full dynamic memory allocation of molecule

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

combine rings and srings to eliminate duplication

fix build script

build script

synchronized with trunk, less openmp lib/include

cleanup of k*.c parameter assignment routines

cleanup and removal of amber and opls

using last pre-openmp source version

branch created

branch for synching up with pymol 1.2

created branches directory

code cleanup

resolved problem in read_sdf, removed omp pragma in ehal

fixed spurious debug output

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

rewrote ehal to remove pow(x,y) function call

more cleanup and code removal

win32 fixes

win32 fixes

preproc

troubleshooting

troubleshooting svn

mpeg

fixes in typeing to pass MMFF validation suite

mpeg encoding

stdin redirection

fixed typing errors - mmff test suite a to c

added aromatic bonds in read_sdf removed TJO bailout

path stuff

added call to type in rd_sdf, fixed problem in type_mmx

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

updated read_sdf type_mmx and first pass at using best practices

fixed typos

minor

minor change

deleting old h files

code merge 20081130

osx doesn't like install -D, but mingw and linux need -D (for licenses/ file)

changes for mingw

changes for mingw

new README.txt for binary distibutions

Makefile.in now cleans Makefile

first check in of pdb2pqr

update README

update README

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

install licenses too

new freemol license file

added psize.py support

licenses folder

add mengine license file

type

freemol.apbs module

readd apbs files after mixup

housekeeping

make apbs executable apbs.exe

directories used by APBS

first commit of APBS

tweak installation scripts

remove include malloc.h for osx compatibility

Don't write_sdf when missing parameters or other errors

correct python script to use mengine.exe

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

tentative libpy folder for Python code

add files for configure and make

move mengine src to reflect new freemol directory structure

header files containg all the data from
mmff94.prm and mmxconst.prm

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.

updated readme

changes for win32

initial checkin of mpeg_encode source

draft design spec

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.

building up freemol root structure

Change to popen3 to be able to capture stderr

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

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.

Sample python code showing how mengine can be called using popen2

Sample file for use with mengine and mengine.py

Tag original source from https://cicc-grid.svn.sourceforge.net/svnroot/cicc-grid/cicc-grid/smi23d/trunk

Tag the original source from https://cicc-grid.svn.sourceforge.net/svnroot/cicc-grid/cicc-grid/smi23d/trunk

Create place for tagged branches

Was an old test

No need to store output file until a test suite is developed.

No need to store executables

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.

test

test add

test

First Commit

First Import