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Revision 57 - Directory Listing
Modified Tue Sep 30 00:49:05 2008 UTC (11 years ago) by tjod

Revision 56 - Directory Listing
Modified Tue Sep 30 00:40:05 2008 UTC (11 years ago) by tjod
osx doesn't like install -D, but mingw and linux need -D (for licenses/ file)

Revision 55 - Directory Listing
Modified Mon Sep 29 23:41:23 2008 UTC (11 years ago) by tjod
changes for mingw

Revision 54 - Directory Listing
Modified Mon Sep 29 23:37:10 2008 UTC (11 years ago) by tjod
changes for mingw

Revision 53 - Directory Listing
Modified Fri Sep 19 16:21:56 2008 UTC (11 years, 1 month ago) by wdelano
new README.txt for binary distibutions
Revision 52 - Directory Listing
Modified Fri Sep 19 16:21:25 2008 UTC (11 years, 1 month ago) by wdelano
Makefile.in now cleans Makefile
Revision 51 - Directory Listing
Modified Fri Sep 19 16:19:32 2008 UTC (11 years, 1 month ago) by wdelano
first check in of pdb2pqr
Revision 50 - Directory Listing
Modified Fri Sep 19 16:18:22 2008 UTC (11 years, 1 month ago) by wdelano
update README
Revision 49 - Directory Listing
Modified Fri Sep 19 16:18:08 2008 UTC (11 years, 1 month ago) by wdelano
update README
Revision 48 - Directory Listing
Modified Thu Jul 31 16:34:52 2008 UTC (11 years, 2 months ago) by tjod
Add modification notice to files modified for Freemol
per mengine/smi23d license requirements

Revision 47 - Directory Listing
Modified Mon Jul 28 20:16:38 2008 UTC (11 years, 2 months ago) by wdelano
install licenses too
Revision 46 - Directory Listing
Modified Mon Jul 28 20:15:22 2008 UTC (11 years, 2 months ago) by wdelano
new freemol license file
Revision 45 - Directory Listing
Modified Mon Jul 28 20:00:34 2008 UTC (11 years, 2 months ago) by wdelano
added psize.py support
Revision 44 - Directory Listing
Modified Mon Jul 28 19:56:02 2008 UTC (11 years, 2 months ago) by wdelano
licenses folder
Revision 43 - Directory Listing
Modified Mon Jul 28 19:54:19 2008 UTC (11 years, 2 months ago) by wdelano
add mengine license file
Revision 42 - Directory Listing
Modified Mon Jul 28 19:15:55 2008 UTC (11 years, 2 months ago) by wdelano
type
Revision 41 - Directory Listing
Modified Mon Jul 28 18:48:54 2008 UTC (11 years, 2 months ago) by wdelano
freemol.apbs module
Revision 40 - Directory Listing
Modified Mon Jul 28 16:23:29 2008 UTC (11 years, 2 months ago) by tjod
readd apbs files after mixup

Revision 39 - Directory Listing
Modified Mon Jul 28 16:22:02 2008 UTC (11 years, 2 months ago) by tjod
housekeeping

Revision 38 - Directory Listing
Modified Fri Jul 25 21:48:14 2008 UTC (11 years, 2 months ago) by tjod
make apbs executable apbs.exe

Revision 37 - Directory Listing
Modified Fri Jul 25 21:27:56 2008 UTC (11 years, 2 months ago) by tjod
directories used by APBS

Revision 36 - Directory Listing
Modified Fri Jul 25 21:17:20 2008 UTC (11 years, 2 months ago) by tjod
first commit of APBS

Revision 35 - Directory Listing
Modified Fri Jul 25 20:49:28 2008 UTC (11 years, 2 months ago) by tjod
tweak installation scripts

Revision 34 - Directory Listing
Modified Wed Jul 23 19:12:47 2008 UTC (11 years, 2 months ago) by tjod
remove include malloc.h for osx compatibility

Revision 33 - Directory Listing
Modified Wed Jul 23 01:04:58 2008 UTC (11 years, 2 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 (11 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 (11 years, 3 months ago) by tjod
When aromatic bonds are encountered generate error on stderr and do not output sdf file.

Revision 30 - Directory Listing
Modified Tue Jul 15 23:40:04 2008 UTC (11 years, 3 months ago) by wdelano
tentative libpy folder for Python code
Revision 29 - Directory Listing
Modified Tue Jul 8 19:22:35 2008 UTC (11 years, 3 months ago) by tjod
add files for configure and make

Revision 28 - Directory Listing
Modified Tue Jul 8 19:15:21 2008 UTC (11 years, 3 months ago) by tjod

Revision 27 - Directory Listing
Modified Tue Jul 8 19:10:25 2008 UTC (11 years, 3 months ago) by tjod
move mengine src to reflect new freemol directory structure

Revision 26 - Directory Listing
Modified Tue Jul 8 17:17:48 2008 UTC (11 years, 3 months ago) by tjod
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, 3 months ago) by tjod
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 24 - Directory Listing
Modified Mon Jul 7 23:29:55 2008 UTC (11 years, 3 months ago) by wdelano
updated readme
Revision 23 - Directory Listing
Modified Mon Jul 7 23:06:52 2008 UTC (11 years, 3 months ago) by wdelano
changes for win32
Revision 22 - Directory Listing
Modified Mon Jul 7 22:16:37 2008 UTC (11 years, 3 months ago) by wdelano
initial checkin of mpeg_encode source
Revision 21 - Directory Listing
Modified Mon Jul 7 20:05:24 2008 UTC (11 years, 3 months ago) by wdelano
draft design spec
Revision 20 - Directory Listing
Modified Mon Jun 30 22:00:43 2008 UTC (11 years, 3 months ago) by tjod
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 19 - Directory Listing
Modified Fri Jun 27 18:12:33 2008 UTC (11 years, 3 months ago) by wdelano
building up freemol root structure
Revision 18 - Directory Listing
Modified Fri Jun 27 18:01:21 2008 UTC (11 years, 3 months ago) by wdelano

Revision 17 - Directory Listing
Modified Mon Jun 23 21:33:34 2008 UTC (11 years, 3 months ago) by tjod
Change to popen3 to be able to capture stderr

Revision 16 - Directory Listing
Modified Mon Jun 23 21:29:26 2008 UTC (11 years, 3 months ago) by tjod
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, 4 months ago) by tjod
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, 4 months ago) by tjod
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, 4 months ago) by tjod
Sample file for use with mengine and mengine.py

Revision 12 - Directory Listing
Modified Thu Jun 19 00:08:11 2008 UTC (11 years, 4 months ago) by tjod
Tag original source from https://cicc-grid.svn.sourceforge.net/svnroot/cicc-grid/cicc-grid/smi23d/trunk
Revision 11 - Directory Listing
Modified Thu Jun 19 00:07:49 2008 UTC (11 years, 4 months ago) by tjod
Tag the original source from https://cicc-grid.svn.sourceforge.net/svnroot/cicc-grid/cicc-grid/smi23d/trunk

Revision 10 - Directory Listing
Modified Thu Jun 19 00:07:22 2008 UTC (11 years, 4 months ago) by tjod
Create place for tagged branches

Revision 9 - Directory Listing
Modified Thu Jun 12 21:50:08 2008 UTC (11 years, 4 months ago) by tjod
Was an old test

Revision 8 - Directory Listing
Modified Thu Jun 12 21:47:53 2008 UTC (11 years, 4 months ago) by tjod
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, 4 months ago) by tjod
No need to store executables

Revision 6 - Directory Listing
Modified Thu Jun 12 21:12:19 2008 UTC (11 years, 4 months ago) by tjod
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 5 - Directory Listing
Modified Mon Jun 9 21:44:31 2008 UTC (11 years, 4 months ago) by tjod
test

Revision 4 - Directory Listing
Modified Mon Jun 9 21:43:12 2008 UTC (11 years, 4 months ago) by wdelano
test add
Revision 3 - Directory Listing
Modified Mon Jun 9 21:38:26 2008 UTC (11 years, 4 months ago) by tjod
test

Revision 2 - Directory Listing
Modified Thu May 22 18:48:23 2008 UTC (11 years, 4 months ago) by wdelano
First Commit
Revision 1 - Directory Listing
Added Thu May 22 18:41:46 2008 UTC (11 years, 4 months ago) by wdelano
First Import