[MMTK] MMTK 2.4.4 and 2.5.10

[khinsen at cea.fr]

Release 2.4.4 of MMTK is now available at the usual location. It is a  
bugfix release that removes the compilation errors in the f2c- 
generated lapack_subset.c with GCC 4.0, which is used in MacOS 20.4  
and many recent Linux distributions.

There is no need to update if you have a functional MMTK installation.

For those using the development releases, the current 2.5.10 contains  
the same GCC compatibility fix. As a reminder of what is different  
int the development releases, here is the change log since 2.4.2:



2.5.9 --> 2.5.10
================

Bug fixes:

- MMTK.Proteins.PeptideChain.replaceResidue() did not update the atom  
list
   of the universe.

- Compiler errors with gcc 4.0

Changes:

- Module "Collection" is now named "Collections" to avoid confusion  
with the
   class "Collection". Application code should not import that module  
directly,
   so there should be no compatibility issues.

2.5.8 --> 2.5.9
===============

Improvements:

- Subspace.RigidMotionSubspace avoids the costly SVD calculation by
   constructing an orthonormal basis immediately.
- Src/lapack_subset.c should compile with gcc 4 now.
- MMTK.Proteins.PeptideChain.replaceResidue() could only be used prior
   to the inclusion of the chain into a protein. Now it can be used  
later
   as well, permitting mutations.

2.5.7 --> 2.5.8
===============

Bug fix:

- Bugs concerning storing certain force field terms in trajectory  
descriptions.
- Universe descriptions didn't contain distance constraints in  
AtomCluster
   objects.

2.5.6 --> 2.5.7
===============

New features:

- Support for force field development in Python

2.5.5 --> 2.5.6
===============

New features:

- Support for force field development with Pyrex.

Bug fixes:

- LAPACK error -13 with certain normal mode and subspace operations  
fixed.
- MMTK.Proteins.Residue.phiPsi() could fail for proline residues.

2.5.4 --> 2.5.5
===============

New features:

- New module MoleculeFactory permits the construction of molecules
   from Python code, without requiring database entries.

- Any object can be written to an XML file that uses CML conventions
   as much as possible, the method to call is writeXML(). These files
   can also be read in using XML.XMLMoleculeFactory.

Bug fixes:

- A few C modules crashed on Opteron systems running Linux in 64 bit  
mode.


2.5.3 --> 2.5.4
===============

New features:

- Reorganization of the normal mode module into a package providing
   vibrational, energetic, and Brownian normal modes.
- New module MMTK.ProteinFriction to go with Brownian modes.


2.4.2 --> 2.5.3
===============

New features:

- Amber 99 force field
- New module MMTK.InternalCoordinates
- New methods phiAngle, psiAngle, chiAngle in MMTK.Proteins.Residue


Konrad.
--


---------------------------------------------------------------------
Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr
---------------------------------------------------------------------