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StollLab/chiLife
New support for icodes breaks repacking if icode is not prepsent in MDA.Universe

  • mtessmer
  • Opened 
    on Feb 18
  • #184

StollLab/chiLife
IntrinsicLabel() does not accept MDAnalysis.AtomGroup as 'spin_atoms', even though the documentation states the opposite

Basically the title. In the code for IntrinsicLabel() there is a check for the type of spin_atoms : https://github.com/StollLab/chiLife/blob/938f173c7fe52ffba32dce18b9c5454befe21aee/src/chilife/IntrinsicLabel.py#L38-L53 ...
  • Mishakolok
  • 1
  • Opened 
    on Dec 26, 2024
  • #176

StollLab/chiLife
MolSysIC.chi_idxs returns unexpected output

  • mtessmer
  • Opened 
    on Dec 5, 2024
  • #171

StollLab/chiLife
xl.mutate only mutates top rotamer or random rotamer. Users should have more fine grained control.

Currently xl.mutate will only place the top rotamer of a rotamer library. More fine grained control would allow users to place specific rotamers or sets of rotamers which would result in a mutated ensemble. ...
  • mtessmer
  • 1
  • Opened 
    on Nov 15, 2024
  • #168

StollLab/chiLife
Save all non-clashing rotamers with the protein

Hello. I am trying to find a way to save the whole protein structures with all rotamers of the mutated residue which don t have clashes. The xl.mutate function uses only the highest probability rotamer. ...
  • amin-sagar
  • 2
  • Opened 
    on Nov 8, 2024
  • #167

StollLab/chiLife
Rotlibs without hydrogens made from RotamerEnsemble.to_library() are not useable.

  • mtessmer
  • Opened 
    on Oct 14, 2024
  • #166

StollLab/chiLife
Bifunctional labels in tutorial can't run

Hi, Chilife is an excellent python package for spin modeling. When I run the Bifunctional labels in tutorial, but: Traceback (most recent call last): File /home/nadou/MD/PycharmProjects/TPT3/tutorial/chiLife-main/examples/09 ...
  • nadounadou
  • 3
  • Opened 
    on Sep 30, 2024
  • #164

StollLab/chiLife
How to handle repack when using SpinLabels made from ORS?

Currently, the repack function uses the SpinLabel.sample() method to sample new label conformations. This method always samples from the underlying rotamer library and not the current state of RotamerEnsemble. ...
  • mtessmer
  • 2
  • Opened 
    on Sep 10, 2024
  • #163

StollLab/chiLife
Support NumPy 2.0

  • stestoll
  • 1
  • Opened 
    on Sep 4, 2024
  • #161

StollLab/chiLife
IntrinsicLabel() with a single atom has no spin_centers set

In the IntrinsicLabel.py file, there is a method spin_centers that calculates the spin center of rotamers in an ensemble. The method uses a check if np.any(self.spin_idx): to determine if there are any ...
  • Mishakolok
  • 1
  • Opened 
    on Aug 27, 2024
  • #159
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