Merge pull request #1983 from nd-02110114/fix-docs-error (b5edbb45) · Commits · 钟慕尧 / deepchem

deepchem/data/datasets.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -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.

+4 −4

Original line number	Diff line number	Diff line
		@@ -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

+2 −2

Original line number	Diff line number	Diff line
		@@ -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.

+2 −2

Original line number	Diff line number	Diff line
		@@ -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]

+7 −7

Original line number	Diff line number	Diff line
		@@ -142,8 +142,8 @@ class CoulombMatrix(Featurizer):

		def randomize_coulomb_matrix(self, m):
		"""
		Randomize a Coulomb matrix as decribed in Montavon et al., _New Journal
		of Physics_ __15__ (2013) 095003:
		Randomize a Coulomb matrix as decribed in Montavon et al.,
		New Journal of Physics, 15, (2013), 095003:

		1. Compute row norms for M in a vector row_norms.
		2. Sample a zero-mean unit-variance noise vector e with dimension