Utilities ========= 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. Data Utilities -------------- Array Utilities ^^^^^^^^^^^^^^^ .. autofunction:: deepchem.utils.data_utils.pad_array Data Directory ^^^^^^^^^^^^^^^ The DeepChem data directory is where downloaded MoleculeNet datasets are stored. .. autofunction:: deepchem.utils.data_utils.get_data_dir URL Handling ^^^^^^^^^^^^ .. autofunction:: deepchem.utils.data_utils.download_url File Handling ^^^^^^^^^^^^^ .. autofunction:: deepchem.utils.data_utils.untargz_file .. autofunction:: deepchem.utils.data_utils.unzip_file .. autofunction:: deepchem.utils.data_utils.load_data .. autofunction:: deepchem.utils.data_utils.load_sdf_files .. autofunction:: deepchem.utils.data_utils.load_csv_files .. autofunction:: deepchem.utils.data_utils.load_json_files .. autofunction:: deepchem.utils.data_utils.load_pickle_files .. autofunction:: deepchem.utils.data_utils.load_from_disk .. autofunction:: deepchem.utils.data_utils.save_to_disk .. autofunction:: deepchem.utils.data_utils.load_dataset_from_disk .. autofunction:: deepchem.utils.data_utils.save_dataset_to_disk Molecular Utilities ------------------- .. autoclass:: deepchem.utils.conformers.ConformerGenerator :members: .. autoclass:: deepchem.utils.rdkit_utils.MoleculeLoadException :members: .. autofunction:: deepchem.utils.rdkit_utils.get_xyz_from_mol .. autofunction:: deepchem.utils.rdkit_utils.add_hydrogens_to_mol .. autofunction:: deepchem.utils.rdkit_utils.compute_charges .. autofunction:: deepchem.utils.rdkit_utils.load_molecule .. autofunction:: deepchem.utils.rdkit_utils.write_molecule Molecular Fragment Utilities ---------------------------- It's often convenient to manipulate subsets of a molecule. The :code:`MolecularFragment` class aids in such manipulations. .. autoclass:: deepchem.utils.fragment_utils.MolecularFragment :members: .. autoclass:: deepchem.utils.fragment_utils.AtomShim :members: .. autofunction:: deepchem.utils.fragment_utils.strip_hydrogens .. autofunction:: deepchem.utils.fragment_utils.merge_molecular_fragments .. autofunction:: deepchem.utils.fragment_utils.get_contact_atom_indices .. autofunction:: deepchem.utils.fragment_utils.reduce_molecular_complex_to_contacts Coordinate Box Utilities ------------------------ .. autoclass:: deepchem.utils.coordinate_box_utils.CoordinateBox :members: .. autofunction:: deepchem.utils.coordinate_box_utils.intersect_interval .. autofunction:: deepchem.utils.coordinate_box_utils.union .. autofunction:: deepchem.utils.coordinate_box_utils.merge_overlapping_boxes .. autofunction:: deepchem.utils.coordinate_box_utils.get_face_boxes Evaluation Utils ---------------- .. autoclass:: deepchem.utils.evaluate.Evaluator :members: .. autoclass:: deepchem.utils.evaluate.GeneratorEvaluator :members: .. autofunction:: deepchem.utils.evaluate.relative_difference Genomic Utilities ----------------- .. autofunction:: deepchem.utils.genomics_utils.seq_one_hot_encode .. autofunction:: deepchem.utils.genomics_utils.encode_bio_sequence .. autofunction:: deepchem.utils.sequence_utils.hhblits .. autofunction:: deepchem.utils.sequence_utils.hhsearch .. autofunction:: deepchem.utils.sequence_utils.MSA_to_dataset Geometry Utilities ------------------ .. autofunction:: deepchem.utils.geometry_utils.unit_vector .. autofunction:: deepchem.utils.geometry_utils.angle_between .. autofunction:: deepchem.utils.geometry_utils.generate_random_unit_vector .. autofunction:: deepchem.utils.geometry_utils.generate_random_rotation_matrix .. autofunction:: deepchem.utils.geometry_utils.is_angle_within_cutoff Graph Utilities --------------- .. autofunction:: deepchem.utils.graph_utils.fourier_encode_dist .. autofunction:: deepchem.utils.graph_utils.aggregate_mean .. autofunction:: deepchem.utils.graph_utils.aggregate_max .. autofunction:: deepchem.utils.graph_utils.aggregate_min .. autofunction:: deepchem.utils.graph_utils.aggregate_std .. autofunction:: deepchem.utils.graph_utils.aggregate_var .. autofunction:: deepchem.utils.graph_utils.aggregate_moment .. autofunction:: deepchem.utils.graph_utils.aggregate_sum .. autofunction:: deepchem.utils.graph_utils.scale_identity .. autofunction:: deepchem.utils.graph_utils.scale_amplification .. autofunction:: deepchem.utils.graph_utils.scale_attenuation Hash Function Utilities ----------------------- .. autofunction:: deepchem.utils.hash_utils.hash_ecfp .. autofunction:: deepchem.utils.hash_utils.hash_ecfp_pair .. autofunction:: deepchem.utils.hash_utils.vectorize Voxel Utils ----------- .. autofunction:: deepchem.utils.voxel_utils.convert_atom_to_voxel .. autofunction:: deepchem.utils.voxel_utils.convert_atom_pair_to_voxel .. autofunction:: deepchem.utils.voxel_utils.voxelize Graph Convolution Utilities --------------------------- .. autofunction:: deepchem.utils.molecule_feature_utils.one_hot_encode .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_type_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.construct_hydrogen_bonding_info .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_hydrogen_bonding_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_is_in_aromatic_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_hybridization_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_total_num_Hs_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_chirality_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_formal_charge .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_partial_charge .. autofunction:: deepchem.utils.molecule_feature_utils.get_atom_total_degree_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_bond_type_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_bond_is_in_same_ring_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_bond_is_conjugated_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_bond_stereo_one_hot .. autofunction:: deepchem.utils.molecule_feature_utils.get_bond_graph_distance_one_hot Grover Utilities ---------------- .. autofunction:: deepchem.utils.grover.extract_grover_attributes Debug Utilities --------------- Docking Utilities ----------------- These utilities assist in file preparation and processing for molecular docking. .. autofunction:: deepchem.utils.docking_utils.write_vina_conf .. autofunction:: deepchem.utils.docking_utils.write_gnina_conf .. autofunction:: deepchem.utils.docking_utils.load_docked_ligands .. autofunction:: deepchem.utils.docking_utils.prepare_inputs .. autofunction:: deepchem.utils.docking_utils.read_gnina_log Print Threshold ^^^^^^^^^^^^^^^ The printing threshold controls how many dataset elements are printed when :code:`dc.data.Dataset` objects are converted to strings or represnted in the IPython repl. .. autofunction:: deepchem.utils.debug_utils.get_print_threshold .. autofunction:: deepchem.utils.debug_utils.set_print_threshold .. autofunction:: deepchem.utils.debug_utils.get_max_print_size .. autofunction:: deepchem.utils.debug_utils.set_max_print_size Fake Data Generator ------------------- The utilities here are used to generate random sample data which can be used for testing model architectures or other purposes. .. autoclass:: deepchem.utils.fake_data_generator.FakeGraphGenerator :members: Electron Sampler ------------------- 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. .. autoclass:: deepchem.utils.electron_sampler.ElectronSampler :members: Density Functional Theory Utilities ----------------------------------- The utilites here are used to create an object that contains information about a system's self-consistent iteration steps and other processes. .. autoclass:: deepchem.utils.dft_utils.Lattice :members: .. autoclass:: deepchem.utils.dft_utils.SpinParam :members: .. autoclass:: deepchem.utils.dft_utils.ValGrad :members: .. autoclass:: deepchem.utils.dft_utils.data.datastruct.CGTOBasis :members: .. autoclass:: deepchem.utils.dft_utils.data.datastruct.AtomCGTOBasis :members: .. autoclass:: deepchem.utils.dft_utils.BaseXC :members: .. autoclass:: deepchem.utils.dft_utils.AddBaseXC :members: .. autoclass:: deepchem.utils.dft_utils.xc.base_xc.MulBaseXC :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc_wrapper.CalcLDALibXCPol :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc_wrapper.CalcLDALibXCUnpol :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc_wrapper.CalcGGALibXCUnpol :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc_wrapper.CalcGGALibXCPol :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc_wrapper.CalcMGGALibXCUnpol :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc_wrapper.CalcMGGALibXCPol :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc.LibXCLDA :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc.LibXCGGA :members: .. autoclass:: deepchem.utils.dft_utils.xc.libxc.LibXCMGGA :members: .. autofunction:: deepchem.utils.dft_utils.api.getxc.get_libxc .. autofunction:: deepchem.utils.dft_utils.api.getxc.get_xc .. autofunction:: deepchem.utils.dft_utils.api.loadbasis.loadbasis .. autofunction:: deepchem.utils.dft_utils.api.loadbasis._read_float .. autofunction:: deepchem.utils.dft_utils.api.loadbasis._get_basis_file .. autofunction:: deepchem.utils.dft_utils.api.loadbasis._normalize_basisname .. autofunction:: deepchem.utils.dft_utils.api.loadbasis._download_basis .. autofunction:: deepchem.utils.dft_utils.api.loadbasis._expand_angmoms .. autoclass:: deepchem.utils.dft_utils.BaseGrid :members: .. autoclass:: deepchem.utils.dft_utils.df.base_df.BaseDF :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.base_hamilton.BaseHamilton :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.lcintwrap.LibcintWrapper :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.lcintwrap.SubsetLibcintWrapper :members: .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.int1e .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.int2c2e .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.int3c2e .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.int2e .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.overlap .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.kinetic .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.nuclattr .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.elrep .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.coul2c .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor.coul3c .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor._check_and_set .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor._get_intgl_optimizer .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor._get_integrals .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor._transpose .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor._swap_list .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor._gather_at_dims .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.molintor._get_uniqueness .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.molintor._Int2cFunction :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.molintor._Int3cFunction :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.molintor._Int4cFunction :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.molintor._cintoptHandler :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.molintor.Intor :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.symmetry.BaseSymmetry :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.symmetry.S1Symmetry :members: .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.symmetry.S4Symmetry :members: .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.utils.np2ctypes .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.utils.int2ctypes .. autoclass:: deepchem.utils.dftutils.KSCalc :members: .. autofunction:: deepchem.utils.dftutils.hashstr .. autoclass:: deepchem.utils.dftutils.BaseGrid :members: .. autoclass:: deepchem.utils.dftutils.BaseQCCalc :members: .. autoclass:: deepchem.utils.dftutils.SpinParam :members: .. autoclass:: deepchem.utils.dft_utils.config._Config :members: .. autoclass:: deepchem.utils.dft_utils.BaseOrbParams :members: .. autoclass:: deepchem.utils.dft_utils.QROrbParams :members: .. autoclass:: deepchem.utils.dft_utils.MatExpOrbParams :members: .. autoclass:: deepchem.utils.dft_utils.api.parser.parse_moldesc :members: .. autoclass:: deepchem.utils.dft_utils.system.base_system.BaseSystem :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.RadialGrid :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.get_xw_integration :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.SlicedRadialGrid :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.BaseGridTransform :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.DE2Transformation :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.LogM3Transformation :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.TreutlerM4Transformation :members: .. autoclass:: deepchem.utils.dft_utils.grid.radial_grid.get_grid_transform :members: .. autoclass:: deepchem.utils.dft_utils.qccalc.hf.HF :members: .. autoclass:: deepchem.utils.dft_utils.qccalc.hf.HFEngine :members: .. autoclass:: deepchem.utils.dft_utils.qccalc.base_qccalc.BaseQCCalc :members: .. autoclass:: deepchem.utils.dft_utils.qccalc.scf_qccalc.SCF_QCCalc :members: .. autoclass:: deepchem.utils.dft_utils.qccalc.scf_qccalc.BaseSCFEngine :members: .. autoclass:: deepchem.utils.dft_utils.qccalc.ks.KS :members: .. autoclass:: deepchem.utils.dft_utils.qccalc.ks.KSEngine :members: .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.gtoft.evl_ft .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.gtoft.eval_gto_ft .. autoclass:: deepchem.utils.dft_utils.hamilton.intor.gtoft._EvalGTO_FT :members: .. autofunction:: deepchem.utils.dft_utils.hamilton.intor.gtoft.gto_ft_evaluator .. autoclass:: deepchem.utils.differentiation_utils.editable_module.EditableModule :members: .. autofunction:: deepchem.utils.differentiation_utils.normalize_bcast_dims .. autofunction:: deepchem.utils.differentiation_utils.get_bcasted_dims .. autofunction:: deepchem.utils.differentiation_utils.match_dim .. autoclass:: deepchem.utils.differentiation_utils.linop.LinearOperator :members: .. autoclass:: deepchem.utils.differentiation_utils.linop.AddLinearOperator :members: .. autoclass:: deepchem.utils.differentiation_utils.linop.MulLinearOperator :members: .. autoclass:: deepchem.utils.differentiation_utils.linop.AdjointLinearOperator :members: .. autoclass:: deepchem.utils.differentiation_utils.linop.MatmulLinearOperator :members: .. autoclass:: deepchem.utils.differentiation_utils.linop.MatrixLinearOperator :members: .. autoclass:: deepchem.utils.differentiation_utils.pure_function.PureFunction :members: .. autoclass:: deepchem.utils.differentiation_utils.pure_function.FunctionPureFunction :members: .. autoclass:: deepchem.utils.differentiation_utils.pure_function.EditableModulePureFunction :members: .. autoclass:: deepchem.utils.differentiation_utils.pure_function.TorchNNPureFunction :members: .. autoclass:: deepchem.utils.differentiation_utils.pure_function.PureFunction :members: .. autofunction:: deepchem.utils.differentiation_utils.pure_function._check_identical_objs .. autofunction:: deepchem.utils.differentiation_utils.pure_function.get_pure_function .. autofunction:: deepchem.utils.differentiation_utils.set_default_option .. autofunction:: deepchem.utils.differentiation_utils.get_and_pop_keys .. autofunction:: deepchem.utils.differentiation_utils.get_method .. autofunction:: deepchem.utils.differentiation_utils.dummy_context_manager .. autofunction:: deepchem.utils.differentiation_utils.assert_runtime .. autofunction:: deepchem.utils.differentiation_utils.symeig._set_initial_v .. autofunction:: deepchem.utils.differentiation_utils.symeig._take_eigpairs .. autofunction:: deepchem.utils.differentiation_utils.symeig.exacteig .. autofunction:: deepchem.utils.differentiation_utils.symeig.degen_symeig .. autofunction:: deepchem.utils.differentiation_utils.symeig.davidson .. autofunction:: deepchem.utils.differentiation_utils.symeig.lsymeig .. autofunction:: deepchem.utils.differentiation_utils.symeig.usymeig .. autofunction:: deepchem.utils.differentiation_utils.symeig.symeig .. autoclass:: deepchem.utils.differentiation_utils.symeig.symeig_torchfcn :members: .. autofunction:: deepchem.utils.differentiation_utils.symeig._check_degen .. autofunction:: deepchem.utils.differentiation_utils.symeig.ortho .. autofunction:: deepchem.utils.differentiation_utils.grad.jac .. autoclass:: deepchem.utils.differentiation_utils.grad._Jac :members: .. autofunction:: deepchem.utils.differentiation_utils.grad._setup_idxs .. autofunction:: deepchem.utils.differentiation_utils.grad.connect_graph .. autofunction:: deepchem.utils.differentiation_utils.solve.wrap_gmres .. autofunction:: deepchem.utils.differentiation_utils.solve.exactsolve .. autofunction:: deepchem.utils.differentiation_utils.solve.solve_ABE .. autofunction:: deepchem.utils.differentiation_utils.solve.get_batchdims .. autofunction:: deepchem.utils.differentiation_utils.solve.setup_precond .. autofunction:: deepchem.utils.differentiation_utils.solve.dot .. autofunction:: deepchem.utils.differentiation_utils.solve.gmres .. autofunction:: deepchem.utils.differentiation_utils.solve.setup_linear_problem .. autofunction:: deepchem.utils.differentiation_utils.solve.safedenom .. autofunction:: deepchem.utils.differentiation_utils.solve.get_largest_eival .. autofunction:: deepchem.utils.differentiation_utils.solve.solve .. autofunction:: deepchem.utils.differentiation_utils.solve.broyden1_solve .. autofunction:: deepchem.utils.differentiation_utils.solve._rootfinder_solve .. autofunction:: deepchem.utils.differentiation_utils.solve.cg .. autofunction:: deepchem.utils.differentiation_utils.solve.bicgstab .. autoclass:: deepchem.utils.differentiation_utils.solve.solve_torchfcn :members: .. autofunction:: deepchem.utils.differentiation_utils.optimize.equilibrium.anderson_acc .. autofunction:: deepchem.utils.differentiation_utils.optimize.minimizer.gd .. autofunction:: deepchem.utils.differentiation_utils.optimize.minimizer.adam .. autofunction:: deepchem.utils.differentiation_utils.optimize.minimizer.TerminationCondition .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver._nonlin_solver .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver.broyden1 .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver.broyden2 .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver.linearmixing .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver._safe_norm .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver._nonline_line_search .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver._scalar_search_armijo .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootsolver.TerminationCondition .. autoclass:: deepchem.utils.differentiation_utils.optimize.jacobian.Jacobian :members: .. autoclass:: deepchem.utils.differentiation_utils.optimize.jacobian.BroydenFirst :members: .. autoclass:: deepchem.utils.differentiation_utils.optimize.jacobian.BroydenSecond :members: .. autoclass:: deepchem.utils.differentiation_utils.optimize.jacobian.LinearMixing :members: .. autoclass:: deepchem.utils.differentiation_utils.optimize.jacobian.LowRankMatrix :members: .. autoclass:: deepchem.utils.differentiation_utils.optimize.jacobian.FullRankMatrix :members: .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootfinder.rootfinder .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootfinder.equilibrium .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootfinder.minimize .. autoclass:: deepchem.utils.differentiation_utils.optimize.rootfinder._RootFinder :members: .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootfinder._get_rootfinder_default_method .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootfinder._get_equilibrium_default_method .. autofunction:: deepchem.utils.differentiation_utils.optimize.rootfinder._get_minimizer_default_method .. autoclass:: deepchem.utils.differentiation_utils.integrate.explicit_rk._Tableau :members: .. autofunction:: deepchem.utils.differentiation_utils.integrate.explicit_rk.explicit_rk .. autofunction:: deepchem.utils.differentiation_utils.integrate.explicit_rk.rk38_ivp .. autofunction:: deepchem.utils.differentiation_utils.integrate.explicit_rk.fwd_euler_ivp .. autofunction:: deepchem.utils.differentiation_utils.integrate.explicit_rk.rk4_ivp .. autofunction:: deepchem.utils.differentiation_utils.integrate.explicit_rk.mid_point_ivp Attribute Utilities ------------------- The utilities here are used to modify the attributes of the classes. Used by differentiation_utils. .. autoclass:: deepchem.utils.attribute_utils.get_attr :members: .. autoclass:: deepchem.utils.attribute_utils.set_attr :members: .. autoclass:: deepchem.utils.attribute_utils.del_attr :members: Polymer Weighted Directed Graph Data Utilities ----------------------------------------- These classes and functions are required to handle converstion of string data to graph data and validation of the same. .. autofunction:: deepchem.utils.poly_wd_graph_utils.handle_hydrogen .. autofunction:: deepchem.utils.poly_wd_graph_utils.make_polymer_mol .. autofunction:: deepchem.utils.poly_wd_graph_utils.parse_polymer_rules .. autofunction:: deepchem.utils.poly_wd_graph_utils.tag_atoms_in_repeating_unit .. autofunction:: deepchem.utils.poly_wd_graph_utils.onek_encoding_unk .. autofunction:: deepchem.utils.poly_wd_graph_utils.remove_wildcard_atoms Polymer Weighted Directed Graph String Validator ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This class validates the input string representation for graphical conversion of polymer data. It splits the input strings, validates their order and values. Upon recieving error it can return meaningful error message to the user indicating the type of error that hinders the conversion process. The format is an extended string representation that is used as input format for Weighted Directed Message Passing Neural Network (wDMPNN) implementation using :code:`polymer-chemprop` python module. For more information and understanding, visit the `github repo `. The format development and implementation is done by Matteo Aldeghi and Connor W. Coley for their work on "A graph representation of molecular ensembles for polymer property prediction". The :code:`dc.utils.PolyWDGStringValidator` class is explicitly useful for validating a Weighted Directed Graph Representaion within a string data for polymers. It validates atom notations in monomer, valid Fragment weights for monomers, and valid polymer rules within the string representation. References: - `Aldeghi M, Coley CW. A graph representation of molecular ensembles for polymer property prediction. Chemical Science. 2022;13(35):10486-98.`_ .. autoclass:: deepchem.utils.poly_wd_graph_utils.PolyWDGStringValidator :members: Polymer Conversion Utilities ---------------------------- These classes and functions are required to handle converstion of PSMILES string data format to WDG string data format and vice versa. .. autoclass:: deepchem.utils.poly_converters.PSMILES2WDGConverter :members: .. autoclass:: deepchem.utils.poly_converters.WDG2PSMILESConverter :members: Pytorch Utilities ----------------- .. autofunction:: deepchem.utils.pytorch_utils.unsorted_segment_sum .. autofunction:: deepchem.utils.pytorch_utils.segment_sum .. autofunction:: deepchem.utils.pytorch_utils.chunkify .. autofunction:: deepchem.utils.pytorch_utils.get_memory .. autofunction:: deepchem.utils.pytorch_utils.gaussian_integral .. autofunction:: deepchem.utils.pytorch_utils.TensorNonTensorSeparator .. autofunction:: deepchem.utils.pytorch_utils.tallqr .. autofunction:: deepchem.utils.pytorch_utils.to_fortran_order .. autofunction:: deepchem.utils.pytorch_utils.get_np_dtype .. autofunction:: deepchem.utils.pytorch_utils.unsorted_segment_max .. autofunction:: deepchem.utils.pytorch_utils.unweighted_coul_ft .. autofunction:: deepchem.utils.pytorch_utils.get_complex_dtype Batch Utilities --------------- The utilites here are used for computing features on batch of data. Can be used inside of default_generator function. .. autofunction:: deepchem.utils.batch_utils.batch_coulomb_matrix_features .. autofunction:: deepchem.utils.batch_utils.batch_elements .. autofunction:: deepchem.utils.batch_utils.create_input_array .. autofunction:: deepchem.utils.batch_utils.create_output_array Periodic Table Utilities ------------------------ The Utilities here are used to computing atomic mass and radii data. These can be used by DFT and many other Molecular Models. .. autofunction:: deepchem.utils.periodic_table_utils.get_atomz Equivariance Utilities ---------------------- 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. .. autofunction:: deepchem.utils.equivariance_utils.su2_generators .. autofunction:: deepchem.utils.equivariance_utils.so3_generators .. autofunction:: deepchem.utils.equivariance_utils.change_basis_real_to_complex .. autofunction:: deepchem.utils.equivariance_utils.wigner_D .. autofunction:: deepchem.utils.equivariance_utils.semifactorial .. autofunction:: deepchem.utils.equivariance_utils.pochhammer .. autofunction:: deepchem.utils.equivariance_utils.lpmv .. autofunction:: deepchem.utils.equivariance_utils.SphericalHarmonics .. autofunction:: deepchem.utils.equivariance_utils.get_matrix_kernel .. autofunction:: deepchem.utils.equivariance_utils.basis_transformation_Q_J .. autofunction:: deepchem.utils.equivariance_utils.get_spherical_from_cartesian .. autofunction:: deepchem.utils.equivariance_utils.kron .. autofunction:: deepchem.utils.equivariance_utils.precompute_sh .. autofunction:: deepchem.utils.equivariance_utils.get_basis .. autofunction:: deepchem.utils.equivariance_utils.get_r .. autofunction:: deepchem.utils.equivariance_utils.get_equivariant_basis_and_r .. autofunction:: deepchem.utils.equivariance_utils.fiber2head .. autoclass:: deepchem.utils.equivariance_utils.LieGroup :members: .. autoclass:: deepchem.utils.equivariance_utils.T :members: .. autofunction:: deepchem.utils.equivariance_utils.sinc .. autofunction:: deepchem.utils.equivariance_utils.sincc .. autofunction:: deepchem.utils.equivariance_utils.cosc .. autofunction:: deepchem.utils.equivariance_utils.coscc .. autofunction:: deepchem.utils.equivariance_utils.sinc_inv .. autofunction:: deepchem.utils.equivariance_utils.cross_matrix .. autofunction:: deepchem.utils.equivariance_utils.uncross_matrix .. autoclass:: deepchem.utils.equivariance_utils.SO3 :members: .. autoclass:: deepchem.utils.equivariance_utils.SE3 :members: Miscellaneous Utilities ----------------------- The utilities here are used for miscellaneous purposes. Initial usecases are for improving the printing format of __repr__. .. autofunction:: deepchem.utils.misc_utils.indent .. autofunction:: deepchem.utils.misc_utils.shape2str .. autofunction:: deepchem.utils.misc_utils.memoize_method .. autoclass:: deepchem.utils.misc_utils.UnimplementedError :members: .. autoclass:: deepchem.utils.misc_utils.GetSetParamsError :members: .. autoclass:: deepchem.utils.misc_utils.ConvergenceWarning :members: .. autoclass:: deepchem.utils.misc_utils.MathWarning :members: .. autoclass:: deepchem.utils.misc_utils.Uniquifier :members: SafeOperations Utilities ------------------------ The utilities here are used for safe operations on tensors. These are used to avoid NaNs and Infs in the output. .. autofunction:: deepchem.utils.safeops_utils.safepow .. autofunction:: deepchem.utils.safeops_utils.safenorm .. autofunction:: deepchem.utils.safeops_utils.occnumber .. autofunction:: deepchem.utils.safeops_utils.get_floor_and_ceil .. autofunction:: deepchem.utils.safeops_utils.safe_cdist Lightning Utilities ------------------ The utilities here are used for lightning specific operations and act as componenets for lightning modules. .. autofunction:: deepchem.utils.lightning_utils.collate_dataset_fn Caching Utils ------------- Caching utilities to reuse computation results across active sessions. These prevent redundant recalculations by saving function outputs to disk or memory, improving performance for expensive and data-heavy operations (e.g., equivariant basis). .. autofunction:: deepchem.utils.cache_utils.FileSystemMutex .. autofunction:: deepchem.utils.cache_utils.cached_dirpklgz