/
RELEASE_NOTES.txt
165 lines (133 loc) · 5.87 KB
/
RELEASE_NOTES.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
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