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Revision 245 - Directory Listing
Modified Wed Oct 12 18:00:37 2011 UTC (6 years, 1 month ago) by thassine
update the Changelog
Revision 244 - Directory Listing
Modified Wed Oct 12 17:52:47 2011 UTC (6 years, 1 month ago) by thassine
finally release the version 3
Revision 243 - Directory Listing
Modified Wed Sep 14 16:49:25 2011 UTC (6 years, 2 months ago) by thassine
add german translation + configuration scripts updated.
Revision 242 - Directory Listing
Modified Mon Nov 2 15:02:08 2009 UTC (8 years ago) by thassine
russian translation added.
Revision 241 - Directory Listing
Modified Fri Sep 11 12:51:40 2009 UTC (8 years, 2 months ago) by thassine
version 2.99.1 released due to a missing file.
Revision 240 - Directory Listing
Modified Fri Sep 4 12:41:29 2009 UTC (8 years, 2 months ago) by thassine
ChangeLog update
Revision 239 - Directory Listing
Modified Fri Sep 4 12:28:47 2009 UTC (8 years, 2 months ago) by thassine
release the version 2.99.1
Revision 238 - Directory Listing
Modified Mon Aug 10 11:22:37 2009 UTC (8 years, 3 months ago) by thassine
translation pt_BR added (thanks to Ulisses)
Revision 237 - Directory Listing
Modified Thu Apr 30 11:01:36 2009 UTC (8 years, 6 months ago) by thassine
an AMBER-param error fixed.
Revision 236 - Directory Listing
Modified Tue Apr 21 11:33:01 2009 UTC (8 years, 6 months ago) by thassine
added translations mk + po ; translation fi updated.
Revision 235 - Directory Listing
Modified Wed Apr 1 05:48:39 2009 UTC (8 years, 7 months ago) by thassine
added assertion_failed() method for fatal error reporting.
Revision 234 - Directory Listing
Modified Tue Dec 9 10:41:48 2008 UTC (8 years, 11 months ago) by thassine
translations added ; Vlado Peshov.
Revision 233 - Directory Listing
Modified Wed Nov 26 11:03:38 2008 UTC (8 years, 11 months ago) by thassine
started adding gettext()-translations ; Vlado Peshov + others.
Revision 232 - Directory Listing
Modified Tue Nov 18 19:19:20 2008 UTC (9 years ago) by thassine
the examples are now tested and updated ; TODO : example3 suffers from libghemical_init() output.
Revision 231 - Directory Listing
Modified Wed Oct 22 09:41:03 2008 UTC (9 years ago) by thassine
configuration update (Daniel Leidert) + minor fixes
Revision 230 - Directory Listing
Modified Wed Aug 6 12:15:28 2008 UTC (9 years, 3 months ago) by thassine
added autogen.sh to EXTRA_DIST.
Revision 229 - Directory Listing
Modified Fri Aug 1 06:56:10 2008 UTC (9 years, 3 months ago) by thassine
configuration fix.
Revision 228 - Directory Listing
Modified Fri Aug 1 06:36:41 2008 UTC (9 years, 3 months ago) by thassine
patched sasaeval to make it compile more reliably.
Revision 227 - Directory Listing
Modified Thu Jul 31 10:29:34 2008 UTC (9 years, 3 months ago) by thassine
forgot the releasedate
Revision 226 - Directory Listing
Modified Thu Jul 31 10:06:12 2008 UTC (9 years, 3 months ago) by thassine
version number changed to 2.98
Revision 225 - Directory Listing
Modified Thu Jul 31 07:59:43 2008 UTC (9 years, 3 months ago) by thassine
removed dependencies to GL/glut.h data types ; GL/gl.h data types dependency is optional.
Revision 224 - Directory Listing
Modified Wed Jul 30 20:18:59 2008 UTC (9 years, 3 months ago) by thassine
added Makefile.in files for clarity...
Revision 223 - Directory Listing
Modified Wed Jul 30 20:11:53 2008 UTC (9 years, 3 months ago) by thassine
added bin/Makefile.in
Revision 222 - Directory Listing
Modified Wed Jul 30 20:10:33 2008 UTC (9 years, 3 months ago) by thassine
added src/Makefile.in for clarity.
Revision 221 - Directory Listing
Modified Wed Jul 30 20:07:42 2008 UTC (9 years, 3 months ago) by thassine
renamed AddAtom_lg() and GetClassName_lg() ; libghemical_init() added ; win32-related changes mostly.
Revision 220 - Directory Listing
Modified Fri Jul 18 08:24:08 2008 UTC (9 years, 4 months ago) by thassine
langevin dynamics is pulled out ; no applications so the implementation is not well tested...
Revision 219 - Directory Listing
Modified Thu May 22 10:59:40 2008 UTC (9 years, 5 months ago) by thassine
added a SASA evaluator ; transferred from the eng1_sf_cg.cpp file.
Revision 218 - Directory Listing
Modified Mon Apr 28 12:11:17 2008 UTC (9 years, 6 months ago) by thassine
some stuff renamed ; unfortunately this will affect ghemical as well...
Revision 217 - Directory Listing
Modified Tue Feb 26 11:32:13 2008 UTC (9 years, 8 months ago) by thassine
should now compile with g++ v4.3
Revision 216 - Directory Listing
Modified Mon Jan 7 13:06:54 2008 UTC (9 years, 10 months ago) by thassine
copyright notice update
Revision 215 - Directory Listing
Modified Mon Jan 7 11:28:25 2008 UTC (9 years, 10 months ago) by thassine
do not use NEWLINE anymore (but simply endl). autogen.sh update.
Revision 214 - Directory Listing
Modified Wed Oct 24 08:43:52 2007 UTC (10 years ago) by thassine
added a fix for gcc4
Revision 213 - Directory Listing
Modified Tue Oct 9 06:10:36 2007 UTC (10 years, 1 month ago) by thassine
fixed the libtool versioninfo
Revision 212 - Directory Listing
Modified Fri Sep 21 09:59:49 2007 UTC (10 years, 1 month ago) by thassine
commit 20070921
Revision 211 - Directory Listing
Modified Fri May 4 09:23:38 2007 UTC (10 years, 6 months ago) by thassine
an another set of AMBER checks/fixes ; should be OK now.
Revision 210 - Directory Listing
Modified Thu May 3 09:04:29 2007 UTC (10 years, 6 months ago) by thassine
added more fixes for the AMBER forcefield
Revision 209 - Directory Listing
Modified Mon Apr 30 10:51:16 2007 UTC (10 years, 6 months ago) by thassine
some AMBER atom type fixes added.
Revision 208 - Directory Listing
Modified Tue Mar 13 08:54:36 2007 UTC (10 years, 8 months ago) by thassine
checked the nonbonded 1,4-scalings ; should be/have been ok ; debug stuff added.
Revision 207 - Directory Listing
Modified Tue Feb 13 08:22:29 2007 UTC (10 years, 9 months ago) by thassine
changes in seq-builder and in engine classes.
Revision 206 - Directory Listing
Modified Thu Feb 1 13:16:07 2007 UTC (10 years, 9 months ago) by thassine
some sequencebuilder tweaks.
Revision 205 - Directory Listing
Modified Tue Jan 30 09:12:50 2007 UTC (10 years, 9 months ago) by thassine
atom::cr_list is protected now ; model::UpdateChains() may ask nucl-acid detection skipped.
Revision 204 - Directory Listing
Modified Thu Jan 25 10:17:08 2007 UTC (10 years, 9 months ago) by thassine
added code for collecting energy components using atom groups.
Revision 203 - Directory Listing
Modified Tue Jan 16 09:05:26 2007 UTC (10 years, 10 months ago) by thassine
various small changes.
Revision 202 - Directory Listing
Modified Mon Jan 15 10:24:20 2007 UTC (10 years, 10 months ago) by thassine
changed the SetTorsionConstraint() method parameters.
Revision 201 - Directory Listing
Modified Mon Jan 15 07:53:53 2007 UTC (10 years, 10 months ago) by thassine
changes for the win32 version.
Revision 200 - Directory Listing
Modified Thu Dec 21 10:40:14 2006 UTC (10 years, 10 months ago) by thassine
minor changes + additions for win32 compilation.
Revision 199 - Directory Listing
Modified Wed Nov 8 12:26:37 2006 UTC (11 years ago) by thassine
some configuration fixes added (thanks Jean).
Revision 198 - Directory Listing
Modified Tue Oct 31 10:48:51 2006 UTC (11 years ago) by thassine
added a new atomflag ; the atomflag values below 256 should be internal (not saved).
Revision 197 - Directory Listing
Modified Thu Oct 26 12:38:48 2006 UTC (11 years ago) by thassine
TSS bugfixes added.
Revision 196 - Directory Listing
Modified Tue Oct 24 12:21:38 2006 UTC (11 years ago) by thassine
removed unnecessary files.
Revision 195 - Directory Listing
Modified Tue Oct 24 12:19:21 2006 UTC (11 years ago) by thassine
removed unnecessary files.
Revision 194 - Directory Listing
Modified Tue Oct 24 11:54:05 2006 UTC (11 years ago) by thassine
added the new files (libghemical-features.h)...
Revision 193 - Directory Listing
Modified Tue Oct 24 11:52:32 2006 UTC (11 years ago) by thassine
added the new files (libghemical-features.h)...
Revision 192 - Directory Listing
Modified Tue Oct 24 11:50:27 2006 UTC (11 years ago) by thassine
added the new files (libghemical-features.h).
Revision 191 - Directory Listing
Modified Tue Oct 24 11:48:28 2006 UTC (11 years ago) by thassine
libghemical-features.h implemented (thanks to Jean Brefort).
Revision 190 - Directory Listing
Modified Thu Oct 19 12:16:25 2006 UTC (11 years, 1 month ago) by thassine
versioninfo added.
Revision 189 - Directory Listing
Modified Wed Oct 11 10:47:22 2006 UTC (11 years, 1 month ago) by thassine
added a method engine::ReadCRD() for looking at engine::crd.
Revision 188 - Directory Listing
Modified Thu Aug 31 11:03:45 2006 UTC (11 years, 2 months ago) by thassine
minor bugfixes added + few comments.
Revision 187 - Directory Listing
Modified Tue Aug 29 08:11:13 2006 UTC (11 years, 2 months ago) by thassine
changelog update
Revision 186 - Directory Listing
Modified Mon Aug 28 12:22:02 2006 UTC (11 years, 2 months ago) by thassine
fixed a memory bug.
Revision 185 - Directory Listing
Modified Mon Aug 28 11:18:40 2006 UTC (11 years, 2 months ago) by thassine
many changes at sequencebuilder
Revision 184 - Directory Listing
Modified Mon Aug 7 12:28:59 2006 UTC (11 years, 3 months ago) by thassine
version number change
Revision 183 - Directory Listing
Modified Mon Aug 7 11:49:27 2006 UTC (11 years, 3 months ago) by thassine
removed the .cvsignore files.
Revision 182 - Directory Listing
Modified Mon Jul 31 10:45:13 2006 UTC (11 years, 3 months ago) by thassine
more changes at seqbuild code.
Revision 181 - Directory Listing
Modified Mon Jul 24 11:40:49 2006 UTC (11 years, 3 months ago) by thassine
the sequence builder code has been updated (no longer compatible with the old one.
Revision 180 - Directory Listing
Modified Wed Jul 12 10:01:20 2006 UTC (11 years, 4 months ago) by thassine
changes in sequence-builder code and data files.
Revision 179 - Directory Listing
Modified Mon Apr 24 12:02:16 2006 UTC (11 years, 6 months ago) by thassine
changed version number after a release.

Revision 178 - Directory Listing
Modified Mon Apr 24 12:00:16 2006 UTC (11 years, 6 months ago) by thassine
this is v2.00

Revision 177 - Directory Listing
Modified Tue Apr 11 09:04:43 2006 UTC (11 years, 7 months ago) by thassine
this is v2.00rc1

Revision 176 - Directory Listing
Modified Wed Mar 29 08:41:31 2006 UTC (11 years, 7 months ago) by thassine
documentation update.

Revision 175 - Directory Listing
Modified Tue Mar 28 16:19:50 2006 UTC (11 years, 7 months ago) by hutchisn
Check for selected atoms before adding hydrogens. If the user has selected atoms,
only add to those atoms.

Revision 174 - Directory Listing
Modified Tue Mar 28 10:49:35 2006 UTC (11 years, 7 months ago) by thassine
cvsignore update.

Revision 173 - Directory Listing
Modified Tue Mar 28 10:36:15 2006 UTC (11 years, 7 months ago) by thassine
removed some unnecessary files.

Revision 172 - Directory Listing
Modified Thu Mar 23 11:42:05 2006 UTC (11 years, 7 months ago) by thassine
fixed a text string.

Revision 171 - Directory Listing
Modified Wed Mar 22 13:01:27 2006 UTC (11 years, 8 months ago) by thassine
a change in mol.dyn.

Revision 170 - Directory Listing
Modified Wed Mar 22 12:21:23 2006 UTC (11 years, 8 months ago) by thassine
added (distance)constraints ; Donald Curtis.

Revision 169 - Directory Listing
Modified Sat Mar 18 17:02:07 2006 UTC (11 years, 8 months ago) by thassine
some mol.dyn. changes.

Revision 168 - Directory Listing
Modified Tue Mar 14 13:47:26 2006 UTC (11 years, 8 months ago) by thassine
a few more mol.dyn. changes.

Revision 167 - Directory Listing
Modified Tue Mar 14 08:45:47 2006 UTC (11 years, 8 months ago) by thassine
added some mol.dyn. improvements ; some missing srand() calls added.

Revision 166 - Directory Listing
Modified Fri Mar 10 12:12:45 2006 UTC (11 years, 8 months ago) by thassine
added a mopac/mpqc patch (Jean Br�fort), and a new Orient() method.

Revision 165 - Directory Listing
Modified Wed Mar 8 10:33:13 2006 UTC (11 years, 8 months ago) by thassine
aclocal.m4 removed ; some mol.dyn. related changes added.

Revision 164 - Directory Listing
Modified Tue Mar 7 13:42:56 2006 UTC (11 years, 8 months ago) by thassine
a bugfix for CheckLocations().

Revision 163 - Directory Listing
Modified Tue Mar 7 13:22:49 2006 UTC (11 years, 8 months ago) by thassine
CheckLocations() changed.

Revision 162 - Directory Listing
Modified Tue Mar 7 10:49:57 2006 UTC (11 years, 8 months ago) by thassine
updated autogen.sh

Revision 161 - Directory Listing
Modified Tue Mar 7 08:44:00 2006 UTC (11 years, 8 months ago) by thassine
added engine::RequestNeighborListUpdate().

Revision 160 - Directory Listing
Modified Mon Mar 6 08:53:00 2006 UTC (11 years, 8 months ago) by thassine
added a method RequestUpdateTerms().

Revision 159 - Directory Listing
Modified Mon Mar 6 07:46:16 2006 UTC (11 years, 8 months ago) by thassine
a minor fix in mol.dyn.

Revision 158 - Directory Listing
Modified Fri Mar 3 12:56:25 2006 UTC (11 years, 8 months ago) by thassine
added Donald's freezed atom changes.

Revision 157 - Directory Listing
Modified Fri Mar 3 12:24:26 2006 UTC (11 years, 8 months ago) by thassine
many changes ; especially at mol.dyn. code ; autogen.sh added

Revision 156 - Directory Listing
Modified Wed Mar 1 12:15:04 2006 UTC (11 years, 8 months ago) by thassine
many changes in mol.dyn. code.

Revision 155 - Directory Listing
Modified Tue Feb 28 12:14:14 2006 UTC (11 years, 8 months ago) by thassine
added cleanups/changes for virial/pressure calculations.

Revision 154 - Directory Listing
Modified Mon Feb 27 11:25:55 2006 UTC (11 years, 8 months ago) by thassine
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.

Revision 153 - Directory Listing
Modified Mon Feb 27 08:29:27 2006 UTC (11 years, 8 months ago) by thassine
a bugfix added...

Revision 152 - Directory Listing
Modified Fri Feb 24 13:50:43 2006 UTC (11 years, 8 months ago) by thassine
fixed a bug in box solvation.

Revision 151 - Directory Listing
Modified Mon Feb 20 12:34:50 2006 UTC (11 years, 8 months ago) by thassine
output-streams-code changed.

Revision 150 - Directory Listing
Modified Fri Feb 17 19:14:53 2006 UTC (11 years, 9 months ago) by hutchisn
        * src/*.cpp: Update to use stringstream and <sstream> headers --
        fixes backwards-compatibility warnings using GCC.

Revision 149 - Directory Listing
Modified Fri Feb 17 16:18:52 2006 UTC (11 years, 9 months ago) by hutchisn
        * 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).

Revision 148 - Directory Listing
Modified Thu Feb 16 09:20:39 2006 UTC (11 years, 9 months ago) by thassine
configure updates.

Revision 147 - Directory Listing
Modified Fri Feb 10 14:22:17 2006 UTC (11 years, 9 months ago) by thassine
many changes...

Revision 146 - Directory Listing
Modified Tue Feb 7 12:44:10 2006 UTC (11 years, 9 months ago) by thassine
data hiding fixes ; no longer need to declare classes of the ghemical app as friend classes ; still no perfect but a good start.

Revision 145 - Directory Listing
Modified Mon Feb 6 14:02:09 2006 UTC (11 years, 9 months ago) by thassine
fixed some friend statements ; these should be cleaned away in future...

Revision 144 - Directory Listing
Modified Mon Feb 6 09:40:32 2006 UTC (11 years, 9 months ago) by thassine
some comments added.

Revision 143 - Directory Listing
Modified Mon Feb 6 08:29:10 2006 UTC (11 years, 9 months ago) by thassine
minor changes.

Revision 142 - Directory Listing
Modified Thu Jan 19 13:38:04 2006 UTC (11 years, 10 months ago) by thassine
removed some unnecessary changes.

Revision 141 - Directory Listing
Modified Thu Jan 19 07:41:22 2006 UTC (11 years, 10 months ago) by thassine
libdefine.h was renamed to libghemicaldefine.h

Revision 140 - Directory Listing
Modified Wed Dec 14 14:10:16 2005 UTC (11 years, 11 months ago) by thassine
minor changes.

Revision 139 - Directory Listing
Modified Tue Nov 29 10:54:35 2005 UTC (11 years, 11 months ago) by thassine
oops ; geomopt.cpp pathed wrong way.

Revision 138 - Directory Listing
Modified Tue Nov 29 10:39:31 2005 UTC (11 years, 11 months ago) by thassine
some changes in the atom flags ; need to separate the user/system level hidden atoms.

Revision 137 - Directory Listing
Modified Thu Nov 17 12:31:05 2005 UTC (12 years ago) by thassine
added an another table.

Revision 136 - Directory Listing
Modified Thu Nov 17 11:56:16 2005 UTC (12 years ago) by thassine
a new table was added for visualization params.

Revision 135 - Directory Listing
Modified Thu Nov 10 10:00:49 2005 UTC (12 years ago) by thassine
changed the version number into 1.92 after a release.

Revision 134 - Directory Listing
Modified Wed Nov 2 12:24:56 2005 UTC (12 years ago) by thassine
minor changes ; needed for the app.

Revision 133 - Directory Listing
Modified Wed Oct 26 21:44:33 2005 UTC (12 years ago) by hutchisn
        * 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).

Revision 131 - Directory Listing
Modified Sat Oct 8 15:12:27 2005 UTC (12 years, 1 month ago) by thassine
OpenGL bugfixes on 64-bit platforms ; just a new value stored in atom objects

Revision 130 - Directory Listing
Modified Mon Sep 26 08:46:49 2005 UTC (12 years, 1 month ago) by thassine
oops! forgot to add some files...

Revision 129 - Directory Listing
Modified Mon Sep 19 09:21:34 2005 UTC (12 years, 2 months ago) by thassine
minor tweaks ; now should compile with the FC4 compiler.

Revision 128 - Directory Listing
Modified Wed Aug 24 09:55:12 2005 UTC (12 years, 2 months ago) by thassine
removed the mm_sf model type.

Revision 127 - Directory Listing
Modified Tue Aug 23 11:27:50 2005 UTC (12 years, 2 months ago) by thassine
now depends on mopac7-1.10 ; also other smaller changes here and there.

Revision 126 - Directory Listing
Modified Wed Jul 6 08:59:11 2005 UTC (12 years, 4 months ago) by thassine
config headers changed to avoid multiple PACKAGE definitions.

Revision 125 - Directory Listing
Modified Tue Jul 5 08:01:39 2005 UTC (12 years, 4 months ago) by thassine
a fix for the f2c.h/g2c.h issue ported form libmopac7 ; tested to compile with g++-3.4 ok

Revision 124 - Directory Listing
Modified Fri Jul 1 12:48:35 2005 UTC (12 years, 4 months ago) by thassine
some last-minute changes before release.

Revision 123 - Directory Listing
Modified Fri Jul 1 10:49:03 2005 UTC (12 years, 4 months ago) by thassine
did the final changes for a release 1.90.

Revision 122 - Directory Listing
Modified Thu Jun 30 13:01:29 2005 UTC (12 years, 4 months ago) by thassine
a lot of changes in configuration.

Revision 121 - Directory Listing
Modified Thu Jun 23 13:19:17 2005 UTC (12 years, 4 months ago) by thassine
the lib/app interface changed.

Revision 120 - Directory Listing
Modified Tue Jun 21 08:14:27 2005 UTC (12 years, 5 months ago) by thassine
added some old fixes.

Revision 119 - Directory Listing
Modified Mon Jun 20 13:07:09 2005 UTC (12 years, 5 months ago) by thassine
disabled some options/features that are not yet usable.

Revision 118 - Directory Listing
Modified Mon Jun 20 10:57:36 2005 UTC (12 years, 5 months ago) by thassine
added some older fixes.

Revision 117 - Directory Listing
Modified Mon Jun 20 09:29:45 2005 UTC (12 years, 5 months ago) by thassine
minor changes related to app multithreading.

Revision 116 - Directory Listing
Modified Tue Jun 14 10:23:27 2005 UTC (12 years, 5 months ago) by thassine
started converting GO and MD into multithreaded versions.

Revision 115 - Directory Listing
Modified Mon Jun 13 10:17:32 2005 UTC (12 years, 5 months ago) by thassine
a complete multi-threaded Random Search added ; others will follow.

Revision 114 - Directory Listing
Modified Mon Jun 13 07:13:53 2005 UTC (12 years, 5 months ago) by thassine
added an initial framework for multithreading.

Revision 113 - Directory Listing
Modified Wed Jun 8 08:40:11 2005 UTC (12 years, 5 months ago) by thassine
some formatting changes and a macro changed in eng1_sf.h

Revision 112 - Directory Listing
Modified Wed May 11 15:14:44 2005 UTC (12 years, 6 months ago) by thassine
minor changes ; added some friend definitions for the app.

Revision 111 - Directory Listing
Modified Mon May 9 06:50:40 2005 UTC (12 years, 6 months ago) by thassine
an initial implementation for a LOCKED atom flag.

Revision 110 - Directory Listing
Modified Fri May 6 10:05:49 2005 UTC (12 years, 6 months ago) by thassine
a speed optimization in the CenterCRDSet() function.

Revision 109 - Directory Listing
Modified Tue May 3 12:12:58 2005 UTC (12 years, 6 months ago) by thassine
some bugfixes added for solvation functions.

Revision 108 - Directory Listing
Modified Thu Apr 28 10:17:04 2005 UTC (12 years, 6 months ago) by thassine
added an initial version for getting the energy in MM as its components.

Revision 107 - Directory Listing
Modified Tue Apr 26 07:20:39 2005 UTC (12 years, 6 months ago) by thassine
some changes added in boundary potential code.

Revision 106 - Directory Listing
Modified Fri Apr 22 13:41:55 2005 UTC (12 years, 6 months ago) by thassine
some class names changed in the app ; sync here.

Revision 105 - Directory Listing
Modified Thu Apr 21 12:24:11 2005 UTC (12 years, 7 months ago) by thassine
made some changes in copyright notices for easier output in the application.

Revision 104 - Directory Listing
Modified Tue Apr 19 12:23:05 2005 UTC (12 years, 7 months ago) by thassine
some files were forgotten from the previous commits ; added them.

Revision 103 - Directory Listing
Modified Tue Apr 19 12:20:57 2005 UTC (12 years, 7 months ago) by thassine
updated the example(s) and added some new ones.

Revision 102 - Directory Listing
Modified Tue Apr 19 08:48:52 2005 UTC (12 years, 7 months ago) by thassine
ported the tripos5.2 force field implementation from ghemical-1.01 into libghemical.

Revision 101 - Directory Listing
Modified Fri Apr 8 14:59:13 2005 UTC (12 years, 7 months ago) by thassine
added an utility function.

Revision 100 - Directory Listing
Modified Mon Mar 21 12:52:08 2005 UTC (12 years, 8 months ago) by thassine
added an alternative simple makefile in src/.

Revision 99 - Directory Listing
Modified Tue Feb 8 07:12:11 2005 UTC (12 years, 9 months ago) by thassine
some updates in conjgrad.cpp Simple linesearch.

Revision 98 - Directory Listing
Modified Thu Feb 3 11:44:35 2005 UTC (12 years, 9 months ago) by thassine
minor changes to make it compile at FC3.

Revision 97 - Directory Listing
Modified Wed Jan 19 11:29:41 2005 UTC (12 years, 10 months ago) by thassine
some minor changes for new stuff of my own ; not yet functional.

Revision 96 - Directory Listing
Modified Tue Jan 4 11:28:37 2005 UTC (12 years, 10 months ago) by thassine
added a new virtual method DoSHAKE() in engine class.

Revision 95 - Directory Listing
Modified Fri Dec 10 15:14:25 2004 UTC (12 years, 11 months ago) by thassine
small fixes added ; depends on libg2c only etc.

Revision 94 - Directory Listing
Modified Mon Sep 13 09:17:54 2004 UTC (13 years, 2 months ago) by thassine
the atom objects now are aware of the model object ; added some stuff to make everything compile.

Revision 93 - Directory Listing
Modified Mon Aug 30 09:28:14 2004 UTC (13 years, 2 months ago) by thassine
the include dir is changed into <prefix>/include/ghemical.

Revision 92 - Directory Listing
Modified Fri Aug 27 12:07:46 2004 UTC (13 years, 2 months ago) by thassine
changed includedir to /ghemical and some other changes ; .pc file not updated?

Revision 91 - Directory Listing
Modified Thu Aug 26 12:34:57 2004 UTC (13 years, 2 months ago) by thassine
added patches to configure/makefiles (Michael Banck).

Revision 90 - Directory Listing
Modified Wed Aug 25 11:13:43 2004 UTC (13 years, 2 months ago) by thassine
added automake-based configuration scripts (M. Banck and J. Brefort).

Revision 89 - Directory Listing
Modified Fri Aug 13 12:14:50 2004 UTC (13 years, 3 months ago) by thassine
added an improved configuration system (Michael Banck and Jean Brefort).

Revision 88 - Directory Listing
Modified Mon Jun 7 19:54:55 2004 UTC (13 years, 5 months ago) by hutchisn
Updated with standardized element colors.

Revision 87 - Directory Listing
Modified Fri May 28 15:10:52 2004 UTC (13 years, 5 months ago) by thassine
some checks added to typerule class.

Revision 86 - Directory Listing
Modified Thu May 13 11:45:27 2004 UTC (13 years, 6 months ago) by thassine
some improvements in configure.in

Revision 85 - Directory Listing
Modified Fri Apr 16 09:24:42 2004 UTC (13 years, 7 months ago) by thassine
added a fix for TRP-residues in sequencebuilder::Identify().

Revision 84 - Directory Listing
Modified Thu Apr 8 10:13:35 2004 UTC (13 years, 7 months ago) by thassine
fixed some compiler warnings.

Revision 83 - Directory Listing
Modified Fri Mar 26 09:05:24 2004 UTC (13 years, 7 months ago) by thassine
added a new GetRange() method for bonds in model class.

Revision 82 - Directory Listing
Modified Thu Mar 18 12:04:44 2004 UTC (13 years, 8 months ago) by thassine
minor changes in resonance_structures class (just a framework, under construction).

Revision 81 - Directory Listing
Modified Mon Mar 15 13:01:13 2004 UTC (13 years, 8 months ago) by thassine
implemented the fc=? test in the typerule class.

Revision 80 - Directory Listing
Modified Tue Mar 9 08:44:38 2004 UTC (13 years, 8 months ago) by thassine
added model::GetRS().

Revision 79 - Directory Listing
Modified Wed Mar 3 13:13:25 2004 UTC (13 years, 8 months ago) by thassine
updated simple_test and other minor changes.

Revision 78 - Directory Listing
Modified Wed Feb 18 11:47:46 2004 UTC (13 years, 9 months ago) by thassine
some tweaks/cleanups in configure/makefiles.

Revision 77 - Directory Listing
Modified Wed Jan 28 08:56:18 2004 UTC (13 years, 9 months ago) by thassine
added the .pc.in file, a simple QM population analysis code, and some framework for resonance structure determination (to be added later).

Revision 76 - Directory Listing
Modified Wed Jan 28 08:53:57 2004 UTC (13 years, 9 months ago) by thassine
remove the mopac sources ; moved into a separate library.

Revision 75 - Directory Listing
Modified Thu Nov 6 11:59:50 2003 UTC (14 years ago) by thassine
added convert_crd for eng1_sf.

Revision 74 - Directory Listing
Modified Wed Sep 24 06:47:29 2003 UTC (14 years, 1 month ago) by thassine
minor improvements in conjgrad search.

Revision 73 - Directory Listing
Modified Thu Sep 11 11:56:26 2003 UTC (14 years, 2 months ago) by thassine
some changes in typerules.

Revision 72 - Directory Listing
Modified Mon Sep 1 09:25:51 2003 UTC (14 years, 2 months ago) by thassine
some bugfixes added.

Revision 71 - Directory Listing
Modified Fri Aug 29 07:39:55 2003 UTC (14 years, 2 months ago) by thassine
added a new set of mol.mech. parameters for testing ; less default force constants than in the prev. one.

Revision 70 - Directory Listing
Modified Thu Aug 21 09:09:45 2003 UTC (14 years, 3 months ago) by thassine
some changes in bp (boundary potential) details.

Revision 69 - Directory Listing
Modified Thu Aug 21 05:35:54 2003 UTC (14 years, 3 months ago) by thassine
a bug related to out-of-plane terms is fixed.

Revision 68 - Directory Listing
Modified Tue Aug 19 13:12:04 2003 UTC (14 years, 3 months ago) by thassine
removed some type checks ; (temporarily).

Revision 67 - Directory Listing
Modified Tue Aug 19 11:20:56 2003 UTC (14 years, 3 months ago) by thassine
the langevin switch works now better in GUI.

Revision 66 - Directory Listing
Modified Mon Aug 18 12:58:07 2003 UTC (14 years, 3 months ago) by thassine
changed the function switch value for angle bending term.

Revision 65 - Directory Listing
Modified Thu Aug 14 09:51:55 2003 UTC (14 years, 3 months ago) by thassine
added a tool for exporting solvent boxes as gromacs input files.

Revision 64 - Directory Listing
Modified Fri Aug 8 06:33:09 2003 UTC (14 years, 3 months ago) by thassine
some changes in Solvate???() functions and eng1_mm_default_mim.

Revision 63 - Directory Listing
Modified Mon Aug 4 06:45:17 2003 UTC (14 years, 3 months ago) by thassine
the new force field parameters added for testing; the old ones are tagged WITH_TRIPOS_FF

Revision 61 - Directory Listing
Modified Tue Jul 29 13:41:03 2003 UTC (14 years, 3 months ago) by thassine
some small changes due to changes in app.

Revision 60 - Directory Listing
Modified Thu Jul 24 08:37:47 2003 UTC (14 years, 3 months ago) by thassine
some changes added due to changes in the app.

Revision 59 - Directory Listing
Modified Tue Jul 15 12:13:43 2003 UTC (14 years, 4 months ago) by thassine
some changes added to model class (required by the app).

Revision 58 - Directory Listing
Modified Fri Jul 11 11:56:51 2003 UTC (14 years, 4 months ago) by thassine
changed the copyright notices a bit; now its just the year when the file was created plus names of the authors.

Revision 57 - Directory Listing
Modified Tue Jun 17 12:53:33 2003 UTC (14 years, 5 months ago) by thassine
bugfixes added to the typerule class ; the next rule was not checked in many cases earlier.

Revision 56 - Directory Listing
Modified Fri Jun 13 10:15:44 2003 UTC (14 years, 5 months ago) by thassine
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).

Revision 55 - Directory Listing
Modified Thu Jun 12 12:53:21 2003 UTC (14 years, 5 months ago) by thassine
added improvements to transition_state_search ; should now work pretty well.

Revision 54 - Directory Listing
Modified Wed Jun 11 10:40:07 2003 UTC (14 years, 5 months ago) by thassine
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.

Revision 53 - Directory Listing
Modified Thu Jun 5 03:08:15 2003 UTC (14 years, 5 months ago) by thassine
added an initial version of the experimental FF parameters; for hydrocarbons only and still incomplete.

Revision 52 - Directory Listing
Modified Mon Jun 2 15:20:39 2003 UTC (14 years, 5 months ago) by thassine
some changes in output at force fields and tabs.

Revision 51 - Directory Listing
Modified Mon Jun 2 14:29:48 2003 UTC (14 years, 5 months ago) by thassine
some changes in MM force fields.

Revision 50 - Directory Listing
Modified Wed May 21 14:32:22 2003 UTC (14 years, 6 months ago) by thassine
added misc changes in mol mech stuff.

Revision 49 - Directory Listing
Modified Mon May 19 07:05:47 2003 UTC (14 years, 6 months ago) by thassine
many changes in MM force fields/tables; the AMBER implementation should be OK now.

Revision 48 - Directory Listing
Modified Fri May 16 10:20:05 2003 UTC (14 years, 6 months ago) by thassine
changes to MM force field ; added one input file.

Revision 47 - Directory Listing
Modified Fri May 16 10:19:11 2003 UTC (14 years, 6 months ago) by thassine
changes to MM force field ; need to make it AMBER-compatible.

Revision 46 - Directory Listing
Modified Mon May 12 09:11:04 2003 UTC (14 years, 6 months ago) by thassine
minor changes to ribbon, etc.

Revision 45 - Directory Listing
Modified Tue Apr 29 10:14:25 2003 UTC (14 years, 6 months ago) by thassine
many changes; now AddHydrogens() is more compatible with seq-builder and forcefield.

Revision 44 - Directory Listing
Modified Fri Apr 25 10:20:24 2003 UTC (14 years, 6 months ago) by thassine
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.

Revision 43 - Directory Listing
Modified Thu Apr 17 07:34:31 2003 UTC (14 years, 7 months ago) by thassine
setup objects were not deleted, causing MOPAC to leave some files around and also memory leaking; fixed now.

Revision 42 - Directory Listing
Modified Wed Apr 16 13:43:57 2003 UTC (14 years, 7 months ago) by thassine
many small changes (including trajectory writing).

Revision 41 - Directory Listing
Modified Thu Apr 10 13:49:09 2003 UTC (14 years, 7 months ago) by thassine
only whitespace changed.

Revision 40 - Directory Listing
Modified Thu Apr 10 12:50:28 2003 UTC (14 years, 7 months ago) by thassine
many changes in molmech tables and parameters (not ready yet).

Revision 39 - Directory Listing
Modified Thu Apr 10 12:48:02 2003 UTC (14 years, 7 months ago) by thassine
configuration files updated.

Revision 38 - Directory Listing
Modified Thu Apr 10 12:46:04 2003 UTC (14 years, 7 months ago) by thassine
changes/additions in data files.

Revision 37 - Directory Listing
Modified Wed Apr 2 06:12:24 2003 UTC (14 years, 7 months ago) by thassine
some changes/additions in the atom class.

Revision 36 - Directory Listing
Modified Tue Mar 18 10:08:46 2003 UTC (14 years, 8 months ago) by thassine
just minor rearrangements.

Revision 35 - Directory Listing
Modified Mon Mar 17 10:13:10 2003 UTC (14 years, 8 months ago) by thassine
added a notice about solvation model (not yet automatically set).

Revision 34 - Directory Listing
Modified Mon Mar 17 10:11:31 2003 UTC (14 years, 8 months ago) by thassine
a bugfix for ribbons added, and some changes in moldyn.

Revision 33 - Directory Listing
Modified Wed Mar 12 07:19:02 2003 UTC (14 years, 8 months ago) by thassine
just some cleanups in comments etc.

Revision 32 - Directory Listing
Modified Tue Mar 11 14:22:44 2003 UTC (14 years, 8 months ago) by thassine
added the frame_save_frq variable to model::DoMoldyn()

Revision 31 - Directory Listing
Modified Tue Mar 11 07:58:00 2003 UTC (14 years, 8 months ago) by thassine
ooops; a function was missing.

Revision 30 - Directory Listing
Modified Fri Mar 7 10:39:37 2003 UTC (14 years, 8 months ago) by thassine
added a simple test suite (with a Makefile of it's own).

Revision 29 - Directory Listing
Modified Fri Feb 14 10:56:39 2003 UTC (14 years, 9 months ago) by thassine
slight changes in output.

Revision 28 - Directory Listing
Modified Fri Feb 14 07:59:50 2003 UTC (14 years, 9 months ago) by thassine
many molecular-dynamics-related changes.

Revision 27 - Directory Listing
Modified Tue Feb 11 14:44:02 2003 UTC (14 years, 9 months ago) by thassine
sf will (later) support both implicit and explicit solvation model; work started now.

Revision 26 - Directory Listing
Modified Sat Feb 8 07:35:19 2003 UTC (14 years, 9 months ago) by thassine
make separate subclasses for boundary-potential and periodic-boundary eng-classes; also some comments added etc.

Revision 25 - Directory Listing
Modified Thu Feb 6 14:50:40 2003 UTC (14 years, 9 months ago) by thassine
many changes (computations-related).

Revision 24 - Directory Listing
Modified Mon Feb 3 09:50:54 2003 UTC (14 years, 9 months ago) by thassine
some changes to MM force field parameters (for H2O) and some important bugfixes in MM connectivity records code; this will affect nonbonded interactions.

Revision 23 - Directory Listing
Modified Fri Jan 31 12:24:13 2003 UTC (14 years, 9 months ago) by thassine
many bugfixes added; it is important to note that model::GetAtomCount() may now be different from engine::GetAtomCount().

Revision 22 - Directory Listing
Modified Fri Jan 31 09:25:44 2003 UTC (14 years, 9 months ago) by thassine
an important bugfix was added to engine::engine(); also some minor fixes.

Revision 21 - Directory Listing
Modified Thu Jan 30 16:31:51 2003 UTC (14 years, 9 months ago) by thassine
several fixes to SF; should now work more or less again.

Revision 20 - Directory Listing
Modified Thu Jan 30 14:14:29 2003 UTC (14 years, 9 months ago) by thassine
many changes in SF.

Revision 19 - Directory Listing
Modified Thu Jan 30 08:29:39 2003 UTC (14 years, 9 months ago) by thassine
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.

Revision 18 - Directory Listing
Modified Mon Jan 27 13:43:20 2003 UTC (14 years, 9 months ago) by thassine
many changes in the way how the setup classes work (not even ready yet but compiles and qm/mm works).

Revision 17 - Directory Listing
Modified Fri Jan 24 08:01:37 2003 UTC (14 years, 9 months ago) by thassine
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.

Revision 16 - Directory Listing
Modified Thu Jan 23 12:55:02 2003 UTC (14 years, 9 months ago) by thassine
some improvements to seqbuilder.

Revision 15 - Directory Listing
Modified Wed Jan 22 11:09:53 2003 UTC (14 years, 9 months ago) by thassine
minor cleanups.

Revision 14 - Directory Listing
Modified Wed Jan 22 09:25:04 2003 UTC (14 years, 9 months ago) by thassine
minor cleanups.

Revision 13 - Directory Listing
Modified Wed Jan 22 09:11:30 2003 UTC (14 years, 9 months ago) by thassine
some cleanups, again.

Revision 12 - Directory Listing
Modified Wed Jan 22 08:28:58 2003 UTC (14 years, 9 months ago) by thassine
added a missing file

Revision 11 - Directory Listing
Modified Wed Jan 22 08:28:00 2003 UTC (14 years, 9 months ago) by thassine
minor cleanups.

Revision 10 - Directory Listing
Modified Wed Jan 22 07:18:27 2003 UTC (14 years, 9 months ago) by thassine
now also make install works.

Revision 9 - Directory Listing
Modified Tue Jan 21 11:42:10 2003 UTC (14 years, 10 months ago) by thassine
various improvements...

Revision 8 - Directory Listing
Modified Tue Jan 21 11:19:37 2003 UTC (14 years, 10 months ago) by thassine
many improvements added but make install does not work yet.

Revision 7 - Directory Listing
Modified Mon Jan 20 14:05:00 2003 UTC (14 years, 10 months ago) by thassine
minor fixes; not ready yet...

Revision 2 - Directory Listing
Modified Mon Jan 20 08:38:46 2003 UTC (14 years, 10 months ago) by thassine
Initial revision

Revision 1 - Directory Listing
Added Mon Jan 20 08:38:46 2003 UTC (14 years, 10 months ago) by (unknown author)
New repository initialized by cvs2svn.