gmso xml equation compare and scaling, and extracting specific data from FFs #698

bc118 · 2022-10-14T18:28:32Z

gmso_equation_compare.py = gmso xml equation compare and scaling for each potential parameter
gmso_specific_ff_to_residue.py = extracting specific data from each force field on a per molecule/residue basis for later use for some file writers.

…rom each force field on a per molecule/residue basis.

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lgtm-com · 2022-10-14T18:34:33Z

This pull request introduces 18 alerts when merging 8a7bf2d into bc557dd - view on LGTM.com

new alerts:

12 for Except block handles 'BaseException'
3 for Unused import
3 for Variable defined multiple times

codecov · 2022-10-14T18:40:59Z

Codecov Report

Base: 91.48% // Head: 92.06% // Increases project coverage by +0.58% 🎉

Coverage data is based on head (ce91160) compared to base (0ba3e94).
Patch coverage: 92.89% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #698      +/-   ##
==========================================
+ Coverage   91.48%   92.06%   +0.58%     
==========================================
  Files          63       65       +2     
  Lines        5450     5838     +388     
==========================================
+ Hits         4986     5375     +389     
+ Misses        464      463       -1

Impacted Files	Coverage Δ
gmso/utils/specific_ff_to_residue.py	`89.66% <89.66%> (ø)`
gmso/utils/equation_compare.py	`97.88% <97.88%> (ø)`
gmso/core/forcefield.py	`96.53% <100.00%> (+1.09%)`	⬆️
gmso/external/convert_mbuild.py	`94.70% <100.00%> (+0.07%)`	⬆️
gmso/parameterization/foyer_utils.py	`100.00% <100.00%> (ø)`
gmso/core/atom.py	`91.78% <0.00%> (+1.36%)`	⬆️
gmso/core/topology.py	`97.87% <0.00%> (+5.66%)`	⬆️

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lgtm-com · 2022-10-28T20:03:54Z

This pull request introduces 18 alerts when merging 9af98ee into bc557dd - view on LGTM.com

new alerts:

12 for Except block handles 'BaseException'
3 for Unused import
3 for Variable defined multiple times

lgtm-com · 2022-11-30T18:27:55Z

This pull request introduces 18 alerts when merging 42c7b71 into 6bcdfcc - view on LGTM.com

new alerts:

12 for Except block handles 'BaseException'
3 for Unused import
3 for Variable defined multiple times

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…case.

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lgtm-com · 2022-12-01T22:15:08Z

This pull request introduces 18 alerts when merging 2dcb2dc into 6bcdfcc - view on LGTM.com

new alerts:

12 for Except block handles 'BaseException'
3 for Unused import
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…t look like elements but don't have the element information included

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lgtm-com · 2022-12-02T22:57:30Z

This pull request introduces 18 alerts when merging 7989b61 into 6bcdfcc - view on LGTM.com

new alerts:

12 for Except block handles 'BaseException'
3 for Unused import
3 for Variable defined multiple times

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CalCraven · 2022-12-05T17:54:46Z

It looks to me like the errors you're seeing for the new xmls you're checking aren't writing out the combining rules. That's the difference in the read and written gmso xmls. To combat this, we need to make some changes to this function or create an xml_writer.py in the forcefield-utilities package.

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lgtm-com · 2022-12-06T00:18:08Z

This pull request introduces 19 alerts when merging 0510ed4 into 6bcdfcc - view on LGTM.com

new alerts:

12 for Except block handles 'BaseException'
4 for Unused import
3 for Variable defined multiple times

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lgtm-com · 2022-12-06T00:53:37Z

This pull request introduces 19 alerts when merging 50c9352 into 6bcdfcc - view on LGTM.com

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4 for Unused import
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lgtm-com · 2022-12-06T00:58:41Z

This pull request introduces 18 alerts when merging 145c040 into 6bcdfcc - view on LGTM.com

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lgtm-com · 2022-12-06T01:28:08Z

This pull request introduces 18 alerts when merging 10c5c01 into 6bcdfcc - view on LGTM.com

new alerts:

12 for Except block handles 'BaseException'
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lgtm-com · 2022-12-08T17:54:07Z

This pull request introduces 18 alerts when merging 67dbd58 into fe321e2 - view on LGTM.com

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…mpare_utils

bc118 · 2023-01-05T21:16:49Z

OK this LGTM now, everything passing, and I successfully tested these files in MoSDeF-GOMC also.

daico007

Some code reformat, will pick up from line 437 (specific_ff_to_residue.py) later.

gmso/utils/specific_ff_to_residue.py

for more information, see https://pre-commit.ci

daico007

LGTM! Some chunk of code could used some refactor (separating molecule in a topology), but I guess that should be handled in a different PR (left a #TODO)

bc118 and others added 2 commits October 14, 2022 14:26

gmso xml equation compare and scaling, and extracting specific data f…

2ca1a8f

…rom each force field on a per molecule/residue basis.

[pre-commit.ci] auto fixes from pre-commit.com hooks

8a7bf2d

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changed sympy code sections to be compatible with sympy 1.11

9af98ee

Merge branch 'mosdef-hub:main' into eqn_compare_utils

42c7b71

bc118 and others added 2 commits December 1, 2022 17:01

added some test cases to specific_ff_to_residue, but still a failing …

bfc8781

…case.

[pre-commit.ci] auto fixes from pre-commit.com hooks

2dcb2dc

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CalCraven and others added 2 commits December 2, 2022 16:47

Fixes for element handling in convert_mbuild and atomtyping sites tha…

c51a3e4

…t look like elements but don't have the element information included

[pre-commit.ci] auto fixes from pre-commit.com hooks

7989b61

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bc118 and others added 3 commits December 5, 2022 19:04

added tests for equation compare and specific_ff_to_residue

8f0f5a6

added tests for equation compare and specific_ff_to_residue

af0539d

[pre-commit.ci] auto fixes from pre-commit.com hooks

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bc118 and others added 8 commits December 5, 2022 19:31

cleaned up specific_ff_to_residue.py

2b42969

cleaned up specific_ff_to_residue.py

365e8a1

cleaned up equation_compare.py

2f23032

cleaned up equation_compare.py

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cleaned up equation_compare.py

bd65f53

cleaned up equation_compare.py

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[pre-commit.ci] auto fixes from pre-commit.com hooks

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cleaned up equation_compare.py

50c9352

bc118 and others added 2 commits December 5, 2022 19:53

cleaned up equation_compare.py

3806bdf

[pre-commit.ci] auto fixes from pre-commit.com hooks

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bc118 and others added 3 commits December 5, 2022 20:16

cleaned up equation_compare.py and specific_eqn_to_ff

93a7928

cleaned up equation_compare.py and specific_eqn_to_ff

4972448

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Merge branch 'main' into eqn_compare_utils

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daico007 and others added 4 commits December 14, 2022 16:25

Merge branch 'main' into eqn_compare_utils

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fix xml test related to newly added XML

81987c5

Merge branch 'main' of https://github.com/mosdef-hub/gmso into eqn_co…

b4713e9

…mpare_utils

Clean up print statement, fix SMARTS string of benzene C

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daico007 reviewed Jan 5, 2023

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some code refactor

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fix typo

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minor edits

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daico007 approved these changes Jan 10, 2023

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Merge branch 'main' into eqn_compare_utils

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daico007 merged commit 2f4be46 into mosdef-hub:main Jan 11, 2023

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gmso xml equation compare and scaling, and extracting specific data from FFs #698

gmso xml equation compare and scaling, and extracting specific data from FFs #698

bc118 commented Oct 14, 2022 •

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gmso xml equation compare and scaling, and extracting specific data from FFs #698

gmso xml equation compare and scaling, and extracting specific data from FFs #698

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