StollLab/chiLife issues and pull requests

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

Issue - State: closed - Opened by Mishakolok over 1 year ago - 4 comments
Labels: bug

#68 - Fix urls

Pull Request - State: closed - Opened by mtessmer over 1 year ago

#67 - Pypi prep

Pull Request - State: closed - Opened by mtessmer over 1 year ago

#66 - Fix bug ignoring rotlibs in certain situations

Pull Request - State: closed - Opened by mtessmer over 1 year ago

#65 - Support Nucleic Acids

Issue - State: closed - Opened by mtessmer over 1 year ago - 2 comments

#64 - Fix bug ignoring minimize=False option

Pull Request - State: closed - Opened by mtessmer over 1 year ago

#63 - Fix bug ignoring minimize=False option

Pull Request - State: closed - Opened by mtessmer over 1 year ago

#62 - Refactor rotlib minimization interface and methodology

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#61 - Update nonbonded attribute to be able to exclude 1-n interactions

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#60 - Fix bug in create_dlibrary not aligning library backbone coordinates before saving.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#59 - Implement new method for bifunctinal rotamer modeling

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#58 - Implement new method for bifunctinal rotamer modeling

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#57 - Implement new method for bifunctinal rotamer modeling

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#56 - Bonds bugfix

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#55 - Fix bug only forcing first occurrence of a prefered dihedral

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#54 - Remove assumptions for sort_pdb and get_internal_coords

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#53 - Lots of small changes and feature additions

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#52 - Refactor dSpinLabel to be based off of dRotamerEnsemble

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#51 - Refactor proteinIC

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#50 - Performance improvements to ProteinIC objects and more.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#49 - Improve Protein object performance.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#48 - Fix bug clipping terminal atoms when sorting pdbs

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#47 - Update exampels. Normalize q-factor when saving PDBs for better visualization. Adjust RotamerEnsemble name to include natural aa if it exists.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#46 - Update pdb format

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#45 - Provide explicit function signatures for numba

Issue - State: closed - Opened by stestoll almost 2 years ago - 2 comments

#44 - Document pdb format string

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#43 - Bugfixes, example and test updates.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#42 - Update and add examples

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#41 - Fix from traj bugs

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#40 - Fix repack bug and associated tests

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#39 - Fix squash and merge issues.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#38 - Allow chilife to use CONECT information from PDBS

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#37 - Refactoring, docstrings, typehints

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#36 - Modift energy_func to accept only one argument. Test refactoring.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#35 - Energy function `energy_func` should only take one parameter

Issue - State: closed - Opened by stestoll almost 2 years ago - 1 comment

#34 - Slow test `test_repack_atoms`

Issue - State: closed - Opened by stestoll almost 2 years ago - 2 comments

#33 - Refactor superimposition->alignment. Refactor tests to be less internet dependent

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#32 - Occasional URL retrieve error in test suite

Issue - State: closed - Opened by stestoll almost 2 years ago - 1 comment

#31 - Slow test `test_save_trajectory`

Issue - State: closed - Opened by stestoll almost 2 years ago - 2 comments

#30 - refactor rotlib test

Pull Request - State: closed - Opened by stestoll almost 2 years ago

#29 - refactor rotamer reweighing

Pull Request - State: closed - Opened by stestoll almost 2 years ago

#28 - small adjustment to fundamental constants

Pull Request - State: closed - Opened by stestoll almost 2 years ago

#27 - Add method to save RotamerEnsembles as rotlibs. Several additional bugfixes.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#26 - Make from_trajectory independent of available rotamer libraries.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#25 - Add functions to list and describe rotamer libraries

Issue - State: closed - Opened by mtessmer almost 2 years ago - 1 comment

#24 - Merge develop into main, fixing several overwrites from upstream gitlab mirror.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#23 - Refactor add_library system to create_library

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#22 - Develop

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#21 - Refactor `add_library` to `create_library` and create an new `add_library` function that adds rotlib files.

Issue - State: closed - Opened by mtessmer almost 2 years ago - 1 comment

#20 - `RotamerEnsemble.from_trajectory` should not be dependent on existing rotamer libraries.

Issue - State: closed - Opened by mtessmer almost 2 years ago - 1 comment

#19 - Create method to save RotamerEnsemble instance as a new rotamer library.

Issue - State: closed - Opened by mtessmer almost 2 years ago - 1 comment

#18 - Remove debugging code from tests

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#17 - Merge develop to fix several broken tests and update main branch with progress on protein object.

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#16 - small doc edit

Pull Request - State: closed - Opened by stestoll almost 2 years ago

#15 - Update README to reflect new add_library behavior.

Issue - State: closed - Opened by mtessmer almost 2 years ago - 1 comment

#14 - Merge Develop with new single file rotlib backend

Pull Request - State: closed - Opened by mtessmer almost 2 years ago

#13 - Each spin label libary should be a single file

Issue - State: closed - Opened by stestoll about 2 years ago

#12 - Decouple library name and residue name

Issue - State: closed - Opened by stestoll about 2 years ago - 1 comment

#11 - `get_dd`: eliminiate positional argument `r`

Issue - State: closed - Opened by stestoll about 2 years ago - 2 comments

#10 - Remove default for `site` keyword argument

Issue - State: closed - Opened by stestoll about 2 years ago - 1 comment

#9 - Spin atoms definitions in separate files instead of central `spin_atoms.txt` file

Issue - State: closed - Opened by stestoll about 2 years ago - 1 comment

#8 - `import chiLife` vs `import chilife`

Issue - State: closed - Opened by stestoll about 2 years ago - 1 comment

#7 - `site` vs `resi`

Issue - State: closed - Opened by stestoll about 2 years ago - 1 comment

#6 - remove unused backbone_atoms

Pull Request - State: closed - Opened by stestoll about 2 years ago

#5 - edits to get_dd/pair_dd/etc

Pull Request - State: closed - Opened by stestoll about 2 years ago

#4 - add str for RotamerEnsemble

Pull Request - State: closed - Opened by stestoll about 2 years ago

#3 - remove _rkappas

Pull Request - State: closed - Opened by stestoll about 2 years ago

#2 - convolve instead of fftconvolve

Pull Request - State: closed - Opened by stestoll about 2 years ago

#1 - χ -> chi

Pull Request - State: closed - Opened by stestoll about 2 years ago

GitHub / StollLab/chiLife issues and pull requests