Closed davidfarinajr closed 4 years ago
Merging #78 into master will increase coverage by
0.27%
. The diff coverage is81.57%
.
@@ Coverage Diff @@
## master #78 +/- ##
==========================================
+ Coverage 64.64% 64.91% +0.27%
==========================================
Files 27 27
Lines 4644 4712 +68
==========================================
+ Hits 3002 3059 +57
- Misses 1642 1653 +11
Impacted Files | Coverage Δ | |
---|---|---|
autotst/calculator/vibrational_analysis.py | 80.76% <78.46%> (-5.54%) |
:arrow_down: |
autotst/calculator/vibrational_analysis_test.py | 85.52% <100.00%> (+2.44%) |
:arrow_up: |
autotst/reaction.py | 80.50% <0.00%> (+0.84%) |
:arrow_up: |
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Also, it looks like you're running into this issue in testing. Might be because you tested with a different branch of RMG? The testing suite uses the binary version.
ERROR: test_validate_by_connecting_the_dots (autotst.calculator.vibrational_analysis_test.VibrationalAnalysisTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/ReactionMechanismGenerator/AutoTST/autotst/calculator/vibrational_analysis_test.py", line 135, in test_validate_by_connecting_the_dots
self.assertTrue(self.vibrational_analysis2.validate_by_connecting_the_dots())
File "/home/travis/build/ReactionMechanismGenerator/AutoTST/autotst/calculator/vibrational_analysis.py", line 314, in validate_by_connecting_the_dots
complex1, complex2 = make_complexes(i)
File "/home/travis/build/ReactionMechanismGenerator/AutoTST/autotst/calculator/vibrational_analysis.py", line 296, in make_complexes
raise_atomtype_exception=False,
File "rmgpy/molecule/molecule.py", line 1706, in rmgpy.molecule.molecule.Molecule.from_xyz
TypeError: from_xyz() got an unexpected keyword argument 'raise_atomtype_exception'
Yes, I guess the binary version doesn't have raise_atomtype_exception
as keyword for from_xyz
. Should I remove that keyword?
Yea, remove it for now and add a comment saying that we should add it in when the binary gets updated. It should be good for now. You may also want to make it into a try and except as well because I'm guessing that argument suppressed errors.
This PR will likely conflict with https://github.com/ReactionMechanismGenerator/AutoTST/pull/79. Lets merge https://github.com/ReactionMechanismGenerator/AutoTST/pull/79 in, then I'll rebase this one.
Well, it looks like this could be merged in automatically and all the checks pass. Shall we merge it in? @davidfarinajr
hmm, interesting. I thought there might be conflicts, but apparently not. Do you want me to rebase it just in case?
If you're willing to -- sure, go for it and rebase. Better safe than sorry. ¯\(ツ)\/¯
I rebased it locally and it looks good, no conflicts. You can go ahead and merge it! Thanks
The main contributions of this PR are 2 new methods to the Vibrational Analysis calculator. 1)
_get_complexes_from_rxn_label()
This method is used invalidate_by_connecting_the_dots()
to obtain the rmg reactant and product complexes, determined by the smiles in the ts reaction label. This method converts all bonds to single in order to check isomorphism to molecules createdfrom_xyz
coords from a log file. 2)validate_by_connecting_the_dots()
This method validates a TS by checking the isomorphism between the reaction label reactant and product complexes (obtained through_get_complexes_from_rxn_label()
) and the two rmgpy.molecule complexes generated usingfrom_xyz
with the coordinates adjusted (plus and minus) by the atom displacements from the negative frequency.I also added unit test for
validate_by_connecting_the_dots()
. Other small changes include 1) addedlog_file
to init a Vibrational Analysis calc 2) addedparser
as Vibrational Analysis calc attribute. 3) addedBr
to obtain_geometries symbol dict