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Convergence tests for protein mutation protocol #95

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Oct 28, 2024
Merged

Convergence tests for protein mutation protocol #95

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67a809c
Neutral protein mutation convergence test
ijpulidos Oct 22, 2024
37520fe
Charge changing protein mutation convergence test
ijpulidos Oct 23, 2024
a4bbde0
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 23, 2024
7419ac1
Using GUFE's JSON decoder
ijpulidos Oct 23, 2024
c58fc53
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 23, 2024
7634135
Using forward-reverse utility function in all tests
ijpulidos Oct 28, 2024
25df867
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 28, 2024
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53 changes: 53 additions & 0 deletions feflow/tests/data/capped_AAs/ARG_capped.pdb
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REMARK 1 CREATED WITH OPENMM 8.1.1, 2024-10-22
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 ARG A 2 1.954 -1.121 0.000 1.00 0.00 N
ATOM 8 H ARG A 2 3.113 -0.999 -0.240 1.00 0.00 H
ATOM 9 CA ARG A 2 1.337 -2.432 -0.001 1.00 0.00 C
ATOM 10 HA ARG A 2 0.663 -2.344 -0.981 1.00 0.00 H
ATOM 11 CB ARG A 2 2.391 -3.535 -0.001 1.00 0.00 C
ATOM 12 HB2 ARG A 2 3.180 -3.267 -0.861 1.00 0.00 H
ATOM 13 HB3 ARG A 2 3.041 -3.594 1.003 1.00 0.00 H
ATOM 14 C ARG A 2 0.461 -2.626 1.229 1.00 0.00 C
ATOM 15 O ARG A 2 -0.621 -3.201 1.139 1.00 0.00 O
ATOM 16 CG ARG A 2 2.084 -5.004 -0.344 1.00 0.00 C
ATOM 17 HG2 ARG A 2 1.598 -5.507 0.625 1.00 0.00 H
ATOM 18 HG3 ARG A 2 3.136 -5.550 -0.506 1.00 0.00 H
ATOM 19 CD ARG A 2 1.099 -5.210 -1.499 1.00 0.00 C
ATOM 20 HD2 ARG A 2 1.752 -5.185 -2.502 1.00 0.00 H
ATOM 21 HD3 ARG A 2 0.191 -4.493 -1.801 1.00 0.00 H
ATOM 22 NE ARG A 2 0.404 -6.514 -1.519 1.00 0.00 N
ATOM 23 HE ARG A 2 -0.766 -6.478 -1.303 1.00 0.00 H
ATOM 24 CZ ARG A 2 0.893 -7.771 -1.573 1.00 0.00 C
ATOM 25 NH1 ARG A 2 2.182 -8.043 -1.320 1.00 0.00 N
ATOM 26 HH11 ARG A 2 2.609 -8.561 -0.336 1.00 0.00 H
ATOM 27 HH12 ARG A 2 2.902 -8.196 -2.257 1.00 0.00 H
ATOM 28 NH2 ARG A 2 0.038 -8.772 -1.831 1.00 0.00 N
ATOM 29 HH21 ARG A 2 -0.588 -8.881 -2.837 1.00 0.00 H
ATOM 30 HH22 ARG A 2 -0.095 -9.737 -1.148 1.00 0.00 H
HETATM 31 N NME A 3 0.933 -2.143 2.381 1.00 0.00 N
HETATM 32 H NME A 3 1.829 -1.678 2.404 1.00 0.00 H
HETATM 33 C NME A 3 0.194 -2.264 3.621 1.00 0.00 C
HETATM 34 H1 NME A 3 -0.745 -2.786 3.436 1.00 0.00 H
HETATM 35 H2 NME A 3 0.786 -2.827 4.344 1.00 0.00 H
HETATM 36 H3 NME A 3 -0.014 -1.271 4.019 1.00 0.00 H
TER 37 NME A 3
CONECT 1 2
CONECT 2 5 1 3 4
CONECT 3 2
CONECT 4 2
CONECT 5 2 6 7
CONECT 6 5
CONECT 7 5
CONECT 14 31
CONECT 31 14 33 32
CONECT 32 31
CONECT 33 34 35 36 31
CONECT 34 33
CONECT 35 33
CONECT 36 33
END
51 changes: 51 additions & 0 deletions feflow/tests/data/capped_AAs/LYS_capped.pdb
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REMARK 1 CREATED WITH OPENMM 8.1.1, 2024-10-22
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 LYS A 2 1.954 -1.121 0.000 1.00 0.00 N
ATOM 8 H LYS A 2 3.122 -1.025 -0.195 1.00 0.00 H
ATOM 9 CA LYS A 2 1.337 -2.432 -0.001 1.00 0.00 C
ATOM 10 HA LYS A 2 0.565 -2.458 -0.915 1.00 0.00 H
ATOM 11 CB LYS A 2 2.391 -3.535 -0.001 1.00 0.00 C
ATOM 12 HB2 LYS A 2 1.702 -4.515 0.088 1.00 0.00 H
ATOM 13 HB3 LYS A 2 3.047 -3.497 0.998 1.00 0.00 H
ATOM 14 C LYS A 2 0.461 -2.626 1.229 1.00 0.00 C
ATOM 15 O LYS A 2 -0.621 -3.201 1.139 1.00 0.00 O
ATOM 16 CG LYS A 2 3.224 -3.837 -1.235 1.00 0.00 C
ATOM 17 HG2 LYS A 2 2.315 -3.880 -2.010 1.00 0.00 H
ATOM 18 HG3 LYS A 2 4.035 -3.108 -1.721 1.00 0.00 H
ATOM 19 CD LYS A 2 4.148 -4.963 -0.767 1.00 0.00 C
ATOM 20 HD2 LYS A 2 4.973 -4.351 -0.150 1.00 0.00 H
ATOM 21 HD3 LYS A 2 3.850 -5.847 -0.026 1.00 0.00 H
ATOM 22 CE LYS A 2 4.914 -5.474 -1.977 1.00 0.00 C
ATOM 23 HE2 LYS A 2 5.858 -5.939 -1.402 1.00 0.00 H
ATOM 24 HE3 LYS A 2 5.434 -4.831 -2.835 1.00 0.00 H
ATOM 25 NZ LYS A 2 4.338 -6.749 -2.436 1.00 0.00 N
ATOM 26 HZ1 LYS A 2 4.059 -6.551 -3.589 1.00 0.00 H
ATOM 27 HZ2 LYS A 2 5.104 -7.672 -2.508 1.00 0.00 H
ATOM 28 HZ3 LYS A 2 3.279 -7.099 -1.995 1.00 0.00 H
HETATM 29 N NME A 3 0.933 -2.143 2.381 1.00 0.00 N
HETATM 30 H NME A 3 1.829 -1.678 2.404 1.00 0.00 H
HETATM 31 C NME A 3 0.194 -2.264 3.621 1.00 0.00 C
HETATM 32 H1 NME A 3 -0.745 -2.786 3.436 1.00 0.00 H
HETATM 33 H2 NME A 3 0.786 -2.827 4.344 1.00 0.00 H
HETATM 34 H3 NME A 3 -0.014 -1.271 4.019 1.00 0.00 H
TER 35 NME A 3
CONECT 1 2
CONECT 2 5 1 3 4
CONECT 3 2
CONECT 4 2
CONECT 5 2 6 7
CONECT 6 5
CONECT 7 5
CONECT 14 29
CONECT 29 14 31 30
CONECT 30 29
CONECT 31 32 33 34 29
CONECT 32 31
CONECT 33 31
CONECT 34 31
END
1 change: 1 addition & 0 deletions feflow/tests/data/capped_AAs/ala_to_arg_mapping.json
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":version:": 1}, "componentA_to_componentB": {"0": 0, "2": 2, "3": 3, "7": 7, "9": 9, "11": 12, "12": 15, "13": 11, "17": 31, "19": 33, "20": 34, "21": 35, "1": 1, "4": 4, "5": 5, "6": 6, "8": 8, "10": 10, "14": 13, "15": 14, "16": 30, "18": 32}, "annotations": "{}", "__qualname__": "LigandAtomMapping", "__module__": "gufe.mapping.ligandatommapping", ":version:": 1}
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