2009-08-10 11:22 thassine * po/LINGUAS, po/pt_BR.po, src/libghemical-features.h: translation pt_BR added (thanks to Ulisses) 2009-04-30 11:01 thassine * po/mk.po, po/sq.po, src/tab_mm_default.cpp: an AMBER-param error fixed. 2009-04-21 11:33 thassine * po/LINGUAS, po/POTFILES, po/POTFILES.in, po/fi.po, po/mk.po, po/sq.po, src/bond.cpp, src/bond.h, src/conjgrad.cpp, src/eng1_mm.cpp, src/eng1_qm_mopac.cpp, src/mfinder.cpp, src/model.cpp, src/seqbuild.cpp, src/seqbuild.h, src/typerule.cpp, src/utility.cpp: added translations mk + po ; translation fi updated. 2009-04-01 05:48 thassine * src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/intcrd.cpp, src/mfinder.cpp, src/model.cpp, src/pop_ana.cpp, src/sasaeval.cpp, src/sasaeval.h, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/typerule.cpp: added assertion_failed() method for fatal error reporting. 2008-12-09 10:41 thassine * INSTALL, po/Makefile.in, po/fi.po, src/atom.cpp, src/bond.cpp, src/chn_info.cpp, src/conjgrad.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp, src/engine.cpp, src/intcrd.cpp, src/libghemical-features.h, src/mfinder.cpp, src/model.cpp, src/notice.cpp, src/notice.h, src/pop_ana.cpp, src/sasaeval.cpp, src/sasaeval.h, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp: translations added ; Vlado Peshov. 2008-11-26 11:03 thassine * Makefile.am, Makefile.in, autogen.sh, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, po, po/LINGUAS, po/Makefile.in, po/Makefile.in.in, po/POTFILES, po/POTFILES.in, po/fi.po, po/stamp-it, src/Makefile.am, src/Makefile.in, src/libghemicalconfig.h.in, src/local_i18n.h, src/model.cpp: started adding gettext()-translations ; Vlado Peshov + others. 2008-11-18 19:19 thassine * src/simple_test/Makefile, src/simple_test/example1.cpp, src/simple_test/example1.h, src/simple_test/example2.cpp, src/simple_test/example2.h, src/simple_test/example3.cpp, src/simple_test/example3.h, src/simple_test/fileio.cpp, src/simple_test/streamio.cpp: the examples are now tested and updated ; TODO : example3 suffers from libghemical_init() output. 2008-10-22 09:41 thassine * INSTALL, Makefile.in, autogen.sh, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.in, src/libghemicalconfig.h.in, src/sasaeval.h, src/tab_mm_default.h: configuration update (Daniel Leidert) + minor fixes 2008-08-06 12:15 thassine * Makefile.am, Makefile.in, src/libghemical-features.h: added autogen.sh to EXTRA_DIST. 2008-08-01 06:56 thassine * Makefile.in, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.in: configuration fix. 2008-08-01 06:36 thassine * src/sasaeval.cpp, src/sasaeval.h: patched sasaeval to make it compile more reliably. 2008-07-31 10:29 thassine * configure, configure.ac, src/libghemical-features.h: forgot the releasedate 2008-07-31 10:06 thassine * configure, configure.ac, src/Makefile.am, src/Makefile.in, src/libghemical-features.h, src/typedef.h: version number changed to 2.98 2008-07-31 07:59 thassine * src/typedef.h: removed dependencies to GL/glut.h data types ; GL/gl.h data types dependency is optional. 2008-07-30 20:18 thassine * bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in: added Makefile.in files for clarity... 2008-07-30 20:11 thassine * bin/Makefile.in: added bin/Makefile.in 2008-07-30 20:10 thassine * src/Makefile.in: added src/Makefile.in for clarity. 2008-07-30 20:07 thassine * Makefile.in, configure, configure.ac, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h, src/utility.h, src/win32_hacks.cpp, src/win32_hacks.h: renamed AddAtom_lg() and GetClassName_lg() ; libghemical_init() added ; win32-related changes mostly. 2008-07-18 08:24 thassine * src/engine.cpp, src/engine.h, src/model.cpp, src/moldyn.cpp, src/moldyn.h: langevin dynamics is pulled out ; no applications so the implementation is not well tested... 2008-05-22 10:59 thassine * src/Makefile.am, src/engine.h, src/sasaeval.cpp, src/sasaeval.h: added a SASA evaluator ; transferred from the eng1_sf_cg.cpp file. 2008-04-28 12:11 thassine * src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/eng1_sf.h: some stuff renamed ; unfortunately this will affect ghemical as well... 2008-02-26 11:32 thassine * src/atom.cpp, src/chn_info.cpp, src/eng1_mm.cpp, src/eng1_qm_mopac.cpp, src/mfinder.cpp, src/model.cpp, src/notice.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp, src/win32_hacks.cpp: should now compile with g++ v4.3 2008-01-07 13:06 thassine * src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/chn_info.cpp, src/chn_info.h, src/conjgrad.cpp, src/conjgrad.h, src/constraint.cpp, src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp, src/eng1_sf_ua.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/libghemicaldefine.h, src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp, src/resonance.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/simple_test/example1.cpp, src/simple_test/example1.h, src/simple_test/example2.cpp, src/simple_test/example2.h, src/simple_test/example3.cpp, src/simple_test/example3.h, src/simple_test/fileio.cpp, src/simple_test/streamio.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h, src/v3d.h, src/win32_hacks.cpp, src/win32_hacks.h: copyright notice update 2008-01-07 11:28 thassine * autogen.sh, src/libghemicaldefine.h, src/model.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp: do not use NEWLINE anymore (but simply endl). autogen.sh update. 2007-10-24 08:43 thassine * src/moldyn.h: added a fix for gcc4 2007-10-09 06:10 thassine * configure.ac, src/Makefile.am, src/libghemical-features.h: fixed the libtool versioninfo 2007-09-21 09:59 thassine * bin/amber/Makefile.am, bin/amber/all_amino02.in, bin/amber/all_amino94_MOD.in, bin/amber/all_aminoct02.in, bin/amber/all_aminoct94.in, bin/amber/all_aminont02.in, bin/amber/all_aminont94.in, bin/amber/all_nuc02.in, bin/amber/all_nuc94_MOD.in, bin/amber/original, bin/amber/original/all_amino94.in, bin/amber/original/all_nuc94.in, bin/amber/original/frcmod.ff99SB, bin/amber/original/parm99.dat, bin/amber/parm99.dat, bin/amber/parm99_frcmod_ff99SB.dat, configure.ac, src/atom.h, src/libghemical-features.h, src/model.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/win32_hacks.cpp: commit 20070921 2007-05-04 09:23 thassine * src/tab_mm_default.cpp: an another set of AMBER checks/fixes ; should be OK now. 2007-05-03 09:04 thassine * bin/amber/all_nuc02.in, src/tab_mm_default.cpp: added more fixes for the AMBER forcefield 2007-04-30 10:51 thassine * src/libghemical-features.h, src/tab_mm_default.cpp: some AMBER atom type fixes added. 2007-03-13 08:54 thassine * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp: checked the nonbonded 1,4-scalings ; should be/have been ok ; debug stuff added. 2007-02-13 08:22 thassine * bin/builder/amino.txt, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h: changes in seq-builder and in engine classes. 2007-02-01 13:16 thassine * bin/builder/amino.txt, bin/builder/nucleic.txt, src/libghemical-features.h, src/seqbuild.cpp, src/seqbuild.h: some sequencebuilder tweaks. 2007-01-30 09:12 thassine * src/atom.h, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/intcrd.cpp, src/mfinder.cpp, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/typerule.cpp, src/utility.cpp: atom::cr_list is protected now ; model::UpdateChains() may ask nucl-acid detection skipped. 2007-01-25 10:17 thassine * src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/utility.h: added code for collecting energy components using atom groups. 2007-01-16 09:05 thassine * bin/builder/amino.txt, src/chn_info.h, src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp, src/model.h, src/seqbuild.h, src/tab_mm_prmfit.h, src/win32_hacks.h: various small changes. 2007-01-15 10:24 thassine * src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_qm_mm.h, src/engine.h, src/libghemical-features.h: changed the SetTorsionConstraint() method parameters. 2007-01-15 07:53 thassine * src/libghemical-features.h, src/model.cpp: changes for the win32 version. 2006-12-21 10:40 thassine * configure.ac, src/Makefile.am, src/eng1_mm.cpp, src/geomopt.h, src/libghemicaldefine.h, src/model.cpp, src/model.h, src/moldyn.h, src/search.cpp, src/win32_hacks.cpp, src/win32_hacks.h: minor changes + additions for win32 compilation. 2006-11-08 12:26 thassine * AUTHORS, configure.ac, libghemical.pc.in: some configuration fixes added (thanks Jean). 2006-10-31 10:48 thassine * src/atom.h: added a new atomflag ; the atomflag values below 256 should be internal (not saved). 2006-10-26 12:38 thassine * src/conjgrad.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/engine.cpp, src/search.cpp, src/search.h: TSS bugfixes added. 2006-10-24 12:21 thassine * src/stamp-h1.in, src/stamp-h2.in: removed unnecessary files. 2006-10-24 12:19 thassine * src/stamp-h2: removed unnecessary files. 2006-10-24 11:54 thassine * src/stamp-h1.in, src/stamp-h2.in: added the new files (libghemical-features.h)... 2006-10-24 11:52 thassine * src/stamp-h2: added the new files (libghemical-features.h)... 2006-10-24 11:50 thassine * src/libghemical-features.h, src/libghemical-features.h.in: added the new files (libghemical-features.h). 2006-10-24 11:48 thassine * configure.ac, src/Makefile.am, src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/chn_info.cpp, src/chn_info.h, src/conjgrad.cpp, src/conjgrad.h, src/constraint.cpp, src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp, src/eng1_sf_ua.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/libghemicalconfig.h.in, src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp, src/resonance.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h: libghemical-features.h implemented (thanks to Jean Brefort). 2006-10-19 12:16 thassine * src/Makefile.am: versioninfo added. 2006-10-11 10:47 thassine * src/engine.cpp, src/engine.h: added a method engine::ReadCRD() for looking at engine::crd. 2006-08-31 11:03 thassine * src/model.cpp, src/utility.cpp: minor bugfixes added + few comments. 2006-08-29 08:11 thassine * ChangeLog, src/seqbuild.cpp: changelog update 2006-08-28 12:22 thassine * src/chn_info.cpp, src/chn_info.h, src/seqbuild.cpp: fixed a memory bug. 2006-08-28 11:18 thassine * INSTALL, bin/builder/amino.txt, bin/builder/nucleic.txt, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/typedef.h: many changes at sequencebuilder 2006-08-07 12:28 thassine * ChangeLog, configure.ac, src/seqbuild.cpp, src/seqbuild.h: version number change 2006-08-07 11:49 thassine * .cvsignore, bin/.cvsignore, bin/amber/.cvsignore, bin/builder/.cvsignore, bin/param_mm/.cvsignore, bin/param_mm/default/.cvsignore, bin/param_mm/prmfit/.cvsignore, bin/param_mm/tripos52/.cvsignore, bin/param_sf/.cvsignore, bin/param_sf/default/.cvsignore, src/.cvsignore: removed the .cvsignore files. 2006-07-31 10:45 thassine * bin/param_mm/tripos52/atomtypes.txt, src/seqbuild.cpp, src/seqbuild.h: more changes at seqbuild code. 2006-07-24 11:40 thassine * bin/builder/amino.txt, configure.ac, src/Makefile.am, src/chn_info.cpp, src/chn_info.h, src/eng1_sf.cpp, src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/utility.cpp: the sequence builder code has been updated (no longer compatible with the old one. 2006-07-12 10:01 thassine * bin/builder/amino.txt, bin/builder/nucleic.txt, src/eng1_sf.cpp, src/seqbuild.cpp, src/seqbuild.h: changes in sequence-builder code and data files. 2006-04-24 12:02 thassine * configure.ac: changed version number after a release. 2006-04-24 12:00 thassine * ChangeLog, configure.ac: this is v2.00 2006-04-11 09:04 thassine * ChangeLog, INSTALL, configure.ac: this is v2.00rc1 2006-03-29 08:41 thassine * INSTALL, src/model.cpp: documentation update. 2006-03-28 16:19 hutchisn * src/model.cpp: Check for selected atoms before adding hydrogens. If the user has selected atoms, only add to those atoms. 2006-03-28 10:49 thassine * ., .cvsignore: cvsignore update. 2006-03-28 10:36 thassine * config.guess, config.sub, ltmain.sh: removed some unnecessary files. 2006-03-23 11:42 thassine * src/model.cpp: fixed a text string. 2006-03-22 13:01 thassine * src/model.cpp: a change in mol.dyn. 2006-03-22 12:21 thassine * src/Makefile.am, src/atom.cpp, src/atom.h, src/constraint.cpp, src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/engine.h, src/model.cpp, src/model.h: added (distance)constraints ; Donald Curtis. 2006-03-18 17:02 thassine * src/eng1_mm_default.cpp, src/model.cpp, src/moldyn.cpp: some mol.dyn. changes. 2006-03-14 13:47 thassine * src/moldyn.h: a few more mol.dyn. changes. 2006-03-14 08:45 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h, src/search.cpp, src/tab_mm_prmfit.cpp: added some mol.dyn. improvements ; some missing srand() calls added. 2006-03-10 12:12 thassine * src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.cpp, src/model.h: added a mopac/mpqc patch (Jean Br�fort), and a new Orient() method. 2006-03-08 10:33 thassine * ., .cvsignore, aclocal.m4, src/eng1_mm.cpp, src/engine.cpp: aclocal.m4 removed ; some mol.dyn. related changes added. 2006-03-07 13:42 thassine * aclocal.m4, src/engine.cpp: a bugfix for CheckLocations(). 2006-03-07 13:22 thassine * aclocal.m4, src/eng1_mm.cpp, src/engine.cpp, src/engine.h: CheckLocations() changed. 2006-03-07 10:49 thassine * aclocal.m4, autogen.sh, config.guess, config.sub, ltmain.sh: updated autogen.sh 2006-03-07 08:44 thassine * aclocal.m4, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/eng1_sf.h, src/engine.h, src/model.cpp: added engine::RequestNeighborListUpdate(). 2006-03-06 08:53 thassine * aclocal.m4, src/engine.h, src/model.cpp: added a method RequestUpdateTerms(). 2006-03-06 07:46 thassine * aclocal.m4, src/moldyn.cpp: a minor fix in mol.dyn. 2006-03-03 12:56 thassine * aclocal.m4, src/atom.cpp, src/atom.h: added Donald's freezed atom changes. 2006-03-03 12:24 thassine * ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, bin, bin/.cvsignore, bin/Makefile.in, bin/amber, bin/amber/.cvsignore, bin/amber/Makefile.in, bin/builder, bin/builder/.cvsignore, bin/builder/Makefile.in, bin/param_mm, bin/param_mm/.cvsignore, bin/param_mm/Makefile.in, bin/param_mm/default, bin/param_mm/default/.cvsignore, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit, bin/param_mm/prmfit/.cvsignore, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore, bin/param_mm/tripos52/Makefile.in, bin/param_sf, bin/param_sf/.cvsignore, bin/param_sf/Makefile.in, bin/param_sf/default, bin/param_sf/default/.cvsignore, bin/param_sf/default/Makefile.in, configure, src, src/.cvsignore, src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h: many changes ; especially at mol.dyn. code ; autogen.sh added 2006-03-01 12:15 thassine * aclocal.m4, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h: many changes in mol.dyn. code. 2006-02-28 12:14 thassine * aclocal.m4, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h: added cleanups/changes for virial/pressure calculations. 2006-02-27 11:25 thassine * aclocal.m4, src/eng1_mm.cpp, src/eng1_qm_mpqc.cpp, src/model.cpp, src/search.cpp, src/tab_mm_prmfit.cpp: tried to do a bit safer stringstream code ; only take the c_str out for copying into a buffer or for passing as a parameter. 2006-02-27 08:29 thassine * aclocal.m4, src/eng1_sf.h: a bugfix added... 2006-02-24 13:50 thassine * aclocal.m4, src/model.cpp: fixed a bug in box solvation. 2006-02-20 12:34 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, src/Makefile.in, src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/model.cpp, src/notice.cpp, src/search.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typedef.h: output-streams-code changed. 2006-02-17 19:14 hutchisn * ChangeLog, src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/model.cpp, src/moldyn.cpp, src/notice.cpp, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp: * src/*.cpp: Update to use stringstream and <sstream> headers -- fixes backwards-compatibility warnings using GCC. 2006-02-17 16:18 hutchisn * ChangeLog, Makefile.in, acinclude.m4, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, config.guess, config.sub, configure, depcomp, install-sh, ltmain.sh, missing, mkinstalldirs, src, src/.cvsignore, src/Makefile.in: * acinclude.m4: Fix underquoted macros to prevent warnings. * aclocal.m4, config.guess, config.sub, configure depcomp, install-sh, ltmain.sh, missing, mkinstalldirs */Makefile.in: Update with latest automake (1.9.6), libtool (1.5.22). 2006-02-16 09:20 thassine * aclocal.m4, config.guess, config.sub, ltmain.sh: configure updates. 2006-02-10 14:22 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, libghemical.pc.in, src/Makefile.am, src/Makefile.in, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp, src/libghemicalconfig.h.in, src/model.cpp, src/pop_ana.cpp, src/seqbuild.cpp, src/seqbuild.h, src/typedef.h, src/utility.cpp, src/utility.h, src/v3d.h: many changes... 2006-02-07 12:44 thassine * src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h: data hiding fixes ; no longer need to declare classes of the ghemical app as friend classes ; still no perfect but a good start. 2006-02-06 14:02 thassine * src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/geomopt.h, src/model.h, src/moldyn.h: fixed some friend statements ; these should be cleaned away in future... 2006-02-06 09:40 thassine * src/utility.cpp: some comments added. 2006-02-06 08:29 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/model.h: minor changes. 2006-01-19 13:38 thassine * src/eng1_sf.cpp, src/eng1_sf.h: removed some unnecessary changes. 2006-01-19 07:41 thassine * src/Makefile.am, src/Makefile.in, src/atom.h, src/bond.h, src/conjgrad.h, src/eng1_sf.cpp, src/eng1_sf.h, src/engine.h, src/intcrd.cpp, src/intcrd.h, src/libdefine.h, src/libghemicaldefine.h, src/model.cpp, src/model.h, src/notice.cpp, src/notice.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h: libdefine.h was renamed to libghemicaldefine.h 2005-12-14 14:10 thassine * src, src/.cvsignore: minor changes. 2005-11-29 10:54 thassine * src/geomopt.cpp: oops ; geomopt.cpp pathed wrong way. 2005-11-29 10:39 thassine * src/atom.h, src/geomopt.cpp, src/model.cpp, src/moldyn.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp: some changes in the atom flags ; need to separate the user/system level hidden atoms. 2005-11-17 12:31 thassine * src/eng1_sf.h: added an another table. 2005-11-17 11:56 thassine * src/eng1_sf.h: a new table was added for visualization params. 2005-11-10 10:00 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, ltmain.sh, src/Makefile.in: changed the version number into 1.92 after a release. 2005-11-02 12:24 thassine * configure, src/model.h: minor changes ; needed for the app. 2005-10-26 21:44 hutchisn * ., .cvsignore, ChangeLog, Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, config.guess, config.sub, configure, configure.ac, ltmain.sh, src, src/.cvsignore, src/Makefile.in: * configure.ac, configure: Update to use openbabel-2.0 check, rather than openbabel. * ltmain.sh, aclocal.m4, */Makefile.in: Update with latest autoconf, libtool (1.5.20). 2005-10-08 15:12 thassine * Makefile.in, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.in, src/atom.cpp, src/atom.h, src/libdefine.h, src/libghemicalconfig.h.in: OpenGL bugfixes on 64-bit platforms ; just a new value stored in atom objects 2005-09-26 08:46 thassine * src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp, src/eng1_sf_ua.h: oops! forgot to add some files... 2005-09-19 09:21 thassine * src/eng1_qm_mopac.cpp, src/search.cpp: minor tweaks ; now should compile with the FC4 compiler. 2005-08-24 09:55 thassine * src/Makefile.am, src/Makefile.in, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/model.cpp: removed the mm_sf model type. 2005-08-23 11:27 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/builder/amino.txt, bin/builder/nucleic.txt, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, depcomp, src/Makefile.am, src/Makefile.in, src/eng1_qm_mopac.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h: now depends on mopac7-1.10 ; also other smaller changes here and there. 2005-07-06 08:59 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.am, src/Makefile.in, src/atom.h, src/bond.h, src/conjgrad.h, src/eng1_mm.h, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.h, src/eng1_qm.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h, src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/intcrd.h, src/libconfig.h.in, src/libdefine.h, src/libghemicalconfig.h.in, src/model.h, src/moldyn.h, src/notice.h, src/pop_ana.h, src/resonance.h, src/search.h, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_prmfit.h, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.h, src/utility.h, src/v3d.h: config headers changed to avoid multiple PACKAGE definitions. 2005-07-05 08:01 thassine * INSTALL, Makefile.in, aclocal.m4, configure, configure.ac, src/Doxyfile, src/eng1_qm_mopac.cpp, src/libconfig.h.in: a fix for the f2c.h/g2c.h issue ported form libmopac7 ; tested to compile with g++-3.4 ok 2005-07-01 12:48 thassine * Makefile.in, src/atom.h, src/bond.h, src/conjgrad.h, src/eng1_mm.h, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.h, src/eng1_qm.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h, src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/intcrd.h, src/libdefine.h, src/model.h, src/moldyn.h, src/notice.h, src/pop_ana.h, src/resonance.h, src/search.h, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_prmfit.h, src/tab_mm_tripos52.h, src/typedef.h, src/utility.cpp, src/utility.h, src/v3d.h: some last-minute changes before release. 2005-07-01 10:49 thassine * ChangeLog, INSTALL, aclocal.m4, configure, configure.ac: did the final changes for a release 1.90. 2005-06-30 13:01 thassine * Makefile.in, acconfig.h, acinclude.m4, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, configure.in, libghemical.pc.in, src/Makefile.in, src/eng1_qm.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/libconfig.h.in: a lot of changes in configuration. 2005-06-23 13:19 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/engine.cpp, src/model.cpp, src/model.h: the lib/app interface changed. 2005-06-21 08:14 thassine * src/engine.h, src/geomopt.h, src/model.cpp, src/moldyn.cpp, src/moldyn.h, src/utility.cpp, src/utility.h: added some old fixes. 2005-06-20 13:07 thassine * src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp: disabled some options/features that are not yet usable. 2005-06-20 10:57 thassine * src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mpqc.cpp, src/seqbuild.h, src/typerule.cpp: added some older fixes. 2005-06-20 09:29 thassine * src/geomopt.h, src/model.cpp, src/model.h: minor changes related to app multithreading. 2005-06-14 10:23 thassine * src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h: started converting GO and MD into multithreaded versions. 2005-06-13 10:17 thassine * src/model.cpp, src/model.h: a complete multi-threaded Random Search added ; others will follow. 2005-06-13 07:13 thassine * config.guess, config.sub, ltmain.sh, src, src/.cvsignore, src/model.cpp, src/model.h, src/search.cpp, src/search.h: added an initial framework for multithreading. 2005-06-08 08:40 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/search.cpp: some formatting changes and a macro changed in eng1_sf.h 2005-05-11 15:14 thassine * src/atom.h, src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/model.h: minor changes ; added some friend definitions for the app. 2005-05-09 06:50 thassine * src/atom.h, src/moldyn.cpp, src/moldyn.h: an initial implementation for a LOCKED atom flag. 2005-05-06 10:05 thassine * src/atom.cpp, src/atom.h, src/model.cpp, src/model.h, src/search.cpp, src/seqbuild.cpp: a speed optimization in the CenterCRDSet() function. 2005-05-03 12:12 thassine * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/model.cpp: some bugfixes added for solvation functions. 2005-04-28 10:17 thassine * src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/engine.h, src/model.cpp: added an initial version for getting the energy in MM as its components. 2005-04-26 07:20 thassine * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h: some changes added in boundary potential code. 2005-04-22 13:41 thassine * Makefile.in, aclocal.m4, src/model.h: some class names changed in the app ; sync here. 2005-04-21 12:24 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.in, src/Makefile.in, src/libconfig.h.in, src/libdefine.h, src/notice.cpp, src/notice.h, src/simple_test/example1.cpp, src/simple_test/example2.cpp, src/simple_test/example3.cpp: made some changes in copyright notices for easier output in the application. 2005-04-19 12:23 thassine * src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/simple_test/example1.cpp, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h: some files were forgotten from the previous commits ; added them. 2005-04-19 12:20 thassine * Makefile.in, aclocal.m4, src/simple_test/Makefile, src/simple_test/example1.h, src/simple_test/example2.cpp, src/simple_test/example2.h, src/simple_test/example3.cpp, src/simple_test/example3.h, src/simple_test/example3_extra, src/simple_test/example3_extra/TestForm.html, src/simple_test/example3_extra/dumpdata.sh, src/simple_test/example3_extra/input_example, src/simple_test/example3_extra/printenv.sh, src/simple_test/st_main.cpp, src/simple_test/st_main.h, src/simple_test/streamio.cpp: updated the example(s) and added some new ones. 2005-04-19 08:48 thassine * Makefile.in, aclocal.m4, bin/README, bin/param_mm/Makefile.am, bin/param_mm/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore, bin/param_mm/tripos52/Makefile.am, bin/param_mm/tripos52/Makefile.in, bin/param_mm/tripos52/atomtypes.txt, bin/param_mm/tripos52/parameters1.txt, bin/param_mm/tripos52/parameters2.txt, bin/param_mm/tripos52/parameters3.txt, bin/param_mm/tripos52/parameters4.txt, bin/param_mm/tripos52/parameters5.txt, config.guess, config.sub, configure, configure.in, ltmain.sh, src/Makefile.am, src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/engine.h, src/libconfig.h.in, src/model.h: ported the tripos5.2 force field implementation from ghemical-1.01 into libghemical. 2005-04-08 14:59 thassine * src/model.cpp, src/model.h: added an utility function. 2005-03-21 12:52 thassine * src/Makefile.SIMPLE: added an alternative simple makefile in src/. 2005-02-08 07:12 thassine * src/conjgrad.cpp: some updates in conjgrad.cpp Simple linesearch. 2005-02-03 11:44 thassine * src/atom.h, src/bond.h, src/engine.cpp, src/search.cpp, src/typedef.h: minor changes to make it compile at FC3. 2005-01-19 11:29 thassine * Makefile.in, src/model.cpp, src/model.h: some minor changes for new stuff of my own ; not yet functional. 2005-01-04 11:28 thassine * aclocal.m4, src/engine.cpp, src/engine.h, src/moldyn.cpp: added a new virtual method DoSHAKE() in engine class. 2004-12-10 15:14 thassine * Makefile.in, aclocal.m4, configure, configure.in, src/eng1_qm_mopac.cpp, src/libconfig.h.in, src/model.h: small fixes added ; depends on libg2c only etc. 2004-09-13 09:17 thassine * Makefile.in, src/atom.cpp, src/atom.h, src/eng1_sf.h, src/model.cpp: the atom objects now are aware of the model object ; added some stuff to make everything compile. 2004-08-30 09:28 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, configure, configure.in: the include dir is changed into <prefix>/include/ghemical. 2004-08-27 12:07 thassine * Makefile.am, Makefile.in, aclocal.m4, libghemical.pc.in, src/Makefile.am, src/Makefile.in: changed includedir to /ghemical and some other changes ; .pc file not updated? 2004-08-26 12:34 thassine * aclocal.m4, configure, configure.in, src/Makefile.am, src/Makefile.in, src/Makefile.include, src/libconfig.h.in: added patches to configure/makefiles (Michael Banck). 2004-08-25 11:13 thassine * AUTHORS, aclocal.m4, bin, bin/.cvsignore, bin/amber, bin/amber/.cvsignore, bin/amber/Makefile.am, bin/amber/Makefile.in, bin/builder, bin/builder/.cvsignore, bin/builder/Makefile.am, bin/builder/Makefile.in, bin/param_mm, bin/param_mm/.cvsignore, bin/param_mm/Makefile.am, bin/param_mm/default, bin/param_mm/default/.cvsignore, bin/param_mm/default/Makefile.am, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit, bin/param_mm/prmfit/.cvsignore, bin/param_mm/prmfit/Makefile.am, bin/param_mm/prmfit/Makefile.in, bin/param_sf, bin/param_sf/.cvsignore, bin/param_sf/default, bin/param_sf/default/.cvsignore, bin/param_sf/default/Makefile.am, bin/param_sf/default/Makefile.in, config.guess, config.sub, configure, configure.in, ltmain.sh, src/Makefile.am, src/Makefile.in, src/Makefile.include, src/model.cpp: added automake-based configuration scripts (M. Banck and J. Brefort). 2004-08-13 12:14 thassine * CHANGES, ChangeLog, Makefile.am, Makefile.in, NEWS, README, acinclude.m4, aclocal.m4, bin/Makefile.am, bin/Makefile.in, bin/amber/Makefile.am, bin/amber/Makefile.in, bin/builder/Makefile.am, bin/builder/Makefile.in, bin/param_mm/Makefile.am, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.am, bin/param_mm/default/Makefile.in, bin/param_sf/Makefile.am, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.am, bin/param_sf/default/Makefile.in, configure, configure.in, ltmain.sh, missing, src/Makefile.am, src/Makefile.in, src/libconfig.h.in: added an improved configuration system (Michael Banck and Jean Brefort). 2004-06-07 19:54 hutchisn * src/atom.cpp: Updated with standardized element colors. 2004-05-28 15:10 thassine * src/typerule.cpp: some checks added to typerule class. 2004-05-13 11:45 thassine * acinclude.m4, aclocal.m4, configure, configure.in, libghemical.pc.in: some improvements in configure.in 2004-04-16 09:24 thassine * src/seqbuild.cpp: added a fix for TRP-residues in sequencebuilder::Identify(). 2004-04-08 10:13 thassine * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_qm_mopac.cpp, src/eng1_sf.cpp, src/eng2_mm_sf.cpp, src/eng2_qm_mm.cpp: fixed some compiler warnings. 2004-03-26 09:05 thassine * src/bond.cpp, src/bond.h, src/model.cpp, src/model.h: added a new GetRange() method for bonds in model class. 2004-03-18 12:04 thassine * src/model.cpp, src/resonance.h: minor changes in resonance_structures class (just a framework, under construction). 2004-03-15 13:01 thassine * src/typerule.cpp: implemented the fc=? test in the typerule class. 2004-03-09 08:44 thassine * src/model.cpp, src/model.h: added model::GetRS(). 2004-03-03 13:13 thassine * src/eng1_mm.cpp, src/engine.cpp, src/engine.h, src/simple_test/Makefile, src/simple_test/st_main.cpp: updated simple_test and other minor changes. 2004-02-18 11:47 thassine * Makefile.in, configure, configure.in, src/Makefile.in, src/libconfig.h.in, src/model.cpp: some tweaks/cleanups in configure/makefiles. 2004-01-28 08:56 thassine * libghemical.pc.in, src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp, src/resonance.h: added the .pc.in file, a simple QM population analysis code, and some framework for resonance structure determination (to be added later). 2004-01-28 08:53 thassine * Makefile.in, bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt, configure, configure.in, src/Makefile.in, src/atom.cpp, src/atom.h, src/eng1_qm_mopac.cpp, src/miniMOPAC, src/model.cpp, src/model.h: remove the mopac sources ; moved into a separate library. 2003-11-06 11:59 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/engine.h: added convert_crd for eng1_sf. 2003-09-24 06:47 thassine * src/conjgrad.cpp: minor improvements in conjgrad search. 2003-09-11 11:56 thassine * src/typerule.cpp, src/typerule.h: some changes in typerules. 2003-09-01 09:25 thassine * src/engine.cpp, src/engine.h, src/model.cpp, src/search.cpp: some bugfixes added. 2003-08-29 07:39 thassine * bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt: added a new set of mol.mech. parameters for testing ; less default force constants than in the prev. one. 2003-08-21 09:09 thassine * src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/engine.cpp, src/engine.h: some changes in bp (boundary potential) details. 2003-08-21 05:35 thassine * src/tab_mm_default.cpp: a bug related to out-of-plane terms is fixed. 2003-08-19 13:12 thassine * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/tab_mm_default.cpp: removed some type checks ; (temporarily). 2003-08-19 11:20 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h: the langevin switch works now better in GUI. 2003-08-18 12:58 thassine * src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp: changed the function switch value for angle bending term. 2003-08-14 09:51 thassine * bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, src/eng1_mm.cpp, src/eng1_mm_default.h, src/model.cpp: added a tool for exporting solvent boxes as gromacs input files. 2003-08-08 06:33 thassine * src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/model.cpp, src/model.h: some changes in Solvate???() functions and eng1_mm_default_mim. 2003-08-04 06:45 thassine * bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/default/parameters5.txt, bin/param_mm/default/parameters6.txt, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h: the new force field parameters added for testing; the old ones are tagged WITH_TRIPOS_FF 2003-07-29 13:41 thassine * src/model.h: some small changes due to changes in app. 2003-07-24 08:37 thassine * src/model.h: some changes added due to changes in the app. 2003-07-15 12:13 thassine * src/model.cpp, src/model.h: some changes added to model class (required by the app). 2003-07-11 11:56 thassine * AUTHORS, CHANGES, configure, src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/simple_test/fileio.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h: changed the copyright notices a bit; now its just the year when the file was created plus names of the authors. 2003-06-17 12:53 thassine * src/typerule.cpp: bugfixes added to the typerule class ; the next rule was not checked in many cases earlier. 2003-06-13 10:15 thassine * AUTHORS, acconfig.h, src/Doxyfile, src/eng1_sf.h, src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h, src/seqbuild.cpp: added more checks where/how the atom_list is sorted. that is important because sorting atom_list may change atom numbering (problem for example TSS). 2003-06-12 12:53 thassine * src/bond.cpp, src/bond.h, src/model.cpp, src/search.cpp, src/search.h: added improvements to transition_state_search ; should now work pretty well. 2003-06-11 10:40 thassine * src/conjgrad.cpp, src/conjgrad.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/model.cpp, src/search.cpp, src/search.h, src/utility.cpp: added transition_state_search and stationary_state_search + many related changes here and there. still need to do some testing, and after that add docs in user-docs and some example molecules. 2003-06-05 03:08 thassine * bin/param_mm/prmfit, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt, src/eng1_mm.cpp, src/model.cpp: added an initial version of the experimental FF parameters; for hydrocarbons only and still incomplete. 2003-06-02 15:20 thassine * src/eng1_mm.cpp, src/eng1_mm_prmfit.h, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: some changes in output at force fields and tabs. 2003-06-02 14:29 thassine * bin/builder/amino.txt, bin/builder/nucleic.txt, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp, src/typerule.h: some changes in MM force fields. 2003-05-21 14:32 thassine * src/eng1_mm_prmfit.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: added misc changes in mol mech stuff. 2003-05-19 07:05 thassine * src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/model.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: many changes in MM force fields/tables; the AMBER implementation should be OK now. 2003-05-16 10:20 thassine * bin/param_mm/default/parameters6.txt: changes to MM force field ; added one input file. 2003-05-16 10:19 thassine * bin/param_mm/default/parameters4.txt, bin/param_mm/default/parameters5.txt, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/model.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: changes to MM force field ; need to make it AMBER-compatible. 2003-05-12 09:11 thassine * src/eng1_sf.h: minor changes to ribbon, etc. 2003-04-29 10:14 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/utility.cpp: many changes; now AddHydrogens() is more compatible with seq-builder and forcefield. 2003-04-25 10:20 thassine * bin/param_mm/default/parameters5.txt, src/atom.cpp, src/atom.h, src/eng1_mm.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h: added an option to molecular mechanics, so that one can use AMBER forcefield charges/parameters for amino/nucleic acids. charges are OK now but other params not yet added. the option is very nifty about correctness of topology, but that will be fixed later. 2003-04-17 07:34 thassine * src/model.cpp, src/seqbuild.cpp: setup objects were not deleted, causing MOPAC to leave some files around and also memory leaking; fixed now. 2003-04-16 13:43 thassine * src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp, src/moldyn.cpp, src/moldyn.h, src/tab_mm_default.cpp: many small changes (including trajectory writing). 2003-04-10 13:49 thassine * src/libconfig.h.in: only whitespace changed. 2003-04-10 12:50 thassine * src/bond.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.h, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp: many changes in molmech tables and parameters (not ready yet). 2003-04-10 12:48 thassine * Makefile.in, configure, configure.in, src/libconfig.h.in: configuration files updated. 2003-04-10 12:46 thassine * bin/amber, bin/amber/README, bin/amber/all_amino02.in, bin/amber/all_aminoct02.in, bin/amber/all_aminont02.in, bin/amber/all_nuc02.in, bin/amber/parm99.dat, bin/builder/amino.txt, bin/builder/nucleic.txt: changes/additions in data files. 2003-04-02 06:12 thassine * src/atom.cpp, src/atom.h, src/eng1_sf.cpp, src/seqbuild.cpp, src/utility.cpp: some changes/additions in the atom class. 2003-03-18 10:08 thassine * src/eng1_sf.cpp, src/eng1_sf.h: just minor rearrangements. 2003-03-17 10:13 thassine * src/eng1_sf.cpp: added a notice about solvation model (not yet automatically set). 2003-03-17 10:11 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h: a bugfix for ribbons added, and some changes in moldyn. 2003-03-12 07:19 thassine * src/eng1_sf.cpp: just some cleanups in comments etc. 2003-03-11 14:22 thassine * src/model.cpp: added the frame_save_frq variable to model::DoMoldyn() 2003-03-11 07:58 thassine * src/model.h: ooops; a function was missing. 2003-03-07 10:39 thassine * src/simple_test, src/simple_test/Makefile, src/simple_test/example_file.gpr, src/simple_test/fileio.cpp, src/simple_test/st_main.cpp, src/simple_test/st_main.h: added a simple test suite (with a Makefile of it's own). 2003-02-14 10:56 thassine * src/eng1_sf.cpp: slight changes in output. 2003-02-14 07:59 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h: many molecular-dynamics-related changes. 2003-02-11 14:44 thassine * src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h: sf will (later) support both implicit and explicit solvation model; work started now. 2003-02-08 07:35 thassine * src/atom.h, src/bond.cpp, src/bond.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_qm_mm.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/tab_mm_default.cpp: make separate subclasses for boundary-potential and periodic-boundary eng-classes; also some comments added etc. 2003-02-06 14:50 thassine * bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters5.txt, src/atom.h, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.h, src/tab_mm_default.cpp: many changes (computations-related). 2003-02-03 09:50 thassine * bin/param_mm/default/parameters5.txt, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/model.cpp, src/model.h, src/moldyn.cpp, src/tab_mm_default.cpp: some changes to MM force field parameters (for H2O) and some important bugfixes in MM connectivity records code; this will affect nonbonded interactions. 2003-01-31 12:24 thassine * src/engine.cpp, src/geomopt.cpp, src/model.h, src/moldyn.cpp, src/utility.cpp, src/utility.h: many bugfixes added; it is important to note that model::GetAtomCount() may now be different from engine::GetAtomCount(). 2003-01-31 09:25 thassine * src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp: an important bugfix was added to engine::engine(); also some minor fixes. 2003-01-30 16:31 thassine * src/eng1_sf.cpp, src/eng1_sf.h: several fixes to SF; should now work more or less again. 2003-01-30 14:14 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp: many changes in SF. 2003-01-30 08:29 thassine * src/Makefile.in, src/atom.cpp, src/atom.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h: many changes in the way how data is stored in different models; compiles but SF-stuff does not work yet; QM and MM should work. 2003-01-27 13:43 thassine * src/atom.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/utility.cpp: many changes in the way how the setup classes work (not even ready yet but compiles and qm/mm works). 2003-01-24 08:01 thassine * src/seqbuild.cpp: a fix to sequence-builder: identify now also includes H atoms to residues that it detects, so that selecting by chain/residue now works as expected. 2003-01-23 12:55 thassine * src/atom.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h: some improvements to seqbuilder. 2003-01-22 11:09 thassine * src, src/.cvsignore: minor cleanups. 2003-01-22 09:25 thassine * src/eng1_mm_prmfit.h: minor cleanups. 2003-01-22 09:11 thassine * src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: some cleanups, again. 2003-01-22 08:28 thassine * src/typedef.h: added a missing file 2003-01-22 08:28 thassine * src/model.cpp, src/model.h: minor cleanups. 2003-01-22 07:18 thassine * Makefile.in, src/Makefile.in, src/eng1_sf.cpp, src/libdefine.h, src/model.cpp, src/model.h, src/notice.cpp, src/notice.h, src/seqbuild.cpp, src/tab_mm_default.cpp: now also make install works. 2003-01-21 11:42 thassine * src/eng2_qm_mm.h, src/errutil.cpp, src/errutil.h, src/libdefine.h: various improvements... 2003-01-21 11:19 thassine * Makefile.in, configure, configure.in, src/Makefile.in, src/atom.h, src/bond.h, src/config.h.in, src/conjgrad.h, src/define.h, src/eng1_mm.h, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_qm.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h, src/engine.h, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/libconfig.h.in, src/libdefine.h, src/model.cpp, src/model.h, src/moldyn.h, src/notice.cpp, src/notice.h, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_prmfit.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h, src/v3d.h: many improvements added but make install does not work yet. 2003-01-20 14:05 thassine * configure, src/engine.h: minor fixes; not ready yet... 2003-01-20 08:38 thassine * ., .cvsignore, AUTHORS, CHANGES, COPYING, INSTALL, Makefile.in, TODO, acconfig.h, aclocal.m4, bin, bin/.cvsignore, bin/builder, bin/builder/amino.txt, bin/builder/nucleic.txt, bin/param_mm, bin/param_mm/default, bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/default/parameters5.txt, bin/param_sf, bin/param_sf/default, bin/param_sf/default/loopdip.txt, bin/param_sf/default/looptor.txt, bin/param_sf/default/nonbonded.txt, config.guess, config.sub, configure, configure.in, install-sh, libghemical.spec, mkinstalldirs, src, src/.cvsignore, src/Doxyfile, src/Makefile.in, src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/config.h.in, src/conjgrad.cpp, src/conjgrad.h, src/define.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/errutil.cpp, src/errutil.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/miniMOPAC, src/miniMOPAC/.cvsignore, src/miniMOPAC/Makefile.in, src/miniMOPAC/README, src/miniMOPAC/aababc.c, src/miniMOPAC/addfck.c, src/miniMOPAC/addhcr.c, src/miniMOPAC/addnuc.c, src/miniMOPAC/analyt.c, src/miniMOPAC/anavib.c, src/miniMOPAC/axis.c, src/miniMOPAC/block.c, src/miniMOPAC/bonds.c, src/miniMOPAC/brlzon.c, src/miniMOPAC/btoc.c, src/miniMOPAC/calpar.c, src/miniMOPAC/capcor.c, src/miniMOPAC/cdiag.c, src/miniMOPAC/chrge.c, src/miniMOPAC/cnvg.c, src/miniMOPAC/compfg.c, src/miniMOPAC/config.log, src/miniMOPAC/consts.c, src/miniMOPAC/cqden.c, src/miniMOPAC/datin.c, src/miniMOPAC/dcart.c, src/miniMOPAC/delmol.c, src/miniMOPAC/delri.c, src/miniMOPAC/denrot.c, src/miniMOPAC/densit.c, src/miniMOPAC/depvar.c, src/miniMOPAC/deri0.c, src/miniMOPAC/deri1.c, src/miniMOPAC/deri2.c, src/miniMOPAC/deri21.c, src/miniMOPAC/deri22.c, src/miniMOPAC/deri23.c, src/miniMOPAC/deritr.c, src/miniMOPAC/deriv.c, src/miniMOPAC/dernvo.c, src/miniMOPAC/ders.c, src/miniMOPAC/dfock2.c, src/miniMOPAC/dfpsav.c, src/miniMOPAC/dgemm.c, src/miniMOPAC/dgemv.c, src/miniMOPAC/dger.c, src/miniMOPAC/dgetf2.c, src/miniMOPAC/dgetrf.c, src/miniMOPAC/dgetri.c, src/miniMOPAC/diag.c, src/miniMOPAC/diat.c, src/miniMOPAC/diat2.c, src/miniMOPAC/diegrd.c, src/miniMOPAC/dielen.c, src/miniMOPAC/diis.c, src/miniMOPAC/dijkl1.c, src/miniMOPAC/dijkl2.c, src/miniMOPAC/dipind.c, src/miniMOPAC/dipole.c, src/miniMOPAC/dlaswp.c, src/miniMOPAC/dofs.c, src/miniMOPAC/dot.c, src/miniMOPAC/drc.c, src/miniMOPAC/drcout.c, src/miniMOPAC/dtrmm.c, src/miniMOPAC/dtrmv.c, src/miniMOPAC/dtrsm.c, src/miniMOPAC/dtrti2.c, src/miniMOPAC/dtrtri.c, src/miniMOPAC/dvfill.c, src/miniMOPAC/ef.c, src/miniMOPAC/enpart.c, src/miniMOPAC/esp.c, src/miniMOPAC/etime.c, src/miniMOPAC/exchng.c, src/miniMOPAC/fdate.c, src/miniMOPAC/ffhpol.c, src/miniMOPAC/flepo.c, src/miniMOPAC/fmat.c, src/miniMOPAC/fock1.c, src/miniMOPAC/fock2.c, src/miniMOPAC/force.c, src/miniMOPAC/formxy.c, src/miniMOPAC/forsav.c, src/miniMOPAC/fortran, src/miniMOPAC/fortran/SIZES, src/miniMOPAC/fortran/aababc.f, 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src/miniMOPAC/fortran/deritr.f, src/miniMOPAC/fortran/deriv.f, src/miniMOPAC/fortran/dernvo.f, src/miniMOPAC/fortran/ders.f, src/miniMOPAC/fortran/dfock2.f, src/miniMOPAC/fortran/dfpsav.f, src/miniMOPAC/fortran/dgemm.f, src/miniMOPAC/fortran/dgemv.f, src/miniMOPAC/fortran/dger.f, src/miniMOPAC/fortran/dgetf2.f, src/miniMOPAC/fortran/dgetrf.f, src/miniMOPAC/fortran/dgetri.f, src/miniMOPAC/fortran/diag.f, src/miniMOPAC/fortran/diat.f, src/miniMOPAC/fortran/diat2.f, src/miniMOPAC/fortran/diegrd.f, src/miniMOPAC/fortran/dielen.f, src/miniMOPAC/fortran/diis.f, src/miniMOPAC/fortran/dijkl1.f, src/miniMOPAC/fortran/dijkl2.f, src/miniMOPAC/fortran/dipind.f, src/miniMOPAC/fortran/dipole.f, src/miniMOPAC/fortran/dlaswp.f, src/miniMOPAC/fortran/dofs.f, src/miniMOPAC/fortran/dot.f, src/miniMOPAC/fortran/drc.f, src/miniMOPAC/fortran/drcout.f, src/miniMOPAC/fortran/dtrmm.f, src/miniMOPAC/fortran/dtrmv.f, src/miniMOPAC/fortran/dtrsm.f, src/miniMOPAC/fortran/dtrti2.f, src/miniMOPAC/fortran/dtrtri.f, 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src/miniMOPAC/fortran/wrttxt.f, src/miniMOPAC/fortran/xerbla.f, src/miniMOPAC/fortran/xyzint.f, src/miniMOPAC/frame.c, src/miniMOPAC/freqcy.c, src/miniMOPAC/geout.c, src/miniMOPAC/geoutg.c, src/miniMOPAC/getgeg.c, src/miniMOPAC/getgeo.c, src/miniMOPAC/getsym.c, src/miniMOPAC/gettxt.c, src/miniMOPAC/gmetry.c, src/miniMOPAC/gover.c, src/miniMOPAC/greenf.c, src/miniMOPAC/grid.c, src/miniMOPAC/h1elec.c, src/miniMOPAC/haddon.c, src/miniMOPAC/hcore.c, src/miniMOPAC/helect.c, src/miniMOPAC/hqrii.c, src/miniMOPAC/ijkl.c, src/miniMOPAC/ilaenv.c, src/miniMOPAC/initsv.c, src/miniMOPAC/interp.c, src/miniMOPAC/iter.c, src/miniMOPAC/jcarin.c, src/miniMOPAC/linmin.c, src/miniMOPAC/local.c, src/miniMOPAC/locmin.c, src/miniMOPAC/lsame.c, src/miniMOPAC/makpol.c, src/miniMOPAC/mamult.c, src/miniMOPAC/matou1.c, src/miniMOPAC/matout.c, src/miniMOPAC/matpak.c, src/miniMOPAC/meci.c, src/miniMOPAC/mecid.c, src/miniMOPAC/mecih.c, src/miniMOPAC/mecip.c, src/miniMOPAC/minimopac.c, src/miniMOPAC/moldat.c, src/miniMOPAC/molval.c, src/miniMOPAC/mullik.c, src/miniMOPAC/mult.c, src/miniMOPAC/nllsq.c, src/miniMOPAC/nuchar.c, src/miniMOPAC/parsav.c, src/miniMOPAC/partxy.c, src/miniMOPAC/pathk.c, src/miniMOPAC/paths.c, src/miniMOPAC/perm.c, src/miniMOPAC/polar.c, src/miniMOPAC/powsav.c, src/miniMOPAC/powsq.c, src/miniMOPAC/prtdrc.c, src/miniMOPAC/quadr.c, src/miniMOPAC/react1.c, src/miniMOPAC/reada.c, src/miniMOPAC/readmo.c, src/miniMOPAC/refer.c, src/miniMOPAC/repp.c, src/miniMOPAC/rotat.c, src/miniMOPAC/rotate.c, src/miniMOPAC/rsp.c, src/miniMOPAC/search.c, src/miniMOPAC/second.c, src/miniMOPAC/setupg.c, src/miniMOPAC/solrot.c, src/miniMOPAC/swap.c, src/miniMOPAC/sympro.c, src/miniMOPAC/symtry.c, src/miniMOPAC/symtrz.c, src/miniMOPAC/thermo.c, src/miniMOPAC/timer.c, src/miniMOPAC/timout.c, src/miniMOPAC/update.c, src/miniMOPAC/upsurf.c, src/miniMOPAC/vecprt.c, src/miniMOPAC/writmo.c, src/miniMOPAC/wrtkey.c, src/miniMOPAC/wrttxt.c, src/miniMOPAC/xerbla.c, src/miniMOPAC/xyzint.c, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h, src/v3d.h: Initial revision 2003-01-20 08:38 * branches, tags, .: New repository initialized by cvs2svn.
