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258 remove strand groups #259

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258 remove strand groups #259

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af17b86
closes #255 matplotlib histogram of nearest neighbor energies
dave-doty Apr 4, 2024
aa6bd70
Update np.py
dave-doty Apr 4, 2024
eaaabf9
Update np.py
dave-doty Apr 4, 2024
36704ac
Update np.py
dave-doty Apr 4, 2024
1e97db9
Update np.py
dave-doty Apr 4, 2024
e3ad89c
Merge pull request #256 from UC-Davis-molecular-computing/255-matplot…
dave-doty Apr 4, 2024
ac5dd26
Update np.py
dave-doty Apr 4, 2024
b3f8140
Update np.py
dave-doty Apr 5, 2024
751bf49
fixed constraints using ThreadPool to only create it if `parallel` is…
dave-doty Apr 5, 2024
31f0b8c
added tests for pfunc and rnaplex
dave-doty Apr 6, 2024
2d8f884
changed many IDT references to vendor_fields
dave-doty Apr 8, 2024
53e7f98
Update constraints.py
dave-doty Apr 8, 2024
d864681
removed strand groups
lia-n2 Apr 24, 2024
afeb66e
Update constraints.py
dave-doty Apr 24, 2024
03d3b38
Updated constraints.py
lia-n2 May 1, 2024
8d91f69
Update constraints.py
dave-doty May 1, 2024
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11 changes: 6 additions & 5 deletions examples/many_strands_no_common_domains.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,8 @@ def main() -> None:
# num_strands = 10
# num_strands = 10
# num_strands = 50
num_strands = 100
# num_strands = 100
num_strands = 200
# num_strands = 355

design = nc.Design()
Expand Down Expand Up @@ -152,8 +153,8 @@ def main() -> None:
params = ns.SearchParameters(constraints=[
# domain_nupack_ss_constraint,
# strand_individual_ss_constraint,
strand_pairs_rna_duplex_constraint,
# strand_pairs_rna_plex_constraint,
# strand_pairs_rna_duplex_constraint,
strand_pairs_rna_plex_constraint,
# strand_pair_nupack_constraint,
# domain_pair_nupack_constraint,
# domain_pairs_rna_plex_constraint,
Expand All @@ -169,8 +170,8 @@ def main() -> None:
# save_report_for_all_updates=True,
# save_design_for_all_updates=True,
force_overwrite=True,
# log_time=True,
scrolling_output=False,
log_time=True,
# scrolling_output=False,
# report_only_violations=False,
)
ns.search_for_sequences(design, params)
Expand Down
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