Closed davidfarinajr closed 4 years ago
This is where we are getting the IndexError in the molecule.is_linear()
method. We are not checking if len(bonds) == 0
for atom in self.vertices:
bonds = list(atom.edges.values())
if len(bonds) == 1:
continue # ok, next atom
if len(bonds) > 2:
break # fail!
if bonds[0].is_single() and bonds[1].is_triple():
continue # ok, next atom
if bonds[1].is_single() and bonds[0].is_triple():
continue # ok, next atom
break # fail if we haven't continued
else:
# didn't fail
return True
Perhaps we should open a PR with rmgpy as well. Although this method is not typically used for rmg molecules with nonbonded atoms
Merging #76 into master will decrease coverage by
0.02%
. The diff coverage is66.66%
.
@@ Coverage Diff @@
## master #76 +/- ##
==========================================
- Coverage 64.66% 64.64% -0.03%
==========================================
Files 27 27
Lines 4641 4644 +3
==========================================
+ Hits 3001 3002 +1
- Misses 1640 1642 +2
Impacted Files | Coverage Δ | |
---|---|---|
autotst/species.py | 72.32% <66.66%> (-0.19%) |
:arrow_down: |
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Looking at the PR itself, it looks good and makes sense. However, there's a weird issue with the decrease in coverage. Once this is addressed and the tests pass, I'm happy to merge this in.
coverage looks fine now. I messed up my first commit and had to force push. Mixed up continue
and pass
🙃
conformer.rmg_molecule.is_linear()
raisesIndexError
for autotst TS's that have atoms with no bonds such as an H_Abstraction by an atom (H, F, Cl, or Br). This commit adds a try and except block to keep it from crashing.