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@@ 159-209 (lines=51) @@
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| 156 |
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self.use_bond_types = use_bond_types |
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self.use_chirality = use_chirality |
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def _transform_mol(self, mol): |
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"""Private method to transform a skchem molecule. |
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Use `transform` for the public method, which genericizes the argument |
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to iterables of mols. |
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Args: |
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mol (skchem.Mol): Molecule to calculate fingerprint for. |
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Returns: |
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np.array or dict: |
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Fingerprint as an array (or a dict if sparse). |
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""" |
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if self.as_bits and self.n_feats > 0: |
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fp = GetMorganFingerprintAsBitVect( |
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mol, self.radius, nBits=self.n_feats, |
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useFeatures=self.use_features, |
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useBondTypes=self.use_bond_types, |
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useChirality=self.use_chirality) |
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res = np.array(0) |
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ConvertToNumpyArray(fp, res) |
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res = res.astype(np.uint8) |
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else: |
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if self.n_feats <= 0: |
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res = GetMorganFingerprint( |
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mol, self.radius, |
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useFeatures=self.use_features, |
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useBondTypes=self.use_bond_types, |
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useChirality=self.use_chirality) |
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res = res.GetNonzeroElements() |
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if self.as_bits: |
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res = {k: int(v > 0) for k, v in res.items()} |
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else: |
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res = GetHashedMorganFingerprint( |
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mol, self.radius, nBits=self.n_feats, |
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useFeatures=self.use_features, |
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useBondTypes=self.use_bond_types, |
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useChirality=self.use_chirality) |
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res = np.array(list(res)) |
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return res |
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@property |
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def name(self): |
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@@ 325-371 (lines=47) @@
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self.as_bits = as_bits |
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self.use_chirality = use_chirality |
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def _transform_mol(self, mol): |
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"""Private method to transform a skchem molecule. |
| 328 |
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Use transform` for the public method, which genericizes the argument to |
| 330 |
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iterables of mols. |
| 331 |
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Args: |
| 333 |
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mol (skchem.Mol): Molecule to calculate fingerprint for. |
| 334 |
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Returns: |
| 336 |
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np.array or dict: |
| 337 |
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Fingerprint as an array (or a dict if sparse). |
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""" |
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if self.as_bits and self.n_feats > 0: |
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fp = GetHashedAtomPairFingerprintAsBitVect( |
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mol, nBits=self.n_feats, minLength=self.min_length, |
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maxLength=self.max_length, includeChirality=self.use_chirality) |
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res = np.array(0) |
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ConvertToNumpyArray(fp, res) |
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res = res.astype(np.uint8) |
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else: |
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if self.n_feats <= 0: |
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res = GetAtomPairFingerprint( |
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mol, nBits=self.n_feats, minLength=self.min_length, |
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maxLength=self.max_length, |
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includeChirality=self.use_chirality) |
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res = res.GetNonzeroElements() |
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if self.as_bits: |
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res = {k: int(v > 0) for k, v in res.items()} |
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else: |
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res = GetHashedAtomPairFingerprint( |
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mol, nBits=self.n_feats, minLength=self.min_length, |
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maxLength=self.max_length, |
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includeChirality=self.use_chirality) |
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res = np.array(list(res)) |
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return res |
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@property |
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def name(self): |
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@@ 422-461 (lines=40) @@
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super(TopologicalTorsionFeaturizer, self).__init__(n_jobs=n_jobs, |
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verbose=verbose) |
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def _transform_mol(self, mol): |
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""" Private method to transform a skchem molecule. |
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Args: |
| 425 |
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mol (skchem.Mol): Molecule to calculate fingerprint for. |
| 426 |
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| 427 |
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Returns: |
| 428 |
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np.array or dict: |
| 429 |
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Fingerprint as an array (or a dict if sparse). |
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""" |
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if self.as_bits and self.n_feats > 0: |
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fp = GetHashedTopologicalTorsionFingerprintAsBitVect( |
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mol, nBits=self.n_feats, targetSize=self.target_size, |
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includeChirality=self.use_chirality) |
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res = np.array(0) |
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ConvertToNumpyArray(fp, res) |
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res = res.astype(np.uint8) |
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else: |
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if self.n_feats <= 0: |
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res = GetTopologicalTorsionFingerprint( |
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mol, nBits=self.n_feats, targetSize=self.target_size, |
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includeChirality=self.use_chirality) |
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res = res.GetNonzeroElements() |
| 451 |
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if self.as_bits: |
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res = {k: int(v > 0) for k, v in res.items()} |
| 453 |
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else: |
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res = GetHashedTopologicalTorsionFingerprint( |
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mol, nBits=self.n_feats, targetSize=self.target_size, |
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includeChirality=self.use_chirality) |
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res = np.array(list(res)) |
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return res |
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@property |
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def names(self): |
richlewis42 /
scikit-chem
