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DasLab
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zetafold
Sandbox for secondary structure modeling
MIT License
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Port unit tests
#29
rhiju
opened
4 years ago
2
EternaFold
#28
rhiju
opened
4 years ago
0
Match Contrafold
#27
rhiju
opened
4 years ago
0
Match Vienna
#26
rhiju
opened
4 years ago
0
S-turns (a.k.a. bulged-G motifs, loop E motifs, sarcin/ricin loop)
#25
rhiju
opened
4 years ago
1
handle dangles & mismatches
#24
rhiju
opened
4 years ago
1
Overflow from large structures
#23
everyday847
closed
4 years ago
1
Rhiju/sum contribs at end
#22
rhiju
closed
5 years ago
0
remove inline derivative stuff
#21
rhiju
closed
5 years ago
0
Rhiju/sum contribs at end
#20
rhiju
closed
5 years ago
0
zetafold simplification
#19
rhiju
opened
5 years ago
0
type annotations
#18
everyday847
opened
5 years ago
0
allow more general definition of motifs (e.g. R = A,G)
#17
rhiju
closed
5 years ago
0
Separate out unit tests into distinct cases for pytest
#16
everyday847
closed
5 years ago
2
`possible_motif_types` to accelerate zetafold with motifs (hopefully dramatically!)
#15
rhiju
closed
5 years ago
0
Speed up by precomputing possible_base_pair_types
#14
rhiju
closed
5 years ago
0
rnasoft/vienna/contrafold/nupack ensemble defects for analysis/
#13
rhiju
closed
5 years ago
0
bug fix with BP specification of C_eff_motif --> C_eff_stack.
#12
rhiju
closed
5 years ago
0
Rhiju/devel: use zetafoldv0.20 for tests
#11
rhiju
closed
5 years ago
0
tiny changes to get tests_zetafold.py to run
#10
rhiju
closed
5 years ago
4
Ramyarangan/python3
#9
ramyarangan
closed
5 years ago
0
prevent overflow by tracking log values not values
#8
rhiju
opened
5 years ago
2
Speed up motifs like internal loops by refactoring them to be like stacked pairs
#7
rhiju
closed
5 years ago
7
Speed up recursions by precomputing `possible_base_pair_types` for each (i,j) once
#6
rhiju
closed
5 years ago
2
Break unit tests into individual cases
#5
everyday847
closed
5 years ago
4
OK, print function and pytest updates, finally
#4
everyday847
closed
5 years ago
4
Rhiju/simplify recursions
#3
rhiju
closed
6 years ago
0
print_function for python2/3 compatibility; some import fixups
#2
everyday847
closed
5 years ago
1
Zero matrix initialization in a one-liner
#1
everyday847
closed
6 years ago
5