UC-Davis-molecular-computing/nuad

Issues

• allow subdomains to have multiple parents

  #252 opened 9 months ago by dave-doty
  1

• remove strand groups

  #258 opened 5 months ago by dave-doty
  0

• matplotlib histogram of nearest neighbor energies

  #255 opened 5 months ago by dave-doty
  0

• merge `Result` and `Evaluation`

  #254 opened 6 months ago by dave-doty
  0

• prevent two strands with the same name

  #228 opened 2 years ago by dave-doty
  0

• generalized dependent domains

  #251 opened 9 months ago by dave-doty
  0

• mismatches

  #250 opened 9 months ago by dave-doty
  2

• do not require `length` parameter to `Domain` constructor when `Domain.dependent` is True and subdomains are independent

  #249 opened 9 months ago by dave-doty
  0

• find/use/compare black box stochastic local search optimization software

  #247 opened 10 months ago by dave-doty
  0

• minimize time spent creating `pint.Quantity` objects

  #233 opened a year ago by dave-doty
  2

• RNAplex output missing lines with sufficiently long input

  #244 opened a year ago by dave-doty
  0

• constraint to specify NUPACK/ViennaRNA non-complementary domain binding affinities

  #240 opened a year ago by dave-doty
  0

• use `_normalize_domains_pairs_disjoint_parameters` and `_normalize_strands_pairs_disjoint_parameters`

  #241 opened a year ago by dave-doty
  0

• add unit test actions for Python 3.10, 3.11, 3.12

  #236 opened a year ago by dave-doty
  0

• add Constraint using RNAplex

  #237 opened a year ago by dave-doty
  0

• How to have DomainPools reuse existing strands when possible and generate new ones if not.

  #231 opened 2 years ago by DurhamSmith
  2

• rename "hard" constraints `NumpyConstraint` and `SequenceConstraint` to `NumpyFilter` and `SequenceFilter`

  #227 opened 2 years ago by dave-doty
  0

• fix readthedocs

  #219 opened 2 years ago by dave-doty
  1

• use `|` instead of `Union` for union type annotations

  #216 opened 2 years ago by dave-doty
  0

• implement parallelism for SingularConstraints

  #133 opened 2 years ago by dave-doty
  0

• display constraints report graphically in jupyter notebook

  #213 opened 2 years ago by dave-doty
  0

• remove declaration of private properties in classes

  #210 opened 2 years ago by dave-doty
  0

• store `StrandPair` instead of `Tuple[Strand, Strand]` in `ConstraintWithStrandPairs` and make `_determine_strand_pairs_to_check` more efficient

  #209 opened 2 years ago by dave-doty
  0

• dependent domains whose independent source is fixed should be fixed

  #208 opened 2 years ago by dave-doty
  0

• implement `SearchParameters.report_only_violations`

  #134 opened 2 years ago by dave-doty
  0

• Domains and pools should be stored per-design

  #175 opened 2 years ago by cgevans
  1

• `DomainPool`'s should have distinct names

  #190 opened 2 years ago by cgevans
  0

• allow quit early optimization even when there is positive probability to keep a higher-scoring change

  #124 opened 3 years ago by dave-doty
  1

• fix protocol for choosing dependent domains to change, and independent domains to be weighted to affect change probability

  #201 opened 2 years ago by dave-doty
  0

• pre-packaged strand pair constraints should allow threshold to depend on number of complementary domains

  #191 opened 2 years ago by dave-doty
  1

• store `DomainPool.possible_sequences` as a single longer sequence and substring length

  #197 opened 2 years ago by dave-doty
  0

• Allow inclusion of other arguments in `description` for constraints.

  #195 opened 2 years ago by cgevans
  3

• Parallel constraints will fail on single-cpu systems

  #192 opened 2 years ago by cgevans
  0

• `info_log_file=True` should create output directory before opening log file

  #182 opened 2 years ago by cgevans
  4

• rna_duplex_multiple causes occasional KeyError with parallel=True

  #181 opened 2 years ago by cgevans
  2

• restart runs with different random seeds

  #183 opened 2 years ago by cgevans
  1

• create tool that allows design to be specified and pre-packaged constraints to be picked without writing Python code

  #147 opened 3 years ago by dave-doty
  0

• simplify API of `evaluate` function in constraint

  #148 opened 3 years ago by dave-doty
  0

• automated release notes

  #138 opened 2 years ago by dave-doty
  0

• make PyPI package that does not include NUPACK or ViennaRNA

  #139 opened 2 years ago by dave-doty
  0

• API for creating report on constraints

  #99 opened 3 years ago by dave-doty
  1

• Correct installation instructions for OSX

  #159 opened 3 years ago by JoshPetrack
  0

• `nupack_complex_base_pair_probability_constraint` falsely flags a noncompetitive domain as competitive if it appears in multiple strands

  #144 opened 3 years ago by UnHumbleBen
  1

• add more unit tests

  #140 opened 3 years ago by dave-doty
  0

• profile parallelism to see if speedups can be obtained

  #132 opened 3 years ago by dave-doty
  0

• add check for NUPACK/ViennaRNA when creating constraints

  #127 opened 3 years ago by dave-doty
  0

• add RNA parameter to pfunc and pre-packaged constraints

  #126 opened 3 years ago by dave-doty
  0

• add tutorial

  #120 opened 3 years ago by dave-doty
  0

• return first sequence passing all SequenceConstraint's

  #109 opened 3 years ago by dave-doty
  0

• remove constraints from Design and make it more straightforward for user to read in Design from serialized .json file

  #98 opened 3 years ago by dave-doty
  0