
Renumbering Sprint and after:
-----------------------------
(August 2013)
dropped support for Biopython < 1.53

Release notes for ModeRNA 1.7.1
-------------------------------
(September 2011)

- compatibility bug with Biopython 1.5.8 fixed.


Release notes for ModeRNA 1.7.0
-------------------------------
(May 2011)

- new command: get_stacking() 
- reformats atom names.
- added recognition of m7G-mRNA-cap
- resi.pucker is available.
- get_base_pairs return BasePairInteraction objects.
- Technical changes:
  - code borrowed from pycogent removed.
  - major refactoring of ModernaFragment and related classes. 
  - get_... methods of Sequence replaced by properties.
  - package structure revised: moderna.analyze and moderna.builder created.
  - package moderna.topology_matcher merged into moderna.analyze.
  - Resolved circulare dependencies: the module moderna.py is now commands.py --> from moderna import * DOES NOT CHANGE.
  - cleanup in the code using pylint.


Release notes for ModeRNA 1.6.0
-------------------------------
(November 2010)

- new command: write_secstruc()
- new command: change_sequence()
- phosphates are fixed by clean_structure() trying to avoid clashes.
- non-terminal phosphates are fixed by clean_structure() as well.
- sequences are no longer equal if they only differ by modifications.
- bug fixed in extend_helix()
- bug fixed in automatic alignment refinement.
- bug fixed in loading fragments with backbone breaks.
- better string representation of structures and alignments in Python shell.
- improved output of geometry analysis.


Release notes for ModeRNA 1.5.2
-------------------------------
(October 2010)

- standard A-RNA helix based on fiber diffraction data added.
- fixed bugs in RNAChain.
- fixed bugs in ligand recognition and structure cleanup.
- added validation of input for all toplevel commands.
- explicit Sequence(seq) in some commands no longer required.
- Bio.PDB warnings are suppressed.


Release notes for ModeRNA 1.5.1
-------------------------------
(August 2010)

- added recognition of ATP, ADP, AMP, GTP, and many more.
- fixed bug in command line interface.
- fixed bug: ions + water not marked as modifications any more.
- improved ligand recognition
- improved structure cleanup
- renamed commands:
    insert_2D_fragment -> insert_two_strand_fragment
    find_loop -> find_fragment
    insert_loop -> insert_fragment
    write_loop_candidates -> write_fragment_candidates
    apply_loop -> apply_indel
    apply_all_loops -> apply_all_indels
- replaced 'stem residue' by 'anchor residue'	


Release notes for ModeRNA 1.5
-----------------------------
(July 2010)

- Many new functions for modeling with secondary structures:
- New command: get_secstruc        -  returns dot-bracket structure.
- New command: extend_helix        -  adds a WC-paired region.
- New command: shrink_helix        -  removes a region between two WC-pairs.
- New command: add_pair_to_base    -  adds a corresponding WC-paired base.
- New command: insert_2D_fragment  -  adds a 2D motif from a file.
- Linker search can be done with secondary structure constraints.
- Command fix_structure() renamed to clean_structure().
- Command clean_structure adds P to residues if it is missing.
- Command match_template_with_alignment() fixes small inaccuracies in the alignment.
- Refactored ModernaAlignment, RNAChain, and RNAResidue.
- Complete documentation checked.
- Lots of small bugfixes and refactorings.


Release notes for ModeRNA 1.4
-----------------------------
(March 2010)
	
- Mac installation proven working.
- ModeRNA can be installed by 'python setup.py install'
- two new commands: fix_structure() and examine_structure()
- improved documentation on the website.
- improved MMTK support & MMTK installation guide.
- criteria for backbone breaks are stricter - more breaks being recognized.
- BackboneBuilder recognizes intra-residue clashes and messy phosphate groups.
- backbones are fixed using Richardsons suite fragments.
- Linker library can be generated without RNAView (uses a list of chains).
- bug in interpreting gaps at alignment ends fixed.
- updated linker library.


Release notes for ModeRNA 1.3
-----------------------------
(February 2010)

- new command: fix_backbone(model)
- improved loop modeling: 50 candidates examined, distances and RMSD and clashes are only criteria for selection.
- improved remodeling of backbones: using PhosphateBuilder and FCCDLoopCloser
- more strict distance criteria what is a discontinuous backbone.
- faster (374 tests pass in 430 sec instead of 950 sec)
- allowed insertion of long fragments (<100nt).
- compatible with Biopython 1.53 (element column of atoms).
- refactored ModernaFragment.py.
- added chmod a+x moderna/moderna.py to docs.


Release notes for ModeRNA 1.2
-----------------------------
(late 2009)
 
- target and template sequences in the alignment file are switched:
--- target ---> the first sequence in the alignment file
--- template ---> the second sequene in the alignment file


Release notes for ModeRNA 1.1
-----------------------------
(mid 2009)

- There is a new command: renumber_chain(model, start_id)
- Linker insertion uses different atoms now - better loops than before. The linker database has been updated.
- automatic alignment can handle more complicated cases:
  CC---AAAUGUUU
  CCAAA---U-UUU
  (adjacent gaps and gaps interrupted by one base)

- The main functions can now be imported by :
>>> from moderna import *
>>> t = load_template('1ehz.ent')

Cleanup & bugfixes:
- Numeric is no longer necessary -> uses Numpy instead.
- Some module names have been changed to be consistently in CamelCase.
- Class and function names made more consistent.
- unnecessary files have been deleted.
- better error messages when files are missing.
- test data files cleaned up.
- PDB Parser no longer contained -> Bio.PDB used
- Dihedral no longer contained -> Bio.PDB used
- rnasuperposition no longer contained -> shifted to main repository.
- many small bugfixes
