Fixing Pymatgen import error and docstrings (60e3f0d9) · Commits · 钟慕尧 / deepchem

deepchem/feat/material_featurizers/lcnn_featurizer.py

+51 −44

Original line number	Diff line number	Diff line
		@@ -64,52 +64,52 @@ class LCNNFeaturizer(MaterialStructureFeaturizer):
		>>> from pymatgen import Structure
		>>> import numpy as np
		>>> PRIMITIVE_CELL = {
		>>> "lattice": [[2.818528, 0.0, 0.0],
		>>> [-1.409264, 2.440917, 0.0],
		>>> [0.0, 0.0, 25.508255]],
		>>> "coords": [[0.66667, 0.33333, 0.090221],
		>>> [0.33333, 0.66667, 0.18043936],
		>>> [0.0, 0.0, 0.27065772],
		>>> [0.66667, 0.33333, 0.36087608],
		>>> [0.33333, 0.66667, 0.45109444],
		>>> [0.0, 0.0, 0.49656991]],
		>>> "species": ['H', 'H', 'H', 'H', 'H', 'He'],
		>>> "site_properties": {'SiteTypes': ['S1', 'S1', 'S1', 'S1', 'S1', 'A1']}
		>>> }
		... "lattice": [[2.818528, 0.0, 0.0],
		... [-1.409264, 2.440917, 0.0],
		... [0.0, 0.0, 25.508255]],
		... "coords": [[0.66667, 0.33333, 0.090221],
		... [0.33333, 0.66667, 0.18043936],
		... [0.0, 0.0, 0.27065772],
		... [0.66667, 0.33333, 0.36087608],
		... [0.33333, 0.66667, 0.45109444],
		... [0.0, 0.0, 0.49656991]],
		... "species": ['H', 'H', 'H', 'H', 'H', 'He'],
		... "site_properties": {'SiteTypes': ['S1', 'S1', 'S1', 'S1', 'S1', 'A1']}
		... }
		>>> PRIMITIVE_CELL_INF0 = {
		>>> "cutoff": np.around(6.00),
		>>> "structure": Structure(**PRIMITIVE_CELL),
		>>> "aos": ['1', '0', '2'],
		>>> "pbc": [True, True, False],
		>>> "ns": 1,
		>>> "na": 1
		>>> }
		... "cutoff": np.around(6.00),
		... "structure": Structure(**PRIMITIVE_CELL),
		... "aos": ['1', '0', '2'],
		... "pbc": [True, True, False],
		... "ns": 1,
		... "na": 1
		... }
		>>> DATA_POINT = {
		>>> "lattice": [[1.409264, -2.440917, 0.0],
		>>> [4.227792, 2.440917, 0.0],
		>>> [0.0, 0.0, 23.17559]],
		>>> "coords": [[0.0, 0.0, 0.099299],
		>>> [0.0, 0.33333, 0.198598],
		>>> [0.5, 0.16667, 0.297897],
		>>> [0.0, 0.0, 0.397196],
		>>> [0.0, 0.33333, 0.496495],
		>>> [0.5, 0.5, 0.099299],
		>>> [0.5, 0.83333, 0.198598],
		>>> [0.0, 0.66667, 0.297897],
		>>> [0.5, 0.5, 0.397196],
		>>> [0.5, 0.83333, 0.496495],
		>>> [0.0, 0.66667, 0.54654766],
		>>> [0.5, 0.16667, 0.54654766]],
		>>> "species": ['H', 'H', 'H', 'H', 'H', 'H',
		>>> 'H', 'H', 'H', 'H', 'He', 'He'],
		>>> "site_properties": {
		>>> "SiteTypes": ['S1', 'S1', 'S1', 'S1', 'S1',
		>>> 'S1', 'S1', 'S1', 'S1', 'S1',
		>>> 'A1', 'A1'],
		>>> "oss": ['-1', '-1', '-1', '-1', '-1', '-1',
		>>> '-1', '-1', '-1', '-1', '0', '2']
		>>> }
		>>> }
		... "lattice": [[1.409264, -2.440917, 0.0],
		... [4.227792, 2.440917, 0.0],
		... [0.0, 0.0, 23.17559]],
		... "coords": [[0.0, 0.0, 0.099299],
		... [0.0, 0.33333, 0.198598],
		... [0.5, 0.16667, 0.297897],
		... [0.0, 0.0, 0.397196],
		... [0.0, 0.33333, 0.496495],
		... [0.5, 0.5, 0.099299],
		... [0.5, 0.83333, 0.198598],
		... [0.0, 0.66667, 0.297897],
		... [0.5, 0.5, 0.397196],
		... [0.5, 0.83333, 0.496495],
		... [0.0, 0.66667, 0.54654766],
		... [0.5, 0.16667, 0.54654766]],
		... "species": ['H', 'H', 'H', 'H', 'H', 'H',
		... 'H', 'H', 'H', 'H', 'He', 'He'],
		... "site_properties": {
		... "SiteTypes": ['S1', 'S1', 'S1', 'S1', 'S1',
		... 'S1', 'S1', 'S1', 'S1', 'S1',
		... 'A1', 'A1'],
		... "oss": ['-1', '-1', '-1', '-1', '-1', '-1',
		... '-1', '-1', '-1', '-1', '0', '2']
		... }
		... }
		>>> featuriser = dc.feat.LCNNFeaturizer(**PRIMITIVE_CELL_INF0)
		>>> print(type(featuriser._featurize(Structure(**DATA_POINT))))
		<class 'deepchem.feat.graph_data.GraphData'>
		@@ -146,6 +146,13 @@ class LCNNFeaturizer(MaterialStructureFeaturizer):
		Cutoff of radius for getting local environment.Only
		used down to 2 digits.
		"""
		try:
		from pymatgen import Structure
		except:
		raise ImportError("This class requires pymatgen to be installed.")

		if type(structure) is not Structure:
		structure = Structure(**structure)
		self.aos = aos
		self.cutoff = np.around(cutoff, 2)
		self.setup_env = _load_primitive_cell(structure, aos, pbc, ns, na, cutoff)

deepchem/molnet/load_function/material_datasets/load_Pt_NO_surface_adsorbate_energy.py

+21 −25

Original line number	Diff line number	Diff line
		@@ -8,8 +8,6 @@ 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"
		PLATINUM_TASKS = ["Formation Energy"]
		@@ -26,14 +24,12 @@ try:
		}
		PRIMITIVE_CELL_INF0 = {
		"cutoff": np.around(6.00),
		"structure": Structure(**PRIMITIVE_CELL),
		"structure": PRIMITIVE_CELL,
		"aos": ['1', '0', '2'],
		"pbc": [True, True, False],
		"ns": 1,
		"na": 1
		}
		except:
		raise ImportError("This class requires pymatgen to be installed.")


		class _PtAdsorptionLoader(_MolnetLoader):

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