DeepChem has a broad collection of utility functions. Many of these maybe be of independent interest to users since they deal with some tricky aspects of processing scientific datatypes.
deepchem.utils.data_utils.pad_array
The DeepChem data directory is where downloaded MoleculeNet datasets are stored.
deepchem.utils.data_utils.get_data_dir
deepchem.utils.data_utils.download_url
deepchem.utils.data_utils.untargz_file
deepchem.utils.data_utils.unzip_file
deepchem.utils.data_utils.load_data
deepchem.utils.data_utils.load_sdf_files
deepchem.utils.data_utils.load_csv_files
deepchem.utils.data_utils.load_json_files
deepchem.utils.data_utils.load_pickle_files
deepchem.utils.data_utils.load_from_disk
deepchem.utils.data_utils.save_to_disk
deepchem.utils.data_utils.load_dataset_from_disk
deepchem.utils.data_utils.save_dataset_to_disk
deepchem.utils.conformers.ConformerGenerator
deepchem.utils.rdkit_utils.MoleculeLoadException
deepchem.utils.rdkit_utils.get_xyz_from_mol
deepchem.utils.rdkit_utils.add_hydrogens_to_mol
deepchem.utils.rdkit_utils.compute_charges
deepchem.utils.rdkit_utils.load_molecule
deepchem.utils.rdkit_utils.write_molecule
It's often convenient to manipulate subsets of a molecule. The MolecularFragment class aids in such manipulations.
deepchem.utils.fragment_utils.MolecularFragment
deepchem.utils.fragment_utils.AtomShim
deepchem.utils.fragment_utils.strip_hydrogens
deepchem.utils.fragment_utils.merge_molecular_fragments
deepchem.utils.fragment_utils.get_contact_atom_indices
deepchem.utils.fragment_utils.reduce_molecular_complex_to_contacts
deepchem.utils.coordinate_box_utils.CoordinateBox
deepchem.utils.coordinate_box_utils.intersect_interval
deepchem.utils.coordinate_box_utils.union
deepchem.utils.coordinate_box_utils.merge_overlapping_boxes
deepchem.utils.coordinate_box_utils.get_face_boxes
deepchem.utils.evaluate.Evaluator
deepchem.utils.evaluate.GeneratorEvaluator
deepchem.utils.evaluate.relative_difference
deepchem.utils.genomics_utils.seq_one_hot_encode
deepchem.utils.genomics_utils.encode_bio_sequence
deepchem.utils.sequence_utils.hhblits
deepchem.utils.sequence_utils.hhsearch
deepchem.utils.sequence_utils.MSA_to_dataset
deepchem.utils.geometry_utils.unit_vector
deepchem.utils.geometry_utils.angle_between
deepchem.utils.geometry_utils.generate_random_unit_vector
deepchem.utils.geometry_utils.generate_random_rotation_matrix
deepchem.utils.geometry_utils.is_angle_within_cutoff
deepchem.utils.graph_utils.fourier_encode_dist
deepchem.utils.graph_utils.aggregate_mean
deepchem.utils.graph_utils.aggregate_max
deepchem.utils.graph_utils.aggregate_min
deepchem.utils.graph_utils.aggregate_std
deepchem.utils.graph_utils.aggregate_var
deepchem.utils.graph_utils.aggregate_moment
deepchem.utils.graph_utils.aggregate_sum
deepchem.utils.graph_utils.scale_identity
deepchem.utils.graph_utils.scale_amplification
deepchem.utils.graph_utils.scale_attenuation
deepchem.utils.hash_utils.hash_ecfp
deepchem.utils.hash_utils.hash_ecfp_pair
deepchem.utils.hash_utils.vectorize
deepchem.utils.voxel_utils.convert_atom_to_voxel
deepchem.utils.voxel_utils.convert_atom_pair_to_voxel
deepchem.utils.voxel_utils.voxelize
deepchem.utils.molecule_feature_utils.one_hot_encode
deepchem.utils.molecule_feature_utils.get_atom_type_one_hot
deepchem.utils.molecule_feature_utils.construct_hydrogen_bonding_info
deepchem.utils.molecule_feature_utils.get_atom_hydrogen_bonding_one_hot
deepchem.utils.molecule_feature_utils.get_atom_is_in_aromatic_one_hot
deepchem.utils.molecule_feature_utils.get_atom_hybridization_one_hot
deepchem.utils.molecule_feature_utils.get_atom_total_num_Hs_one_hot
deepchem.utils.molecule_feature_utils.get_atom_chirality_one_hot
deepchem.utils.molecule_feature_utils.get_atom_formal_charge
deepchem.utils.molecule_feature_utils.get_atom_partial_charge
deepchem.utils.molecule_feature_utils.get_atom_total_degree_one_hot
deepchem.utils.molecule_feature_utils.get_bond_type_one_hot
deepchem.utils.molecule_feature_utils.get_bond_is_in_same_ring_one_hot
deepchem.utils.molecule_feature_utils.get_bond_is_conjugated_one_hot
deepchem.utils.molecule_feature_utils.get_bond_stereo_one_hot
deepchem.utils.molecule_feature_utils.get_bond_graph_distance_one_hot
deepchem.utils.grover.extract_grover_attributes
These utilities assist in file preparation and processing for molecular docking.
deepchem.utils.docking_utils.write_vina_conf
deepchem.utils.docking_utils.write_gnina_conf
deepchem.utils.docking_utils.load_docked_ligands
deepchem.utils.docking_utils.prepare_inputs
deepchem.utils.docking_utils.read_gnina_log
The printing threshold controls how many dataset elements are printed when dc.data.Dataset objects are converted to strings or represnted in the IPython repl.
deepchem.utils.debug_utils.get_print_threshold
deepchem.utils.debug_utils.set_print_threshold
deepchem.utils.debug_utils.get_max_print_size
deepchem.utils.debug_utils.set_max_print_size
The utilities here are used to generate random sample data which can be used for testing model architectures or other purposes.
deepchem.utils.fake_data_generator.FakeGraphGenerator
The utilities here are used to sample electrons in a given molecule and update it using monte carlo methods, which can be used for methods like Variational Monte Carlo, etc.
deepchem.utils.electron_sampler.ElectronSampler
The utilites here are used to create an object that contains information about a system's self-consistent iteration steps and other processes.
deepchem.utils.dft_utils.Lattice
deepchem.utils.dft_utils.SpinParam
deepchem.utils.dft_utils.ValGrad
deepchem.utils.dft_utils.data.datastruct.CGTOBasis
deepchem.utils.dft_utils.data.datastruct.AtomCGTOBasis
deepchem.utils.dft_utils.BaseXC
deepchem.utils.dft_utils.AddBaseXC
deepchem.utils.dft_utils.xc.base_xc.MulBaseXC
deepchem.utils.dft_utils.BaseGrid
deepchem.utils.dft_utils.df.base_df.BaseDF
deepchem.utils.dft_utils.hamilton.base_hamilton.BaseHamilton
deepchem.utils.dftutils.KSCalc
deepchem.utils.dftutils.hashstr
deepchem.utils.dftutils.BaseGrid
deepchem.utils.dftutils.BaseQCCalc
deepchem.utils.dftutils.SpinParam
deepchem.utils.dft_utils.config._Config
deepchem.utils.dft_utils.BaseOrbParams
deepchem.utils.dft_utils.QROrbParams
deepchem.utils.dft_utils.MatExpOrbParams
deepchem.utils.dft_utils.api.parser.parse_moldesc
deepchem.utils.dft_utils.system.base_system.BaseSystem
deepchem.utils.dft_utils.grid.radial_grid.RadialGrid
deepchem.utils.dft_utils.grid.radial_grid.get_xw_integration
deepchem.utils.dft_utils.grid.radial_grid.SlicedRadialGrid
deepchem.utils.dft_utils.grid.radial_grid.BaseGridTransform
deepchem.utils.dft_utils.grid.radial_grid.DE2Transformation
deepchem.utils.dft_utils.grid.radial_grid.LogM3Transformation
deepchem.utils.dft_utils.grid.radial_grid.TreutlerM4Transformation
deepchem.utils.dft_utils.grid.radial_grid.get_grid_transform
deepchem.utils.differentiation_utils.editable_module.EditableModule
deepchem.utils.differentiation_utils.normalize_bcast_dims
deepchem.utils.differentiation_utils.get_bcasted_dims
deepchem.utils.differentiation_utils.match_dim
deepchem.utils.differentiation_utils.linop.LinearOperator
deepchem.utils.differentiation_utils.linop.AddLinearOperator
deepchem.utils.differentiation_utils.linop.MulLinearOperator
deepchem.utils.differentiation_utils.linop.AdjointLinearOperator
deepchem.utils.differentiation_utils.linop.MatmulLinearOperator
deepchem.utils.differentiation_utils.linop.MatrixLinearOperator
deepchem.utils.differentiation_utils.pure_function.PureFunction
deepchem.utils.differentiation_utils.pure_function.FunctionPureFunction
deepchem.utils.differentiation_utils.pure_function.EditableModulePureFunction
deepchem.utils.differentiation_utils.pure_function.TorchNNPureFunction
deepchem.utils.differentiation_utils.pure_function.PureFunction
deepchem.utils.differentiation_utils.pure_function._check_identical_objs
deepchem.utils.differentiation_utils.pure_function.get_pure_function
deepchem.utils.differentiation_utils.set_default_option
deepchem.utils.differentiation_utils.get_and_pop_keys
deepchem.utils.differentiation_utils.get_method
deepchem.utils.differentiation_utils.dummy_context_manager
deepchem.utils.differentiation_utils.assert_runtime
deepchem.utils.differentiation_utils.symeig._set_initial_v
deepchem.utils.differentiation_utils.symeig._take_eigpairs
deepchem.utils.differentiation_utils.symeig.exacteig
deepchem.utils.differentiation_utils.symeig.degen_symeig
deepchem.utils.differentiation_utils.symeig.davidson
deepchem.utils.differentiation_utils.symeig.lsymeig
deepchem.utils.differentiation_utils.symeig.usymeig
deepchem.utils.differentiation_utils.symeig.symeig
deepchem.utils.differentiation_utils.symeig.symeig_torchfcn
deepchem.utils.differentiation_utils.symeig._check_degen
deepchem.utils.differentiation_utils.symeig.ortho
deepchem.utils.differentiation_utils.grad.jac
deepchem.utils.differentiation_utils.grad._Jac
deepchem.utils.differentiation_utils.grad._setup_idxs
deepchem.utils.differentiation_utils.grad.connect_graph
deepchem.utils.differentiation_utils.solve.wrap_gmres
deepchem.utils.differentiation_utils.solve.exactsolve
deepchem.utils.differentiation_utils.solve.solve_ABE
deepchem.utils.differentiation_utils.solve.get_batchdims
deepchem.utils.differentiation_utils.solve.setup_precond
deepchem.utils.differentiation_utils.solve.dot
deepchem.utils.differentiation_utils.solve.gmres
deepchem.utils.differentiation_utils.solve.setup_linear_problem
deepchem.utils.differentiation_utils.solve.safedenom
deepchem.utils.differentiation_utils.solve.get_largest_eival
deepchem.utils.differentiation_utils.solve.solve
deepchem.utils.differentiation_utils.solve.broyden1_solve
deepchem.utils.differentiation_utils.solve._rootfinder_solve
deepchem.utils.differentiation_utils.solve.cg
deepchem.utils.differentiation_utils.solve.bicgstab
deepchem.utils.differentiation_utils.solve.solve_torchfcn
deepchem.utils.differentiation_utils.optimize.equilibrium.anderson_acc
deepchem.utils.differentiation_utils.optimize.minimizer.gd
deepchem.utils.differentiation_utils.optimize.minimizer.adam
deepchem.utils.differentiation_utils.optimize.minimizer.TerminationCondition
deepchem.utils.differentiation_utils.optimize.rootsolver._nonlin_solver
deepchem.utils.differentiation_utils.optimize.rootsolver.broyden1
deepchem.utils.differentiation_utils.optimize.rootsolver.broyden2
deepchem.utils.differentiation_utils.optimize.rootsolver.linearmixing
deepchem.utils.differentiation_utils.optimize.rootsolver._safe_norm
deepchem.utils.differentiation_utils.optimize.rootsolver._nonline_line_search
deepchem.utils.differentiation_utils.optimize.rootsolver._scalar_search_armijo
deepchem.utils.differentiation_utils.optimize.rootsolver.TerminationCondition
deepchem.utils.differentiation_utils.optimize.jacobian.Jacobian
deepchem.utils.differentiation_utils.optimize.jacobian.BroydenFirst
deepchem.utils.differentiation_utils.optimize.jacobian.BroydenSecond
deepchem.utils.differentiation_utils.optimize.jacobian.LinearMixing
deepchem.utils.differentiation_utils.optimize.jacobian.LowRankMatrix
deepchem.utils.differentiation_utils.optimize.jacobian.FullRankMatrix
deepchem.utils.differentiation_utils.optimize.rootfinder.rootfinder
deepchem.utils.differentiation_utils.optimize.rootfinder.equilibrium
deepchem.utils.differentiation_utils.optimize.rootfinder.minimize
deepchem.utils.differentiation_utils.optimize.rootfinder._RootFinder
deepchem.utils.differentiation_utils.optimize.rootfinder._get_rootfinder_default_method
deepchem.utils.differentiation_utils.optimize.rootfinder._get_equilibrium_default_method
deepchem.utils.differentiation_utils.optimize.rootfinder._get_minimizer_default_method
The utilities here are used to modify the attributes of the classes. Used by differentiation_utils.
deepchem.utils.attribute_utils.get_attr
deepchem.utils.attribute_utils.set_attr
deepchem.utils.attribute_utils.del_attr
deepchem.utils.pytorch_utils.unsorted_segment_sum
deepchem.utils.pytorch_utils.segment_sum
deepchem.utils.pytorch_utils.chunkify
deepchem.utils.pytorch_utils.get_memory
deepchem.utils.pytorch_utils.gaussian_integral
deepchem.utils.pytorch_utils.TensorNonTensorSeparator
deepchem.utils.pytorch_utils.tallqr
deepchem.utils.pytorch_utils.to_fortran_order
deepchem.utils.pytorch_utils.get_np_dtype
The utilites here are used for computing features on batch of data. Can be used inside of default_generator function.
deepchem.utils.batch_utils.batch_coulomb_matrix_features
deepchem.utils.batch_utils.batch_elements
deepchem.utils.batch_utils.create_input_array
deepchem.utils.batch_utils.create_output_array
The Utilities here are used to computing atomic mass and radii data. These can be used by DFT and many other Molecular Models.
deepchem.utils.periodic_table_utils.get_atomz
The utilities here refer to equivariance tools that play a vital role in mathematics and applied sciences. They excel in preserving the relationships between objects or data points when undergoing transformations such as rotations or scaling.
You can refer to the tutorials for additional information regarding equivariance and Deepchem's support for equivariance.
deepchem.utils.equivariance_utils.su2_generators
deepchem.utils.equivariance_utils.so3_generators
deepchem.utils.equivariance_utils.change_basis_real_to_complex
deepchem.utils.equivariance_utils.wigner_D
The utilities here are used for miscellaneous purposes. Initial usecases are for improving the printing format of __repr__.
deepchem.utils.misc_utils.indent
deepchem.utils.misc_utils.shape2str
deepchem.utils.misc_utils.UnimplementedError
deepchem.utils.misc_utils.GetSetParamsError
deepchem.utils.misc_utils.ConvergenceWarning
deepchem.utils.misc_utils.MathWarning
deepchem.utils.misc_utils.Uniquifier
The utilities here are used for safe operations on tensors. These are used to avoid NaNs and Infs in the output.
deepchem.utils.safeops_utils.safepow
deepchem.utils.safeops_utils.safenorm
deepchem.utils.safeops_utils.occnumber
deepchem.utils.safeops_utils.get_floor_and_ceil
deepchem.utils.safeops_utils.safe_cdist