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refactor to rdFingerprintGenerator #226

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merged 6 commits into from
Jun 10, 2024
Merged

refactor to rdFingerprintGenerator #226

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dd953df
refactor to rdFingerprintGenerator
zhu0619 May 28, 2024
18ddc51
update default parameter
zhu0619 May 28, 2024
176fce9
update atompair parameters
zhu0619 May 28, 2024
96bb89c
fix errors and add no_rdkit_log decorator
maclandrol Jun 9, 2024
b2c8dde
change matrix testing
maclandrol Jun 9, 2024
9210ec9
wip
maclandrol Jun 9, 2024
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178 changes: 95 additions & 83 deletions datamol/fp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
from rdkit.Chem import rdReducedGraphs
from rdkit.Chem.EState import Fingerprinter as EStateFingerprinter
from rdkit.Avalon import pyAvalonTools
from rdkit.Chem import rdFingerprintGenerator

from rdkit.DataStructs.cDataStructs import SparseBitVect
from rdkit.DataStructs.cDataStructs import UIntSparseIntVect
Expand All @@ -20,25 +21,28 @@
from rdkit.DataStructs.cDataStructs import ExplicitBitVect
from rdkit.DataStructs.cDataStructs import ULongSparseIntVect

_FP_GENERATORS = {
"ecfp": rdFingerprintGenerator.GetMorganGenerator,
"fcfp": rdFingerprintGenerator.GetMorganGenerator,
"topological": rdFingerprintGenerator.GetTopologicalTorsionGenerator,
"atompair": rdFingerprintGenerator.GetAtomPairGenerator,
"rdkit": rdFingerprintGenerator.GetRDKitFPGenerator,
"ecfp-count": rdFingerprintGenerator.GetMorganGenerator,
"fcfp-count": rdFingerprintGenerator.GetMorganGenerator,
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"topological-count": rdFingerprintGenerator.GetTopologicalTorsionGenerator,
"atompair-count": rdFingerprintGenerator.GetAtomPairGenerator,
"rdkit-count": rdFingerprintGenerator.GetRDKitFPGenerator,
}

_FP_FUNCS = {
"maccs": rdMolDescriptors.GetMACCSKeysFingerprint,
"ecfp": rdMolDescriptors.GetMorganFingerprintAsBitVect,
"fcfp": rdMolDescriptors.GetMorganFingerprintAsBitVect,
"topological": rdMolDescriptors.GetHashedTopologicalTorsionFingerprintAsBitVect,
"atompair": rdMolDescriptors.GetHashedAtomPairFingerprintAsBitVect,
"rdkit": rdmolops.RDKFingerprint,
"pattern": rdmolops.PatternFingerprint,
"layered": rdmolops.LayeredFingerprint,
"erg": rdReducedGraphs.GetErGFingerprint,
# NOTE(hadim): bad for pickling?
"estate": lambda x, **args: EStateFingerprinter.FingerprintMol(x)[0],
"avalon-count": pyAvalonTools.GetAvalonCountFP,
"rdkit-count": rdmolops.UnfoldedRDKFingerprintCountBased,
"ecfp-count": rdMolDescriptors.GetHashedMorganFingerprint,
"fcfp-count": rdMolDescriptors.GetHashedMorganFingerprint,
"topological-count": rdMolDescriptors.GetHashedTopologicalTorsionFingerprint,
"atompair-count": rdMolDescriptors.GetHashedAtomPairFingerprint,
**_FP_GENERATORS,
}

_FP_DEFAULT_ARGS = {
Expand All @@ -51,59 +55,60 @@
},
"ecfp": {
"radius": 3, # ECFP6 - not the RDKit default (ECFP4)
"nBits": 2048,
"invariants": [],
"fromAtoms": [],
"useChirality": False,
"fpSize": 2048,
"includeChirality": False,
"useBondTypes": True,
"useFeatures": False,
"countSimulation": False,
"countBounds": None,
"atomInvariantsGenerator": None,
"bondInvariantsGenerator": None,
},
"fcfp": {
"radius": 2, # FCFP4
"nBits": 2048,
"invariants": [], # you may want to provide features invariance
"fromAtoms": [],
"useChirality": False,
"radius": 2,
"fpSize": 2048,
"includeChirality": False,
"useBondTypes": True,
"useFeatures": True,
"countSimulation": False,
"countBounds": None,
"atomInvariantsGenerator": rdFingerprintGenerator.GetMorganFeatureAtomInvGen(),
"bondInvariantsGenerator": None,
},
"topological": {
"nBits": 2048,
"targetSize": 4,
"fromAtoms": 0,
"ignoreAtoms": 0,
"atomInvariants": 0,
"nBitsPerEntry": 4,
"includeChirality": False,
"torsionAtomCount": 4,
"countSimulation": False,
"countBounds": None,
"fpSize": 2048,
"atomInvariantsGenerator": None,
},
"atompair": {
"nBits": 2048,
"minLength": 1,
"maxLength": 30,
"fromAtoms": 0,
"ignoreAtoms": 0,
"atomInvariants": 0,
"nBitsPerEntry": 4,
"minDistance": 1,
"maxDistance": 30,
"includeChirality": False,
"use2D": True,
"confId": -1,
"countSimulation": True,
"countBounds": None,
"fpSize": 2048,
"atomInvariantsGenerator": None,
},
"rdkit": {
"minPath": 1,
"maxPath": 7,
"fpSize": 2048,
"nBitsPerHash": 2,
"useHs": True,
"tgtDensity": 0.0,
"minSize": 128,
"branchedPaths": True,
"useBondOrder": True,
"atomInvariants": 0,
"fromAtoms": 0,
"atomBits": None,
"bitInfo": None,
"countSimulation": False,
"countBounds": None,
"fpSize": 2048,
"numBitsPerFeature": 2,
"atomInvariantsGenerator": None,
},
"pattern": {
"fpSize": 2048,
"atomCounts": [],
"setOnlyBits": None,
"tautomerFingerprints": False,
},
"pattern": {"fpSize": 2048, "atomCounts": [], "setOnlyBits": None},
"layered": {
"fpSize": 2048,
"minPath": 1,
Expand All @@ -126,60 +131,60 @@
"erg": {"atomTypes": 0, "fuzzIncrement": 0.3, "minPath": 1, "maxPath": 15},
"estate": {},
# COUNTING FP
"avalon-count": {
"nBits": 512,
"isQuery": False,
"bitFlags": pyAvalonTools.avalonSimilarityBits,
},
"ecfp-count": {
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"radius": 2, # ECFP4
"nBits": 2048,
"invariants": [],
"fromAtoms": [],
"useChirality": False,
"radius": 3, # ECFP6 - not the RDKit default (ECFP4)
"fpSize": 2048,
"includeChirality": False,
"useBondTypes": True,
"useFeatures": False,
"includeRedundantEnvironments": False,
"countSimulation": False,
"countBounds": None,
"atomInvariantsGenerator": None,
"bondInvariantsGenerator": None,
},
"fcfp-count": {
"radius": 2, # FCFP4
"nBits": 2048,
"invariants": [], # you may want to provide features invariance
"fromAtoms": [],
"useChirality": False,
"radius": 2,
"fpSize": 2048,
"includeChirality": False,
"useBondTypes": True,
"useFeatures": True,
"includeRedundantEnvironments": False,
"countSimulation": False,
"countBounds": None,
"atomInvariantsGenerator": rdFingerprintGenerator.GetMorganFeatureAtomInvGen(),
"bondInvariantsGenerator": None,
},
"topological-count": {
"nBits": 2048,
"targetSize": 4,
"fromAtoms": 0,
"ignoreAtoms": 0,
"atomInvariants": 0,
"includeChirality": False,
"torsionAtomCount": 4,
"countSimulation": False,
"countBounds": None,
"fpSize": 2048,
"atomInvariantsGenerator": None,
},
"avalon-count": {
"nBits": 512,
"isQuery": False,
"bitFlags": pyAvalonTools.avalonSimilarityBits,
"atompair-count": {
"minDistance": 1,
"maxDistance": 30,
"includeChirality": False,
"use2D": True,
"countSimulation": True,
"countBounds": None,
"fpSize": 2048,
"atomInvariantsGenerator": None,
},
"rdkit-count": {
"minPath": 1,
"maxPath": 7,
"useHs": True,
"branchedPaths": True,
"useBondOrder": True,
"atomInvariants": 0,
"fromAtoms": 0,
"atomBits": None,
"bitInfo": None,
},
"atompair-count": {
"nBits": 2048,
"minLength": 1,
"maxLength": 30,
"fromAtoms": 0,
"ignoreAtoms": 0,
"atomInvariants": 0,
"includeChirality": False,
"use2D": True,
"confId": -1,
"countSimulation": False,
"countBounds": None,
"fpSize": 2048,
"numBitsPerFeature": 1,
"atomInvariantsGenerator": None,
},
}

Expand Down Expand Up @@ -279,7 +284,14 @@ def to_fp(
fp_args.setdefault(key, value)

# Compute the fingerprint
fp = fp_func(mol, **fp_args)
if fp_type in _FP_GENERATORS:
fp_func = fp_func(**fp_args)
if fp_type.endswith("-count"):
fp = fp_func.GetCountFingerprint(mol)
else:
fp = fp_func.GetFingerprint(mol)
else:
fp = fp_func(mol, **fp_args)

# Fold the fp if needed.
if fold_size is not None:
Expand Down
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