Merge branch 'fix-deepchem-build' of ssh://github.com/nd-02110114/deepchem into fix-deepchem-build (c50693b9) · Commits · 钟慕尧 / deepchem

README.md

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		@@ -5,7 +5,7 @@
		[![Anaconda-Server Badge](https://anaconda.org/conda-forge/deepchem/badges/version.svg)](https://anaconda.org/conda-forge/deepchem)
		[![PyPI version](https://badge.fury.io/py/deepchem.svg)](https://badge.fury.io/py/deepchem)

		[Website](https://deepchem.io/) \| [Documentation (master)](https://deepchem.readthedocs.io/en/latest/)) \| [Colab Tutorial](https://github.com/deepchem/deepchem/tree/master/examples/tutorials) \| [Discussion Forum](https://forum.deepchem.io/) \| [Gitter](https://gitter.im/deepchem/Lobby)
		[Website](https://deepchem.io/) \| [Documentation (master)](https://deepchem.readthedocs.io/en/latest/) \| [Colab Tutorial](https://github.com/deepchem/deepchem/tree/master/examples/tutorials) \| [Discussion Forum](https://forum.deepchem.io/) \| [Gitter](https://gitter.im/deepchem/Lobby)

		DeepChem aims to provide a high quality open-source toolchain
		that democratizes the use of deep-learning in drug discovery,
		@@ -58,6 +58,7 @@ DeepChem has a number of "soft" requirements. These are packages which are neede
		- [RDKit](http://www.rdkit.org/docs/Install.html)
		- [simdna](https://github.com/kundajelab/simdna)
		- [XGBoost](https://xgboost.readthedocs.io/en/latest/)
		- [Weights & Biases](https://docs.wandb.com/)
		- [Tensorflow Probability](https://www.tensorflow.org/probability)

		## Installation

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		@@ -412,8 +412,8 @@ class Dataset(object):

		Returns
		-------
		If `X_stats == True`, returns `(X_means, X_stds)`. If `y_stats ==
		True`, returns `(y_means, y_stds)`. If both are true, returns
		If `X_stats == True`, returns `(X_means, X_stds)`. If `y_stats == True`,
		returns `(y_means, y_stds)`. If both are true, returns
		`(X_means, X_stds, y_means, y_stds)`.
		"""
		X_means = 0.0
		@@ -1160,8 +1160,8 @@ class DiskDataset(Dataset):
		`math.ceil(len(dataset)/batch_size)`. Each minibatch is returned as
		a tuple of four numpy arrays: `(X, y, w, ids)`.

		Parameters:
		-----------
		Parameters
		----------
		batch_size: int
		Number of elements in a batch. If None, then it yields batches
		with size equal to the size of each individual shard.

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		@@ -18,8 +18,8 @@ logger = logging.getLogger(__name__)
		def extract_active_site(protein_file, ligand_file, cutoff=4):
		"""Extracts a box for the active site.

		Params
		------
		Parameters
		----------
		protein_file: str
		Location of protein PDB
		ligand_file: str
		@@ -116,8 +116,8 @@ class ConvexHullPocketFinder(BindingPocketFinder):
		face of the hull is converted into a coordinate box used for
		binding.

		Params
		------
		Parameters
		----------
		macromolecule_file: str
		Location of the macromolecule file to load

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		@@ -93,8 +93,8 @@ class VinaPoseGenerator(PoseGenerator):
		def __init__(self, sixty_four_bits=True, pocket_finder=None):
		"""Initializes Vina Pose Generator

		Params
		------
		Parameters
		----------
		sixty_four_bits: bool, optional (default True)
		Specifies whether this is a 64-bit machine. Needed to download
		the correct executable.

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		@@ -70,8 +70,8 @@ class BindingPocketFeaturizer(Featurizer):
		"""
		Calculate atomic coodinates.

		Params
		------
		Parameters
		----------
		protein_file: str
		Location of PDB file. Will be loaded by MDTraj
		pockets: list[CoordinateBox]