Moltemplate

-Fixed a bug in the ".matrix()" and ".quatT()" coordinate transforms.
-Added the "-orientations", "-quaternions", and "-helix-angles" arguments
to genpoly_lt.py.
-Updated the documentation.
(I doubt these are popular features, hence I don't think anyone will notice.)

added the .matrix() feature, allowing arbitrary linear transformations on molecule coordinates. Fixed a bug in the .quat() coordinate transformation. Updated the moltemplate_manual.

This performs additional post-processing for users of the MOLC coarse-grained model.
(Thanks to Otello M Roscioni and possibly Matteo Ricci at U.Bologna for contributing this feature!)

Fixed a bug preventing imports with absolute paths from working. (I'm referring to the "import" command in moltemplate, not the "import" command in python.) Thanks to Otello M. Roscioni for reporting the bug.

1) new feature: added the "create_static_var" command.
2) fixed a bug in ltemplify.py's python API.
3) added a complex new DNA example into the "examples/coarse_grained" subdirectory.

Simplified the scoping rules for Object definitions and static counter variables (eg aton:C, bond:CH, angle:HCH, ...). Hopefully this should make it easier to create LT files using namespaces and (nested) class definitions which behave in a way which is more similar to languages like python.

(This may eventually ease the transition to creating a version of moltemplate where static node definitions are implemented as python class definitions. It would be nice to have a version of moltemplate which can be run from within python itself.)