e3fp package

Subpackages

• e3fp.config package
  • Submodules
    • e3fp.config.params module
      • get_default_value()
      • get_value()
      • params_to_sections_dict()
      • read_params()
      • update_params()
      • write_params()
  • Module contents
• e3fp.conformer package
  • Submodules
    • e3fp.conformer.generate module
      • generate_conformers()
      • main()
      • run()
      • values_to_hdf5()
    • e3fp.conformer.generator module
      • ConformerGenerator
        • ConformerGenerator.embed_molecule()
        • ConformerGenerator.filter_conformers()
        • ConformerGenerator.generate_conformers()
        • ConformerGenerator.get_conformer_energies()
        • ConformerGenerator.get_molecule_force_field()
        • ConformerGenerator.get_num_conformers()
        • ConformerGenerator.minimize_conformers()
        • ConformerGenerator.reverse_enumerate()
    • e3fp.conformer.protonation module
      • smiles_dict_to_proto_smiles_dict()
      • smiles_list_to_proto_smiles_list()
      • smiles_to_proto_smiles()
    • e3fp.conformer.util module
      • MolItemName
        • MolItemName.conf_name
        • MolItemName.copy()
        • MolItemName.from_str()
        • MolItemName.from_tuple()
        • MolItemName.mol_item_name
        • MolItemName.mol_item_name_to_dict()
        • MolItemName.mol_name
        • MolItemName.proto_name
        • MolItemName.to_conf_name()
        • MolItemName.to_mol_name()
        • MolItemName.to_proto_name()
        • MolItemName.to_str()
        • MolItemName.to_tuple()
      • MolItemTuple
        • MolItemTuple.conf_num
        • MolItemTuple.mol_name
        • MolItemTuple.proto_state_num
      • add_conformer_energies_to_mol()
      • dict_to_smiles()
      • get_conformer_energies_from_mol()
      • iter_to_smiles()
      • mol2_generator()
      • mol_from_mol2()
      • mol_from_sdf()
      • mol_from_smiles()
      • mol_to_sdf()
      • mol_to_standardised_mol()
      • smiles_generator()
      • smiles_to_dict()
  • Module contents
• e3fp.fingerprint package
  • Subpackages
    • e3fp.fingerprint.metrics package
      • Submodules
        • e3fp.fingerprint.metrics.array_metrics module
          • cosine()
          • dice()
          • pearson()
          • soergel()
          • tanimoto()
        • e3fp.fingerprint.metrics.fprint_metrics module
          • cosine()
          • dice()
          • distance()
          • hamming()
          • pearson()
          • soergel()
          • tanimoto()
      • Module contents
        • cosine()
        • dice()
        • pearson()
        • soergel()
        • tanimoto()
  • Submodules
    • e3fp.fingerprint.array_ops module
      • as_unit()
      • calculate_angles()
      • make_distance_matrix()
      • make_rotation_matrix()
      • make_transform_matrix()
      • pad_array()
      • project_to_plane()
      • quaternion_to_transform_matrix()
      • rotate_angles()
      • transform_array()
      • transform_matrix_to_quaternion()
      • unpad_array()
    • e3fp.fingerprint.db module
      • FingerprintDatabase
        • FingerprintDatabase.add_fingerprints()
        • FingerprintDatabase.as_type()
        • FingerprintDatabase.bits
        • FingerprintDatabase.fold()
        • FingerprintDatabase.fp_num
        • FingerprintDatabase.from_array()
        • FingerprintDatabase.get_density()
        • FingerprintDatabase.get_prop()
        • FingerprintDatabase.get_subset()
        • FingerprintDatabase.load()
        • FingerprintDatabase.save()
        • FingerprintDatabase.savetxt()
        • FingerprintDatabase.savez()
        • FingerprintDatabase.set_prop()
        • FingerprintDatabase.update_names_map()
        • FingerprintDatabase.update_props()
      • concat()
    • e3fp.fingerprint.fprint module
      • CountFingerprint
        • CountFingerprint.counts
        • CountFingerprint.fold()
        • CountFingerprint.from_counts()
        • CountFingerprint.from_fingerprint()
        • CountFingerprint.from_indices()
        • CountFingerprint.get_count()
        • CountFingerprint.mean()
        • CountFingerprint.reset()
        • CountFingerprint.std()
        • CountFingerprint.vector_dtype
      • Fingerprint
        • Fingerprint.bit_count
        • Fingerprint.bits
        • Fingerprint.clear()
        • Fingerprint.counts
        • Fingerprint.density
        • Fingerprint.fold()
        • Fingerprint.from_bitstring()
        • Fingerprint.from_fingerprint()
        • Fingerprint.from_indices()
        • Fingerprint.from_rdkit()
        • Fingerprint.from_vector()
        • Fingerprint.get_count()
        • Fingerprint.get_folding_index_map()
        • Fingerprint.get_prop()
        • Fingerprint.get_unfolding_index_map()
        • Fingerprint.index_id_map
        • Fingerprint.indices
        • Fingerprint.level
        • Fingerprint.mean()
        • Fingerprint.mol
        • Fingerprint.name
        • Fingerprint.props
        • Fingerprint.reset()
        • Fingerprint.set_prop()
        • Fingerprint.std()
        • Fingerprint.to_bitstring()
        • Fingerprint.to_bitvector()
        • Fingerprint.to_rdkit()
        • Fingerprint.to_vector()
        • Fingerprint.unfold()
        • Fingerprint.update_props()
        • Fingerprint.vector_dtype
      • FloatFingerprint
        • FloatFingerprint.counts
        • FloatFingerprint.vector_dtype
      • add()
      • coerce_to_valid_dtype()
      • diff_counts_dict()
      • dtype_from_fptype()
      • fptype_from_dtype()
      • load()
      • loadz()
      • mean()
      • save()
      • savez()
      • sum_counts_dict()
    • e3fp.fingerprint.fprinter module
      • Fingerprinter
        • Fingerprinter.current_level
        • Fingerprinter.get_fingerprint_at_level()
        • Fingerprinter.get_shells_at_level()
        • Fingerprinter.initialize_conformer()
        • Fingerprinter.initialize_identifiers()
        • Fingerprinter.initialize_mol()
        • Fingerprinter.next()
        • Fingerprinter.reset()
        • Fingerprinter.reset_conf()
        • Fingerprinter.reset_mol()
        • Fingerprinter.run()
        • Fingerprinter.substructs_to_pdb()
      • ShellsGenerator
        • ShellsGenerator.back()
        • ShellsGenerator.get_match_atoms()
        • ShellsGenerator.get_shells_at_level()
        • ShellsGenerator.next()
      • atom_tuples_from_shell()
      • bound_atoms_from_mol()
      • coords_from_atoms()
      • get_first_unique_tuple_inds()
      • hash_int64_array()
      • identifier_from_shell()
      • identifiers_from_invariants()
      • invariants_from_atom()
      • pick_y()
      • pick_z()
      • quad_indicators_from_coords()
      • rdkit_invariants_from_atom()
      • signed_to_unsigned_int()
      • stereo_indicators_from_shell()
    • e3fp.fingerprint.generate module
      • fprints_dict_from_mol()
      • fprints_dict_from_sdf()
      • main()
      • run()
    • e3fp.fingerprint.structs module
      • FormatError
      • Shell
        • Shell.atoms
        • Shell.center_atom
        • Shell.from_substruct()
        • Shell.shells
        • Shell.substruct
      • Substruct
        • Substruct.atoms
        • Substruct.center_atom
        • Substruct.from_shell()
      • shell_to_pdb()
    • e3fp.fingerprint.util module
      • E3FPBitsValueError
      • E3FPCountsError
      • E3FPInvalidFingerprintError
      • E3FPMolError
      • E3FPOptionError
  • Module contents

Submodules

• e3fp.pipeline module
  • confs_from_smiles()
  • fprints_from_fprints_dict()
  • fprints_from_mol()
  • fprints_from_sdf()
  • fprints_from_smiles()
  • params_to_dicts()
  • sdf_from_smiles()
• e3fp.util module
  • E3FPDeprecationWarning
  • E3FPEfficiencyWarning
  • E3FPError
  • E3FPWarning
  • deprecated
    • deprecated.deprecate_function()
    • deprecated.update_docstring()
  • maybe_jit()

Module contents