GilsonLabUCSD/pAPRika

Issues

• Codacy Code Analysis

  #203 opened 2 months ago by jaketanderson
  0

• Quality of life time estimation

  #171 opened 2 months ago by jaketanderson
  7

• Numpy Error in Tutorial

  #198 opened 3 months ago by enrobinson
  9

• Binding affinity in cb6-but-pbc very different

  #199 opened 3 months ago by martinj80
  11

• correct way to run amber MPI executables?

  #200 opened 3 months ago by camattelaer
  1

• Comment about "6.6 is wrong"

  #85 opened 2 years ago by nhenriksen
  0

• Problem with letting through invalid restraints

  #73 opened 2 years ago by jlomibao
  1

• Index should not be win_idx

  #54 opened 2 years ago by nhenriksen
  1

• Tleap not work properly

  #165 opened 2 years ago by rehan1988
  16

• error in paprika tutorial cb6-but

  #185 opened 2 years ago by mauramalinka01
  4

• Add example on running pAPRika through PropertyEstimator via Dask

  #114 opened 2 years ago by slochower
  1

• [WIP] Additional test cases

  #105 opened 6 years ago by slochower
  0

• [TODO] Evaluate center of mass restraints

  #97 opened 2 years ago by slochower
  1

• Integrate Pint units into pAPRika

  #135 opened 3 years ago by jeff231li
  3

• pAPRika error

  #163 opened 3 years ago by rehan1988
  25

• Add osx-arm64 builds to conda-forge recipe

  #161 opened 4 years ago by slochower
  1

• module build not found

  #160 opened 4 years ago by 2young-2simple-sometimes-naive
  7

• Can I perform a antibody-antigen binding free energy calculation on pAPRika?

  #158 opened 4 years ago by meetxinzhang
  3

• Refactor build-related modules into one common namespace?

  #156 opened 4 years ago by jeff231li
  1

• [TODO] Split `analysis.py`

  #96 opened 6 years ago by slochower
  2

• Migrate to Github Actions

  #150 opened 4 years ago by jeff231li
  1

• filter_template function makes loading multiple PDB files impossible

  #141 opened 4 years ago by tuckerburgin
  4

• Images in README.md are missing

  #142 opened 4 years ago by slochower
  4

• Blackify code base

  #134 opened 4 years ago by slochower
  1

• Possible issue with `mbar-block` and `fractions`

  #87 opened 6 years ago by slochower
  2

• Simplify checking if a restraint is changing

  #53 opened 5 years ago by slochower
  0

• Should `_identify_active_rest` be method of the restraint class?

  #52 opened 5 years ago by slochower
  1

• Update all docstrings to NumPy style

  #94 opened 5 years ago by slochower
  1

• Consider migrating to Data Classes

  #113 opened 5 years ago by slochower
  0

• (Current) limitations of `paprika.setup()` convenience feature with OpenMM

  #107 opened 5 years ago by slochower
  0

• I think we should able to index restraint by window

  #101 opened 5 years ago by slochower
  1

• [WIP] OpenFF API design

  #106 opened 6 years ago by slochower
  1

• Store PMF data for `endpoints` method

  #100 opened 6 years ago by nhenriksen
  0

• Undo erroneous README.md regression after merging `k-cl`

  #103 opened 6 years ago by slochower
  1

• Visualization of restraints

  #63 opened 6 years ago by slochower
  1

• Installing from `conda-forge` does not have ParmEd

  #102 opened 6 years ago by slochower
  9

• Add `jupyter` to the conda file.

  #79 opened 6 years ago by slochower
  2

• Repository root directory `environment` may no longer be necessary.

  #89 opened 6 years ago by slochower
  1

• We should adjust `pt.distance()` to use `image=True`

  #90 opened 6 years ago by slochower
  0

• Reference material for NPT replica exchange

  #86 opened 6 years ago by nhenriksen
  2

• Travis builds are taking way too long

  #77 opened 6 years ago by slochower
  6

• Create `simulation.save_input()`

  #88 opened 6 years ago by slochower
  1

• Update tutorials regarding explicit release phases

  #80 opened 6 years ago by slochower
  1

• Put files for tutorial in separate subdirectory

  #78 opened 6 years ago by slochower
  0

• Python .instances() appears to be shared among running jupyter notebooks

  #56 opened 6 years ago by slochower
  1

• Stop analysis if the topology does not match the trajectories

  #72 opened 6 years ago by slochower
  0

• Can pytraj open smirnoff `prmtop`s?

  #55 opened 6 years ago by slochower
  1

• `continuous_apr` is broken for release

  #64 opened 6 years ago by slochower
  4

• Release restraint ordering seems to wrong

  #65 opened 6 years ago by slochower
  1

• Unable to determine changing restraints with no pull phase

  #66 opened 6 years ago by slochower
  3