2003-11-06 14:22 thassine * src/fileio.cpp: a minor fix in file-IO; still need to save secondary structures for SF? 2003-11-06 14:09 thassine * src/fileio.cpp: a minor fix in file-IO; still need to save secondary structures for SF? 2003-10-10 11:56 thassine * src/: gnome_project.cpp, gnome_views.cpp, gnome_views.h: a new menu itm (experimental) was added. 2003-10-10 11:53 thassine * src/: gnome_project.cpp, gnome_views.cpp, gnome_views.h: added a new (experimental) menu item. 2003-10-03 16:32 thassine * src/project.cpp: fixed a bug in drawing mouse tool. 2003-10-03 16:29 thassine * src/project.cpp: fixed a drawing tool bug. 2003-09-12 13:34 thassine * src/: gnome_project.cpp, plane.cpp, plane.h, project.cpp, surface.cpp, surface.h: improved planes/surfaces ; now adapt better for charged molecules. 2003-09-12 13:32 thassine * src/: gnome_project.cpp, plane.cpp, plane.h, project.cpp, surface.cpp, surface.h: improvements in plane/surface plots; now adapt better for charged molecules. 2003-09-10 15:04 thassine * src/: appdefine.h, gnome_project.cpp, gnome_project.h, project.cpp: a rendering bug was fixed, and LABEL_RESIDUE was implemented. 2003-09-10 15:02 thassine * src/: appdefine.h, gnome_project.cpp, gnome_project.h, project.cpp: a rendering bug fixed and LABEL_RESIDUE added. 2003-09-01 12:43 thassine * src/project.cpp: added some bugfixes/comments 2003-09-01 12:41 thassine * src/project.cpp: some bugfixes/comments added 2003-08-08 09:55 thassine * src/: fileio.cpp, gnome_project.cpp, project.cpp, project.h: the Solvate??() functions have changed. 2003-08-08 09:43 thassine * src/: gnome_project.cpp, project.cpp, project.h: the Solvate???() functions changed. 2003-07-30 13:11 thassine * src/: camera.cpp, gnome_dialog.cpp, gnome_project.cpp, gnome_project.h, project.cpp, 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 16:48 thassine * src/: camera.cpp, camera.h, gnome_views.cpp, gnome_views.h, objects.cpp, objects.h, plane.cpp, plane.h, project.cpp, project.h, ribbon.cpp, ribbon.h, surface.cpp, surface.h, views.cpp, views.h: the project_view now works reasonably well ; also popup-menus added to project_view pages. 2003-07-24 13:12 thassine * src/: gnome_project.cpp, gnome_project.h, gnome_views.cpp, gnome_views.h, project.cpp, project.h, 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 15:18 thassine * src/: gnome_project.cpp, gnome_project.h, gnome_views.cpp, gnome_views.h, project.cpp, project.h, views.cpp, views.h: the message log now works (more or less) and project_view work started. 2003-07-14 12:20 thassine * src/: gnome_dialog.cpp, gnome_project.cpp, gnome_project.h, gnome_views.cpp, 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 12:28 thassine * GNOME_Ghemical.server: added the .server file (bonobo-activation). 2003-07-11 16:01 thassine * configure, configure.in, bin/ghemical-ui.xml, src/Makefile.in, src/fileio.cpp, src/filetrans.cpp, src/filetrans.h, src/ghemical-server.cpp, src/ghemical-server.h, src/ghemical.cpp, src/ghemical.h, src/glade_dialog.cpp, src/gnome_dialog.cpp, src/gnome_project.cpp, src/gnome_project.h, src/gnome_views.cpp, src/gnome_views.h, src/main.cpp, src/main.h, src/notice.cpp, src/notice.h, src/plane.h, src/project.cpp, src/project.h, src/ribbon.cpp, src/ribbon.h, src/surface.h, src/views.cpp, src/views.h: started porting to gnome2 and converting into bonobo. 2003-06-13 13:18 thassine * AUTHORS, acconfig.h, src/Doxyfile, src/camera.cpp, src/gnome_project.cpp, src/project.cpp: more checks added for atom_list sorting. also misc cleanups. 2003-06-12 16:12 thassine * src/: gnome_views.cpp, gnome_views.h, project.cpp, views.cpp, views.h: added imrovements to transition_state_search + other search tools, and added examples for TSS. 2003-06-11 14:06 thassine * src/: gnome_project.cpp, gnome_project.h, gnome_views.cpp, gnome_views.h, project.cpp, project.h, views.cpp, views.h: added transition_state_search and stationary_state_search ; user-docs and examples will follow in a few days. 2003-05-19 10:09 thassine * src/project.cpp: some debugging-label options added. 2003-05-13 16:44 thassine * src/gnome_project.cpp: removed some redundant DefineSecondaryStructure() runs. 2003-05-12 12:13 thassine * src/: project.cpp, ribbon.cpp, ribbon.h: minor changes in ribbon object. 2003-05-06 16:59 thassine * src/target3/t3docv.cpp: removed some unnecessary output. 2003-04-29 13:22 thassine * src/: gnome_project.cpp, project.cpp, project.h, ribbon.cpp: many changes in lib, adaptaptations to those added. 2003-04-17 10:37 thassine * src/gnome_project.cpp: added better defaults for glade dialogs. 2003-04-16 16:46 thassine * src/: gnome_project.cpp, gnome_views.cpp, gnome_views.h, project.cpp: many small changes (including trajectory reading). 2003-04-10 17:02 thassine * Makefile.in, configure, configure.in, src/appconfig.h.in, src/appdefine.h, src/gnome_project.cpp, src/gnome_project.h, src/project.cpp: changes in configure script (now tested to work with --enable-mpqc). 2003-04-02 09:14 thassine * src/ribbon.cpp: changes in ribbon due to changes in atom class. 2003-03-07 13:37 thassine * src/fileio.cpp: a minor addition to fileio.cpp 2003-03-07 11:11 thassine * src/fileio.cpp: the functions in fileio.cpp now handle data using member functions, not direclty (so that they now are more portable). 2003-03-05 14:20 thassine * src/: gnome_project.cpp, main.cpp: added some changes related to gcc-3.2 2003-03-05 13:43 thassine * src/target3/: t3docv.cpp, t3main.cpp, t3prefs.cpp, t3views.cpp: added changes related to gcc-3.2 2003-02-14 16:51 thassine * src/fileio.cpp: just cleanups, no real changes. 2003-02-14 10:02 thassine * src/project.cpp: sf virtual bonds now rendered also using wireframes. 2003-02-06 16:53 thassine * src/: gnome_project.cpp, main.cpp, notice.cpp, project.cpp: many changes; for example added tool for adding solvent (not ready yet). 2003-02-03 11:54 thassine * src/: gnome_project.cpp, gnome_project.h: added tools for solvation (using H2O). 2003-02-03 11:46 thassine * src/common/: mm1eng.cpp, mm1eng.h, mm1eng1.cpp, mm1eng9.cpp: a bugfix added to mol.mech. connectivity record tables; will affect to nonbonded interactions. 2003-01-31 14:06 thassine * src/: filetrans.cpp, project.cpp, project.h: some bugfixes were added; mostly because of changes in model::GetAtomCount() and engine::GetAtomCount(). 2003-01-30 10:31 thassine * src/: Makefile.in, fileio.cpp, gnome_project.cpp, project.cpp, project.h: changes in SF-stuff rendering and file operations. 2003-01-27 15:45 thassine * src/: fileio.cpp, project.cpp, project.h, ribbon.cpp: some additions to graphics code (how the new flags work). 2003-01-23 15:02 thassine * src/: camera.cpp, camera.h, gnome_project.cpp, gnome_views.cpp, gnome_views.h, main.cpp, main.h, mtools.cpp, mtools.h, project.cpp, project.h, views.cpp, 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 13:25 thassine * Makefile.in: make install also works now. 2003-01-22 13:11 thassine * src/.cvsignore: minor cleanups added. 2003-01-22 13:06 thassine * Makefile.in, configure, configure.in, src/Makefile.in, src/appconfig.h.in, src/appdefine.h, src/camera.cpp, src/camera.h, src/color.h, src/config.h.in, src/fileio.cpp, src/filetrans.cpp, src/filetrans.h, src/glade_dialog.cpp, src/glade_dialog.h, src/gnome_dialog.cpp, src/gnome_dialog.h, src/gnome_project.cpp, src/gnome_project.h, src/gnome_views.cpp, src/gnome_views.h, src/main.cpp, src/main.h, src/mtools.cpp, src/mtools.h, src/notice.cpp, src/notice.h, src/objects.cpp, src/objects.h, src/plane.cpp, src/plane.h, src/project.cpp, src/project.h, src/ribbon.cpp, src/ribbon.h, src/spline.cpp, src/spline.h, src/surface.cpp, src/surface.h, src/views.cpp, src/views.h: added the missing files; some changes have happened in the filenames. 2003-01-21 12:05 thassine * bin/parameters/builder/: amino.txt, nucleic.txt: removed bin/prameters since it is now contained in libghemical. 2003-01-20 16:08 thassine * configure, configure.in: many changes all over the tree; does not compile yet... 2003-01-20 11:22 thassine * src/: graphics/.cvsignore, graphics/Makefile.OLD, graphics/Makefile.in, graphics/camera.cpp, graphics/camera.h, graphics/color.h, graphics/mtools.cpp, graphics/mtools.h, graphics/objects.cpp, graphics/objects.h, graphics/plane.cpp, graphics/plane.h, graphics/project.cpp, graphics/project.h, graphics/ribbon.cpp, graphics/ribbon.h, graphics/spline.cpp, graphics/spline.h, graphics/surface.cpp, graphics/surface.h, graphics/views.cpp, graphics/views.h, target3/.cvsignore, target3/Makefile.OLD, target3/Makefile.in, target3/config.h.OLD, target3/glade_dialog.cpp, target3/glade_dialog.h, target3/t3dialog.cpp, target3/t3dialog.h, target3/t3errutil.cpp, target3/t3errutil.h, target3/t3main.cpp, target3/t3main.h, target3/t3prefs.cpp, target3/t3prefs.h, target3/t3project.cpp, target3/t3project.h, target3/t3views.cpp, target3/t3views.h: moved the contents of src/graphics and src/target3 to src/. 2003-01-20 11:17 thassine * src/target3/pixmaps/: .cvsignore, angle.xpm, bond.xpm, chain.xpm, dihedral.xpm, distance.xpm, draw.xpm, element.xpm, erase.xpm, invert.xpm, molecule.xpm, orb_xy.xpm, orb_z.xpm, residue.xpm, rot_xy.xpm, rot_z.xpm, select.xpm, trans_xy.xpm, trans_z.xpm, zoom.xpm: moved the src/target3/pixmaps to src/pixmaps. 2003-01-20 11:13 thassine * Makefile.in, src/target3/glade/.cvsignore, src/target3/glade/Makefile.OLD, src/target3/glade/Makefile.in, src/target3/glade/README, src/target3/glade/file_export_dialog.cpp, src/target3/glade/file_export_dialog.glade, src/target3/glade/file_export_dialog.h, src/target3/glade/file_import_dialog.cpp, src/target3/glade/file_import_dialog.glade, src/target3/glade/file_import_dialog.h, src/target3/glade/geomopt_dialog.cpp, src/target3/glade/geomopt_dialog.glade, src/target3/glade/geomopt_dialog.h, src/target3/glade/moldyn_dialog.cpp, src/target3/glade/moldyn_dialog.glade, src/target3/glade/moldyn_dialog.h, src/target3/glade/setup_druid.cpp, src/target3/glade/setup_druid.glade, src/target3/glade/setup_druid.h, src/target3/glade/trajview_dialog.cpp, src/target3/glade/trajview_dialog.glade, src/target3/glade/trajview_dialog.h: moved the /src/target3/glade to /src/glade. 2003-01-20 11:05 thassine * src/common/: .cvsignore, Makefile.OLD, Makefile.in, atom.cpp, atom.h, bond.cpp, bond.h, conjgrad.cpp, conjgrad.h, define.h, eng1_mm.cpp, eng1_mm.h, eng1_mm_default.cpp, eng1_mm_default.h, eng1_mm_prmfit.cpp, eng1_mm_prmfit.h, eng1_qm.cpp, eng1_qm.h, eng1_qm_mopac.cpp, eng1_qm_mopac.h, eng1_qm_mpqc.cpp, eng1_qm_mpqc.h, eng1_sf.cpp, eng1_sf.h, eng2_mm_sf.cpp, eng2_mm_sf.h, eng2_qm_mm.cpp, eng2_qm_mm.h, engine.cpp, engine.h, errutil.cpp, errutil.h, factory.cpp, factory.h, filetrans.cpp, filetrans.h, geomopt.cpp, geomopt.h, intcrd.cpp, intcrd.h, matrix.h, model.cpp, model.h, moldyn.cpp, moldyn.h, notice.cpp, notice.h, oldfiles.cpp, prefs.cpp, prefs.h, search.cpp, search.h, seqbuild.cpp, seqbuild.h, tab_mm_default.cpp, tab_mm_default.h, tab_mm_prmfit.cpp, tab_mm_prmfit.h, typedef.h, typerule.cpp, typerule.h, utility.cpp, utility.h, v3d.h: removed the common-directory (now in libghemical). 2003-01-20 10:49 thassine * BUGLIST, Makefile.in, PROJECT, configure.in, miniMOPAC/.cvsignore, miniMOPAC/Makefile.OLD, miniMOPAC/Makefile.in, miniMOPAC/README, miniMOPAC/aababc.c, miniMOPAC/addfck.c, miniMOPAC/addhcr.c, miniMOPAC/addnuc.c, miniMOPAC/analyt.c, miniMOPAC/anavib.c, miniMOPAC/axis.c, miniMOPAC/block.c, miniMOPAC/bonds.c, miniMOPAC/brlzon.c, miniMOPAC/btoc.c, miniMOPAC/calpar.c, miniMOPAC/capcor.c, miniMOPAC/cdiag.c, miniMOPAC/chrge.c, miniMOPAC/cnvg.c, miniMOPAC/compfg.c, miniMOPAC/consts.c, miniMOPAC/cqden.c, miniMOPAC/datin.c, miniMOPAC/dcart.c, miniMOPAC/delmol.c, miniMOPAC/delri.c, miniMOPAC/denrot.c, miniMOPAC/densit.c, miniMOPAC/depvar.c, miniMOPAC/deri0.c, miniMOPAC/deri1.c, miniMOPAC/deri2.c, miniMOPAC/deri21.c, miniMOPAC/deri22.c, miniMOPAC/deri23.c, miniMOPAC/deritr.c, miniMOPAC/deriv.c, miniMOPAC/dernvo.c, miniMOPAC/ders.c, miniMOPAC/dfock2.c, miniMOPAC/dfpsav.c, miniMOPAC/dgemm.c, miniMOPAC/dgemv.c, miniMOPAC/dger.c, miniMOPAC/dgetf2.c, miniMOPAC/dgetrf.c, miniMOPAC/dgetri.c, miniMOPAC/diag.c, miniMOPAC/diat.c, miniMOPAC/diat2.c, miniMOPAC/diegrd.c, miniMOPAC/dielen.c, miniMOPAC/diis.c, miniMOPAC/dijkl1.c, miniMOPAC/dijkl2.c, miniMOPAC/dipind.c, miniMOPAC/dipole.c, miniMOPAC/dlaswp.c, miniMOPAC/dofs.c, miniMOPAC/dot.c, miniMOPAC/drc.c, miniMOPAC/drcout.c, miniMOPAC/dtrmm.c, miniMOPAC/dtrmv.c, miniMOPAC/dtrsm.c, miniMOPAC/dtrti2.c, miniMOPAC/dtrtri.c, miniMOPAC/dvfill.c, miniMOPAC/ef.c, miniMOPAC/enpart.c, miniMOPAC/esp.c, miniMOPAC/etime.c, miniMOPAC/exchng.c, miniMOPAC/fdate.c, miniMOPAC/ffhpol.c, miniMOPAC/flepo.c, miniMOPAC/fmat.c, miniMOPAC/fock1.c, miniMOPAC/fock2.c, miniMOPAC/force.c, miniMOPAC/formxy.c, miniMOPAC/forsav.c, miniMOPAC/frame.c, miniMOPAC/freqcy.c, miniMOPAC/geout.c, miniMOPAC/geoutg.c, miniMOPAC/getgeg.c, miniMOPAC/getgeo.c, miniMOPAC/getsym.c, miniMOPAC/gettxt.c, miniMOPAC/gmetry.c, miniMOPAC/gover.c, miniMOPAC/greenf.c, miniMOPAC/grid.c, miniMOPAC/h1elec.c, miniMOPAC/haddon.c, miniMOPAC/hcore.c, miniMOPAC/helect.c, miniMOPAC/hqrii.c, miniMOPAC/ijkl.c, miniMOPAC/ilaenv.c, miniMOPAC/initsv.c, miniMOPAC/interp.c, miniMOPAC/iter.c, miniMOPAC/jcarin.c, miniMOPAC/linmin.c, miniMOPAC/local.c, miniMOPAC/locmin.c, miniMOPAC/lsame.c, miniMOPAC/makpol.c, miniMOPAC/mamult.c, miniMOPAC/matou1.c, miniMOPAC/matout.c, miniMOPAC/matpak.c, miniMOPAC/meci.c, miniMOPAC/mecid.c, miniMOPAC/mecih.c, miniMOPAC/mecip.c, miniMOPAC/minimopac.c, miniMOPAC/moldat.c, miniMOPAC/molval.c, miniMOPAC/mullik.c, miniMOPAC/mult.c, miniMOPAC/nllsq.c, miniMOPAC/nuchar.c, miniMOPAC/parsav.c, miniMOPAC/partxy.c, miniMOPAC/pathk.c, miniMOPAC/paths.c, miniMOPAC/perm.c, miniMOPAC/polar.c, miniMOPAC/powsav.c, miniMOPAC/powsq.c, miniMOPAC/prtdrc.c, miniMOPAC/quadr.c, miniMOPAC/react1.c, miniMOPAC/reada.c, miniMOPAC/readmo.c, miniMOPAC/refer.c, miniMOPAC/repp.c, miniMOPAC/rotat.c, miniMOPAC/rotate.c, miniMOPAC/rsp.c, miniMOPAC/search.c, miniMOPAC/second.c, miniMOPAC/setupg.c, miniMOPAC/solrot.c, miniMOPAC/swap.c, miniMOPAC/sympro.c, miniMOPAC/symtry.c, miniMOPAC/symtrz.c, miniMOPAC/thermo.c, miniMOPAC/timer.c, miniMOPAC/timout.c, miniMOPAC/update.c, miniMOPAC/upsurf.c, miniMOPAC/vecprt.c, miniMOPAC/writmo.c, miniMOPAC/wrtkey.c, miniMOPAC/wrttxt.c, miniMOPAC/xerbla.c, miniMOPAC/xyzint.c, miniMOPAC/fortran/SIZES, miniMOPAC/fortran/aababc.f, miniMOPAC/fortran/addfck.f, miniMOPAC/fortran/addhcr.f, miniMOPAC/fortran/addnuc.f, miniMOPAC/fortran/analyt.f, miniMOPAC/fortran/anavib.f, miniMOPAC/fortran/axis.f, miniMOPAC/fortran/block.f, miniMOPAC/fortran/bonds.f, miniMOPAC/fortran/brlzon.f, miniMOPAC/fortran/btoc.f, miniMOPAC/fortran/calpar.f, miniMOPAC/fortran/capcor.f, miniMOPAC/fortran/cdiag.f, miniMOPAC/fortran/chrge.f, miniMOPAC/fortran/cnvg.f, miniMOPAC/fortran/compfg.f, miniMOPAC/fortran/consts.f, miniMOPAC/fortran/cqden.f, miniMOPAC/fortran/datin.f, miniMOPAC/fortran/dcart.f, miniMOPAC/fortran/delmol.f, miniMOPAC/fortran/delri.f, miniMOPAC/fortran/denrot.f, miniMOPAC/fortran/densit.f, miniMOPAC/fortran/depvar.f, miniMOPAC/fortran/deri0.f, miniMOPAC/fortran/deri1.f, miniMOPAC/fortran/deri2.f, miniMOPAC/fortran/deri21.f, miniMOPAC/fortran/deri22.f, miniMOPAC/fortran/deri23.f, miniMOPAC/fortran/deritr.f, miniMOPAC/fortran/deriv.f, miniMOPAC/fortran/dernvo.f, miniMOPAC/fortran/ders.f, miniMOPAC/fortran/dfock2.f, miniMOPAC/fortran/dfpsav.f, miniMOPAC/fortran/dgemm.f, miniMOPAC/fortran/dgemv.f, miniMOPAC/fortran/dger.f, miniMOPAC/fortran/dgetf2.f, miniMOPAC/fortran/dgetrf.f, miniMOPAC/fortran/dgetri.f, miniMOPAC/fortran/diag.f, miniMOPAC/fortran/diat.f, miniMOPAC/fortran/diat2.f, miniMOPAC/fortran/diegrd.f, miniMOPAC/fortran/dielen.f, miniMOPAC/fortran/diis.f, miniMOPAC/fortran/dijkl1.f, miniMOPAC/fortran/dijkl2.f, miniMOPAC/fortran/dipind.f, miniMOPAC/fortran/dipole.f, miniMOPAC/fortran/dlaswp.f, miniMOPAC/fortran/dofs.f, miniMOPAC/fortran/dot.f, miniMOPAC/fortran/drc.f, miniMOPAC/fortran/drcout.f, miniMOPAC/fortran/dtrmm.f, miniMOPAC/fortran/dtrmv.f, miniMOPAC/fortran/dtrsm.f, miniMOPAC/fortran/dtrti2.f, miniMOPAC/fortran/dtrtri.f, miniMOPAC/fortran/dvfill.f, miniMOPAC/fortran/ef.f, miniMOPAC/fortran/enpart.f, miniMOPAC/fortran/esp.f, miniMOPAC/fortran/etime.c, miniMOPAC/fortran/exchng.f, miniMOPAC/fortran/fdate.c, miniMOPAC/fortran/ffhpol.f, miniMOPAC/fortran/flepo.f, miniMOPAC/fortran/fmat.f, miniMOPAC/fortran/fock1.f, miniMOPAC/fortran/fock2.f, miniMOPAC/fortran/force.f, miniMOPAC/fortran/formxy.f, miniMOPAC/fortran/forsav.f, miniMOPAC/fortran/frame.f, miniMOPAC/fortran/freqcy.f, miniMOPAC/fortran/geout.f, miniMOPAC/fortran/geoutg.f, miniMOPAC/fortran/getgeg.f, miniMOPAC/fortran/getgeo.f, miniMOPAC/fortran/getsym.f, miniMOPAC/fortran/gettxt.f, miniMOPAC/fortran/gmetry.f, miniMOPAC/fortran/gover.f, miniMOPAC/fortran/greenf.f, miniMOPAC/fortran/grid.f, miniMOPAC/fortran/h1elec.f, miniMOPAC/fortran/haddon.f, miniMOPAC/fortran/hcore.f, miniMOPAC/fortran/helect.f, miniMOPAC/fortran/hqrii.f, miniMOPAC/fortran/ijkl.f, miniMOPAC/fortran/ilaenv.f, miniMOPAC/fortran/initsv.f, miniMOPAC/fortran/interp.f, miniMOPAC/fortran/iter.f, miniMOPAC/fortran/jcarin.f, miniMOPAC/fortran/linmin.f, miniMOPAC/fortran/local.f, miniMOPAC/fortran/locmin.f, miniMOPAC/fortran/lsame.f, miniMOPAC/fortran/makpol.f, miniMOPAC/fortran/mamult.f, miniMOPAC/fortran/matou1.f, miniMOPAC/fortran/matout.f, miniMOPAC/fortran/matpak.f, miniMOPAC/fortran/meci.f, miniMOPAC/fortran/mecid.f, miniMOPAC/fortran/mecih.f, miniMOPAC/fortran/mecip.f, miniMOPAC/fortran/minimopac.f, miniMOPAC/fortran/moldat.f, miniMOPAC/fortran/molval.f, miniMOPAC/fortran/mopac.f, miniMOPAC/fortran/mullik.f, miniMOPAC/fortran/mult.f, miniMOPAC/fortran/nllsq.f, miniMOPAC/fortran/nuchar.f, miniMOPAC/fortran/parsav.f, miniMOPAC/fortran/partxy.f, miniMOPAC/fortran/pathk.f, miniMOPAC/fortran/paths.f, miniMOPAC/fortran/perm.f, miniMOPAC/fortran/polar.f, miniMOPAC/fortran/powsav.f, miniMOPAC/fortran/powsq.f, miniMOPAC/fortran/prtdrc.f, miniMOPAC/fortran/quadr.f, miniMOPAC/fortran/react1.f, miniMOPAC/fortran/reada.f, miniMOPAC/fortran/readmo.f, miniMOPAC/fortran/refer.f, miniMOPAC/fortran/repp.f, miniMOPAC/fortran/rotat.f, miniMOPAC/fortran/rotate.f, miniMOPAC/fortran/rsp.f, miniMOPAC/fortran/search.f, miniMOPAC/fortran/second.f, miniMOPAC/fortran/setupg.f, miniMOPAC/fortran/solrot.f, miniMOPAC/fortran/swap.f, miniMOPAC/fortran/sympro.f, miniMOPAC/fortran/symtry.f, miniMOPAC/fortran/symtrz.f, miniMOPAC/fortran/thermo.f, miniMOPAC/fortran/timer.f, miniMOPAC/fortran/timout.f, miniMOPAC/fortran/update.f, miniMOPAC/fortran/upsurf.f, miniMOPAC/fortran/vecprt.f, miniMOPAC/fortran/writmo.f, miniMOPAC/fortran/wrtkey.f, miniMOPAC/fortran/wrttxt.f, miniMOPAC/fortran/xerbla.f, miniMOPAC/fortran/xyzint.f, src/Makefile.OLD, src/common/Makefile.in, src/graphics/Makefile.in, src/some-extra-files/newfile.cpp, src/some-extra-files/newfile.h, src/target1/Makefile.OLD, src/target1/config.h.OLD, src/target1/t1m_param_mm_cpp.h, src/target1/t1m_param_mm_h.h, src/target1/t1m_param_sf_cpp.h, src/target1/t1m_param_sf_h.h, src/target1/t1main.cpp, src/target1/t1main.h, src/target2/.cvsignore, src/target2/Makefile.OLD, src/target2/config.h.OLD, src/target2/t2main.cpp, src/target2/t2main.h, src/target2/t2project.cpp, src/target2/t2project.h, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/Makefile.in, src/target3/glade/Makefile.in: some directories removed; this stuff is either moved into the new libghemical library, or (target1/target2) is discarded. 2003-01-15 17:35 thassine * src/common/matrix.h: added matrix.h back (from v1.0 source tree). 2003-01-03 13:11 thassine * src/common/: utility.cpp, utility.h: superimpose is no longer a virtual class; only one class needed since there's only one model class. 2003-01-02 15:55 thassine * src/common/moldyn.h: minor improvements to MD. 2002-12-12 09:34 thassine * src/common/model.cpp: some extra checks were added (for simplified force field, does not affect all-atom stuff). 2002-12-11 15:12 thassine * src/common/: model.cpp, seqbuild.cpp: bugfix; adding ribbons re-ordered the atoms (via seqbuild::Identify()) but this is now fixed. 2002-12-09 11:01 thassine * src/: common/eng1_qm_mopac.cpp, common/eng1_qm_mpqc.cpp, target3/glade/Makefile.in: added a bugfix (now builds with --enable-mpqc) and added some comments about MPQC/MOPAC output. 2002-12-09 10:59 thassine * src/common/: qm1e_mopac.cpp, qm1e_mpqc.cpp: added comments about MPQC/MOPAC output. 2002-12-05 13:44 thassine * configure, configure.in, src/common/define.h: changed the version number to 1.51 2002-12-05 13:43 thassine * configure, configure.in, src/common/define.h: changed the version number to 1.01 2002-12-04 09:47 thassine * CHANGES: updated the changelog 2002-12-04 09:45 thassine * INSTALL, ghemical.spec, bin/user-docs/ribbon.html, bin/user-docs/images/aa_builder_ci.png, bin/user-docs/images/aa_builder_menu.png, bin/user-docs/images/aa_builder_note.png, bin/user-docs/images/aa_builder_w_h.png, bin/user-docs/images/aa_builder_wo_h.png, bin/user-docs/images/ci_plane.png, bin/user-docs/images/ribbon.png: final fixes before release as v1.50 2002-12-03 10:49 thassine * CHANGES, INSTALL, ghemical.spec: the final fixes added... 2002-12-03 10:07 thassine * src/common/define.h: set the releasedate; this is released as v1.00 unless there are some last-minute problems 2002-12-03 09:50 thassine * Makefile.in: minor fixes to make install. 2002-12-03 09:44 thassine * Makefile.in: minor fixes to make install. 2002-12-03 09:42 thassine * bin/user-docs/: geometry_optimization.html, index.html, introduction.html, measure.html, references.html, sequence_builder.html, using_mm.html, using_qm.html, using_sf.html, visualization.html, images/geometry_opimization_console.png, images/sequence_builder_console.png: added the improved docs from Christopher also here. 2002-12-03 09:41 thassine * bin/user-docs/references.html: minor fixes to docs... 2002-12-03 09:30 thassine * bin/user-docs/: geometry_optimization.html, index.html, measure.html, references.html, ribbon.html, sequence_builder.html, using_mm.html, using_qm.html, visualization.html, images/aa_builder_ci.png, images/aa_builder_menu.png, images/aa_builder_note.png, images/aa_builder_w_h.png, images/aa_builder_wo_h.png, images/ci_plane.png, images/geometry_opimization_console.png, images/ribbon.png, images/sequence_builder_console.png: added the latest improvements to user's manual by Christopher. 2002-11-22 11:02 thassine * .cvsignore, miniMOPAC/.cvsignore, openbabel/.cvsignore, openbabel/aromatic.h, openbabel/aromatic.txt, openbabel/extable.h, openbabel/extable.txt, src/common/model.cpp, src/target3/glade/.cvsignore: synchronized openbabel with the v1.0 tree, and added a notice about incompleteness of the file format. 2002-11-21 00:26 hutchisn * .cvsignore, miniMOPAC/.cvsignore, openbabel/.cvsignore, openbabel/aromatic.h, openbabel/aromatic.txt, openbabel/extable.h, openbabel/extable.txt, src/target3/glade/.cvsignore: Minor updates. 2002-11-20 17:54 thassine * bin/examples/: 2-chlorobutane.gpr, 3-phenylpropanal.gpr, PeriodicTable.gpr, acetylsalicylic_acid.gpr, alpha-pinene.gpr, bromobenzene.gpr, camphor.gpr, cinnamaldehyde.gpr, cis-2-pentene.gpr, cyclohexane.gpr, naphtalene.gpr: added also the new example files. 2002-11-20 17:53 thassine * bin/examples/1gar.mm2gp, bin/examples/1hcl.mm2gp, bin/examples/2-chlorobutane.mm1gp, bin/examples/3-phenylpropanal.mm1gp, bin/examples/4rhn.mm2gp, bin/examples/PeriodicTable.mm1gp, bin/examples/acetylsalicylic_acid.mm1gp, bin/examples/alpha-pinene.mm1gp, bin/examples/bromobenzene.mm1gp, bin/examples/camphor.mm1gp, bin/examples/cinnamaldehyde.mm1gp, bin/examples/cis-2-pentene.mm1gp, bin/examples/cyclohexane.mm1gp, bin/examples/naphtalene.mm1gp, openbabel/extable.h, openbabel/extable.txt, openbabel/ghemical.cpp, src/common/model.cpp, src/common/model.h, src/common/oldfiles.cpp, src/common/tab_mm_prmfit.cpp, src/graphics/project.cpp, src/target1/t1m_param_mm_cpp.h, src/target1/t1main.cpp, src/target3/t3dialog.cpp, src/target3/t3main.cpp, src/target3/t3project.cpp, src/target3/t3project.h: the file format detection is now fixed; now can read the current (.gpr) and old (.mm1gp) v1.0 files. 2002-11-20 17:49 thassine * bin/examples/2-chlorobutane.gpr, bin/examples/3-phenylpropanal.gpr, bin/examples/PeriodicTable.gpr, bin/examples/acetylsalicylic_acid.gpr, bin/examples/alpha-pinene.gpr, bin/examples/bromobenzene.gpr, bin/examples/camphor.gpr, bin/examples/cinnamaldehyde.gpr, bin/examples/cis-2-pentene.gpr, bin/examples/cyclohexane.gpr, bin/examples/naphtalene.gpr, openbabel/extable.h, openbabel/extable.txt, openbabel/ghemical.cpp, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm1tab9.cpp, src/common/mm2mdl.cpp, src/common/mm2mdl.h, src/common/mm3mdl.h, src/common/model.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/common/qm2mdl.h, src/graphics/docview.cpp, src/target1/t1m_mm1param_cpp.h, src/target1/t1main.cpp, src/target3/t3docv.cpp, src/target3/t3docv.h, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h: now both MM and QM projects use the same file format (.gpr) that is the same as the old .mm1gp file format; this is consistent with arrangements in v1.50. 2002-11-20 12:38 thassine * Makefile.in: make install now installs the docs correctly. 2002-11-14 15:00 thassine * bin/user-docs/: MD.html, MD_viewer.html, aa_table.html, add_hydrogens.html, basic_mm.html, conf_search_tools.html, energy_vs_torsion.html, enlevdiag.jpg, filetypes.html, formula.html, geometry_optimization.html, index.html, labels.html, mdi_mode.html, measure.html, perspective.html, references.html, sequence_builder.html, using_cs_tools.html, using_cs_tools01.jpg, using_cs_tools02.jpg, using_cs_tools03.jpg, using_cs_tools04.jpg, using_cs_tools05.jpg, using_mm.html, using_qm.html, using_sf.html, visualization.html, images/energy_vs_torsion1.png, images/energy_vs_torsion2.png, images/energy_vs_torsion3.png, images/energy_vs_torsion4.png, images/enlevdiag.png, images/esp-plane_mm.png, images/esp-plane_qm.png, images/esp-plane_select.png, images/esp-plane_select_obj.png: updated the documentation. 2002-11-14 14:50 thassine * bin/user-docs/: MD.html, MD_viewer.html, aa_table.html, add_hydrogens.html, basic_mm.html, conf_search_tools.html, energy_vs_torsion.html, enlevdiag.jpg, filetypes.html, formula.html, geometry_optimization.html, index.html, labels.html, mdi_mode.html, measure.html, perspective.html, projects.html, references.html, sequence_builder.html, using_cs_tools.html, using_cs_tools01.jpg, using_cs_tools02.jpg, using_cs_tools03.jpg, using_cs_tools04.jpg, using_cs_tools05.jpg, using_mm.html, using_qm.html, using_sf.html, visualization.html, images/energy_vs_torsion1.png, images/energy_vs_torsion2.png, images/energy_vs_torsion3.png, images/energy_vs_torsion4.png, images/enlevdiag.png, images/esp-plane_mm.png, images/esp-plane_qm.png, images/esp-plane_select.png, images/esp-plane_select_obj.png: updated the documentation. 2002-11-14 11:16 thassine * bin/user-docs/: basic_mm.html, index.html, introduction.html, maintools.jpg, images/mainmenu.png, images/maintools.png: the chapter 1. introduction seems to be ok now. 2002-11-14 11:03 thassine * bin/user-docs/: basic_mm.html, index.html, introduction.html, maintools.jpg, references.html, images/mainmenu.png, images/maintools.png: the chapter 1. introduction seems to be ok now. 2002-11-14 09:59 thassine * bin/user-docs/: index.html: oops! fixed the absolute links from index.html 2002-11-13 10:39 thassine * configure, configure.in, bin/parameters/mm1param/stable/parameters1.txt, bin/parameters/mm1param/stable/parameters2.txt, bin/parameters/mm1param/unstable/parameters1.txt, bin/parameters/mm1param/unstable/parameters2.txt, src/common/define.h: added some halogen MM parameters, and changed the version number. 2002-11-13 10:32 thassine * configure, configure.in, src/common/define.h: added some halogen MM parameters, and changed the version number. 2002-11-11 15:18 thassine * src/graphics/: mm1docv.cpp, mm1docv.h: a broken feature fixed ; it's now again possible to calculate final energies of 1d/2d energy vs torsion plots using QM methods. 2002-11-11 11:22 thassine * src/: Doxyfile, graphics/views.cpp: changed doxygen settings, and added some fixes for gcc-3.2 2002-11-11 11:21 thassine * openbabel/: Makefile.in, Vector.cpp, Vector.h, alchemy.cpp, aromatic.h, atom.cpp, atomtyp.h, atomtyp.txt, balst.cpp, base.h, bin2hex.pl, binary.h, binary_io.h, bitgrid.h, bitvec.h, bond.txt, c3d.cpp, cacao.cpp, chains.cpp, chains.h, chiral.h, commandline.h, ctransform.h, cwrap.cpp, cwrap.h, data.cpp, data.h, element.h, element.txt, extable.h, extable.txt, fileformat.cpp, fileformat.h, generic.cpp, generic.h, grid.h, main.cpp, matrix.h, mol.cpp, mol.h, mol2.cpp, molchrg.h, molvector.cpp, molvector.h, obifstream.h, obutil.cpp, obutil.h, parsmart.cpp, parsmart.h, patty.h, pdb.cpp, phmodel.cpp, phmodel.h, phmodeldata.h, resdata.h, ring.h, rotor.h, smarts.cpp, smarts.h, smi.h, typer.cpp, typer.h, types.h, types.txt: the openbabel tree is now in sync with v1.00 2002-11-11 11:16 thassine * src/: Doxyfile, Makefile.OLD: the docs generator is now doxygen also here. 2002-11-06 12:29 thassine * bin/user-docs/: MD.html, MD_viewer.html, aa_table.html, add_hydrogens.html, basic_mm.html, documentation.css, filetypes.html, formula.html, geometry_optimization.html, import_types.html, index.html, introduction.html, labels.html, mdi_mode.html, measure.html, perspective.html, references.html, sequence_builder.html, images/2atoms_bond.png, images/2atoms_unbonded.png, images/add_hydrogens.png, images/add_hydrogens_select.png, images/change_bond_dialog.png, images/change_bond_select.png, images/cyclohexane1.png, images/cyclohexane2.png, images/cyclohexane_optimized.png, images/cyclohexane_unoptimized.png, images/draw_button.png, images/draw_hydrogens.png, images/first_atom.png, images/formula.png, images/formula_select.png, images/geometry_op_dialog.png, images/geometry_opimization_console.png, images/geometry_optimization_select.png, images/labels_menu.png, images/md_dialog.png, images/modal.png, images/new_mm.png, images/notebook.png, images/optimized_ethane.png, images/periodic_button.png, images/periodic_table.png, images/remove_hydrogens.png, images/sequence_builder.png, images/sequence_builder_console.png, images/toplevel.png, images/traj_dialog.png, images/window.png, projects.html: added the Christopher's new docs. 2002-11-05 10:48 thassine * AUTHORS, src/target2/Makefile.OLD, src/target3/Makefile.OLD, src/target3/t3main.cpp: added some new libs (reported that a modified RedHat7.3 needed these; should be added to configure system as well) : -lXt -lSM -lICE 2002-10-31 16:09 thassine * src/: graphics/project.cpp, graphics/surface.cpp, graphics/surface.h, target2/t2project.cpp: various small fixes added to plane/surface/etc objects. 2002-10-31 15:11 thassine * src/: graphics/mm1docv.cpp, graphics/mm2docv.cpp, graphics/qm1docv.cpp, graphics/surface.cpp, graphics/surface.h, target2/t2mm1docv.cpp, target2/t2mm2docv.cpp, target2/t2qm1docv.cpp: various small improvements done for plane/surface/etc objects. 2002-10-31 12:26 thassine * src/common/eng1_sf.h, src/target1/t1m_param_sf_h.h, src/common/engine.h, src/common/mm2eng.h, src/common/mm2mdl.h, src/common/mm2util.h, src/graphics/mm2docv.cpp, src/target1/t1m_mm2param_h.h, src/target2/t2main.cpp, src/target3/t3main.cpp, bin/user-docs/index.html: just terminology changes: reduced now changed to simplified in strings. 2002-10-29 12:11 thassine * src/common/model.cpp: a bugfix added that makes model.cpp compile with the configure script. 2002-10-28 16:28 thassine * src/: common/interface.cpp, common/interface.h, common/mm1eng.cpp, common/mm1mdl.cpp, common/mm2mdl.cpp, target3/t3dialog.cpp, target3/glade/trajview_dialog.cpp: moldyn now uses logbox; changed the simpl. forcef. moldyn default settings. 2002-10-28 15:38 thassine * src/: common/model.cpp, target3/t3dialog.cpp, target3/glade/trajview_dialog.cpp: moldyn now also uses logbox. 2002-10-28 14:45 thassine * src/: common/eng1_mm.cpp, common/eng1_qm.cpp, common/eng1_sf.cpp, graphics/project.cpp: bugfixes added. 2002-10-25 16:02 thassine * src/target3/t3project.cpp: optimized the default settings for planes/surfaces etc. 2002-10-25 15:59 thassine * src/target3/: t3mm1docv.cpp, t3mm2docv.cpp, t3qm1docv.cpp: optimized the default settings for planes/surfaces. 2002-10-24 16:06 thassine * src/: graphics/mm1docv.cpp, target3/t3mm1docv.cpp, target3/t3mm1docv.h: seq-builder has a command string. 2002-10-24 16:02 thassine * src/: graphics/project.cpp, target3/t3project.cpp, target3/t3project.h: seq-builder now has a command string. 2002-10-24 15:09 thassine * src/: graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/views.cpp, target3/t3mm1docv.cpp: the 1d and 2d energy plots now have command strings. 2002-10-24 15:01 thassine * src/: graphics/project.cpp, graphics/project.h, graphics/views.cpp, target3/t3project.cpp: the 1d and 2d plots now have command strings. 2002-10-23 17:44 thassine * src/: common/mm1mdl.cpp, target3/t3qm1docv.cpp: the colour of eldens-plot changed, add hydrogens-message is now displayed. 2002-10-23 17:38 thassine * src/: common/model.cpp, graphics/project.cpp, graphics/project.h, target3/t3project.cpp, target3/t3project.h, target3/t3views.cpp: qm-related planes/surfaces added, enlev-diagram addded. 2002-10-23 12:01 thassine * src/: common/mm1mdl.cpp, graphics/mm1docv.cpp, graphics/qm1docv.cpp, target3/t3views.cpp: some output moved to logbox. 2002-10-23 10:52 thassine * src/: graphics/mm2docv.cpp, graphics/qm1docv.cpp, target3/t3mm2docv.cpp, target3/t3qm1docv.cpp: all plane/volrend/surface objects are now managed using the command strings. 2002-10-22 18:40 thassine * src/: graphics/project.cpp, target3/t3project.cpp: plane/volrend/surface command strings added. 2002-10-22 18:38 thassine * src/: graphics/docview.cpp, graphics/mm1docv.cpp, graphics/mm2docv.cpp, graphics/mm3docv.cpp, graphics/qm1docv.cpp, graphics/qm2docv.cpp, target3/t3mm1docv.cpp: added commands for plane/volrend/surface objects (not quite complete yet). 2002-10-21 13:43 thassine * src/: common/model.cpp, common/model.h, common/search.cpp, graphics/project.cpp, target2/t2project.cpp, target3/t3project.cpp: added the random/systematic/montecarlo conformational search commands. 2002-10-21 13:39 thassine * src/: common/mm1alg.cpp, common/mm1mdl.cpp, common/mm1mdl.h, graphics/mm1docv.cpp, graphics/qm1docv.cpp, target2/t2mm1docv.cpp, target3/t3mm1docv.cpp: added the set_current_orbital command, and commands for random/systematic/montecarlo searchs. 2002-10-21 11:20 thassine * src/: graphics/qm1docv.cpp, target3/t3qm1docv.cpp: the set_current_orbital now works without console. 2002-10-21 10:53 thassine * src/: graphics/project.cpp, target3/t3project.cpp, target3/t3views.cpp: the add light-operation is a bit improved. 2002-10-21 10:52 thassine * src/: graphics/docview.cpp, target3/t3mm1docv.cpp, target3/t3mm2docv.cpp, target3/t3views.cpp: added some improvements to add light-operation. 2002-10-17 17:17 thassine * src/: graphics/project.cpp, graphics/project.h, target3/t3dialog.cpp, target3/t3dialog.h, target3/t3project.cpp, target3/t3project.h, target3/t3views.cpp: the command interpreter added; now initially only commands help and add light works. 2002-10-17 17:09 thassine * src/: common/mm2mdl.h, common/mm3mdl.h, common/qm1mdl.h, common/qm2mdl.h, graphics/docview.cpp, graphics/docview.h, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/mm2docv.cpp, graphics/mm2docv.h, graphics/mm3docv.cpp, graphics/mm3docv.h, graphics/qm1docv.cpp, graphics/qm1docv.h, graphics/qm2docv.cpp, graphics/qm2docv.h, target3/t3dialog.cpp, target3/t3dialog.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3mm2docv.cpp, target3/t3mm2docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h, target3/t3views.cpp: the command interpreter dialog is added; commands help and add light work now. 2002-10-16 11:15 thassine * src/: common/mm1eng1.cpp, common/mm1eng9.cpp, common/mm1tab1.cpp, common/mm1tab9.cpp, target3/t3docv.cpp, target3/t3docv.h, target3/glade/setup_mm1_dialog.cpp, target3/glade/setup_qm1_dialog.cpp: now the setup changes and possible error messages from mol.mech. calculations are displayed in the new logbox. 2002-10-16 11:08 thassine * src/: common/eng1_mm_default.cpp, common/eng1_mm_prmfit.cpp, common/tab_mm_default.cpp, common/tab_mm_prmfit.cpp, target3/t3project.cpp, target3/t3project.h, target3/glade/setup_druid.cpp: setup changes and possible mol.mech. error messages are now displayed in the new logbox. 2002-10-15 11:48 thassine * src/: common/mm1mdl.cpp, common/mm2mdl.cpp, common/qm1mdl.cpp, target3/t3docv.cpp: moved console output to the new output box; all CalcEnergy and GeomOpt variants how handled. 2002-10-15 11:46 thassine * src/: common/model.cpp, target3/t3project.cpp: moved output from console to output box; CalcEnergy and GeomOpt. 2002-10-14 15:55 thassine * src/: common/model.cpp, common/model.h, target3/t3project.cpp, target3/t3project.h, target3/t3views.cpp: a text log box was added to the GUI. works now for CalcEnergy and GeomOpt operations. 2002-10-14 15:48 thassine * src/: common/mm1mdl.cpp, common/model.h, target3/t3docv.cpp, target3/t3docv.h, target3/t3views.cpp: a new text log box was added to GUI; works now for mol.mech. CalculateEnergy and GeometryOptimization operations. 2002-10-05 11:31 thassine * src/: common/model.cpp, target3/t3dialog.cpp: after the aa2sf conversion, the setup is automatically set suitable for doing calculations with the simplified model. 2002-10-04 15:18 thassine * src/common/: eng1_sf.cpp, model.cpp: the values of model::sf_types array are now the same as those in the atom::sf_atmtp records. 2002-10-04 13:52 thassine * src/: common/eng1_sf.cpp, common/eng1_sf.h, common/typedef.h, graphics/plane.cpp, graphics/plane.h, graphics/project.cpp, graphics/project.h, graphics/ribbon.cpp, graphics/ribbon.h, graphics/spline.cpp, graphics/spline.h: the use of typedef- or template-based arrays (see typedef.h) seems to be a continuous source of memory-handling bugs. therefore removed all such constructs and banned their future use as well (removed from typedef.h). 2002-10-04 11:10 thassine * src/common/model.cpp: more fixes to aa2sf conversion (temporary coordinate handling). 2002-10-04 10:20 thassine * src/common/: model.cpp, model.h: a potential bug related to aa2sf conversion is fixed. 2002-10-03 15:12 thassine * src/common/: model.cpp, utility.cpp: a few changes here and there... 2002-10-03 12:09 thassine * src/common/oldfiles.cpp: the oldfiles.cpp file was added. 2002-10-03 11:27 thassine * src/: common/Makefile.OLD, common/Makefile.in, common/eng1_mm.cpp, common/eng1_mm.h, common/eng1_qm.cpp, common/eng1_qm.h, common/eng1_sf.cpp, common/eng1_sf.h, common/eng2_mm_sf.cpp, common/eng2_mm_sf.h, common/eng2_qm_mm.cpp, common/eng2_qm_mm.h, common/engine.h, common/model.cpp, common/model.h, target3/glade/setup_druid.cpp: an initial version of the new file format is now added; needs some futher testing however. 2002-09-12 13:50 thassine * src/target3/t3dialog.cpp: a warning message was added (readpdb). 2002-09-12 13:45 thassine * src/target3/: t3mm1docv.cpp, t3mm2docv.cpp: a warning message was added about readpdb. 2002-09-11 17:35 thassine * src/: graphics/ribbon.cpp, target3/t3dialog.cpp, target3/t3project.cpp, 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. 2002-09-11 13:24 thassine * src/graphics/mm1rbn.cpp: all-atoms ribbon colouring is now done using secodary structure assignments, as it has been in the simplified model (mm2) earlier. 2002-09-10 17:36 thassine * bin/parameters/builder/amino.txt, src/common/seqbuild.cpp, src/common/utility.cpp: the DefineSecondaryStructure() function now works with simplified residues as well; also a ribbon bug is fixed. 2002-09-10 17:30 thassine * bin/parameters/builder/amino.txt, src/common/mm1util.cpp: a bug was fixed that caused ribbon object creation crash in some cases. now the ribbons should work if 1) there are more than 3 residues in each chain 2) the chains are properly gapped with -NH3 and -COO groups 3) the chain consists of proper (-NH-C-CO-) units. 2002-09-10 11:47 thassine * src/common/: model.cpp, seqbuild.cpp, seqbuild.h: the seqbuilder::Identify() now handles correctly also the simplified chains. 2002-09-08 13:05 thassine * src/: Doxyfile, Makefile.OLD, common/atom.h, common/bond.h, common/conjgrad.h, common/eng1_sf.h, common/engine.h, 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 11:25 thassine * src/target1/: t1m_mm2param_cpp.h, t1m_mm2param_h.h: removed some old files from the console target. 2002-09-07 11:24 thassine * src/target1/: t1m_mm1param_cpp.h, t1m_mm1param_h.h, t1m_param_mm_cpp.h, t1m_param_mm_h.h, t1m_param_sf_cpp.h, t1m_param_sf_h.h, t1main.cpp, t1main.h: some filenames changed at the console target... 2002-09-06 12:07 thassine * src/common/: atom.cpp, atom.h, eng1_sf.cpp, model.cpp: the sf is now in sync with the version in MANY_PROJECTS_BRANCH. 2002-09-06 12:06 thassine * src/common/mm2eng.cpp: the simplified ff is now in sync with the HEAD branch one. 2002-09-05 16:47 thassine * src/common/: eng1_sf.cpp, eng1_sf.h: in sf, all terms except the solvation one works like before. 2002-09-05 13:18 thassine * src/common/: eng1_sf.cpp, eng1_sf.h: the nbt1 terms work now in sf. 2002-09-05 10:26 thassine * src/common/eng1_sf.cpp: minor bugs fixed in bonded-term creation in the sf. 2002-09-04 16:56 thassine * src/common/: eng1_sf.cpp, eng1_sf.h: continued to port the sf stuff. 2002-09-03 13:45 thassine * src/: common/atom.cpp, common/eng1_mm.cpp, common/eng1_mm_default.cpp, common/eng1_mm_prmfit.cpp, common/eng1_qm.cpp, common/eng1_qm.h, common/eng1_qm_mopac.cpp, common/eng1_qm_mpqc.cpp, common/eng1_sf.h, common/eng2_mm_sf.h, common/eng2_qm_mm.h, common/engine.cpp, common/filetrans.cpp, common/intcrd.cpp, common/model.cpp, common/seqbuild.cpp, common/tab_mm_prmfit.cpp, graphics/project.cpp, graphics/ribbon.cpp, target1/t1m_mm1param_cpp.h, target1/t1m_mm2param_cpp.h, target3/glade_dialog.cpp, target3/t3dialog.cpp, target3/t3main.cpp, target3/t3project.cpp, target3/glade/setup_druid.cpp: checked the bug report messages in various little run-time tests; they now all carry a BUG: tag. 2002-09-03 12:39 thassine * src/: common/atom.h, common/bond.cpp, common/bond.h, common/eng1_sf.cpp, common/eng1_sf.h, common/engine.cpp, common/model.cpp, graphics/project.cpp: some improvements added to sf. 2002-09-02 16:28 thassine * src/: common/bond.cpp, common/bond.h, common/eng1_sf.cpp, common/eng1_sf.h, common/model.cpp, graphics/project.cpp: the all-atoms -> simplified conversion seems to work now. 2002-08-31 12:57 thassine * src/: common/eng1_qm_mpqc.cpp, common/eng2_qm_mm.cpp, common/eng2_qm_mm.h, target3/glade/setup_druid.cpp, target3/glade/setup_druid.glade: updated the mpqc-related stuff; now there are qm/mm engine classes for both mopac and mpqc. they seem to work technically fine, but without any glue code the qm and mm parts are not interacting at all. yet. 2002-08-31 11:39 thassine * src/common/: eng1_mm.cpp, eng1_mm.h, eng1_mm_default.cpp, 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 18:33 thassine * src/: common/eng1_mm.cpp, common/eng1_mm.h, common/eng1_mm_default.cpp, common/eng1_mm_prmfit.cpp, common/eng1_qm.cpp, common/eng1_qm.h, common/eng1_qm_mopac.cpp, common/eng1_qm_mopac.h, common/eng1_sf.cpp, common/eng1_sf.h, common/eng2_qm_mm.cpp, common/engine.cpp, common/engine.h, common/model.h, common/tab_mm_default.cpp, common/tab_mm_prmfit.cpp, target2/t2project.cpp: the eng classes now use local instead of global atom numbering (more like the old system). there is a nonbonded-term bug in qmmm but otherwise it looks good. sf only compiles. 2002-08-30 13:54 thassine * src/: common/eng1_mm.cpp, common/eng1_mm.h, common/eng1_qm.cpp, common/eng1_qm.h, common/eng1_sf.cpp, common/eng1_sf.h, common/eng2_mm_sf.cpp, common/eng2_mm_sf.h, common/eng2_qm_mm.cpp, common/eng2_qm_mm.h, common/engine.cpp, common/engine.h, target2/t2project.cpp, target2/t2project.h, target3/glade/setup_druid.cpp: the setup classes are now initialized correctly. setup::GetMaxEngineIndex() renamed to setup::GetEngineCount(). 2002-08-30 12:36 thassine * src/: common/Makefile.OLD, common/Makefile.in, common/eng1_sf.cpp, common/eng1_sf.h, common/eng2_mm_sf.cpp, common/eng2_mm_sf.h, target3/glade/setup_druid.cpp: ok, everything compiles now, including the simplified forcefield stuff. 2002-08-30 09:27 thassine * src/: common/atom.cpp, common/atom.h, common/eng1_sf.cpp, common/eng1_sf.h, common/engine.cpp, common/model.cpp, common/model.h, common/seqbuild.cpp, common/tab_mm_default.cpp, common/tab_mm_prmfit.cpp, graphics/project.cpp, 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 09:30 thassine * src/: common/model.cpp, common/seqbuild.cpp, target1/Makefile.OLD, target1/t1m_mm1param_cpp.h, target1/t1m_mm1param_h.h, target1/t1main.cpp, target2/t2project.cpp, target3/t3project.cpp: the new model::UpdateChains() function now updates the chain/residue information. all targets brought up-to-date again. 2002-08-28 17:40 thassine * src/: common/atom.cpp, common/atom.h, common/eng1_mm.cpp, common/model.cpp, common/model.h, common/search.cpp, common/seqbuild.cpp, graphics/project.cpp, target2/t2project.cpp, target3/glade/setup_druid.glade: many changes added. GatherGroups() renamed to UpdateGroups(). is_index_clean and is_groups_clean flags are added so that it would be better defined whether groups/chains/etc information is up-to-date or not. 2002-08-28 12:59 thassine * src/: common/eng1_mm.cpp, common/eng1_mm.h, common/eng1_qm.cpp, common/eng1_qm.h, common/eng1_sf.cpp, common/eng1_sf.h, common/eng2_qm_mm.cpp, common/eng2_qm_mm.h, common/engine.h, common/model.h, target3/glade/setup_druid.cpp, target3/glade/setup_druid.glade, 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 17:54 thassine * src/common/: atom.cpp, eng1_sf.h, intcrd.cpp, model.cpp: some bugfixes added; the conformational search tools should work now. 2002-08-27 14:41 thassine * src/target3/: t3dialog.cpp, t3dialog.h, t3project.cpp, t3project.h, glade/file_import_dialog.cpp: added the File/ExtraTools also here. 2002-08-27 14:37 thassine * src/target3/: t3mm1docv.cpp, t3mm1docv.h, t3mm2docv.cpp, t3mm2docv.h, t3qm1docv.cpp, t3qm1docv.h, glade/file_import_dialog.cpp: added to popup-menu new items File/ExtraTools where one has an alternate way to read in PDB files; that way might be quite slow (can take many minutes) but the resulting files (usually?) are compatible to the ribbon drawing tool (so that the ribbons work). that's because the ribbon tool must have intact (-NH-CHR-CO-) protein/peptide main chains and proper amino -NH3+ and carboxy -COO- groups. 2002-08-21 10:32 thassine * src/: common/eng1_sf.cpp, common/model.cpp, common/model.h, common/seqbuild.cpp, common/seqbuild.h, graphics/ribbon.cpp, target2/t2project.cpp, target3/t3project.cpp: improvements added to the seqbuilder and chn_info classes. 2002-08-21 10:31 thassine * src/: common/mm1mdl.cpp, common/mm1util.cpp, common/mm1util.h, graphics/mm1rbn.cpp, target2/t2mm1docv.cpp, target3/t3mm1docv.cpp: improvements added to the sequence builder. 2002-08-01 10:31 thassine * src/common/: engine.cpp, intcrd.cpp, 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). 2002-08-01 09:28 thassine * src/common/: mm1eng.cpp, mm2eng.cpp, qm1eng.cpp: bounds-checking was added to CopyCRD() functions. 2002-07-31 13:09 thassine * src/graphics/camera.cpp: the fps counter added also to HEAD. 2002-07-31 12:53 thassine * src/graphics/camera.cpp: a simple frame rate counter was added for graphics optimization purposes (at camera.cpp, commented out). uncomment it, and use for example orbit_xy tool continuously to update graphics; will print frame rates at 30 frame intervals. 2002-07-30 10:07 thassine * src/: common/atom.cpp, common/atom.h, common/eng1_mm.cpp, common/eng1_qm.cpp, common/eng1_qm_mopac.cpp, common/engine.cpp, common/filetrans.cpp, common/intcrd.cpp, common/intcrd.h, common/model.cpp, common/model.h, common/seqbuild.cpp, common/tab_mm_prmfit.cpp, common/utility.cpp, graphics/project.cpp, graphics/ribbon.cpp, 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. 2002-07-30 09:48 thassine * src/common/: mm1alg.cpp, mm1mdl.cpp: added description of a bug that might affect intcrd objects when coordinate sets are added. 2002-07-25 11:37 thassine * src/common/: mm1alg.cpp, mm1mdl.cpp: added some improvements to monte carlo search. 2002-07-24 13:24 thassine * openbabel/c3d.cpp, src/graphics/views.cpp: added some fixes that gcc-3.1 needs; just types specified like in sqrt(a) -> sqrt((double) a); should not really change anything. 2002-07-23 15:27 thassine * src/: common/model.cpp, common/model.h, graphics/project.cpp, target2/t2project.cpp: the memory management scheme of crd_set objects is now simpler. 2002-07-23 15:24 thassine * src/: common/mm1mdl.cpp, common/mm2mdl.cpp, common/model.cpp, common/model.h, common/qm1mdl.cpp, graphics/mm1docv.cpp, graphics/mm2docv.cpp, graphics/qm1docv.cpp, target2/t2mm1docv.cpp, target2/t2mm2docv.cpp, target2/t2qm1docv.cpp: the memory management of crd_set objects is now simpler. 2002-07-23 12:34 thassine * src/: common/engine.h, common/model.cpp, common/model.h, common/search.cpp, common/search.h, target2/t2project.cpp, target3/t3project.cpp, target3/t3project.h: the search tool improvements ported also here. 2002-07-23 12:04 thassine * src/common/: eng1_sf.cpp, eng1_sf.h, engine.h: added some fixes to SF, althought it does not even compile yet; therefore the ENABLE_SIMPLIFIED macro is disabled at config.h 2002-07-22 16:19 thassine * src/: common/mm1alg.cpp, common/mm1alg.h, common/mm1mdl.cpp, common/mm1mdl.h, target2/t2mm1docv.cpp, target3/t3mm1docv.cpp, target3/t3mm1docv.h: added systematic and montecarlo search tools. for my part the v1.00 is feature-complete, so i will move into bugfixes and gui enhancements. 2002-07-20 16:13 thassine * src/common/: mm1eng.cpp, mm1eng1.cpp, mm1eng9.cpp, mm2eng.cpp, qm1alg.cpp, qm1eng.cpp: started adding improvements that remove the dependence of console input; changed a few error messages into graphical ones. 2002-06-27 23:21 hutchisn * src/common/: filetrans.cpp, filetrans.h, mm1mdl.cpp: Add support to file_trans::Synchronize to allow only creating new atoms/bonds rather than modifying existing ones. Use this for AddHydrogens. 2002-06-21 21:37 hutchisn * openbabel/mol.cpp, src/common/mm1mdl.cpp, src/target3/t3prefs.cpp: Add fixes for library widget bug. 2002-06-20 16:52 thassine * configure, configure.in, src/common/define.h: changed the version number to 0.91 2002-06-20 16:48 thassine * src/: common/prefs.h, target3/t3prefs.cpp, target3/t3prefs.h, target3/t3project.cpp: added the v0.90 bugfixes also to HEAD. 2002-06-20 14:27 thassine * INSTALL, src/common/prefs.h, src/common/utility.cpp, src/graphics/mm2docv.cpp, src/graphics/views.cpp, src/target3/t3mm1docv.cpp, src/target3/t3prefs.cpp, src/target3/t3prefs.h: added some final fixes and comments. 2002-06-20 10:54 thassine * ghemical.spec: updated also the .spec file. 2002-06-20 10:36 thassine * CHANGES, src/common/define.h: updated the changelog; this is soon released as v0.90 if no problems are found. 2002-06-20 10:25 thassine * INSTALL: updated the documentation. 2002-06-20 00:18 hutchisn * miniMOPAC/Makefile.in, openbabel/Makefile.in, openbabel/Vector.cpp, openbabel/Vector.h, openbabel/alchemy.cpp, openbabel/amber.cpp, openbabel/aromatic.h, openbabel/aromatic.txt, openbabel/atom.cpp, openbabel/atomtyp.h, openbabel/atomtyp.txt, openbabel/balst.cpp, openbabel/base.cpp, openbabel/base.h, openbabel/bgf.cpp, openbabel/bin2hex.pl, openbabel/binary.cpp, openbabel/binary.h, openbabel/binary_io.cpp, openbabel/binary_io.h, openbabel/bitgrid.cpp, openbabel/bitgrid.h, openbabel/bitvec.h, openbabel/bond.cpp, openbabel/box.cpp, openbabel/c3d.cpp, openbabel/cacao.cpp, openbabel/cache.cpp, openbabel/car.cpp, openbabel/chains.cpp, openbabel/chains.h, openbabel/chdrw.cpp, openbabel/chiral.cpp, openbabel/chiral.h, openbabel/cml.cpp, openbabel/commandline.h, openbabel/csr.cpp, openbabel/cssr.cpp, openbabel/ctransform.cpp, openbabel/ctransform.h, openbabel/cwrap.cpp, openbabel/cwrap.h, openbabel/data.cpp, openbabel/data.h, openbabel/dmol.cpp, openbabel/element.h, openbabel/element.txt, openbabel/extable.h, openbabel/extable.txt, openbabel/feat.cpp, openbabel/fh.cpp, openbabel/fileformat.cpp, openbabel/fileformat.h, openbabel/gamess.cpp, openbabel/gaussian.cpp, openbabel/generic.cpp, openbabel/generic.h, openbabel/ghemical.cpp, openbabel/grid.h, openbabel/gromos96.cpp, openbabel/hin.cpp, openbabel/jaguar.cpp, openbabel/main.cpp, openbabel/matrix.cpp, openbabel/matrix.h, openbabel/mmod.cpp, openbabel/mol.cpp, openbabel/mol.h, openbabel/mol2.cpp, openbabel/molchrg.cpp, openbabel/molchrg.h, openbabel/molvector.cpp, openbabel/molvector.h, openbabel/mopac.cpp, openbabel/mpqc.cpp, openbabel/nwchem.cpp, openbabel/obifstream.h, openbabel/oblib.dsp, openbabel/obutil.cpp, openbabel/obutil.h, openbabel/parsmart.cpp, openbabel/parsmart.h, openbabel/parsmi.cpp, openbabel/patty.cpp, openbabel/patty.h, openbabel/pdb.cpp, openbabel/phmodel.cpp, openbabel/phmodel.h, openbabel/phmodel.txt, openbabel/phmodeldata.h, openbabel/qchem.cpp, openbabel/report.cpp, openbabel/resdata.h, openbabel/ring.cpp, openbabel/ring.h, openbabel/rotor.cpp, openbabel/rotor.h, openbabel/smarts.cpp, openbabel/smarts.h, openbabel/smi.cpp, openbabel/smi.h, openbabel/tinker.cpp, openbabel/tokenst.cpp, openbabel/typer.cpp, openbabel/typer.h, openbabel/types.h, openbabel/types.txt, openbabel/unichem.cpp, openbabel/viewmol.cpp, openbabel/xed.cpp, openbabel/xyz.cpp, src/common/Makefile.in, src/graphics/Makefile.in: Updating Open Babel version with fixes, new formats for next ghemical release. 2002-06-19 15:56 thassine * src/: common/Makefile.OLD, common/Makefile.in, common/atom.cpp, common/atom.h, common/eng1_mm.h, common/eng1_sf.cpp, common/eng1_sf.h, common/engine.h, common/model.cpp, common/moldyn.cpp, common/seqbuild.h, graphics/project.cpp, target1/config.h.OLD, target2/config.h.OLD, target2/t2project.cpp, 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... 2002-06-19 13:06 thassine * src/target3/glade/trajview_dialog.glade: destroy-event added to trajview dialog; now closes properly. 2002-06-17 13:55 thassine * src/target3/glade_dialog.h: whitespace cleanup... 2002-06-17 13:40 thassine * Makefile.in, src/common/define.h, src/common/eng1_sf.cpp, src/common/model.cpp, src/common/model.h, src/common/tab_mm_default.cpp, src/target3/glade_dialog.cpp, src/target3/glade_dialog.h, src/target3/t3dialog.cpp, src/target3/t3project.cpp, src/target3/glade/file_export_dialog.cpp, src/target3/glade/file_export_dialog.h, src/target3/glade/file_import_dialog.cpp, src/target3/glade/file_import_dialog.h, src/target3/glade/geomopt_dialog.cpp, src/target3/glade/geomopt_dialog.h, src/target3/glade/moldyn_dialog.cpp, src/target3/glade/moldyn_dialog.h, src/target3/glade/setup_druid.cpp, src/target3/glade/setup_druid.h, src/target3/glade/trajview_dialog.cpp, src/target3/glade/trajview_dialog.h: the glade files are now installed correctly by make install. 2002-06-17 12:52 thassine * Makefile.in, src/common/define.h, src/common/mm1tab1.cpp, src/common/mm2eng.cpp, src/common/model.cpp, src/common/model.h, src/target3/Makefile.OLD, src/target3/Makefile.in, src/target3/glade_callbacks.cpp, src/target3/glade_callbacks.h, src/target3/glade_dialog.cpp, src/target3/glade_dialog.h, src/target3/glade_interface.cpp, src/target3/glade_interface.h, src/target3/glade_support.cpp, src/target3/glade_support.h, src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp, src/target3/glade/file_export_dialog.cpp, src/target3/glade/file_export_dialog.h, src/target3/glade/file_import_dialog.cpp, src/target3/glade/file_import_dialog.h, src/target3/glade/geomopt_dialog.cpp, src/target3/glade/geomopt_dialog.h, src/target3/glade/moldyn_dialog.cpp, src/target3/glade/moldyn_dialog.h, src/target3/glade/setup_mm1_dialog.cpp, src/target3/glade/setup_mm1_dialog.h, src/target3/glade/setup_qm1_dialog.cpp, src/target3/glade/setup_qm1_dialog.h, src/target3/glade/trajview_dialog.cpp, src/target3/glade/trajview_dialog.h: removed the old glade code + files. 2002-06-14 14:47 thassine * src/Makefile.OLD: fixed src/Makefile.OLD clean: also in HEAD. 2002-06-14 14:42 thassine * src/Makefile.OLD: the src/Makefile.OLD returned errors in clean: 2002-06-13 16:09 thassine * src/common/: conjgrad.cpp, conjgrad.h: also copied conjgrad changes to HEAD. 2002-06-13 15:37 thassine * src/: common/conjgrad.cpp, common/conjgrad.h, graphics/mm2docv.cpp, target2/Makefile.OLD, target2/t2main.cpp: added some improvements to conjgrad, and something was still missing from mm2_mdl mouse rot/trans tool. 2002-06-11 13:06 thassine * src/graphics/: mm2docv.cpp, mm2docv.h: added the simple rotation/translation operations for selected VA's also into mm2_mdl (like it has been in mm1_mdl for a long time already). 2002-06-08 12:01 thassine * src/target3/: t3main.cpp, glade/setup_druid.cpp, glade/setup_druid.glade, glade/setup_druid.h: the setup_druid can now correctly change the pages with prev/next buttons. 2002-06-07 15:49 thassine * src/target3/: t3project.cpp, glade/Makefile.OLD, glade/Makefile.in, glade/setup_druid.cpp, glade/setup_druid.glade, glade/setup_druid.h: added an initial version of the setup druid (nothing except cancel works). 2002-06-07 13:54 thassine * src/target3/: glade_callbacks.cpp, glade_callbacks.h, glade_interface.cpp, glade_interface.h, glade_support.cpp, glade_support.h, t3main.cpp, t3mm1docv.cpp, t3qm1docv.cpp, glade/Makefile.OLD, glade/Makefile.in, glade/ghemical.glade, glade/setup_mm1_dialog.cpp, glade/setup_mm1_dialog.glade, glade/setup_mm1_dialog.h, glade/setup_qm1_dialog.cpp, glade/setup_qm1_dialog.glade, glade/setup_qm1_dialog.h: the setup dialogs also are now libglade dialogs; none of the old-style dialogs are no longer needed, and the old code is commented out. the old code can be removed once we have the .glade file installation working (and tested a bit). 2002-06-07 11:26 thassine * src/target3/: t3project.cpp, glade/Makefile.OLD, glade/Makefile.in, glade/file_export_dialog.cpp, glade/file_export_dialog.glade, glade/file_export_dialog.h, glade/file_import_dialog.cpp, glade/file_import_dialog.glade, glade/file_import_dialog.h: added the file import/export dialogs. 2002-06-07 11:19 thassine * src/target3/: t3mm1docv.cpp, glade/Makefile.OLD, glade/Makefile.in, glade/file_export_dialog.cpp, glade/file_export_dialog.glade, glade/file_export_dialog.h, glade/file_import_dialog.cpp, glade/file_import_dialog.glade, glade/file_import_dialog.h: file import/export dialogs converted to libglade. 2002-06-07 09:38 thassine * src/target3/: t3dialog.cpp, t3dialog.h, t3main.cpp, t3project.cpp, t3project.h, glade/Makefile.OLD, glade/Makefile.in, glade/geomopt_dialog.cpp, glade/geomopt_dialog.glade, glade/geomopt_dialog.h, glade/moldyn_dialog.cpp, glade/moldyn_dialog.glade, glade/moldyn_dialog.h, glade/trajview_dialog.cpp, glade/trajview_dialog.glade, glade/trajview_dialog.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. 2002-06-07 09:35 thassine * src/target3/: t3dialog.cpp, t3dialog.h, t3main.cpp, t3mm1docv.cpp, t3mm2docv.cpp, glade/Makefile.OLD, glade/Makefile.in, glade/geomopt_dialog.cpp, glade/geomopt_dialog.glade, glade/geomopt_dialog.h, glade/moldyn_dialog.cpp, glade/moldyn_dialog.glade, glade/moldyn_dialog.h, glade/trajview_dialog.cpp, glade/trajview_dialog.glade, glade/trajview_dialog.h: moldyn + trajview dialogs also now libglade dialogs. trajview is a modeless one, so one can rotate,zoom,etc when using the dialog. also memory leaks related to dialogs should be gone now. 2002-06-05 15:10 thassine * Makefile.in, configure, configure.in, src/Makefile.OLD, src/target3/Makefile.OLD, src/target3/Makefile.in, src/target3/glade_dialog.cpp, src/target3/glade_dialog.h, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp, src/target3/glade/Makefile.OLD, src/target3/glade/Makefile.in, src/target3/glade/README, src/target3/glade/geomopt_dialog.cpp, src/target3/glade/geomopt_dialog.glade, src/target3/glade/geomopt_dialog.h: back-ported the libglade-based geomopt dialog. 2002-06-05 14:39 thassine * src/Makefile.OLD: added some Makefile tweaks. 2002-06-05 13:25 thassine * src/target3/: glade_dialog.h, t3project.cpp, glade/Makefile.OLD, glade/geomopt_dialog.cpp, glade/geomopt_dialog.glade, glade/geomopt_dialog.h: the geomopt dialog now works using libglade. 2002-06-03 13:23 thassine * openbabel/fileformat.h: oops, my mistake. of course there were nothing wrong with fileformat.h but I had an obsolete Makefile. the changes are reverted. 2002-06-03 12:50 thassine * openbabel/fileformat.h: there were some undefined functions at fileformat.cpp; just made some dummy functions in fileformat.h so that OB can be compiled... 2002-05-31 19:34 hutchisn * configure, configure.in, miniMOPAC/Makefile.in, src/common/Makefile.in, src/graphics/Makefile.in, src/target3/Makefile.in, src/target3/glade/Makefile.in, src/target3/glade/geomopt_dialog.h: Updated makefiles for libglade, etc. 2002-05-31 19:31 hutchisn * openbabel/: Makefile.in, Vector.cpp, Vector.h, alchemy.cpp, amber.cpp, aromatic.h, aromatic.txt, atom.cpp, atomtyp.h, atomtyp.txt, balst.cpp, base.cpp, base.h, bgf.cpp, bin2hex.pl, binary.cpp, binary.h, binary_io.cpp, binary_io.h, bitgrid.cpp, bitgrid.h, bitvec.h, bond.cpp, bond.txt, box.cpp, c3d.cpp, cacao.cpp, cache.cpp, car.cpp, chains.cpp, chdrw.cpp, chiral.cpp, chiral.h, cml.cpp, commandline.h, csr.cpp, cssr.cpp, ctransform.cpp, ctransform.h, data.cpp, data.h, dmol.cpp, element.h, extable.h, extable.txt, feat.cpp, fh.cpp, fileformat.cpp, fileformat.h, gamess.cpp, gaussian.cpp, generic.cpp, generic.h, ghemical.cpp, grid.h, gromos96.cpp, hin.cpp, jaguar.cpp, main.cpp, matrix.cpp, matrix.h, mmod.cpp, mol.cpp, mol.h, molchrg.cpp, molchrg.h, molvector.cpp, molvector.h, mopac.cpp, mpqc.cpp, nwchem.cpp, obifstream.h, oblib.dsp, obutil.cpp, obutil.h, parsmart.cpp, parsmart.h, parsmi.cpp, patty.cpp, patty.h, pdb.cpp, phmodel.cpp, phmodel.h, phmodel.txt, phmodeldata.h, qchem.cpp, report.cpp, resdata.h, ring.cpp, ring.h, rotor.cpp, rotor.h, smarts.cpp, smarts.h, smi.cpp, smi.h, tinker.cpp, tokenst.cpp, typer.cpp, typer.h, types.h, unichem.cpp, viewmol.cpp, xed.cpp, xyz.cpp: Merge in current Open Babel (w/ CML and proper namespace support). 2002-05-31 11:12 thassine * src/: common/Makefile.in, graphics/Makefile.in, target3/Makefile.in, target3/glade/Makefile.in: fixes added to makefiles; now the configuration works otherwise except that libglade incs and libs are missing. 2002-05-31 10:52 thassine * src/: common/Makefile.in, graphics/Makefile.in, target3/Makefile.in: some cleanups done in makefiles. 2002-05-30 15:43 thassine * configure, configure.in, src/common/define.h: promoted the version number to 0.85 in the HEAD branch. 2002-05-30 15:37 thassine * configure, configure.in, src/common/define.h: promoted the version number to 0.90 in the MANY_PROJECTS_BRANCH, to avoid confusion between the branches. 2002-05-30 14:07 thassine * Makefile.in, configure, configure.in, src/common/Makefile.in, src/common/eng1_sf.cpp, src/common/tab_mm_default.cpp, src/graphics/Makefile.in, src/target3/Makefile.in, src/target3/glade/Makefile.in: minor fixes like changed directories etc added. 2002-05-30 12:39 thassine * src/some-extra-files/: newfile.cpp, newfile.h: added new files to bin/parameters and some minor stuff. 2002-05-30 12:34 thassine * bin/parameters/: mm1param/stable/atomtypes.txt, mm1param/stable/parameters1.txt, mm1param/stable/parameters2.txt, mm1param/stable/parameters3.txt, mm1param/stable/parameters4.txt, mm1param/stable/parameters5.txt, mm1param/unstable/atomtypes.txt, mm1param/unstable/parameters1.txt, mm1param/unstable/parameters2.txt, mm1param/unstable/parameters3.txt, mm1param/unstable/parameters4.txt, mm1param/unstable/parameters5.txt, mm2param/loopdip.txt, mm2param/looptor.txt, mm2param/nonbonded.txt: removed old files under bin/parameters. 2002-05-30 12:29 thassine * src/: common/atom.cpp, common/atom.h, common/bond.cpp, common/bond.h, common/define.h, common/eng1_mm.cpp, common/eng1_mm.h, common/eng1_mm_default.cpp, common/eng1_mm_default.h, common/eng1_mm_prmfit.cpp, common/eng1_mm_prmfit.h, common/eng1_qm.cpp, common/eng1_qm.h, common/eng1_qm_mopac.cpp, common/eng1_qm_mopac.h, common/eng1_qm_mpqc.cpp, common/eng1_qm_mpqc.h, common/eng1_sf.cpp, common/eng1_sf.h, common/eng2_qm_mm.cpp, common/eng2_qm_mm.h, common/engine.cpp, common/engine.h, common/filetrans.cpp, common/filetrans.h, common/geomopt.cpp, common/geomopt.h, common/intcrd.cpp, common/intcrd.h, common/model.cpp, common/model.h, common/moldyn.cpp, common/moldyn.h, common/search.cpp, common/search.h, common/seqbuild.cpp, common/seqbuild.h, common/tab_mm_default.cpp, common/tab_mm_default.h, common/tab_mm_prmfit.cpp, common/tab_mm_prmfit.h, common/typedef.h, common/typerule.cpp, common/typerule.h, common/utility.cpp, common/utility.h, graphics/camera.cpp, graphics/camera.h, graphics/color.h, graphics/mtools.cpp, graphics/plane.cpp, graphics/plane.h, graphics/project.cpp, graphics/project.h, graphics/ribbon.cpp, graphics/ribbon.h, graphics/surface.cpp, graphics/surface.h, graphics/views.cpp, graphics/views.h, target1/t1main.cpp, target2/t2main.cpp, target2/t2main.h, target2/t2project.cpp, target2/t2project.h, target2/t2views.cpp, target2/t2views.h, target3/glade_dialog.cpp, target3/glade_dialog.h, target3/t3dialog.cpp, target3/t3dialog.h, target3/t3main.cpp, target3/t3main.h, target3/t3project.cpp, target3/t3project.h, target3/t3views.cpp, target3/t3views.h: added the new files. 2002-05-30 12:18 thassine * src/: common/interface.cpp, common/interface.h, common/matrix.h, common/mm1alg.cpp, common/mm1alg.h, common/mm1eng.cpp, common/mm1eng.h, common/mm1eng1.cpp, common/mm1eng1.h, common/mm1eng9.cpp, common/mm1eng9.h, common/mm1ic.cpp, common/mm1ic.h, common/mm1mdl.cpp, common/mm1mdl.h, common/mm1tab1.cpp, common/mm1tab1.h, common/mm1tab9.cpp, common/mm1tab9.h, common/mm1util.cpp, common/mm1util.h, common/mm2alg.cpp, common/mm2alg.h, common/mm2eng.cpp, common/mm2eng.h, common/mm2mdl.cpp, common/mm2mdl.h, common/mm2util.cpp, common/mm2util.h, common/mm3mdl.cpp, common/mm3mdl.h, common/qm1alg.cpp, common/qm1alg.h, common/qm1e_mopac.cpp, common/qm1e_mopac.h, common/qm1e_mpqc.cpp, common/qm1e_mpqc.h, common/qm1eng.cpp, common/qm1eng.h, common/qm1mdl.cpp, common/qm1mdl.h, common/qm2eng.cpp, common/qm2eng.h, common/qm2mdl.cpp, common/qm2mdl.h, graphics/docview.cpp, graphics/docview.h, graphics/io-jpg.cpp, graphics/io-jpg.h, graphics/io-png.cpp, graphics/io-png.h, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/mm1rbn.cpp, graphics/mm1rbn.h, graphics/mm2docv.cpp, graphics/mm2docv.h, graphics/mm2rbn.cpp, graphics/mm2rbn.h, graphics/mm3docv.cpp, graphics/mm3docv.h, graphics/qm1docv.cpp, graphics/qm1docv.h, graphics/qm2docv.cpp, graphics/qm2docv.h, target2/t2docv.cpp, target2/t2docv.h, target2/t2mm1docv.cpp, target2/t2mm1docv.h, target2/t2mm2docv.cpp, target2/t2mm2docv.h, target2/t2mm3docv.cpp, target2/t2mm3docv.h, target2/t2qm1docv.cpp, target2/t2qm1docv.h, target2/t2qm2docv.cpp, target2/t2qm2docv.h, target3/glade_callbacks.cpp, target3/glade_callbacks.h, target3/glade_interface.cpp, target3/glade_interface.h, target3/glade_support.cpp, target3/glade_support.h, target3/t3docv.cpp, target3/t3docv.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3mm2docv.cpp, target3/t3mm2docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h, target3/t3qm2docv.cpp, target3/t3qm2docv.h: the old/renamed files are removed. 2002-05-30 11:29 thassine * src/target3/glade/README: update the glade README 2002-05-30 11:27 thassine * src/: target1/config.h.OLD, target2/config.h.OLD, target3/config.h.OLD, target3/glade/Makefile.OLD, target3/glade/Makefile.in, target3/glade/geomopt_dialog.cpp, target3/glade/geomopt_dialog.glade, target3/glade/geomopt_dialog.h, target3/glade/ghemical.glade: added changes to config.h.OLD files and src/target3/glade dir. 2002-05-30 11:17 thassine * src/: Makefile.OLD, common/Makefile.OLD, common/Makefile.in, graphics/Makefile.OLD, graphics/Makefile.in, target2/Makefile.OLD, target3/Makefile.OLD, target3/Makefile.in: the makefiles are updated. 2002-05-30 10:40 thassine * CHANGES: the changelog is updated. 2002-05-30 10:39 thassine * CHANGES: updated the changelog 2002-05-30 10:35 thassine * src/Makefile.OLD: test; this goes to HEAD branch... 2002-05-30 10:35 thassine * src/Makefile.OLD: test; should show in branch only... 2002-05-30 09:45 thassine * CHANGES: Ok, changed my mind. The current version is now moved into MANY_PROJECTS_BRANCH at CVS; this might be easier in the long run. 2002-05-29 11:11 thassine * CHANGES: again testing that the OSP_BRANCH is separate; seems to be but cvs2cl picks all commits to the log; I'll start using OSP: identifier when working with the branch in the future. 2002-05-29 11:08 thassine * CHANGES: more branches practicing... 2002-05-29 10:48 thassine * CHANGES: first test commit in the branch. 2002-05-28 12:03 thassine * CHANGES: updated the changelog (using cvs2cl again). 2002-05-28 10:57 thassine * src/common/define.h: ooop, reverted the previous. 2002-05-28 10:55 thassine * src/common/define.h: just testing how the branches work. 2002-05-27 16:36 thassine * bin/parameters/mm2param/loopdip.txt, bin/parameters/mm2param/looptor.txt, bin/parameters/mm2param/nonbonded.txt, small-utilities/getpdb_cd.cpp, small-utilities/getpdb_ftp.cpp, src/common/Makefile.OLD, src/common/Makefile.in, src/common/mm1mdl.h, src/common/mm1util.h, src/common/mm2alg.h, src/common/mm2eng.cpp, src/common/mm2eng.h, src/common/mm2mdl.cpp, src/common/mm2mdl.h, src/common/mm2util.cpp, src/common/mm2util.h, src/common/mm3mdl.cpp, src/common/mm3mdl.h, src/graphics/Makefile.OLD, src/graphics/Makefile.in, src/graphics/mm2docv.cpp, src/graphics/mm3docv.cpp, src/graphics/mm3docv.h, src/graphics/views.h, src/target1/Makefile.OLD, src/target1/t1m_mm2param_cpp.h, src/target2/Makefile.OLD, src/target2/t2main.cpp, src/target2/t2main.h, src/target2/t2mm2docv.cpp, src/target2/t2mm3docv.cpp, src/target2/t2mm3docv.h, src/target3/Makefile.OLD, src/target3/Makefile.in: added some of my own works; not all of this stuff is ready, but I need to start converting them to fit into single-project environment. 2002-05-22 10:23 thassine * Makefile.in, configure, configure.in: configure script now updated, scripts now compatible with autoconf 2.53 2002-05-21 14:06 thassine * aclocal.m4, configure.in, src/config.h.in, src/common/Makefile.OLD, src/common/qm1e_mpqc.cpp, src/common/qm1e_mpqc.h, src/graphics/Makefile.OLD, src/graphics/Makefile.in, src/target1/Makefile.OLD, src/target1/config.h.OLD, src/target2/Makefile.OLD, src/target2/config.h.OLD, src/target3/Makefile.OLD, src/target3/Makefile.in, src/target3/config.h.OLD: added the configuration system for MPQC v1/v2 (thanks to Michael); BTW you still have to run autoconf to update the configure script. 2002-05-20 10:45 thassine * src/: common/Makefile.OLD, common/qm1e_mpqc.cpp, common/qm1e_mpqc.h, graphics/Makefile.OLD, target1/Makefile.OLD, target2/Makefile.OLD, target3/Makefile.OLD: support for MPQC v2 was added (but ./configure still needs update). 2002-05-20 09:17 thassine * src/target1/: t1m_mm1param_cpp.h, t1m_mm1param_h.h: oops, forgot to add some files last time. 2002-05-17 10:30 thassine * src/: common/mm1eng9.cpp, common/mm1eng9.h, common/mm1mdl.cpp, common/mm1mdl.h, common/mm1tab9.cpp, common/mm1tab9.h, target1/t1main.cpp, target1/t1main.h, 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 17:03 thassine * src/: common/define.h, graphics/mm2docv.cpp, target2/t2mm2docv.cpp, target3/t3mm2docv.cpp, target3/t3mm2docv.h: added LABEL_RESIDUE for mm2_docv. 2002-04-17 13:24 thassine * src/common/: mm2util.cpp, 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 09:56 thassine * src/: common/mm2mdl.cpp, graphics/mm2docv.cpp: some comments and minor fixes added to mm2_mdl. 2002-04-09 13:18 thassine * src/: graphics/mm2docv.cpp, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3mm2docv.cpp, target3/t3mm2docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h: some colour/label mode improvements added. 2002-04-08 17:32 thassine * src/graphics/: mm2docv.cpp, mm2docv.h, mm2rbn.cpp: some cleanups added to the mm2_docv rendering code - should not change the looks/anything. 2002-04-04 15:18 thassine * BUGLIST, TODO: the BUGLIST and TODO files are now CSV text files - use a spreadsheet program like Gnumeric or StarOffice/Calc to read and/or modify them. 2002-04-04 11:43 thassine * src/graphics/camera.cpp: some cleanups done for the stereo modes; now the effect seems to be independent of orientation. 2002-03-26 20:27 hutchisn * openbabel/: mol.cpp, pdb.cpp: Fixes OpenBabel PDB import problems (PR #529744 for OpenBabel). 2002-02-28 13:43 thassine * ghemical.spec: the .spec file updated; the RPM now does the installation with prefix /usr instead of /usr/local. 2002-02-27 11:26 thassine * miniMOPAC/Makefile.in: modified miniMOPAC/Makefile.in so that -O optimization is forced in the miniMOPAC directory. 2002-02-26 10:28 thassine * ghemical.spec: some updates added to .spec file. 2002-02-25 13:29 thassine * AUTHORS, ghemical.spec, bin/ghemical.xpm: added the files for building RedHat binary packages, contributed by Radek Liboska. 2002-02-22 16:09 thassine * configure, configure.in, src/common/define.h, src/common/notice.cpp: switch back to development settings. 2002-02-22 12:36 thassine * CHANGES, INSTALL, src/common/define.h: changelog updated and all settings are now ready for release as v0.82 2002-02-22 10:29 thassine * src/target3/t3mm1docv.cpp: a small fix added to the library widget generation code. 2002-02-21 16:26 thassine * bin/user-docs/: index.html, using_cs_tools.html, using_cs_tools01.jpg, using_cs_tools02.jpg, using_cs_tools03.jpg, using_cs_tools04.jpg, using_cs_tools05.jpg: user's manual is enhanced; it now contains a section about 1D and 2D energy plots. 2002-02-20 12:34 thassine * INSTALL, src/common/mm1alg.h, src/common/mm1mdl.cpp, src/common/mm2alg.h, src/common/mm2mdl.cpp, src/common/qm1alg.h, src/common/qm1mdl.cpp, src/target1/Makefile.OLD, src/target2/Makefile.OLD, src/target2/t2mm1docv.cpp, src/target2/t2mm2docv.cpp, src/target2/t2qm1docv.cpp, src/target3/Makefile.OLD, src/target3/glade_callbacks.cpp, src/target3/glade_interface.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp: old makefiles updated, and the code added for geomopt dialogs + calculations that separates the different termination criteria and makes them optional. it also prints out which criteria was used to terminate the optimization. 2002-02-18 19:06 hutchisn * openbabel/pdb.cpp: Don't try to run PerceiveBondOrders yet... this seems to be very buggy. 2002-02-18 18:53 hutchisn * openbabel/: Makefile.in, alchemy.cpp, amber.cpp, aromatic.txt, atom.cpp, balst.cpp, box.cpp, c3d.cpp, cacao.cpp, car.cpp, ccc.cpp, commandline.h, ctransform.h, data.cpp, data.h, dmol.cpp, element.h, element.txt, extable.h, extable.txt, feat.cpp, gamess.cpp, gaussian.cpp, ghemical.cpp, grid.h, hin.cpp, jaguar.cpp, main.cpp, mol.cpp, mol.h, mopac.cpp, mpqc.cpp, nwchem.cpp, obutil.cpp, obutil.h, patty.cpp, pdb.cpp, phmodel.cpp, qchem.cpp, report.cpp, rotor.cpp, smarts.h, typer.cpp, unichem.cpp, version.h.in, xyz.cpp: Updated Open Babel code, including preliminary bond-order perception. 2002-01-31 15:50 thassine * miniMOPAC/README: some documentation fixes for miniMOPAC. 2002-01-31 14:25 thassine * src/target3/: glade_interface.cpp, glade/ghemical.glade: the check boxes for different termination criteria were added to the geomopt GLADE dialog; their states are not yet checked however. 2002-01-25 18:09 hutchisn * small-utilities/: Makefile, README, symmetry.c: Add Symmetry program (from Sergei Pachkovsky, who gave OK to use in Ghemical) 2002-01-25 15:42 thassine * src/: common/Makefile.OLD, common/define.h, common/qm1mdl.cpp, graphics/Makefile.OLD, target1/Makefile.OLD, target2/Makefile.OLD, target3/Makefile.OLD: some comments added, and old makefiles are fixed/updated. 2002-01-25 06:39 hutchisn * src/target3/: glade_callbacks.cpp, t3mm1docv.cpp: Make sure we actually set the optimization limits after the dialog completes... 2002-01-25 06:35 hutchisn * openbabel/unichem.cpp: Fix unichem XYZ support (read should expect atomic numbers in Unichem files). 2002-01-22 17:27 thassine * src/target3/: glade_interface.h, glade_support.cpp: verified that /target3 and /target3/glade/src keep in sync... 2002-01-22 00:23 hutchisn * src/: common/mm1alg.h, common/mm1mdl.cpp, common/mm2alg.h, common/qm1alg.h, common/qm1mdl.cpp, target3/glade_interface.cpp, target3/t3mm1docv.cpp, target3/t3mm2docv.cpp, target3/t3qm1docv.cpp, target3/glade/ghemical.glade: 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 13:45 thassine * src/common/: mm1mdl.cpp, qm1mdl.cpp: the geomopt output now displays accurate gradient vector lengths. 2002-01-21 09:44 thassine * INSTALL: removed .cvsignore from the oelib directory. 2002-01-18 21:59 hutchisn * src/common/: mm1mdl.cpp, 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 11:12 thassine * src/graphics/mm1docv.cpp: in the 1D and 2D energy plotting tools of mm1_docv it is now possible to select a smaller range of angles if needed, and the final energy can be calculated also using QM methods (so now it's possible to compare MM results against QM results as well as compare different QM results). 2002-01-14 21:10 thassine * src/: common/Makefile.OLD, graphics/Makefile.OLD, target1/Makefile.OLD, target2/Makefile.OLD, target3/Makefile.OLD: converted the old makefiles to use the new openbabel-paths. 2002-01-14 20:12 hutchisn * src/common/filetrans.cpp: Delete filename at appropriate time--Babel uses it for a Title when exporting. 2002-01-14 05:57 hutchisn * configure, configure.in: Add almost-forgotten configure tests contributed by Michael Banck--check for f2c if g2c is not found (and give an error if neither is found). 2002-01-11 17:20 hutchisn * src/: common/Makefile.in, graphics/Makefile.in, target3/Makefile.in: Makefile fixes. 2002-01-11 01:04 hutchisn * configure, configure.in, src/common/Makefile.in, src/target3/Makefile.in: Added support for Michael Banck's SC autoconf macros to simplify building MPQC. 2002-01-11 00:45 hutchisn * Makefile.in, PROJECT, config.guess, config.sub, configure, configure.in, openbabel/Makefile.in, openbabel/StdAfx.cpp, openbabel/StdAfx.h, openbabel/Vector.cpp, openbabel/Vector.h, openbabel/alchemy.cpp, openbabel/amber.cpp, openbabel/aromatic.h, openbabel/aromatic.txt, openbabel/atom.cpp, openbabel/atomtyp.h, openbabel/atomtyp.txt, openbabel/balst.cpp, openbabel/base.cpp, openbabel/base.h, openbabel/bgf.cpp, openbabel/bin2hex.pl, openbabel/binary.cpp, openbabel/binary.h, openbabel/binary_io.cpp, openbabel/binary_io.h, openbabel/bitgrid.cpp, openbabel/bitgrid.h, openbabel/bitvec.cpp, openbabel/bitvec.h, openbabel/bond.cpp, openbabel/box.cpp, openbabel/c3d.cpp, openbabel/cacao.cpp, openbabel/cache.cpp, openbabel/car.cpp, openbabel/ccc.cpp, openbabel/chains.cpp, openbabel/chains.h, openbabel/chdrw.cpp, openbabel/chiral.cpp, openbabel/chiral.h, openbabel/commandline.cpp, openbabel/commandline.h, openbabel/csr.cpp, openbabel/cssr.cpp, openbabel/ctransform.cpp, openbabel/ctransform.h, openbabel/cwrap.cpp, openbabel/cwrap.h, openbabel/data.cpp, openbabel/data.h, openbabel/dmol.cpp, openbabel/element.h, openbabel/element.txt, openbabel/extable.h, openbabel/extable.txt, openbabel/feat.cpp, openbabel/fh.cpp, openbabel/fileformat.cpp, openbabel/fileformat.h, openbabel/gamess.cpp, openbabel/gaussian.cpp, openbabel/generic.cpp, openbabel/generic.h, openbabel/ghemical.cpp, openbabel/grid.cpp, openbabel/grid.h, openbabel/gromos96.cpp, openbabel/hin.cpp, openbabel/jaguar.cpp, openbabel/main.cpp, openbabel/matrix.cpp, openbabel/matrix.h, openbabel/mdl.cpp, openbabel/mmod.cpp, openbabel/mol.cpp, openbabel/mol.h, openbabel/mol2.cpp, openbabel/molchrg.cpp, openbabel/molchrg.h, openbabel/molvector.cpp, openbabel/molvector.h, openbabel/mopac.cpp, openbabel/mpqc.cpp, openbabel/nwchem.cpp, openbabel/obifstream.h, openbabel/oblib.dsp, openbabel/oblib.dsw, openbabel/obutil.cpp, openbabel/obutil.h, openbabel/parsmart.cpp, openbabel/parsmart.h, openbabel/parsmi.cpp, openbabel/patty.cpp, openbabel/patty.h, openbabel/pdb.cpp, openbabel/phmodel.cpp, openbabel/phmodel.h, openbabel/phmodel.txt, openbabel/phmodeldata.h, openbabel/qchem.cpp, openbabel/quat.c, openbabel/rand.cpp, openbabel/report.cpp, openbabel/resdata.h, openbabel/resdata.txt, openbabel/ring.cpp, openbabel/ring.h, openbabel/rotor.cpp, openbabel/rotor.h, openbabel/smarts.cpp, openbabel/smarts.h, openbabel/smi.cpp, openbabel/smi.h, openbabel/tinker.cpp, openbabel/tokenst.cpp, openbabel/typer.cpp, openbabel/typer.h, openbabel/types.h, openbabel/types.txt, openbabel/unichem.cpp, openbabel/version.h, openbabel/xed.cpp, openbabel/xyz.cpp, src/common/Makefile.in, src/common/filetrans.cpp, src/common/filetrans.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/notice.cpp, src/common/utility.cpp, src/graphics/Makefile.in, src/graphics/docview.cpp, src/target3/Makefile.in: Updated with OpenBabel replacing OELib. 2002-01-10 20:28 hutchisn * src/graphics/: mtools.h, views.cpp, views.h: Add data types for select modes and measure modes. 2002-01-07 15:51 thassine * src/common/: mm1mdl.cpp, mm1mdl.h, mm2mdl.cpp, mm2mdl.h, qm1mdl.cpp, qm1mdl.h: some cleanups for the model classes, plus some documentation updates. 2002-01-06 01:00 hutchisn * aclocal.m4: Added Michael Banck's contributed SC tests. These have not yet been implemented into configure.in yet. 2002-01-02 16:40 thassine * INSTALL, src/common/Makefile.OLD, src/graphics/Makefile.OLD, src/target1/Makefile.OLD, src/target2/Makefile.OLD, src/target3/Makefile.OLD: converted the old makefiles to use the Scientific Computation toolkit (SC toolkit) of MPQC, instead of the MPQC object files and headers directly. 2001-12-31 15:19 thassine * src/: common/interface.cpp, common/interface.h, common/mm1mdl.cpp, common/mm1mdl.h, common/qm1mdl.cpp, common/qm1mdl.h, target3/t3mm1docv.cpp, 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 16:56 thassine * src/: graphics/camera.cpp, graphics/camera.h, graphics/docview.cpp, graphics/objects.cpp, graphics/objects.h, graphics/views.h, target3/t3mm1docv.cpp, target3/t3qm1docv.cpp, target3/t3views.cpp: the convert-project-to-QM/MM and attach/detach-this-view operations now retain the graphics settings. 2001-12-29 13:51 thassine * src/graphics/views.cpp: the GLUT stroke fonts now make readable text in all cases, but 3D text (as in labels) is still misaligned. 2001-12-28 15:43 thassine * src/graphics/: camera.cpp, mm1docv.cpp, mm2docv.cpp, qm1docv.cpp, views.cpp, 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 13:11 thassine * src/graphics/: mm1docv.cpp, views.cpp, views.h: the plots are now checked and commented; should work but UI is still console-based. 2001-12-19 16:47 thassine * src/graphics/: mm1docv.cpp, mtools.cpp, views.cpp, views.h: now it's possible to scale colors of plot2d_view (using zoom mousetool), and the plot views now store and display the strcutures (using select/orbit/rotate tools); still need to do some testing for the plots but they look good for symmterical molecules. 2001-12-19 13:45 thassine * src/graphics/: docview.cpp, docview.h, mtools.cpp, qm1docv.cpp, qm1docv.h, views.cpp, 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 17:20 thassine * src/common/: mm1eng1.cpp, mm1eng9.cpp: just docs clarified a bit... 2001-12-18 14:43 thassine * src/: common/mm1eng1.cpp, common/mm1eng9.cpp, common/mm1mdl.cpp, graphics/mm1docv.cpp: a better tor-constraints added to mm1_eng classes for the 1d and 2d plots. 2001-12-18 09:53 thassine * INSTALL: updated the installation docs. 2001-12-17 17:17 thassine * src/: common/intcrd.cpp, common/intcrd.h, common/mm1mdl.cpp, common/mm1mdl.h, graphics/docview.h, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/views.cpp, graphics/views.h, target2/t2mm1docv.cpp, target2/t2views.cpp, target2/t2views.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3views.cpp, 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 14:35 thassine * bin/user-docs/index.html, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/views.cpp, src/graphics/views.h, src/target2/t2qm1docv.cpp, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/t3docv.cpp, src/target3/t3docv.h, src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp, src/target3/t3views.cpp, src/target3/t3views.h: added attach/detach feature for gnome_graphics_views. earlier it was somewhat difficult to use multiple views, because only one at a time could be looked at the GtkNotebook. now the views can be detached from the notebook to separate windows, and attached back to notebook as well. also some GLUT and plotting improvements are added. 2001-12-10 15:27 thassine * src/: common/mm1mdl.cpp, common/mm1mdl.h, common/model.cpp, common/model.h, common/qm1alg.cpp, common/qm1alg.h, common/qm1e_mopac.cpp, common/qm1eng.h, common/qm1mdl.cpp, common/qm1mdl.h, target2/t2mm1docv.cpp, 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 15:56 thassine * src/: common/model.h, common/qm1mdl.cpp, graphics/qm1docv.cpp, target2/t2mm1docv.cpp, target2/t2mm2docv.cpp, target2/t2qm1docv.cpp: some t2 cleanups added, and improved qm1_mdl support for multiple crd-sets. 2001-12-05 18:11 thassine * src/common/: mm1eng.h, mm1eng1.cpp, mm1eng1.h, mm1eng9.cpp, mm1eng9.h: added an initial framework for adding torsional constraints in molecular mechanics force fields; the old stuff should work as usual. 2001-12-05 16:53 thassine * src/: common/errutil.cpp, common/notice.h, common/typedef.h, graphics/mm2rbn.cpp: added some Alpha platform fixes from Bob Williams. 2001-11-27 07:35 hutchisn * Makefile.in: Added distclean target and changed help destination to smooth with Debian package. 2001-11-27 07:32 hutchisn * src/target3/: t3mm1docv.cpp, t3mm1docv.h, t3prefs.cpp: Added Selection Mode submenu (w/radio items) and fixed library error message. 2001-11-27 01:31 hutchisn * src/target3/: t3mm1docv.cpp, t3mm1docv.h: Updated library feature to be fully user-configurable (# levels, directory path) Now also add submenus for subdirectories! 2001-11-26 11:05 thassine * src/target3/: t3mm1docv.cpp, t3views.h: minor fixes for 'Library', and some cleanups. 2001-11-21 07:28 hutchisn * src/target3/: t3mm1docv.cpp, t3mm1docv.h, 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 14:27 thassine * INSTALL, src/common/mm1mdl.h, src/common/mm2mdl.h, src/common/qm1mdl.h, src/common/qm2mdl.h, src/graphics/docview.h, src/graphics/mm1docv.cpp, src/graphics/mm1docv.h, src/graphics/mm2docv.cpp, src/graphics/mm2docv.h, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3qm1docv.cpp, src/target3/t3views.cpp: made the SelectNone feature as a combination of SelectAll and InvertSelection (less code this way), and added some enhancements to FileOpen (graphics update forced, and possibly selected new atoms now replace the old selection). 2001-11-12 18:20 hutchisn * src/: common/mm1mdl.cpp, common/mm1mdl.h, common/mm2mdl.cpp, common/mm2mdl.h, common/model.h, common/qm1mdl.h, graphics/docview.h, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/mm2docv.cpp, graphics/mm2docv.h, graphics/qm1docv.cpp, graphics/qm1docv.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3qm1docv.cpp, target3/t3views.cpp, target3/t3views.h: Added SelectNone() and support for "inserting" files (open with molecules selected). 2001-11-09 20:32 hutchisn * 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 12:19 thassine * configure, configure.in, src/common/define.h: back to devel settings, version number changed to 0.82. 2001-11-08 09:51 thassine * CHANGES, src/common/define.h: some final changes for the new release; this is released as 0.81. 2001-11-07 11:43 thassine * CHANGES, INSTALL, bin/user-docs/index.html: some documentation updates added. 2001-10-29 17:48 thassine * src/: common/define.h, common/mm2mdl.cpp, common/mm2mdl.h, common/qm1mdl.cpp, common/qm1mdl.h, graphics/mm1docv.cpp, target2/t2mm1docv.cpp, target2/t2mm2docv.cpp, target3/t3docv.h, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3mm2docv.cpp, target3/t3mm2docv.h, target3/t3qm1docv.cpp: some generic improvements added: some t3 file operations added and mm1_mdl labels feature improved. 2001-10-23 16:10 thassine * src/: common/mm1eng.cpp, common/mm1eng.h, common/mm1eng1.cpp, common/mm1eng1.h, common/mm1eng9.cpp, common/mm1eng9.h, common/mm1mdl.cpp, common/mm1tab1.cpp, common/mm1tab1.h, common/mm1tab9.cpp, common/mm1tab9.h, common/mm1util.cpp, common/mm2eng.cpp, common/mm2eng.h, common/mm2mdl.cpp, common/model.cpp, graphics/mm2docv.cpp, graphics/plane.cpp, graphics/surface.cpp, target1/t1m_mm2param_cpp.h, target1/t1main.cpp, target3/t3mm1docv.cpp, 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 18:01 thassine * src/common/: mm1eng.cpp, mm1eng.h, mm1eng1.cpp, mm1eng1.h, mm1eng9.cpp, 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 17:39 thassine * bin/parameters/mm1param/stable/atomtypes.txt, bin/parameters/mm1param/stable/parameters1.txt, bin/parameters/mm1param/stable/parameters2.txt, bin/parameters/mm1param/stable/parameters3.txt, bin/parameters/mm1param/stable/parameters4.txt, bin/parameters/mm1param/stable/parameters5.txt, bin/parameters/mm1param/unstable/atomtypes.txt, bin/parameters/mm1param/unstable/parameters1.txt, bin/parameters/mm1param/unstable/parameters2.txt, bin/parameters/mm1param/unstable/parameters3.txt, bin/parameters/mm1param/unstable/parameters4.txt, bin/parameters/mm1param/unstable/parameters5.txt, src/common/mm1eng1.h, src/common/mm1eng9.h, src/common/mm1mdl.cpp, src/common/mm1tab1.cpp, src/common/mm1tab1.h, src/common/mm1tab9.cpp, src/common/mm1tab9.h: made some rearrangements at mm1_eng classes that make expermimentation with the classes easier; also the parameter files have been changed so you should do the #make install# for this version. 2001-10-03 13:56 thassine * CHANGES, PROJECT: changed the old manually maintained changes-file to a newer log that is maintained using a cvs2cl.pl utility; it makes a logfile using cvs log information; see http://www.red-bean.com/cvs2cl/ 2001-10-03 13:47 thassine * src/: common/mm2mdl.h, common/qm2mdl.h, target3/t3main.cpp, 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 06:50 hutchisn * src/: common/mm1mdl.cpp, common/mm1mdl.h, common/mm2mdl.h, common/model.h, common/qm1mdl.h, target3/glade_callbacks.cpp, target3/t3main.cpp: Moved import code into mm1model so it can be called from other parts of the code. Added support for command-line flags, e.g. -f opens a ghemical file, -i imports a file. And any remaining arguments are assumed to be filenames to import. (Keep in mind that we can import a .mm1gp or .qm1gp anyway.) Allows $PATH/ghemical to be used as a web helper application. 2001-09-27 15:57 thassine * src/common/define.h: changed the main web address to www.bioinformatics.org 2001-09-27 15:14 thassine * CHANGES, miniMOPAC/README, miniMOPAC/iter.c, miniMOPAC/fortran/iter.f: 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 17:35 thassine * CHANGES, INSTALL, miniMOPAC/README, miniMOPAC/esp.c, miniMOPAC/iter.c, miniMOPAC/minimopac.c, miniMOPAC/fortran/esp.f, miniMOPAC/fortran/iter.f, miniMOPAC/fortran/minimopac.f, miniMOPAC/fortran/mopac.f, 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 17:21 thassine * src/graphics/: docview.cpp, docview.h, mm1docv.cpp, qm1docv.cpp: added to measure tool a set if model-independent measurement functions in an effort to make it simpler. 2001-09-24 16:10 thassine * BUGLIST, src/target2/t2qm1docv.cpp, src/target3/glade_callbacks.cpp, src/target3/glade_interface.cpp, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h: a new known bug was added; qm1 geomopt dialog was added for gnome version. 2001-09-15 00:17 hutchisn * Makefile.in, bin/ghemical.png, src/common/Makefile.in, src/graphics/Makefile.in, src/target3/Makefile.in: Add distclean targets to Makefiles 2001-09-14 16:08 thassine * src/graphics/views.cpp: the energy level diagram now tries to detect degenerate energy levels (like in N2 or F2) and draw them side by side rather than overlapped. 2001-09-14 13:44 thassine * src/graphics/: docview.cpp, mm1docv.cpp: completed the fixes for known mem leaks at docview.cpp 2001-09-08 02:20 hutchisn * src/: common/filetrans.cpp, graphics/docview.cpp, graphics/mm1docv.cpp, graphics/views.cpp, target3/t3prefs.cpp: Fix a few memory leaks and bugs. 2001-09-07 16:22 thassine * CHANGES, configure, configure.in, src/common/define.h: development starts again, promoted version number to 0.81 2001-09-06 10:21 thassine * CHANGES, INSTALL, bin/user-docs/index.html, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/target2/t2mm1docv.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h: did a last-minute addition of random conformational search; this is released as version 0.80 2001-09-05 16:37 thassine * CHANGES, INSTALL, bin/user-docs/index.html: final fixes to documentation etc... 2001-09-04 12:38 thassine * src/common/: mm1eng1.cpp, mm1eng9.cpp, mm1mdl.h, mm1tab1.cpp, mm1tab9.cpp: some cleanups at MM eng/tab classes. 2001-09-04 11:07 thassine * src/common/: mm1eng.h, mm1tab1.cpp, mm1tab9.cpp: minor changes and cleanups. 2001-09-03 13:01 thassine * src/common/: mm1tab1.cpp, mm1tab9.cpp, mm1util.cpp, mm1util.h: a minor cleanup for mm1_typerule. 2001-09-03 10:06 thassine * miniMOPAC/README, src/common/mm1mdl.h: minor additions to mm1_mdl and MOPAC docs. 2001-08-30 07:22 hutchisn * src/common/filetrans.cpp: Update with new OELib code -- a few new filetypes, cleanups and better bonding for QM files. 2001-08-29 16:21 thassine * AUTHORS, src/graphics/camera.cpp, src/graphics/camera.h, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp, src/target3/t3views.cpp, src/target3/t3views.h: added an alternative way for camera setup in stereo viewing modes; copyright notices etc updated. 2001-08-29 13:18 thassine * src/target3/: t3mm1docv.cpp, t3views.cpp, t3views.h: added Mike's stereo code (under target3). 2001-08-29 13:18 thassine * src/graphics/: camera.cpp, camera.h: added Mike's stereo code (under graphics). 2001-08-29 10:08 thassine * configure, configure.in, src/common/define.h, src/common/qm1e_mopac.cpp, src/common/qm1e_mopac.h, src/common/qm1mdl.cpp: a safer mopac locking mechanism added, version number promoted to 0.80. 2001-08-28 10:04 thassine * INSTALL, miniMOPAC/README, miniMOPAC/minimopac.c, miniMOPAC/fortran/minimopac.f, 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 15:35 thassine * bin/user-docs/: enlevdiag.jpg, index.html, maintools.jpg: user's manual quickly updated. 2001-08-27 12:26 thassine * src/common/qm1e_mopac.cpp: added comments about a specifig bug in mopac. 2001-08-27 11:13 thassine * src/common/: mm1mdl.cpp, mm1mdl.h, mm2mdl.cpp, qm1e_mopac.cpp, qm1e_mopac.h, qm1e_mpqc.cpp, qm1e_mpqc.h, qm1mdl.cpp, qm1mdl.h: hamiltonian/basis set selection added for QM engs. 2001-08-26 12:45 thassine * src/common/: mm1alg.cpp, mm2alg.cpp, qm1alg.cpp, qm1e_mopac.cpp, 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 17:48 thassine * src/: common/qm1e_mopac.cpp, common/qm1e_mpqc.cpp, common/qm1mdl.cpp, common/qm1mdl.h, target3/glade_callbacks.cpp, target3/glade_interface.cpp, target3/glade/ghemical.glade: now the total charge can be specified in QM models; also checking added for QM setup. 2001-08-25 14:50 thassine * src/common/qm1e_mpqc.cpp: energy level diagram now works for ab initio as well. 2001-08-24 16:12 thassine * src/common/: qm1e_mopac.cpp, qm1e_mpqc.cpp, qm1e_mpqc.h: force calculations + algorithms added for MPQC. 2001-08-24 11:34 thassine * src/common/: qm1e_mopac.cpp, qm1mdl.cpp: fixed a gradient scaling bug in MOPAC engine; the geometry optimization is much more robust now. 2001-08-23 21:06 hutchisn * src/: graphics/mm1docv.cpp, graphics/mm2docv.cpp, graphics/qm1docv.cpp, graphics/views.cpp, target3/t3mm1docv.cpp, target3/t3mm2docv.cpp, target3/t3qm1docv.cpp: Migrate general "Graphics" prefs section to MM1Graphics, etc. 2001-08-23 15:38 thassine * src/: common/engine.h, common/mm1eng.cpp, common/mm1eng.h, common/mm2eng.cpp, common/mm2eng.h, common/qm1e_mopac.cpp, common/qm1e_mopac.h, common/qm1e_mpqc.cpp, common/qm1e_mpqc.h, common/qm1eng.cpp, common/qm1eng.h, common/qm1mdl.cpp, graphics/views.cpp, target2/t2mm1docv.cpp, target2/t2qm1docv.cpp: many smaller cleanups/fixes... 2001-08-23 01:21 hutchisn * src/graphics/: mm1docv.cpp, qm1docv.cpp: add QM measure functionality 2001-08-23 01:20 hutchisn * src/common/: mm1mdl.cpp, mm2mdl.cpp, qm1mdl.cpp: Use sprintf to give a standardized output to the geometry opt. output. 2001-08-22 19:31 hutchisn * src/: common/qm1mdl.cpp, target3/t3qm1docv.cpp: Use the same methods for ImportMM command as "convert" routines--and make sure we update the title! 2001-08-22 16:27 thassine * src/: common/mm1mdl.h, common/qm1mdl.cpp, common/qm1mdl.h, graphics/docview.cpp, graphics/docview.h, graphics/mm1docv.cpp, graphics/qm1docv.cpp, target3/t3docv.cpp, target3/t3mm1docv.cpp, target3/t3qm1docv.cpp: various smaller changes... 2001-08-22 14:18 thassine * CHANGES, src/common/qm1e_mopac.cpp, src/common/qm1e_mopac.h, src/common/qm1e_mpqc.cpp, src/common/qm1e_mpqc.h, src/common/qm1eng.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/graphics/mtools.cpp, src/graphics/mtools.h, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/graphics/views.cpp, src/graphics/views.h, src/target2/t2qm1docv.cpp, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3views.cpp, src/target3/t3views.h: an initial version of energy-level diagrams for QM models added (now works for mopac only). 2001-08-21 18:07 hutchisn * src/: graphics/mm2docv.cpp, target3/t3qm1docv.cpp: Add more config use in QM and MM2 modes. 2001-08-21 18:07 hutchisn * src/target3/t3mm1docv.cpp: Add minimal MM -> QM conversion code. Doesn't quite set the filename correctly but otherwise pretty much correct. 2001-08-20 14:03 thassine * CHANGES, miniMOPAC/esp.c, miniMOPAC/fortran/esp.f, src/common/qm1e_mopac.cpp, src/common/qm1e_mpqc.cpp, src/graphics/qm1docv.cpp, src/target2/t2qm1docv.cpp, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h: the rest of qm1_eng_mopac plots added, and a scaling bug in MO plots fixed. 2001-08-18 12:45 thassine * CHANGES, miniMOPAC/README, miniMOPAC/minimopac.c, miniMOPAC/fortran/minimopac.f, src/common/qm1e_mopac.cpp: some cleanups done in qm1_eng_mopac (the fortran and C code are now better separated, easier to maintain). 2001-08-18 10:01 thassine * miniMOPAC/fortran/SIZES: ooops, forgot to add the SIZES file. 2001-08-17 20:17 thassine * miniMOPAC/fortran/: esp.f, minimopac.f: added all changes to mopac fortran source before 2001-08-17. 2001-08-17 20:12 thassine * miniMOPAC/fortran/: aababc.f, addfck.f, addhcr.f, addnuc.f, analyt.f, anavib.f, axis.f, block.f, bonds.f, brlzon.f, btoc.f, calpar.f, capcor.f, cdiag.f, chrge.f, cnvg.f, compfg.f, consts.f, cqden.f, datin.f, dcart.f, delmol.f, delri.f, denrot.f, densit.f, depvar.f, deri0.f, deri1.f, deri2.f, deri21.f, deri22.f, deri23.f, deritr.f, deriv.f, dernvo.f, ders.f, dfock2.f, dfpsav.f, dgemm.f, dgemv.f, dger.f, dgetf2.f, dgetrf.f, dgetri.f, diag.f, diat.f, diat2.f, diegrd.f, dielen.f, diis.f, dijkl1.f, dijkl2.f, dipind.f, dipole.f, dlaswp.f, dofs.f, dot.f, drc.f, drcout.f, dtrmm.f, dtrmv.f, dtrsm.f, dtrti2.f, dtrtri.f, dvfill.f, ef.f, enpart.f, esp.f, etime.c, exchng.f, fdate.c, ffhpol.f, flepo.f, fmat.f, fock1.f, fock2.f, force.f, formxy.f, forsav.f, frame.f, freqcy.f, geout.f, geoutg.f, getgeg.f, getgeo.f, getsym.f, gettxt.f, gmetry.f, gover.f, greenf.f, grid.f, h1elec.f, haddon.f, hcore.f, helect.f, hqrii.f, ijkl.f, ilaenv.f, initsv.f, interp.f, iter.f, jcarin.f, linmin.f, local.f, locmin.f, lsame.f, makpol.f, mamult.f, matou1.f, matout.f, matpak.f, meci.f, mecid.f, mecih.f, mecip.f, moldat.f, molval.f, mopac.f, mullik.f, mult.f, nllsq.f, nuchar.f, parsav.f, partxy.f, pathk.f, paths.f, perm.f, polar.f, powsav.f, powsq.f, prtdrc.f, quadr.f, react1.f, reada.f, readmo.f, refer.f, repp.f, rotat.f, rotate.f, rsp.f, search.f, second.f, setupg.f, solrot.f, swap.f, sympro.f, symtry.f, symtrz.f, thermo.f, timer.f, timout.f, update.f, upsurf.f, vecprt.f, writmo.f, wrtkey.f, wrttxt.f, xerbla.f, xyzint.f: added the original mopac-7.01-4 fortran source, since it seems to be impossible to maintain this stuff from f2c'd source. 2001-08-17 16:44 thassine * miniMOPAC/esp.c, src/common/qm1e_mopac.cpp: miniMOPAC tweaks; ESP plot drawing is now faster, plus MO plotting added. 2001-08-16 13:40 thassine * CHANGES, miniMOPAC/README: added some documentation about the mopac ESP plots. 2001-08-15 16:04 thassine * miniMOPAC/esp.c, src/common/qm1e_mopac.cpp: ESP plotting added to MOPAC-engine (1st working version). 2001-08-13 16:14 thassine * src/: common/Makefile.OLD, common/Makefile.in, common/interface.cpp, common/interface.h, common/mm1mdl.cpp, common/mm1mdl.h, common/mm2mdl.cpp, common/mm2mdl.h, target2/t2mm2docv.cpp, target3/glade_callbacks.cpp, target3/t3mm1docv.cpp, target3/t3mm2docv.cpp, target3/t3mm2docv.h: trajectory viewer for mm2_mdl added (and fixed the timestep of MD). 2001-08-09 11:30 thassine * CHANGES, src/target3/t3mm2docv.cpp, src/target3/t3mm2docv.h: the plotting stuff for mm2_mdl is now also added. 2001-08-08 16:29 thassine * CHANGES, src/common/mm2mdl.cpp, src/target2/t2mm1docv.cpp, src/target2/t2mm1docv.h, src/target2/t2mm2docv.cpp, src/target2/t2mm2docv.h, src/target3/glade_callbacks.cpp, src/target3/glade_interface.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3mm2docv.cpp, src/target3/t3mm2docv.h: algorithms for mm2_mdl are added. 2001-08-08 13:36 thassine * src/target3/: glade_callbacks.cpp, glade_interface.cpp, t3docv.cpp, t3docv.h, t3mm1docv.cpp, t3mm1docv.h, t3qm1docv.cpp, t3qm1docv.h: glade_modal_dialog_owner moved into glade_docv class, in order to make the dialogs work with multiple mdl-classes. 2001-08-04 00:04 hutchisn * src/graphics/: docview.cpp, docview.h, mm1docv.cpp, mm2docv.cpp, mm2docv.h, qm1docv.cpp, qm1docv.h, qm2docv.cpp, qm2docv.h: Moved InitGL() to parent DocumentView class--allows all classes to inherit config code easily. 2001-08-03 16:09 thassine * src/target3/: glade_callbacks.cpp, glade_callbacks.h, glade_interface.cpp, glade_interface.h, t3mm1docv.cpp, glade/README, glade/ghemical.glade: rebuilt the glade code; some docs added for the glade stuff. 2001-08-02 14:36 thassine * src/: common/qm1e_mpqc.cpp, target2/t2mm1docv.cpp, target2/t2mm2docv.cpp, target2/t2qm1docv.cpp, target3/t3mm1docv.cpp, target3/t3qm1docv.cpp, target3/t3qm1docv.h: ESP plotting added to qm1_eng_mpqc. 2001-08-01 16:46 thassine * CHANGES, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm2alg.h, src/common/mm2mdl.cpp, src/common/mm2mdl.h, src/common/qm1e_mpqc.cpp, src/common/qm1eng.cpp, src/common/qm1eng.h, src/target2/t2mm1docv.cpp, src/target2/t2mm2docv.cpp, src/target2/t2qm1docv.cpp: small improvements for mm2_mdl and qm1_eng_mpqc but nothing ready yet. 2001-07-30 15:07 thassine * src/: graphics/mm1docv.cpp, graphics/mm2docv.cpp, graphics/qm1docv.cpp, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h: the 4 first shortcut buttons work now. 2001-07-30 11:14 thassine * src/graphics/: mm1docv.cpp, mm2docv.cpp, qm2docv.cpp, qm2docv.h: added MeasureEvent() also to (obsolete) qm2_mdl. 2001-07-28 21:46 hutchisn * src/: graphics/camera.cpp, graphics/docview.h, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/mm1rbn.cpp, graphics/mm2docv.cpp, graphics/mm2docv.h, graphics/qm1docv.cpp, graphics/qm1docv.h, target3/t3mm1docv.cpp: Add preliminary measure tool code. Works well--need to add "modes" 2001-07-24 20:04 hutchisn * src/graphics/: docview.h, mm1docv.cpp, mm1docv.h, mtools.cpp: Change rendering to support more prefs--including passing prefs for element colors. 2001-07-24 20:00 hutchisn * src/graphics/: camera.cpp, camera.h: Improve selection with wireframe slightly and add Measure enum. 2001-07-24 19:56 hutchisn * src/common/: utility.cpp, utility.h: Change elements to allow prefs class to override colors and VdW radii. 2001-07-24 19:55 hutchisn * src/: common/prefs.cpp, common/prefs.h, target3/t3prefs.cpp, target3/t3prefs.h: Add Color methods 2001-07-24 19:55 hutchisn * src/common/: filetrans.cpp, mm1mdl.cpp: Fix OELib bond synchronization and switch hydrogens to use OELib method. 2001-07-24 02:10 hutchisn * src/target3/: t3main.cpp, pixmaps/bond.xpm, pixmaps/chain.xpm, pixmaps/element.xpm, pixmaps/invert.xpm, pixmaps/molecule.xpm, pixmaps/residue.xpm: Added sample pixmaps for shortcut bar. 2001-07-22 17:28 thassine * src/target1/: t1m_mm2param_cpp.h, t1m_mm2param_h.h: added some files for mm2_mdl. 2001-07-22 16:37 thassine * miniMOPAC/README, miniMOPAC/dgetf2.c, miniMOPAC/dgetri.c, miniMOPAC/dlaswp.c, miniMOPAC/dtrti2.c, miniMOPAC/ef.c, src/common/Makefile.OLD, src/common/factory.cpp, src/common/factory.h, src/common/prefs.cpp, src/common/prefs.h, src/common/qm1e_mopac.cpp, src/common/qm1e_mopac.h, src/common/qm1e_mpqc.cpp, src/graphics/Makefile.OLD, src/target1/Makefile.OLD, src/target2/Makefile.OLD, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/Makefile.OLD, src/target3/t3mm1docv.cpp, src/target3/t3prefs.cpp, src/target3/t3prefs.h, src/target3/t3qm1docv.cpp, src/target3/t3views.h: some mopac/mpqc conflicts fixed, and mopac intermediate files FOR005 FOR006 SHUTDOWN cleaned. 2001-07-20 22:30 hutchisn * src/: common/factory.h, common/model.cpp, common/model.h, graphics/mm1docv.cpp, target3/t3prefs.cpp, target3/t3prefs.h, target3/t3views.cpp, 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 16:07 thassine * src/: common/mm1mdl.cpp, common/mm1mdl.h, common/mm2mdl.cpp, common/mm2mdl.h, common/model.cpp, common/model.h, common/qm1mdl.cpp, graphics/camera.cpp, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/mm2docv.cpp, graphics/mm2docv.h, graphics/qm1docv.cpp, graphics/views.cpp, target2/t2mm1docv.cpp: some comments added and arrangements done for stereo image viewing. 2001-06-29 15:15 thassine * src/common/: intcrd.cpp, intcrd.h, mm1ic.cpp, mm1ic.h: ooops, forgot to add some files in the last commit. 2001-06-29 15:12 thassine * src/: common/Makefile.OLD, common/Makefile.in, common/mm1alg.cpp, common/mm1alg.h, common/mm1mdl.cpp, common/mm1mdl.h, common/mm2mdl.cpp, common/model.cpp, common/model.h, common/qm1mdl.cpp, target2/t2mm1docv.cpp: some groundwork added for mm1_mdl multiple crd_sets and conformational search tools. 2001-06-25 14:21 thassine * bin/user-docs/index.html, src/common/notice.cpp, src/common/notice.h, src/target3/t3main.cpp: minor updates in user's manual and copyright notices (MOPAC included). 2001-06-21 11:49 thassine * CHANGES, src/graphics/camera.cpp, src/graphics/docview.cpp, src/graphics/docview.h, src/target3/t3docv.cpp, src/target3/t3docv.h, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3mm2docv.cpp, src/target3/t3mm2docv.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3views.cpp, src/target3/t3views.h: gnome MDI system revised; one view/child (GtkNotebook container), project views now grouped together. 2001-06-19 16:15 thassine * miniMOPAC/etime.c, src/common/conjgrad.h, src/common/errutil.cpp, src/common/factory.cpp, src/common/filetrans.cpp, src/common/filetrans.h, src/common/mm1eng.cpp, src/common/mm1eng.h, src/common/mm1eng1.cpp, src/common/mm1eng1.h, src/common/mm1eng9.cpp, src/common/mm1eng9.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm1tab1.cpp, src/common/mm1tab1.h, src/common/mm1tab9.cpp, src/common/mm1tab9.h, src/common/mm1util.cpp, src/common/mm1util.h, src/common/mm2eng.cpp, src/common/mm2eng.h, src/common/mm2mdl.h, src/common/mm2util.h, src/common/model.cpp, src/common/model.h, src/common/notice.cpp, src/common/notice.h, src/common/prefs.cpp, src/common/qm1e_mopac.cpp, src/common/qm1e_mpqc.cpp, src/common/qm1e_mpqc.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/common/typedef.h, src/common/utility.cpp, src/common/v3d.h, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/mm1docv.cpp, src/graphics/mm2docv.cpp, src/graphics/objects.cpp, src/graphics/objects.h, src/graphics/plane.cpp, src/graphics/surface.cpp, src/graphics/surface.h, src/target2/t2main.h, src/target2/t2mm1docv.cpp, src/target2/t2mm2docv.cpp, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/glade_callbacks.cpp, src/target3/glade_interface.cpp, src/target3/t3dialog.cpp, src/target3/t3docv.cpp, src/target3/t3docv.h, src/target3/t3errutil.cpp, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp, src/target3/t3prefs.cpp, src/target3/t3qm1docv.cpp, src/target3/t3views.cpp, src/target3/t3views.h: some cleanups done for redhat7.1 (seems to work) and gcc3.0 (still some stl/namespace problems?). 2001-06-13 16:30 thassine * src/target3/: t3mm1docv.cpp, t3mm1docv.h, t3mm2docv.cpp, t3mm2docv.h, t3qm1docv.cpp, t3qm1docv.h: some menuitems added, and an initial mm1gp <-> qm1gp conversion feature 2001-05-28 15:47 thassine * src/common/filetrans.cpp: some comments added 2001-05-23 16:28 thassine * src/: common/factory.h, common/mm1mdl.cpp, common/mm1mdl.h, common/mm2mdl.cpp, target2/t2views.h, target3/t3views.h: just some cleanups here and there 2001-05-21 17:45 thassine * src/common/mm1mdl.cpp: again some readpdb tweaks. 2001-05-21 13:39 thassine * src/common/: mm1mdl.cpp, mm1mdl.h: some readpdb changes again 2001-05-18 16:09 thassine * src/common/: factory.cpp, factory.h: ooops, forgot to add the class_factory files... 2001-05-18 16:07 thassine * CHANGES, src/common/Makefile.OLD, src/common/Makefile.in, src/common/errutil.cpp, src/common/errutil.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm2mdl.cpp, src/common/mm2mdl.h, src/common/model.cpp, src/common/model.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/common/qm2mdl.cpp, src/common/qm2mdl.h, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/mm1docv.cpp, src/graphics/mm1docv.h, src/graphics/mm2docv.cpp, src/graphics/mm2docv.h, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/graphics/qm2docv.cpp, src/graphics/qm2docv.h, src/graphics/views.h, src/target1/t1main.cpp, src/target2/t2docv.cpp, src/target2/t2docv.h, src/target2/t2main.cpp, src/target2/t2mm1docv.cpp, src/target2/t2mm1docv.h, src/target2/t2mm2docv.cpp, src/target2/t2mm2docv.h, src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h, src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/t3docv.cpp, src/target3/t3docv.h, src/target3/t3errutil.cpp, src/target3/t3errutil.h, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3mm2docv.cpp, src/target3/t3mm2docv.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h, src/target3/t3views.cpp, src/target3/t3views.h: many factory classes combined to class_factory. 2001-05-16 14:30 thassine * src/target3/t3main.cpp: just added some buttons, to see what it looks like... 2001-05-16 06:56 hutchisn * src/: common/Makefile.in, common/prefs.cpp, common/prefs.h, target3/Makefile.in, target3/t3prefs.cpp, target3/t3prefs.h: Add new "prefs" class to interface with gnome-config to allow user-config for various things. 2001-05-15 14:57 thassine * src/common/mm1mdl.cpp: again some fixes to readpdb 2001-05-15 11:49 thassine * src/common/mm1mdl.cpp: just some fixes added to readpdb 2001-05-14 12:10 thassine * src/: common/mm1mdl.cpp, target3/t3mm1docv.cpp: organized menus a bit, some changes to readpdb 2001-05-11 18:18 hutchisn * src/target3/: t3mm1docv.cpp, t3mm1docv.h: Add stubs for export graphics, as well as "zap all" and "compute formula" 2001-05-11 15:10 thassine * src/: graphics/mtools.cpp, graphics/mtools.h, graphics/views.cpp, graphics/views.h, target3/t3main.cpp, target3/t3main.h: switched to a single measure tool, multiple toolbars added. 2001-05-08 14:25 thassine * miniMOPAC/Makefile: miniMOPAC/Makefile removed; configure will update it. 2001-05-08 14:22 thassine * miniMOPAC/Makefile, miniMOPAC/Makefile.OLD, src/Makefile.OLD, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm2mdl.cpp, src/common/mm2mdl.h, src/common/model.h, src/target2/t2mm2docv.cpp: some improvements to readpdb; it now reads multiple crd-sets present in NMR entries 2001-05-07 17:33 hutchisn * src/graphics/Makefile.in: Remove io-* from build list until GNOME catches up (!) 2001-05-04 23:32 hutchisn * src/target3/: t3main.cpp, t3main.h: Add buttons for measure tools. 2001-05-04 23:31 hutchisn * src/graphics/: mtools.cpp, mtools.h, views.cpp, views.h: Add tools for measurements. 2001-05-04 23:30 hutchisn * src/target3/pixmaps/: .cvsignore, angle.xpm, dihedral.xpm, distance.xpm, draw.xpm, erase.xpm, orb_xy.xpm, orb_z.xpm, rot_xy.xpm, rot_z.xpm, select.xpm, trans_xy.xpm, trans_z.xpm, zoom.xpm: Add transparency to button pics and buttons for measure tools. 2001-05-04 21:28 hutchisn * src/: graphics/docview.cpp, graphics/docview.h, target3/t3docv.cpp, target3/t3docv.h: Changes to make sure window titles update when importing. 2001-05-04 21:27 hutchisn * src/target3/Makefile.in: Make sure miniMOPAC is compiled in. 2001-05-04 21:26 hutchisn * src/graphics/Makefile.in: Compile io-* for exporting. 2001-05-04 19:39 hutchisn * src/common/: mm1mdl.cpp, mm1mdl.h: Added CLear and DoFormula methods. 2001-05-04 19:38 hutchisn * src/common/Makefile.in: Remove EXTERN_GLOBALS -- not needed 2001-05-04 19:37 hutchisn * src/graphics/: io-jpg.cpp, io-jpg.h, io-png.cpp, io-png.h: Add GNOME code for exporting GdkPixbuf -> PNG or JPEG files. 2001-05-03 19:52 hutchisn * Makefile.in, configure, configure.in, miniMOPAC/Makefile.in: Update for miniMOPAC, test for g2c/f2c library (hopefully). 2001-05-03 19:50 hutchisn * src/target3/glade/ghemical.glade: Add Element options dialog to glade. 2001-05-02 12:31 thassine * src/common/mm1mdl.cpp: added a small fix to readpdb so that it can read also NMR entries. 2001-04-30 13:58 thassine * src/common/: mm1mdl.cpp, mm1mdl.h: some improvements to readpdb-functions. 2001-04-27 15:40 thassine * src/: common/mm1mdl.cpp, common/mm1mdl.h, target2/t2mm1docv.cpp, target2/t2mm2docv.cpp: revived ImportENT_OLD and changed them to readpdb-functions (for advanced PDB file imports) 2001-04-24 14:10 thassine * INSTALL, src/common/Makefile.OLD, src/target3/t3dialog.cpp: documentation, old makefile, t3 bondtype dialog fixed a bit. 2001-04-20 13:11 thassine * src/: common/Makefile.OLD, common/Makefile.in, common/mm1mdl.cpp, common/mm1mdl.h, common/mm2alg.cpp, common/mm2alg.h, common/mm2mdl.h, common/model.h, target2/t2mm2docv.cpp: continued merging the mm2_mdl. 2001-04-19 13:16 thassine * src/: common/mm1mdl.h, common/mm2eng.h, common/mm2mdl.cpp, common/mm2mdl.h, common/mm2util.cpp, common/mm2util.h, common/model.cpp, common/model.h, common/qm1mdl.h, graphics/mm2docv.cpp, graphics/mm2docv.h, graphics/qm2docv.h, target2/t2mm1docv.h, target2/t2mm2docv.cpp, target2/t2qm1docv.h, target2/t2qm2docv.h: continued merging the mm2_mdl, plus some cleanups. 2001-04-18 14:04 thassine * CHANGES, bin/parameters/mm2param/loopdip.txt, bin/parameters/mm2param/looptor.txt, src/common/Makefile.OLD, src/common/Makefile.in, src/common/mm1mdl.h, src/common/mm1util.h, src/common/mm2eng.cpp, src/common/mm2eng.h, src/common/mm2mdl.cpp, src/common/mm2mdl.h, src/graphics/mm2docv.cpp, src/graphics/mm2docv.h, src/target2/t2mm1docv.cpp, src/target2/t2mm2docv.cpp, src/target2/t2mm2docv.h, src/target3/t3mm2docv.cpp, src/target3/t3mm2docv.h: started merging the mm2_mdl code (accepted for publication :) 2001-04-18 11:22 thassine * CHANGES, miniMOPAC/Makefile, miniMOPAC/Makefile.OLD, miniMOPAC/README, miniMOPAC/aababc.c, miniMOPAC/addfck.c, miniMOPAC/addhcr.c, miniMOPAC/addnuc.c, miniMOPAC/analyt.c, miniMOPAC/anavib.c, miniMOPAC/axis.c, miniMOPAC/block.c, miniMOPAC/bonds.c, miniMOPAC/brlzon.c, miniMOPAC/btoc.c, miniMOPAC/calpar.c, miniMOPAC/capcor.c, miniMOPAC/cdiag.c, miniMOPAC/chrge.c, miniMOPAC/cnvg.c, miniMOPAC/compfg.c, miniMOPAC/consts.c, miniMOPAC/cqden.c, miniMOPAC/datin.c, miniMOPAC/dcart.c, miniMOPAC/delmol.c, miniMOPAC/delri.c, miniMOPAC/denrot.c, miniMOPAC/densit.c, miniMOPAC/depvar.c, miniMOPAC/deri0.c, miniMOPAC/deri1.c, miniMOPAC/deri2.c, miniMOPAC/deri21.c, miniMOPAC/deri22.c, miniMOPAC/deri23.c, miniMOPAC/deritr.c, miniMOPAC/deriv.c, miniMOPAC/dernvo.c, miniMOPAC/ders.c, miniMOPAC/dfock2.c, miniMOPAC/dfpsav.c, miniMOPAC/dgemm.c, miniMOPAC/dgemv.c, miniMOPAC/dger.c, miniMOPAC/dgetf2.c, miniMOPAC/dgetrf.c, miniMOPAC/dgetri.c, miniMOPAC/diag.c, miniMOPAC/diat.c, miniMOPAC/diat2.c, miniMOPAC/diegrd.c, miniMOPAC/dielen.c, miniMOPAC/diis.c, miniMOPAC/dijkl1.c, miniMOPAC/dijkl2.c, miniMOPAC/dipind.c, miniMOPAC/dipole.c, miniMOPAC/dlaswp.c, miniMOPAC/dofs.c, miniMOPAC/dot.c, miniMOPAC/drc.c, miniMOPAC/drcout.c, miniMOPAC/dtrmm.c, miniMOPAC/dtrmv.c, miniMOPAC/dtrsm.c, miniMOPAC/dtrti2.c, miniMOPAC/dtrtri.c, miniMOPAC/dvfill.c, miniMOPAC/ef.c, miniMOPAC/enpart.c, miniMOPAC/esp.c, miniMOPAC/etime.c, miniMOPAC/exchng.c, miniMOPAC/fdate.c, miniMOPAC/ffhpol.c, miniMOPAC/flepo.c, miniMOPAC/fmat.c, miniMOPAC/fock1.c, miniMOPAC/fock2.c, miniMOPAC/force.c, miniMOPAC/formxy.c, miniMOPAC/forsav.c, miniMOPAC/frame.c, miniMOPAC/freqcy.c, miniMOPAC/geout.c, miniMOPAC/geoutg.c, miniMOPAC/getgeg.c, miniMOPAC/getgeo.c, miniMOPAC/getsym.c, miniMOPAC/gettxt.c, miniMOPAC/gmetry.c, miniMOPAC/gover.c, miniMOPAC/greenf.c, miniMOPAC/grid.c, miniMOPAC/h1elec.c, miniMOPAC/haddon.c, miniMOPAC/hcore.c, miniMOPAC/helect.c, miniMOPAC/hqrii.c, miniMOPAC/ijkl.c, miniMOPAC/ilaenv.c, miniMOPAC/initsv.c, miniMOPAC/interp.c, miniMOPAC/iter.c, miniMOPAC/jcarin.c, miniMOPAC/linmin.c, miniMOPAC/local.c, miniMOPAC/locmin.c, miniMOPAC/lsame.c, miniMOPAC/makpol.c, miniMOPAC/mamult.c, miniMOPAC/matou1.c, miniMOPAC/matout.c, miniMOPAC/matpak.c, miniMOPAC/meci.c, miniMOPAC/mecid.c, miniMOPAC/mecih.c, miniMOPAC/mecip.c, miniMOPAC/minimopac.c, miniMOPAC/moldat.c, miniMOPAC/molval.c, miniMOPAC/mullik.c, miniMOPAC/mult.c, miniMOPAC/nllsq.c, miniMOPAC/nuchar.c, miniMOPAC/parsav.c, miniMOPAC/partxy.c, miniMOPAC/pathk.c, miniMOPAC/paths.c, miniMOPAC/perm.c, miniMOPAC/polar.c, miniMOPAC/powsav.c, miniMOPAC/powsq.c, miniMOPAC/prtdrc.c, miniMOPAC/quadr.c, miniMOPAC/react1.c, miniMOPAC/reada.c, miniMOPAC/readmo.c, miniMOPAC/refer.c, miniMOPAC/repp.c, miniMOPAC/rotat.c, miniMOPAC/rotate.c, miniMOPAC/rsp.c, miniMOPAC/search.c, miniMOPAC/second.c, miniMOPAC/setupg.c, miniMOPAC/solrot.c, miniMOPAC/swap.c, miniMOPAC/sympro.c, miniMOPAC/symtry.c, miniMOPAC/symtrz.c, miniMOPAC/thermo.c, miniMOPAC/timer.c, miniMOPAC/timout.c, miniMOPAC/update.c, miniMOPAC/upsurf.c, miniMOPAC/vecprt.c, miniMOPAC/writmo.c, miniMOPAC/wrtkey.c, miniMOPAC/wrttxt.c, miniMOPAC/xerbla.c, miniMOPAC/xyzint.c, src/common/Makefile.OLD, src/common/Makefile.in, src/common/errutil.cpp, src/common/qm1alg.cpp, src/common/qm1alg.h, src/common/qm1e_mopac.cpp, src/common/qm1e_mopac.h, src/common/qm1e_mpqc.cpp, src/common/qm1e_mpqc.h, src/common/qm1eng.cpp, src/common/qm1eng.h, src/common/qm1eng1.cpp, src/common/qm1eng1.h, src/common/qm1eng9.cpp, src/common/qm1eng9.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/graphics/camera.h, src/graphics/mm1docv.cpp, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/target1/Makefile.OLD, src/target2/Makefile.OLD, src/target2/t2mm1docv.h, src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h, src/target3/Makefile.OLD, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h: added miniMOPAC and QM geometry optimization. 2001-03-30 13:21 thassine * configure, configure.in, src/common/define.h: switched back to devel settings; the version number is now 0.43 2001-03-30 11:30 thassine * CHANGES, src/common/define.h, src/common/notice.cpp, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm2docv.cpp, src/target3/t3qm1docv.cpp: minor cleanups; this is released as 0.42 2001-03-28 14:08 thassine * src/: common/model.cpp, common/typedef.h, graphics/mm1docv.cpp, target1/Makefile.OLD, target2/Makefile.OLD, target3/Makefile.OLD: some comments added, X11/ogl headers and libs removed from TARGET1. 2001-03-22 18:43 hutchisn * src/graphics/mm1docv.cpp: Add new multiple-bond rendering. Now uses line stipple to render conjugated bonds fairly well. 2001-03-22 17:51 thassine * src/: common/mm1util.h, graphics/mm1rbn.cpp, target2/t2mm1docv.cpp, target3/t3mm1docv.cpp: the bug with ribbon objects should now be fixed. 2001-03-19 13:46 thassine * src/common/: filetrans.cpp, filetrans.h: added syncronization for bonds into file_trans::Synchronize(). 2001-03-16 14:17 thassine * src/: common/filetrans.cpp, common/mm1mdl.cpp, common/utility.cpp, common/utility.h, target2/t2mm1docv.cpp: oelib syncronization and other small improvements. 2001-03-15 20:50 hutchisn * src/common/filetrans.cpp: Fix "the bug" with calling extab before it was properly set. 2001-03-15 13:15 thassine * src/common/: filetrans.cpp, filetrans.h: switched to a less complicated way to do oelib compatibility 2001-03-14 18:40 hutchisn * bin/examples/PeriodicTable.mm1gp, src/common/utility.cpp, src/common/utility.h: Fixed atom colors and add example Periodic Table. 2001-03-14 15:00 thassine * CHANGES, configure, configure.in, src/common/define.h, src/common/filetrans.cpp, src/common/filetrans.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/utility.cpp, src/common/utility.h, src/graphics/Makefile.OLD, src/graphics/Makefile.in, src/target1/Makefile.OLD, src/target2/Makefile.OLD, src/target2/t2mm1docv.cpp, src/target3/Makefile.OLD, src/target3/Makefile.in: some mm1_mdl <=> oelib compatibility features started. 2001-03-12 14:00 thassine * BUGLIST, CHANGES, INSTALL, PROJECT, bin/examples/2-chlorobutane.mm1gp, bin/examples/3-phenylpropanal.mm1gp, bin/examples/acetylsalicylic_acid.mm1gp, bin/examples/alpha-pinene.mm1gp, bin/examples/bromobenzene.mm1gp, bin/examples/camphor.mm1gp, bin/examples/cinnamaldehyde.mm1gp, bin/examples/cis-2-pentene.mm1gp, bin/examples/cyclohexane.mm1gp, bin/examples/naphtalene.mm1gp, src/common/mm1mdl.cpp, src/graphics/docview.cpp, src/graphics/docview.h, src/target3/t3docv.h, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3views.cpp: this is released as version 0.41 2001-03-09 00:54 hutchisn * src/: common/define.h, graphics/mm1docv.cpp, target3/t3mm1docv.cpp, target3/t3mm1docv.h: Add support for label Atom IDs 2001-03-09 00:53 hutchisn * src/common/mm1mdl.cpp: ReadStream changes to support reading charges 2001-03-09 00:53 hutchisn * src/common/notice.cpp: Update copyright with OELib info. 2001-03-09 00:51 hutchisn * src/common/filetrans.cpp: Update for new OELib changes. 2001-03-09 00:49 hutchisn * Makefile.in: Add target for help files. 2001-03-08 16:59 thassine * CHANGES, src/common/notice.cpp, src/common/notice.h, src/target3/t3main.cpp, src/target3/t3main.h: added the Help/Help item to the main menu, copyright notices updated to include OELib 2001-03-08 15:51 thassine * bin/user-docs/: index.html, maintools.jpg: updated the user's manual 2001-02-16 17:14 thassine * src/Makefile.OLD: this will make quick test builds easier. 2001-02-16 16:29 thassine * bin/user-docs/index.html: added some framework for the user manual 2001-02-13 16:32 thassine * INSTALL, src/target3/t3main.cpp, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h: added some quick improvements to qm1-model to boost its ease of use. 2001-02-12 19:07 hutchisn * configure, configure.in: Solved configure problems with MPQC and oelib. 2001-02-12 18:25 hutchisn * configure, configure.in: Fix problem with configure in srcdir. 2001-02-12 11:41 thassine * src/: common/Makefile.OLD, common/qm1eng1.cpp, common/qm1mdl.cpp, graphics/Makefile.OLD, graphics/camera.cpp, graphics/docview.cpp, graphics/mm1docv.cpp, graphics/mm1rbn.cpp, graphics/mm2docv.cpp, graphics/mm2rbn.cpp, graphics/mtools.cpp, graphics/objects.cpp, graphics/plane.cpp, graphics/qm1docv.cpp, graphics/qm2docv.cpp, graphics/surface.cpp, graphics/views.cpp, target1/Makefile.OLD, target1/config.h.OLD, target2/Makefile.OLD, target2/config.h.OLD, target3/Makefile.OLD, target3/config.h.OLD: a bug that affected MPQC front end compilation is now fixed (thanks Mark). 2001-02-11 16:36 thassine * CHANGES, bin/examples/1gar.mm2gp, bin/examples/1hcl.mm2gp, bin/examples/4rhn.mm2gp, src/common/Makefile.OLD, src/common/Makefile.in, src/common/mm2mdl.cpp, src/common/mm2mdl.h, src/common/mm2util.cpp, src/common/mm2util.h, src/common/model.h, src/graphics/Makefile.OLD, src/graphics/Makefile.in, src/graphics/mm2docv.cpp, src/graphics/mm2docv.h, src/graphics/mm2rbn.cpp, src/graphics/mm2rbn.h, src/graphics/views.h, src/target2/Makefile.OLD, src/target2/t2main.cpp, src/target2/t2main.h, src/target2/t2mm2docv.cpp, src/target2/t2mm2docv.h, src/target3/Makefile.OLD, src/target3/Makefile.in, src/target3/t3docv.h, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm2docv.cpp, src/target3/t3mm2docv.h, src/target3/t3views.h: tadaall added a preview version of the reduced protein modelling thing. 2001-02-10 17:09 thassine * INSTALL, configure, configure.in, src/common/define.h, src/common/engine.h, src/common/mm1mdl.cpp, src/common/qm1mdl.cpp, src/target3/t3views.cpp: changed back to devel settings (version number, releasedate); small fixes appled here and there. 2001-02-07 11:24 thassine * small-utilities/README, small-utilities/gp2mpqc.cpp, src/graphics/spline.h, src/graphics/views.h: added some final fixes to documentation; this is released as 0.40 2001-02-06 20:24 hutchisn * src/common/filetrans.cpp: Fix bug with GetImportDescription. 2001-02-06 15:10 thassine * src/: common/mm1mdl.cpp, common/mm1mdl.h, graphics/docview.h, graphics/mm1docv.cpp, graphics/mm1docv.h, target2/t2docv.h, target3/t3docv.h, target3/t3errutil.h, target3/t3main.h, target3/t3mm1docv.h, target3/t3qm1docv.h, target3/t3views.h: added some more DOC++ style documentation. 2001-02-06 11:21 thassine * AUTHORS, CHANGES, INSTALL, PROJECT: revised/updated some documentation. 2001-02-06 10:44 thassine * configure, configure.in, src/common/define.h, src/common/notice.cpp, src/target3/glade_callbacks.cpp, src/target3/glade_interface.cpp, src/target3/glade_interface.h: some cleanups at glade optionmenus; the version number promoted to 0.40 2001-02-06 08:17 hutchisn * src/target3/glade_callbacks.cpp: Use file_trans methods to specifically request a file type when the user picks it or "Automatic" based on the file name. 2001-02-06 08:16 hutchisn * src/common/: filetrans.cpp, filetrans.h: Add support for specifically requesting an import or export type (by index #). 2001-02-05 17:26 thassine * src/target3/glade_callbacks.cpp: the file import/export dialogs seem to work now... 2001-02-05 16:48 thassine * src/target3/: glade_callbacks.cpp, glade_interface.cpp, glade_interface.h: the filename change is done also in oelib; the file import/export dialogs almost work now. 2001-02-05 15:55 thassine * src/target3/: glade_callbacks.cpp, glade_callbacks.h, glade_interface.cpp, glade_interface.h, t3mm1docv.cpp, t3qm1docv.cpp, glade/ghemical.glade: changed the glade project and code so that each dialog (and most important widgets) have their own simple namespace. 2001-02-04 20:30 thassine * src/: common/qm1eng.cpp, common/qm1eng.h, common/qm1mdl.cpp, common/qm1mdl.h, common/qm2eng.cpp, common/qm2eng.h, common/qm2mdl.cpp, common/qm2mdl.h, graphics/qm1docv.cpp, graphics/qm1docv.h, graphics/qm2docv.cpp, graphics/qm2docv.h, target2/t2qm1docv.cpp, target2/t2qm1docv.h, target2/t2qm2docv.cpp, target2/t2qm2docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h, target3/t3qm2docv.cpp, target3/t3qm2docv.h: some files were lost in the last commit; added them back... 2001-02-04 20:11 thassine * CHANGES, INSTALL, bin/examples/2-chlorobutane.gpMM, bin/examples/2-chlorobutane.mm1gp, bin/examples/3-phenylpropanal.gpMM, bin/examples/3-phenylpropanal.mm1gp, bin/examples/acetylsalicylic_acid.gpMM, bin/examples/acetylsalicylic_acid.mm1gp, bin/examples/alpha-pinene.gpMM, bin/examples/alpha-pinene.mm1gp, bin/examples/bromobenzene.gpMM, bin/examples/bromobenzene.mm1gp, bin/examples/camphor.gpMM, bin/examples/camphor.mm1gp, bin/examples/cinnamaldehyde.gpMM, bin/examples/cinnamaldehyde.mm1gp, bin/examples/cis-2-pentene.gpMM, bin/examples/cis-2-pentene.mm1gp, bin/examples/cyclohexane.gpMM, bin/examples/cyclohexane.mm1gp, bin/examples/naphtalene.gpMM, bin/examples/naphtalene.mm1gp, src/common/Makefile.OLD, src/common/Makefile.in, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/model.h, src/common/qm1eng.cpp, src/common/qm1eng.h, src/common/qm1eng1.cpp, src/common/qm1eng1.h, src/common/qm1eng9.cpp, src/common/qm1eng9.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/common/qm2eng.cpp, src/common/qm2eng.h, src/common/qm2eng1.cpp, src/common/qm2eng1.h, src/common/qm2eng9.cpp, src/common/qm2eng9.h, src/common/qm2mdl.cpp, src/common/qm2mdl.h, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/graphics/qm2docv.cpp, src/graphics/qm2docv.h, src/target1/t1main.cpp, src/target2/t2main.cpp, src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h, src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h, src/target3/glade_callbacks.cpp, src/target3/glade_interface.cpp, src/target3/glade_interface.h, src/target3/t3docv.h, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h, src/target3/t3views.h, src/target3/glade/ghemical.glade: 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 18:27 thassine * src/: common/mm1alg.h, common/mm1mdl.cpp, target2/t2mm1docv.cpp, target3/glade_callbacks.cpp, target3/glade_interface.cpp, target3/t3dialog.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/glade/ghemical.glade: the trajectory viewer works now (as a modal dialog, but anyway). 2001-01-31 19:32 thassine * CHANGES, src/common/errutil.cpp, src/common/errutil.h, src/common/mm1alg.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/model.h, src/common/qm2mdl.cpp, src/common/qm2mdl.h, src/graphics/docview.h, src/graphics/mm1docv.cpp, src/graphics/mm1docv.h, src/graphics/qm2docv.cpp, src/graphics/qm2docv.h, src/target2/t2mm1docv.cpp, src/target2/t2mm1docv.h, src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h, src/target3/t3errutil.cpp, src/target3/t3errutil.h, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h: changed MM trajectory file format; some Do???-functions moved to model (and are now accessible in TARGET1 also). 2001-01-30 21:44 hutchisn * src/: common/filetrans.cpp, common/filetrans.h, common/utility.cpp, target3/glade_interface.cpp, target3/t3mm1docv.cpp, target3/t3mm1docv.h: Switch to new GLADE-designed import/export boxes. 2001-01-30 17:21 thassine * src/: common/mm1alg.h, graphics/mm1docv.cpp, graphics/mm1docv.h, target2/t2mm1docv.cpp, target2/t2mm1docv.h, target3/glade_callbacks.cpp, target3/glade_callbacks.h, target3/glade_interface.cpp, target3/glade_interface.h, target3/glade_support.cpp, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/glade/ghemical.glade: the geomopt/moldyn dialogs should now mostly work (except the traj filename). 2001-01-29 17:54 thassine * src/target3/: glade_interface.cpp, glade_interface.h, t3mm1docv.cpp, glade/ghemical.glade: added geomopt and moldyn dialogs, but wont work yet (just press cancel) 2001-01-25 15:45 thassine * src/: common/conjgrad.h, common/define.h, common/engine.h, common/errutil.h, common/mm1alg.h, common/mm1eng.h, common/mm1eng1.cpp, common/mm1eng1.h, common/mm1eng9.cpp, common/mm1eng9.h, common/mm1mdl.h, common/mm1tab1.cpp, common/mm1tab1.h, common/mm1tab9.cpp, common/mm1tab9.h, common/mm1util.h, common/model.h, common/qm1eng.h, common/qm1mdl.h, common/qm2eng.h, common/qm2eng1.h, common/qm2mdl.h, common/typedef.h, common/utility.h, common/v3d.h, graphics/camera.h, graphics/color.h, graphics/docview.cpp, graphics/docview.h, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/mm1rbn.cpp, graphics/mm1rbn.h, graphics/mtools.cpp, graphics/mtools.h, graphics/objects.cpp, graphics/objects.h, graphics/plane.cpp, graphics/plane.h, graphics/qm1docv.cpp, graphics/qm1docv.h, graphics/qm2docv.cpp, graphics/qm2docv.h, graphics/spline.cpp, graphics/spline.h, graphics/surface.cpp, graphics/surface.h, graphics/views.cpp, graphics/views.h, target1/config.h.OLD, target1/t1main.cpp, target1/t1main.h, target2/config.h.OLD, target2/t2docv.cpp, target2/t2docv.h, target2/t2main.cpp, target2/t2main.h, target2/t2mm1docv.cpp, target2/t2mm1docv.h, target2/t2qm1docv.cpp, target2/t2qm1docv.h, target2/t2qm2docv.cpp, target2/t2qm2docv.h, target2/t2views.cpp, target2/t2views.h, target3/config.h.OLD, target3/glade_callbacks.cpp, target3/glade_interface.cpp, target3/t3dialog.cpp, target3/t3dialog.h, target3/t3docv.cpp, target3/t3docv.h, target3/t3errutil.cpp, target3/t3errutil.h, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h, target3/t3qm2docv.cpp, target3/t3qm2docv.h, target3/t3views.cpp, target3/t3views.h: all documentation is now in DOC++ form, it's a bit sparse, but usable. 2001-01-24 16:08 thassine * src/: common/qm1eng.cpp, common/qm1eng.h, common/qm1mdl.cpp, common/qm1mdl.h, common/qm2eng.cpp, common/qm2eng.h, common/qm2eng1.cpp, common/qm2eng1.h, common/qm2eng9.cpp, common/qm2eng9.h, common/qm2mdl.cpp, common/qm2mdl.h, common/typedef.h, common/utility.cpp, common/utility.h, common/v3d.h, graphics/camera.cpp, graphics/camera.h, graphics/color.h: some more documentation converted into DOC++ form 2001-01-22 09:52 thassine * src/: Makefile.OLD, common/conjgrad.cpp, common/conjgrad.h, common/define.h, common/engine.cpp, common/engine.h, common/errutil.cpp, common/errutil.h, common/filetrans.cpp, common/filetrans.h, common/matrix.h, common/mm1alg.cpp, common/mm1alg.h, common/mm1eng.cpp, common/mm1eng.h, common/mm1eng1.cpp, common/mm1eng1.h, common/mm1eng9.cpp, common/mm1eng9.h, common/mm1mdl.cpp, common/mm1mdl.h, common/mm1tab1.cpp, common/mm1tab1.h, common/mm1tab9.cpp, common/mm1tab9.h, common/mm1util.cpp, common/mm1util.h, common/model.cpp, common/model.h, common/notice.cpp, common/notice.h, graphics/objects.cpp, graphics/objects.h, target3/t3mm1docv.cpp: started to convert comments into a form suitable to DOC++ 2001-01-20 08:19 hutchisn * PROJECT, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h: [no log message] 2001-01-20 08:19 hutchisn * src/target3/: glade_callbacks.cpp, glade_callbacks.h, glade_interface.cpp, glade_interface.h, glade_support.cpp, glade/ghemical.glade: Added new import/export dialogues using Glade. (Still need to figure out how to update the option menu appropriately.) 2001-01-13 23:29 hutchisn * src/common/utility.cpp: Small modifications to vdW radii to be closer to literature (Bondi) values 2001-01-13 23:28 hutchisn * src/common/filetrans.cpp: Use filename for molecule title -- we don't currently have another way of titling. 2001-01-06 00:38 hutchisn * acconfig.h, configure, configure.in, src/config.h.in, src/target3/Makefile.in: Fix build environment 2001-01-05 17:34 thassine * src/: common/mm1mdl.cpp, common/mm1mdl.h, common/qm2eng.h, common/qm2eng1.h, common/qm2eng9.cpp, common/qm2mdl.cpp, common/qm2mdl.h, graphics/docview.h, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/plane.cpp, graphics/plane.h, graphics/qm2docv.cpp, graphics/qm2docv.h, graphics/surface.cpp, graphics/surface.h, target1/Makefile.OLD, target1/t1main.cpp, target2/t2qm2docv.cpp, target3/glade_callbacks.cpp, target3/t3qm2docv.cpp: added a simple TARGET1 example, the QM setup dialog should also now work. 2001-01-03 19:09 thassine * src/: common/mm1mdl.cpp, graphics/mm1docv.cpp, graphics/mm1docv.h, graphics/qm2docv.cpp, graphics/qm2docv.h, target3/glade_callbacks.cpp, target3/glade_callbacks.h, target3/glade_interface.cpp, target3/glade_interface.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3qm2docv.cpp, target3/t3qm2docv.h, target3/glade/ghemical.glade: the setup dialog should now work for MM. 2001-01-03 12:03 thassine * CHANGES, src/target3/glade_callbacks.cpp, src/target3/glade_interface.cpp, src/target3/glade_interface.h, src/target3/glade/ghemical.glade: dialogs; read from glade/src/Makefile how to retain your changes in GLADE code. 2001-01-02 18:00 thassine * src/: common/mm1mdl.cpp, common/mm1mdl.h, common/qm2mdl.cpp, common/qm2mdl.h, graphics/mm1docv.cpp, graphics/mm1docv.h: some preliminary stuff for the setup dialogs 2001-01-02 14:42 thassine * INSTALL, PROJECT, src/target3/Makefile.OLD, src/target3/glade_callbacks.cpp, src/target3/glade_callbacks.h, src/target3/glade_interface.cpp, src/target3/glade_interface.h, src/target3/glade_support.cpp, src/target3/glade_support.h, src/target3/t3dialog.cpp, src/target3/glade/ghemical.glade: started making some dialogs using GLADE... 2001-01-01 15:53 thassine * AUTHORS, INSTALL, PROJECT, src/common/Makefile.OLD, src/common/mm1mdl.h, src/common/qm1eng.cpp, src/common/qm1eng.h, src/common/qm2eng.h, src/common/qm2eng1.h, src/common/qm2mdl.h, src/graphics/Makefile.OLD, src/target1/Makefile.OLD, src/target2/Makefile.OLD, src/target3/Makefile.OLD: just some cleanups and some improvements to documentation 2001-01-01 13:30 thassine * small-utilities/: Makefile, getpdb_cd.cpp, getpdb_ftp.cpp, gp2mpqc.cpp: HAPPY NEW YEAR; some small-utilities added... 2000-12-27 15:59 thassine * src/: graphics/camera.cpp, graphics/docview.cpp, graphics/docview.h, graphics/mm1docv.cpp, graphics/views.h, target2/t2docv.cpp, target2/t2docv.h, target2/t2main.cpp, target2/t2mm1docv.cpp, target2/t2mm1docv.h, target2/t2qm1docv.cpp, target2/t2qm1docv.h, target2/t2qm2docv.cpp, target2/t2qm2docv.h, target2/t2views.cpp, target2/t2views.h, target3/t3docv.cpp, target3/t3docv.h, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h, target3/t3qm2docv.cpp, target3/t3qm2docv.h, target3/t3views.cpp, target3/t3views.h: some cleanups; status bars now work in the GNOME version 2000-12-22 17:09 thassine * src/target3/: t3docv.cpp, t3docv.h: added some missing files... 2000-12-22 16:47 thassine * CHANGES, src/graphics/camera.cpp, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/mm1docv.cpp, src/graphics/mm1docv.h, src/graphics/mtools.cpp, src/graphics/qm1docv.h, src/graphics/qm2docv.h, src/graphics/views.cpp, src/graphics/views.h, src/target2/Makefile.OLD, src/target2/t2docv.cpp, src/target2/t2docv.h, src/target2/t2mm1docv.cpp, src/target2/t2mm1docv.h, src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h, src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/Makefile.OLD, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h, src/target3/t3views.cpp, src/target3/t3views.h: added target-dependent middle classes for docviews and views; simplifies the base-classes a bit 2000-12-22 13:34 thassine * BUGLIST, src/graphics/docview.cpp, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1docv.cpp, src/target3/t3qm2docv.cpp, src/target3/t3views.cpp: treelist works now pretty well (see BUGLIST for some details) 2000-12-21 19:16 thassine * src/: graphics/docview.cpp, graphics/docview.h, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3qm2docv.cpp, target3/t3views.cpp, target3/t3views.h: improved proper model closing/cleanup in GNOME version, but still problems (try File/Close and File/Exit) 2000-12-21 15:19 thassine * src/: graphics/docview.cpp, graphics/docview.h, graphics/views.h, target3/t3views.cpp, target3/t3views.h: treelist (now actually works) - added subtrees and lights 2000-12-20 17:01 thassine * src/: graphics/docview.cpp, graphics/views.h, target3/t3main.h, target3/t3views.cpp, target3/t3views.h: treelist - now shows objects (planes etc), and selection is possible 2000-12-19 18:57 thassine * CHANGES, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/views.cpp, src/graphics/views.h, src/target2/t2main.cpp, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3qm2docv.cpp, src/target3/t3views.cpp, src/target3/t3views.h: added framework for tree/list views, and smaller changes 2000-12-19 14:45 thassine * src/: common/notice.cpp, graphics/docview.h, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3qm2docv.cpp, target3/t3views.cpp: the toolbar buttons work again as toggle buttons 2000-12-18 17:24 thassine * src/: common/filetrans.cpp, target3/t3main.cpp: changes for old makefiles, and a statusbar added (which is empty so far) 2000-12-08 19:22 hutchisn * src/: common/filetrans.cpp, common/filetrans.h, target3/t3mm1docv.cpp: Use new OEFileFormat code to check if formats are valid. 2000-12-08 18:41 thassine * src/: common/filetrans.cpp, graphics/camera.cpp, graphics/docview.cpp, graphics/docview.h, graphics/mm1docv.cpp, graphics/mtools.cpp, graphics/qm2docv.cpp, target2/t2mm1docv.cpp, target2/t2qm2docv.cpp, target2/t2views.cpp, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3qm2docv.cpp, target3/t3views.cpp: various fixes (like exit-command) - oelib? 2000-12-02 02:29 hutchisn * src/target3/t3mm1docv.cpp: OKEvent should return true for now. 2000-12-02 02:28 hutchisn * src/target3/: t3dialog.cpp, t3dialog.h, t3mm1docv.cpp, t3mm1docv.h, t3qm2docv.cpp, t3qm2docv.h: OKEvent should return bool in case there's a problem (e.g. file doesn't exist, save might overwrite a file, format is not supported, etc.) 2000-12-02 02:27 hutchisn * src/common/Makefile.in: One more bug fix--really get the logic in initialization correct! 2000-12-01 23:49 hutchisn * Makefile.in, configure, configure.in, src/common/Makefile.in, src/common/filetrans.cpp: Update OELib to use GHEMICAL_DIR environment variable or specified directories installed by "make install" target. 2000-12-01 15:27 thassine * src/: common/Makefile.OLD, target1/Makefile.OLD, target2/Makefile.OLD, target3/Makefile.OLD: updated the old makefiles... 2000-12-01 02:13 hutchisn * src/: common/Makefile.in, common/define.h, common/filetrans.cpp, common/filetrans.h, common/model.cpp, graphics/Makefile.in, target3/Makefile.in, target3/t3main.cpp, target3/t3mm1docv.cpp: add support for import/export methods using oelib 2000-11-30 14:18 thassine * src/: common/Makefile.OLD, common/qm2mdl.h, graphics/Makefile.OLD, graphics/mm1docv.h, target3/t3main.cpp, target3/t3main.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3qm2docv.cpp, target3/t3qm2docv.h: GNOME erase-tool fixed, STATICpopupmenu removed, all popup-items enabled again 2000-11-29 19:18 thassine * src/: graphics/docview.h, graphics/views.h, target3/t3mm1docv.cpp, target3/t3mm1docv.h, target3/t3qm1docv.cpp, target3/t3qm1docv.h, target3/t3qm2docv.cpp, target3/t3qm2docv.h, target3/t3views.cpp, target3/t3views.h: GNOME popup menu callbacks finished - but some items are still disabled 2000-11-29 16:43 thassine * src/target3/: t3mm1docv.cpp, t3qm2docv.cpp, t3views.cpp, t3views.h: popup-menu callbacks changed (for model-independent items) 2000-11-29 15:10 thassine * src/: common/model.cpp, common/model.h, graphics/views.cpp, graphics/views.h, target2/t2views.cpp, target2/t2views.h, target3/t3main.cpp, target3/t3views.cpp, target3/t3views.h: OpenGL initialization in GNOME fixed (so that we have colors back). 2000-11-28 19:43 hutchisn * src/target3/: t3mm1docv.cpp, t3mm1docv.h, t3views.cpp: Add import/export menu items, center command and move things to "build" submenu. 2000-11-28 19:42 hutchisn * src/target3/t3main.cpp: Can't pass VERSION since it's a double. Run it through sprintf first. 2000-11-28 19:40 hutchisn * acconfig.h, configure, configure.in, src/config.h.in, src/graphics/Makefile.in: Fix build environment to define appropriate flags, etc. 2000-11-28 17:41 thassine * CHANGES, src/common/conjgrad.h, src/common/errutil.h, src/common/mm1alg.h, src/common/mm1eng.h, src/common/mm1eng1.h, src/common/mm1mdl.h, src/common/mm1util.h, src/common/model.h, src/common/qm2eng.h, src/common/qm2eng9.h, src/common/qm2mdl.h, src/common/v3d.h, src/graphics/mtools.h, src/graphics/views.h, src/target2/t2mm1docv.cpp, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/t3main.h, src/target3/t3qm2docv.cpp, src/target3/t3views.cpp, src/target3/t3views.h: some cleanups : public data changed protected in many classes 2000-11-28 14:18 thassine * CHANGES, src/common/define.h, src/graphics/Makefile.OLD, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/views.h, src/target2/t2views.cpp, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1docv.cpp, src/target3/t3views.cpp, src/target3/t3views.h: any things broken/mixed up, but we have a standard GNOME MDI app now 2000-11-27 18:50 hutchisn * src/target3/: t3dialog.cpp, t3dialog.h: Modify dialog to show which element is currently selected. 2000-11-27 18:48 hutchisn * src/common/: filetrans.cpp, filetrans.h, mm1mdl.cpp, mm1mdl.h: Remove import functions from mm1mdl and use new filetrans code through OELib. 2000-11-27 18:47 hutchisn * Makefile.in, acconfig.h, configure, configure.in, src/config.h.in, src/common/Makefile.in, src/graphics/Makefile.in, src/target3/Makefile.in: Add changes to support linking in OELib and slightly cleaned up build system. 2000-11-27 10:51 thassine * configure, configure.in, src/common/Makefile.in, src/graphics/Makefile.in, src/target3/Makefile.in: Makefile.in -files updated (configure still broken) 2000-11-26 15:05 thassine * CHANGES, src/graphics/camera.cpp, src/graphics/camera.h, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/mm1docv.cpp, src/graphics/mm1docv.h, src/graphics/mm1rbn.cpp, src/graphics/mm1rbn.h, src/graphics/mtools.cpp, src/graphics/mtools.h, src/graphics/objects.cpp, src/graphics/objects.h, src/graphics/plane.cpp, src/graphics/plane.h, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/graphics/qm2docv.cpp, src/graphics/qm2docv.h, src/graphics/surface.cpp, src/graphics/surface.h, src/graphics/views.cpp, src/graphics/views.h, src/target2/config.h.OLD, src/target2/t2mm1docv.cpp, src/target2/t2qm1docv.cpp, src/target2/t2qm2docv.cpp, src/target2/t2views.cpp, src/target3/config.h.OLD, src/target3/t3mm1docv.cpp, src/target3/t3qm1docv.cpp, src/target3/t3qm2docv.cpp, src/target3/t3views.cpp: 3rd stage of doc/view changes 2000-11-24 15:36 thassine * CHANGES, src/graphics/camera.cpp, src/graphics/camera.h, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/mm1docv.cpp, src/graphics/mm1docv.h, src/graphics/mm1rbn.cpp, src/graphics/mm1rbn.h, src/graphics/mtools.cpp, src/graphics/mtools.h, src/graphics/plane.cpp, src/graphics/plane.h, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/graphics/qm2docv.cpp, src/graphics/qm2docv.h, src/graphics/surface.cpp, src/graphics/surface.h, src/graphics/views.cpp, src/graphics/views.h, src/target2/t2main.cpp, src/target2/t2mm1docv.cpp, src/target2/t2mm1docv.h, src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h, src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h, src/target2/t2views.cpp, src/target2/t2views.h, src/target3/t3main.cpp, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h, src/target3/t3views.cpp, src/target3/t3views.h: 2nd stage of doc/view reorganization 2000-11-23 17:07 thassine * CHANGES, src/common/Makefile.OLD, src/common/conjgrad.h, src/common/engbase.cpp, src/common/engbase.h, src/common/engine.cpp, src/common/engine.h, src/common/mdlbase.cpp, src/common/mdlbase.h, src/common/mm1eng.cpp, src/common/mm1eng.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm1tab1.cpp, src/common/mm1tab9.cpp, src/common/mm1util.cpp, src/common/model.cpp, src/common/model.h, src/common/qm1eng.cpp, src/common/qm1eng.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/common/qm2eng.cpp, src/common/qm2eng.h, src/common/qm2mdl.cpp, src/common/qm2mdl.h, src/graphics/Makefile.OLD, src/graphics/camera.cpp, src/graphics/camera.h, src/graphics/docview.cpp, src/graphics/docview.h, src/graphics/guibase.cpp, src/graphics/guibase.h, src/graphics/mm1docv.cpp, src/graphics/mm1docv.h, src/graphics/mm1gui.cpp, src/graphics/mm1gui.h, src/graphics/mm1rbn.cpp, src/graphics/mm1rbn.h, src/graphics/mtools.cpp, src/graphics/mtools.h, src/graphics/objects.cpp, src/graphics/objects.h, src/graphics/plane.cpp, src/graphics/plane.h, src/graphics/qm1docv.cpp, src/graphics/qm1docv.h, src/graphics/qm1gui.cpp, src/graphics/qm1gui.h, src/graphics/qm2docv.cpp, src/graphics/qm2docv.h, src/graphics/qm2gui.cpp, src/graphics/qm2gui.h, src/graphics/surface.cpp, src/graphics/surface.h, src/graphics/viewing.cpp, src/graphics/viewing.h, src/graphics/views.cpp, src/graphics/views.h, src/graphics/window.cpp, src/graphics/window.h, src/target1/Makefile.OLD, src/target2/Makefile.OLD, src/target2/t2main.h, src/target2/t2mm1docv.cpp, src/target2/t2mm1docv.h, src/target2/t2mm1gui.cpp, src/target2/t2mm1gui.h, src/target2/t2qm1docv.cpp, src/target2/t2qm1docv.h, src/target2/t2qm1gui.cpp, src/target2/t2qm1gui.h, src/target2/t2qm2docv.cpp, src/target2/t2qm2docv.h, src/target2/t2qm2gui.cpp, src/target2/t2qm2gui.h, src/target2/t2views.cpp, src/target2/t2views.h, src/target2/t2window.cpp, src/target2/t2window.h, src/target3/Makefile.OLD, src/target3/t3main.h, src/target3/t3mm1docv.cpp, src/target3/t3mm1docv.h, src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h, src/target3/t3qm1docv.cpp, src/target3/t3qm1docv.h, src/target3/t3qm1gui.cpp, src/target3/t3qm1gui.h, src/target3/t3qm2docv.cpp, src/target3/t3qm2docv.h, src/target3/t3qm2gui.cpp, src/target3/t3qm2gui.h, src/target3/t3views.cpp, src/target3/t3views.h, src/target3/t3window.cpp, src/target3/t3window.h: 1st round of doc/view changes (will break the configure-script) 2000-11-20 12:18 thassine * src/: common/qm2mdl.cpp, graphics/guibase.h, graphics/mm1gui.cpp, graphics/mm1gui.h, graphics/mm1rbn.cpp, graphics/qm2gui.cpp, graphics/qm2gui.h: fixed QM import bug + some potential graphics bugs 2000-11-16 17:06 hutchisn * Makefile.in: Removed configure target--something is strange with the timestamps. 2000-11-16 13:55 thassine * src/: common/Makefile.OLD, common/errorutil.cpp, common/errorutil.h, common/errutil.cpp, common/errutil.h, common/mdlbase.cpp, common/mdlbase.h, common/mm1mdl.cpp, common/mm1mdl.h, common/qm1mdl.cpp, common/qm1mdl.h, common/qm2mdl.cpp, common/qm2mdl.h, graphics/Makefile.OLD, graphics/guibase.cpp, graphics/guibase.h, graphics/mm1gui.cpp, graphics/mm1gui.h, graphics/qm1gui.cpp, graphics/qm1gui.h, graphics/qm2gui.cpp, graphics/qm2gui.h, target2/Makefile.OLD, target2/t2main.cpp, target2/t2mm1gui.cpp, target2/t2mm1gui.h, target2/t2qm1gui.cpp, target2/t2qm1gui.h, target2/t2qm2gui.cpp, target2/t2qm2gui.h, target2/t2window.cpp, target3/Makefile.OLD, target3/t3errorutil.cpp, target3/t3errorutil.h, target3/t3errutil.cpp, target3/t3errutil.h, target3/t3main.cpp, target3/t3mm1gui.cpp, target3/t3mm1gui.h, target3/t3qm1gui.cpp, target3/t3qm1gui.h, target3/t3qm2gui.cpp, target3/t3qm2gui.h, target3/t3window.cpp: added err_util for all models 2000-11-15 17:01 hutchisn * src/: common/Makefile.in, common/errorutil.cpp, common/errorutil.h, target3/Makefile.in, target3/t3errorutil.cpp, target3/t3errorutil.h: Add error-handling classes with support for GNOME. 2000-11-14 23:32 hutchisn * src/target3/: t3mm1gui.cpp, t3mm1gui.h, t3window.cpp: Added menu items and user-visible feedback for menu choices. 2000-11-14 23:23 hutchisn * Makefile.in, configure.in: Add makefile targets to ensure configure script and Makefiles are updated properly. Also add AC_PREREQ to configure.in to ensure configure script isn't updated by an old version of autoconf. 2000-11-10 21:56 hutchisn * src/target3/: t3mm1gui.cpp, t3mm1gui.h, t3window.cpp: Remove menu items for import HIN and PDB files (soon to be done through OELib) Add menu items and support for render labels and coloring and quick update mode. 2000-11-10 18:48 hutchisn * bin/examples/: 2-chlorobutane.gpMM, 3-phenylpropanal.gpMM, acetylsalicylic_acid.gpMM, alpha-pinene.gpMM, bromobenzene.gpMM, camphor.gpMM, cinnamaldehyde.gpMM, cis-2-pentene.gpMM, cyclohexane.gpMM, naphtalene.gpMM: Update examples to new file format (read in and re-saved). 2000-11-10 14:46 thassine * CHANGES, src/common/mdlbase.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm1util.cpp, src/common/qm1mdl.h, src/common/qm2mdl.h: 1st round of mm1_mdl file format revision 2000-11-09 14:42 thassine * BUGLIST, CHANGES, src/Makefile.OLD, src/common/typedef.h, src/common/utility.cpp, src/graphics/color.h, src/graphics/guibase.cpp, src/graphics/guibase.h, src/graphics/mm1gui.cpp, src/graphics/mm1rbn.h, src/graphics/objects.cpp, src/graphics/objects.h, src/graphics/plane.cpp, src/graphics/plane.h, src/graphics/qm1gui.cpp, src/graphics/qm2gui.cpp, src/graphics/surface.cpp, src/graphics/surface.h, src/graphics/viewing.cpp, src/graphics/viewing.h, src/target2/t2mm1gui.cpp, src/target2/t2qm2gui.cpp, src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h, src/target3/t3qm2gui.cpp, src/target3/t3window.cpp: graphics improvements, volume rendering added 2000-11-08 23:30 hutchisn * src/common/: utility.cpp, 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 22:00 hutchisn * src/target3/t3dialog.cpp: Add feedback for currently selected bondtype and element in dialogues. 2000-11-07 21:59 hutchisn * src/target3/: t3mm1gui.cpp, t3qm2gui.cpp: Temporarily fix bug for open file filters--don't supply a filter until GTK is fixed. 2000-11-02 16:34 thassine * src/: common/define.h, target3/t3main.cpp: fixed those about-dialog crashes... 2000-11-01 14:43 thassine * CHANGES, src/common/define.h, src/common/mdlbase.cpp, src/common/mdlbase.h, src/common/mm1mdl.cpp, src/common/mm1tab1.cpp, src/common/mm1tab9.cpp, src/common/mm1util.cpp, src/target3/Makefile.OLD: added primary/secondary paths for parameter files 2000-11-01 00:37 hutchisn * src/: common/utility.cpp, graphics/mm1gui.cpp: Enter real vdW radii from several sources and update GUI to draw accordingly 2000-11-01 00:34 hutchisn * src/target3/t3dialog.cpp: Fixed bug with elements beyond #105. 2000-10-31 19:55 hutchisn * configure, configure.in: Another attempt to pick up Xmu and glut appropirately. 2000-10-31 10:17 thassine * src/Makefile.OLD: revieved the /src/Makefile.OLD 2000-10-30 18:41 hutchisn * configure, configure.in, src/Makefile.OLD, src/target3/Makefile.in: Bugfixes for the autoconf changes--should now work on systems needing -Xmu. 2000-10-30 17:10 thassine * src/Makefile.OLD: added yet another Makefile.OLD 2000-10-30 15:50 hutchisn * INSTALL, Makefile.in, acconfig.h, aclocal.m4, configure, configure.in, install-sh, mkinstalldirs, src/Makefile, src/config.h.in, src/common/Makefile.in, src/common/define.h, src/graphics/Makefile.in, src/target3/Makefile.in, src/target3/t3main.cpp: Changes to move to an autoconf-derived configure script. 2000-10-25 12:06 thassine * src/common/: conjgrad.cpp, utility.cpp: added some missing header files 2000-10-25 11:45 thassine * CHANGES, src/common/conjgrad.cpp, src/common/utility.cpp, src/target3/t3main.cpp, src/target3/t3mm1gui.cpp, src/target3/t3qm2gui.cpp: better GnomeUIInfo initialization (the RH7-patch from GH) 2000-10-25 10:47 thassine * CHANGES, src/graphics/guibase.cpp, src/graphics/mm1gui.cpp: the multiple view management bug fixed (at last) 2000-10-25 03:03 hutchisn * src/: common/conjgrad.cpp, common/utility.cpp, target3/t3main.cpp, target3/t3mm1gui.cpp, target3/t3qm2gui.cpp: Minor changes to allow compilation on RH7. 2000-10-25 03:02 hutchisn * bin/.cvsignore, src/.cvsignore, src/common/.cvsignore, src/graphics/.cvsignore, src/target2/.cvsignore, src/target3/.cvsignore: CVS ignore files to remove common build objects, etc. 2000-10-24 12:28 thassine * src/: graphics/mm1gui.cpp, graphics/mm1gui.h, target2/t2mm1gui.cpp, target3/t3mm1gui.cpp: cleaned some graphics code 2000-10-23 17:20 thassine * src/: new.cpp, new.h, some-extra-files/newfile.cpp, some-extra-files/newfile.h: moved some conflicting files to some-extra-files 2000-10-23 11:59 thassine * CHANGES, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm1util.cpp, src/common/mm1util.h, src/graphics/mm1rbn.cpp: improved mm1_chn_info 2000-10-21 13:14 thassine * src/common/: Makefile, color.h, config.h, guibase.cpp, guibase.h, mm1gui.cpp, mm1gui.h, mm1rbn.cpp, mm1rbn.h, mtools.cpp, mtools.h, objects.cpp, objects.h, plane.cpp, plane.h, qm1gui.cpp, qm1gui.h, qm2gui.cpp, qm2gui.h, spline.cpp, spline.h, surface.cpp, surface.h, viewing.cpp, viewing.h, window.cpp, window.h: removed some duplicate files 2000-10-21 12:42 thassine * CHANGES, src/Makefile, src/common/Makefile.OLD, src/common/conjgrad.cpp, src/common/conjgrad.h, src/common/define.h, src/common/engbase.cpp, src/common/engbase.h, src/common/mdlbase.cpp, src/common/mdlbase.h, src/common/mm1alg.cpp, src/common/mm1alg.h, src/common/mm1eng.cpp, src/common/mm1eng.h, src/common/mm1eng1.cpp, src/common/mm1eng1.h, src/common/mm1eng9.cpp, src/common/mm1eng9.h, src/common/mm1mdl.cpp, src/common/mm1mdl.h, src/common/mm1tab1.cpp, src/common/mm1tab1.h, src/common/mm1tab9.cpp, src/common/mm1tab9.h, src/common/mm1util.cpp, src/common/mm1util.h, src/common/qm1eng.cpp, src/common/qm1eng.h, src/common/qm1mdl.cpp, src/common/qm1mdl.h, src/common/qm2eng.cpp, src/common/qm2eng.h, src/common/qm2eng1.cpp, src/common/qm2eng1.h, src/common/qm2eng9.cpp, src/common/qm2eng9.h, src/common/qm2mdl.cpp, src/common/qm2mdl.h, src/common/typedef.h, src/common/utility.cpp, src/common/utility.h, src/common/v3d.h, src/graphics/Makefile.OLD, src/graphics/color.h, src/graphics/guibase.cpp, src/graphics/guibase.h, src/graphics/mm1gui.cpp, src/graphics/mm1gui.h, src/graphics/mm1rbn.cpp, src/graphics/mm1rbn.h, src/graphics/mtools.cpp, src/graphics/mtools.h, src/graphics/objects.cpp, src/graphics/objects.h, src/graphics/plane.cpp, src/graphics/plane.h, src/graphics/qm1gui.cpp, src/graphics/qm1gui.h, src/graphics/qm2gui.cpp, src/graphics/qm2gui.h, src/graphics/spline.cpp, src/graphics/spline.h, src/graphics/surface.cpp, src/graphics/surface.h, src/graphics/viewing.cpp, src/graphics/viewing.h, src/graphics/window.cpp, src/graphics/window.h, src/target1/Makefile, src/target1/Makefile.OLD, src/target1/config.h, src/target1/config.h.OLD, src/target2/Makefile, src/target2/Makefile.OLD, src/target2/config.h, src/target2/config.h.OLD, src/target3/Makefile, src/target3/Makefile.OLD, src/target3/config.h, src/target3/config.h.OLD: new source tree with old makefiles 2000-10-21 11:16 thassine * CHANGES, src/common/guibase.cpp, src/common/guibase.h, src/common/viewing.cpp, src/target3/t3dialog.cpp, src/target3/t3dialog.h, src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h, src/target3/t3qm2gui.cpp, src/target3/t3qm2gui.h, src/target3/t3window.cpp: file save dialogs added, selection bug fixed 2000-10-18 17:13 thassine * CHANGES, bin/examples/2-chlorobutane.gpMM, bin/examples/2-chlorobutane.mm1gp, bin/examples/3-phenylpropanal.gpMM, bin/examples/3-phenylpropanal.mm1gp, bin/examples/acetylsalicylic_acid.gpMM, bin/examples/acetylsalicylic_acid.mm1gp, bin/examples/alpha-pinene.gpMM, bin/examples/alpha-pinene.mm1gp, bin/examples/bromobenzene.gpMM, bin/examples/bromobenzene.mm1gp, bin/examples/camphor.gpMM, bin/examples/camphor.mm1gp, bin/examples/cinnamaldehyde.gpMM, bin/examples/cinnamaldehyde.mm1gp, bin/examples/cis-2-pentene.gpMM, bin/examples/cis-2-pentene.mm1gp, bin/examples/cyclohexane.gpMM, bin/examples/cyclohexane.mm1gp, bin/examples/naphtalene.gpMM, bin/examples/naphtalene.mm1gp, src/common/guibase.cpp, src/common/guibase.h, src/common/mm1gui.cpp, src/common/mm1gui.h, src/common/qm1gui.cpp, src/common/qm1gui.h, src/common/qm2gui.cpp, src/common/qm2gui.h, src/target2/t2main.cpp, src/target3/t3dialog.cpp, src/target3/t3dialog.h, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h, src/target3/t3qm2gui.cpp, src/target3/t3qm2gui.h, src/target3/t3window.cpp, src/target3/t3window.h: added file dialogs for GNOME version, changed examples 2000-10-16 10:07 thassine * src/common/config.h: merged the patches from GH 2000-09-09 17:49 thassine * CHANGES, src/common/config.h, src/target1/Makefile: just a few minor changes 2000-09-09 15:17 thassine * BUGLIST, CHANGES, INSTALL, PROJECT, src/new.h, src/common/Makefile, src/common/qm2gui.cpp, src/target2/Makefile, src/target3/Makefile, src/target3/t3main.cpp, src/target3/t3mm1gui.cpp, src/target3/t3qm2gui.cpp, src/target3/t3qm2gui.h, src/target3/t3window.cpp: improvements in gt3. this is released as 0.2.2 2000-09-06 12:02 thassine * src/Makefile: made some changes in makefiles 2000-09-06 11:38 thassine * AUTHORS, BUGLIST, CHANGES, COPYING, INSTALL, PROJECT, bin/examples/2-chlorobutane.mm1gp, bin/examples/3-phenylpropanal.mm1gp, bin/examples/acetylsalicylic_acid.mm1gp, bin/examples/alpha-pinene.mm1gp, bin/examples/bromobenzene.mm1gp, bin/examples/camphor.mm1gp, bin/examples/cinnamaldehyde.mm1gp, bin/examples/cis-2-pentene.mm1gp, bin/examples/cyclohexane.mm1gp, bin/examples/naphtalene.mm1gp, bin/parameters/builder/amino.txt, bin/parameters/builder/nucleic.txt, bin/parameters/mm1param/stable/atomtypes.txt, bin/parameters/mm1param/stable/parameters1.txt, bin/parameters/mm1param/stable/parameters2.txt, bin/parameters/mm1param/stable/parameters3.txt, bin/parameters/mm1param/stable/parameters4.txt, bin/parameters/mm1param/stable/parameters5.txt, bin/parameters/mm1param/unstable/atomtypes.txt, bin/parameters/mm1param/unstable/parameters1.txt, bin/parameters/mm1param/unstable/parameters2.txt, bin/parameters/mm1param/unstable/parameters3.txt, bin/parameters/mm1param/unstable/parameters4.txt, bin/parameters/mm1param/unstable/parameters5.txt, src/Makefile, src/new.cpp, src/new.h, src/common/Makefile, src/common/color.h, src/common/config.h, src/common/guibase.cpp, src/common/guibase.h, src/common/matrix.h, src/common/mm1gui.cpp, src/common/mm1gui.h, src/common/mm1rbn.cpp, src/common/mm1rbn.h, src/common/mtools.cpp, src/common/mtools.h, src/common/notice.cpp, src/common/notice.h, src/common/objects.cpp, src/common/objects.h, src/common/plane.cpp, src/common/plane.h, src/common/qm1gui.cpp, src/common/qm1gui.h, src/common/qm2gui.cpp, src/common/qm2gui.h, src/common/spline.cpp, src/common/spline.h, src/common/surface.cpp, src/common/surface.h, src/common/viewing.cpp, src/common/viewing.h, src/common/window.cpp, src/common/window.h, src/target1/Makefile, src/target1/config.h, src/target1/t1main.cpp, src/target1/t1main.h, src/target2/Makefile, src/target2/config.h, src/target2/t2main.cpp, src/target2/t2main.h, src/target2/t2mm1gui.cpp, src/target2/t2mm1gui.h, src/target2/t2qm1gui.cpp, src/target2/t2qm1gui.h, src/target2/t2qm2gui.cpp, src/target2/t2qm2gui.h, src/target2/t2window.cpp, src/target2/t2window.h, src/target3/Makefile, src/target3/config.h, src/target3/t3dialog.cpp, src/target3/t3dialog.h, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h, src/target3/t3qm1gui.cpp, src/target3/t3qm1gui.h, src/target3/t3qm2gui.cpp, src/target3/t3qm2gui.h, src/target3/t3window.cpp, src/target3/t3window.h, src/target3/pixmaps/draw.xpm, src/target3/pixmaps/erase.xpm, src/target3/pixmaps/orb_xy.xpm, src/target3/pixmaps/orb_z.xpm, src/target3/pixmaps/rot_xy.xpm, src/target3/pixmaps/rot_z.xpm, src/target3/pixmaps/select.xpm, src/target3/pixmaps/trans_xy.xpm, src/target3/pixmaps/trans_z.xpm, src/target3/pixmaps/zoom.xpm: Initial revision 2000-09-06 11:38 thassine * AUTHORS, BUGLIST, CHANGES, COPYING, INSTALL, PROJECT, bin/examples/2-chlorobutane.mm1gp, bin/examples/3-phenylpropanal.mm1gp, bin/examples/acetylsalicylic_acid.mm1gp, bin/examples/alpha-pinene.mm1gp, bin/examples/bromobenzene.mm1gp, bin/examples/camphor.mm1gp, bin/examples/cinnamaldehyde.mm1gp, bin/examples/cis-2-pentene.mm1gp, bin/examples/cyclohexane.mm1gp, bin/examples/naphtalene.mm1gp, bin/parameters/builder/amino.txt, bin/parameters/builder/nucleic.txt, bin/parameters/mm1param/stable/atomtypes.txt, bin/parameters/mm1param/stable/parameters1.txt, bin/parameters/mm1param/stable/parameters2.txt, bin/parameters/mm1param/stable/parameters3.txt, bin/parameters/mm1param/stable/parameters4.txt, bin/parameters/mm1param/stable/parameters5.txt, bin/parameters/mm1param/unstable/atomtypes.txt, bin/parameters/mm1param/unstable/parameters1.txt, bin/parameters/mm1param/unstable/parameters2.txt, bin/parameters/mm1param/unstable/parameters3.txt, bin/parameters/mm1param/unstable/parameters4.txt, bin/parameters/mm1param/unstable/parameters5.txt, src/Makefile, src/new.cpp, src/new.h, src/common/Makefile, src/common/color.h, src/common/config.h, src/common/guibase.cpp, src/common/guibase.h, src/common/matrix.h, src/common/mm1gui.cpp, src/common/mm1gui.h, src/common/mm1rbn.cpp, src/common/mm1rbn.h, src/common/mtools.cpp, src/common/mtools.h, src/common/notice.cpp, src/common/notice.h, src/common/objects.cpp, src/common/objects.h, src/common/plane.cpp, src/common/plane.h, src/common/qm1gui.cpp, src/common/qm1gui.h, src/common/qm2gui.cpp, src/common/qm2gui.h, src/common/spline.cpp, src/common/spline.h, src/common/surface.cpp, src/common/surface.h, src/common/viewing.cpp, src/common/viewing.h, src/common/window.cpp, src/common/window.h, src/target1/Makefile, src/target1/config.h, src/target1/t1main.cpp, src/target1/t1main.h, src/target2/Makefile, src/target2/config.h, src/target2/t2main.cpp, src/target2/t2main.h, src/target2/t2mm1gui.cpp, src/target2/t2mm1gui.h, src/target2/t2qm1gui.cpp, src/target2/t2qm1gui.h, src/target2/t2qm2gui.cpp, src/target2/t2qm2gui.h, src/target2/t2window.cpp, src/target2/t2window.h, src/target3/Makefile, src/target3/config.h, src/target3/t3dialog.cpp, src/target3/t3dialog.h, src/target3/t3main.cpp, src/target3/t3main.h, src/target3/t3mm1gui.cpp, src/target3/t3mm1gui.h, src/target3/t3qm1gui.cpp, src/target3/t3qm1gui.h, src/target3/t3qm2gui.cpp, src/target3/t3qm2gui.h, src/target3/t3window.cpp, src/target3/t3window.h, src/target3/pixmaps/draw.xpm, src/target3/pixmaps/erase.xpm, src/target3/pixmaps/orb_xy.xpm, src/target3/pixmaps/orb_z.xpm, src/target3/pixmaps/rot_xy.xpm, src/target3/pixmaps/rot_z.xpm, src/target3/pixmaps/select.xpm, src/target3/pixmaps/trans_xy.xpm, src/target3/pixmaps/trans_z.xpm, src/target3/pixmaps/zoom.xpm: start : the initial version
distrib
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Mandriva
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10.0
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i586
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media
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contrib
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by-pkgid
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91e2cdb90b9e1ef9b484dbb91d4aae7a
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files
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6
