/unichem.cpp,
trunk/openbabel/viewmol.cpp, trunk/openbabel/xed.cpp,
trunk/openbabel/xyz.cpp: Merge in current Open Babel (w/ CML and
proper namespace support).
2002-05-31 thassine
* trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
trunk/src/target3/Makefile.in,
trunk/src/target3/glade/Makefile.in: fixes added to makefiles;
now the configuration works otherwise except that libglade incs
and libs are missing.
2002-05-30 thassine
* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
promoted the version number to 0.85 in the HEAD branch.
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/src/common/Makefile.in, trunk/src/common/eng1_sf.cpp,
trunk/src/common/tab_mm_default.cpp,
trunk/src/graphics/Makefile.in, trunk/src/target3/Makefile.in,
trunk/src/target3/glade/Makefile.in: minor fixes like changed
directories etc added.
* trunk/bin/parameters/param_mm,
trunk/bin/parameters/param_mm/default,
trunk/bin/parameters/param_mm/default/atomtypes.txt,
trunk/bin/parameters/param_mm/default/parameters1.txt,
trunk/bin/parameters/param_mm/default/parameters2.txt,
trunk/bin/parameters/param_mm/default/parameters3.txt,
trunk/bin/parameters/param_mm/default/parameters4.txt,
trunk/bin/parameters/param_mm/default/parameters5.txt,
trunk/bin/parameters/param_sf,
trunk/bin/parameters/param_sf/default,
trunk/bin/parameters/param_sf/default/loopdip.txt,
trunk/bin/parameters/param_sf/default/looptor.txt,
trunk/bin/parameters/param_sf/default/nonbonded.txt,
trunk/src/some-extra-files/newfile.cpp,
trunk/src/some-extra-files/newfile.h: added new files to
bin/parameters and some minor stuff.
* trunk/bin/parameters/mm1param, trunk/bin/parameters/mm2param:
removed old files under bin/parameters.
* trunk/src/common/atom.cpp, trunk/src/common/atom.h,
trunk/src/common/bond.cpp, trunk/src/common/bond.h,
trunk/src/common/define.h, trunk/src/common/eng1_mm.cpp,
trunk/src/common/eng1_mm.h,
trunk/src/common/eng1_mm_default.cpp,
trunk/src/common/eng1_mm_default.h,
trunk/src/common/eng1_mm_prmfit.cpp,
trunk/src/common/eng1_mm_prmfit.h, trunk/src/common/eng1_qm.cpp,
trunk/src/common/eng1_qm.h, trunk/src/common/eng1_qm_mopac.cpp,
trunk/src/common/eng1_qm_mopac.h,
trunk/src/common/eng1_qm_mpqc.cpp,
trunk/src/common/eng1_qm_mpqc.h, trunk/src/common/eng1_sf.cpp,
trunk/src/common/eng1_sf.h, trunk/src/common/eng2_qm_mm.cpp,
trunk/src/common/eng2_qm_mm.h, trunk/src/common/engine.cpp,
trunk/src/common/engine.h, trunk/src/common/filetrans.cpp,
trunk/src/common/filetrans.h, trunk/src/common/geomopt.cpp,
trunk/src/common/geomopt.h, trunk/src/common/intcrd.cpp,
trunk/src/common/intcrd.h, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/moldyn.cpp,
trunk/src/common/moldyn.h, trunk/src/common/search.cpp,
trunk/src/common/search.h, trunk/src/common/seqbuild.cpp,
trunk/src/common/seqbuild.h,
trunk/src/common/tab_mm_default.cpp,
trunk/src/common/tab_mm_default.h,
trunk/src/common/tab_mm_prmfit.cpp,
trunk/src/common/tab_mm_prmfit.h, trunk/src/common/typedef.h,
trunk/src/common/typerule.cpp, trunk/src/common/typerule.h,
trunk/src/common/utility.cpp, trunk/src/common/utility.h,
trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h,
trunk/src/graphics/color.h, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/plane.cpp, trunk/src/graphics/plane.h,
trunk/src/graphics/project.cpp, trunk/src/graphics/project.h,
trunk/src/graphics/ribbon.cpp, trunk/src/graphics/ribbon.h,
trunk/src/graphics/surface.cpp, trunk/src/graphics/surface.h,
trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
trunk/src/target1/t1main.cpp, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2main.h, trunk/src/target2/t2project.cpp,
trunk/src/target2/t2project.h, trunk/src/target2/t2views.cpp,
trunk/src/target2/t2views.h, trunk/src/target3/glade_dialog.cpp,
trunk/src/target3/glade_dialog.h,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3project.cpp, trunk/src/target3/t3project.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
added the new files.
* trunk/src/common/interface.cpp, trunk/src/common/interface.h,
trunk/src/common/matrix.h, trunk/src/common/mm1alg.cpp,
trunk/src/common/mm1alg.h, trunk/src/common/mm1eng.cpp,
trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.cpp,
trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.cpp,
trunk/src/common/mm1eng9.h, trunk/src/common/mm1ic.cpp,
trunk/src/common/mm1ic.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.cpp,
trunk/src/common/mm1util.h, trunk/src/common/mm2alg.cpp,
trunk/src/common/mm2alg.h, trunk/src/common/mm2eng.cpp,
trunk/src/common/mm2eng.h, trunk/src/common/mm2mdl.cpp,
trunk/src/common/mm2mdl.h, trunk/src/common/mm2util.cpp,
trunk/src/common/mm2util.h, trunk/src/common/mm3mdl.cpp,
trunk/src/common/mm3mdl.h, trunk/src/common/qm1alg.cpp,
trunk/src/common/qm1alg.h, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1eng.cpp,
trunk/src/common/qm1eng.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.cpp,
trunk/src/common/qm2eng.h, trunk/src/common/qm2mdl.cpp,
trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/io-jpg.cpp,
trunk/src/graphics/io-jpg.h, trunk/src/graphics/io-png.cpp,
trunk/src/graphics/io-png.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm2docv.h, trunk/src/graphics/mm2rbn.cpp,
trunk/src/graphics/mm2rbn.h, trunk/src/graphics/mm3docv.cpp,
trunk/src/graphics/mm3docv.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h, trunk/src/target2/t2docv.cpp,
trunk/src/target2/t2docv.h, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2mm2docv.h, trunk/src/target2/t2mm3docv.cpp,
trunk/src/target2/t2mm3docv.h, trunk/src/target2/t2qm1docv.cpp,
trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.cpp,
trunk/src/target2/t2qm2docv.h,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_callbacks.h,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/glade_support.cpp,
trunk/src/target3/glade_support.h, trunk/src/target3/t3docv.cpp,
trunk/src/target3/t3docv.h, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3mm2docv.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3qm2docv.cpp,
trunk/src/target3/t3qm2docv.h: the old/renamed files are removed.
* trunk/src/target3/glade/README: update the glade README
* trunk/src/target1/config.h.OLD, trunk/src/target2/config.h.OLD,
trunk/src/target3/config.h.OLD,
trunk/src/target3/glade/Makefile.OLD,
trunk/src/target3/glade/Makefile.in,
trunk/src/target3/glade/geomopt_dialog.cpp,
trunk/src/target3/glade/geomopt_dialog.glade,
trunk/src/target3/glade/geomopt_dialog.h,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src: added changes to config.h.OLD files
and src/target3/glade dir.
* trunk/src/Makefile.OLD, trunk/src/common/Makefile.OLD,
trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.OLD,
trunk/src/graphics/Makefile.in, trunk/src/target2/Makefile.OLD,
trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in:
the makefiles are updated.
* trunk/CHANGES: the changelog is updated.
* trunk/src/Makefile.OLD: test; this goes to HEAD branch...
2002-05-29 thassine
* trunk/CHANGES: again testing that the OSP_BRANCH is separate;
seems to be but cvs2cl picks all commits to the log; I'll start
using OSP: identifier when working with the branch in the future.
2002-05-28 thassine
* trunk/CHANGES: updated the changelog (using cvs2cl again).
* trunk/src/common/define.h: ooop, reverted the previous.
* trunk/src/common/define.h: just testing how the branches work.
2002-05-27 thassine
* trunk/bin/parameters/mm2param/loopdip.txt,
trunk/bin/parameters/mm2param/looptor.txt,
trunk/bin/parameters/mm2param/nonbonded.txt,
trunk/small-utilities/getpdb_cd.cpp,
trunk/small-utilities/getpdb_ftp.cpp,
trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.h,
trunk/src/common/mm2alg.h, trunk/src/common/mm2eng.cpp,
trunk/src/common/mm2eng.h, trunk/src/common/mm2mdl.cpp,
trunk/src/common/mm2mdl.h, trunk/src/common/mm2util.cpp,
trunk/src/common/mm2util.h, trunk/src/common/mm3mdl.cpp,
trunk/src/common/mm3mdl.h, trunk/src/graphics/Makefile.OLD,
trunk/src/graphics/Makefile.in, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm3docv.cpp, trunk/src/graphics/mm3docv.h,
trunk/src/graphics/views.h, trunk/src/target1/Makefile.OLD,
trunk/src/target1/t1m_mm2param_cpp.h,
trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2main.h, trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2mm3docv.cpp, trunk/src/target2/t2mm3docv.h,
trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in:
added some of my own works; not all of this stuff is ready, but
I need to start converting them to fit into single-project
environment.
2002-05-22 thassine
* trunk/Makefile.in, trunk/configure, trunk/configure.in:
configure script now updated, scripts now compatible with
autoconf 2.53
2002-05-21 thassine
* trunk/aclocal.m4, trunk/configure.in,
trunk/src/common/Makefile.OLD, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1e_mpqc.h, trunk/src/config.h.in,
trunk/src/graphics/Makefile.OLD, trunk/src/graphics/Makefile.in,
trunk/src/target1/Makefile.OLD, trunk/src/target1/config.h.OLD,
trunk/src/target2/Makefile.OLD, trunk/src/target2/config.h.OLD,
trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in,
trunk/src/target3/config.h.OLD: added the configuration system
for MPQC v1/v2 (thanks to Michael); BTW you still have to run
autoconf to update the configure script.
2002-05-20 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1e_mpqc.h, trunk/src/graphics/Makefile.OLD,
trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
trunk/src/target3/Makefile.OLD: support for MPQC v2 was added
(but ./configure still needs update).
* trunk/src/target1/t1m_mm1param_cpp.h,
trunk/src/target1/t1m_mm1param_h.h: oops, forgot to add some
files last time.
2002-05-17 thassine
* trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1tab9.h,
trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h,
trunk/src/target2/t2mm1docv.cpp: added my (so far incomplete)
system for fitting MM force field parameters; this stuff is not
really working yet.
2002-04-29 thassine
* trunk/src/common/define.h, trunk/src/graphics/mm2docv.cpp,
trunk/src/target2/t2mm2docv.cpp,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
added LABEL_RESIDUE for mm2_docv.
2002-04-17 thassine
* trunk/src/common/mm2util.cpp, trunk/src/common/model.cpp: a few
bugs that freed memory multiple times were fixed. there still
remains maaany memory leaks, but they are less dangerous than
these.
2002-04-16 thassine
* trunk/src/common/mm2mdl.cpp, trunk/src/graphics/mm2docv.cpp:
some comments and minor fixes added to mm2_mdl.
2002-04-09 thassine
* trunk/src/graphics/mm2docv.cpp, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3mm2docv.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm1docv.h: some colour/label mode
improvements added.
2002-04-08 thassine
* trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
trunk/src/graphics/mm2rbn.cpp: some cleanups added to the
mm2_docv rendering code - should not change the looks/anything.
2002-04-04 thassine
* trunk/BUGLIST, trunk/TODO: the BUGLIST and TODO files are now
CSV text files - use a spreadsheet program like Gnumeric or
StarOffice/Calc to read and/or modify them.
* trunk/src/graphics/camera.cpp: some cleanups done for the stereo
modes; now the effect seems to be independent of orientation.
2002-03-26 hutchisn
* trunk/openbabel/mol.cpp, trunk/openbabel/pdb.cpp: Fixes
OpenBabel PDB import problems (PR #529744 for OpenBabel).
2002-02-28 thassine
* trunk/ghemical.spec: the .spec file updated; the RPM now does
the installation with prefix /usr instead of /usr/local.
2002-02-27 thassine
* trunk/miniMOPAC/Makefile.in: modified miniMOPAC/Makefile.in so
that -O optimization is forced in the miniMOPAC directory.
2002-02-26 thassine
* trunk/ghemical.spec: some updates added to .spec file.
2002-02-25 thassine
* trunk/AUTHORS, trunk/bin/ghemical.xpm, trunk/ghemical.spec:
added the files for building RedHat binary packages, contributed
by Radek Liboska.
2002-02-22 thassine
* trunk/configure, trunk/configure.in, trunk/src/common/define.h,
trunk/src/common/notice.cpp: switch back to development settings.
* trunk/CHANGES, trunk/INSTALL, trunk/src/common/define.h:
changelog updated and all settings are now ready for release as
v0.82
* trunk/src/target3/t3mm1docv.cpp: a small fix added to the
library widget generation code.
2002-02-21 thassine
* trunk/bin/user-docs/index.html,
trunk/bin/user-docs/using_cs_tools.html,
trunk/bin/user-docs/using_cs_tools01.jpg,
trunk/bin/user-docs/using_cs_tools02.jpg,
trunk/bin/user-docs/using_cs_tools03.jpg,
trunk/bin/user-docs/using_cs_tools04.jpg,
trunk/bin/user-docs/using_cs_tools05.jpg: user's manual is
enhanced; it now contains a section about 1D and 2D energy plots.
2002-02-20 thassine
* trunk/INSTALL, trunk/src/common/mm1alg.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm2alg.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/qm1alg.h,
trunk/src/common/qm1mdl.cpp, trunk/src/target1/Makefile.OLD,
trunk/src/target2/Makefile.OLD, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target3/Makefile.OLD,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3qm1docv.cpp: old makefiles updated, and the
code added for geomopt dialogs + calculations that separates the
different termination criteria and makes them optional. it also
prints out which criteria was used to terminate the optimization.
2002-02-18 hutchisn
* trunk/openbabel/pdb.cpp: Don't try to run PerceiveBondOrders
yet... this seems to be very buggy.
* trunk/openbabel/Makefile.in, trunk/openbabel/alchemy.cpp,
trunk/openbabel/amber.cpp, trunk/openbabel/aromatic.txt,
trunk/openbabel/atom.cpp, trunk/openbabel/balst.cpp,
trunk/openbabel/box.cpp, trunk/openbabel/c3d.cpp,
trunk/openbabel/cacao.cpp, trunk/openbabel/car.cpp,
trunk/openbabel/ccc.cpp, trunk/openbabel/commandline.h,
trunk/openbabel/ctransform.h, trunk/openbabel/data.cpp,
trunk/openbabel/data.h, trunk/openbabel/dmol.cpp,
trunk/openbabel/element.h, trunk/openbabel/element.txt,
trunk/openbabel/extable.h, trunk/openbabel/extable.txt,
trunk/openbabel/feat.cpp, trunk/openbabel/gamess.cpp,
trunk/openbabel/gaussian.cpp, trunk/openbabel/ghemical.cpp,
trunk/openbabel/grid.h, trunk/openbabel/hin.cpp,
trunk/openbabel/jaguar.cpp, trunk/openbabel/main.cpp,
trunk/openbabel/mol.cpp, trunk/openbabel/mol.h,
trunk/openbabel/mopac.cpp, trunk/openbabel/mpqc.cpp,
trunk/openbabel/nwchem.cpp, trunk/openbabel/obutil.cpp,
trunk/openbabel/obutil.h, trunk/openbabel/patty.cpp,
trunk/openbabel/pdb.cpp, trunk/openbabel/phmodel.cpp,
trunk/openbabel/qchem.cpp, trunk/openbabel/report.cpp,
trunk/openbabel/rotor.cpp, trunk/openbabel/smarts.h,
trunk/openbabel/typer.cpp, trunk/openbabel/unichem.cpp,
trunk/openbabel/version.h.in, trunk/openbabel/xyz.cpp: Updated
Open Babel code, including preliminary bond-order perception.
2002-01-31 thassine
* trunk/miniMOPAC/README: some documentation fixes for miniMOPAC.
* trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade_interface.cpp: the check boxes for
different termination criteria were added to the geomopt GLADE
dialog; their states are not yet checked however.
2002-01-25 hutchisn
* trunk/small-utilities/Makefile, trunk/small-utilities/README,
trunk/small-utilities/symmetry.c: Add Symmetry program (from
Sergei Pachkovsky, who gave OK to use in Ghemical)
2002-01-25 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/define.h,
trunk/src/common/qm1mdl.cpp, trunk/src/graphics/Makefile.OLD,
trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
trunk/src/target3/Makefile.OLD: some comments added, and old
makefiles are fixed/updated.
2002-01-25 hutchisn
* trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/t3mm1docv.cpp: Make sure we actually set the
optimization limits after the dialog completes...
* trunk/openbabel/unichem.cpp: Fix unichem XYZ support (read
should expect atomic numbers in Unichem files).
2002-01-22 thassine
* trunk/src/target3/glade_interface.h,
trunk/src/target3/glade_support.cpp: verified that /target3 and
/target3/glade/src keep in sync...
2002-01-21 hutchisn
* trunk/src/common/mm1alg.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm2alg.h, trunk/src/common/qm1alg.h,
trunk/src/common/qm1mdl.cpp,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_support.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3qm1docv.cpp: Add support for terminating
geometry optimizations "early" based on delta E or
small gradient. Currently does not have a UI for termination
based on small
step, and this is set to 1.0e-12 so this should never happen.
2002-01-21 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/qm1mdl.cpp: the
geomopt output now displays accurate gradient vector lengths.
* trunk/INSTALL, trunk/oelib: removed .cvsignore from the oelib
directory.
2002-01-18 hutchisn
* trunk/src/common/mm1mdl.cpp, trunk/src/common/qm1mdl.cpp: Added
user-friendly display of the step-size, displacement and delta E
in geom opt.
Seems to indicate that most geom opt can quit early with tests
for displ. and/or delta E.
2002-01-15 thassine
* trunk/src/graphics/mm1docv.cpp: in the 1D and 2D energy plotting
tools of mm1_docv it is now possible to select a smaller range
of angles if needed, and the final energy can be calculated also
using QM methods (so now it's possible to compare MM results
against QM results as well as compare different QM results).
2002-01-14 thassine
* trunk/src/common/Makefile.OLD, trunk/src/graphics/Makefile.OLD,
trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
trunk/src/target3/Makefile.OLD: converted the old makefiles to
use the new openbabel-paths.
2002-01-14 hutchisn
* trunk/src/common/filetrans.cpp: Delete filename at appropriate
time--Babel uses it for a Title when exporting.
* trunk/configure, trunk/configure.in: Add almost-forgotten
configure tests contributed by Michael Banck--check for f2c if
g2c is not found (and give an error if neither is found).
2002-01-11 hutchisn
* trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
trunk/src/target3/Makefile.in: Makefile fixes.
2002-01-10 hutchisn
* trunk/configure, trunk/configure.in,
trunk/src/common/Makefile.in, trunk/src/target3/Makefile.in:
Added support for Michael Banck's SC autoconf macros to simplify
building MPQC.
* trunk/Makefile.in, trunk/PROJECT, trunk/config.guess,
trunk/config.sub, trunk/configure, trunk/configure.in,
trunk/oelib/GNULICENSE.txt, trunk/oelib/Makefile.in,
trunk/oelib/OELibPrimer.html, trunk/oelib/StdAfx.cpp,
trunk/oelib/StdAfx.h, trunk/oelib/Vector.cpp,
trunk/oelib/Vector.h, trunk/oelib/alchemy.cpp,
trunk/oelib/amber.cpp, trunk/oelib/aromatic.h,
trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
trunk/oelib/atomtyp.h, trunk/oelib/atomtyp.txt,
trunk/oelib/balst.cpp, trunk/oelib/base.cpp, trunk/oelib/base.h,
trunk/oelib/bgf.cpp, trunk/oelib/bin2hex.pl,
trunk/oelib/binary.cpp, trunk/oelib/binary.h,
trunk/oelib/binary_io.cpp, trunk/oelib/binary_io.h,
trunk/oelib/bitgrid.cpp, trunk/oelib/bitgrid.h,
trunk/oelib/bitvec.cpp, trunk/oelib/bitvec.h,
trunk/oelib/bond.cpp, trunk/oelib/box.cpp, trunk/oelib/c3d.cpp,
trunk/oelib/cacao.cpp, trunk/oelib/cache.cpp,
trunk/oelib/car.cpp, trunk/oelib/ccc.cpp,
trunk/oelib/chains.cpp, trunk/oelib/chains.h,
trunk/oelib/chdrw.cpp, trunk/oelib/chiral.cpp,
trunk/oelib/chiral.h, trunk/oelib/commandline.cpp,
trunk/oelib/commandline.h, trunk/oelib/configure,
trunk/oelib/csr.cpp, trunk/oelib/cssr.cpp,
trunk/oelib/ctransform.cpp, trunk/oelib/ctransform.h,
trunk/oelib/cwrap.cpp, trunk/oelib/cwrap.h,
trunk/oelib/data.cpp, trunk/oelib/data.h, trunk/oelib/dmol.cpp,
trunk/oelib/element.h, trunk/oelib/element.txt,
trunk/oelib/extable.h, trunk/oelib/extable.txt,
trunk/oelib/feat.cpp, trunk/oelib/fh.cpp,
trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
trunk/oelib/gamess.cpp, trunk/oelib/gaussian.cpp,
trunk/oelib/generic.cpp, trunk/oelib/generic.h,
trunk/oelib/ghemical.cpp, trunk/oelib/globals.cpp,
trunk/oelib/grid.cpp, trunk/oelib/grid.h,
trunk/oelib/gromos96.cpp, trunk/oelib/hin.cpp,
trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
trunk/oelib/matrix.cpp, trunk/oelib/matrix.h,
trunk/oelib/mdl.cpp, trunk/oelib/mmod.cpp, trunk/oelib/mol.cpp,
trunk/oelib/mol.h, trunk/oelib/mol2.cpp,
trunk/oelib/molchrg.cpp, trunk/oelib/molchrg.h,
trunk/oelib/molvector.cpp, trunk/oelib/molvector.h,
trunk/oelib/mopac.cpp, trunk/oelib/mpqc.cpp,
trunk/oelib/nwchem.cpp, trunk/oelib/oeifstream.h,
trunk/oelib/oelib.dsp, trunk/oelib/oelib.dsw,
trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
trunk/oelib/parsmart.cpp, trunk/oelib/parsmart.h,
trunk/oelib/parsmi.cpp, trunk/oelib/patty.cpp,
trunk/oelib/patty.h, trunk/oelib/pdb.cpp,
trunk/oelib/phmodel.cpp, trunk/oelib/phmodel.h,
trunk/oelib/phmodel.txt, trunk/oelib/phmodeldata.h,
trunk/oelib/qchem.cpp, trunk/oelib/quat.c, trunk/oelib/rand.cpp,
trunk/oelib/report.cpp, trunk/oelib/resdata.h,
trunk/oelib/resdata.txt, trunk/oelib/ring.cpp,
trunk/oelib/ring.h, trunk/oelib/rotor.cpp, trunk/oelib/rotor.h,
trunk/oelib/smarts.cpp, trunk/oelib/smarts.h,
trunk/oelib/smi.cpp, trunk/oelib/smi.h, trunk/oelib/tinker.cpp,
trunk/oelib/tokenst.cpp, trunk/oelib/typer.cpp,
trunk/oelib/typer.h, trunk/oelib/types.h, trunk/oelib/types.txt,
trunk/oelib/unichem.cpp, trunk/oelib/version.h,
trunk/oelib/xed.cpp, trunk/oelib/xyz.cpp, trunk/openbabel,
trunk/openbabel/Makefile.in, trunk/openbabel/StdAfx.cpp,
trunk/openbabel/StdAfx.h, trunk/openbabel/Vector.cpp,
trunk/openbabel/Vector.h, trunk/openbabel/alchemy.cpp,
trunk/openbabel/amber.cpp, trunk/openbabel/aromatic.h,
trunk/openbabel/aromatic.txt, trunk/openbabel/atom.cpp,
trunk/openbabel/atomtyp.h, trunk/openbabel/atomtyp.txt,
trunk/openbabel/balst.cpp, trunk/openbabel/base.cpp,
trunk/openbabel/base.h, trunk/openbabel/bgf.cpp,
trunk/openbabel/bin2hex.pl, trunk/openbabel/binary.cpp,
trunk/openbabel/binary.h, trunk/openbabel/binary_io.cpp,
trunk/openbabel/binary_io.h, trunk/openbabel/bitgrid.cpp,
trunk/openbabel/bitgrid.h, trunk/openbabel/bitvec.cpp,
trunk/openbabel/bitvec.h, trunk/openbabel/bond.cpp,
trunk/openbabel/box.cpp, trunk/openbabel/c3d.cpp,
trunk/openbabel/cacao.cpp, trunk/openbabel/cache.cpp,
trunk/openbabel/car.cpp, trunk/openbabel/ccc.cpp,
trunk/openbabel/chains.cpp, trunk/openbabel/chains.h,
trunk/openbabel/chdrw.cpp, trunk/openbabel/chiral.cpp,
trunk/openbabel/chiral.h, trunk/openbabel/commandline.cpp,
trunk/openbabel/commandline.h, trunk/openbabel/csr.cpp,
trunk/openbabel/cssr.cpp, trunk/openbabel/ctransform.cpp,
trunk/openbabel/ctransform.h, trunk/openbabel/cwrap.cpp,
trunk/openbabel/cwrap.h, trunk/openbabel/data.cpp,
trunk/openbabel/data.h, trunk/openbabel/dmol.cpp,
trunk/openbabel/element.h, trunk/openbabel/element.txt,
trunk/openbabel/extable.h, trunk/openbabel/extable.txt,
trunk/openbabel/feat.cpp, trunk/openbabel/fh.cpp,
trunk/openbabel/fileformat.cpp, trunk/openbabel/fileformat.h,
trunk/openbabel/gamess.cpp, trunk/openbabel/gaussian.cpp,
trunk/openbabel/generic.cpp, trunk/openbabel/generic.h,
trunk/openbabel/ghemical.cpp, trunk/openbabel/grid.cpp,
trunk/openbabel/grid.h, trunk/openbabel/gromos96.cpp,
trunk/openbabel/hin.cpp, trunk/openbabel/jaguar.cpp,
trunk/openbabel/main.cpp, trunk/openbabel/matrix.cpp,
trunk/openbabel/matrix.h, trunk/openbabel/mdl.cpp,
trunk/openbabel/mmod.cpp, trunk/openbabel/mol.cpp,
trunk/openbabel/mol.h, trunk/openbabel/mol2.cpp,
trunk/openbabel/molchrg.cpp, trunk/openbabel/molchrg.h,
trunk/openbabel/molvector.cpp, trunk/openbabel/molvector.h,
trunk/openbabel/mopac.cpp, trunk/openbabel/mpqc.cpp,
trunk/openbabel/nwchem.cpp, trunk/openbabel/obifstream.h,
trunk/openbabel/oblib.dsp, trunk/openbabel/oblib.dsw,
trunk/openbabel/obutil.cpp, trunk/openbabel/obutil.h,
trunk/openbabel/parsmart.cpp, trunk/openbabel/parsmart.h,
trunk/openbabel/parsmi.cpp, trunk/openbabel/patty.cpp,
trunk/openbabel/patty.h, trunk/openbabel/pdb.cpp,
trunk/openbabel/phmodel.cpp, trunk/openbabel/phmodel.h,
trunk/openbabel/phmodel.txt, trunk/openbabel/phmodeldata.h,
trunk/openbabel/qchem.cpp, trunk/openbabel/quat.c,
trunk/openbabel/rand.cpp, trunk/openbabel/report.cpp,
trunk/openbabel/resdata.h, trunk/openbabel/resdata.txt,
trunk/openbabel/ring.cpp, trunk/openbabel/ring.h,
trunk/openbabel/rotor.cpp, trunk/openbabel/rotor.h,
trunk/openbabel/smarts.cpp, trunk/openbabel/smarts.h,
trunk/openbabel/smi.cpp, trunk/openbabel/smi.h,
trunk/openbabel/tinker.cpp, trunk/openbabel/tokenst.cpp,
trunk/openbabel/typer.cpp, trunk/openbabel/typer.h,
trunk/openbabel/types.h, trunk/openbabel/types.txt,
trunk/openbabel/unichem.cpp, trunk/openbabel/version.h,
trunk/openbabel/xed.cpp, trunk/openbabel/xyz.cpp,
trunk/src/common/Makefile.in, trunk/src/common/filetrans.cpp,
trunk/src/common/filetrans.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/notice.cpp,
trunk/src/common/utility.cpp, trunk/src/graphics/Makefile.in,
trunk/src/graphics/docview.cpp, trunk/src/target3/Makefile.in:
Updated with OpenBabel replacing OELib.
* trunk/src/graphics/mtools.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h: Add data types for select modes and
measure modes.
* trunk/oelib/gamess.cpp: Small fix for GAMESS file format.
(this is a temporary issue until OpenBabel is imported in a day
or so.)
2002-01-07 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h: some
cleanups for the model classes, plus some documentation updates.
2002-01-05 hutchisn
* trunk/aclocal.m4: Added Michael Banck's contributed SC tests.
These have not yet been implemented into configure.in yet.
2002-01-02 thassine
* trunk/INSTALL, trunk/src/common/Makefile.OLD,
trunk/src/graphics/Makefile.OLD, trunk/src/target1/Makefile.OLD,
trunk/src/target2/Makefile.OLD, trunk/src/target3/Makefile.OLD:
converted the old makefiles to use the Scientific Computation
toolkit (SC toolkit) of MPQC, instead of the MPQC object files
and headers directly.
2001-12-31 thassine
* trunk/src/common/interface.cpp, trunk/src/common/interface.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp: the all_atoms_interface is now
implemented. it works as a bridge between MM and QM models, and
offers a stadard set of functions to access atoms and bonds in
them. the convert-to-MM/QM feature is now implemented using
all_atoms_interface, and also the OELib/OpenBabel complatibility
methods might fit into it.
2001-12-29 thassine
* trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h,
trunk/src/graphics/docview.cpp, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/graphics/views.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp:
the convert-project-to-QM/MM and attach/detach-this-view
operations now retain the graphics settings.
* trunk/src/graphics/views.cpp: the GLUT stroke fonts now make
readable text in all cases, but 3D text (as in labels) is still
misaligned.
2001-12-28 thassine
* trunk/src/graphics/camera.cpp, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/views.cpp, trunk/src/graphics/views.h: tried
to simplify the text rendering functions; also an initial
support for line-based font rendering (using glutStrokeBitmap())
but it's still quite broken.
2001-12-20 thassine
* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h: the plots are now checked and
commented; should work but UI is still console-based.
2001-12-19 thassine
* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/views.cpp, trunk/src/graphics/views.h: now
it's possible to scale colors of plot2d_view (using zoom
mousetool), and the plot views now store and display the
strcutures (using select/orbit/rotate tools); still need to do
some testing for the plots but they look good for symmterical
molecules.
* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/graphics/mtools.cpp, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h: moved the enlevdiag_view class to
the newly created plotting_view class family; now there is a
consistent way to handle non-graphics (energy-level diagram,
plot1d, plot2d) views.
2001-12-18 thassine
* trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng9.cpp: just
docs clarified a bit...
* trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng9.cpp,
trunk/src/common/mm1mdl.cpp, trunk/src/graphics/mm1docv.cpp: a
better tor-constraints added to mm1_eng classes for the 1d and
2d plots.
* trunk/INSTALL: updated the installation docs.
2001-12-17 thassine
* trunk/src/common/intcrd.cpp, trunk/src/common/intcrd.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
added 1D and 2D energy vs. torsion angles-plotting feature; it
compiles and even more or less works, but it still needs a lot
of finishing.
2001-12-12 thassine
* trunk/bin/user-docs/index.html, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/target2/t2qm1docv.cpp,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: added attach/detach feature for
gnome_graphics_views. earlier it was somewhat difficult to use
multiple views, because only one at a time could be looked at
the GtkNotebook. now the views can be detached from the notebook
to separate windows, and attached back to notebook as well. also
some GLUT and plotting improvements are added.
2001-12-10 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/common/qm1alg.cpp, trunk/src/common/qm1alg.h,
trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1eng.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2qm1docv.cpp: a simple transition state
search tool added for qm1_mdl; at the moment it's badly
documented and only works in the GLUT user interface (target2).
2001-12-07 thassine
* trunk/src/common/model.h, trunk/src/common/qm1mdl.cpp,
trunk/src/graphics/qm1docv.cpp, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2qm1docv.cpp: some t2 cleanups added, and
improved qm1_mdl support for multiple crd-sets.
2001-12-05 thassine
* trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.cpp,
trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.cpp,
trunk/src/common/mm1eng9.h: added an initial framework for
adding torsional constraints in molecular mechanics force
fields; the old stuff should work as usual.
* trunk/src/common/errutil.cpp, trunk/src/common/notice.h,
trunk/src/common/typedef.h, trunk/src/graphics/mm2rbn.cpp: added
some Alpha platform fixes from Bob Williams.
2001-11-27 hutchisn
* trunk/Makefile.in: Added distclean target and changed help
destination to smooth with Debian package.
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3prefs.cpp: Added Selection Mode submenu
(w/radio items) and fixed library error message.
2001-11-26 hutchisn
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
Updated library feature to be fully user-configurable (# levels,
directory path)
Now also add submenus for subdirectories!
2001-11-26 thassine
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3views.h:
minor fixes for 'Library', and some cleanups.
2001-11-21 hutchisn
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3views.h: Add "library submenu" as a first
draft--still needs to be user-configurable
(recursive function to establish the menu) and still buggy.
2001-11-13 thassine
* trunk/INSTALL, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.h, trunk/src/common/qm1mdl.h,
trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp:
made the SelectNone feature as a combination of SelectAll and
InvertSelection (less code this way), and added some
enhancements to FileOpen (graphics update forced, and possibly
selected new atoms now replace the old selection).
2001-11-12 hutchisn
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/common/model.h, trunk/src/common/qm1mdl.h,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
Added SelectNone() and support for "inserting" files (open with
molecules selected).
2001-11-09 hutchisn
* trunk/oelib/mol.cpp, trunk/src/common/filetrans.cpp: Fix bug
with OELib making Kekule structures. OELib now no longer clears
flags
for perceived Aromatic bonds and atoms. Our code makes bonds
conjugated if
OE has marked the bond as aromatic.
2001-11-08 thassine
* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
back to devel settings, version number changed to 0.82.
* trunk/CHANGES, trunk/src/common/define.h: some final changes for
the new release; this is released as 0.81.
2001-11-07 thassine
* trunk/CHANGES, trunk/INSTALL, trunk/bin/user-docs/index.html:
some documentation updates added.
2001-10-29 thassine
* trunk/src/common/define.h, trunk/src/common/mm2mdl.cpp,
trunk/src/common/mm2mdl.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp, trunk/src/target3/t3docv.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
trunk/src/target3/t3qm1docv.cpp: some generic improvements
added: some t3 file operations added and mm1_mdl labels feature
improved.
2001-10-23 thassine
* trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.cpp,
trunk/src/common/mm2eng.cpp, trunk/src/common/mm2eng.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/model.cpp,
trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/plane.cpp,
trunk/src/graphics/surface.cpp,
trunk/src/target1/t1m_mm2param_cpp.h,
trunk/src/target1/t1main.cpp, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h: did some cleanups for eng-classes
(removed some old unnecessary parts); nothing should have
changed in how the classes actually work. also tried to improve
code readability generally. in summary: everything should still
work as it used to...
2001-10-18 thassine
* trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h: a new
energy term for out of plane bending must be added soon to
forcefield; added an empty framework for the new term.
2001-10-08 thassine
* trunk/bin/parameters/mm1param/stable/atomtypes.txt,
trunk/bin/parameters/mm1param/stable/parameters1.txt,
trunk/bin/parameters/mm1param/stable/parameters2.txt,
trunk/bin/parameters/mm1param/stable/parameters3.txt,
trunk/bin/parameters/mm1param/stable/parameters4.txt,
trunk/bin/parameters/mm1param/stable/parameters5.txt,
trunk/bin/parameters/mm1param/unstable/atomtypes.txt,
trunk/bin/parameters/mm1param/unstable/parameters1.txt,
trunk/bin/parameters/mm1param/unstable/parameters2.txt,
trunk/bin/parameters/mm1param/unstable/parameters3.txt,
trunk/bin/parameters/mm1param/unstable/parameters4.txt,
trunk/bin/parameters/mm1param/unstable/parameters5.txt,
trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
trunk/src/common/mm1tab9.h: made some rearrangements at mm1_eng
classes that make expermimentation with the classes easier; also
the parameter files have been changed so you should do the #make
install# for this version.
2001-10-03 thassine
* trunk/CHANGES, trunk/PROJECT: changed the old manually
maintained changes-file to a newer log that is maintained using
a cvs2cl.pl utility; it makes a logfile using cvs log
information; see http://www.red-bean.com/cvs2cl/
* trunk/src/common/mm2mdl.h, trunk/src/common/qm2mdl.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3prefs.cpp: a
temporary modification done for colour prefs at t3prefs.cpp
where the default values are just quickly returned (a quick fix
to improve graphics performance of 0.80 compared to 0.42).
2001-10-01 hutchisn
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.h, trunk/src/common/model.h,
trunk/src/common/qm1mdl.h,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/t3main.cpp: Moved import code into mm1model so
it can be called from other parts of the code.
Added support for command-line flags, e.g. -f opens a ghemical
file, -i imports a file.
And any remaining arguments are assumed to be filenames to
import.
(Keep in mind that we can import a .mm1gp or .qm1gp anyway.)
Allows $PATH/ghemical to be used as a web helper application.
* trunk/oelib/data.cpp: Fix bugs with extension handling--make
sure to lowercase before comparisons.
Fixes problems, e.g. .PDB = .pdb
* trunk/oelib/element.txt: Fix max valence on P to allow PF6, etc.
2001-09-27 thassine
* trunk/src/common/define.h: changed the main web address to
www.bioinformatics.org
* trunk/CHANGES, trunk/miniMOPAC/README,
trunk/miniMOPAC/fortran/iter.f, trunk/miniMOPAC/iter.c: mopac
iter.f changed so that the program is not closed even if SCF
convergence problems; the mopac geometry optimization is now
much more resistant to crashes.
2001-09-26 thassine
* trunk/CHANGES, trunk/INSTALL, trunk/miniMOPAC/README,
trunk/miniMOPAC/esp.c, trunk/miniMOPAC/fortran/esp.f,
trunk/miniMOPAC/fortran/iter.f,
trunk/miniMOPAC/fortran/minimopac.f,
trunk/miniMOPAC/fortran/mopac.f, trunk/miniMOPAC/iter.c,
trunk/miniMOPAC/minimopac.c, trunk/src/common/qm1e_mopac.cpp:
some MOPAC fortran code cleanups; unnecessary file operations
removed, and output is now directed to console. now works also
with redhat 7.1???
2001-09-24 thassine
* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/qm1docv.cpp:
added to measure tool a set if model-independent measurement
functions in an effort to make it simpler.
* trunk/BUGLIST, trunk/src/target2/t2qm1docv.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
a new known bug was added; qm1 geomopt dialog was added for
gnome version.
2001-09-14 hutchisn
* trunk/Makefile.in, trunk/bin/ghemical.png,
trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
trunk/src/target3/Makefile.in: Add distclean targets to Makefiles
2001-09-14 thassine
* trunk/src/graphics/views.cpp: the energy level diagram now tries
to detect degenerate energy levels (like in N2 or F2) and draw
them side by side rather than overlapped.
* trunk/src/graphics/docview.cpp, trunk/src/graphics/mm1docv.cpp:
completed the fixes for known mem leaks at docview.cpp
2001-09-07 hutchisn
* trunk/oelib, trunk/oelib/.cvsignore, trunk/oelib/configure,
trunk/oelib/dmol.cpp, trunk/src/common/filetrans.cpp,
trunk/src/graphics/docview.cpp, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/views.cpp, trunk/src/target3/t3prefs.cpp: Fix
a few memory leaks and bugs.
2001-09-07 thassine
* trunk/CHANGES, trunk/configure, trunk/configure.in,
trunk/src/common/define.h: development starts again, promoted
version number to 0.81
2001-09-06 thassine
* trunk/CHANGES, trunk/INSTALL, trunk/bin/user-docs/index.html,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
did a last-minute addition of random conformational search; this
is released as version 0.80
2001-09-05 thassine
* trunk/CHANGES, trunk/INSTALL, trunk/bin/user-docs/index.html:
final fixes to documentation etc...
2001-09-04 thassine
* trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng9.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab9.cpp: some cleanups at MM eng/tab
classes.
* trunk/src/common/mm1eng.h, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab9.cpp: minor changes and cleanups.
2001-09-03 thassine
* trunk/src/common/mm1tab1.cpp, trunk/src/common/mm1tab9.cpp,
trunk/src/common/mm1util.cpp, trunk/src/common/mm1util.h: a
minor cleanup for mm1_typerule.
* trunk/miniMOPAC/README, trunk/src/common/mm1mdl.h: minor
additions to mm1_mdl and MOPAC docs.
2001-08-30 hutchisn
* trunk/oelib/Makefile.in, trunk/oelib/atom.cpp,
trunk/oelib/base.cpp, trunk/oelib/base.h,
trunk/oelib/binary.cpp, trunk/oelib/binary_io.cpp,
trunk/oelib/binary_io.h, trunk/oelib/bitgrid.cpp,
trunk/oelib/bond.cpp, trunk/oelib/chains.cpp,
trunk/oelib/chiral.cpp, trunk/oelib/ctransform.cpp,
trunk/oelib/ctransform.h, trunk/oelib/data.cpp,
trunk/oelib/data.h, trunk/oelib/element.h,
trunk/oelib/element.txt, trunk/oelib/gamess.cpp,
trunk/oelib/generic.cpp, trunk/oelib/generic.h,
trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
trunk/oelib/mdl.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
trunk/oelib/parsmart.cpp, trunk/oelib/parsmart.h,
trunk/oelib/parsmi.cpp, trunk/oelib/patty.cpp,
trunk/oelib/patty.h, trunk/oelib/phmodel.cpp,
trunk/oelib/phmodel.txt, trunk/oelib/ring.cpp,
trunk/oelib/ring.h, trunk/oelib/smarts.cpp,
trunk/oelib/smarts.h, trunk/oelib/smi.cpp,
trunk/oelib/tokenst.cpp, trunk/oelib/typer.cpp,
trunk/src/common/filetrans.cpp: Update with new OELib code -- a
few new filetypes, cleanups and better bonding
for QM files.
2001-08-29 thassine
* trunk/AUTHORS, trunk/src/graphics/camera.cpp,
trunk/src/graphics/camera.h, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: added an alternative way for camera
setup in stereo viewing modes; copyright notices etc updated.
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: added Mike's stereo code (under
target3).
* trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h:
added Mike's stereo code (under graphics).
* trunk/configure, trunk/configure.in, trunk/src/common/define.h,
trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mopac.h,
trunk/src/common/qm1mdl.cpp: a safer mopac locking mechanism
added, version number promoted to 0.80.
2001-08-28 thassine
* trunk/INSTALL, trunk/miniMOPAC/README,
trunk/miniMOPAC/fortran/minimopac.f,
trunk/miniMOPAC/minimopac.c, trunk/src/common/qm1e_mopac.cpp:
mopac engine now survives from change of molecule (the fortran
variables NUMCAL and ISOK were handled wrong), and some docs
updated.
2001-08-27 thassine
* trunk/bin/user-docs/enlevdiag.jpg,
trunk/bin/user-docs/index.html,
trunk/bin/user-docs/maintools.jpg: user's manual quickly updated.
* trunk/src/common/qm1e_mopac.cpp: added comments about a specifig
bug in mopac.
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h: hamiltonian/basis set selection added
for QM engs.
2001-08-26 thassine
* trunk/src/common/mm1alg.cpp, trunk/src/common/mm2alg.cpp,
trunk/src/common/qm1alg.cpp, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1mdl.cpp: minor bugs fixed in
mm1/qm1_geomopt::GetValue() where it calculated gradient when
only energy was needed. also qm1_eng_mopac and qm1_geomopt
settings are optimized for speed/stability (now simple molecules
with good starting geometries are quite safe).
2001-08-25 thassine
* trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp: now the total charge can
be specified in QM models; also checking added for QM setup.
* trunk/src/common/qm1e_mpqc.cpp: energy level diagram now works
for ab initio as well.
2001-08-24 thassine
* trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1e_mpqc.h: force calculations + algorithms
added for MPQC.
* trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1mdl.cpp:
fixed a gradient scaling bug in MOPAC engine; the geometry
optimization is much more robust now.
2001-08-23 hutchisn
* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/views.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3qm1docv.cpp: Migrate general "Graphics"
prefs section to MM1Graphics, etc.
2001-08-23 thassine
* trunk/src/common/engine.h, trunk/src/common/mm1eng.cpp,
trunk/src/common/mm1eng.h, trunk/src/common/mm2eng.cpp,
trunk/src/common/mm2eng.h, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1eng.cpp,
trunk/src/common/qm1eng.h, trunk/src/common/qm1mdl.cpp,
trunk/src/graphics/views.cpp, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2qm1docv.cpp: many smaller cleanups/fixes...
2001-08-22 hutchisn
* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/qm1docv.cpp:
add QM measure functionality
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm2mdl.cpp,
trunk/src/common/qm1mdl.cpp: Use sprintf to give a standardized
output to the geometry opt. output.
* trunk/src/common/qm1mdl.cpp, trunk/src/target3/t3qm1docv.cpp:
Use the same methods for ImportMM command as "convert"
routines--and make sure we update the title!
2001-08-22 thassine
* trunk/src/common/mm1mdl.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/qm1docv.cpp, trunk/src/target3/t3docv.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp: various smaller changes...
* trunk/CHANGES, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/common/qm1e_mpqc.h, trunk/src/common/qm1eng.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/graphics/mtools.cpp, trunk/src/graphics/mtools.h,
trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2views.cpp,
trunk/src/target2/t2views.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: an initial version of energy-level
diagrams for QM models added (now works for mopac only).
2001-08-21 hutchisn
* trunk/src/graphics/mm2docv.cpp, trunk/src/target3/t3qm1docv.cpp:
Add more config use in QM and MM2 modes.
* trunk/src/target3/t3mm1docv.cpp: Add minimal MM -> QM conversion
code. Doesn't quite set the filename correctly
but otherwise pretty much correct.
2001-08-20 thassine
* trunk/CHANGES, trunk/miniMOPAC/esp.c,
trunk/miniMOPAC/fortran/esp.f, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1e_mpqc.cpp, trunk/src/graphics/qm1docv.cpp,
trunk/src/target2/t2qm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
the rest of qm1_eng_mopac plots added, and a scaling bug in MO
plots fixed.
2001-08-18 thassine
* trunk/CHANGES, trunk/miniMOPAC/README,
trunk/miniMOPAC/fortran/minimopac.f,
trunk/miniMOPAC/minimopac.c, trunk/src/common/qm1e_mopac.cpp:
some cleanups done in qm1_eng_mopac (the fortran and C code are
now better separated, easier to maintain).
* trunk/miniMOPAC/fortran/SIZES: ooops, forgot to add the SIZES
file.
2001-08-17 thassine
* trunk/miniMOPAC/fortran/esp.f,
trunk/miniMOPAC/fortran/minimopac.f: added all changes to mopac
fortran source before 2001-08-17.
* trunk/miniMOPAC/fortran, trunk/miniMOPAC/fortran/aababc.f,
trunk/miniMOPAC/fortran/addfck.f,
trunk/miniMOPAC/fortran/addhcr.f,
trunk/miniMOPAC/fortran/addnuc.f,
trunk/miniMOPAC/fortran/analyt.f,
trunk/miniMOPAC/fortran/anavib.f,
trunk/miniMOPAC/fortran/axis.f, trunk/miniMOPAC/fortran/block.f,
trunk/miniMOPAC/fortran/bonds.f,
trunk/miniMOPAC/fortran/brlzon.f,
trunk/miniMOPAC/fortran/btoc.f,
trunk/miniMOPAC/fortran/calpar.f,
trunk/miniMOPAC/fortran/capcor.f,
trunk/miniMOPAC/fortran/cdiag.f,
trunk/miniMOPAC/fortran/chrge.f, trunk/miniMOPAC/fortran/cnvg.f,
trunk/miniMOPAC/fortran/compfg.f,
trunk/miniMOPAC/fortran/consts.f,
trunk/miniMOPAC/fortran/cqden.f,
trunk/miniMOPAC/fortran/datin.f,
trunk/miniMOPAC/fortran/dcart.f,
trunk/miniMOPAC/fortran/delmol.f,
trunk/miniMOPAC/fortran/delri.f,
trunk/miniMOPAC/fortran/denrot.f,
trunk/miniMOPAC/fortran/densit.f,
trunk/miniMOPAC/fortran/depvar.f,
trunk/miniMOPAC/fortran/deri0.f,
trunk/miniMOPAC/fortran/deri1.f,
trunk/miniMOPAC/fortran/deri2.f,
trunk/miniMOPAC/fortran/deri21.f,
trunk/miniMOPAC/fortran/deri22.f,
trunk/miniMOPAC/fortran/deri23.f,
trunk/miniMOPAC/fortran/deritr.f,
trunk/miniMOPAC/fortran/deriv.f,
trunk/miniMOPAC/fortran/dernvo.f,
trunk/miniMOPAC/fortran/ders.f,
trunk/miniMOPAC/fortran/dfock2.f,
trunk/miniMOPAC/fortran/dfpsav.f,
trunk/miniMOPAC/fortran/dgemm.f,
trunk/miniMOPAC/fortran/dgemv.f, trunk/miniMOPAC/fortran/dger.f,
trunk/miniMOPAC/fortran/dgetf2.f,
trunk/miniMOPAC/fortran/dgetrf.f,
trunk/miniMOPAC/fortran/dgetri.f,
trunk/miniMOPAC/fortran/diag.f, trunk/miniMOPAC/fortran/diat.f,
trunk/miniMOPAC/fortran/diat2.f,
trunk/miniMOPAC/fortran/diegrd.f,
trunk/miniMOPAC/fortran/dielen.f,
trunk/miniMOPAC/fortran/diis.f,
trunk/miniMOPAC/fortran/dijkl1.f,
trunk/miniMOPAC/fortran/dijkl2.f,
trunk/miniMOPAC/fortran/dipind.f,
trunk/miniMOPAC/fortran/dipole.f,
trunk/miniMOPAC/fortran/dlaswp.f,
trunk/miniMOPAC/fortran/dofs.f, trunk/miniMOPAC/fortran/dot.f,
trunk/miniMOPAC/fortran/drc.f, trunk/miniMOPAC/fortran/drcout.f,
trunk/miniMOPAC/fortran/dtrmm.f,
trunk/miniMOPAC/fortran/dtrmv.f,
trunk/miniMOPAC/fortran/dtrsm.f,
trunk/miniMOPAC/fortran/dtrti2.f,
trunk/miniMOPAC/fortran/dtrtri.f,
trunk/miniMOPAC/fortran/dvfill.f, trunk/miniMOPAC/fortran/ef.f,
trunk/miniMOPAC/fortran/enpart.f, trunk/miniMOPAC/fortran/esp.f,
trunk/miniMOPAC/fortran/etime.c,
trunk/miniMOPAC/fortran/exchng.f,
trunk/miniMOPAC/fortran/fdate.c,
trunk/miniMOPAC/fortran/ffhpol.f,
trunk/miniMOPAC/fortran/flepo.f, trunk/miniMOPAC/fortran/fmat.f,
trunk/miniMOPAC/fortran/fock1.f,
trunk/miniMOPAC/fortran/fock2.f,
trunk/miniMOPAC/fortran/force.f,
trunk/miniMOPAC/fortran/formxy.f,
trunk/miniMOPAC/fortran/forsav.f,
trunk/miniMOPAC/fortran/frame.f,
trunk/miniMOPAC/fortran/freqcy.f,
trunk/miniMOPAC/fortran/geout.f,
trunk/miniMOPAC/fortran/geoutg.f,
trunk/miniMOPAC/fortran/getgeg.f,
trunk/miniMOPAC/fortran/getgeo.f,
trunk/miniMOPAC/fortran/getsym.f,
trunk/miniMOPAC/fortran/gettxt.f,
trunk/miniMOPAC/fortran/gmetry.f,
trunk/miniMOPAC/fortran/gover.f,
trunk/miniMOPAC/fortran/greenf.f,
trunk/miniMOPAC/fortran/grid.f,
trunk/miniMOPAC/fortran/h1elec.f,
trunk/miniMOPAC/fortran/haddon.f,
trunk/miniMOPAC/fortran/hcore.f,
trunk/miniMOPAC/fortran/helect.f,
trunk/miniMOPAC/fortran/hqrii.f, trunk/miniMOPAC/fortran/ijkl.f,
trunk/miniMOPAC/fortran/ilaenv.f,
trunk/miniMOPAC/fortran/initsv.f,
trunk/miniMOPAC/fortran/interp.f,
trunk/miniMOPAC/fortran/iter.f,
trunk/miniMOPAC/fortran/jcarin.f,
trunk/miniMOPAC/fortran/linmin.f,
trunk/miniMOPAC/fortran/local.f,
trunk/miniMOPAC/fortran/locmin.f,
trunk/miniMOPAC/fortran/lsame.f,
trunk/miniMOPAC/fortran/makpol.f,
trunk/miniMOPAC/fortran/mamult.f,
trunk/miniMOPAC/fortran/matou1.f,
trunk/miniMOPAC/fortran/matout.f,
trunk/miniMOPAC/fortran/matpak.f,
trunk/miniMOPAC/fortran/meci.f, trunk/miniMOPAC/fortran/mecid.f,
trunk/miniMOPAC/fortran/mecih.f,
trunk/miniMOPAC/fortran/mecip.f,
trunk/miniMOPAC/fortran/moldat.f,
trunk/miniMOPAC/fortran/molval.f,
trunk/miniMOPAC/fortran/mopac.f,
trunk/miniMOPAC/fortran/mullik.f,
trunk/miniMOPAC/fortran/mult.f, trunk/miniMOPAC/fortran/nllsq.f,
trunk/miniMOPAC/fortran/nuchar.f,
trunk/miniMOPAC/fortran/parsav.f,
trunk/miniMOPAC/fortran/partxy.f,
trunk/miniMOPAC/fortran/pathk.f,
trunk/miniMOPAC/fortran/paths.f, trunk/miniMOPAC/fortran/perm.f,
trunk/miniMOPAC/fortran/polar.f,
trunk/miniMOPAC/fortran/powsav.f,
trunk/miniMOPAC/fortran/powsq.f,
trunk/miniMOPAC/fortran/prtdrc.f,
trunk/miniMOPAC/fortran/quadr.f,
trunk/miniMOPAC/fortran/react1.f,
trunk/miniMOPAC/fortran/reada.f,
trunk/miniMOPAC/fortran/readmo.f,
trunk/miniMOPAC/fortran/refer.f, trunk/miniMOPAC/fortran/repp.f,
trunk/miniMOPAC/fortran/rotat.f,
trunk/miniMOPAC/fortran/rotate.f, trunk/miniMOPAC/fortran/rsp.f,
trunk/miniMOPAC/fortran/search.f,
trunk/miniMOPAC/fortran/second.f,
trunk/miniMOPAC/fortran/setupg.f,
trunk/miniMOPAC/fortran/solrot.f,
trunk/miniMOPAC/fortran/swap.f,
trunk/miniMOPAC/fortran/sympro.f,
trunk/miniMOPAC/fortran/symtry.f,
trunk/miniMOPAC/fortran/symtrz.f,
trunk/miniMOPAC/fortran/thermo.f,
trunk/miniMOPAC/fortran/timer.f,
trunk/miniMOPAC/fortran/timout.f,
trunk/miniMOPAC/fortran/update.f,
trunk/miniMOPAC/fortran/upsurf.f,
trunk/miniMOPAC/fortran/vecprt.f,
trunk/miniMOPAC/fortran/writmo.f,
trunk/miniMOPAC/fortran/wrtkey.f,
trunk/miniMOPAC/fortran/wrttxt.f,
trunk/miniMOPAC/fortran/xerbla.f,
trunk/miniMOPAC/fortran/xyzint.f: added the original
mopac-7.01-4 fortran source, since it seems to be impossible to
maintain this stuff from f2c'd source.
* trunk/miniMOPAC/esp.c, trunk/src/common/qm1e_mopac.cpp:
miniMOPAC tweaks; ESP plot drawing is now faster, plus MO
plotting added.
2001-08-16 thassine
* trunk/CHANGES, trunk/miniMOPAC/README: added some documentation
about the mopac ESP plots.
2001-08-15 thassine
* trunk/miniMOPAC/esp.c, trunk/src/common/qm1e_mopac.cpp: ESP
plotting added to MOPAC-engine (1st working version).
2001-08-13 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/interface.cpp, trunk/src/common/interface.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/target2/t2mm2docv.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
trajectory viewer for mm2_mdl added (and fixed the timestep of
MD).
2001-08-09 thassine
* trunk/CHANGES, trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3mm2docv.h: the plotting stuff for mm2_mdl is
now also added.
2001-08-08 thassine
* trunk/CHANGES, trunk/src/common/mm2mdl.cpp,
trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2mm2docv.h,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
algorithms for mm2_mdl are added.
* trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
glade_modal_dialog_owner moved into glade_docv class, in order
to make the dialogs work with multiple mdl-classes.
2001-08-03 hutchisn
* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h: Moved InitGL() to parent
DocumentView class--allows all classes to inherit config code
easily.
2001-08-03 thassine
* trunk/src/target3/glade/README,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/Makefile,
trunk/src/target3/glade/src/glade_callbacks.cpp,
trunk/src/target3/glade/src/glade_callbacks.h,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_interface.h,
trunk/src/target3/glade/src/glade_support.cpp,
trunk/src/target3/glade/src/main.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_callbacks.h,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/t3mm1docv.cpp: rebuilt the glade code; some
docs added for the glade stuff.
2001-08-02 thassine
* trunk/src/common/qm1e_mpqc.cpp, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2qm1docv.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
ESP plotting added to qm1_eng_mpqc.
2001-08-01 thassine
* trunk/CHANGES, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm2alg.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/common/qm1e_mpqc.cpp, trunk/src/common/qm1eng.cpp,
trunk/src/common/qm1eng.h, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2qm1docv.cpp: small improvements for mm2_mdl
and qm1_eng_mpqc but nothing ready yet.
2001-07-30 thassine
* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/qm1docv.cpp, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm1docv.h: the 4 first shortcut buttons work
now.
* trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h:
added MeasureEvent() also to (obsolete) qm2_mdl.
2001-07-28 hutchisn
* trunk/src/graphics/camera.cpp, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
trunk/src/graphics/mm1rbn.cpp, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/target3/t3mm1docv.cpp:
Add preliminary measure tool code. Works well--need to add
"modes"
2001-07-24 hutchisn
* trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mtools.cpp:
Change rendering to support more prefs--including passing prefs
for element colors.
* trunk/src/graphics/camera.cpp, trunk/src/graphics/camera.h:
Improve selection with wireframe slightly and add Measure enum.
* trunk/src/common/utility.cpp, trunk/src/common/utility.h: Change
elements to allow prefs class to override colors and VdW radii.
* trunk/src/common/prefs.cpp, trunk/src/common/prefs.h,
trunk/src/target3/t3prefs.cpp, trunk/src/target3/t3prefs.h: Add
Color methods
* trunk/src/common/filetrans.cpp, trunk/src/common/mm1mdl.cpp: Fix
OELib bond synchronization and switch hydrogens to use OELib
method.
2001-07-23 hutchisn
* trunk/src/target3/pixmaps/bond.xpm,
trunk/src/target3/pixmaps/chain.xpm,
trunk/src/target3/pixmaps/element.xpm,
trunk/src/target3/pixmaps/invert.xpm,
trunk/src/target3/pixmaps/molecule.xpm,
trunk/src/target3/pixmaps/residue.xpm,
trunk/src/target3/t3main.cpp: Added sample pixmaps for shortcut
bar.
2001-07-22 thassine
* trunk/src/target1/t1m_mm2param_cpp.h,
trunk/src/target1/t1m_mm2param_h.h: added some files for mm2_mdl.
* trunk/miniMOPAC/README, trunk/miniMOPAC/dgetf2.c,
trunk/miniMOPAC/dgetri.c, trunk/miniMOPAC/dlaswp.c,
trunk/miniMOPAC/dtrti2.c, trunk/miniMOPAC/ef.c,
trunk/src/common/Makefile.OLD, trunk/src/common/factory.cpp,
trunk/src/common/factory.h, trunk/src/common/prefs.cpp,
trunk/src/common/prefs.h, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1e_mopac.h, trunk/src/common/qm1e_mpqc.cpp,
trunk/src/graphics/Makefile.OLD, trunk/src/target1/Makefile.OLD,
trunk/src/target2/Makefile.OLD, trunk/src/target2/t2views.cpp,
trunk/src/target2/t2views.h, trunk/src/target3/Makefile.OLD,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3prefs.cpp,
trunk/src/target3/t3prefs.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3views.h: some mopac/mpqc conflicts fixed,
and mopac intermediate files FOR005 FOR006 SHUTDOWN cleaned.
2001-07-20 hutchisn
* trunk/src/common/factory.h, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/target3/t3prefs.cpp, trunk/src/target3/t3prefs.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
Finished implementation of prefs class through GNOME config
classes. Currently nothing sets prefs from the code, and
rendering is an example of accessing pref values.
2001-07-09 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/common/qm1mdl.cpp, trunk/src/graphics/camera.cpp,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/views.cpp,
trunk/src/target2/t2mm1docv.cpp: some comments added and
arrangements done for stereo image viewing.
2001-06-29 thassine
* trunk/src/common/intcrd.cpp, trunk/src/common/intcrd.h,
trunk/src/common/mm1ic.cpp, trunk/src/common/mm1ic.h: ooops,
forgot to add some files in the last commit.
* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/mm1alg.cpp, trunk/src/common/mm1alg.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/qm1mdl.cpp,
trunk/src/target2/t2mm1docv.cpp: some groundwork added for
mm1_mdl multiple crd_sets and conformational search tools.
2001-06-25 thassine
* trunk/bin/user-docs/index.html, trunk/src/common/notice.cpp,
trunk/src/common/notice.h, trunk/src/target3/t3main.cpp: minor
updates in user's manual and copyright notices (MOPAC included).
2001-06-21 thassine
* trunk/CHANGES, trunk/src/graphics/camera.cpp,
trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3mm2docv.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: gnome MDI system revised; one
view/child (GtkNotebook container), project views now grouped
together.
2001-06-19 thassine
* trunk/miniMOPAC/etime.c, trunk/src/common/conjgrad.h,
trunk/src/common/errutil.cpp, trunk/src/common/factory.cpp,
trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm1tab1.cpp, trunk/src/common/mm1tab1.h,
trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1tab9.h,
trunk/src/common/mm1util.cpp, trunk/src/common/mm1util.h,
trunk/src/common/mm2eng.cpp, trunk/src/common/mm2eng.h,
trunk/src/common/mm2mdl.h, trunk/src/common/mm2util.h,
trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/common/notice.cpp, trunk/src/common/notice.h,
trunk/src/common/prefs.cpp, trunk/src/common/qm1e_mopac.cpp,
trunk/src/common/qm1e_mpqc.cpp, trunk/src/common/qm1e_mpqc.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/common/typedef.h, trunk/src/common/utility.cpp,
trunk/src/common/v3d.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/surface.cpp, trunk/src/graphics/surface.h,
trunk/src/target2/t2main.h, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2views.cpp,
trunk/src/target2/t2views.h,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3docv.cpp,
trunk/src/target3/t3docv.h, trunk/src/target3/t3errutil.cpp,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3prefs.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: some cleanups done for redhat7.1
(seems to work) and gcc3.0 (still some stl/namespace problems?).
2001-06-13 thassine
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
some menuitems added, and an initial mm1gp <-> qm1gp conversion
feature
2001-05-28 thassine
* trunk/src/common/filetrans.cpp: some comments added
2001-05-23 thassine
* trunk/src/common/factory.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm2mdl.cpp,
trunk/src/target2/t2views.h, trunk/src/target3/t3views.h: just
some cleanups here and there
2001-05-21 thassine
* trunk/src/common/mm1mdl.cpp: again some readpdb tweaks.
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: some
readpdb changes again
2001-05-18 thassine
* trunk/src/common/factory.cpp, trunk/src/common/factory.h: ooops,
forgot to add the class_factory files...
* trunk/CHANGES, trunk/src/common/Makefile.OLD,
trunk/src/common/Makefile.in, trunk/src/common/errutil.cpp,
trunk/src/common/errutil.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm2mdl.cpp,
trunk/src/common/mm2mdl.h, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h, trunk/src/common/qm2mdl.cpp,
trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h, trunk/src/graphics/views.h,
trunk/src/target1/t1main.cpp, trunk/src/target2/t2docv.cpp,
trunk/src/target2/t2docv.h, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2mm2docv.h,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: many
factory classes combined to class_factory.
2001-05-16 thassine
* trunk/src/target3/t3main.cpp: just added some buttons, to see
what it looks like...
2001-05-16 hutchisn
* trunk/src/common/Makefile.in, trunk/src/common/prefs.cpp,
trunk/src/common/prefs.h, trunk/src/target3/Makefile.in,
trunk/src/target3/t3prefs.cpp, trunk/src/target3/t3prefs.h: Add
new "prefs" class to interface with gnome-config
to allow user-config for various things.
2001-05-15 thassine
* trunk/src/common/mm1mdl.cpp: again some fixes to readpdb
* trunk/src/common/mm1mdl.cpp: just some fixes added to readpdb
2001-05-14 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/target3/t3mm1docv.cpp:
organized menus a bit, some changes to readpdb
2001-05-11 hutchisn
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
Add stubs for export graphics, as well as "zap all" and "compute
formula"
2001-05-11 thassine
* trunk/src/graphics/mtools.cpp, trunk/src/graphics/mtools.h,
trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h:
switched to a single measure tool, multiple toolbars added.
2001-05-08 thassine
* trunk/miniMOPAC/Makefile: miniMOPAC/Makefile removed; configure
will update it.
* trunk/miniMOPAC/Makefile, trunk/miniMOPAC/Makefile.OLD,
trunk/src/Makefile.OLD, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm2mdl.cpp,
trunk/src/common/mm2mdl.h, trunk/src/common/model.h,
trunk/src/target2/t2mm2docv.cpp: some improvements to readpdb;
it now reads multiple crd-sets present in NMR entries
2001-05-07 hutchisn
* trunk/src/graphics/Makefile.in: Remove io-* from build list
until GNOME catches up (!)
2001-05-04 hutchisn
* trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h: Add
buttons for measure tools.
* trunk/src/graphics/mtools.cpp, trunk/src/graphics/mtools.h,
trunk/src/graphics/views.cpp, trunk/src/graphics/views.h: Add
tools for measurements.
* trunk/src/target3/pixmaps, trunk/src/target3/pixmaps/.cvsignore,
trunk/src/target3/pixmaps/angle.xpm,
trunk/src/target3/pixmaps/dihedral.xpm,
trunk/src/target3/pixmaps/distance.xpm,
trunk/src/target3/pixmaps/draw.xpm,
trunk/src/target3/pixmaps/erase.xpm,
trunk/src/target3/pixmaps/orb_xy.xpm,
trunk/src/target3/pixmaps/orb_z.xpm,
trunk/src/target3/pixmaps/rot_xy.xpm,
trunk/src/target3/pixmaps/rot_z.xpm,
trunk/src/target3/pixmaps/select.xpm,
trunk/src/target3/pixmaps/trans_xy.xpm,
trunk/src/target3/pixmaps/trans_z.xpm,
trunk/src/target3/pixmaps/zoom.xpm: Add transparency to button
pics and buttons for measure tools.
* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h:
Changes to make sure window titles update when importing.
* trunk/src/target3/Makefile.in: Make sure miniMOPAC is compiled
in.
* trunk/src/graphics/Makefile.in: Compile io-* for exporting.
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: Added
CLear and DoFormula methods.
* trunk/src/common/Makefile.in: Remove EXTERN_GLOBALS -- not needed
* trunk/src/graphics/io-jpg.cpp, trunk/src/graphics/io-jpg.h,
trunk/src/graphics/io-png.cpp, trunk/src/graphics/io-png.h: Add
GNOME code for exporting GdkPixbuf -> PNG or JPEG files.
* trunk/oelib/aromatic.h, trunk/oelib/atom.cpp,
trunk/oelib/atomtyp.h, trunk/oelib/bin2hex.pl,
trunk/oelib/binary.cpp, trunk/oelib/binary.h,
trunk/oelib/binary_io.cpp, trunk/oelib/binary_io.h,
trunk/oelib/chains.cpp, trunk/oelib/chains.h,
trunk/oelib/configure, trunk/oelib/ctransform.cpp,
trunk/oelib/ctransform.h, trunk/oelib/data.cpp,
trunk/oelib/data.h, trunk/oelib/dmol.cpp, trunk/oelib/element.h,
trunk/oelib/extable.h, trunk/oelib/extable.txt,
trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
trunk/oelib/gaussian.cpp, trunk/oelib/generic.cpp,
trunk/oelib/generic.h, trunk/oelib/ghemical.cpp,
trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
trunk/oelib/matrix.cpp, trunk/oelib/matrix.h,
trunk/oelib/mdl.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
trunk/oelib/mol2.cpp, trunk/oelib/mopac.cpp,
trunk/oelib/nwchem.cpp, trunk/oelib/oelib.dsp,
trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
trunk/oelib/parsmart.cpp, trunk/oelib/parsmi.cpp,
trunk/oelib/phmodel.cpp, trunk/oelib/phmodeldata.h,
trunk/oelib/report.cpp, trunk/oelib/resdata.h,
trunk/oelib/rotor.cpp, trunk/oelib/smi.cpp,
trunk/oelib/typer.cpp, trunk/oelib/types.h: Update with current
OELib version.
2001-05-03 hutchisn
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/miniMOPAC/Makefile.in, trunk/oelib/Makefile.in: Update for
miniMOPAC, test for g2c/f2c library (hopefully).
* trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_interface.h,
trunk/src/target3/glade/src/glade_support.cpp: Add Element
options dialog to glade.
2001-05-02 thassine
* trunk/src/common/mm1mdl.cpp: added a small fix to readpdb so
that it can read also NMR entries.
2001-04-30 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: some
improvements to readpdb-functions.
2001-04-27 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp: revived ImportENT_OLD and
changed them to readpdb-functions (for advanced PDB file imports)
2001-04-24 thassine
* trunk/INSTALL, trunk/src/common/Makefile.OLD,
trunk/src/target3/t3dialog.cpp: documentation, old makefile, t3
bondtype dialog fixed a bit.
2001-04-20 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm2alg.cpp, trunk/src/common/mm2alg.h,
trunk/src/common/mm2mdl.h, trunk/src/common/model.h,
trunk/src/target2/t2mm2docv.cpp: continued merging the mm2_mdl.
2001-04-19 thassine
* trunk/src/common/mm1mdl.h, trunk/src/common/mm2eng.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/common/mm2util.cpp, trunk/src/common/mm2util.h,
trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/common/qm1mdl.h, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm2docv.h, trunk/src/graphics/qm2docv.h,
trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.h:
continued merging the mm2_mdl, plus some cleanups.
2001-04-18 thassine
* trunk/CHANGES, trunk/bin/parameters/mm2param,
trunk/bin/parameters/mm2param/loopdip.txt,
trunk/bin/parameters/mm2param/looptor.txt,
trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.h,
trunk/src/common/mm2eng.cpp, trunk/src/common/mm2eng.h,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2docv.h,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm2docv.cpp, trunk/src/target2/t2mm2docv.h,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h:
started merging the mm2_mdl code (accepted for publication :)
* trunk/CHANGES, trunk/miniMOPAC, trunk/miniMOPAC/Makefile,
trunk/miniMOPAC/Makefile.OLD, trunk/miniMOPAC/README,
trunk/miniMOPAC/aababc.c, trunk/miniMOPAC/addfck.c,
trunk/miniMOPAC/addhcr.c, trunk/miniMOPAC/addnuc.c,
trunk/miniMOPAC/analyt.c, trunk/miniMOPAC/anavib.c,
trunk/miniMOPAC/axis.c, trunk/miniMOPAC/block.c,
trunk/miniMOPAC/bonds.c, trunk/miniMOPAC/brlzon.c,
trunk/miniMOPAC/btoc.c, trunk/miniMOPAC/calpar.c,
trunk/miniMOPAC/capcor.c, trunk/miniMOPAC/cdiag.c,
trunk/miniMOPAC/chrge.c, trunk/miniMOPAC/cnvg.c,
trunk/miniMOPAC/compfg.c, trunk/miniMOPAC/consts.c,
trunk/miniMOPAC/cqden.c, trunk/miniMOPAC/datin.c,
trunk/miniMOPAC/dcart.c, trunk/miniMOPAC/delmol.c,
trunk/miniMOPAC/delri.c, trunk/miniMOPAC/denrot.c,
trunk/miniMOPAC/densit.c, trunk/miniMOPAC/depvar.c,
trunk/miniMOPAC/deri0.c, trunk/miniMOPAC/deri1.c,
trunk/miniMOPAC/deri2.c, trunk/miniMOPAC/deri21.c,
trunk/miniMOPAC/deri22.c, trunk/miniMOPAC/deri23.c,
trunk/miniMOPAC/deritr.c, trunk/miniMOPAC/deriv.c,
trunk/miniMOPAC/dernvo.c, trunk/miniMOPAC/ders.c,
trunk/miniMOPAC/dfock2.c, trunk/miniMOPAC/dfpsav.c,
trunk/miniMOPAC/dgemm.c, trunk/miniMOPAC/dgemv.c,
trunk/miniMOPAC/dger.c, trunk/miniMOPAC/dgetf2.c,
trunk/miniMOPAC/dgetrf.c, trunk/miniMOPAC/dgetri.c,
trunk/miniMOPAC/diag.c, trunk/miniMOPAC/diat.c,
trunk/miniMOPAC/diat2.c, trunk/miniMOPAC/diegrd.c,
trunk/miniMOPAC/dielen.c, trunk/miniMOPAC/diis.c,
trunk/miniMOPAC/dijkl1.c, trunk/miniMOPAC/dijkl2.c,
trunk/miniMOPAC/dipind.c, trunk/miniMOPAC/dipole.c,
trunk/miniMOPAC/dlaswp.c, trunk/miniMOPAC/dofs.c,
trunk/miniMOPAC/dot.c, trunk/miniMOPAC/drc.c,
trunk/miniMOPAC/drcout.c, trunk/miniMOPAC/dtrmm.c,
trunk/miniMOPAC/dtrmv.c, trunk/miniMOPAC/dtrsm.c,
trunk/miniMOPAC/dtrti2.c, trunk/miniMOPAC/dtrtri.c,
trunk/miniMOPAC/dvfill.c, trunk/miniMOPAC/ef.c,
trunk/miniMOPAC/enpart.c, trunk/miniMOPAC/esp.c,
trunk/miniMOPAC/etime.c, trunk/miniMOPAC/exchng.c,
trunk/miniMOPAC/fdate.c, trunk/miniMOPAC/ffhpol.c,
trunk/miniMOPAC/flepo.c, trunk/miniMOPAC/fmat.c,
trunk/miniMOPAC/fock1.c, trunk/miniMOPAC/fock2.c,
trunk/miniMOPAC/force.c, trunk/miniMOPAC/formxy.c,
trunk/miniMOPAC/forsav.c, trunk/miniMOPAC/frame.c,
trunk/miniMOPAC/freqcy.c, trunk/miniMOPAC/geout.c,
trunk/miniMOPAC/geoutg.c, trunk/miniMOPAC/getgeg.c,
trunk/miniMOPAC/getgeo.c, trunk/miniMOPAC/getsym.c,
trunk/miniMOPAC/gettxt.c, trunk/miniMOPAC/gmetry.c,
trunk/miniMOPAC/gover.c, trunk/miniMOPAC/greenf.c,
trunk/miniMOPAC/grid.c, trunk/miniMOPAC/h1elec.c,
trunk/miniMOPAC/haddon.c, trunk/miniMOPAC/hcore.c,
trunk/miniMOPAC/helect.c, trunk/miniMOPAC/hqrii.c,
trunk/miniMOPAC/ijkl.c, trunk/miniMOPAC/ilaenv.c,
trunk/miniMOPAC/initsv.c, trunk/miniMOPAC/interp.c,
trunk/miniMOPAC/iter.c, trunk/miniMOPAC/jcarin.c,
trunk/miniMOPAC/linmin.c, trunk/miniMOPAC/local.c,
trunk/miniMOPAC/locmin.c, trunk/miniMOPAC/lsame.c,
trunk/miniMOPAC/makpol.c, trunk/miniMOPAC/mamult.c,
trunk/miniMOPAC/matou1.c, trunk/miniMOPAC/matout.c,
trunk/miniMOPAC/matpak.c, trunk/miniMOPAC/meci.c,
trunk/miniMOPAC/mecid.c, trunk/miniMOPAC/mecih.c,
trunk/miniMOPAC/mecip.c, trunk/miniMOPAC/minimopac.c,
trunk/miniMOPAC/moldat.c, trunk/miniMOPAC/molval.c,
trunk/miniMOPAC/mullik.c, trunk/miniMOPAC/mult.c,
trunk/miniMOPAC/nllsq.c, trunk/miniMOPAC/nuchar.c,
trunk/miniMOPAC/parsav.c, trunk/miniMOPAC/partxy.c,
trunk/miniMOPAC/pathk.c, trunk/miniMOPAC/paths.c,
trunk/miniMOPAC/perm.c, trunk/miniMOPAC/polar.c,
trunk/miniMOPAC/powsav.c, trunk/miniMOPAC/powsq.c,
trunk/miniMOPAC/prtdrc.c, trunk/miniMOPAC/quadr.c,
trunk/miniMOPAC/react1.c, trunk/miniMOPAC/reada.c,
trunk/miniMOPAC/readmo.c, trunk/miniMOPAC/refer.c,
trunk/miniMOPAC/repp.c, trunk/miniMOPAC/rotat.c,
trunk/miniMOPAC/rotate.c, trunk/miniMOPAC/rsp.c,
trunk/miniMOPAC/search.c, trunk/miniMOPAC/second.c,
trunk/miniMOPAC/setupg.c, trunk/miniMOPAC/solrot.c,
trunk/miniMOPAC/swap.c, trunk/miniMOPAC/sympro.c,
trunk/miniMOPAC/symtry.c, trunk/miniMOPAC/symtrz.c,
trunk/miniMOPAC/thermo.c, trunk/miniMOPAC/timer.c,
trunk/miniMOPAC/timout.c, trunk/miniMOPAC/update.c,
trunk/miniMOPAC/upsurf.c, trunk/miniMOPAC/vecprt.c,
trunk/miniMOPAC/writmo.c, trunk/miniMOPAC/wrtkey.c,
trunk/miniMOPAC/wrttxt.c, trunk/miniMOPAC/xerbla.c,
trunk/miniMOPAC/xyzint.c, trunk/src/common/Makefile.OLD,
trunk/src/common/Makefile.in, trunk/src/common/errutil.cpp,
trunk/src/common/qm1alg.cpp, trunk/src/common/qm1alg.h,
trunk/src/common/qm1e_mopac.cpp, trunk/src/common/qm1e_mopac.h,
trunk/src/common/qm1e_mpqc.cpp, trunk/src/common/qm1e_mpqc.h,
trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
trunk/src/common/qm1eng1.cpp, trunk/src/common/qm1eng1.h,
trunk/src/common/qm1eng9.cpp, trunk/src/common/qm1eng9.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/graphics/camera.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2qm1docv.cpp,
trunk/src/target2/t2qm1docv.h, trunk/src/target3/Makefile.OLD,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
added miniMOPAC and QM geometry optimization.
2001-03-30 thassine
* trunk/configure, trunk/configure.in, trunk/src/common/define.h:
switched back to devel settings; the version number is now 0.43
* trunk/CHANGES, trunk/src/common/define.h,
trunk/src/common/notice.cpp, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm2docv.cpp,
trunk/src/target3/t3qm1docv.cpp: minor cleanups; this is
released as 0.42
2001-03-28 thassine
* trunk/src/common/model.cpp, trunk/src/common/typedef.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/target1/Makefile.OLD,
trunk/src/target2/Makefile.OLD, trunk/src/target3/Makefile.OLD:
some comments added, X11/ogl headers and libs removed from
TARGET1.
2001-03-23 hutchisn
* trunk/oelib/jaguar.cpp: Fix problems with Jaguar translator.
2001-03-22 hutchisn
* trunk/src/graphics/mm1docv.cpp: Add new multiple-bond rendering.
Now uses line stipple to render conjugated bonds fairly well.
* trunk/oelib/Makefile, trunk/oelib/Makefile.in,
trunk/oelib/data.cpp, trunk/oelib/data.h, trunk/oelib/dmol.cpp,
trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
trunk/oelib/fileformat.h, trunk/oelib/gamess.cpp,
trunk/oelib/ghemical.cpp: Added Dmol format and cleanups.
2001-03-22 thassine
* trunk/src/common/mm1util.h, trunk/src/graphics/mm1rbn.cpp,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target3/t3mm1docv.cpp: the bug with ribbon objects
should now be fixed.
2001-03-19 thassine
* trunk/oelib/Makefile, trunk/src/common/filetrans.cpp,
trunk/src/common/filetrans.h: added syncronization for bonds
into file_trans::Synchronize().
2001-03-16 thassine
* trunk/oelib/Makefile, trunk/src/common/filetrans.cpp,
trunk/src/common/mm1mdl.cpp, trunk/src/common/utility.cpp,
trunk/src/common/utility.h, trunk/src/target2/t2mm1docv.cpp:
oelib syncronization and other small improvements.
2001-03-15 hutchisn
* trunk/oelib/ghemical.cpp, trunk/oelib/xyz.cpp: Fix minor bugs in
file translators.
* trunk/src/common/filetrans.cpp: Fix "the bug" with calling extab
before it was properly set.
* trunk/oelib/alchemy.cpp, trunk/oelib/amber.cpp,
trunk/oelib/atomtyp.h, trunk/oelib/atomtyp.txt,
trunk/oelib/element.h, trunk/oelib/element.txt,
trunk/oelib/extable.h, trunk/oelib/ghemical.cpp,
trunk/oelib/hin.cpp, trunk/oelib/jaguar.cpp,
trunk/oelib/mpqc.cpp, trunk/oelib/oelib.dsp,
trunk/oelib/phmodeldata.h, trunk/oelib/qchem.cpp,
trunk/oelib/tinker.cpp, trunk/oelib/types.h,
trunk/oelib/types.txt, trunk/oelib/unichem.cpp,
trunk/oelib/xyz.cpp: Added fixes to the translators--now much
better about getting elements correct for rare atoms (e.g. Pb).
2001-03-15 thassine
* trunk/oelib/Makefile, trunk/oelib/atom.cpp, trunk/oelib/mol.h,
trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h:
switched to a less complicated way to do oelib compatibility
2001-03-14 hutchisn
* trunk/bin/examples/PeriodicTable.mm1gp,
trunk/src/common/utility.cpp, trunk/src/common/utility.h: Fixed
atom colors and add example Periodic Table.
2001-03-14 thassine
* trunk/CHANGES, trunk/configure, trunk/configure.in,
trunk/oelib/atom.cpp, trunk/oelib/mol.h,
trunk/src/common/define.h, trunk/src/common/filetrans.cpp,
trunk/src/common/filetrans.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/utility.cpp,
trunk/src/common/utility.h, trunk/src/graphics/Makefile.OLD,
trunk/src/graphics/Makefile.in, trunk/src/target1/Makefile.OLD,
trunk/src/target2/Makefile.OLD, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target3/Makefile.OLD, trunk/src/target3/Makefile.in:
some mm1_mdl <=> oelib compatibility features started.
2001-03-12 thassine
* trunk/BUGLIST, trunk/CHANGES, trunk/INSTALL, trunk/PROJECT,
trunk/bin/examples/2-chlorobutane.mm1gp,
trunk/bin/examples/3-phenylpropanal.mm1gp,
trunk/bin/examples/acetylsalicylic_acid.mm1gp,
trunk/bin/examples/alpha-pinene.mm1gp,
trunk/bin/examples/bromobenzene.mm1gp,
trunk/bin/examples/camphor.mm1gp,
trunk/bin/examples/cinnamaldehyde.mm1gp,
trunk/bin/examples/cis-2-pentene.mm1gp,
trunk/bin/examples/cyclohexane.mm1gp,
trunk/bin/examples/naphtalene.mm1gp, trunk/oelib/Makefile,
trunk/src/common/mm1mdl.cpp, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/target3/t3docv.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3views.cpp: this is released as version 0.41
2001-03-08 hutchisn
* trunk/src/common/define.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
Add support for label Atom IDs
* trunk/src/common/mm1mdl.cpp: ReadStream changes to support
reading charges
* trunk/src/common/notice.cpp: Update copyright with OELib info.
* trunk/src/common/filetrans.cpp: Update for new OELib changes.
* trunk/Makefile.in: Add target for help files.
* trunk/oelib/Makefile.in, trunk/oelib/Vector.cpp,
trunk/oelib/Vector.h, trunk/oelib/alchemy.cpp,
trunk/oelib/amber.cpp, trunk/oelib/aromatic.h,
trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
trunk/oelib/atomtyp.h, trunk/oelib/atomtyp.txt,
trunk/oelib/balst.cpp, trunk/oelib/bgf.cpp,
trunk/oelib/bin2hex.pl, trunk/oelib/binary.cpp,
trunk/oelib/binary.h, trunk/oelib/bitgrid.cpp,
trunk/oelib/bitgrid.h, trunk/oelib/bitvec.cpp,
trunk/oelib/bitvec.h, trunk/oelib/bond.cpp, trunk/oelib/box.cpp,
trunk/oelib/c3d.cpp, trunk/oelib/cacao.cpp,
trunk/oelib/cache.cpp, trunk/oelib/car.cpp, trunk/oelib/ccc.cpp,
trunk/oelib/chdrw.cpp, trunk/oelib/chiral.cpp,
trunk/oelib/chiral.h, trunk/oelib/commandline.cpp,
trunk/oelib/commandline.h, trunk/oelib/configure,
trunk/oelib/csr.cpp, trunk/oelib/cssr.cpp,
trunk/oelib/cwrap.cpp, trunk/oelib/cwrap.h,
trunk/oelib/data.cpp, trunk/oelib/data.h, trunk/oelib/element.h,
trunk/oelib/extable.h, trunk/oelib/extable.txt,
trunk/oelib/feat.cpp, trunk/oelib/fh.cpp,
trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
trunk/oelib/gamess.cpp, trunk/oelib/ghemical.cpp,
trunk/oelib/grid.cpp, trunk/oelib/grid.h,
trunk/oelib/gromos96.cpp, trunk/oelib/hin.cpp,
trunk/oelib/jaguar.cpp, trunk/oelib/main.cpp,
trunk/oelib/matrix.cpp, trunk/oelib/matrix.h,
trunk/oelib/mdl.cpp, trunk/oelib/mmod.cpp, trunk/oelib/mol.cpp,
trunk/oelib/mol.h, trunk/oelib/mol2.cpp,
trunk/oelib/molchrg.cpp, trunk/oelib/molchrg.h,
trunk/oelib/molvector.cpp, trunk/oelib/molvector.h,
trunk/oelib/mpqc.cpp, trunk/oelib/oeifstream.h,
trunk/oelib/oelib.dsp, trunk/oelib/oeutil.cpp,
trunk/oelib/oeutil.h, trunk/oelib/parsmart.cpp,
trunk/oelib/parsmart.h, trunk/oelib/parsmi.cpp,
trunk/oelib/patty.cpp, trunk/oelib/patty.h, trunk/oelib/pdb.cpp,
trunk/oelib/phmodel.cpp, trunk/oelib/phmodel.h,
trunk/oelib/phmodel.txt, trunk/oelib/phmodeldata.h,
trunk/oelib/qchem.cpp, trunk/oelib/rand.cpp,
trunk/oelib/resdata.h, trunk/oelib/ring.cpp, trunk/oelib/ring.h,
trunk/oelib/rotor.cpp, trunk/oelib/rotor.h, trunk/oelib/smi.cpp,
trunk/oelib/smi.h, trunk/oelib/tokenst.cpp,
trunk/oelib/typer.cpp, trunk/oelib/typer.h, trunk/oelib/types.h,
trunk/oelib/version.h, trunk/oelib/xed.cpp: Updates to oelib
files.
2001-03-08 thassine
* trunk/CHANGES, trunk/src/common/notice.cpp,
trunk/src/common/notice.h, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3main.h: added the Help/Help item to the main
menu, copyright notices updated to include OELib
* trunk/bin/user-docs/index.html,
trunk/bin/user-docs/maintools.jpg: updated the user's manual
2001-02-16 thassine
* trunk/src/Makefile.OLD: this will make quick test builds easier.
* trunk/bin/user-docs, trunk/bin/user-docs/index.html: added some
framework for the user manual
2001-02-13 thassine
* trunk/INSTALL, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h:
added some quick improvements to qm1-model to boost its ease of
use.
2001-02-12 hutchisn
* trunk/configure, trunk/configure.in: Solved configure problems
with MPQC and oelib.
* trunk/configure, trunk/configure.in: Fix problem with configure
in srcdir.
2001-02-12 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/qm1eng1.cpp,
trunk/src/common/qm1mdl.cpp, trunk/src/graphics/Makefile.OLD,
trunk/src/graphics/camera.cpp, trunk/src/graphics/docview.cpp,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1rbn.cpp,
trunk/src/graphics/mm2docv.cpp, trunk/src/graphics/mm2rbn.cpp,
trunk/src/graphics/mtools.cpp, trunk/src/graphics/objects.cpp,
trunk/src/graphics/plane.cpp, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/surface.cpp,
trunk/src/graphics/views.cpp, trunk/src/target1/Makefile.OLD,
trunk/src/target1/config.h.OLD, trunk/src/target2/Makefile.OLD,
trunk/src/target2/config.h.OLD, trunk/src/target3/Makefile.OLD,
trunk/src/target3/config.h.OLD: a bug that affected MPQC front
end compilation is now fixed (thanks Mark).
2001-02-11 thassine
* trunk/CHANGES, trunk/bin/examples/1gar.mm2gp,
trunk/bin/examples/1hcl.mm2gp, trunk/bin/examples/4rhn.mm2gp,
trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/mm2mdl.cpp, trunk/src/common/mm2mdl.h,
trunk/src/common/mm2util.cpp, trunk/src/common/mm2util.h,
trunk/src/common/model.h, trunk/src/graphics/Makefile.OLD,
trunk/src/graphics/Makefile.in, trunk/src/graphics/mm2docv.cpp,
trunk/src/graphics/mm2docv.h, trunk/src/graphics/mm2rbn.cpp,
trunk/src/graphics/mm2rbn.h, trunk/src/graphics/views.h,
trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2main.h, trunk/src/target2/t2mm2docv.cpp,
trunk/src/target2/t2mm2docv.h, trunk/src/target3/Makefile.OLD,
trunk/src/target3/Makefile.in, trunk/src/target3/t3docv.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm2docv.cpp, trunk/src/target3/t3mm2docv.h,
trunk/src/target3/t3views.h: tadaall added a preview version of
the reduced protein modelling thing.
2001-02-10 thassine
* trunk/INSTALL, trunk/configure, trunk/configure.in,
trunk/src/common/define.h, trunk/src/common/engine.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/qm1mdl.cpp,
trunk/src/target3/t3views.cpp: changed back to devel settings
(version number, releasedate); small fixes appled here and there.
2001-02-07 thassine
* trunk/small-utilities/README, trunk/small-utilities/gp2mpqc.cpp,
trunk/src/graphics/spline.h, trunk/src/graphics/views.h: added
some final fixes to documentation; this is released as 0.40
2001-02-06 hutchisn
* trunk/oelib/extable.txt: Add sorted extable to make menus more
user-friendly.
* trunk/src/common/filetrans.cpp: Fix bug with
GetImportDescription.
* trunk/oelib/data.cpp: Fix problem with GetType from an
integer--table lookup was in the wrong place!
2001-02-06 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/target2/t2docv.h,
trunk/src/target3/t3docv.h, trunk/src/target3/t3errutil.h,
trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3views.h:
added some more DOC++ style documentation.
* trunk/AUTHORS, trunk/CHANGES, trunk/INSTALL, trunk/PROJECT:
revised/updated some documentation.
* trunk/configure, trunk/configure.in, trunk/oelib/Makefile,
trunk/src/common/define.h, trunk/src/common/notice.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h: some cleanups at glade
optionmenus; the version number promoted to 0.40
2001-02-06 hutchisn
* trunk/src/target3/glade_callbacks.cpp: Use file_trans methods to
specifically request a file type when the user picks it or
"Automatic" based on the file name.
* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h:
Add support for specifically requesting an import or export type
(by index #).
* trunk/oelib/Makefile.in: Add target to rebuild Makefile if
Makefile.in or configure script changes.
2001-02-05 thassine
* trunk/src/target3/glade_callbacks.cpp: the file import/export
dialogs seem to work now...
* trunk/oelib/data.cpp, trunk/oelib/extable.txt,
trunk/oelib/ghemical.cpp, trunk/oelib/mol.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h: the filename change is done
also in oelib; the file import/export dialogs almost work now.
* trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_callbacks.cpp,
trunk/src/target3/glade/src/glade_callbacks.h,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_interface.h,
trunk/src/target3/glade/src/main.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_callbacks.h,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp: changed the glade project and
code so that each dialog (and most important widgets) have their
own simple namespace.
2001-02-04 thassine
* trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/common/qm2eng.cpp, trunk/src/common/qm2eng.h,
trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
trunk/src/graphics/qm1docv.cpp, trunk/src/graphics/qm1docv.h,
trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
some files were lost in the last commit; added them back...
* trunk/CHANGES, trunk/INSTALL,
trunk/bin/examples/2-chlorobutane.gpMM,
trunk/bin/examples/2-chlorobutane.mm1gp,
trunk/bin/examples/3-phenylpropanal.gpMM,
trunk/bin/examples/3-phenylpropanal.mm1gp,
trunk/bin/examples/acetylsalicylic_acid.gpMM,
trunk/bin/examples/acetylsalicylic_acid.mm1gp,
trunk/bin/examples/alpha-pinene.gpMM,
trunk/bin/examples/alpha-pinene.mm1gp,
trunk/bin/examples/bromobenzene.gpMM,
trunk/bin/examples/bromobenzene.mm1gp,
trunk/bin/examples/camphor.gpMM,
trunk/bin/examples/camphor.mm1gp,
trunk/bin/examples/cinnamaldehyde.gpMM,
trunk/bin/examples/cinnamaldehyde.mm1gp,
trunk/bin/examples/cis-2-pentene.gpMM,
trunk/bin/examples/cis-2-pentene.mm1gp,
trunk/bin/examples/cyclohexane.gpMM,
trunk/bin/examples/cyclohexane.mm1gp,
trunk/bin/examples/naphtalene.gpMM,
trunk/bin/examples/naphtalene.mm1gp,
trunk/src/common/Makefile.OLD, trunk/src/common/Makefile.in,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/model.h, trunk/src/common/qm1eng.cpp,
trunk/src/common/qm1eng.h, trunk/src/common/qm1eng1.cpp,
trunk/src/common/qm1eng1.h, trunk/src/common/qm1eng9.cpp,
trunk/src/common/qm1eng9.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.cpp,
trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.cpp,
trunk/src/common/qm2eng1.h, trunk/src/common/qm2eng9.cpp,
trunk/src/common/qm2eng9.h, trunk/src/common/qm2mdl.cpp,
trunk/src/common/qm2mdl.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h, trunk/src/target1/t1main.cpp,
trunk/src/target2/t2main.cpp, trunk/src/target2/t2qm1docv.cpp,
trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.cpp,
trunk/src/target2/t2qm2docv.h,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_interface.h,
trunk/src/target3/glade/src/main.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h, trunk/src/target3/t3docv.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
trunk/src/target3/t3views.h: swapped the classnames qm1* and qm2
(as well as filenames) in an effort to make the class naming
scheme more reasonnable (now we have a clear division in mm/qm,
and the all-atoms classes (most used) have numbers 1); also
changed nicer filename extensions.
2001-02-02 thassine
* trunk/src/common/mm1alg.h, trunk/src/common/mm1mdl.cpp,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3dialog.h, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h: the trajectory viewer works now
(as a modal dialog, but anyway).
2001-01-31 thassine
* trunk/CHANGES, trunk/src/common/errutil.cpp,
trunk/src/common/errutil.h, trunk/src/common/mm1alg.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/model.h, trunk/src/common/qm2mdl.cpp,
trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h,
trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
changed MM trajectory file format; some Do???-functions moved to
model (and are now accessible in TARGET1 also).
2001-01-30 hutchisn
* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
trunk/src/common/utility.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
Switch to new GLADE-designed import/export boxes.
* trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
trunk/oelib/atomtyp.txt, trunk/oelib/binary.cpp,
trunk/oelib/bond.cpp, trunk/oelib/csr.cpp, trunk/oelib/data.cpp,
trunk/oelib/data.h, trunk/oelib/extable.txt,
trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
trunk/oelib/gamess.cpp, trunk/oelib/ghemical.cpp,
trunk/oelib/hin.cpp, trunk/oelib/main.cpp, trunk/oelib/mdl.cpp,
trunk/oelib/mol.cpp, trunk/oelib/mol.h, trunk/oelib/mpqc.cpp,
trunk/oelib/oeutil.cpp, trunk/oelib/parsmart.cpp,
trunk/oelib/patty.cpp, trunk/oelib/patty.h, trunk/oelib/pdb.cpp,
trunk/oelib/quat.c, trunk/oelib/ring.cpp, trunk/oelib/ring.h,
trunk/oelib/rotor.cpp, trunk/oelib/smi.cpp,
trunk/oelib/typer.cpp, trunk/oelib/typer.h,
trunk/oelib/types.txt: Synch with current OELib code.
2001-01-30 thassine
* trunk/src/common/mm1alg.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm1docv.h,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/Makefile,
trunk/src/target3/glade/src/glade_callbacks.cpp,
trunk/src/target3/glade/src/glade_callbacks.h,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_callbacks.h,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/glade_support.cpp,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h:
the geomopt/moldyn dialogs should now mostly work (except the
traj filename).
2001-01-29 thassine
* trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_interface.h,
trunk/src/target3/glade/src/glade_support.cpp,
trunk/src/target3/glade/src/main.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/t3mm1docv.cpp: added geomopt and moldyn
dialogs, but wont work yet (just press cancel)
2001-01-25 thassine
* trunk/src/common/conjgrad.h, trunk/src/common/define.h,
trunk/src/common/engine.h, trunk/src/common/errutil.h,
trunk/src/common/mm1alg.h, trunk/src/common/mm1eng.h,
trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.h,
trunk/src/common/model.h, trunk/src/common/qm1eng.h,
trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.h,
trunk/src/common/qm2eng1.h, trunk/src/common/qm2mdl.h,
trunk/src/common/typedef.h, trunk/src/common/utility.h,
trunk/src/common/v3d.h, trunk/src/graphics/camera.h,
trunk/src/graphics/color.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h, trunk/src/graphics/spline.cpp,
trunk/src/graphics/spline.h, trunk/src/graphics/surface.cpp,
trunk/src/graphics/surface.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/target1/config.h.OLD,
trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h,
trunk/src/target2/config.h.OLD, trunk/src/target2/t2docv.cpp,
trunk/src/target2/t2docv.h, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2main.h, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2mm1docv.h, trunk/src/target2/t2qm1docv.cpp,
trunk/src/target2/t2qm1docv.h, trunk/src/target2/t2qm2docv.cpp,
trunk/src/target2/t2qm2docv.h, trunk/src/target2/t2views.cpp,
trunk/src/target2/t2views.h, trunk/src/target3/config.h.OLD,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: all
documentation is now in DOC++ form, it's a bit sparse, but
usable.
2001-01-24 thassine
* trunk/oelib/Makefile, trunk/oelib/data.cpp,
trunk/oelib/mpqc.cpp, trunk/src/common/qm1eng.cpp,
trunk/src/common/qm1eng.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h, trunk/src/common/qm2eng.cpp,
trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.cpp,
trunk/src/common/qm2eng1.h, trunk/src/common/qm2eng9.cpp,
trunk/src/common/qm2eng9.h, trunk/src/common/qm2mdl.cpp,
trunk/src/common/qm2mdl.h, trunk/src/common/typedef.h,
trunk/src/common/utility.cpp, trunk/src/common/utility.h,
trunk/src/common/v3d.h, trunk/src/graphics/camera.cpp,
trunk/src/graphics/camera.h, trunk/src/graphics/color.h: some
more documentation converted into DOC++ form
2001-01-22 hutchisn
* trunk/oelib/Makefile.in, trunk/oelib/data.cpp,
trunk/oelib/data.h, trunk/oelib/extable.txt,
trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
trunk/oelib/mpqc.cpp, trunk/oelib/tinker.cpp,
trunk/oelib/unichem.cpp: Added unichem and mpqc formats.
2001-01-22 thassine
* trunk/oelib/Makefile, trunk/oelib/tinker.cpp,
trunk/src/Makefile.OLD, trunk/src/common/conjgrad.cpp,
trunk/src/common/conjgrad.h, trunk/src/common/define.h,
trunk/src/common/engine.cpp, trunk/src/common/engine.h,
trunk/src/common/errutil.cpp, trunk/src/common/errutil.h,
trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
trunk/src/common/matrix.h, trunk/src/common/mm1alg.cpp,
trunk/src/common/mm1alg.h, trunk/src/common/mm1eng.cpp,
trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.cpp,
trunk/src/common/mm1eng1.h, trunk/src/common/mm1eng9.cpp,
trunk/src/common/mm1eng9.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab1.h, trunk/src/common/mm1tab9.cpp,
trunk/src/common/mm1tab9.h, trunk/src/common/mm1util.cpp,
trunk/src/common/mm1util.h, trunk/src/common/model.cpp,
trunk/src/common/model.h, trunk/src/common/notice.cpp,
trunk/src/common/notice.h, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/target3/t3mm1docv.cpp:
started to convert comments into a form suitable to DOC++
2001-01-20 hutchisn
* trunk/PROJECT, trunk/oelib/Makefile.in, trunk/oelib/data.cpp,
trunk/oelib/tinker.cpp, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h: *** empty log message ***
* trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/glade_callbacks.cpp,
trunk/src/target3/glade/src/glade_callbacks.h,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_interface.h,
trunk/src/target3/glade/src/glade_support.cpp,
trunk/src/target3/glade/src/main.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_callbacks.h,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/glade_support.cpp: Added new import/export
dialogues using Glade.
(Still need to figure out how to update the option menu
appropriately.)
* trunk/oelib/data.h, trunk/oelib/extable.txt: Added all options
from Babel 1.6
2001-01-19 hutchisn
* trunk/oelib/Makefile.in, trunk/oelib/fileformat.cpp,
trunk/oelib/qchem.cpp: Added export to QChem input files.
2001-01-16 hutchisn
* trunk/oelib/data.cpp, trunk/oelib/data.h,
trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
trunk/oelib/fileformat.h, trunk/oelib/qchem.cpp: Added a QChem
file export translator.
* trunk/oelib/data.cpp, trunk/oelib/data.h,
trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
trunk/oelib/fileformat.h: More OELib updates--removing
incomplete formats for now.
* trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
trunk/oelib/gamess.cpp, trunk/oelib/hin.cpp: More OELib cleanups.
2001-01-13 hutchisn
* trunk/oelib/Makefile.in, trunk/oelib/data.cpp,
trunk/oelib/data.h, trunk/oelib/extable.txt,
trunk/oelib/fileformat.cpp, trunk/oelib/fileformat.h,
trunk/oelib/gamess.cpp, trunk/oelib/ghemical.cpp,
trunk/oelib/hin.cpp, trunk/oelib/main.cpp, trunk/oelib/mol.h,
trunk/oelib/mpqc.cpp, trunk/oelib/oelib.dsp,
trunk/oelib/oelib.dsw, trunk/oelib/pdb.cpp, trunk/oelib/quat.c,
trunk/oelib/rotor.cpp, trunk/oelib/typer.cpp,
trunk/oelib/xyz.cpp: Added new translators, updated to be in
sync with OpenEyes code.
* trunk/src/common/utility.cpp: Small modifications to vdW radii
to be closer to literature (Bondi) values
* trunk/src/common/filetrans.cpp: Use filename for molecule title
-- we don't currently have another way of titling.
2001-01-05 hutchisn
* trunk/acconfig.h, trunk/configure, trunk/configure.in,
trunk/src/config.h.in, trunk/src/target3/Makefile.in: Fix build
environment
2001-01-05 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.h,
trunk/src/common/qm2eng9.cpp, trunk/src/common/qm2mdl.cpp,
trunk/src/common/qm2mdl.h, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
trunk/src/graphics/plane.cpp, trunk/src/graphics/plane.h,
trunk/src/graphics/qm2docv.cpp, trunk/src/graphics/qm2docv.h,
trunk/src/graphics/surface.cpp, trunk/src/graphics/surface.h,
trunk/src/target1/Makefile.OLD, trunk/src/target1/t1main.cpp,
trunk/src/target2/t2qm2docv.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/t3qm2docv.cpp: added a simple TARGET1 example,
the QM setup dialog should also now work.
2001-01-03 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h,
trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/Makefile,
trunk/src/target3/glade/src/glade_callbacks.cpp,
trunk/src/target3/glade/src/glade_callbacks.h,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_callbacks.h,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
the setup dialog should now work for MM.
* trunk/CHANGES, trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src/Makefile,
trunk/src/target3/glade/src/glade_callbacks.cpp,
trunk/src/target3/glade/src/glade_callbacks.h,
trunk/src/target3/glade/src/glade_interface.cpp,
trunk/src/target3/glade/src/glade_interface.h,
trunk/src/target3/glade/src/glade_support.cpp,
trunk/src/target3/glade/src/glade_support.h,
trunk/src/target3/glade/src/main.cpp,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h: dialogs; read from
glade/src/Makefile how to retain your changes in GLADE code.
2001-01-02 thassine
* trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h:
some preliminary stuff for the setup dialogs
* trunk/INSTALL, trunk/PROJECT, trunk/src/target3/Makefile.OLD,
trunk/src/target3/glade, trunk/src/target3/glade/ghemical.glade,
trunk/src/target3/glade/src,
trunk/src/target3/glade/src/Makefile,
trunk/src/target3/glade_callbacks.cpp,
trunk/src/target3/glade_callbacks.h,
trunk/src/target3/glade_interface.cpp,
trunk/src/target3/glade_interface.h,
trunk/src/target3/glade_support.cpp,
trunk/src/target3/glade_support.h,
trunk/src/target3/t3dialog.cpp: started making some dialogs
using GLADE...
2001-01-01 thassine
* trunk/AUTHORS, trunk/INSTALL, trunk/PROJECT,
trunk/src/common/Makefile.OLD, trunk/src/common/mm1mdl.h,
trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
trunk/src/common/qm2eng.h, trunk/src/common/qm2eng1.h,
trunk/src/common/qm2mdl.h, trunk/src/graphics/Makefile.OLD,
trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
trunk/src/target3/Makefile.OLD: just some cleanups and some
improvements to documentation
* trunk/small-utilities, trunk/small-utilities/Makefile,
trunk/small-utilities/getpdb_cd.cpp,
trunk/small-utilities/getpdb_ftp.cpp,
trunk/small-utilities/gp2mpqc.cpp: HAPPY NEW YEAR; some
small-utilities added...
2000-12-27 thassine
* trunk/src/graphics/camera.cpp, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/views.h, trunk/src/target2/t2docv.cpp,
trunk/src/target2/t2docv.h, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: some
cleanups; status bars now work in the GNOME version
2000-12-22 thassine
* trunk/src/target3/t3docv.cpp, trunk/src/target3/t3docv.h: added
some missing files...
* trunk/CHANGES, trunk/src/graphics/camera.cpp,
trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mm1docv.h,
trunk/src/graphics/mtools.cpp, trunk/src/graphics/qm1docv.h,
trunk/src/graphics/qm2docv.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/target2/Makefile.OLD,
trunk/src/target2/t2docv.cpp, trunk/src/target2/t2docv.h,
trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/Makefile.OLD, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3qm2docv.cpp,
trunk/src/target3/t3qm2docv.h, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: added target-dependent middle
classes for docviews and views; simplifies the base-classes a bit
* trunk/BUGLIST, trunk/src/graphics/docview.cpp,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
treelist works now pretty well (see BUGLIST for some details)
2000-12-21 thassine
* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: improved proper model
closing/cleanup in GNOME version, but still problems (try
File/Close and File/Exit)
* trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/graphics/views.h, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: treelist (now actually works) -
added subtrees and lights
2000-12-20 thassine
* trunk/src/graphics/docview.cpp, trunk/src/graphics/views.h,
trunk/src/target3/t3main.h, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: treelist - now shows objects
(planes etc), and selection is possible
2000-12-19 thassine
* trunk/CHANGES, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: added framework for tree/list
views, and smaller changes
* trunk/src/common/notice.cpp, trunk/src/graphics/docview.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
the toolbar buttons work again as toggle buttons
2000-12-18 thassine
* trunk/oelib/Makefile, trunk/src/common/filetrans.cpp,
trunk/src/target3/t3main.cpp: changes for old makefiles, and a
statusbar added (which is empty so far)
2000-12-08 hutchisn
* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
trunk/src/target3/t3mm1docv.cpp: Use new OEFileFormat code to
check if formats are valid.
* trunk/oelib/Makefile, trunk/oelib/Makefile.in,
trunk/oelib/aromatic.txt, trunk/oelib/binary.cpp,
trunk/oelib/data.cpp, trunk/oelib/data.h,
trunk/oelib/extable.txt, trunk/oelib/fileformat.cpp,
trunk/oelib/fileformat.h, trunk/oelib/globals.cpp,
trunk/oelib/main.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
trunk/oelib/molvector.cpp, trunk/oelib/oeutil.h,
trunk/oelib/rotor.cpp, trunk/oelib/rotor.h,
trunk/oelib/typer.cpp, trunk/oelib/xyz.cpp: Synched with current
oelib version--fixed bugs finding data files.
2000-12-08 thassine
* trunk/oelib/Makefile, trunk/oelib/mol.h,
trunk/src/common/filetrans.cpp, trunk/src/graphics/camera.cpp,
trunk/src/graphics/docview.cpp, trunk/src/graphics/docview.h,
trunk/src/graphics/mm1docv.cpp, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/qm2docv.cpp, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2views.cpp,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
various fixes (like exit-command) - oelib?
2000-12-02 hutchisn
* trunk/src/target3/t3mm1docv.cpp: OKEvent should return true for
now.
* trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
OKEvent should return bool in case there's a problem
(e.g. file doesn't exist, save might overwrite a file, format is
not supported, etc.)
* trunk/oelib/data.cpp, trunk/oelib/mol.h, trunk/oelib/pdb.cpp,
trunk/oelib/rotor.cpp, trunk/oelib/typer.cpp,
trunk/src/common/Makefile.in: One more bug fix--really get the
logic in initialization correct!
2000-12-01 hutchisn
* trunk/oelib/data.cpp, trunk/oelib/pdb.cpp,
trunk/oelib/rotor.cpp, trunk/oelib/typer.cpp: Ensure that the
directory is checked AND the environment variable is checked
when initializing.
* trunk/Makefile.in, trunk/configure, trunk/configure.in,
trunk/oelib/Makefile, trunk/oelib/Vector.cpp,
trunk/oelib/configure, trunk/oelib/data.cpp, trunk/oelib/data.h,
trunk/oelib/extable.txt, trunk/oelib/gromos96.cpp,
trunk/oelib/main.cpp, trunk/oelib/mol.cpp, trunk/oelib/mol.h,
trunk/oelib/oeutil.cpp, trunk/oelib/pdb.cpp,
trunk/oelib/rotor.cpp, trunk/oelib/rotor.h,
trunk/oelib/typer.cpp, trunk/oelib/typer.h,
trunk/src/common/Makefile.in, trunk/src/common/filetrans.cpp:
Update OELib to use GHEMICAL_DIR environment variable or
specified directories
installed by "make install" target.
2000-12-01 thassine
* trunk/oelib/Makefile, trunk/src/common/Makefile.OLD,
trunk/src/target1/Makefile.OLD, trunk/src/target2/Makefile.OLD,
trunk/src/target3/Makefile.OLD: updated the old makefiles...
2000-12-01 hutchisn
* trunk/src/common/Makefile.in, trunk/src/common/define.h,
trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
trunk/src/common/model.cpp, trunk/src/graphics/Makefile.in,
trunk/src/target3/Makefile.in, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3mm1docv.cpp: add support for import/export
methods using oelib
2000-11-30 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/qm2mdl.h,
trunk/src/graphics/Makefile.OLD, trunk/src/graphics/mm1docv.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h:
GNOME erase-tool fixed, STATICpopupmenu removed, all popup-items
enabled again
2000-11-29 thassine
* trunk/src/graphics/docview.h, trunk/src/graphics/views.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h:
GNOME popup menu callbacks finished - but some items are still
disabled
* trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: popup-menu callbacks changed (for
model-independent items)
* trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/graphics/views.cpp, trunk/src/graphics/views.h,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: OpenGL initialization in GNOME
fixed (so that we have colors back).
2000-11-28 hutchisn
* trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3views.cpp: Add import/export menu items,
center command and move things to "build" submenu.
* trunk/src/target3/t3main.cpp: Can't pass VERSION since it's a
double. Run it through sprintf first.
* trunk/acconfig.h, trunk/configure, trunk/configure.in,
trunk/src/config.h.in, trunk/src/graphics/Makefile.in: Fix build
environment to define appropriate flags, etc.
* trunk/oelib/quat.c: fixed problem with undeclared memset
2000-11-28 thassine
* trunk/CHANGES, trunk/src/common/conjgrad.h,
trunk/src/common/errutil.h, trunk/src/common/mm1alg.h,
trunk/src/common/mm1eng.h, trunk/src/common/mm1eng1.h,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.h,
trunk/src/common/model.h, trunk/src/common/qm2eng.h,
trunk/src/common/qm2eng9.h, trunk/src/common/qm2mdl.h,
trunk/src/common/v3d.h, trunk/src/graphics/mtools.h,
trunk/src/graphics/views.h, trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3main.h, trunk/src/target3/t3qm2docv.cpp,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: some
cleanups : public data changed protected in many classes
* trunk/CHANGES, trunk/src/common/define.h,
trunk/src/graphics/Makefile.OLD, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/views.h,
trunk/src/target2/t2views.cpp, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3main.h, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h: any
things broken/mixed up, but we have a standard GNOME MDI app now
2000-11-27 hutchisn
* trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h:
Modify dialog to show which element is currently selected.
* trunk/src/common/filetrans.cpp, trunk/src/common/filetrans.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h: Remove
import functions from mm1mdl and use new filetrans code through
OELib.
* trunk/Makefile.in, trunk/acconfig.h, trunk/configure,
trunk/configure.in, trunk/oelib/Makefile.in,
trunk/oelib/configure, trunk/src/common/Makefile.in,
trunk/src/config.h.in, trunk/src/graphics/Makefile.in,
trunk/src/target3/Makefile.in: Add changes to support linking in
OELib and slightly cleaned up build system.
2000-11-27 thassine
* trunk/configure, trunk/configure.in,
trunk/src/common/Makefile.in, trunk/src/graphics/Makefile.in,
trunk/src/target3/Makefile.in: Makefile.in -files updated
(configure still broken)
2000-11-26 thassine
* trunk/CHANGES, trunk/src/graphics/camera.cpp,
trunk/src/graphics/camera.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h, trunk/src/graphics/surface.cpp,
trunk/src/graphics/surface.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/target2/config.h.OLD,
trunk/src/target2/t2mm1docv.cpp,
trunk/src/target2/t2qm1docv.cpp,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2views.cpp,
trunk/src/target3/config.h.OLD, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3views.cpp:
3rd stage of doc/view changes
2000-11-24 thassine
* trunk/CHANGES, trunk/src/graphics/camera.cpp,
trunk/src/graphics/camera.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1rbn.cpp,
trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/mtools.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h, trunk/src/graphics/surface.cpp,
trunk/src/graphics/surface.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1docv.cpp,
trunk/src/target3/t3mm1docv.h, trunk/src/target3/t3qm1docv.cpp,
trunk/src/target3/t3qm1docv.h, trunk/src/target3/t3qm2docv.cpp,
trunk/src/target3/t3qm2docv.h, trunk/src/target3/t3views.cpp,
trunk/src/target3/t3views.h: 2nd stage of doc/view reorganization
2000-11-23 thassine
* trunk/CHANGES, trunk/src/common/Makefile.OLD,
trunk/src/common/conjgrad.h, trunk/src/common/engbase.cpp,
trunk/src/common/engbase.h, trunk/src/common/engine.cpp,
trunk/src/common/engine.h, trunk/src/common/mdlbase.cpp,
trunk/src/common/mdlbase.h, trunk/src/common/mm1eng.cpp,
trunk/src/common/mm1eng.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1util.cpp,
trunk/src/common/model.cpp, trunk/src/common/model.h,
trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/common/qm2eng.cpp, trunk/src/common/qm2eng.h,
trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
trunk/src/graphics/Makefile.OLD, trunk/src/graphics/camera.cpp,
trunk/src/graphics/camera.h, trunk/src/graphics/docview.cpp,
trunk/src/graphics/docview.h, trunk/src/graphics/guibase.cpp,
trunk/src/graphics/guibase.h, trunk/src/graphics/mm1docv.cpp,
trunk/src/graphics/mm1docv.h, trunk/src/graphics/mm1gui.cpp,
trunk/src/graphics/mm1gui.h, trunk/src/graphics/mm1rbn.cpp,
trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/plane.h, trunk/src/graphics/qm1docv.cpp,
trunk/src/graphics/qm1docv.h, trunk/src/graphics/qm1gui.cpp,
trunk/src/graphics/qm1gui.h, trunk/src/graphics/qm2docv.cpp,
trunk/src/graphics/qm2docv.h, trunk/src/graphics/qm2gui.cpp,
trunk/src/graphics/qm2gui.h, trunk/src/graphics/surface.cpp,
trunk/src/graphics/surface.h, trunk/src/graphics/viewing.cpp,
trunk/src/graphics/viewing.h, trunk/src/graphics/views.cpp,
trunk/src/graphics/views.h, trunk/src/graphics/window.cpp,
trunk/src/graphics/window.h, trunk/src/target1/Makefile.OLD,
trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.h,
trunk/src/target2/t2mm1docv.cpp, trunk/src/target2/t2mm1docv.h,
trunk/src/target2/t2mm1gui.cpp, trunk/src/target2/t2mm1gui.h,
trunk/src/target2/t2qm1docv.cpp, trunk/src/target2/t2qm1docv.h,
trunk/src/target2/t2qm1gui.cpp, trunk/src/target2/t2qm1gui.h,
trunk/src/target2/t2qm2docv.cpp, trunk/src/target2/t2qm2docv.h,
trunk/src/target2/t2qm2gui.cpp, trunk/src/target2/t2qm2gui.h,
trunk/src/target2/t2views.cpp, trunk/src/target2/t2views.h,
trunk/src/target2/t2window.cpp, trunk/src/target2/t2window.h,
trunk/src/target3/Makefile.OLD, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1docv.cpp, trunk/src/target3/t3mm1docv.h,
trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
trunk/src/target3/t3qm1docv.cpp, trunk/src/target3/t3qm1docv.h,
trunk/src/target3/t3qm1gui.cpp, trunk/src/target3/t3qm1gui.h,
trunk/src/target3/t3qm2docv.cpp, trunk/src/target3/t3qm2docv.h,
trunk/src/target3/t3qm2gui.cpp, trunk/src/target3/t3qm2gui.h,
trunk/src/target3/t3views.cpp, trunk/src/target3/t3views.h,
trunk/src/target3/t3window.cpp, trunk/src/target3/t3window.h:
1st round of doc/view changes (will break the configure-script)
2000-11-20 thassine
* trunk/src/common/qm2mdl.cpp, trunk/src/graphics/guibase.h,
trunk/src/graphics/mm1gui.cpp, trunk/src/graphics/mm1gui.h,
trunk/src/graphics/mm1rbn.cpp, trunk/src/graphics/qm2gui.cpp,
trunk/src/graphics/qm2gui.h: fixed QM import bug + some
potential graphics bugs
2000-11-16 hutchisn
* trunk/Makefile.in: Removed configure target--something is
strange with the timestamps.
2000-11-16 thassine
* trunk/src/common/Makefile.OLD, trunk/src/common/errorutil.cpp,
trunk/src/common/errorutil.h, trunk/src/common/errutil.cpp,
trunk/src/common/errutil.h, trunk/src/common/mdlbase.cpp,
trunk/src/common/mdlbase.h, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/qm1mdl.cpp,
trunk/src/common/qm1mdl.h, trunk/src/common/qm2mdl.cpp,
trunk/src/common/qm2mdl.h, trunk/src/graphics/Makefile.OLD,
trunk/src/graphics/guibase.cpp, trunk/src/graphics/guibase.h,
trunk/src/graphics/mm1gui.cpp, trunk/src/graphics/mm1gui.h,
trunk/src/graphics/qm1gui.cpp, trunk/src/graphics/qm1gui.h,
trunk/src/graphics/qm2gui.cpp, trunk/src/graphics/qm2gui.h,
trunk/src/target2/Makefile.OLD, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2mm1gui.cpp, trunk/src/target2/t2mm1gui.h,
trunk/src/target2/t2qm1gui.cpp, trunk/src/target2/t2qm1gui.h,
trunk/src/target2/t2qm2gui.cpp, trunk/src/target2/t2qm2gui.h,
trunk/src/target2/t2window.cpp, trunk/src/target3/Makefile.OLD,
trunk/src/target3/t3errorutil.cpp,
trunk/src/target3/t3errorutil.h,
trunk/src/target3/t3errutil.cpp, trunk/src/target3/t3errutil.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1gui.cpp,
trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm1gui.cpp,
trunk/src/target3/t3qm1gui.h, trunk/src/target3/t3qm2gui.cpp,
trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp:
added err_util for all models
2000-11-15 hutchisn
* trunk/src/common/Makefile.in, trunk/src/common/errorutil.cpp,
trunk/src/common/errorutil.h, trunk/src/target3/Makefile.in,
trunk/src/target3/t3errorutil.cpp,
trunk/src/target3/t3errorutil.h: Add error-handling classes with
support for GNOME.
* trunk/oelib/Makefile, trunk/oelib/Makefile.in,
trunk/oelib/data.cpp, trunk/oelib/data.h,
trunk/oelib/extable.txt, trunk/oelib/ghemical.cpp,
trunk/oelib/mol.cpp, trunk/oelib/mol.h: Add read/write for
ghemical file format.
2000-11-14 hutchisn
* trunk/oelib, trunk/oelib/.cvsignore, trunk/oelib/GNULICENSE.txt,
trunk/oelib/Makefile, trunk/oelib/Makefile.in,
trunk/oelib/OELibPrimer.html, trunk/oelib/StdAfx.cpp,
trunk/oelib/StdAfx.h, trunk/oelib/Vector.cpp,
trunk/oelib/Vector.h, trunk/oelib/alchemy.cpp,
trunk/oelib/aromatic.txt, trunk/oelib/atom.cpp,
trunk/oelib/atomtyp.txt, trunk/oelib/balst.cpp,
trunk/oelib/bgf.cpp, trunk/oelib/binary.cpp,
trunk/oelib/binary.h, trunk/oelib/bitgrid.cpp,
trunk/oelib/bitgrid.h, trunk/oelib/bitvec.cpp,
trunk/oelib/bitvec.h, trunk/oelib/bond.cpp, trunk/oelib/box.cpp,
trunk/oelib/c3d.cpp, trunk/oelib/cacao.cpp,
trunk/oelib/cache.cpp, trunk/oelib/ccc.cpp,
trunk/oelib/chdrw.cpp, trunk/oelib/chiral.cpp,
trunk/oelib/chiral.h, trunk/oelib/commandline.cpp,
trunk/oelib/commandline.h, trunk/oelib/configure,
trunk/oelib/csr.cpp, trunk/oelib/cssr.cpp,
trunk/oelib/cwrap.cpp, trunk/oelib/cwrap.h,
trunk/oelib/data.cpp, trunk/oelib/data.h,
trunk/oelib/element.txt, trunk/oelib/extable.txt,
trunk/oelib/feat.cpp, trunk/oelib/fh.cpp, trunk/oelib/grid.cpp,
trunk/oelib/grid.h, trunk/oelib/gromos96.cpp,
trunk/oelib/main.cpp, trunk/oelib/matrix.cpp,
trunk/oelib/matrix.h, trunk/oelib/mdl.cpp, trunk/oelib/mmod.cpp,
trunk/oelib/mol.cpp, trunk/oelib/mol.h, trunk/oelib/mol2.cpp,
trunk/oelib/molchrg.cpp, trunk/oelib/molchrg.h,
trunk/oelib/molvector.cpp, trunk/oelib/molvector.h,
trunk/oelib/oeutil.cpp, trunk/oelib/oeutil.h,
trunk/oelib/parsmart.cpp, trunk/oelib/parsmart.h,
trunk/oelib/parsmi.cpp, trunk/oelib/patty.cpp,
trunk/oelib/patty.h, trunk/oelib/pdb.cpp, trunk/oelib/quat.c,
trunk/oelib/rand.cpp, trunk/oelib/resdata.txt,
trunk/oelib/ring.cpp, trunk/oelib/ring.h, trunk/oelib/rotor.cpp,
trunk/oelib/rotor.h, trunk/oelib/smi.cpp, trunk/oelib/smi.h,
trunk/oelib/tokenst.cpp, trunk/oelib/typer.cpp,
trunk/oelib/typer.h, trunk/oelib/types.txt,
trunk/oelib/version.h: Initial revision
* trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
trunk/src/target3/t3window.cpp: Added menu items and
user-visible feedback for menu choices.
* trunk/Makefile.in, trunk/configure.in: Add makefile targets to
ensure configure script and Makefiles are updated properly.
Also add AC_PREREQ to configure.in to ensure configure script
isn't updated by
an old version of autoconf.
2000-11-10 hutchisn
* trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
trunk/src/target3/t3window.cpp: Remove menu items for import HIN
and PDB files (soon to be done through OELib)
Add menu items and support for render labels and coloring and
quick update mode.
* trunk/bin/examples/2-chlorobutane.gpMM,
trunk/bin/examples/3-phenylpropanal.gpMM,
trunk/bin/examples/acetylsalicylic_acid.gpMM,
trunk/bin/examples/alpha-pinene.gpMM,
trunk/bin/examples/bromobenzene.gpMM,
trunk/bin/examples/camphor.gpMM,
trunk/bin/examples/cinnamaldehyde.gpMM,
trunk/bin/examples/cis-2-pentene.gpMM,
trunk/bin/examples/cyclohexane.gpMM,
trunk/bin/examples/naphtalene.gpMM: Update examples to new file
format (read in and re-saved).
2000-11-10 thassine
* trunk/CHANGES, trunk/src/common/mdlbase.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm1util.cpp, trunk/src/common/qm1mdl.h,
trunk/src/common/qm2mdl.h: 1st round of mm1_mdl file format
revision
2000-11-09 thassine
* trunk/BUGLIST, trunk/CHANGES, trunk/src/Makefile.OLD,
trunk/src/common/typedef.h, trunk/src/common/utility.cpp,
trunk/src/graphics/color.h, trunk/src/graphics/guibase.cpp,
trunk/src/graphics/guibase.h, trunk/src/graphics/mm1gui.cpp,
trunk/src/graphics/mm1rbn.h, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/plane.h, trunk/src/graphics/qm1gui.cpp,
trunk/src/graphics/qm2gui.cpp, trunk/src/graphics/surface.cpp,
trunk/src/graphics/surface.h, trunk/src/graphics/viewing.cpp,
trunk/src/graphics/viewing.h, trunk/src/target2/t2mm1gui.cpp,
trunk/src/target2/t2qm2gui.cpp, trunk/src/target3/t3mm1gui.cpp,
trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm2gui.cpp,
trunk/src/target3/t3window.cpp: graphics improvements, volume
rendering added
2000-11-08 hutchisn
* trunk/src/common/utility.cpp, trunk/src/common/utility.h: Add
back correct symbol for element 110. This may cause problems
with atom
type rules, but how many rules involve element 110 anyway?
2000-11-07 hutchisn
* trunk/src/target3/t3dialog.cpp: Add feedback for currently
selected bondtype and element in dialogues.
* trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3qm2gui.cpp:
Temporarily fix bug for open file filters--don't supply a filter
until GTK is
fixed.
2000-11-02 thassine
* trunk/src/common/define.h, trunk/src/target3/t3main.cpp: fixed
those about-dialog crashes...
2000-11-01 thassine
* trunk/CHANGES, trunk/src/common/define.h,
trunk/src/common/mdlbase.cpp, trunk/src/common/mdlbase.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1tab1.cpp,
trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1util.cpp,
trunk/src/target3/Makefile.OLD: added primary/secondary paths
for parameter files
2000-10-31 hutchisn
* trunk/src/common/utility.cpp, trunk/src/graphics/mm1gui.cpp:
Enter real vdW radii from several sources and update GUI to draw
accordingly
* trunk/src/target3/t3dialog.cpp: Fixed bug with elements beyond
#105.
* trunk/configure, trunk/configure.in: Another attempt to pick up
Xmu and glut appropirately.
2000-10-31 thassine
* trunk/src/Makefile.OLD: revieved the /src/Makefile.OLD
2000-10-30 hutchisn
* trunk/configure, trunk/configure.in, trunk/src/Makefile.OLD,
trunk/src/target3/Makefile.in: Bugfixes for the autoconf
changes--should now work on systems needing -Xmu.
2000-10-30 thassine
* trunk/src/Makefile.OLD: added yet another Makefile.OLD
2000-10-30 hutchisn
* trunk/INSTALL, trunk/Makefile.in, trunk/acconfig.h,
trunk/aclocal.m4, trunk/configure, trunk/configure.in,
trunk/install-sh, trunk/mkinstalldirs, trunk/src/Makefile,
trunk/src/common/Makefile.in, trunk/src/common/define.h,
trunk/src/config.h.in, trunk/src/graphics/Makefile.in,
trunk/src/target3/Makefile.in, trunk/src/target3/t3main.cpp:
Changes to move to an autoconf-derived configure script.
2000-10-25 thassine
* trunk/src/common/conjgrad.cpp, trunk/src/common/utility.cpp:
added some missing header files
* trunk/CHANGES, trunk/src/common/conjgrad.cpp,
trunk/src/common/utility.cpp, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3qm2gui.cpp:
better GnomeUIInfo initialization (the RH7-patch from GH)
* trunk/CHANGES, trunk/src/graphics/guibase.cpp,
trunk/src/graphics/mm1gui.cpp: the multiple view management bug
fixed (at last)
2000-10-25 hutchisn
* trunk/src/common/conjgrad.cpp, trunk/src/common/utility.cpp,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3mm1gui.cpp,
trunk/src/target3/t3qm2gui.cpp: Minor changes to allow
compilation on RH7.
* trunk/bin, trunk/bin/.cvsignore, trunk/src,
trunk/src/.cvsignore, trunk/src/common,
trunk/src/common/.cvsignore, trunk/src/graphics,
trunk/src/graphics/.cvsignore, trunk/src/target2,
trunk/src/target2/.cvsignore, trunk/src/target3,
trunk/src/target3/.cvsignore: CVS ignore files to remove common
build objects, etc.
2000-10-24 thassine
* trunk/src/graphics/mm1gui.cpp, trunk/src/graphics/mm1gui.h,
trunk/src/target2/t2mm1gui.cpp, trunk/src/target3/t3mm1gui.cpp:
cleaned some graphics code
2000-10-23 thassine
* trunk/src/new.cpp, trunk/src/new.h, trunk/src/some-extra-files,
trunk/src/some-extra-files/newfile.cpp,
trunk/src/some-extra-files/newfile.h: moved some conflicting
files to some-extra-files
* trunk/CHANGES, trunk/src/common/mm1mdl.cpp,
trunk/src/common/mm1mdl.h, trunk/src/common/mm1util.cpp,
trunk/src/common/mm1util.h, trunk/src/graphics/mm1rbn.cpp:
improved mm1_chn_info
2000-10-21 thassine
* trunk/src/common/Makefile, trunk/src/common/color.h,
trunk/src/common/config.h, trunk/src/common/guibase.cpp,
trunk/src/common/guibase.h, trunk/src/common/mm1gui.cpp,
trunk/src/common/mm1gui.h, trunk/src/common/mm1rbn.cpp,
trunk/src/common/mm1rbn.h, trunk/src/common/mtools.cpp,
trunk/src/common/mtools.h, trunk/src/common/objects.cpp,
trunk/src/common/objects.h, trunk/src/common/plane.cpp,
trunk/src/common/plane.h, trunk/src/common/qm1gui.cpp,
trunk/src/common/qm1gui.h, trunk/src/common/qm2gui.cpp,
trunk/src/common/qm2gui.h, trunk/src/common/spline.cpp,
trunk/src/common/spline.h, trunk/src/common/surface.cpp,
trunk/src/common/surface.h, trunk/src/common/viewing.cpp,
trunk/src/common/viewing.h, trunk/src/common/window.cpp,
trunk/src/common/window.h: removed some duplicate files
* trunk/src/common/library: removed library-dir
* trunk/CHANGES, trunk/src/Makefile,
trunk/src/common/Makefile.OLD, trunk/src/common/conjgrad.cpp,
trunk/src/common/conjgrad.h, trunk/src/common/define.h,
trunk/src/common/engbase.cpp, trunk/src/common/engbase.h,
trunk/src/common/mdlbase.cpp, trunk/src/common/mdlbase.h,
trunk/src/common/mm1alg.cpp, trunk/src/common/mm1alg.h,
trunk/src/common/mm1eng.cpp, trunk/src/common/mm1eng.h,
trunk/src/common/mm1eng1.cpp, trunk/src/common/mm1eng1.h,
trunk/src/common/mm1eng9.cpp, trunk/src/common/mm1eng9.h,
trunk/src/common/mm1mdl.cpp, trunk/src/common/mm1mdl.h,
trunk/src/common/mm1tab1.cpp, trunk/src/common/mm1tab1.h,
trunk/src/common/mm1tab9.cpp, trunk/src/common/mm1tab9.h,
trunk/src/common/mm1util.cpp, trunk/src/common/mm1util.h,
trunk/src/common/qm1eng.cpp, trunk/src/common/qm1eng.h,
trunk/src/common/qm1mdl.cpp, trunk/src/common/qm1mdl.h,
trunk/src/common/qm2eng.cpp, trunk/src/common/qm2eng.h,
trunk/src/common/qm2eng1.cpp, trunk/src/common/qm2eng1.h,
trunk/src/common/qm2eng9.cpp, trunk/src/common/qm2eng9.h,
trunk/src/common/qm2mdl.cpp, trunk/src/common/qm2mdl.h,
trunk/src/common/typedef.h, trunk/src/common/utility.cpp,
trunk/src/common/utility.h, trunk/src/common/v3d.h,
trunk/src/graphics, trunk/src/graphics/Makefile.OLD,
trunk/src/graphics/color.h, trunk/src/graphics/guibase.cpp,
trunk/src/graphics/guibase.h, trunk/src/graphics/mm1gui.cpp,
trunk/src/graphics/mm1gui.h, trunk/src/graphics/mm1rbn.cpp,
trunk/src/graphics/mm1rbn.h, trunk/src/graphics/mtools.cpp,
trunk/src/graphics/mtools.h, trunk/src/graphics/objects.cpp,
trunk/src/graphics/objects.h, trunk/src/graphics/plane.cpp,
trunk/src/graphics/plane.h, trunk/src/graphics/qm1gui.cpp,
trunk/src/graphics/qm1gui.h, trunk/src/graphics/qm2gui.cpp,
trunk/src/graphics/qm2gui.h, trunk/src/graphics/spline.cpp,
trunk/src/graphics/spline.h, trunk/src/graphics/surface.cpp,
trunk/src/graphics/surface.h, trunk/src/graphics/viewing.cpp,
trunk/src/graphics/viewing.h, trunk/src/graphics/window.cpp,
trunk/src/graphics/window.h, trunk/src/target1/Makefile,
trunk/src/target1/Makefile.OLD, trunk/src/target1/config.h,
trunk/src/target1/config.h.OLD, trunk/src/target2/Makefile,
trunk/src/target2/Makefile.OLD, trunk/src/target2/config.h,
trunk/src/target2/config.h.OLD, trunk/src/target3/Makefile,
trunk/src/target3/Makefile.OLD, trunk/src/target3/config.h,
trunk/src/target3/config.h.OLD: new source tree with old
makefiles
* trunk/CHANGES, trunk/src/common/guibase.cpp,
trunk/src/common/guibase.h, trunk/src/common/library/define.h,
trunk/src/common/library/mdlbase.cpp,
trunk/src/common/library/mdlbase.h,
trunk/src/common/viewing.cpp, trunk/src/target3/t3dialog.cpp,
trunk/src/target3/t3dialog.h, trunk/src/target3/t3mm1gui.cpp,
trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm2gui.cpp,
trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp:
file save dialogs added, selection bug fixed
2000-10-18 thassine
* trunk/CHANGES, trunk/bin/examples/2-chlorobutane.gpMM,
trunk/bin/examples/2-chlorobutane.mm1gp,
trunk/bin/examples/3-phenylpropanal.gpMM,
trunk/bin/examples/3-phenylpropanal.mm1gp,
trunk/bin/examples/acetylsalicylic_acid.gpMM,
trunk/bin/examples/acetylsalicylic_acid.mm1gp,
trunk/bin/examples/alpha-pinene.gpMM,
trunk/bin/examples/alpha-pinene.mm1gp,
trunk/bin/examples/bromobenzene.gpMM,
trunk/bin/examples/bromobenzene.mm1gp,
trunk/bin/examples/camphor.gpMM,
trunk/bin/examples/camphor.mm1gp,
trunk/bin/examples/cinnamaldehyde.gpMM,
trunk/bin/examples/cinnamaldehyde.mm1gp,
trunk/bin/examples/cis-2-pentene.gpMM,
trunk/bin/examples/cis-2-pentene.mm1gp,
trunk/bin/examples/cyclohexane.gpMM,
trunk/bin/examples/cyclohexane.mm1gp,
trunk/bin/examples/naphtalene.gpMM,
trunk/bin/examples/naphtalene.mm1gp,
trunk/src/common/guibase.cpp, trunk/src/common/guibase.h,
trunk/src/common/library/mm1mdl.cpp,
trunk/src/common/library/qm1mdl.cpp,
trunk/src/common/library/qm2mdl.cpp,
trunk/src/common/mm1gui.cpp, trunk/src/common/mm1gui.h,
trunk/src/common/qm1gui.cpp, trunk/src/common/qm1gui.h,
trunk/src/common/qm2gui.cpp, trunk/src/common/qm2gui.h,
trunk/src/target2/t2main.cpp, trunk/src/target3/t3dialog.cpp,
trunk/src/target3/t3dialog.h, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3main.h, trunk/src/target3/t3mm1gui.cpp,
trunk/src/target3/t3mm1gui.h, trunk/src/target3/t3qm2gui.cpp,
trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp,
trunk/src/target3/t3window.h: added file dialogs for GNOME
version, changed examples
2000-10-16 thassine
* trunk/src/common/config.h, trunk/src/common/library/config.h,
trunk/src/common/library/mm1mdl.cpp,
trunk/src/common/library/mm1util.cpp,
trunk/src/common/library/utility.cpp,
trunk/src/common/library/utility.h: merged the patches from GH
2000-09-09 thassine
* trunk/CHANGES, trunk/src/common/config.h,
trunk/src/common/library/config.h,
trunk/src/common/library/define.h, trunk/src/target1/Makefile:
just a few minor changes
* trunk/BUGLIST, trunk/CHANGES, trunk/INSTALL, trunk/PROJECT,
trunk/src/common/Makefile, trunk/src/common/library/Makefile,
trunk/src/common/library/define.h, trunk/src/common/qm2gui.cpp,
trunk/src/new.h, trunk/src/target2/Makefile,
trunk/src/target3/Makefile, trunk/src/target3/t3main.cpp,
trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3qm2gui.cpp,
trunk/src/target3/t3qm2gui.h, trunk/src/target3/t3window.cpp:
improvements in gt3. this is released as 0.2.2
2000-09-06 thassine
* trunk/src/Makefile: made some changes in makefiles
* trunk/AUTHORS, trunk/BUGLIST, trunk/CHANGES, trunk/COPYING,
trunk/INSTALL, trunk/PROJECT, trunk/bin, trunk/bin/examples,
trunk/bin/examples/2-chlorobutane.mm1gp,
trunk/bin/examples/3-phenylpropanal.mm1gp,
trunk/bin/examples/acetylsalicylic_acid.mm1gp,
trunk/bin/examples/alpha-pinene.mm1gp,
trunk/bin/examples/bromobenzene.mm1gp,
trunk/bin/examples/camphor.mm1gp,
trunk/bin/examples/cinnamaldehyde.mm1gp,
trunk/bin/examples/cis-2-pentene.mm1gp,
trunk/bin/examples/cyclohexane.mm1gp,
trunk/bin/examples/naphtalene.mm1gp, trunk/bin/parameters,
trunk/bin/parameters/builder,
trunk/bin/parameters/builder/amino.txt,
trunk/bin/parameters/builder/nucleic.txt,
trunk/bin/parameters/mm1param,
trunk/bin/parameters/mm1param/stable,
trunk/bin/parameters/mm1param/stable/atomtypes.txt,
trunk/bin/parameters/mm1param/stable/parameters1.txt,
trunk/bin/parameters/mm1param/stable/parameters2.txt,
trunk/bin/parameters/mm1param/stable/parameters3.txt,
trunk/bin/parameters/mm1param/stable/parameters4.txt,
trunk/bin/parameters/mm1param/stable/parameters5.txt,
trunk/bin/parameters/mm1param/unstable,
trunk/bin/parameters/mm1param/unstable/atomtypes.txt,
trunk/bin/parameters/mm1param/unstable/parameters1.txt,
trunk/bin/parameters/mm1param/unstable/parameters2.txt,
trunk/bin/parameters/mm1param/unstable/parameters3.txt,
trunk/bin/parameters/mm1param/unstable/parameters4.txt,
trunk/bin/parameters/mm1param/unstable/parameters5.txt,
trunk/src, trunk/src/Makefile, trunk/src/common,
trunk/src/common/Makefile, trunk/src/common/color.h,
trunk/src/common/config.h, trunk/src/common/guibase.cpp,
trunk/src/common/guibase.h, trunk/src/common/library,
trunk/src/common/library/Makefile,
trunk/src/common/library/config.h,
trunk/src/common/library/conjgrad.cpp,
trunk/src/common/library/conjgrad.h,
trunk/src/common/library/define.h,
trunk/src/common/library/engbase.cpp,
trunk/src/common/library/engbase.h,
trunk/src/common/library/mdlbase.cpp,
trunk/src/common/library/mdlbase.h,
trunk/src/common/library/mm1alg.cpp,
trunk/src/common/library/mm1alg.h,
trunk/src/common/library/mm1eng.cpp,
trunk/src/common/library/mm1eng.h,
trunk/src/common/library/mm1eng1.cpp,
trunk/src/common/library/mm1eng1.h,
trunk/src/common/library/mm1eng9.cpp,
trunk/src/common/library/mm1eng9.h,
trunk/src/common/library/mm1mdl.cpp,
trunk/src/common/library/mm1mdl.h,
trunk/src/common/library/mm1tab1.cpp,
trunk/src/common/library/mm1tab1.h,
trunk/src/common/library/mm1tab9.cpp,
trunk/src/common/library/mm1tab9.h,
trunk/src/common/library/mm1util.cpp,
trunk/src/common/library/mm1util.h,
trunk/src/common/library/qm1eng.cpp,
trunk/src/common/library/qm1eng.h,
trunk/src/common/library/qm1mdl.cpp,
trunk/src/common/library/qm1mdl.h,
trunk/src/common/library/qm2eng.cpp,
trunk/src/common/library/qm2eng.h,
trunk/src/common/library/qm2eng1.cpp,
trunk/src/common/library/qm2eng1.h,
trunk/src/common/library/qm2eng9.cpp,
trunk/src/common/library/qm2eng9.h,
trunk/src/common/library/qm2mdl.cpp,
trunk/src/common/library/qm2mdl.h,
trunk/src/common/library/typedef.h,
trunk/src/common/library/utility.cpp,
trunk/src/common/library/utility.h,
trunk/src/common/library/v3d.h, trunk/src/common/matrix.h,
trunk/src/common/mm1gui.cpp, trunk/src/common/mm1gui.h,
trunk/src/common/mm1rbn.cpp, trunk/src/common/mm1rbn.h,
trunk/src/common/mtools.cpp, trunk/src/common/mtools.h,
trunk/src/common/notice.cpp, trunk/src/common/notice.h,
trunk/src/common/objects.cpp, trunk/src/common/objects.h,
trunk/src/common/plane.cpp, trunk/src/common/plane.h,
trunk/src/common/qm1gui.cpp, trunk/src/common/qm1gui.h,
trunk/src/common/qm2gui.cpp, trunk/src/common/qm2gui.h,
trunk/src/common/spline.cpp, trunk/src/common/spline.h,
trunk/src/common/surface.cpp, trunk/src/common/surface.h,
trunk/src/common/viewing.cpp, trunk/src/common/viewing.h,
trunk/src/common/window.cpp, trunk/src/common/window.h,
trunk/src/new.cpp, trunk/src/new.h, trunk/src/target1,
trunk/src/target1/Makefile, trunk/src/target1/config.h,
trunk/src/target1/t1main.cpp, trunk/src/target1/t1main.h,
trunk/src/target2, trunk/src/target2/Makefile,
trunk/src/target2/config.h, trunk/src/target2/t2main.cpp,
trunk/src/target2/t2main.h, trunk/src/target2/t2mm1gui.cpp,
trunk/src/target2/t2mm1gui.h, trunk/src/target2/t2qm1gui.cpp,
trunk/src/target2/t2qm1gui.h, trunk/src/target2/t2qm2gui.cpp,
trunk/src/target2/t2qm2gui.h, trunk/src/target2/t2window.cpp,
trunk/src/target2/t2window.h, trunk/src/target3,
trunk/src/target3/Makefile, trunk/src/target3/config.h,
trunk/src/target3/pixmaps, trunk/src/target3/pixmaps/draw.xpm,
trunk/src/target3/pixmaps/erase.xpm,
trunk/src/target3/pixmaps/orb_xy.xpm,
trunk/src/target3/pixmaps/orb_z.xpm,
trunk/src/target3/pixmaps/rot_xy.xpm,
trunk/src/target3/pixmaps/rot_z.xpm,
trunk/src/target3/pixmaps/select.xpm,
trunk/src/target3/pixmaps/trans_xy.xpm,
trunk/src/target3/pixmaps/trans_z.xpm,
trunk/src/target3/pixmaps/zoom.xpm,
trunk/src/target3/t3dialog.cpp, trunk/src/target3/t3dialog.h,
trunk/src/target3/t3main.cpp, trunk/src/target3/t3main.h,
trunk/src/target3/t3mm1gui.cpp, trunk/src/target3/t3mm1gui.h,
trunk/src/target3/t3qm1gui.cpp, trunk/src/target3/t3qm1gui.h,
trunk/src/target3/t3qm2gui.cpp, trunk/src/target3/t3qm2gui.h,
trunk/src/target3/t3window.cpp, trunk/src/target3/t3window.h:
Initial revision
2000-09-06
* branches, tags, trunk: New repository initialized by cvs2svn.
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