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Merge pull request #65 from OpenFreeEnergy/fix_hybridization_ring_filter
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Fix ring hybridization filter
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@jthorton
jthorton authored Nov 18, 2024
2 parents ca54878 + f670838 commit cd226b6
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Showing 5 changed files with 504 additions and 3 deletions.
5 changes: 3 additions & 2 deletions src/kartograf/filters/ring_changes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -156,8 +156,9 @@ def get_atom_ring_hybridization_map(rdmol: Chem.Mol) -> dict[int, bool]:
# Filtering Mapping
filtered_mapping = {}
for ai, aj in mapping.items():
ai_only_arom_sys = atomA_ring_hyb_map[ai]
aj_only_arom_sys = atomB_ring_hyb_map[aj]
# if the atom is not in a ring return False
ai_only_arom_sys = atomA_ring_hyb_map.get(ai, False)
aj_only_arom_sys = atomB_ring_hyb_map.get(aj, False)

if ai_only_arom_sys == aj_only_arom_sys:
filtered_mapping[ai] = aj
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6 changes: 6 additions & 0 deletions src/kartograf/tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,3 +119,9 @@ def fused_ring_mols() -> tuple[SmallMoleculeComponent, SmallMoleculeComponent]:
mol_a, mol_b = [SmallMoleculeComponent.from_rdkit(m) for m in rd_mols]
mol_b_to_a = align_mol_shape(mol_b, ref_mol=mol_a)
return mol_a, mol_b_to_a

@pytest.fixture(scope="session")
def shp2_hybridization_ligands() -> tuple[SmallMoleculeComponent, SmallMoleculeComponent]:
with resources.files("kartograf.tests.data") as d:
mols = [SmallMoleculeComponent.from_sdf_file(str(f)) for f in [d / "lig_E6.sdf", d / "lig_E29.sdf"]]
return mols[0], mols[1]
241 changes: 241 additions & 0 deletions src/kartograf/tests/data/lig_E29.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,241 @@

RDKit 3D

47 49 0 0 0 0 0 0 0 0999 V2000
18.7754 40.1099 3.8002 H 0 0 0 0 0 0 0 0 0 0 0 0
18.6777 40.2314 4.8706 C 0 0 0 0 0 0 0 0 0 0 0 0
19.7468 40.6158 5.5946 C 0 0 0 0 0 0 0 0 0 0 0 0
21.0192 40.8818 4.9003 C 0 0 0 0 0 0 0 0 0 0 0 0
21.0171 41.8873 3.9945 N 0 0 0 0 0 0 0 0 0 0 0 0
22.1653 42.0916 3.3156 C 0 0 0 0 0 0 0 0 0 0 0 0
22.1055 42.8603 2.5624 H 0 0 0 0 0 0 0 0 0 0 0 0
23.3293 41.3033 3.5193 C 0 0 0 0 0 0 0 0 0 0 0 0
24.4899 41.4562 2.7256 N 0 0 0 0 0 0 0 0 0 0 0 0
24.8188 42.7417 2.1171 C 0 0 0 0 0 0 0 0 0 0 0 0
23.9776 43.4260 2.0503 H 0 0 0 0 0 0 0 0 0 0 0 0
25.1240 42.5624 1.0869 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9528 43.4192 2.9002 C 0 0 0 0 0 0 0 0 0 0 0 0
25.5856 43.6625 3.8981 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1980 44.3696 2.4255 H 0 0 0 0 0 0 0 0 0 0 0 0
27.2087 42.5229 3.0068 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8970 42.3874 1.6345 C 0 0 0 0 0 0 0 0 0 0 0 0
27.2619 41.8998 0.8938 H 0 0 0 0 0 0 0 0 0 0 0 0
28.8113 41.7942 1.7084 H 0 0 0 0 0 0 0 0 0 0 0 0
28.1702 43.3626 1.2287 H 0 0 0 0 0 0 0 0 0 0 0 0
28.1742 43.1538 3.9230 N 0 0 0 0 0 0 0 0 0 0 0 0
27.7769 43.2322 4.8532 H 0 0 0 0 0 0 0 0 0 0 0 0
29.0207 42.6059 3.9644 H 0 0 0 0 0 0 0 0 0 0 0 0
26.7863 41.1434 3.5786 C 0 0 0 0 0 0 0 0 0 0 0 0
27.6286 40.4533 3.5771 H 0 0 0 0 0 0 0 0 0 0 0 0
26.4880 41.2540 4.6208 H 0 0 0 0 0 0 0 0 0 0 0 0
25.6075 40.5174 2.8072 C 0 0 0 0 0 0 0 0 0 0 0 0
25.3237 39.5633 3.2539 H 0 0 0 0 0 0 0 0 0 0 0 0
25.9197 40.2722 1.7921 H 0 0 0 0 0 0 0 0 0 0 0 0
23.3267 40.3222 4.4587 N 0 0 0 0 0 0 0 0 0 0 0 0
22.1821 40.1114 5.1371 C 0 0 0 0 0 0 0 0 0 0 0 0
22.2060 39.0712 6.0662 N 0 0 0 0 0 0 0 0 0 0 0 0
21.3655 38.7600 6.5286 H 0 0 0 0 0 0 0 0 0 0 0 0
23.0367 38.5080 6.2095 H 0 0 0 0 0 0 0 0 0 0 0 0
19.6371 40.8386 7.1028 C 0 0 0 0 0 0 0 0 0 0 0 0
20.1496 40.0245 7.6191 H 0 0 0 0 0 0 0 0 0 0 0 0
20.1702 41.7537 7.3603 H 0 0 0 0 0 0 0 0 0 0 0 0
18.1832 40.9556 7.5993 C 0 0 0 0 0 0 0 0 0 0 0 0
18.1577 40.8839 8.6877 H 0 0 0 0 0 0 0 0 0 0 0 0
17.7698 41.9259 7.3434 H 0 0 0 0 0 0 0 0 0 0 0 0
17.2981 39.8754 6.9782 C 0 0 0 0 0 0 0 0 0 0 0 0
16.2781 39.9423 7.3565 H 0 0 0 0 0 0 0 0 0 0 0 0
17.6808 38.9089 7.3029 H 0 0 0 0 0 0 0 0 0 0 0 0
17.3046 39.9236 5.4417 C 0 0 0 0 0 0 0 0 0 0 0 0
16.6078 40.6774 5.0802 H 0 0 0 0 0 0 0 0 0 0 0 0
16.9636 38.9714 5.0364 H 0 0 0 0 0 0 0 0 0 0 0 0
28.3916 44.0828 3.5817 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 44 1 0
2 3 2 0
3 4 1 0
3 35 1 0
4 31 1 0
4 5 2 0
5 6 1 0
6 7 1 0
6 8 2 0
8 9 1 0
8 30 1 0
9 27 1 0
9 10 1 0
10 11 1 0
10 12 1 0
10 13 1 0
13 14 1 0
13 15 1 0
13 16 1 0
16 17 1 0
16 21 1 0
16 24 1 0
17 18 1 0
17 19 1 0
17 20 1 0
21 22 1 0
21 23 1 0
21 47 1 0
24 25 1 0
24 26 1 0
24 27 1 0
27 28 1 0
27 29 1 0
30 31 2 0
31 32 1 0
32 33 1 0
32 34 1 0
35 36 1 0
35 37 1 0
35 38 1 0
38 39 1 0
38 40 1 0
38 41 1 0
41 42 1 0
41 43 1 0
41 44 1 0
44 45 1 0
44 46 1 0
M CHG 1 21 1
M END

> <atom.dprop.PartialCharge>
0.13163000139150213 -0.1050800031169932 -0.21353000608530451 0.31494998725804879 -0.58587998357859061 0.23794999512586187 0.035829996492000339 0.50832998546514108 -0.75827998128977225
0.19682000371369909 0.06843999567184042 0.06843999567184042 -0.10818000343885828 0.072059994365306607 0.072059994365306607 0.15586000474843573 -0.13655999508943964 0.080199999536605587
0.080199999536605587 0.080199999536605587 -0.85518998113718436 0.45449000390920236 0.45449000390920236 -0.10818000343885828 0.072059994365306607 0.072059994365306607 0.19682000371369909
0.06843999567184042 0.06843999567184042 -0.74010998216715262 0.57174998315724923 -0.93444997278299735 0.43125000389966561 0.43125000389966561 -0.032640001003412487 0.051699997659059284
0.051699997659059284 -0.078700000618366489 0.049989996279807804 0.049989996279807804 -0.078590000246433506 0.046179996605249164 0.046179996605249164 -0.059940001194147351
0.060529997374149082 0.060529997374149082 0.45449000390920236

> <b_lp_Chiralities_Consistent>
1

> <i_epik_Tot_Q>
1

> <i_epik_Tot_abs_Q>
1

> <i_f3d_flags>
0

> <i_i_glide_confnum>
19

> <i_i_glide_lignum>
17

> <i_i_glide_posenum>
7

> <i_i_glide_rotatable_bonds>
2

> <i_lp_mmshare_version>
53161

> <i_m_source_file_index>
17

> <ofe-name>
lig_E29

> <r_epik_Charging_Adjusted_Penalty>
0.013028700000000001

> <r_epik_Ionization_Penalty>
0.0133

> <r_epik_Ionization_Penalty_Charging>
0.0130

> <r_epik_Ionization_Penalty_Neutral>
0.0002

> <r_epik_State_Penalty>
-0.0000

> <r_i_docking_score>
-7.6957134029427996

> <r_i_glide_ecoul>
-11.862565994262701

> <r_i_glide_eff_state_penalty>
0

> <r_i_glide_einternal>
0.703849077224731

> <r_i_glide_emodel>
-89.9225863409645

> <r_i_glide_energy>
-57.240186691284201

> <r_i_glide_erotb>
0.43741369017076498

> <r_i_glide_esite>
0

> <r_i_glide_evdw>
-45.377620697021499

> <r_i_glide_gscore>
-7.6957134029427996

> <r_i_glide_hbond>
-0.43198977661645799

> <r_i_glide_ligand_efficiency>
-0.36646254299727599

> <r_i_glide_ligand_efficiency_ln>
-1.9027495882244501

> <r_i_glide_ligand_efficiency_sa>
-1.0110423685872401

> <r_i_glide_lipo>
-1.92524055991004

> <r_i_glide_metal>
0

> <r_i_glide_rewards>
-1.72763082259658

> <r_i_glide_rmsd>
0.098280273803711807

> <r_lp_Energy>
44.176299999999998

> <r_lp_tautomer_probability>
1

> <s_epik_cmdline>
J2VwaWtfcHl0aG9uJywgJy1waHQnLCAnMC4wJywgJy1waCcsICc3LjQnLCAnLXRuJywgJzgnLCAnLW1hJywgJzUwMCcsICctaW1hZScsICc8aW5maWxlLm1hZT4nLCAnLW9tYWUnLCAnPG91dGZpbGUubWFlPic=

> <s_epik_input>
W0NIMl0xW0NIMl1bQ0gyXVtDSDJdW0NIXT1DMWMybltjSF1jKG5jMltOSDJdKU4oW0NIMl1bQ0gyXTMpW0NIMl1bQ0gyXUMzKFtDSDNdKVtOSDJd

> <s_glide_core_constrain_type>
snapped_core_restrain

> <s_i_glide_gridfile>
glide-grid_SHP2-5EHR

> <s_lp_Force_Field>
S-OPLS

> <s_lp_Variant>
lig_E29-1

> <s_m_source_file>
ligprep_shp2.smi

$$$$
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