Made CensusJob work well with non-SCOP structures.
forCeSymmTm should call generallySymmetric.
Set count too!
Merge branch 'master' of https://github.com/rcsb/symmetry
Use StructureName to figure out isScopDomain.
Use the new rotationallySymmetricSmart.
Use 3 digits, not 2.
Implemented helical symmetry detection and refactored symmetry related
classes to accommodate changes. Fixed a bug in C2SymmetrySolver. Changed
the way pseudosymmetry is assigned. Added a default gray scale coloring
subunits that are asymmetric in case of local symmetry.
adding gitignore
merging fixes from peter
resolving merge conflicts
Merge branch 'master' of github.com:rcsb/symmetry
version 0.3.1 now supports the detection of Helical symmetries
Merge branch 'master' of https://github.com/rcsb/symmetry
updating API to latest version
Adopted clustering of protein chains for two structures
Merge branch 'master' of https://github.com/rcsb/symmetry
Fixed CensusJobTest.
Changed the criteria to differentiate between helical and cyclic
symmetry. For example, 3J4F has both C2 and helical symmetry. Since the
helical RMSD is lower than the cylic RMSD, now helical symmetry is
assigned in this case.

A new parameter: helixRmsdThreshold was added to QuatSymmetryParameters
that can be used to adjust the preference of helical vs cyclic RMSD.

This update also fixes and an array of of bounds exception in helical
symmetry detection.
Merge branch 'master' of https://github.com/pwrose/symmetry