Loading deepchem/feat/one_hot.pydeleted 100644 → 0 +0 −148 Original line number Diff line number Diff line import numpy as np from deepchem.feat import Featurizer zinc_charset = [ ' ', '#', ')', '(', '+', '-', '/', '1', '3', '2', '5', '4', '7', '6', '8', '=', '@', 'C', 'B', 'F', 'I', 'H', 'O', 'N', 'S', '[', ']', '\\', 'c', 'l', 'o', 'n', 'p', 's', 'r' ] class OneHotFeaturizer(Featurizer): """ NOTE(LESWING) Not Thread Safe in initialization of charset """ def __init__(self, charset=None, padlength=120): """ Parameters ---------- charset: obj:`list` of obj:`str` Each string is length 1 padlength: int length to pad the smile strings to """ self.charset = charset self.pad_length = padlength def featurize(self, mols, verbose=True, log_every_n=1000): """ Parameters ---------- mols: obj List of rdkit Molecule Objects verbose: bool How much logging log_every_n: How often to log Returns ------- obj numpy array of features """ from rdkit import Chem smiles = [Chem.MolToSmiles(mol) for mol in mols] if self.charset is None: self.charset = self._create_charset(smiles) return np.array([self.one_hot_encoded(smile) for smile in smiles]) def one_hot_array(self, i): """ Create a one hot array with bit i set to 1 Parameters ---------- i: int bit to set to 1 Returns ------- obj:`list` of obj:`int` length len(self.charset) """ return [int(x) for x in [ix == i for ix in range(len(self.charset))]] def one_hot_index(self, c): """ TODO(LESWING) replace with map lookup vs linear scan Parameters ---------- c character whose index we want Returns ------- int index of c in self.charset """ return self.charset.index(c) def pad_smile(self, smile): """ Pad A Smile String to self.pad_length Parameters ---------- smile: str Returns ------- str smile string space padded to self.pad_length """ return smile.ljust(self.pad_length) def one_hot_encoded(self, smile): """ One Hot Encode an entire SMILE string Parameters ---------- smile: str smile string to encode Returns ------- object np.array of one hot encoded arrays for each character in smile """ return np.array([ self.one_hot_array(self.one_hot_index(x)) for x in self.pad_smile(smile) ]) def untransform(self, z): """ Convert from one hot representation back to SMILE Parameters ---------- z: obj:`list` list of one hot encoded features Returns ------- Smile Strings picking MAX for each one hot encoded array """ z1 = [] for i in range(len(z)): s = "" for j in range(len(z[i])): oh = np.argmax(z[i][j]) s += self.charset[oh] z1.append([s.strip()]) return z1 def _create_charset(self, smiles): """ create the charset from smiles Parameters ---------- smiles: obj:`list` of obj:`str` list of smile strings Returns ------- obj:`list` of obj:`str` List of length one strings that are characters in smiles. No duplicates """ s = set() for smile in smiles: for c in smile: s.add(c) return [' '] + sorted(list(s)) deepchem/feat/tests/test_basic.pydeleted 100644 → 0 +0 −53 Original line number Diff line number Diff line """ Test basic molecular features. """ import numpy as np import unittest from deepchem.feat.basic import MolecularWeight, RDKitDescriptors class TestMolecularWeight(unittest.TestCase): """ Test MolecularWeight. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) self.engine = MolecularWeight() def testMW(self): """ Test MW. """ assert np.allclose(self.engine([self.mol]), 180, atol=0.1) class TestRDKitDescriptors(unittest.TestCase): """ Test RDKitDescriptors. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) self.engine = RDKitDescriptors() def testRDKitDescriptors(self): """ Test simple descriptors. """ descriptors = self.engine([self.mol]) assert np.allclose( descriptors[0, self.engine.descriptors.index('ExactMolWt')], 180, atol=0.1) Loading
deepchem/feat/one_hot.pydeleted 100644 → 0 +0 −148 Original line number Diff line number Diff line import numpy as np from deepchem.feat import Featurizer zinc_charset = [ ' ', '#', ')', '(', '+', '-', '/', '1', '3', '2', '5', '4', '7', '6', '8', '=', '@', 'C', 'B', 'F', 'I', 'H', 'O', 'N', 'S', '[', ']', '\\', 'c', 'l', 'o', 'n', 'p', 's', 'r' ] class OneHotFeaturizer(Featurizer): """ NOTE(LESWING) Not Thread Safe in initialization of charset """ def __init__(self, charset=None, padlength=120): """ Parameters ---------- charset: obj:`list` of obj:`str` Each string is length 1 padlength: int length to pad the smile strings to """ self.charset = charset self.pad_length = padlength def featurize(self, mols, verbose=True, log_every_n=1000): """ Parameters ---------- mols: obj List of rdkit Molecule Objects verbose: bool How much logging log_every_n: How often to log Returns ------- obj numpy array of features """ from rdkit import Chem smiles = [Chem.MolToSmiles(mol) for mol in mols] if self.charset is None: self.charset = self._create_charset(smiles) return np.array([self.one_hot_encoded(smile) for smile in smiles]) def one_hot_array(self, i): """ Create a one hot array with bit i set to 1 Parameters ---------- i: int bit to set to 1 Returns ------- obj:`list` of obj:`int` length len(self.charset) """ return [int(x) for x in [ix == i for ix in range(len(self.charset))]] def one_hot_index(self, c): """ TODO(LESWING) replace with map lookup vs linear scan Parameters ---------- c character whose index we want Returns ------- int index of c in self.charset """ return self.charset.index(c) def pad_smile(self, smile): """ Pad A Smile String to self.pad_length Parameters ---------- smile: str Returns ------- str smile string space padded to self.pad_length """ return smile.ljust(self.pad_length) def one_hot_encoded(self, smile): """ One Hot Encode an entire SMILE string Parameters ---------- smile: str smile string to encode Returns ------- object np.array of one hot encoded arrays for each character in smile """ return np.array([ self.one_hot_array(self.one_hot_index(x)) for x in self.pad_smile(smile) ]) def untransform(self, z): """ Convert from one hot representation back to SMILE Parameters ---------- z: obj:`list` list of one hot encoded features Returns ------- Smile Strings picking MAX for each one hot encoded array """ z1 = [] for i in range(len(z)): s = "" for j in range(len(z[i])): oh = np.argmax(z[i][j]) s += self.charset[oh] z1.append([s.strip()]) return z1 def _create_charset(self, smiles): """ create the charset from smiles Parameters ---------- smiles: obj:`list` of obj:`str` list of smile strings Returns ------- obj:`list` of obj:`str` List of length one strings that are characters in smiles. No duplicates """ s = set() for smile in smiles: for c in smile: s.add(c) return [' '] + sorted(list(s))
deepchem/feat/tests/test_basic.pydeleted 100644 → 0 +0 −53 Original line number Diff line number Diff line """ Test basic molecular features. """ import numpy as np import unittest from deepchem.feat.basic import MolecularWeight, RDKitDescriptors class TestMolecularWeight(unittest.TestCase): """ Test MolecularWeight. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) self.engine = MolecularWeight() def testMW(self): """ Test MW. """ assert np.allclose(self.engine([self.mol]), 180, atol=0.1) class TestRDKitDescriptors(unittest.TestCase): """ Test RDKitDescriptors. """ def setUp(self): """ Set up tests. """ smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O' from rdkit import Chem self.mol = Chem.MolFromSmiles(smiles) self.engine = RDKitDescriptors() def testRDKitDescriptors(self): """ Test simple descriptors. """ descriptors = self.engine([self.mol]) assert np.allclose( descriptors[0, self.engine.descriptors.index('ExactMolWt')], 180, atol=0.1)
