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Revision 111 - Directory Listing
Modified Thu Mar 12 14:12:33 2009 UTC (11 years, 7 months ago) by gilbertke
more atom localization
Revision 110 - Directory Listing
Modified Thu Mar 12 01:43:50 2009 UTC (11 years, 7 months ago) by gilbertke
further cleanup and localization of atom data
Revision 109 - Directory Listing
Modified Fri Mar 6 21:18:36 2009 UTC (11 years, 7 months ago) by wdelano

Revision 108 - Directory Listing
Modified Fri Mar 6 21:16:52 2009 UTC (11 years, 7 months ago) by wdelano

Revision 107 - Directory Listing
Modified Sun Feb 22 16:04:49 2009 UTC (11 years, 8 months ago) by gilbertke
fixed read_sdf to use tabulator for electrostatics keyword, added read of dielectric constant
Revision 106 - Directory Listing
Modified Fri Feb 20 21:04:40 2009 UTC (11 years, 8 months ago) by wdelano
KEG_OPENMP ext
Revision 105 - Directory Listing
Modified Fri Feb 20 21:01:21 2009 UTC (11 years, 8 months ago) by gilbertke
add job_contro.h
Revision 104 - Directory Listing
Modified Fri Feb 20 14:09:46 2009 UTC (11 years, 8 months ago) by gilbertke
full dynamic memory allocation of molecule
Revision 103 - Directory Listing
Modified Thu Feb 19 01:37:38 2009 UTC (11 years, 8 months ago) by gilbertke
major rewrite - removing global data, adding electrostatics tag to read_sdf
Revision 102 - Directory Listing
Modified Tue Jan 20 18:02:33 2009 UTC (11 years, 9 months ago) by gilbertke
combine rings and srings to eliminate duplication
Revision 98 - Directory Listing
Modified Mon Jan 19 01:04:10 2009 UTC (11 years, 9 months ago) by gilbertke
cleanup of k*.c parameter assignment routines
Revision 97 - Directory Listing
Modified Sun Jan 18 16:44:49 2009 UTC (11 years, 9 months ago) by gilbertke
cleanup and removal of amber and opls
Revision 90 - Directory Listing
Modified Fri Jan 16 21:55:34 2009 UTC (11 years, 9 months ago) by gilbertke
code cleanup
Revision 89 - Directory Listing
Modified Thu Jan 15 14:13:58 2009 UTC (11 years, 9 months ago) by gilbertke
resolved problem in read_sdf, removed omp pragma in ehal
Revision 88 - Directory Listing
Modified Thu Jan 15 02:54:42 2009 UTC (11 years, 9 months ago) by wdelano
fixed spurious debug output
Revision 87 - Directory Listing
Modified Mon Jan 12 17:11:11 2009 UTC (11 years, 9 months ago) by gilbertke
fixed corruption in mengine.c and bug in ehal.c
Revision 86 - Directory Listing
Modified Mon Jan 12 16:21:45 2009 UTC (11 years, 9 months ago) by gilbertke
rewrote ehal to remove pow(x,y) function call
Revision 85 - Directory Listing
Modified Mon Jan 12 15:05:44 2009 UTC (11 years, 9 months ago) by gilbertke
more cleanup and code removal
Revision 75 - Directory Listing
Modified Mon Dec 15 18:03:29 2008 UTC (11 years, 10 months ago) by gilbertke
fixes in typeing to pass MMFF validation suite
Revision 68 - Directory Listing
Modified Wed Dec 10 15:37:34 2008 UTC (11 years, 10 months ago) by gilbertke
fixed typing errors - mmff test suite a to c
Revision 67 - Directory Listing
Modified Fri Dec 5 14:18:02 2008 UTC (11 years, 10 months ago) by gilbertke
added aromatic bonds in read_sdf removed TJO bailout
Revision 65 - Directory Listing
Modified Fri Dec 5 02:21:07 2008 UTC (11 years, 10 months ago) by gilbertke
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 (11 years, 10 months ago) by gilbertke
fixed bug in routine to recognize delocalized bonds in kbond.c
Revision 63 - Directory Listing
Modified Wed Dec 3 03:46:32 2008 UTC (11 years, 10 months ago) by gilbertke
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 (11 years, 11 months ago) by wdelano
fixed typos
Revision 61 - Directory Listing
Modified Mon Dec 1 22:23:40 2008 UTC (11 years, 11 months ago) by wdelano
minor
Revision 60 - Directory Listing
Modified Mon Dec 1 22:21:53 2008 UTC (11 years, 11 months ago) by wdelano
minor change
Revision 59 - Directory Listing
Modified Mon Dec 1 22:17:35 2008 UTC (11 years, 11 months ago) by gilbertke
deleting old h files
Revision 58 - Directory Listing
Modified Mon Dec 1 06:44:59 2008 UTC (11 years, 11 months ago) by wdelano
code merge 20081130
Revision 48 - Directory Listing
Modified Thu Jul 31 16:34:52 2008 UTC (12 years, 3 months ago) by tjod
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 (12 years, 3 months ago) by wdelano
add mengine license file
Revision 34 - Directory Listing
Modified Wed Jul 23 19:12:47 2008 UTC (12 years, 3 months ago) by tjod
remove include malloc.h for osx compatibility

Revision 33 - Directory Listing
Modified Wed Jul 23 01:04:58 2008 UTC (12 years, 3 months ago) by tjod
Don't write_sdf when missing parameters or other errors

Revision 32 - Directory Listing
Modified Fri Jul 18 18:50:15 2008 UTC (12 years, 3 months ago) by tjod
correct python script to use mengine.exe

Revision 31 - Directory Listing
Modified Fri Jul 18 18:47:27 2008 UTC (12 years, 3 months ago) by tjod
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 (12 years, 3 months ago) by tjod
add files for configure and make

Revision 27 - Directory Listing
Modified Tue Jul 8 19:10:25 2008 UTC (12 years, 3 months ago) by tjod
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 (12 years, 3 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 (12 years, 3 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 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 (12 years, 4 months ago) by tjod
Original Path: trunk/smi23d/src/mengine
test