Merge pull request #99 from rbharath/transformer (4d759c16) · Commits · 钟慕尧 / deepchem

.travis.yml

+6 −1

Original line number	Diff line number	Diff line
		@@ -20,7 +20,12 @@ install:
		- conda install -c omnia keras
		- conda install seaborn
		- conda install six
		- pip install --user git+https://github.com/uqfoundation/pathos
		- conda install dill
		- conda install runipy
		- conda install ipyparallel
		- pip install runipy
		- pip install nglview
		- conda install -c omnia mdtraj
		- python setup.py install
		script:
		- nosetests -v deepchem

datasets/desc_canvas_aug30.csv

0 → 100644

+1523 −0

File added.

Preview size limit exceeded, changes collapsed.

deepchem/featurizers/featurize.py

+12 −26

Original line number	Diff line number	Diff line
		@@ -19,10 +19,8 @@ from deepchem.utils.save import load_from_disk
		from deepchem.utils.save import load_pandas_from_disk
		from deepchem.utils import ScaffoldGenerator
		from deepchem.featurizers.nnscore import NNScoreComplexFeaturizer
		from pathos.multiprocessing import ProcessingPool
		import multiprocessing as mp
		from functools import partial
		import multiprocess
		import dill

		def generate_scaffold(smiles, include_chirality=False):
		@@ -116,7 +114,8 @@ class DataFeaturizer(object):
		self.verbose = verbose
		self.log_every_n = log_every_n

		def featurize(self, input_file, feature_dir, samples_dir, shard_size=128, worker_pool=None):
		def featurize(self, input_file, feature_dir, samples_dir,
		shard_size=128, worker_pool=None):
		"""Featurize provided file and write to specified location."""
		input_type = _get_input_type(input_file)

		@@ -138,8 +137,10 @@ class DataFeaturizer(object):
		0, nb_sample, np.ceil(float(nb_sample)/shard_size)+1, dtype=int)
		shard_files = []
		for j in range(len(interval_points)-1):
		log("Sharding and standardizing into shard-%s / %s shards" % (str(j+1), len(interval_points)-1), self.verbose)
		log("Sharding and standardizing into shard-%s / %s shards"
		% (str(j+1), len(interval_points)-1), self.verbose)
		raw_df_shard = raw_df.iloc[range(interval_points[j], interval_points[j+1])]

		df = self._standardize_df(raw_df_shard)

		for compound_featurizer in self.compound_featurizers:
		@@ -199,12 +200,9 @@ class DataFeaturizer(object):
		df["ligand_pdb"] = ori_df[[self.ligand_pdb_field]]
		if self.ligand_mol2_field is not None:
		df["ligand_mol2"] = ori_df[[self.ligand_mol2_field]]
		if self.user_specified_features is not None:
		log("Aggregating User-Specified Features", self.verbose)
		self._add_user_specified_features(df)
		self._add_user_specified_features(df, ori_df)
		return df


		def _featurize_complexes(self, df, featurizer, parallel=True,
		worker_pool=None):
		"""Generates circular fingerprints for dataset."""
		@@ -222,11 +220,6 @@ class DataFeaturizer(object):
		features = []
		for ligand_protein_pdb_tuple in zip(ligand_pdbs, protein_pdbs):
		features.append(featurize_wrapper(ligand_protein_pdb_tuple))
		else:
		if worker_pool is None:
		worker_pool = ProcessingPool(mp.cpu_count())
		features = worker_pool.map(featurize_wrapper,
		zip(ligand_pdbs, protein_pdbs))
		else:
		features = worker_pool.map_sync(featurize_wrapper,
		zip(ligand_pdbs, protein_pdbs))
		@@ -258,30 +251,22 @@ class DataFeaturizer(object):
		feature = featurizer.featurize([mol])
		return feature

		if worker_pool is None:
		dilled_featurizer = dill.dumps(featurizer)
		worker_pool = ProcessingPool(mp.cpu_count())
		featurize_wrapper_partial = partial(featurize_wrapper,
		dilled_featurizer=dilled_featurizer)
		features = []
		for smiles in sample_smiles:
		features.append(featurize_wrapper_partial(smiles))
		else:
		features = worker_pool.map_sync(featurize_wrapper,
		sample_smiles)

		df[featurizer.__class__.__name__] = features

		def _add_user_specified_features(self, df):
		def _add_user_specified_features(self, df, ori_df):
		"""Merge user specified features.

		Merge features included in dataset provided by user
		into final features dataframe
		"""
		if self.user_specified_features is not None:
		log("Aggregating User-Specified Features", self.verbose)
		#log("Adding user-defined features.", self.verbose)
		features_data = []
		for _, row in df.iterrows():
		for ind, row in ori_df.iterrows():
		# pandas rows are tuples (row_num, row_data)
		feature_list = []
		for feature_name in self.user_specified_features:
		@@ -294,7 +279,8 @@ def map_function(data_tuple, featurizer):
		featurizer = NNScoreComplexFeaturizer()
		ind, ligand_pdb, protein_pdb = data_tuple
		print("Mapping on ind %d" % ind)
		print("ind, type(ligand_pdb), type(protein_pdb): %s " % str((ind, type(ligand_pdb), type(protein_pdb))))
		print("ind, type(ligand_pdb), type(protein_pdb): %s " %
		str((ind, type(ligand_pdb), type(protein_pdb))))
		return featurizer.featurize_complexes([ligand_pdb], [protein_pdb])

		class FeaturizedSamples(object):
		@@ -517,7 +503,7 @@ class FeaturizedSamples(object):
		for ind, row in self.compounds_df.iterrows():
		if row["split"].lower() == "train":
		train_inds.append(ind)
		elif row["split"].lower() == "validation":
		elif row["split"].lower() in ["valid", "validation"]:
		valid_inds.append(ind)
		elif row["split"].lower() == "test":
		test_inds.append(ind)

deepchem/featurizers/featurize_old.py

deleted100644 → 0

+0 −443

Original line number	Diff line number	Diff line
		"""
		Process an input dataset into a format suitable for machine learning.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals
		import os
		import gzip
		import pandas as pd
		import numpy as np
		import csv
		from rdkit import Chem
		from deepchem.featurizers.fingerprints import CircularFingerprint
		from deepchem.featurizers.basic import RDKitDescriptors
		from deepchem.utils.save import log
		from deepchem.utils.save import save_to_disk
		from deepchem.utils.save import load_from_disk
		from deepchem.utils.save import load_pandas_from_disk
		from deepchem.utils import ScaffoldGenerator
		from deepchem.featurizers.nnscore import NNScoreComplexFeaturizer
		import multiprocessing as mp
		from pathos.multiprocessing import ProcessingPool
		from functools import partial


		def generate_scaffold(smiles, include_chirality=False):
		"""Compute the Bemis-Murcko scaffold for a SMILES string."""
		mol = Chem.MolFromSmiles(smiles)
		engine = ScaffoldGenerator(include_chirality=include_chirality)
		scaffold = engine.get_scaffold(mol)
		return scaffold

		def _check_validity(compounds_df):
		"""Ensure that columns of compound_df contain required elements."""
		if not set(FeaturizedSamples.colnames).issubset(compounds_df.keys()):
		raise ValueError("Compound dataframe does not contain required columns")

		def _process_field(val):
		"""Parse data in a field."""
		if isinstance(val, float) or isinstance(val, np.ndarray):
		return val
		elif isinstance(val, list):
		return [_process_field(elt) for elt in val]
		elif isinstance(val, str):
		try:
		return float(val)
		except ValueError:
		return val
		else:
		raise ValueError("Field of unrecognized type: %s" % str(val))

		def _get_input_type(input_file):
		"""Get type of input file. Must be csv/pkl.gz/sdf file."""
		filename, file_extension = os.path.splitext(input_file)
		# If gzipped, need to compute extension again
		if file_extension == ".gz":
		filename, file_extension = os.path.splitext(filename)
		if file_extension == ".csv":
		return "csv"
		elif file_extension == ".pkl":
		return "pandas-pickle"
		elif file_extension == ".joblib":
		return "pandas-joblib"
		else:
		raise ValueError("Unrecognized extension %s" % file_extension)

		def _get_fields(input_file):
		"""Get the names of fields and field_types for input data."""
		# If CSV input, assume that first row contains labels
		input_type = _get_input_type(input_file)
		if input_type == "csv":
		with open(input_file, "rb") as inp_file_obj:
		return csv.reader(inp_file_obj).next()
		elif input_type == "pandas-joblib":
		df = load_from_disk(input_file)
		return df.keys()
		elif input_type == "pandas-pickle":
		df = load_pickle_from_disk(input_file)
		return df.keys()
		else:
		raise ValueError("Unrecognized extension for %s" % input_file)

		class DataFeaturizer(object):
		"""
		Handles loading/featurizing of chemical samples (datapoints).

		Currently knows how to load csv-files/pandas-dataframes/SDF-files. Writes a
		dataframe object to disk as output.
		"""

		def __init__(self, tasks, smiles_field, split_field=None,
		id_field=None, threshold=None, user_specified_features=None,
		protein_pdb_field=None, ligand_pdb_field=None,
		ligand_mol2_field=None,
		compound_featurizers=[], complex_featurizers=[],
		verbose=False, log_every_n=1000):
		"""Extracts data from input as Pandas data frame"""
		if not isinstance(tasks, list):
		raise ValueError("tasks must be a list.")
		self.tasks = tasks
		self.smiles_field = smiles_field
		self.split_field = split_field
		if id_field is None:
		self.id_field = smiles_field
		else:
		self.id_field = id_field
		self.threshold = threshold
		self.protein_pdb_field = protein_pdb_field
		self.ligand_pdb_field = ligand_pdb_field
		self.ligand_mol2_field = ligand_mol2_field
		self.user_specified_features = user_specified_features
		self.compound_featurizers = compound_featurizers
		self.complex_featurizers = complex_featurizers
		self.verbose = verbose
		self.log_every_n = log_every_n

		def featurize(self, input_file, feature_dir, samples_dir, shard_size=128):
		"""Featurize provided file and write to specified location."""
		input_type = _get_input_type(input_file)

		log("Loading raw samples now.", self.verbose)
		raw_df = load_pandas_from_disk(input_file)
		fields = raw_df.keys()
		log("Loaded raw data frame from file.", self.verbose)

		def process_raw_sample_helper(row, fields, input_type):
		return self._process_raw_sample(input_type, row, fields)
		process_raw_sample_helper_partial = partial(process_raw_sample_helper,
		fields=fields,
		input_type=input_type)


		#processed_rows = raw_df.apply(process_raw_sample_helper_partial, axis=1)
		raw_df = raw_df.apply(process_raw_sample_helper_partial, axis=1, reduce=False)
		#raw_df = pd.DataFrame.from_records(processed_rows)

		nb_sample = raw_df.shape[0]
		interval_points = np.linspace(
		0, nb_sample, np.ceil(float(nb_sample)/shard_size)+1, dtype=int)
		shard_files = []
		for j in range(len(interval_points)-1):
		log("Sharding and standardizing into shard-%s / %s shards" % (str(j+1), len(interval_points)-1), self.verbose)
		raw_df_shard = raw_df.iloc[range(interval_points[j], interval_points[j+1])]

		df = self._standardize_df(raw_df_shard)
		log("Aggregating User-Specified Features", self.verbose)
		self._add_user_specified_features(df)

		for compound_featurizer in self.compound_featurizers:
		log("Currently feauturizing feature_type: %s"
		% compound_featurizer.__class__.__name__, self.verbose)
		self._featurize_compounds(df, compound_featurizer)

		for complex_featurizer in self.complex_featurizers:
		log("Currently feauturizing feature_type: %s"
		% complex_featurizer.__class__.__name__, self.verbose)
		self._featurize_complexes(df, complex_featurizer)

		shard_out = os.path.join(feature_dir, "features_shard%d.joblib" % j)
		save_to_disk(df, shard_out)
		shard_files.append(shard_out)

		featurizers = self.compound_featurizers + self.complex_featurizers
		samples = FeaturizedSamples(samples_dir=samples_dir, featurizers=featurizers,
		dataset_files=shard_files,
		reload_data=False)

		return samples

		def _process_raw_sample(self, input_type, row, fields):
		"""Extract information from row data."""
		data = {}
		if input_type == "csv":
		for ind, field in enumerate(fields):
		data[field] = _process_field(row[ind])
		elif input_type in ["pandas-pickle", "pandas-joblib"]:
		for field in fields:
		data[field] = _process_field(row[field])
		else:
		raise ValueError("Unrecognized input_type")
		if self.threshold is not None:
		for task in self.tasks:
		raw = _process_field(data[task])
		if not isinstance(raw, float):
		raise ValueError("Cannot threshold non-float fields.")
		data[field] = 1 if raw > self.threshold else 0
		return data

		def _standardize_df(self, ori_df):
		"""Copy specified columns to new df with standard column names."""
		df = pd.DataFrame(ori_df[[self.id_field]])
		df.columns = ["mol_id"]
		df["smiles"] = ori_df[[self.smiles_field]]
		for task in self.tasks:
		df[task] = ori_df[[task]]
		if self.split_field is not None:
		df["split"] = ori_df[[self.split_field]]
		if self.protein_pdb_field is not None:
		df["protein_pdb"] = ori_df[[self.protein_pdb_field]]
		if self.ligand_pdb_field is not None:
		df["ligand_pdb"] = ori_df[[self.ligand_pdb_field]]
		if self.ligand_mol2_field is not None:
		df["ligand_mol2"] = ori_df[[self.ligand_mol2_field]]
		return df

		def _featurize_complexes(self, df, featurizer, parallel=True):
		"""Generates circular fingerprints for dataset."""
		protein_pdbs = list(df["protein_pdb"])
		ligand_pdbs = list(df["ligand_pdb"])
		complexes = zip(ligand_pdbs, protein_pdbs)

		def featurize_wrapper(ligand_protein_pdb_tuple):
		ligand_pdb, protein_pdb = ligand_protein_pdb_tuple
		molecule_features = featurizer.featurize_complexes([ligand_pdb], [protein_pdb])
		return featurizer.featurize_complexes([ligand_pdb], [protein_pdb])

		features = ProcessingPool(mp.cpu_count()).map(featurize_wrapper,
		zip(ligand_pdbs, protein_pdbs))
		#features = featurize_wrapper(zip(ligand_pdbs, protein_pdbs))
		df[featurizer.__class__.__name__] = list(features)

		def _featurize_compounds(self, df, featurizer, parallel=True):
		"""Featurize individual compounds.

		Given a featurizer that operates on individual chemical compounds
		or macromolecules, compute & add features for that compound to the
		features dataframe
		"""
		sample_smiles = df["smiles"].tolist()

		if not parallel:
		features = []
		for ind, smiles in enumerate(sample_smiles):
		if ind % self.log_every_n == 0:
		log("Featurizing sample %d" % ind, self.verbose)
		mol = Chem.MolFromSmiles(smiles)
		features.append(featurizer.featurize([mol]))
		else:
		def featurize_wrapper(smiles):
		mol = Chem.MolFromSmiles(smiles)
		return featurizer.featurize([mol])

		features = ProcessingPool(mp.cpu_count()).map(featurize_wrapper,
		sample_smiles)

		df[featurizer.__class__.__name__] = features

		def _add_user_specified_features(self, df):
		"""Merge user specified features.

		Merge features included in dataset provided by user
		into final features dataframe
		"""
		if self.user_specified_features is not None:
		log("Adding user-defined features.", self.verbose)
		features_data = []
		for _, row in df.iterrows():
		# pandas rows are tuples (row_num, row_data)
		feature_list = []
		for feature_name in self.user_specified_features:
		feature_list.append(row[feature_name])
		features_data.append({"user-specified-features": np.array(feature_list)})
		df["user-specified-features"] = pd.DataFrame(features_data)


		def map_function(data_tuple, featurizer):
		featurizer = NNScoreComplexFeaturizer()
		ind, ligand_pdb, protein_pdb = data_tuple
		#print("Mapping on ind %d" % ind)
		#print("ind, type(ligand_pdb), type(protein_pdb): %s " % str((ind, type(ligand_pdb), type(protein_pdb))))
		return featurizer.featurize_complexes([ligand_pdb], [protein_pdb])

		class FeaturizedSamples(object):
		"""
		Wrapper class for featurized data on disk.
		"""
		# The standard columns for featurized data.
		colnames = ["mol_id", "smiles", "split"]
		optional_colnames = ["protein_pdb", "ligand_pdb", "ligand_mol2"]

		def __init__(self, samples_dir, featurizers, dataset_files=None,
		overwrite=True, reload_data=False):
		"""
		Initialiize FeaturizedSamples

		If samples_dir does not exist, must specify dataset_files. Then samples_dir
		is created and populated. If samples_dir exists (created by previous call to
		FeaturizedSamples), then dataset_files cannot be specified. If overwrite is
		set and dataset_files is provided, will overwrite old dataset_files with
		new.
		"""
		self.dataset_files = dataset_files
		self.feature_types = (
		["user-specified-features"] +
		[featurizer.__class__.__name__ for featurizer in featurizers])

		self.featurizers = featurizers

		if not os.path.exists(samples_dir):
		os.makedirs(samples_dir)
		self.samples_dir = samples_dir
		if os.path.exists(self._get_compounds_filename()) and reload_data:
		compounds_df = load_from_disk(self._get_compounds_filename())
		else:
		compounds_df = self._get_compounds()
		# compounds_df is not altered by any method after initialization, so it's
		# safe to keep a copy in memory and on disk.
		save_to_disk(compounds_df, self._get_compounds_filename())
		_check_validity(compounds_df)
		self.compounds_df = compounds_df

		if os.path.exists(self._get_dataset_paths_filename()):
		if dataset_files is not None:
		if overwrite:
		save_to_disk(dataset_files, self._get_dataset_paths_filename())
		else:
		raise ValueError("Can't change dataset_files already stored on disk")
		self.dataset_files = load_from_disk(self._get_dataset_paths_filename())
		else:
		save_to_disk(dataset_files, self._get_dataset_paths_filename())

		def _get_compounds_filename(self):
		"""
		Get standard location for file listing compounds in this dataframe.
		"""
		return os.path.join(self.samples_dir, "compounds.joblib")

		def _get_dataset_paths_filename(self):
		"""
		Get standard location for file listing dataset_files.
		"""
		return os.path.join(self.samples_dir, "datasets.joblib")

		def _get_compounds(self):
		"""
		Create dataframe containing metadata about compounds.
		"""
		compound_rows = []
		for dataset_file in self.dataset_files:
		df = load_from_disk(dataset_file)
		compound_ids = list(df["mol_id"])
		smiles = list(df["smiles"])
		if "split" in df.keys():
		splits = list(df["split"])
		else:
		splits = [None] * len(smiles)
		compound_rows += [list(elt) for elt in zip(compound_ids, smiles, splits)]

		compounds_df = pd.DataFrame(compound_rows,
		columns=("mol_id", "smiles", "split"))
		return compounds_df

		def _set_compound_df(self, df):
		"""Internal method used to replace compounds_df."""
		_check_validity(df)
		save_to_disk(df, self._get_compounds_filename())
		self.compounds_df = df

		# TODO(rbharath): Might this be inefficient?
		def itersamples(self):
		"""
		Provides an iterator over samples.

		Each sample from the iterator is a dataframe of samples.
		"""
		compound_ids = set(list(self.compounds_df["mol_id"]))
		for df_file in self.dataset_files:
		df = load_from_disk(df_file)
		visible_inds = []
		for ind, row in df.iterrows():
		if row["mol_id"] in compound_ids:
		visible_inds.append(ind)
		yield df.loc[visible_inds]

		def train_test_split(self, splittype, train_dir, test_dir, seed=None,
		frac_train=.8):
		"""
		Splits self into train/test sets and returns two FeaturizedDatsets
		"""
		if splittype == "random":
		train_inds, test_inds = self._train_test_random_split(seed=seed, frac_train=frac_train)
		elif splittype == "scaffold":
		train_inds, test_inds = self._train_test_scaffold_split(frac_train=frac_train)
		elif splittype == "specified":
		train_inds, test_inds = self._train_test_specified_split()
		else:
		raise ValueError("improper splittype.")
		train_samples = FeaturizedSamples(samples_dir=train_dir,
		dataset_files=self.dataset_files,
		featurizers=self.featurizers)
		train_samples._set_compound_df(self.compounds_df.iloc[train_inds])
		test_samples = FeaturizedSamples(samples_dir=test_dir,
		dataset_files=self.dataset_files,
		featurizers=self.featurizers)
		test_samples._set_compound_df(self.compounds_df.iloc[test_inds])

		return train_samples, test_samples

		def _train_test_random_split(self, seed=None, frac_train=.8):
		"""
		Splits internal compounds randomly into train/test.
		"""
		np.random.seed(seed)
		train_cutoff = frac_train * len(self.compounds_df)
		shuffled = np.random.permutation(range(len(self.compounds_df)))
		return shuffled[:train_cutoff], shuffled[train_cutoff:]

		def _train_test_scaffold_split(self, frac_train=.8):
		"""
		Splits internal compounds into train/test by scaffold.
		"""
		scaffolds = {}
		for ind, row in self.compounds_df.iterrows():
		scaffold = generate_scaffold(row["smiles"])
		if scaffold not in scaffolds:
		scaffolds[scaffold] = [ind]
		else:
		scaffolds[scaffold].append(ind)
		# Sort from largest to smallest scaffold sets
		scaffold_sets = [scaffold_set for (scaffold, scaffold_set) in
		sorted(scaffolds.items(), key=lambda x: -len(x[1]))]
		train_cutoff = frac_train * len(self.compounds_df)
		train_inds, test_inds = [], []
		for scaffold_set in scaffold_sets:
		if len(train_inds) + len(scaffold_set) > train_cutoff:
		test_inds += scaffold_set
		else:
		train_inds += scaffold_set
		return train_inds, test_inds

		def _train_test_specified_split(self):
		"""
		Splits internal compounds into train/test by user-specification.
		"""
		train_inds, test_inds = [], []
		for ind, row in self.compounds_df.iterrows():
		if row["split"].lower() == "train":
		train_inds.append(ind)
		elif row["split"].lower() == "test":
		test_inds.append(ind)
		else:
		raise ValueError("Missing required split information.")
		return train_inds, test_inds

deepchem/featurizers/nnscore.py

+7 −0

Original line number	Diff line number	Diff line
		@@ -714,32 +714,39 @@ class NNScoreComplexFeaturizer(ComplexFeaturizer):
		"""
		Compute Binana fingerprint for complex.
		"""
		print("In _featurize_complex")
		mol_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
		with open(mol_pdb_file.name, "w") as mol_f:
		mol_f.writelines(mol_pdb)
		protein_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
		with open(protein_pdb_file.name, "w") as protein_f:
		protein_f.writelines(protein_pdb)
		print("Written temp pdb files")

		mol_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
		mol_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
		hydrogenate_and_compute_partial_charges(
		mol_pdb_file.name, "pdb", mol_hyd_file.name,
		mol_pdbqt_file.name)
		print("Hydrogenated mol file")

		protein_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
		protein_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
		hydrogenate_and_compute_partial_charges(
		protein_pdb_file.name, "pdb", protein_hyd_file.name,
		protein_pdbqt_file.name)
		print("Hydrogenated protein file")

		mol_pdb_obj = PDB()
		mol_pdb_obj.load_from_files(mol_pdb_file.name, mol_pdbqt_file.name)
		print("Loaded mol pdb object")

		protein_pdb_obj = PDB()
		protein_pdb_obj.load_from_files(
		protein_pdb_file.name, protein_pdbqt_file.name)
		print("Loaded protein pdb object")

		features = self.binana.compute_input_vector(mol_pdb_obj, protein_pdb_obj)
		print("Computed binana features.")

		return features

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