Peptacular

Added:
- Full ProForma2.0 support
- proforma.py for handling ProForma strings (full support for ProForma2.0)
- Support for all types of internal fragment ions (ax, ay, bx, bx...)
- isotope.py for generating isotope distributions
- apply_static_mod and apply_variable_mods now support n/c term mods
- gno, resid, and xlmod support
- randomizer.py for generating random proforma sequences
- added mods module to handle loading obo files and finding mods
- added fragmenter to fragment.py

Changed:
- Terminal modifications notation has been changed to use []- and -[] for N- and C-terminal modifications, respectively
- All internal modifications now use [] notation
- Element masses/isotopes are generated using physics.nist.gov db
- Move static/var mod builders to mod_builder.py
- Moved combinatorics funcs to combinatorics.py
- All public functions are accessible from peptacular base (suggest using import peptacular as pt)
- Most functions now support a ProFormaAnnotation object
- Improved digest and fragment performance
- Improved docs

Added:
- Permutation / Combination / Product functions in sequence.py
- Immonium Ion support to fragment.py

Added:
- Added support for custom aa masses to mass.py and fragment.py

Added:
- Added isotopes and loss to fragment.py

Added:
- speed_test.py to examples and more examples!
- more term functions! pop_c_term & pop_n_term & _get_c_term_index & _get_n_term_index
- split_sequence function to sequence.py, which splits a sequence into a list of modified single residues
- pop_modifications function to sequence.py, since it's useful!

Changed
- fragment.fragment now returns a list rather than a generator
- identify_cleavage_sites no longer returns cleavage sites at the beginning or end of the sequence (x)PEPTIDE(x)
- removed the x's appended onto sequence when calculating sites
- fixed bug with non-specific digestion
- made term functions more robust, using _get_c_term_index & _get_n_term_index when possible
- split term.py into term.modification and term.residue (it just got too large)

Added:
- term.py - a module for handling terminal modifications
- readthedocs 'sphynx-style' documentation
- examples folder

Changed:
- split up sequence module into sequence and digest
- split mass module into fragment and mass
- updated term modification notation to use square brackets
- renamed most functions... again
- updated documentation to be compatible with sphynx