Revision 127 - (view) (annotate) - [select for diffs]
Modified Fri Jun 19 18:18:02 2009 UTC (11 years ago) by gilbertke
File length: 6039 byte(s)
Diff to previous 119

ran mmff94.sdf test suite on latest code - fixed errors in rings.c

Revision 119 - (view) (annotate) - [select for diffs]
Modified Tue Jun 16 21:36:00 2009 UTC (11 years, 1 month ago) by wdelano
File length: 6057 byte(s)
Diff to previous 116

printf( to fprintf(pcmlogfile,

Revision 116 - (view) (annotate) - [select for diffs]
Modified Thu May 14 14:04:15 2009 UTC (11 years, 2 months ago) by gilbertke
File length: 6031 byte(s)
Diff to previous 113

added number of connections and total bond order to atom definition in preparation for AM1BCC code

Revision 113 - (view) (annotate) - [select for diffs]
Modified Mon Apr 13 13:58:10 2009 UTC (11 years, 3 months ago) by gilbertke
File length: 5911 byte(s)
Diff to previous 110

added monitor tag and timer code to minimizer

Revision 110 - (view) (annotate) - [select for diffs]
Modified Thu Mar 12 01:43:50 2009 UTC (11 years, 4 months ago) by gilbertke
File length: 5770 byte(s)
Diff to previous 103

further cleanup and localization of atom data

Revision 103 - (view) (annotate) - [select for diffs]
Modified Thu Feb 19 01:37:38 2009 UTC (11 years, 4 months ago) by gilbertke
File length: 5496 byte(s)
Diff to previous 89

major rewrite - removing global data, adding electrostatics tag to read_sdf

Revision 89 - (view) (annotate) - [select for diffs]
Modified Thu Jan 15 14:13:58 2009 UTC (11 years, 6 months ago) by gilbertke
File length: 5903 byte(s)
Diff to previous 87

resolved problem in read_sdf, removed omp pragma in ehal

Revision 87 - (view) (annotate) - [select for diffs]
Modified Mon Jan 12 17:11:11 2009 UTC (11 years, 6 months ago) by gilbertke
File length: 5815 byte(s)
Diff to previous 85

fixed corruption in mengine.c and bug in ehal.c

Revision 85 - (view) (annotate) - [select for diffs]
Modified Mon Jan 12 15:05:44 2009 UTC (11 years, 6 months ago) by gilbertke
File length: 5427 byte(s)
Diff to previous 75

more cleanup and code removal

Revision 75 - (view) (annotate) - [select for diffs]
Modified Mon Dec 15 18:03:29 2008 UTC (11 years, 7 months ago) by gilbertke
File length: 9839 byte(s)
Diff to previous 68

fixes in typeing to pass MMFF validation suite

Revision 68 - (view) (annotate) - [select for diffs]
Modified Wed Dec 10 15:37:34 2008 UTC (11 years, 7 months ago) by gilbertke
File length: 9947 byte(s)
Diff to previous 67

fixed typing errors - mmff test suite a to c

Revision 67 - (view) (annotate) - [select for diffs]
Modified Fri Dec 5 14:18:02 2008 UTC (11 years, 7 months ago) by gilbertke
File length: 9849 byte(s)
Diff to previous 65

added aromatic bonds in read_sdf removed TJO bailout

Revision 65 - (view) (annotate) - [select for diffs]
Modified Fri Dec 5 02:21:07 2008 UTC (11 years, 7 months ago) by gilbertke
File length: 9863 byte(s)
Diff to previous 64

added call to type in rd_sdf, fixed problem in type_mmx

Revision 64 - (view) (annotate) - [select for diffs]
Modified Thu Dec 4 02:03:23 2008 UTC (11 years, 7 months ago) by gilbertke
File length: 9860 byte(s)
Diff to previous 63

fixed bug in routine to recognize delocalized bonds in kbond.c

Revision 63 - (view) (annotate) - [select for diffs]
Modified Wed Dec 3 03:46:32 2008 UTC (11 years, 7 months ago) by gilbertke
File length: 10930 byte(s)
Diff to previous 58

updated read_sdf type_mmx and first pass at using best practices

Revision 58 - (view) (annotate) - [select for diffs]
Modified Mon Dec 1 06:44:59 2008 UTC (11 years, 7 months ago) by wdelano
File length: 14633 byte(s)
Diff to previous 48

code merge 20081130

Revision 48 - (view) (annotate) - [select for diffs]
Modified Thu Jul 31 16:34:52 2008 UTC (11 years, 11 months ago) by tjod
File length: 14648 byte(s)
Diff to previous 33

Add modification notice to files modified for Freemol
per mengine/smi23d license requirements

Revision 33 - (view) (annotate) - [select for diffs]
Modified Wed Jul 23 01:04:58 2008 UTC (11 years, 11 months ago) by tjod
File length: 14573 byte(s)
Diff to previous 31

Don't write_sdf when missing parameters or other errors

Revision 31 - (view) (annotate) - [select for diffs]
Modified Fri Jul 18 18:47:27 2008 UTC (11 years, 11 months ago) by tjod
File length: 14567 byte(s)
Diff to previous 27

When aromatic bonds are encountered generate error on stderr and do not output sdf file.

Revision 27 - (view) (annotate) - [select for diffs]
Modified Tue Jul 8 19:10:25 2008 UTC (12 years ago) by tjod
File length: 14392 byte(s)
Diff to previous 25

move mengine src to reflect new freemol directory structure

Revision 25 - (view) (annotate) - [select for diffs]
Modified Tue Jul 8 15:38:24 2008 UTC (12 years ago) by tjod
Original Path: trunk/smi23d/src/mengine/gmmx_run.c
File length: 14392 byte(s)
Diff to previous 20

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 - (view) (annotate) - [select for diffs]
Modified Mon Jun 30 22:00:43 2008 UTC (12 years ago) by tjod
Original Path: trunk/smi23d/src/mengine/gmmx_run.c
File length: 14385 byte(s)
Diff to previous 16

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 16 - (view) (annotate) - [select for diffs]
Modified Mon Jun 23 21:29:26 2008 UTC (12 years ago) by tjod
Original Path: trunk/smi23d/src/mengine/gmmx_run.c
File length: 14239 byte(s)
Diff to previous 15

Add back the command line options -d -i -x for dipole moment, vibrational data and logp.  Have error.log directed to stdout.

Revision 15 - (view) (annotate) - [select for diffs]
Modified Thu Jun 19 00:26:16 2008 UTC (12 years ago) by tjod
Original Path: trunk/smi23d/src/mengine/gmmx_run.c
File length: 14330 byte(s)
Diff to previous 3

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 3 - (view) (annotate) - [select for diffs]
Added Mon Jun 9 21:38:26 2008 UTC (12 years, 1 month ago) by tjod
Original Path: trunk/smi23d/src/mengine/gmmx_run.c
File length: 14887 byte(s)

test