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Fix 164 #165

Merged
merged 18 commits into from
Feb 22, 2024
Merged

Fix 164 #165

merged 18 commits into from
Feb 22, 2024

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chryswoods
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This pull request fixes issue #164

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
  • I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@lohedges

Any additional context of information?

This includes feature_improve_boresch so that we can save CI.

chryswoods and others added 16 commits February 20, 2024 19:58
@chryswoods
Can now detect when the AmberPrm file changes the atom order because of
820e501 
non-contiguous molecules. The reordering info is passed to the frame parsers
when the files are loaded so that they can transparently reorder the
frame data as it is read.
@chryswoods
Added a progress bar and unit test for the amber topology renumbering…
e3440be 
… code.

It all looks like it is working.

Also updated the wrappers with the new Frame function

Also added map support for perturbable properties in GroTop
@chryswoods
Improve flexibility of boresch function
845ac02 
This allows the user to pass in equilibrium values as well as
force constants. In addition, the likely stability of the restraints
is assessed.
@chryswoods
Clear up import and type errors in _restraints.py
3aaa5c7
@chryswoods
Fix bug in boresch return value
8575a6c 
If a name was supplied, BoreschRestraint was called instead of
BoreschRestraints.
@chryswoods
Add tests for boresch plus minor tweaks to boresch
0c5c7cb
@chryswoods
Add Boresch analytical correction and test
7886876
@chryswoods
Improve formatting of examples in boresch and get_standard_state_corr…
412c1eb 
…ection doc strings
@chryswoods
Fix typo in name of sphinx-issues in development guide
202c51a
@chryswoods
Add missing space in boresch example
679c4a4
@chryswoods
Allow boresch arguments to be passed using a map
19b3981
@chryswoods
Tiny tweak to how default temperature is specified
ab55975
@chryswoods
Add Boresch restraints to the tutorial
258e249
@chryswoods
Update changelog
c7a6c2b
@chryswoods
Autoformatting changes [ci skip]
a30d7b7 
Also remove forgotten breakpoint.
@chryswoods
Can now detect when the AmberPrm file changes the atom order because of
3defa43 
non-contiguous molecules. The reordering info is passed to the frame parsers
when the files are loaded so that they can transparently reorder the
frame data as it is read.
@chryswoods chryswoods linked an issue Feb 21, 2024 that may be closed by this pull request
[BUG] AmberPrm reader reorders atoms when molecules are not contiguous in the file #164
Closed
@chryswoods
Added in the SDF scoring fix, and also added the update to Cursor so …
ba41af4 
…that it

is easier to get and set the potential expression of an internal
@chryswoods chryswoods merged commit 72a8c85 into devel Feb 22, 2024
@chryswoods chryswoods deleted the fix_164 branch February 22, 2024 17:43
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Successfully merging this pull request may close these issues.

[BUG] AmberPrm reader reorders atoms when molecules are not contiguous in the file
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@chryswoods