Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Nuclinfo Major Pair and Minor Pair overhaul #3735

Merged
merged 45 commits into from
Oct 10, 2023
Merged
Show file tree
Hide file tree
Changes from 33 commits
Commits
Show all changes
45 commits
Select commit Hold shift + click to select a range
01d08a9
commit major pair and minor pair classes
ALescoulie Jun 17, 2022
cc12345
add minor pair test
ALescoulie Jun 17, 2022
9d3f644
commit major pair dist
ALescoulie Jun 17, 2022
2de4021
update CHANGELOG
ALescoulie Jun 26, 2022
16abe7b
bring up to PEP8
ALescoulie Jun 26, 2022
7215d49
Merge branch 'MDAnalysis:develop' into nuclinfo_dist_rebuild
ALescoulie Jun 26, 2022
c4936b9
Merge branch 'develop' into nuclinfo_dist_rebuild
Aug 19, 2023
c408c69
fix documentation formatting
ALescoulie Aug 20, 2023
ea6bec0
refactor to use select_strand_atoms staticmethod
ALescoulie Aug 20, 2023
7f6600c
fix major and minor pair selections
ALescoulie Aug 21, 2023
1b1f387
refactor tests to use pytest approx
ALescoulie Aug 21, 2023
9165810
remove dihedral import
ALescoulie Aug 21, 2023
a42ae89
fix WCDist not passing all kwargs into selector
ALescoulie Aug 21, 2023
9caa888
add test for empty AtomGroup error
ALescoulie Aug 21, 2023
1973092
update atom names in pair distance classes
Aug 21, 2023
25acf3f
fix whitespace for pep8
Aug 21, 2023
dfdc45d
use typealias for union[residue, reiduegroup]
Aug 21, 2023
0255fb2
revert kwargs names to preserve old api
Aug 28, 2023
6784ba0
update NucPairDist.select_strand_atoms add docs
Aug 29, 2023
572ce2e
refactor results dict and clarify result structure
Aug 29, 2023
ca8e12e
include versionadded in major and minor pair dists
Aug 29, 2023
764da51
refactor WatsonCrickDist to raise
Aug 30, 2023
207f784
make error messages consistent
Aug 30, 2023
dfb9d62
update CHANGELOG
Aug 30, 2023
8d24e1c
Merge branch 'develop' into nuclinfo_dist_rebuild
orbeckst Sep 2, 2023
facde32
fix type alias import issue
Sep 4, 2023
739f3f0
Merge branch 'develop' into nuclinfo_dist_rebuild
ALescoulie Sep 4, 2023
c0d2879
Update author list in changelog
ALescoulie Sep 5, 2023
3d50e12
Update features list in changelog
ALescoulie Sep 5, 2023
eecbf76
Add future decrication notice to WCDist
ALescoulie Sep 5, 2023
21aa853
update documentation with more detailed
Sep 11, 2023
fd35fcb
fix DeprecationWarning in WCDist for case where
Sep 11, 2023
8792223
add verification helper method to WCDist init to
Sep 12, 2023
c9cdf40
Add deprecation notice to docs and changelog for
Sep 25, 2023
8c901cb
fix deprecation_warn test and add test for strand
Sep 25, 2023
d43cbb9
fix docs issues
Sep 27, 2023
815c76f
fix formatting
Sep 27, 2023
78a1ef1
simplify tests
Sep 27, 2023
32af022
Merge branch 'develop' into nuclinfo_dist_rebuild
IAlibay Sep 29, 2023
087c8d6
Update CHANGELOG
orbeckst Oct 9, 2023
2d612c2
Update docs in nucleicacids.py
orbeckst Oct 10, 2023
d7a23f0
Apply suggestions from code review
orbeckst Oct 10, 2023
d625933
fix pep8
Oct 10, 2023
4b908ab
fix pep8 after rebase
Oct 10, 2023
ee44dca
fix pep8 after rebase
Oct 10, 2023
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 9 additions & 1 deletion package/CHANGELOG
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,10 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, richardjgowers

??/??/?? IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, richardjgowers,
ALescoulie


* 2.7.0

Expand All @@ -26,6 +29,8 @@ Fixes
RMSD of None

Enhancements
* Add faster nucleic acid Major and Minor pair distance calculators using
AnalysisBase for updated nucleicacids module (Issue #3720, PR #3735)
* Updated lib.qcprot.CalcRMSDRotationalMatrix to accept either float32 or float64
inputs
* Added a warning about charge neutrality to the documentation of
Expand Down Expand Up @@ -64,6 +69,9 @@ Changes
as DEF is deprecated as of Cython>=3.0 (Issue #4237, PR #4246)

Deprecations
* using `List[Residue]` as input for `analysis.nucleicacids.WatsonCrickDist()` is
deprecated and will be removed in release 3.0.0; instead use a `ResidueGroup`
(Issue #3720, PR #3735)


08/15/23 IAlibay, jaclark5, MohitKumar020291, orionarcher, xhgchen,
Expand Down
Loading