Fixed several mistakes. Added the PYTHONPATH trick.
Merge pull request #8 from gui11aume/patch-1

Fixed several mistakes. Added the PYTHONPATH trick.
fix consistency writing
fix consistency wtiting. fix write cmm
FIX: write density
Unfinished FIXES around eqv position
merged
mcl clustering now faster. Clustering excludes singletons
fixes #9 for clustering, now random caracters a added to tmp file name
completed Gui11aume s solution to fix #7 . This problem is really specific to IMP installation in Debian machines, on MAC or Fedora the (nice) PYTHONPATH trick may not be necessary.
Fix doc, thanks to Davide s comments
many changes in doc: merge from Davide revision
resolution of #3 for particles of structral models
Resolves #10
resolution of #3 Chromosome.visualize
unfunctional commit, improving for #3. better alignment drawing
Fix alignment problem due to TADs starting at 0. Fix drawing of aligned experiments at different resolutions
draw alignment working. Needs to think about esthetics now...
more efficient check of zero columns. Draw alignment 5 times faster
FIX clustering: problem RMSD vs dRMSD