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Bug fixes SuCOS score (#42)
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SuCOS module:
- ensure score not larger than 1
- handle molecules without features - will only use shape overlap
- add references to RDKit blog and papers for feature map-based similarity metrics
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@maabuu
maabuu authored Jul 10, 2024
1 parent 77433ea commit 7d9f377
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Showing 12 changed files with 599 additions and 13 deletions.
2 changes: 1 addition & 1 deletion posebusters/__init__.py
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Expand Up @@ -24,4 +24,4 @@
"check_volume_overlap",
]

__version__ = "0.2.14"
__version__ = "0.2.15"
36 changes: 25 additions & 11 deletions posebusters/modules/sucos.py
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Expand Up @@ -34,22 +34,30 @@ def get_feature_map_score(
) -> float:
"""Calculate the feature map score between two molecules.
Good introduction:
https://greglandrum.github.io/rdkit-blog/posts/2023-02-24-using-feature-maps.html
References:
Putta et al, 2005: https://pubs.acs.org/doi/abs/10.1021/jm049066l
Landrum et al, 2007: https://link.springer.com/article/10.1007/s10822-006-9085-8
Landrum Greg, 2017: https://rdkit.blogspot.com/2017/11/using-feature-maps.html
Landrum Greg, 2023: https://greglandrum.github.io/rdkit-blog/posts/2023-02-24-using-feature-maps.html
"""

# raw features
# list features
features_small = [f for f in FACTORY.GetFeaturesForMol(mol_small, confId=conf_id_small) if f.GetFamily() in KEEP]
features_large = [f for f in FACTORY.GetFeaturesForMol(mol_large, confId=conf_id_large) if f.GetFamily() in KEEP]

# feature map based on small molecule
# create feature map based on small molecule
feature_map = FeatMaps.FeatMap(feats=features_small, weights=[1] * len(features_small), params=PARAMETERS)
feature_map.scoreMode = FeatMaps.FeatMapScoreMode.Best

# score feature in large molecule present in small molecule
feature_map_score = feature_map.ScoreFeats(features_large) / min(feature_map.GetNumFeatures(), len(features_large))
# score features of large molecule present in small molecule
feature_score = feature_map.ScoreFeats(features_large)

return feature_map_score
# normalize score
normalization_constant = min(feature_map.GetNumFeatures(), len(features_large))
if normalization_constant > 0:
return feature_score / normalization_constant

return np.nan


def get_sucos_score(
Expand All @@ -68,9 +76,9 @@ def get_sucos_score(
Returns:
SuCOS score.
Notes:
SuCOS described in https://chemrxiv.org/engage/chemrxiv/article-details/60c741a99abda23230f8bed5
Adapted from https://github.com/MarcMoesser/SuCOS/blob/master/calc_SuCOS_normalized.py
References:
Leung et al, 2019: https://chemrxiv.org/engage/chemrxiv/article-details/60c741a99abda23230f8bed5
Moesser, Marc: https://github.com/MarcMoesser/SuCOS/blob/master/calc_SuCOS_normalized.py
"""

# explicit or implicit hydrogens should be same for both molecules
Expand All @@ -92,7 +100,13 @@ def get_sucos_score(
vdwScale=0.8,
ignoreHs=True,
)
sucos_score = float(0.5 * feature_map_score + 0.5 * (1 - protrusion_distance))
shape_overlap = max(1 - protrusion_distance, 0)

# if no features, base on shape alone
if not np.isnan(feature_map_score):
sucos_score = 0.5 * feature_map_score + 0.5 * shape_overlap
else:
sucos_score = shape_overlap

return sucos_score

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30 changes: 30 additions & 0 deletions tests/conftest.py
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Expand Up @@ -195,3 +195,33 @@ def mol_small_7brv_f5r_7wb6_f5r():
@pytest.fixture
def mol_large_7brv_f5r_7wb6_f5r():
return MolFromMolFile("tests/conftest/7BRV_F5R_7WB6_F5R/7BRV_F5R_7WB6_F5R_larger_ligand.sdf", removeHs=True)


@pytest.fixture
def mol_065():
return MolFromMolFile("tests/conftest/mol_065_ideal.sdf")


@pytest.fixture
def mol_065_left():
return MolFromMolFile("tests/conftest/mol_065_left.sdf")


@pytest.fixture
def mol_065_right():
return MolFromMolFile("tests/conftest/mol_065_right.sdf")


@pytest.fixture
def mol_TMO():
return MolFromMolFile("tests/conftest/mol_TMO.sdf")


@pytest.fixture
def mol_2YU():
return MolFromMolFile("tests/conftest/mol_2YU.mol")


@pytest.fixture
def mol_HQT():
return MolFromMolFile("tests/conftest/mol_HQT.mol")
174 changes: 174 additions & 0 deletions tests/conftest/mol_065_ideal.sdf
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@@ -0,0 +1,174 @@
065
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M END
> <OPENEYE_ISO_SMILES>
CC(C)CN(C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc5c(c4)OCO5

> <OPENEYE_INCHI>
InChI=1S/C28H36N2O9S/c1-18(2)14-30(40(33,34)20-8-9-24-25(13-20)38-17-37-24)15-23(31)22(12-19-6-4-3-5-7-19)29-28(32)39-26-16-36-27-21(26)10-11-35-27/h3-9,13,18,21-23,26-27,31H,10-12,14-17H2,1-2H3,(H,29,32)/t21-,22-,23+,26-,27+/m0/s1

> <OPENEYE_INCHIKEY>
HNEIRZJZTYYDES-VPZBFSRCSA-N

> <FORMULA>
C28H36N2O9S

$$$$
90 changes: 90 additions & 0 deletions tests/conftest/mol_065_left.sdf
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@@ -0,0 +1,90 @@

RDKit 3D

40 44 0 0 0 0 0 0 0 0999 V2000
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M END
$$$$
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