Fixed bug in parseMSA.
Merge branch 'master' of ssh://bitbucket.org/abakan/prody

Conflicts:
	lib/prody/sequence/msaio.c
Merge branch 'devel'
Replaced len func with numAtoms, since len does not give num atoms for chains.
Added CVS version line.
Updated homepage.
Added handling of segment names.
ProDy writes segment names in NMD files.
Fixed saveAtoms key error problem when bonds are set but fragindices are not.
NMD parser can handle segment names.
Improved handling of potential timeout problems, pep8 revisions.
Revised changelog.
Cleaned up code. Removed lines for changing conf file name.
Fixes issue #53, when HOME is not set, no exceptions, just a log message.
Changed order of log messages.
Trimmed whitespace.
Updated changelog.