StollLab/chiLife

Issues

• Rotlibs without hydrogens made from RotamerEnsemble.to_library() are not useable.

  #166 opened 2 months ago by mtessmer
  0

• Bifunctional labels in tutorial can't run

  #164 opened 3 months ago by nadounadou
  2

• How to handle repack when using SpinLabels made from ORS?

  #163 opened 4 months ago by mtessmer
  2

• Support NumPy 2.0

  #161 opened 4 months ago by stestoll
  0

• Add description of PDB-file organization to docs

  #81 opened 2 years ago by mtessmer
  0

• Residues that use different names to diffierentiate alternate charge sates are not recognized when repacking.

  #89 opened 2 years ago by mtessmer
  0

• Complete basic documentation

  #99 opened 4 months ago by mtessmer
  0

• Update docs for version 0.3.0

  #142 opened 4 months ago by mtessmer
  0

• IntrinsicLabel() with a single atom has no spin_centers set

  #159 opened 4 months ago by Mishakolok
  1

• MMM rotlibs are missing N-terminal hydrogen.

  #155 opened 5 months ago by mtessmer
  0

• Implement optional Jax backend

  #152 opened 5 months ago by mtessmer
  0

• Support Nucleic Acids

  #65 opened 6 months ago by mtessmer
  2

• Add bigger docs link to README

  #146 opened 6 months ago by mtessmer
  1

• register chiLife as MDAKit?

  #148 opened 6 months ago by orbeckst
  2

• How to add support for more elements

  #150 opened 6 months ago by aminsagar
  1

• Add conda install instructions to README

  #145 opened 7 months ago by mtessmer
  0

• xl.save distorts ensemble structures when using a pdb file that does not have chain/segment IDs

  #111 opened 7 months ago by mtessmer
  1

• The alpha hydrogen of monofunctional spin labels seems to be moving when chi1 is altered

  #138 opened 7 months ago by mtessmer
  1

• The alpha hydrogen of monofunctional spin labels seems to be moving when chi1 is altered

  #137 opened 7 months ago by mtessmer
  1

• How to save repacked conformations?

  #129 opened 8 months ago by amin-sagar
  4

• MolSys Residue objects have wrong chain ID when iterating.

  #124 opened a year ago by mtessmer
  1

• A SpinLabel object from a xl.repack trajectory: AttributeError: 'SpinLabel' object has no attribute 'spin_atoms'

  #122 opened a year ago by BelyaevaJuly
  3

• write_atoms function fails to pass file object.

  #120 opened a year ago by mtessmer
  1

• Refactor protein and trajectory backends to be macromolecule type independent

  #100 opened a year ago by mtessmer
  1

• Spin label default name gets wrong native residue type when using an atom selection that excludes residues before the spin label site.

  #114 opened a year ago by mtessmer
  1

• Add dRotamerEnsemble examples

  #108 opened a year ago by mtessmer
  1

• xl.save fails when saveing chiLife.Protein if fname does not exist. Also assigning fname after constructin results in an infinte loop

  #109 opened a year ago by mtessmer
  1

• Add rotamer libraries page to docs

  #82 opened a year ago by mtessmer
  0

• Add a FAQ section to docs

  #85 opened a year ago by mtessmer
  0

• Deploy new internal coordinates backend

  #98 opened a year ago by mtessmer
  1

• Migrate from networkx to igraph

  #101 opened a year ago by mtessmer
  1

• Create function to print a detalied description of a rotamer library

  #84 opened a year ago by mtessmer
  1

• Add descriptions to default rotamer libraries

  #86 opened 2 years ago by mtessmer
  1

• Add functions to list and describe rotamer libraries

  #25 opened 2 years ago by mtessmer
  1

• Provide explicit function signatures for numba

  #45 opened 2 years ago by stestoll
  2

• RotamerEnsemble Lennard-Jones parameters taking up too much memory when sampling.

  #73 opened 2 years ago by mtessmer
  1

• Using non-PDB Universe: "AttributeError: 'Topology' object has no attribute 'altLocs'"

  #69 opened 2 years ago by Mishakolok
  4

• `get_dd`: eliminiate positional argument `r`

  #11 opened 2 years ago by stestoll
  2

• Slow test `test_repack_atoms`

  #34 opened 2 years ago by stestoll
  2

• Energy function `energy_func` should only take one parameter

  #35 opened 2 years ago by stestoll
  1

• Slow test `test_save_trajectory`

  #31 opened 2 years ago by stestoll
  2

• Occasional URL retrieve error in test suite

  #32 opened 2 years ago by stestoll
  1

• Create method to save RotamerEnsemble instance as a new rotamer library.

  #19 opened 2 years ago by mtessmer
  1

• `RotamerEnsemble.from_trajectory` should not be dependent on existing rotamer libraries.

  #20 opened 2 years ago by mtessmer
  1

• Remove default for `site` keyword argument

  #10 opened 2 years ago by stestoll
  1

• Refactor `add_library` to `create_library` and create an new `add_library` function that adds rotlib files.

  #21 opened 2 years ago by mtessmer
  1

• Update README to reflect new add_library behavior.

  #15 opened 2 years ago by mtessmer
  1

• Decouple library name and residue name

  #12 opened 2 years ago by stestoll
  1

• Spin atoms definitions in separate files instead of central `spin_atoms.txt` file

  #9 opened 2 years ago by stestoll
  1

• Each spin label libary should be a single file

  #13 opened 2 years ago by stestoll
  0