Fixed docstrings and removed test functions (867f0aab) · Commits · 钟慕尧 / deepchem

deepchem/feat/material_featurizers/lcnn_featurizer.py

+6 −21

Original line number	Diff line number	Diff line
		@@ -5,6 +5,8 @@ from collections import defaultdict
		from typing import List, Dict, Tuple, DefaultDict, Any
		from deepchem.utils.typing import PymatgenStructure
		from deepchem.feat.graph_data import GraphData
		from scipy.spatial.distance import pdist, squareform, cdist
		from scipy.spatial.transform import Rotation


		class LCNNFeaturizer(MaterialStructureFeaturizer):
		@@ -17,10 +19,10 @@ class LCNNFeaturizer(MaterialStructureFeaturizer):
		determined by first extracting a site local environment from the primitive cell,
		and perform graph matching and distance matching to find neighbors.
		First, the template of the Primitive cell needs to be defined along with periodic
		boundary conditions and active and specator site details. structure(Data Point
		boundary conditions and active and spectator site details. structure(Data Point
		i.e different configuration of adsorbate atoms) is passed for featurization.

		This particular featurisation produces a regular-graph (equal number of Neighbors)
		This particular featurization produces a regular-graph (equal number of Neighbors)
		along with its permutation in 6 symmetric axis. This transformation can be
		applied when orderering of neighboring of nodes around a site play an important role
		in the propert predictions. Due to consideration of local neighbor environment,
		@@ -226,10 +228,6 @@ class _SiteEnvironment(object):
		import networkx.algorithms.isomorphism as iso
		except:
		raise ImportError("This class requires networkx to be installed.")
		try:
		from scipy.spatial.distance import pdist, squareform
		except:
		raise ImportError("This class requires scipy to be installed.")
		self.pos = pos
		self.sitetypes = sitetypes
		self.activesiteidx = [i for i, s in enumerate(self.sitetypes) if 'A' in s]
		@@ -294,11 +292,6 @@ class _SiteEnvironment(object):
		except:
		raise ImportError("This class requires networkx to be installed.")

		try:
		from scipy.spatial.distance import cdist, pdist
		except:
		raise ImportError("This class requires scipy to be installed.")

		# construct graph
		G = nx.Graph()
		dists = cdist([[0, 0, 0]], pos - np.mean(pos, 0))[0]
		@@ -347,10 +340,6 @@ class _SiteEnvironment(object):
		import networkx.algorithms.isomorphism as iso
		except:
		raise ImportError("This class requires networkx to be installed.")
		try:
		from scipy.spatial.transform import Rotation
		except:
		raise ImportError("This class requires scipy to be installed.")
		# construct graph

		G = self._construct_graph(env['pos'], env['sitetypes'])
		@@ -635,10 +624,6 @@ def _get_SiteEnvironments(struct: PymatgenStructure,
		except:
		raise ImportError("This class requires pymatgen to be installed.")

		try:
		from scipy.spatial.distance import cdist
		except:
		raise ImportError("This class requires scipy to be installed.")
		pbc = np.array(PBC)
		structure = struct
		neighbors = structure.get_all_neighbors(cutoff, include_index=True)

deepchem/feat/tests/data/test_platinum_adsorption.json

deleted100644 → 0

+0 −486

Original line number	Diff line number	Diff line
		{
		"primitive_cell": {
		"cutoff": 6.0,
		"structure": {
		"@module":
		"pymatgen.core.structure",
		"@class":
		"Structure",
		"charge":
		null,
		"lattice": {
		"matrix": [[2.818528, 0.0, 0.0], [-1.409264, 2.440917, 0.0],
		[0.0, 0.0, 25.508255]],
		"a":
		2.818528,
		"b":
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		"c":
		25.508255,
		"alpha":
		90.0,
		"beta":
		90.0,
		"gamma":
		119.99999846803924,
		"volume":
		175.4915118999615
		},
		"sites": [{
		"species": [{
		"element": "H",
		"occu": 1
		}],
		"abc": [0.66667, 0.33333, 0.090221],
		"xyz":
		[1.4092780926400001, 0.8136308636099999, 2.3013802743549996],
		"label":
		"H",
		"properties": {
		"SiteTypes": "S1"
		}
		}, {
		"species": [{
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		}],
		"abc": [0.33333, 0.66667, 0.18043936],
		"xyz":
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		"label":
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		"label":
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		"properties": {
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		}, {
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		"abc": [0.0, 0.0, 0.49656991],
		"xyz": [0.0, 0.0, 12.66663188960705],
		"label": "He",
		"properties": {
		"SiteTypes": "A1"
		}
		}]
		},
		"aos": ["1", "0", "2"],
		"pbc": [true, true, false],
		"ns": 1,
		"na": 1
		},
		"data point": {
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		"pymatgen.core.structure",
		"@class":
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		"lattice": {
		"matrix": [[-4.227792, -2.440917, 0.0], [2.818528, -4.881834, 0.0],
		[0.0, 0.0, 23.17559]],
		"a":
		4.881833773916621,
		"b":
		5.637056261058603,
		"c":
		23.17559,
		"alpha":
		90.0,
		"beta":
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		"gamma":
		89.99999693607845,
		"volume":
		637.7730390845832
		},
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		}],
		"abc": [0.33333, 0.5, 0.099298999982],
		"xyz":
		[1.4092640000074041e-5, -3.2545478636099996, 2.301312910992839],
		"label":
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		"properties": {
		"SiteTypes": "S1",
		"oss": "-1"
		}
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		"abc": [0.0, 0.5, 0.198598000008],
		"xyz": [1.409264, -2.440917, 4.602625823005404],
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		"abc": [0.16667, 0.25, 0.297897000033],
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		"label":
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		}

deepchem/feat/tests/test_lcnn_featurizer.py

deleted100644 → 0

+0 −26

Original line number	Diff line number	Diff line
		import os
		import json
		import numpy as np
		from deepchem.feat.material_featurizers.lcnn_featurizer import LCNNFeaturizer
		try:
		from pymatgen import Structure
		except:
		raise ImportError("This class requires pymatgen to be installed.")


		def test_LCNNFeaturizer():
		current_dir = os.path.dirname(os.path.realpath(__file__))
		structure_file = os.path.join(current_dir, 'data',
		'test_platinum_adsorption.json')
		with open(structure_file, 'r') as f:
		test_data = json.load(f)
		test_data["primitive_cell"]["structure"] = Structure.from_dict(
		test_data["primitive_cell"]["structure"])
		test_data["data point"] = Structure.from_dict(test_data["data point"])

		featuriser = LCNNFeaturizer(**test_data["primitive_cell"])
		data = featuriser._featurize(test_data["data point"])
		assert np.all(data.node_features == np.array(test_data["node_feature"]))
		assert np.all(data.edge_index == test_data["edges"])
		assert data.node_features.shape == (4, 3)
		assert data.edge_index.shape == (2, 456)

deepchem/molnet/load_function/material_datasets/load_Pt_NO_surface_adsorbate_energy.py

+25 −22

Original line number	Diff line number	Diff line
		@@ -8,6 +8,7 @@ from deepchem.molnet.load_function.molnet_loader import TransformerGenerator, _M
		from deepchem.feat.material_featurizers.lcnn_featurizer import LCNNFeaturizer
		from deepchem.data import Dataset
		from typing import List, Optional, Tuple, Union
		try:
		from pymatgen import Structure

		PLATINUM_URL = "https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/Platinum_adsorption.tar.gz"
		@@ -31,6 +32,8 @@ PRIMITIVE_CELL_INF0 = {
		"ns": 1,
		"na": 1
		}
		except:
		raise ImportError("This class requires pymatgen to be installed.")


		class _PtAdsorptionLoader(_MolnetLoader):

docs/source/api_reference/featurizers.rst

+3 −1

Original line number	Diff line number	Diff line
		@@ -290,10 +290,12 @@ CGCNNFeaturizer
		:inherited-members:

		LCNNFeaturizer
		^^^^^^^^^^^^^^^^^^^^^^^^
		^^^^^^^^^^^^^^

		.. autoclass:: deepchem.feat.LCNNFeaturizer
		:members:
		:inherited-members:


		MaterialCompositionFeaturizer
		-----------------------------

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