Cleanup (ecc4af56) · Commits · 钟慕尧 / deepchem

deepchem/init.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -15,3 +15,4 @@ import deepchem.utils
		import deepchem.dock
		import deepchem.molnet
		import deepchem.rl
		import deepchem.applications

deepchem/molnet/dnasim.py→deepchem/applications/genomics/dnasim.py

+0 −0

File moved.

View file

deepchem/molnet/init.py

+0 −6

Original line number	Diff line number	Diff line
		@@ -32,12 +32,6 @@ from deepchem.molnet.load_function.thermosol_datasets import load_thermosol
		from deepchem.molnet.load_function.hppb_datasets import load_hppb
		from deepchem.molnet.load_function.chembl25_datasets import load_chembl25

		from deepchem.molnet.dnasim import simulate_motif_density_localization
		from deepchem.molnet.dnasim import simulate_motif_counting
		from deepchem.molnet.dnasim import simple_motif_embedding
		from deepchem.molnet.dnasim import motif_density
		from deepchem.molnet.dnasim import simulate_single_motif_detection

		from deepchem.molnet.run_benchmark import run_benchmark
		#from deepchem.molnet.run_benchmark_low_data import run_benchmark_low_data
		from deepchem.molnet import run_benchmark_models

deepchem/molnet/run_benchmark.py

+35 −35

Original line number	Diff line number	Diff line
		@@ -15,42 +15,8 @@ from deepchem.molnet.preset_hyper_parameters import hps

		logger = logging.getLogger(__name__)

		# Loading functions available
		loading_functions = {
		'bace_c': deepchem.molnet.load_bace_classification,
		'bace_r': deepchem.molnet.load_bace_regression,
		'bbbp': deepchem.molnet.load_bbbp,
		'chembl': deepchem.molnet.load_chembl,
		'clearance': deepchem.molnet.load_clearance,
		'clintox': deepchem.molnet.load_clintox,
		'delaney': deepchem.molnet.load_delaney,
		'factors': deepchem.molnet.load_factors,
		'hiv': deepchem.molnet.load_hiv,
		'hopv': deepchem.molnet.load_hopv,
		'hppb': deepchem.molnet.load_hppb,
		'kaggle': deepchem.molnet.load_kaggle,
		'kinase': deepchem.molnet.load_kinase,
		'lipo': deepchem.molnet.load_lipo,
		'muv': deepchem.molnet.load_muv,
		'nci': deepchem.molnet.load_nci,
		'pcba': deepchem.molnet.load_pcba,
		'pcba_146': deepchem.molnet.load_pcba_146,
		'pcba_2475': deepchem.molnet.load_pcba_2475,
		'pdbbind': deepchem.molnet.load_pdbbind_grid,
		'ppb': deepchem.molnet.load_ppb,
		'qm7': deepchem.molnet.load_qm7_from_mat,
		'qm7b': deepchem.molnet.load_qm7b_from_mat,
		'qm8': deepchem.molnet.load_qm8,
		'qm9': deepchem.molnet.load_qm9,
		'sampl': deepchem.molnet.load_sampl,
		'sider': deepchem.molnet.load_sider,
		'thermosol': deepchem.molnet.load_thermosol,
		'tox21': deepchem.molnet.load_tox21,
		'toxcast': deepchem.molnet.load_toxcast,
		'uv': deepchem.molnet.load_uv,
		}


		# Loading functions available
		def run_benchmark(datasets,
		model,
		split=None,
		@@ -115,6 +81,40 @@ def run_benchmark(datasets,
		reload: boolean, optional(default=True)
		whether to save and reload featurized datasets
		"""
		loading_functions = {
		'bace_c': deepchem.molnet.load_bace_classification,
		'bace_r': deepchem.molnet.load_bace_regression,
		'bbbp': deepchem.molnet.load_bbbp,
		'chembl': deepchem.molnet.load_chembl,
		'clearance': deepchem.molnet.load_clearance,
		'clintox': deepchem.molnet.load_clintox,
		'delaney': deepchem.molnet.load_delaney,
		'factors': deepchem.molnet.load_factors,
		'hiv': deepchem.molnet.load_hiv,
		'hopv': deepchem.molnet.load_hopv,
		'hppb': deepchem.molnet.load_hppb,
		'kaggle': deepchem.molnet.load_kaggle,
		'kinase': deepchem.molnet.load_kinase,
		'lipo': deepchem.molnet.load_lipo,
		'muv': deepchem.molnet.load_muv,
		'nci': deepchem.molnet.load_nci,
		'pcba': deepchem.molnet.load_pcba,
		'pcba_146': deepchem.molnet.load_pcba_146,
		'pcba_2475': deepchem.molnet.load_pcba_2475,
		'pdbbind': deepchem.molnet.load_pdbbind_grid,
		'ppb': deepchem.molnet.load_ppb,
		'qm7': deepchem.molnet.load_qm7_from_mat,
		'qm7b': deepchem.molnet.load_qm7b_from_mat,
		'qm8': deepchem.molnet.load_qm8,
		'qm9': deepchem.molnet.load_qm9,
		'sampl': deepchem.molnet.load_sampl,
		'sider': deepchem.molnet.load_sider,
		'thermosol': deepchem.molnet.load_thermosol,
		'tox21': deepchem.molnet.load_tox21,
		'toxcast': deepchem.molnet.load_toxcast,
		'uv': deepchem.molnet.load_uv,
		}

		for dataset in datasets:
		if dataset in [
		'bace_c', 'bbbp', 'clintox', 'hiv', 'muv', 'pcba', 'pcba_146',

docs/applications.rst

0 → 100644

+34 −0

Original line number	Diff line number	Diff line
		Applications
		============
		To use DeepChem models on downstream applications tasks, it's often necessary
		to have additional infrastructure to apply DeepChem effectively to scientific
		problems of interest. The :code:`dc.applications` module contains an assortment
		of non-machine-learning code that facilitates the use of DeepChem for
		applications.

		Genomics
		--------

		DeepChem currently has utilities to generate synthetic datasets for genomics
		applications.

		DNA Simulation
		^^^^^^^^^^^^^^
		DeepChem uses the :code:`simdna` package to simulate some synthetic DNA
		distributions of interest.

		.. autofunction:: deepchem.applications.genomics.dnasim.simple_motif_embedding

		.. autofunction:: deepchem.applications.genomics.dnasim.motif_density

		.. autofunction:: deepchem.applications.genomics.dnasim.simulate_single_motif_detection

		.. autofunction:: deepchem.applications.genomics.dnasim.simulate_motif_counting

		.. autofunction:: deepchem.applications.genomics.dnasim.simulate_motif_density_localization

		.. autofunction:: deepchem.applications.genomics.dnasim.simulate_multi_motif_embedding

		.. autofunction:: deepchem.applications.genomics.dnasim.simulate_differential_accessibility

		.. autofunction:: deepchem.applications.genomics.dnasim.simulate_heterodimer_grammar

Admin message