Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
Inversion fixes and amber mostly working
Fixed a bug in BlockSnapshotManager.
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
MPI thermodynamic integration works now.
fixed some version info and the copyright date
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
nothing
Still had some globals toUpper problems - these changes should fix those...
rewrite Globals
fixed the spacing on the banner. Vanity.
Version string in banner (and version numbers in config.h)
xemacs has been drafted to perform our indentation services
avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps
Updated copyright information
moved Package variable into subdirectory makefiles to speed up the building process
Fixed publication details in banner
formatting
merging new_design branch into OOPSE-2.0
define DEV_ROOT as relative path
change Makefile to relative path
change directory structure of application. Every executable file is replaced in seperate directory