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Revision 99 - Directory Listing
Modified Mon Jan 19 04:31:29 2009 UTC (10 years, 8 months ago) by wdelano
synchronized with trunk, less openmp lib/include
Revision 96 - Directory Listing
Modified Sat Jan 17 23:40:13 2009 UTC (10 years, 8 months ago) by wdelano
Copied from: trunk/src/mengine/src revision 88
using last pre-openmp source version
Revision 88 - Directory Listing
Modified Thu Jan 15 02:54:42 2009 UTC (10 years, 8 months ago) by wdelano
Original Path: trunk/src/mengine/src
fixed spurious debug output
Revision 87 - Directory Listing
Modified Mon Jan 12 17:11:11 2009 UTC (10 years, 8 months ago) by gilbertke
Original Path: trunk/src/mengine/src
fixed corruption in mengine.c and bug in ehal.c
Revision 86 - Directory Listing
Modified Mon Jan 12 16:21:45 2009 UTC (10 years, 8 months ago) by gilbertke
Original Path: trunk/src/mengine/src
rewrote ehal to remove pow(x,y) function call
Revision 85 - Directory Listing
Modified Mon Jan 12 15:05:44 2009 UTC (10 years, 8 months ago) by gilbertke
Original Path: trunk/src/mengine/src
more cleanup and code removal
Revision 75 - Directory Listing
Modified Mon Dec 15 18:03:29 2008 UTC (10 years, 9 months ago) by gilbertke
Original Path: trunk/src/mengine/src
fixes in typeing to pass MMFF validation suite
Revision 68 - Directory Listing
Modified Wed Dec 10 15:37:34 2008 UTC (10 years, 9 months ago) by gilbertke
Original Path: trunk/src/mengine/src
fixed typing errors - mmff test suite a to c
Revision 67 - Directory Listing
Modified Fri Dec 5 14:18:02 2008 UTC (10 years, 9 months ago) by gilbertke
Original Path: trunk/src/mengine/src
added aromatic bonds in read_sdf removed TJO bailout
Revision 65 - Directory Listing
Modified Fri Dec 5 02:21:07 2008 UTC (10 years, 9 months ago) by gilbertke
Original Path: trunk/src/mengine/src
added call to type in rd_sdf, fixed problem in type_mmx
Revision 64 - Directory Listing
Modified Thu Dec 4 02:03:23 2008 UTC (10 years, 9 months ago) by gilbertke
Original Path: trunk/src/mengine/src
fixed bug in routine to recognize delocalized bonds in kbond.c
Revision 63 - Directory Listing
Modified Wed Dec 3 03:46:32 2008 UTC (10 years, 9 months ago) by gilbertke
Original Path: trunk/src/mengine/src
updated read_sdf type_mmx and first pass at using best practices
Revision 62 - Directory Listing
Modified Tue Dec 2 07:28:56 2008 UTC (10 years, 9 months ago) by wdelano
Original Path: trunk/src/mengine/src
fixed typos
Revision 61 - Directory Listing
Modified Mon Dec 1 22:23:40 2008 UTC (10 years, 9 months ago) by wdelano
Original Path: trunk/src/mengine/src
minor
Revision 60 - Directory Listing
Modified Mon Dec 1 22:21:53 2008 UTC (10 years, 9 months ago) by wdelano
Original Path: trunk/src/mengine/src
minor change
Revision 59 - Directory Listing
Modified Mon Dec 1 22:17:35 2008 UTC (10 years, 9 months ago) by gilbertke
Original Path: trunk/src/mengine/src
deleting old h files
Revision 58 - Directory Listing
Modified Mon Dec 1 06:44:59 2008 UTC (10 years, 9 months ago) by wdelano
Original Path: trunk/src/mengine/src
code merge 20081130
Revision 48 - Directory Listing
Modified Thu Jul 31 16:34:52 2008 UTC (11 years, 1 month ago) by tjod
Original Path: trunk/src/mengine/src
Add modification notice to files modified for Freemol
per mengine/smi23d license requirements

Revision 43 - Directory Listing
Modified Mon Jul 28 19:54:19 2008 UTC (11 years, 1 month ago) by wdelano
Original Path: trunk/src/mengine/src
add mengine license file
Revision 34 - Directory Listing
Modified Wed Jul 23 19:12:47 2008 UTC (11 years, 1 month ago) by tjod
Original Path: trunk/src/mengine/src
remove include malloc.h for osx compatibility

Revision 33 - Directory Listing
Modified Wed Jul 23 01:04:58 2008 UTC (11 years, 1 month ago) by tjod
Original Path: trunk/src/mengine/src
Don't write_sdf when missing parameters or other errors

Revision 32 - Directory Listing
Modified Fri Jul 18 18:50:15 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/src/mengine/src
correct python script to use mengine.exe

Revision 31 - Directory Listing
Modified Fri Jul 18 18:47:27 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/src/mengine/src
When aromatic bonds are encountered generate error on stderr and do not output sdf file.

Revision 29 - Directory Listing
Modified Tue Jul 8 19:22:35 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/src/mengine/src
add files for configure and make

Revision 27 - Directory Listing
Modified Tue Jul 8 19:10:25 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/src/mengine/src
Copied from: trunk/smi23d/src/mengine revision 26
move mengine src to reflect new freemol directory structure

Revision 26 - Directory Listing
Modified Tue Jul 8 17:17:48 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
header files containg all the data from
mmff94.prm and mmxconst.prm

Revision 25 - Directory Listing
Modified Tue Jul 8 15:38:24 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Incoporate the parameter files mmff94.prm and mmxconst.prm
into the mengine code by turning them into header files.
Each line becomes a string array element that is parsed in
place of lines in the .prm files.  The .prm files are no
longer needed, but are not deleted from the repository.

Revision 20 - Directory Listing
Modified Mon Jun 30 22:00:43 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Add -a switch to cause H atoms to be added, deleting existing ones.
With -a, mengine behaves as the original.
Formal charges are not always preserved, by the original or
the modified mengine with or without the -a switch.
It appears that negative charges are preserved (benzoic acid).
A positive charge on a N atom (an amine) is not preserved.
Charges are recognized in CHG records and in atom records.
Charges are output only in atom records.

Revision 17 - Directory Listing
Modified Mon Jun 23 21:33:34 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Change to popen3 to be able to capture stderr

Revision 16 - Directory Listing
Modified Mon Jun 23 21:29:26 2008 UTC (11 years, 2 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Add back the command line options -d -i -x for dipole moment, vibrational data and logp.  Have error.log directed to stdout.

Revision 15 - Directory Listing
Modified Thu Jun 19 00:26:16 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Create new main program, mengine.c to replace gmmx.c
simplifying command line parsing (none).
Make mengine read stdin (sdf) and write stdout (sdf) instead
of files.  Makefile reflects change from gmmx to mengine.

Revision 14 - Directory Listing
Modified Thu Jun 19 00:21:04 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Sample python code showing how mengine can be called using popen2

Revision 13 - Directory Listing
Modified Thu Jun 19 00:20:24 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Sample file for use with mengine and mengine.py

Revision 9 - Directory Listing
Modified Thu Jun 12 21:50:08 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Was an old test

Revision 8 - Directory Listing
Modified Thu Jun 12 21:47:53 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
No need to store output file until a test suite is developed.

Revision 7 - Directory Listing
Modified Thu Jun 12 21:46:15 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
No need to store executables

Revision 6 - Directory Listing
Modified Thu Jun 12 21:12:19 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
Two mods to compile properly under mingw without
breaking linux compile.
Comments in source near /* TJO ... */
gmmx.c handle null-termination of file name string properly.
pcmod.h #include <stdio.h> to define FILE type.

Revision 3 - Directory Listing
Added Mon Jun 9 21:38:26 2008 UTC (11 years, 3 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
test