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pre-commit-ci[bot] committed Oct 31, 2024
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54 changes: 27 additions & 27 deletions feflow/tests/data/capped_AAs/GLU_capped.pdb
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Original file line number Diff line number Diff line change
@@ -1,31 +1,31 @@
REMARK 1 CREATED WITH OPENMM 8.1.1, 2024-10-31
HETATM 1 H1 ACE A 1 1.328 2.173 0.000 1.00 0.00 H
HETATM 2 CH3 ACE A 1 2.006 1.318 0.000 1.00 0.00 C
HETATM 3 H2 ACE A 1 2.634 1.352 0.890 1.00 0.00 H
HETATM 4 H3 ACE A 1 2.634 1.352 -0.890 1.00 0.00 H
HETATM 5 C ACE A 1 1.229 0.000 0.000 1.00 0.00 C
HETATM 6 O ACE A 1 0.000 0.000 0.000 1.00 0.00 O
ATOM 7 N GLU A 2 1.954 -1.121 0.000 1.00 0.00 N
ATOM 8 H GLU A 2 3.130 -0.996 -0.122 1.00 0.00 H
ATOM 9 CA GLU A 2 1.337 -2.432 -0.001 1.00 0.00 C
ATOM 10 HA GLU A 2 0.639 -2.510 -0.966 1.00 0.00 H
ATOM 11 CB GLU A 2 2.391 -3.535 -0.001 1.00 0.00 C
ATOM 12 HB2 GLU A 2 3.174 -3.442 0.897 1.00 0.00 H
ATOM 13 HB3 GLU A 2 1.733 -4.520 0.169 1.00 0.00 H
ATOM 14 C GLU A 2 0.461 -2.626 1.229 1.00 0.00 C
ATOM 15 O GLU A 2 -0.621 -3.201 1.139 1.00 0.00 O
ATOM 16 CG GLU A 2 3.224 -3.837 -1.235 1.00 0.00 C
ATOM 17 HG2 GLU A 2 2.633 -4.297 -2.167 1.00 0.00 H
ATOM 18 HG3 GLU A 2 3.897 -2.967 -1.700 1.00 0.00 H
ATOM 19 CD GLU A 2 4.148 -4.963 -0.767 1.00 0.00 C
ATOM 20 OE1 GLU A 2 3.726 -5.953 -0.125 1.00 0.00 O
ATOM 21 OE2 GLU A 2 5.218 -4.912 -1.414 1.00 0.00 O
HETATM 22 N NME A 3 0.933 -2.143 2.381 1.00 0.00 N
HETATM 23 H NME A 3 1.829 -1.678 2.404 1.00 0.00 H
HETATM 24 C NME A 3 0.194 -2.264 3.621 1.00 0.00 C
HETATM 25 H1 NME A 3 -0.745 -2.786 3.436 1.00 0.00 H
HETATM 26 H2 NME A 3 0.786 -2.827 4.344 1.00 0.00 H
HETATM 27 H3 NME A 3 -0.014 -1.271 4.019 1.00 0.00 H
HETATM 1 H1 ACE A 1 1.328 2.173 0.000 1.00 0.00 H
HETATM 2 CH3 ACE A 1 2.006 1.318 0.000 1.00 0.00 C
HETATM 3 H2 ACE A 1 2.634 1.352 0.890 1.00 0.00 H
HETATM 4 H3 ACE A 1 2.634 1.352 -0.890 1.00 0.00 H
HETATM 5 C ACE A 1 1.229 0.000 0.000 1.00 0.00 C
HETATM 6 O ACE A 1 0.000 0.000 0.000 1.00 0.00 O
ATOM 7 N GLU A 2 1.954 -1.121 0.000 1.00 0.00 N
ATOM 8 H GLU A 2 3.130 -0.996 -0.122 1.00 0.00 H
ATOM 9 CA GLU A 2 1.337 -2.432 -0.001 1.00 0.00 C
ATOM 10 HA GLU A 2 0.639 -2.510 -0.966 1.00 0.00 H
ATOM 11 CB GLU A 2 2.391 -3.535 -0.001 1.00 0.00 C
ATOM 12 HB2 GLU A 2 3.174 -3.442 0.897 1.00 0.00 H
ATOM 13 HB3 GLU A 2 1.733 -4.520 0.169 1.00 0.00 H
ATOM 14 C GLU A 2 0.461 -2.626 1.229 1.00 0.00 C
ATOM 15 O GLU A 2 -0.621 -3.201 1.139 1.00 0.00 O
ATOM 16 CG GLU A 2 3.224 -3.837 -1.235 1.00 0.00 C
ATOM 17 HG2 GLU A 2 2.633 -4.297 -2.167 1.00 0.00 H
ATOM 18 HG3 GLU A 2 3.897 -2.967 -1.700 1.00 0.00 H
ATOM 19 CD GLU A 2 4.148 -4.963 -0.767 1.00 0.00 C
ATOM 20 OE1 GLU A 2 3.726 -5.953 -0.125 1.00 0.00 O
ATOM 21 OE2 GLU A 2 5.218 -4.912 -1.414 1.00 0.00 O
HETATM 22 N NME A 3 0.933 -2.143 2.381 1.00 0.00 N
HETATM 23 H NME A 3 1.829 -1.678 2.404 1.00 0.00 H
HETATM 24 C NME A 3 0.194 -2.264 3.621 1.00 0.00 C
HETATM 25 H1 NME A 3 -0.745 -2.786 3.436 1.00 0.00 H
HETATM 26 H2 NME A 3 0.786 -2.827 4.344 1.00 0.00 H
HETATM 27 H3 NME A 3 -0.014 -1.271 4.019 1.00 0.00 H
TER 28 NME A 3
CONECT 1 2
CONECT 2 5 1 3 4
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52 changes: 26 additions & 26 deletions feflow/tests/data/capped_AAs/PRO_capped.pdb
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Original file line number Diff line number Diff line change
@@ -1,30 +1,30 @@
REMARK 1 CREATED WITH OPENMM 8.1.1, 2024-10-29
HETATM 1 H1 ACE A 1 1.328 2.173 0.000 1.00 0.00 H
HETATM 2 CH3 ACE A 1 2.006 1.318 0.000 1.00 0.00 C
HETATM 3 H2 ACE A 1 2.634 1.352 0.890 1.00 0.00 H
HETATM 4 H3 ACE A 1 2.634 1.352 -0.890 1.00 0.00 H
HETATM 5 C ACE A 1 1.229 0.000 0.000 1.00 0.00 C
HETATM 6 O ACE A 1 0.000 0.000 0.000 1.00 0.00 O
ATOM 7 N PRO A 2 1.954 -1.121 0.000 1.00 0.00 N
ATOM 8 CA PRO A 2 1.337 -2.432 -0.001 1.00 0.00 C
ATOM 9 HA PRO A 2 0.612 -2.550 -0.943 1.00 0.00 H
ATOM 10 CB PRO A 2 2.391 -3.535 -0.001 1.00 0.00 C
ATOM 11 HB2 PRO A 2 2.914 -3.999 0.970 1.00 0.00 H
ATOM 12 HB3 PRO A 2 1.966 -4.516 -0.542 1.00 0.00 H
ATOM 13 C PRO A 2 0.461 -2.626 1.229 1.00 0.00 C
ATOM 14 O PRO A 2 -0.621 -3.201 1.139 1.00 0.00 O
ATOM 15 CD PRO A 2 3.378 -1.375 -0.101 1.00 0.00 C
ATOM 16 HD2 PRO A 2 4.099 -1.236 0.843 1.00 0.00 H
ATOM 17 HD3 PRO A 2 3.939 -0.750 -0.954 1.00 0.00 H
ATOM 18 CG PRO A 2 3.469 -2.740 -0.790 1.00 0.00 C
ATOM 19 HG2 PRO A 2 3.305 -2.861 -1.971 1.00 0.00 H
ATOM 20 HG3 PRO A 2 4.567 -3.189 -0.609 1.00 0.00 H
HETATM 21 N NME A 3 0.933 -2.143 2.381 1.00 0.00 N
HETATM 22 H NME A 3 1.829 -1.678 2.404 1.00 0.00 H
HETATM 23 C NME A 3 0.194 -2.264 3.621 1.00 0.00 C
HETATM 24 H1 NME A 3 -0.745 -2.786 3.436 1.00 0.00 H
HETATM 25 H2 NME A 3 0.786 -2.827 4.344 1.00 0.00 H
HETATM 26 H3 NME A 3 -0.014 -1.271 4.019 1.00 0.00 H
HETATM 1 H1 ACE A 1 1.328 2.173 0.000 1.00 0.00 H
HETATM 2 CH3 ACE A 1 2.006 1.318 0.000 1.00 0.00 C
HETATM 3 H2 ACE A 1 2.634 1.352 0.890 1.00 0.00 H
HETATM 4 H3 ACE A 1 2.634 1.352 -0.890 1.00 0.00 H
HETATM 5 C ACE A 1 1.229 0.000 0.000 1.00 0.00 C
HETATM 6 O ACE A 1 0.000 0.000 0.000 1.00 0.00 O
ATOM 7 N PRO A 2 1.954 -1.121 0.000 1.00 0.00 N
ATOM 8 CA PRO A 2 1.337 -2.432 -0.001 1.00 0.00 C
ATOM 9 HA PRO A 2 0.612 -2.550 -0.943 1.00 0.00 H
ATOM 10 CB PRO A 2 2.391 -3.535 -0.001 1.00 0.00 C
ATOM 11 HB2 PRO A 2 2.914 -3.999 0.970 1.00 0.00 H
ATOM 12 HB3 PRO A 2 1.966 -4.516 -0.542 1.00 0.00 H
ATOM 13 C PRO A 2 0.461 -2.626 1.229 1.00 0.00 C
ATOM 14 O PRO A 2 -0.621 -3.201 1.139 1.00 0.00 O
ATOM 15 CD PRO A 2 3.378 -1.375 -0.101 1.00 0.00 C
ATOM 16 HD2 PRO A 2 4.099 -1.236 0.843 1.00 0.00 H
ATOM 17 HD3 PRO A 2 3.939 -0.750 -0.954 1.00 0.00 H
ATOM 18 CG PRO A 2 3.469 -2.740 -0.790 1.00 0.00 C
ATOM 19 HG2 PRO A 2 3.305 -2.861 -1.971 1.00 0.00 H
ATOM 20 HG3 PRO A 2 4.567 -3.189 -0.609 1.00 0.00 H
HETATM 21 N NME A 3 0.933 -2.143 2.381 1.00 0.00 N
HETATM 22 H NME A 3 1.829 -1.678 2.404 1.00 0.00 H
HETATM 23 C NME A 3 0.194 -2.264 3.621 1.00 0.00 C
HETATM 24 H1 NME A 3 -0.745 -2.786 3.436 1.00 0.00 H
HETATM 25 H2 NME A 3 0.786 -2.827 4.344 1.00 0.00 H
HETATM 26 H3 NME A 3 -0.014 -1.271 4.019 1.00 0.00 H
TER 27 NME A 3
CONECT 1 2
CONECT 2 5 1 3 4
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11 changes: 8 additions & 3 deletions feflow/tests/test_protein_mutation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,7 @@ def pro_capped():
protein_comp = ProteinComponent.from_pdb_file(input_pdb)
return protein_comp


@pytest.fixture(scope="session")
def glu_capped():
"""ProteinComponent for Glutamic Acid residue capped by ACE and NME."""
Expand Down Expand Up @@ -525,7 +526,9 @@ def test_charge_changing_convergence(
f"6 * dDDG ({6 * arg_lys_diff_error})"
)

def test_proline_mutation_fails(self, ala_capped_system, pro_capped_system, ala_to_pro_mapping):
def test_proline_mutation_fails(
self, ala_capped_system, pro_capped_system, ala_to_pro_mapping
):
"""Test that attempting to make a protein mutation that involves proline (or ring breaking
transformations) is not handled and results in an error.
Expand Down Expand Up @@ -556,7 +559,9 @@ def test_proline_mutation_fails(self, ala_capped_system, pro_capped_system, ala_
mapping=ala_to_pro_mapping,
)

def test_double_charge_fails(self, lys_capped_system, glu_capped_system, lys_to_glu_mapping):
def test_double_charge_fails(
self, lys_capped_system, glu_capped_system, lys_to_glu_mapping
):
"""
Test that attempting a mutation with a double charge change between lysine and glutamate
systems raises a `NotSupportedError`.
Expand Down Expand Up @@ -587,4 +592,4 @@ def test_double_charge_fails(self, lys_capped_system, glu_capped_system, lys_to_
stateB=glu_capped_system,
name="Invalid proline mutation",
mapping=lys_to_glu_mapping,
)
)

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