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ChangeLog
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2011-02-11 Ann Giammona <[email protected]>
* NEWS: Update for version 2.2.9
2011-02-11 Ann Giammona <[email protected]>
* libMEADsolvate/Makefile.in: Makefile template for libMEADsolvate.
* libMEADsolvate/meadsolvate.h: Header for meadsolvate.cc
* libMEADsolvate/meadsolinprot.h: Header for meadsolinprot.cc
* libMEADsolvate/meadsolvate.cc: Library version of solvate.
* libMEADsolvate/meadsolinprot.cc: Library version of solinprot.
* libMEADsolvate/domeadsolvate.cc:
Library version of solvate suitable for calling from FORTRAN.
* libMEADsolvate/domeadsolinprot.cc:
Library version of solinprot suitable for calling from FORTRAN.
2011-02-10 Ann Giammona <[email protected]>
* TODO: potint out-of-grid DONE.
* NOTES: Checkin for version 2.2.9
* Makefile.in: Added directives to build libMEADsolvate.a
* libmead/FDGridLevel.h, libmead/FDGridLevel.cc:
Added a boolean, ZeroForOutOfRange, and methods to set and get its value.
This variable controls whether FDGridLevel::potint returns a zero or
throws an error when point-out-of-range.
* configure.in: Bump version number to 2.2.9.
Version 2.2.9 includes the initial implementation of libMEADsolvate and
modification of FDGridLevel::potint to allow return of zero instead
of throwing an error when point-out-of-range.
2009-09-15 Don Bashford <bashford@hc-bashford>
* NOTES: Check in for version 2.2.8
* TODO: potint out-of-grid TODO
* README: A bit more on coming up with charges and radii,
and a minor correction re COPYING file.
* configure.in: Check in prelim to 2.2.8a
2009-02-22 Don Bashford <bashford@hc-bashford>
* libmead/FDGridLevel.h: Fix bug in get_avsScaleFactor.
2008-11-06 Don Bashford <bashford@hc-bashford>
* libmead/DielCubeRep.cc, libmead/AtomSet.cc:
Explicit inclusion of C string header for functions like
strncmp and memset. See Teixeira emails starting 5 Nov. 2008.
2008-03-04 Don Bashford <bashford@hc-bashford>
* ChangeLog, NOTES: Check in for tagging release 2.2.7
* Makefile.in:
Do the right thing if user types "make install" before "make"
* README: Fix a nit in the distro making instructions.
* libmead/Makefile.in, configure.in:
Deal with the need for libmead.a to be -fpic and sharable if it's
to be used to make the Python shared library, MEADc.so
2008-03-04 [email protected] <bashford@hc-bashford>
* NOTES: Check in for tagging release 2.2.7
* Makefile.in:
Do the right thing if user types "make install" before "make"
* README: Fix a nit in the distro making instructions.
* libmead/Makefile.in, configure.in:
Deal with the need for libmead.a to be -fpic and sharable if it's
to be used to make the Python shared library, MEADc.so
2008-03-04 [email protected] <bashford@hc-bashford>
* Makefile.in:
Do the right thing if user types "make install" before "make"
* README: Fix a nit in the distro making instructions.
* libmead/Makefile.in, configure.in:
Deal with the need for libmead.a to be -fpic and sharable if it's
to be used to make the Python shared library, MEADc.so
2008-02-29 [email protected] <bashford@hc-bashford>
* configure.in: bump version number in advance.
* apps/pair_interactions/Makefile.in, apps/potscan/Makefile.in, apps/solinprot/Makefile.in, apps/solvate/Makefile.in, apps/sav-driver/Makefile.in, apps/potential/Makefile.in:
Fix for change in Gnu Make 3.81
2008-02-28 [email protected] <bashford@hc-bashford>
* libmead/SphericalHarmonic.h: Maybe fix a type clash.
2007-11-27 [email protected] <bashford@hc-bashford>
* ChangeLog: Bring up to date for release.
* libmead/posix_using.cc: Posix_using is no longer needed
* 0README.FIRST:
Various updates, esp w.r.t. building and binaries no longer provided.
* configure.in: Bump up the version number
* NOTES: Check in for tag/release.
* TODO: Check in for tagging/release.
* swig/Makefile.in: Removal of unused stuff.
* Makefile.in:
Modified the dist target to put the distro files one level up from the
working dir. Some other cleaning up.
2007-11-27 [email protected] <bashford@hc-bashford>
* libmead/posix_using.cc: Posix_using is no longer needed
* 0README.FIRST:
Various updates, esp w.r.t. building and binaries no longer provided.
* configure.in: Bump up the version number
* NOTES: Check in for tag/release.
* TODO: Check in for tagging/release.
* swig/Makefile.in: Removal of unused stuff.
* Makefile.in:
Modified the dist target to put the distro files one level up from the
working dir. Some other cleaning up.
2007-11-26 [email protected] <bashford@hc-bashford>
* libmead/Makefile.in: Removal of posix_using.cc
* libmead/globals.h:
Removal of posix_using.cc functions, fexists and fdelete.
* libmead/globals.cc, apps/potential/potential.cc:
Replace use of removed fexists function with ifstream open attempt.
2007-10-08 [email protected] <bashford@hc-bashford>
* NOTES: prepare for version 2.2.6
* configure.in: bump up MEAD version number.
* config.sub, install-sh, config.guess:
New config.guess config.sub and install-sh from autoconf-2.61
2007-05-28 [email protected] <bashford@hc-bashford>
* libmead/Polynomial.h, libmead/Potat.cc, libmead/SAVanal_calc.cc, libmead/Sausage.cc, libmead/SphericalHarmonic.cc, libmead/SphericalHarmonic.h, libmead/TPShell.h, libmead/globals.cc, libmead/posix_using.cc, libmead/sor.cc, swig/premade_MEAD_shadow.cc, libmead/CLShell.h, libmead/ChargeCubeRep.cc, libmead/ChargeCubeRep.h, libmead/ChargeDist.cc, libmead/ChargeDist.h, libmead/Coord.h, libmead/Debye.cc, libmead/DielCubeRep.h, libmead/ElectrolyteByAtoms.cc, libmead/ElectrolyteByAtoms.h, libmead/ElstatPotCombination.cc, libmead/FDGridLevel.cc, libmead/FDGridLevel.h, libmead/ManyPointCharge.h, libmead/MomentAnalysis.cc, libmead/MomentAnalysis.h, libmead/MomentAnalysis_tmplts.h, libmead/OnePointCharge.cc, libmead/OnePointCharge.h, libmead/Pair.h, libmead/PairGenBorn.cc, libmead/PhysCond.h, libmead/Polynomial.cc, libmead/AnalySlab.cc, libmead/AnalySphere.cc, libmead/AnalySphere.h, libmead/Angle.h, libmead/AtomChargeSet.cc, libmead/AtomChargeSet.h, libmead/AvsScalarField.cc, libmead/AvsScalarField_input.cc:
Merge-in of the winbranch-2-2-5
2007-05-27 [email protected] <bashford@hc-bashford>
* NOTES: Check in for tagging winmerge-2-2-5
* apps/redti/redti.c, apps/redti/rfixpro.c:
Correct some non-conformant C-library usage.
* TODO: Checkin before merge
* NOTES: Checkin before a merge.
2007-02-22 [email protected] <bashford@hc-bashford>
* libmead/FDGridLevel.cc, libmead/FDGridLevel.h, libmead/FinDiffElstatPot.cc, libmead/FinDiffElstatPot.h, libmead/ManyPointCharge.cc, libmead/ManyPointCharge.h, libmead/OnePointCharge.cc, libmead/OnePointCharge.h, libmead/SAVanal_calc.cc, libmead/globals.cc, libmead/globals.h, libmead/sor.cc, swig/tat.py, ChangeLog, NOTES, README, TODO, apps/libmso/FlexiSite.cc, apps/potential/potential.cc, libmead/AtomChargeSet.cc, libmead/AtomChargeSet.h, libmead/AtomSet.h, libmead/ChargeDist.cc, libmead/ChargeDist.h:
Merged in main-branch changes as of 21 Feb 07
* libmead/OnePointCharge.h, libmead/Pair.h, libmead/PairGenBorn.cc, libmead/PhysCond.h, libmead/Polynomial.cc, libmead/Polynomial.h, libmead/Potat.cc, libmead/SAVanal_calc.cc, libmead/Sausage.cc, libmead/SphericalHarmonic.cc, libmead/SphericalHarmonic.h, libmead/TPShell.h, libmead/globals.cc, libmead/posix_using.cc, libmead/sor.cc, libmead/ChargeCubeRep.cc, libmead/ChargeCubeRep.h, libmead/ChargeDist.cc, libmead/ChargeDist.h, libmead/Coord.h, libmead/Debye.cc, libmead/DielCubeRep.h, libmead/ElectrolyteByAtoms.cc, libmead/ElectrolyteByAtoms.h, libmead/ElstatPotCombination.cc, libmead/FDGridLevel.cc, libmead/FDGridLevel.h, libmead/ManyPointCharge.h, libmead/MomentAnalysis.cc, libmead/MomentAnalysis.h, libmead/MomentAnalysis_tmplts.h, libmead/OnePointCharge.cc, libmead/AnalySlab.cc, libmead/AnalySphere.cc, libmead/AnalySphere.h, libmead/Angle.h, libmead/AtomChargeSet.cc, libmead/AtomChargeSet.h, libmead/AvsScalarField.cc, libmead/AvsScalarField_input.cc, libmead/CLShell.h:
Various changes for compilation under MSVC 7.1. See NOTES of
6 Feb 2007
* swig/premade_MEAD_shadow.cc:
Ugh! Had to hand-edit this for comilation with MSVC!
Added numerous BEGIN/END_CPLUSPLUS_SECTION macro calls and
_USE_MATH_DEFINES to get M_PI etc. from math.h
2007-02-21 [email protected] <bashford@hc-bashford>
* apps/libmso/FlexiSite.cc:
Fix a bug discovered by vivek sharma (email of Feb 21, 2007)
in which rewinding the conf file fails because it was in a non-good
state prior to the rewind. Also put in some error checking on
the state of this fstream and fixed a bit of blabbing output.
2007-02-05 [email protected] <bashford@hc-bashford>
* libmead/FinDiffElstatPot.h, libmead/FinDiffElstatPot.cc:
Changes really done around 25 May 2006 involving "ownership"
of pointed-to AnalyticEP.
2007-02-04 [email protected] <bashford@hc-bashford>
* libmead/SAVanal_calc.cc: Write vertex warnings to blab2, not cerr.
* libmead/OnePointCharge.h, libmead/OnePointCharge.cc, libmead/ManyPointCharge.h, libmead/ManyPointCharge.cc, libmead/FDGridLevel.cc, libmead/ChargeDist.h, libmead/ChargeDist.cc, libmead/AtomChargeSet.h, libmead/AtomChargeSet.cc:
The ChargeDist clsses' get_cuberep function now has an option
to suppress warnings about charges outside the lattice and FDGridLevel
uses it on all levels but the outermost. This avoids spurious
warnings.
2006-05-29 [email protected] <bashford@hc-bashford>
* libmead/sor.cc:
const qualifier on flat iteration pointers to help vectorizer.
2006-05-23 [email protected] <bashford@hc-bashford>
* libmead/AtomSet.h: Better error messages from operator[]
* libmead/globals.cc, libmead/globals.h: error takes string arguments
2006-05-04 [email protected] <bashford@hc-bashford>
* NOTES: check in for May-2006 tag
* ChangeLog: update via VC
* TODO: More stuff to do.
* README: Clarifications on pqr format, esp. w.r.t. chainID.
The -AvsScaleFactor for potential, and some rewording of other stuff
there.
* libmead/FDGridLevel.h, libmead/FDGridLevel.cc, apps/potential/potential.cc:
Added feature, AvsScaleFactor for units control.
(Changes made 7 Dec 05, check in much later)
2006-05-04 [email protected] <bashford@hc-bashford>
* TODO: More stuff to do.
* README: Clarifications on pqr format, esp. w.r.t. chainID.
The -AvsScaleFactor for potential, and some rewording of other stuff
there.
* libmead/FDGridLevel.h, libmead/FDGridLevel.cc, apps/potential/potential.cc:
Added feature, AvsScaleFactor for units control.
(Changes made 7 Dec 05, check in much later)
2005-11-10 [email protected] <bashford@hc-bashford>
* configure.in: Bump version number to 2.2.5
* acinclude.m4:
Fix underquoting per new, more strict aclocal requirements.
2005-11-09 [email protected] <bashford@hc-bashford>
* TODO: Check in for version 2.2.5
* NOTES: Check in for tag v-2-2-5
* utilities/README: Fix a typo (actually done 24 Jan. 2005).
* libmead/MomentAnalysis_tmplts.h:
Increase the default value of ninter in sphereint.
* libmead/AtomSet.cc:
Fixed a bug that was preventing recognition of HETATM records
(Actual date was 15 April 2005)
* apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Now even the David L stuff compiles and runs.
* apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Changes so it all compiles and runs, without commenting-out code
except for some Dave L derived stuff at end.
* apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Under gcc 3.4, Fedora Core 3, only the parts using testAnal are
confirmed to compile, but it runs and results look good.
(The last changes to this file were 21 Feb 2005).
* apps/mulsidecomp/mulsidecomp.cc:
Some minor bug fixes and improvements really made on 15 April 2005.
2005-06-02 [email protected] <bashford@hc-bashford>
* README:
Some clarifications about the interpretation of ATOM and HETATM lines
and the ouput of "potential".
2005-03-25 [email protected] <bashford@hc-bashford>
* utilities/assign_parse_radch.pl: Correct typos in usage
2005-01-25 [email protected] <bashford@hc-bashford>
* libmead/Bigmem.cc:
Change ptr member of MemNode from void* to char* since deletes
on the former are possibly meaningless.
* libmead/posix_using.cc: moved define of _POSIX_SOURCE to top.
This used to break old Sun C++ compilers, but now just do it.
2005-01-21 [email protected] <bashford@hc-bashford>
* testing/expect/sphere-test-solvate-epsin4, testing/expect/sphere-test-solvate-epsin1:
Stop spurious diffs on dirnames.
* testing/expect/sphere-test-solinprot: stop spurious diffs on dirnames
* testing/expect/multiflex-lyso-glu7-test:
Stop spurious diffs on dirnames.
* Makefile.in: remove any .cvsignore files from dist.
* TODO: Check in for 2.2.4 release.
* .cvsignore: Initial version
* apps/libmso/AtomRegex.h, apps/libmso/AtomRegex.cc:
Allow for chainid to be specified in .sites file
Here this requires extension of the AtomRegex format.
* apps/libmso/SiteInMulti.h, apps/libmso/SiteInMulti.cc:
Allow for chainid to be specified in .sites file
* NOTES: Check in for 2.2.4 release
* NEWS: Bring up to date for 2.2.4
* README: Document chainid features
* configure.in: Bump up version number
2005-01-16 [email protected] <bashford@hc-bashford>
* apps/solvate/Makefile.in: Don't try building the obsolete solvate2
(see 6 Jan 05 email from [email protected])
* libmead/ManyPointCharge.h:
Include OnePointCharge, per error report of gerwald jogl
on a Fedora Core 3 system.
2004-12-10 [email protected] <bashford@hc-bashford>
* INSTALLATION: Small correction
* libmead/Makefile.in: Get rid of pair-subopt-rule
* Makefile.in: Sleep a bit befor tar to allow writes to finish.
* ChangeLog: Check in for release 2.3.3
* NOTES: check in for new release
* configure.in:
Get rid of the pair-subopt-rule thing now that Pair.cc is fixed.
* INSTALLATION: Update about status on Linux and Mac.
* swig/sol.py: Don't blab
* libmead/Pair.cc:
Fix a possible significant bug: In the "subsequent cleanup" lists,
cur could be deleted before being used in cur = cur->next.
* acinclude.m4: Bug fix
* apps/libmso/Makefile.in, libmead/Makefile.in: Use ranlib
* Makefile.in:
Fix some distdelete stuff and infinite recursions triggered
by non-distributed dirs.
* swig/interact.py:
Remove blatent syntax errors, but it's still not a working example.
* libmead/MomentAnalysis.cc:
The isnan test is non-portable, so get rid if it.
Trigtrim should take care of it.
2004-12-10 [email protected] <[email protected]>
* NOTES: check in for new release
* configure.in:
Get rid of the pair-subopt-rule thing now that Pair.cc is fixed.
* INSTALLATION: Update about status on Linux and Mac.
* swig/sol.py: Don't blab
* libmead/Pair.cc:
Fix a possible significant bug: In the "subsequent cleanup" lists,
cur could be deleted before being used in cur = cur->next.
* acinclude.m4: Bug fix
* apps/libmso/Makefile.in, libmead/Makefile.in: Use ranlib
* Makefile.in:
Fix some distdelete stuff and infinite recursions triggered
by non-distributed dirs.
* swig/interact.py:
Remove blatent syntax errors, but it's still not a working example.
* libmead/MomentAnalysis.cc:
The isnan test is non-portable, so get rid if it.
Trigtrim should take care of it.
2004-12-09 [email protected] <[email protected]>
* Makefile.in: Python stuff and update new configure features.
* configure.in, acinclude.m4:
Overhaul of pyton handling. Attempts swig, but that's broken anyway
by swig version skew.
* swig/Makefile.in:
Changes corresponding to reworking of configure.in and acinclude.in
* swig/swig_shadow.rule:
Makefile rule for generatying MEAD_shadow.cc and MEAD.py
by running swig et al.
* swig/copy_shadow.rule:
Makefile rule for generatying MEAD_shadow.cc and MEAD.py
by copying from a premade version.
* swig/premade_MEAD.py:
Premade MEAD.py for builds where wrapping via swig et al is not done.
Since swig wrapping is currently broken, this is from a wrapping
from an earlier version.
2004-12-09 [email protected] <[email protected]>
* Makefile.in: Python stuff and update new configure features.
* configure.in, acinclude.m4:
Overhaul of pyton handling. Attempts swig, but that's broken anyway
by swig version skew.
* swig/Makefile.in:
Changes corresponding to reworking of configure.in and acinclude.in
* swig/swig_shadow.rule:
Makefile rule for generatying MEAD_shadow.cc and MEAD.py
by running swig et al.
* swig/copy_shadow.rule:
Makefile rule for generatying MEAD_shadow.cc and MEAD.py
by copying from a premade version.
* swig/premade_MEAD.py:
Premade MEAD.py for builds where wrapping via swig et al is not done.
Since swig wrapping is currently broken, this is from a wrapping
from an earlier version.
2004-12-07 [email protected] <[email protected]>
* configure.in: Bump version to 2.2.3
* libmead/AccTag.h, libmead/Polynomial.h: Typo
2004-12-06 [email protected] <[email protected]>
* acinclude.m4: Simplify finding include dirs for python2
* swig/premade_MEAD_shadow.cc:
Initial is the version generated with MEAD-2.2.2.
* swig/Python_funcs.h: typename qualifier added in various places
* acinclude.m4: Use python2, since numeric only no longer supports 1.5
* Makefile.in: Allow for "make dist" without configuring for python
* NOTES: Another check in for tagging.
* libmead/TPShell.h, libmead/TPShell.cc, libmead/sor.cc, libmead/SolvAccVol.h, libmead/SolvAccVol.cc, libmead/Shell.h, libmead/Shell.cc, libmead/Sausage.h, libmead/Sausage.cc, libmead/Potat.h, libmead/Potat.cc, libmead/PhysCond.h, libmead/PhysCond.cc, libmead/Pair.h, libmead/Pair.cc, libmead/globals.h, libmead/globals.cc, libmead/FinDiffMethod.h, libmead/FinDiffMethod.cc, libmead/FinDiffElstatPot.h, libmead/FinDiffElstatPot.cc, libmead/FDGridLevel.h, libmead/FDGridLevel.cc, libmead/FDChargeIterator.h, libmead/FDChargeIterator.cc, libmead/ElstatPot.h, libmead/ElstatPotCombination.h, libmead/ElstatPot.cc, libmead/ElectrolyteEnvironment.h, libmead/ElectrolyteEnvironment.cc, libmead/DielectricEnvironment.h, libmead/DielectricEnvironment.cc, libmead/DielCubeRep.h, libmead/DielCubeRep.cc, libmead/CubeLatSpec.h, libmead/CubeLatSpec.cc, libmead/CLShell.h, libmead/CLShell.cc, libmead/ChargeDist.h, libmead/ChargeDist.cc, libmead/ChargeCubeRep.h, libmead/ChargeCubeRep.cc, libmead/AvsScalarField.h, libmead/AvsScalarField.cc, libmead/AtomSet.h, libmead/AtomSet.cc, libmead/AtomID.h, libmead/AtomID.cc, libmead/Atom.h, libmead/AtomChargeSet.h, libmead/AtomChargeSet.cc, libmead/Atom.cc, libmead/AnalySlab.h, libmead/AnalySlab.cc, apps/libmso/SiteInMulti.h, apps/libmso/SiteInMulti.cc, apps/libmso/MultiSiteMolecule.h, apps/libmso/MultiSiteMolecule.cc, apps/libmso/MultiFlexiSiteMol.h, apps/libmso/MultiFlexiSiteMol.cc, apps/libmso/FlexiSite.h, apps/libmso/FlexiSite.cc, apps/libmso/AtomRegex.h, apps/libmso/AtomRegex.cc:
Removed pragma interface/implementation stuff (see NOTES).
* NOTES, TODO: Check in for tagging
2004-11-19 [email protected] <[email protected]>
* libmead/Makefile.in, libdevel/Makefile.in, apps/Makefile.common.in:
Don't put "-o $@" in CXXLINK, instead put it in uses of CXXLINK.
This removes redundant -o options in makefile commands.
2004-11-15 [email protected] <[email protected]>
* libmead/TPShell.h, libmead/SphericalHarmonic.cc, libmead/SolvAccVol.cc, libmead/Shell.h, libmead/Potat.cc, libmead/Pair.h, libmead/OnePointCharge.h, libmead/OnePointCharge.cc, libmead/ElstatPotCombination.cc, libmead/ElstatPot.cc, libmead/CubeLatSpec.cc, libmead/Coord.h, libmead/CLShell.h, libmead/AvsScalarField_input.cc, libmead/AvsSF_read_header.cc, libmead/AtomSet.cc, libmead/AnalySphere.cc, apps/solvate/solvate.cc, apps/solinprot/solinprot.cc, apps/sav-driver/sav-driver.cc, apps/potscan/potscan.cc, apps/potential/potential.cc, apps/pair_interactions/pair_interactions.cc, apps/multiflex/multiflex.cc, apps/mulsidecomp/mulsidecomp.cc, apps/libmso/SiteInMulti.cc, apps/libmso/AtomRegex.h, apps/libmso/AtomRegex.cc:
In various files, change from strstream to stringstream (noting that
ostreamstrings usually need to be finished up with a flush, not
an endl, before pulling out their strings.
Also fstreams no longer have nocreate attributes and bin has become
binary.
Not excactly a g++ 3.1 issue, but get rid of Coord(int) and
Coord(float*) ctors (and all uses), which had much potential for error.
* libmead/Coord.h: Remove ctor Coord(int), which was little used.
2003-10-21 [email protected] <[email protected]>
* TODO: Final item and check-in for scripps-last tag
* NOTES: Final notes and checkin for scripps-last tag
* TODO: Several new items added over the last several months
* NOTES: Check in some very old notes from Oct 01 and May 02
* swig/test.py: Account for installation under PyMead package.
* apps/potential/potential.cc:
Prevent spurious warning when fpt file is not given,
but coarsegrid is output.
* README: Added documentation of .fpt file format. Noted availability
of ISCOPE paper on the FTP site. Change addresses to stjude.
* 0README.FIRST: Add stuff about some data files to reproduce papers.
Remove stuff about precompiled executables that aren't really there.
Change my email to stjude.
2003-05-13 [email protected] <[email protected]>
* utilities/assign_charmm_radch.pl:
Stop using depricated split feature.
2003-01-18 [email protected] <[email protected]>
* configure.in: Bump up version number
* NOTES: Checkin for v-2-2-0p2 tage and release
* README: Bump up version number and dates
* INSTALLATION:
Note that it works now on gcc-2.3 and with some newer Pythons
2003-01-17 [email protected] <[email protected]>
* configure.in: MEADVERSION indicates a testing status
* swig/swigpp.el:
Don't rely on C preprocessor to nuke comments while preserving line count.
* NOTES: Notes about some work on python/swig stuff for newer boxes
* apps/sav-driver/sav-driver.cc, apps/potential/potential.cc:
main must return an int
* libmead/OnePointCharge.h: friend syntax fix
* libmead/AvsScalarField_input.cc, libmead/Potat.cc, libmead/SolvAccVol.cc:
Don't use non standard ios stuff like ios::bin
* acinclude.m4:
Look for pyconfig.h if config.h not found in Python dirs.
* configure.in: Use srcdir instead of top_srcdir
* NOTES: Notes about the Vlad patches and new tag on a patch branch
2002-02-03 [email protected] <[email protected]>
* swig/meadtypes.i:
Bug fix: LIST_PTR_OUT was wrapping up pointers to pointers, then
deleting the list of pointers. Removing an & operator fixes it.
2001-09-11 Don Bashford <[email protected]>
* /export/cvsroot/mead/TODO: Check in for tagging
2001-09-10 Don Bashford <[email protected]>
* /export/cvsroot/mead/swig/Makefile.in:
Fix bug causing MEAD.py to come out as C++ code!
* /export/cvsroot/mead/configure.in: bump up version number to 2.2.2
* /export/cvsroot/mead/swig/Makefile.in:
clean ups and better support of dist making
* /export/cvsroot/mead/libmead/MomentAnalysis.cc, /export/cvsroot/mead/libmead/SphericalHarmonic.cc, /export/cvsroot/mead/libmead/MomentAnalysis_tmplts.h, /export/cvsroot/mead/libmead/SphericalHarmonic.h, /export/cvsroot/mead/libmead/MomentAnalysis.h:
Minor corrections to satisfy SGI compiler
2001-09-07 Don Bashford <[email protected]>
* /export/cvsroot/mead/PROBLEMS: Notes about the python interface
* /export/cvsroot/mead/0README.FIRST: mention iscope paper.
* /export/cvsroot/mead/0README.FIRST: Update for the 2.2.0p2 release
2001-09-05 Don Bashford <[email protected]>
* /export/cvsroot/mead/apps/Makefile.in, /export/cvsroot/mead/Makefile.in:
Replace ";" with "&&" in several multi-step commands for more robustness.
* /export/cvsroot/mead/PROBLEMS:
Stuff about Red Hat, gcc versions and Portland Group compiler.
2001-08-24 Don Bashford <[email protected]>
* /export/cvsroot/mead/configure.in: No -g flag by default
* /export/cvsroot/mead/configure.in:
Bump up patch number in MEADVERSION
2001-08-23 Thien-Thi Nguyen, 49614 <ttnttn@gage>
* /export/cvsroot/mead/TODO: Add `top_srcdir' kludge removal item.
2001-08-20 Don Bashford <[email protected]>
* /export/cvsroot/mead/libmead/Angle.h:
Comment out annoying "zero length" warning.
* /export/cvsroot/mead/configure.in:
Update optimization/cpu flags for SGIs
2001-07-13 Don Bashford <[email protected]>
* /export/cvsroot/mead/NOTES, /export/cvsroot/mead/TODO:
Check in before vacation.
* /export/cvsroot/mead/configure.in:
Provide CXX_NOOPTFLAGS, for when optimization should be turned
off (like in compiling the huge, autogenerated MEAD_shadow.cc).
* /export/cvsroot/mead/libmead/SphericalHarmonic.h:
nowraps on friends and assignment operators to stop swig whining.
* /export/cvsroot/mead/swig/meadtypes.i:
Add typemaps for string and x by 4 numeric arrays
* /export/cvsroot/mead/swig/Makefile.in:
Make a reasonable chain of implicit rules for getting from
.h to .j files. Preserve intermediate files.
* /export/cvsroot/mead/swig/MEAD.j: Add MomentAnalysis module.
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Moved some local functions out to MomentAnalysis in libmead
and make the generally useful.
* /export/cvsroot/mead/libmead/Makefile.in:
Add MomentAnalysis.o to MEAD_OBJECTS
* /export/cvsroot/mead/libmead/MomentAnalysis.h:
Many changes. Moved templates out to MomentAnalysis_tmplts.h,
and some functions to MomentAnalysis.cc. Added some analysis
functions and arithmetic operators. Stuff for Python/NumPy.
* /export/cvsroot/mead/libmead/MomentAnalysis_tmplts.h:
Some templates that don't need to be in the regular interface
moved out of MomentAnalysis.h
* /export/cvsroot/mead/libmead/MomentAnalysis.cc:
Some function implemtations moved out of MomentAnalysis.h
2001-07-13 Don Bashford <[email protected]>
* /export/cvsroot/mead/NOTES, /export/cvsroot/mead/TODO:
Check in before vacation.
* /export/cvsroot/mead/configure.in:
Provide CXX_NOOPTFLAGS, for when optimization should be turned
off (like in compiling the huge, autogenerated MEAD_shadow.cc).
* /export/cvsroot/mead/libmead/SphericalHarmonic.h:
nowraps on friends and assignment operators to stop swig whining.
* /export/cvsroot/mead/swig/meadtypes.i:
Add typemaps for string and x by 4 numeric arrays
* /export/cvsroot/mead/swig/Makefile.in:
Make a reasonable chain of implicit rules for getting from
.h to .j files. Preserve intermediate files.
* /export/cvsroot/mead/swig/MEAD.j: Add MomentAnalysis module.
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Moved some local functions out to MomentAnalysis in libmead
and make the generally useful.
* /export/cvsroot/mead/libmead/Makefile.in:
Add MomentAnalysis.o to MEAD_OBJECTS
* /export/cvsroot/mead/libmead/MomentAnalysis.h:
Many changes. Moved templates out to MomentAnalysis_tmplts.h,
and some functions to MomentAnalysis.cc. Added some analysis
functions and arithmetic operators. Stuff for Python/NumPy.
* /export/cvsroot/mead/libmead/MomentAnalysis_tmplts.h:
Some templates that don't need to be in the regular interface
moved out of MomentAnalysis.h
* /export/cvsroot/mead/libmead/MomentAnalysis.cc:
Some function implemtations moved out of MomentAnalysis.h
2001-07-07 Don Bashford <[email protected]>
* /export/cvsroot/mead/swig/Makefile.in:
Add MomentAnalysis.j to list of .j files
2001-07-06 Don Bashford <[email protected]>
* /export/cvsroot/mead/configure.in:
add Makefile generation in apps/sphericalHarmonic_test
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Add tests featuring ChargeDists, ElstatPots and their analysis
using MomentAnalysis.h stuff. (File very messy, but stuff works!)
* /export/cvsroot/mead/libmead/globals.cc:
make ::error blab to standard error, even with USE_EXCEPTIONS.
* /export/cvsroot/mead/libmead/Angle.h:
Supress warning about zero-length vector in Angle ctor.
* /export/cvsroot/mead/libmead/SphericalHarmonic.cc, /export/cvsroot/mead/libmead/SphericalHarmonic.h:
Handle negative m indices for SphericalHarmonics.
New class representing series of SphericalHarmonics.
* /export/cvsroot/mead/libmead/MomentAnalysis.h:
Tools for analyzing charge distributions, scalar fields
(including ElstatPots), and spherical functions in terms of spherical
moments and spherical harmonics.
2001-07-05 Don Bashford <[email protected]>
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Add code for testing SphericalHarmonic class, including
integrator over unit sphere, and generalization of normalization
tests to handle different return types (like complex) different
expected norms and different integration functions.
* /export/cvsroot/mead/libmead/SphericalHarmonic.cc:
Added SphericalHarmonic class.
Provide for Poly to alter the "x" string used for output.
* /export/cvsroot/mead/libmead/SphericalHarmonic.h:
Added SphericalHarmonic class.
Provide for Poly to alter the "x" string used for output.
Important bug fix:
PreSpheHarm copy ctor takes a const reference, not a non-const.
2001-07-04 Don Bashford <[email protected]>
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Deleted the commented-out ModSpheHarm stuff.
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Implementation of classes AssocLegendre and PreSpheHarm moved
out to files SphericalHarmonic.{h,cc} in libmead.
* /export/cvsroot/mead/libmead/SphericalHarmonic.cc, /export/cvsroot/mead/libmead/SphericalHarmonic.h:
Implementation of classes AssocLegendre and PreSpheHarm moved
in from file sphericalHarmonic_test.
* /export/cvsroot/mead/libmead/SphericalHarmonic.cc:
Fix recursive Fibonacci-like slowness in Legendre(int,int) ctor.
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Change SimPreSH name to PreSpheHarm, and comment out all things
pertaining to (now abandoned) ModSpheHarm.
2001-07-03 Don Bashford <[email protected]>
* /export/cvsroot/mead/libmead/SphericalHarmonic.cc:
Fix awful bug in Polynomial subtract operator.
For lagging compilers: <cmath> abs() --> <math.h> fabs(). (Yuk.)
* /export/cvsroot/mead/libmead/SphericalHarmonic.h:
Add memfun to get coefficients of a polynomial.
Add using std::ostream
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Added lots of experimental code --- AssocLegendre class,
and two variants of a Pre-spherical-harmonic class,
and code to test it. At this point all seems to work.
2001-07-03 John Bergsma <[email protected]>
* /export/cvsroot/mead/docs/pymead.tex: The PyMead User Manual
* /export/cvsroot/mead/swig/README:
Added a small reference to the HOWTO-WRAPPING notes
* /export/cvsroot/mead/swig/HOWTO-WRAPPING:
Notes on wrapping using the programs and typemaps created by John Bergsma
2001-07-02 John Bergsma <[email protected]>
* /export/cvsroot/mead/swig/mkoverloaded.pl:
Use J_FILE name as basename for the _overloaded.py and _defs.defs temporary files.
* /export/cvsroot/mead/libmead/Atom.h:
Added a Python write() method.
* /export/cvsroot/mead/libmead/Coord.h: Added a Python write() method
* /export/cvsroot/mead/libmead/AtomSet.h:
Changed values() to return a list of pointers to preserve Python references
Commented out items() because it leaks memory. Has something to do with converting to a list of tuples.
* /export/cvsroot/mead/swig/meadtypes.i:
Added typemaps for converting list of pointers to deal with preserving Python references
* /export/cvsroot/mead/swig/Python_funcs.h:
Return lists of pointers so that Python references are preserved in dict operations like values()
2001-06-29 Don Bashford <[email protected]>
* /export/cvsroot/mead/apps/sphericalHarmonic_test/Makefile.in:
Makefile.in for sphericalHarmonic_test
* /export/cvsroot/mead/apps/sphericalHarmonic_test/sphericalHarmonic_test.cc:
Test driver for classes in SphericalHarmonic.h
* /export/cvsroot/mead/libmead/Polynomial.h, /export/cvsroot/mead/libmead/Polynomial.cc:
Improve some const-ness
* /export/cvsroot/mead/libmead/Makefile.in:
Add SphericalHarmonic.o to MEAD_OBJECTS
* /export/cvsroot/mead/libmead/AnalySphere.cc:
No real changes, just adding comments
* /export/cvsroot/mead/libmead/AtomChargeSet.cc:
Fix bug in total_charge
* /export/cvsroot/mead/swig/MEAD.j:
Add SphericalHarmonic to the list of includes
* /export/cvsroot/mead/swig/Makefile.in:
Fixes to support compilation in separate directory.
Add SphericalHarmonic to the list of headers to wrap.
* /export/cvsroot/mead/swig/meadtypes.i:
Added support for in/out vectors of wrapped class objects via
some macros provided by John, and used it to get a typemap
for vector<Legendre>.
* /export/cvsroot/mead/libmead/SphericalHarmonic.cc, /export/cvsroot/mead/libmead/SphericalHarmonic.h:
Ultimately this should implement spherical harmonics.
For now, just a general polynomial base class, Poly,
and Legendre polynomials.
2001-06-29 John Bergsma <[email protected]>
* /export/cvsroot/mead/swig/mkoperators.pl:
Added operator() support (ie __call__) with the limitation of accepting
at most 2 arguments. It can, however, be multiply defined.
2001-06-29 Don Bashford <[email protected]>
* /export/cvsroot/mead/configure.in: Bump up MEADVERSION by p1
* /export/cvsroot/mead/libmead/AnalySphere.cc:
Bug fix: use internally stored epext, not the one in PhysCond.
* /export/cvsroot/mead/libmead/AtomChargeSet.cc:
Fix bug in total_charge
2001-06-28 John Bergsma <[email protected]>
* /export/cvsroot/mead/swig/mkoverloaded.pl:
No longer derives a class from itself to overload methods, but rather
creates dummy classes and assigns methods from the dummy class to the base
class. This has the advantage of allowing dir(classname) to report all
methods available in the class.
* /export/cvsroot/mead/swig/mkoperators.pl:
Now properly handles both member and non-member operator overloading.
2001-06-27 Don Bashford <[email protected]>
* /export/cvsroot/mead/libmead/AnalySphere.cc:
Bug fix, take the epsext set by the ctor, not from PhysCond
2001-06-26 John Bergsma <[email protected]>
* /export/cvsroot/mead/apps/solvate/Makefile.in:
Needed to specify appname for clean
* /export/cvsroot/mead/swig/Makefile.in:
Added cleanup command for the *_overloaded.py intermediate files
* /export/cvsroot/mead/apps/pair_interactions/Makefile.in:
Added the srcdir definitions for this new application
* /export/cvsroot/mead/apps/solvate/Makefile.in:
Fixed specification of the two appnames
* /export/cvsroot/mead/swig/genpot.py, /export/cvsroot/mead/swig/meadtypes.i, /export/cvsroot/mead/swig/mkoperators.pl, /export/cvsroot/mead/swig/mkoverloaded.pl, /export/cvsroot/mead/swig/removedefs.pl, /export/cvsroot/mead/swig/sol.py, /export/cvsroot/mead/swig/swigpp.el, /export/cvsroot/mead/swig/tat.py, /export/cvsroot/mead/swig/test.py, /export/cvsroot/mead/libmead/PointCharge.h, /export/cvsroot/mead/libmead/SolvAccVol.cc, /export/cvsroot/mead/libmead/SolvAccVol.h, /export/cvsroot/mead/libmead/UniformDielectric.h, /export/cvsroot/mead/libmead/UniformElectrolyte.h, /export/cvsroot/mead/libmead/globals.cc, /export/cvsroot/mead/swig/AccTag.py, /export/cvsroot/mead/swig/CenteringStyle.py, /export/cvsroot/mead/swig/MEAD.j, /export/cvsroot/mead/swig/MEAD_shadow.pat, /export/cvsroot/mead/swig/MEADexcept.py, /export/cvsroot/mead/swig/Makefile.in, /export/cvsroot/mead/swig/PhysCondInstance.py, /export/cvsroot/mead/swig/Python_funcs.h, /export/cvsroot/mead/swig/doctest.py, /export/cvsroot/mead/libmead/ElstatPot.h, /export/cvsroot/mead/libmead/ElstatPotCombination.cc, /export/cvsroot/mead/libmead/ElstatPotCombination.h, /export/cvsroot/mead/libmead/ElySphere.h, /export/cvsroot/mead/libmead/FinDiffElstatPot.h, /export/cvsroot/mead/libmead/FinDiffMethod.cc, /export/cvsroot/mead/libmead/FinDiffMethod.h, /export/cvsroot/mead/libmead/MEADexcept.h, /export/cvsroot/mead/libmead/Makefile.in, /export/cvsroot/mead/libmead/ManyPointCharge.cc, /export/cvsroot/mead/libmead/ManyPointCharge.h, /export/cvsroot/mead/libmead/OnePointCharge.cc, /export/cvsroot/mead/libmead/OnePointCharge.h, /export/cvsroot/mead/libmead/PhysCond.h, /export/cvsroot/mead/libmead/ChargeDist.h, /export/cvsroot/mead/libmead/Coord.h, /export/cvsroot/mead/libmead/CubeLatSpec.h, /export/cvsroot/mead/libmead/Debye.h, /export/cvsroot/mead/libmead/DielByAtoms.h, /export/cvsroot/mead/libmead/DielMembAtoms.h, /export/cvsroot/mead/libmead/DielectricEnvironment.cc, /export/cvsroot/mead/libmead/DielectricEnvironment.h, /export/cvsroot/mead/libmead/DielectricSlab.h, /export/cvsroot/mead/libmead/DielectricSphere.h, /export/cvsroot/mead/libmead/ElectrolyteByAtoms.h, /export/cvsroot/mead/libmead/ElectrolyteEnvironment.cc, /export/cvsroot/mead/libmead/ElectrolyteEnvironment.h, /export/cvsroot/mead/libmead/ElstatPot.cc, /export/cvsroot/mead/libmead/Atom.h, /export/cvsroot/mead/libmead/AtomChargeSet.cc, /export/cvsroot/mead/libmead/AtomChargeSet.h, /export/cvsroot/mead/libmead/AtomID.cc, /export/cvsroot/mead/libmead/AtomID.h, /export/cvsroot/mead/libmead/AtomSet.cc, /export/cvsroot/mead/libmead/AtomSet.h, /export/cvsroot/mead/libmead/ChargeDist.cc, /export/cvsroot/mead/apps/solvate/solvate.cc, /export/cvsroot/mead/apps/solvate/solvate2.cc, /export/cvsroot/mead/libmead/AnalySlab.h, /export/cvsroot/mead/libmead/AnalySphere.cc, /export/cvsroot/mead/libmead/AnalySphere.h, /export/cvsroot/mead/libmead/Atom.cc, /export/cvsroot/mead/apps/Makefile.in, /export/cvsroot/mead/apps/pair_enerdens_test/pair_enerdens_test.cc, /export/cvsroot/mead/apps/solvate/Makefile.in, /export/cvsroot/mead/configure.in, /export/cvsroot/mead/acinclude.m4:
Changes to enable the new Python Interface - tagged as v-2-2-1
* /export/cvsroot/mead/apps/pair_interactions/Makefile.in, /export/cvsroot/mead/apps/pair_interactions/pair_interactions.cc, /export/cvsroot/mead/apps/pair_interactions/pair_interactions.py:
New MEAD application
* /export/cvsroot/mead/apps/pair_interactions/Makefile.in, /export/cvsroot/mead/apps/pair_interactions/pair_interactions.cc, /export/cvsroot/mead/apps/pair_interactions/pair_interactions.py:
New file.
2001-06-16 Don Bashford <[email protected]>
* /export/cvsroot/mead/INSTALLATION:
mention about VPATH feature of make
* /export/cvsroot/mead/PROBLEMS: add stuff about make problems
* /export/cvsroot/mead/apps/Makefile.common.in:
Don't wipe out conventional SUFFIXES.
Use more standard implicit rule syntax in place of % : %.o
* /export/cvsroot/mead/apps/redti/Makefile.in:
Remember to set appname so install will work
2001-06-14 Don Bashford <[email protected]>
* /export/cvsroot/mead/NOTES: Check-in for the 2.2.0 release
* /export/cvsroot/mead/Makefile.in:
Don't distribute (highly preliminary) docs subdir.
* /export/cvsroot/mead/NEWS: added news for the 2.2.0 release
* /export/cvsroot/mead/TODO: The PyMEAD directory thing got done.
Added a todo about AVS stuff.
* /export/cvsroot/mead/PROBLEMS: Major update
* /export/cvsroot/mead/README: Major rewrite of top sections.
* /export/cvsroot/mead/INSTALLATION: Major update
2001-06-13 Don Bashford <[email protected]>
* /export/cvsroot/mead/swig/Makefile.in:
MEAD module should live in PyMead package
* /export/cvsroot/mead/swig/tat.py:
Remove because sol.py and genpot.py do the same thing more clearly
* /export/cvsroot/mead/swig/genpot.py, /export/cvsroot/mead/swig/sol.py, /export/cvsroot/mead/swig/bug.py:
MEAD module should live in PyMead package
* /export/cvsroot/mead/configure.in: Bumped version number up to 2.2.0
* /export/cvsroot/mead/apps/Makefile.common.in:
Fix bug causing mkinstalldirs not to be found.
2001-06-01 Don Bashford <[email protected]>
* /export/cvsroot/mead/apps/solvate/Makefile.in, /export/cvsroot/mead/apps/solinprot/Makefile.in, /export/cvsroot/mead/apps/sav-driver/Makefile.in, /export/cvsroot/mead/apps/redti/Makefile.in, /export/cvsroot/mead/apps/potscan/Makefile.in, /export/cvsroot/mead/apps/potential/Makefile.in, /export/cvsroot/mead/apps/pair_enerdens_test/Makefile.in, /export/cvsroot/mead/apps/multiflex/Makefile.in, /export/cvsroot/mead/apps/mulsidecomp/Makefile.in, /export/cvsroot/mead/apps/kirkwood_test/Makefile.in, /export/cvsroot/mead/apps/gbtest/Makefile.in, /export/cvsroot/mead/apps/debye_test/Makefile.in, /export/cvsroot/mead/apps/add_charge_test/Makefile.in, /export/cvsroot/mead/apps/Makefile.common.in:
srcdir and top_srcdir must be defined from the local Makefiles,
not the common one. (Fixes bug when building in separate directory.)
* /export/cvsroot/mead/examples/lysozyme/README:
added the old lysozyme example
* /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del7, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del8, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del9, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.eps, /export/cvsroot/mead/examples/myoglobin/CTgly.st, /export/cvsroot/mead/examples/myoglobin/GLU.st, /export/cvsroot/mead/examples/myoglobin/HISdel.st, /export/cvsroot/mead/examples/myoglobin/HISeps.st, /export/cvsroot/mead/examples/myoglobin/LYS.st, /export/cvsroot/mead/examples/myoglobin/NTval.st, /export/cvsroot/mead/examples/myoglobin/PROPA.st, /export/cvsroot/mead/examples/myoglobin/PROPD.st, /export/cvsroot/mead/examples/myoglobin/README, /export/cvsroot/mead/examples/myoglobin/TYR.st, /export/cvsroot/mead/examples/myoglobin/collect-curves.pl, /export/cvsroot/mead/examples/myoglobin/make-globals.pl, /export/cvsroot/mead/examples/myoglobin/master.sh, /export/cvsroot/mead/examples/myoglobin/run_mol_multimead.sh, /export/cvsroot/mead/examples/myoglobin/runmcti.sh, /export/cvsroot/mead/examples/solvacc/sav-test.sh, /export/cvsroot/mead/examples/solvacc/trna.pqr, /export/cvsroot/mead/examples/br/GLU.st, /export/cvsroot/mead/examples/br/HE.mgm, /export/cvsroot/mead/examples/br/HE.ogm, /export/cvsroot/mead/examples/br/HE.pqr, /export/cvsroot/mead/examples/br/HE.sites, /export/cvsroot/mead/examples/br/LYR.st, /export/cvsroot/mead/examples/br/LYS.st, /export/cvsroot/mead/examples/br/README, /export/cvsroot/mead/examples/br/RU.mgm, /export/cvsroot/mead/examples/br/RU.ogm, /export/cvsroot/mead/examples/br/RU.pqr, /export/cvsroot/mead/examples/br/RU.sites, /export/cvsroot/mead/examples/br/TYR.st, /export/cvsroot/mead/examples/myoglobin/ARG.st, /export/cvsroot/mead/examples/myoglobin/ASP.st, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.mgm, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.ogm, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.pqr, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del1, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del10, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del11, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del2, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del3, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del4, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del5, /export/cvsroot/mead/examples/myoglobin/COx-AmberBondi.sites.del6, /export/cvsroot/mead/examples/born/README, /export/cvsroot/mead/examples/born/born.ogm, /export/cvsroot/mead/examples/born/born.pqr, /export/cvsroot/mead/examples/br/ARG.st, /export/cvsroot/mead/examples/br/ASP.st, /export/cvsroot/mead/examples/br/ASX.st:
Add files for reproducing lit results from ~/newmead/std-tests/reproduce
* /export/cvsroot/mead/examples/lysozyme/ASPsgl.st, /export/cvsroot/mead/examples/lysozyme/CTLEUsgl.st, /export/cvsroot/mead/examples/lysozyme/GLUsgl.st, /export/cvsroot/mead/examples/lysozyme/HSCsgl.st, /export/cvsroot/mead/examples/lysozyme/LYSsgl.st, /export/cvsroot/mead/examples/lysozyme/NTLYSsgl.st, /export/cvsroot/mead/examples/lysozyme/TYRsgl.st, /export/cvsroot/mead/examples/lysozyme/tric.mgm, /export/cvsroot/mead/examples/lysozyme/tric.ogm, /export/cvsroot/mead/examples/lysozyme/tric.pqr, /export/cvsroot/mead/examples/lysozyme/tric.sites:
added the old lysozyme example
2001-05-10 Don Bashford <[email protected]>
* /export/cvsroot/mead/Makefile.in: try a bug fix
* /export/cvsroot/mead/Makefile.in: bug fix
* /export/cvsroot/mead/swig/Makefile.in: Bug fixes
* /export/cvsroot/mead/ChangeLog, /export/cvsroot/mead/NOTES:
Check in for tag
* /export/cvsroot/mead/libmead/Makefile.in:
Provide for installation of include files.