API ReferenceΒΆ
The API reference is split into two parts. Start with the Key API for a curated, per-module list of the most commonly used functions. The Full API Reference below documents every module exhaustively.
Full API Reference
- qm_atlas
DEFAULT_SCRget_scratch_dir()are_equal()has_macrocycle()conformer_is_3d()remove_conformers()has_hydrogens()as_float()meta_func()store_atom_indices()get_atom_indices_map()restore_atom_indices()is_zwitterion()intervals_overlap()remove_salt()get_python_activation_command()get_cosmo_solvents_dir_key()SoftwareEnvironmentget_env_from_modules()EnvironmentManagerget_config_file()load_environment_manager()SoftwareConfigget_moka_model()get_cosmo_solvents_dirs()
- Command Line
PipelineSubmissionConfigPipelineConfigload_config()run_pipeline()submit()main()CalculationInputSubmissionConfigBaseInterfaceConfigapply_software_config()setup_logging()validate_results_dir()get_input_worker_paths()get_reference_worker_paths()get_conformer_property_worker_paths()get_cosmo_property_worker_paths()get_solvent_screening_worker_paths()missing_reference_optimizations()worker_path_completed()extract_worker_paths()extract_cpd_dirs()
- Tasks
generate_corina_conformers()generate_omega_conformers()generate_moe_conformers()generate_macromodel_conformers()generate_macrocycle_conformers()generate_rdkit_conformers()ConformerGeneratorOptionsMacromodelOptionsOmegaOptionsMoeOptionsCorinaOptionsRdkitOptionsMacrocycleOptionsget_generator_function()deserialize_conformer_generator_config()join_conformers()generate_conformers_with_fallback()generate_joint_conformer_set()ConformerGenerationOptionsgenerate_conformers()PropertyCalculatorOptionsXtbSinglePointOptionsTurbomoleSinglePointOptionsTurbomoleFreehOptionsTurbomoleFukuiOptionsTurbomoleNmrShieldingOptionsTurbomoleVcdOptionsJaguarHydrogenAbstractionOptionsJaguarQmDescriptorsOptionscreate_calculation_config()calculate_property()calculate_property_conformer()calculate_property_mol()calculate_property_mols()extract_cosmo_output()get_xtb_energies_and_weights()OptimizationOptionsXtbOptionsJobexOptionsXtbTurbomoleOptionsoptimize_with_fallback()optimize_conformer()optimize_mol()optimize_mols()update_mol()adapt_positions()check_displacement()CosmoConfigCosmoLogPConfigCosmoDeltaGConfigCosmoDescriptorsConfigCosmoPsaConfigCosmoPermConfigcalculate_cosmo_psa()calculate_logp()calculate_delta_g()calculate_descriptors()calculate_perm()run_cosmo_calculation()generate_tautomers()generate_tautomer_conformers()select_stable_tautomers()ProtomerEntryProtonationPkaTransitionProtonationResultProtonationOptionsMokaBlabberConfigMokaIonicSpeciesConfigMokaSingleChargeConfigdeserialize_protonation_config()run_protonation()energy_to_j_per_mol()compute_boltzmann_weights()compute_relative_energies()plain_average()weighted_average()PropertyScalarPropertyTensorPropertyAtomBasedPropertyBondBasedPropertyStringPropertyBoolProperty
- Workflows
- Wrappers