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Bump version for dependabot warnings. #39

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Merged
andrewtarzia merged 3 commits into from
Apr 8, 2026
Merged

Bump version for dependabot warnings. #39

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b31a305
Bump version for dependabot warnings.
andrewtarzia Apr 7, 2026
61040d3
Handle mypy unreachable error, due to bad typing above, but requires …
andrewtarzia Apr 8, 2026
b04f687
Update ensemble with changing coordinates from, I am assuming, update…
andrewtarzia Apr 8, 2026
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14 changes: 7 additions & 7 deletions src/cgexplore/_internal/systems_optimisation/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ def get_forcefield(self) -> ForceField: # noqa: C901, PLR0912
term = self.definer_dict[key_] # type: ignore[assignment]

if term[0] == "bond":
bond_terms.append(
bond_terms.append( # type: ignore[unreachable]
define_bond(
interaction_key=key_,
interaction_list=term,
Expand All @@ -151,7 +151,7 @@ def get_forcefield(self) -> ForceField: # noqa: C901, PLR0912
)

elif term[0] == "angle":
angle_terms.append(
angle_terms.append( # type: ignore[unreachable]
define_angle(
interaction_key=key_,
interaction_list=term,
Expand All @@ -160,7 +160,7 @@ def get_forcefield(self) -> ForceField: # noqa: C901, PLR0912
)

elif term[0] == "pyramid":
angle_terms.append(
angle_terms.append( # type: ignore[unreachable]
define_pyramid_angle(
interaction_key=key_,
interaction_list=term,
Expand All @@ -169,7 +169,7 @@ def get_forcefield(self) -> ForceField: # noqa: C901, PLR0912
)

elif term[0] == "cosine":
angle_terms.append(
angle_terms.append( # type: ignore[unreachable]
define_cosine_angle(
interaction_key=key_,
interaction_list=term,
Expand All @@ -178,7 +178,7 @@ def get_forcefield(self) -> ForceField: # noqa: C901, PLR0912
)

elif term[0] == "tors":
torsion_terms.append(
torsion_terms.append( # type: ignore[unreachable]
define_torsion(
interaction_key=key_,
interaction_list=term,
Expand All @@ -187,7 +187,7 @@ def get_forcefield(self) -> ForceField: # noqa: C901, PLR0912
)

elif term[0] == "nb":
nonbonded_terms.append(
nonbonded_terms.append( # type: ignore[unreachable]
define_nonbonded(
interaction_key=key_,
interaction_list=term,
Expand All @@ -196,7 +196,7 @@ def get_forcefield(self) -> ForceField: # noqa: C901, PLR0912
)

elif term[0] == "custom-lj":
nonbonded_terms.append(
nonbonded_terms.append( # type: ignore[unreachable]
define_lennardjones(
interaction_key=key_,
interaction_list=term,
Expand Down
48 changes: 24 additions & 24 deletions tests/ensemble/output/known_ensemble0_base.mol
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Original file line number Diff line number Diff line change
Expand Up @@ -5,30 +5,30 @@
M V30 BEGIN CTAB
M V30 COUNTS 24 25 0 0 0
M V30 BEGIN ATOM
M V30 1 C 3.2837 0.2527 -0.0954 0
M V30 2 N 2.0396 -0.4859 -0.1743 0
M V30 3 C 2.0133 -1.8194 -0.4109 0
M V30 4 N 0.7256 -2.2326 -0.4299 0
M V30 5 C -0.0438 -1.1523 -0.2046 0
M V30 6 C 0.7723 -0.0501 -0.0428 0
M V30 7 C 0.2623 1.2109 0.2037 0
M V30 8 O 1.0252 2.1869 0.3453 0
M V30 9 N -1.0694 1.3223 0.2801 0
M V30 10 C -1.6327 2.6239 0.5361 0
M V30 11 C -1.9024 0.2791 0.1295 0
M V30 12 O -3.1286 0.4429 0.2107 0
M V30 13 N -1.3785 -0.9392 -0.1100 0
M V30 14 C -2.2249 -2.1162 -0.2838 0
M V30 15 H 4.0080 -0.1038 -0.8694 0
M V30 16 H 3.1496 1.3447 -0.1457 0
M V30 17 H 3.7888 0.0409 0.8907 0
M V30 18 H 2.8699 -2.4813 -0.5652 0
M V30 19 H -1.8644 2.8035 1.6042 0
M V30 20 H -0.9430 3.4627 0.2275 0
M V30 21 H -2.5465 2.8220 -0.0865 0
M V30 22 H -2.2213 -2.7337 0.6489 0
M V30 23 H -3.2356 -1.8851 -0.6200 0
M V30 24 H -1.7472 -2.7930 -1.0382 0
M V30 1 C 3.2961 0.2829 -0.0872 0
M V30 2 N 2.0719 -0.4774 -0.1861 0
M V30 3 C 2.0072 -1.8047 -0.4504 0
M V30 4 N 0.7145 -2.2048 -0.4738 0
M V30 5 C -0.0498 -1.1346 -0.2246 0
M V30 6 C 0.8044 -0.0466 -0.0434 0
M V30 7 C 0.2779 1.2025 0.2313 0
M V30 8 O 1.0244 2.1894 0.3969 0
M V30 9 N -1.0624 1.3147 0.3130 0
M V30 10 C -1.6179 2.6190 0.6001 0
M V30 11 C -1.8926 0.2690 0.1393 0
M V30 12 O -3.1304 0.4372 0.2278 0
M V30 13 N -1.3829 -0.9680 -0.1322 0
M V30 14 C -2.2353 -2.1181 -0.3260 0
M V30 15 H 3.9967 -0.1572 -0.8347 0
M V30 16 H 3.1506 1.3592 -0.2177 0
M V30 17 H 3.7583 0.0988 0.9139 0
M V30 18 H 2.8847 -2.4322 -0.6154 0
M V30 19 H -1.8605 2.7835 1.6498 0
M V30 20 H -0.9206 3.4269 0.2699 0
M V30 21 H -2.5167 2.7694 -0.0634 0
M V30 22 H -2.3067 -2.6925 0.6298 0
M V30 23 H -3.2479 -1.8893 -0.6676 0
M V30 24 H -1.7629 -2.8270 -1.0494 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
Expand Down
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