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