Merge pull request #1513 from VIGS25/symmetry-rename (4589009d) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+1 −1

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		@@ -18,7 +18,7 @@ from deepchem.feat.fingerprints import CircularFingerprint
		from deepchem.feat.basic import RDKitDescriptors
		from deepchem.feat.coulomb_matrices import CoulombMatrix
		from deepchem.feat.coulomb_matrices import CoulombMatrixEig
		from deepchem.feat.coulomb_matrices import BPSymmetryFunction
		from deepchem.feat.coulomb_matrices import BPSymmetryFunctionInput
		from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer
		from deepchem.feat.nnscore_utils import hydrogenate_and_compute_partial_charges
		from deepchem.feat.binding_pocket_features import BindingPocketFeaturizer

+1 −1

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		@@ -17,7 +17,7 @@ from deepchem.utils import pad_array
		from deepchem.feat.atomic_coordinates import AtomicCoordinates


		class BPSymmetryFunction(Featurizer):
		class BPSymmetryFunctionInput(Featurizer):
		"""
		Calculate Symmetry Function for each atom in the molecules
		Methods described in https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.98.146401

+1 −1

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		@@ -533,7 +533,7 @@ class TestEstimators(unittest.TestCase):
		def test_bpsymm_regression_model(self):
		"""Test creating an estimator for BPSymmetry Regression model."""
		tasks, dataset, transformers = dc.molnet.load_qm7_from_mat(
		featurizer='BPSymmetryFunction', move_mean=False)
		featurizer='BPSymmetryFunctionInput', move_mean=False)

		num_samples_to_use = 5
		train, _, _ = dataset

+3 −3

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		@@ -208,7 +208,7 @@ CheckFeaturizer = {
		('qm7', 'weave_regression'): ['Weave', 75],
		('qm7', 'tf_regression_ft'): ['CoulombMatrix', [23, 23]],
		('qm7', 'dtnn'): ['CoulombMatrix', [23, 23]],
		('qm7', 'ani'): ['BPSymmetryFunction', [23, 4]],
		('qm7', 'ani'): ['BPSymmetryFunctionInput', [23, 4]],
		('qm7b', 'tf_regression_ft'): ['CoulombMatrix', [23, 23]],
		('qm7b', 'krr_ft'): ['CoulombMatrix', 1024],
		('qm7b', 'dtnn'): ['CoulombMatrix', [23, 23]],
		@@ -219,7 +219,7 @@ CheckFeaturizer = {
		('qm8', 'tf_regression_ft'): ['CoulombMatrix', [26, 26]],
		('qm8', 'krr_ft'): ['CoulombMatrix', 1024],
		('qm8', 'dtnn'): ['CoulombMatrix', [26, 26]],
		('qm8', 'ani'): ['BPSymmetryFunction', [26, 4]],
		('qm8', 'ani'): ['BPSymmetryFunctionInput', [26, 4]],
		('qm8', 'mpnn'): ['MP', [70, 8]],
		('qm8', 'weave_regression'): ['Weave', 75],
		('qm8', 'textcnn_regression'): ['Raw', None],
		@@ -230,7 +230,7 @@ CheckFeaturizer = {
		('qm9', 'tf_regression_ft'): ['CoulombMatrix', [29, 29]],
		('qm9', 'krr_ft'): ['CoulombMatrix', 1024],
		('qm9', 'dtnn'): ['CoulombMatrix', [29, 29]],
		('qm9', 'ani'): ['BPSymmetryFunction', [29, 4]],
		('qm9', 'ani'): ['BPSymmetryFunctionInput', [29, 4]],
		('qm9', 'mpnn'): ['MP', [70, 8]],
		('qm9', 'weave_regression'): ['Weave', 75],
		('qm9', 'textcnn_regression'): ['Raw', None]

+1 −1

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		@@ -42,7 +42,7 @@ def load_qm7_from_mat(featurizer='CoulombMatrix',
		y = dataset['T']
		w = np.ones_like(y)
		dataset = deepchem.data.DiskDataset.from_numpy(X, y, w, ids=None)
		elif featurizer == 'BPSymmetryFunction':
		elif featurizer == 'BPSymmetryFunctionInput':
		dataset_file = os.path.join(data_dir, "qm7.mat")

		if not os.path.exists(dataset_file):