Index

A

abundance (qm_atlas.tasks.protonation.ProtomerEntry attribute) abundance_threshold (qm_atlas.tasks.protonation.MokaBlabberConfig attribute) ACIDIC (qm_atlas.wrappers.moka.moka.PkaTypes attribute) action_lines (qm_atlas.wrappers.cosmotherm.cosmo_utils.CosmoSettings attribute) adapt_positions() (in module qm_atlas.tasks.optimize) add_compound() (qm_atlas.wrappers.moka.process.PkaCalculationInfo method) add_pka_center() (qm_atlas.wrappers.moka.process.PkaCalculationInfo method) add_solvents() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method) ALLOWED_GLOBAL_SETTINGS_KEYS (qm_atlas.software_environment.EnvironmentManager attribute) ALLOWED_SUBMISSION_KEYS (qm_atlas.software_environment.EnvironmentManager attribute)

angles_fixed (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) apply_software_config() (in module qm_atlas.command_line.base_config) are_equal() (in module qm_atlas.utils) as_float() (in module qm_atlas.utils) atom_idcs (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) atom_index (qm_atlas.tasks.protonation.ProtonationPkaTransition attribute) (qm_atlas.wrappers.moka.moka.PredictedPKA attribute) AtomBasedProperty (class in qm_atlas.tasks.common) available (qm_atlas.software_environment.SoftwareEnvironment attribute) average_sigma_density_and_charges() (in module qm_atlas.wrappers.cosmotherm.cpsa)

B

backend (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute) (qm_atlas.tasks.conformer_generation.CorinaOptions attribute) (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) (qm_atlas.tasks.conformer_generation.MoeOptions attribute) (qm_atlas.tasks.conformer_generation.OmegaOptions attribute) (qm_atlas.tasks.conformer_generation.RdkitOptions attribute) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoPermConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) (qm_atlas.tasks.protonation.MokaBlabberConfig attribute) (qm_atlas.tasks.protonation.MokaIonicSpeciesConfig attribute) (qm_atlas.tasks.protonation.MokaSingleChargeConfig attribute)

BaseInterfaceConfig (class in qm_atlas.command_line.base_config) BASIC (qm_atlas.wrappers.moka.moka.PkaTypes attribute) basis (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) BondBasedProperty (class in qm_atlas.tasks.common) bonds_fixed (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) BoolProperty (class in qm_atlas.tasks.common)

C

calculate_cosmo_psa() (in module qm_atlas.tasks.cosmo_properties) calculate_cosmoperm() (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) calculate_cosmotherm() (in module qm_atlas.wrappers.cosmotherm.interface) calculate_delta_g() (in module qm_atlas.tasks.cosmo_properties) (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) calculate_descriptors() (in module qm_atlas.tasks.cosmo_properties) (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) (in module qm_atlas.wrappers.jaguar.qm_descriptors) calculate_descriptors_df() (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) calculate_freeh() (in module qm_atlas.wrappers.turbomole.freeh) calculate_fukui (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute) calculate_fukui() (in module qm_atlas.wrappers.turbomole.fukui) calculate_logp() (in module qm_atlas.tasks.cosmo_properties) (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) calculate_mass_fractions() (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) calculate_nmr_shieldings() (in module qm_atlas.wrappers.turbomole.nmr_shielding) calculate_perm() (in module qm_atlas.tasks.cosmo_properties) calculate_pka() (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) calculate_property() (in module qm_atlas.tasks.calculate_properties) calculate_property_conformer() (in module qm_atlas.tasks.calculate_properties) calculate_property_mol() (in module qm_atlas.tasks.calculate_properties) calculate_property_mols() (in module qm_atlas.tasks.calculate_properties) calculate_single_point() (in module qm_atlas.wrappers.xtb) calculate_solubility() (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) calculate_solubility_mixture() (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) calculate_vcd() (in module qm_atlas.wrappers.turbomole.vcd) CalculationInput (class in qm_atlas.command_line.base_config) center_type (qm_atlas.wrappers.moka.process.PkaCenter attribute) charge_schemes (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) check_displacement() (in module qm_atlas.tasks.optimize) check_error() (in module qm_atlas.wrappers.openeye) check_fukui() (in module qm_atlas.wrappers.turbomole.fukui) check_input_conformers() (in module qm_atlas.wrappers.cosmotherm.cosmo_utils) check_jobex() (in module qm_atlas.wrappers.turbomole.jobex) check_licenses() (in module qm_atlas.wrappers.helpers) check_ridft() (in module qm_atlas.wrappers.turbomole.single_point) check_solvation() (qm_atlas.tasks.optimize.XtbOptions method) check_tmol_generic() (in module qm_atlas.wrappers.turbomole.utils) check_xtb_run() (in module qm_atlas.wrappers.xtb) check_xtb_tm_optimization() (in module qm_atlas.wrappers.turbomole.xtb_opt) child_name (qm_atlas.wrappers.moka.process.PkaCenter attribute)

child_smiles (qm_atlas.tasks.protonation.ProtonationPkaTransition attribute) COCRYSTAL_SETTINGS (in module qm_atlas.wrappers.cosmotherm.cosmo_cocrystal) combination_name (qm_atlas.tasks.conformer_generation.ConformerGenerationOptions attribute) command_available() (qm_atlas.software_environment.EnvironmentManager method) command_lines (qm_atlas.wrappers.cosmotherm.cosmo_utils.CosmoSettings attribute) commands (qm_atlas.software_environment.SoftwareEnvironment attribute) comment_line (qm_atlas.wrappers.cosmotherm.cosmo_utils.CosmoSettings attribute) compound_directories (qm_atlas.command_line.base_config.CalculationInput attribute) compute_boltzmann_weights() (in module qm_atlas.tasks.boltzmann) compute_relative_energies() (in module qm_atlas.tasks.boltzmann) conf_gens (qm_atlas.tasks.conformer_generation.ConformerGenerationOptions attribute) conformer_is_3d() (in module qm_atlas.utils) ConformerGenerationOptions (class in qm_atlas.tasks.conformer_generation) ConformerGeneratorOptions (class in qm_atlas.tasks.conformer_generation) constrain (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) CONSTRAIN_BLOCK_TEMPLATE (in module qm_atlas.wrappers.xtb) control_template (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) convert_to_mae() (in module qm_atlas.wrappers.jaguar.common) (in module qm_atlas.wrappers.macromodel.utils) cores_per_task (qm_atlas.command_line.base_config.SubmissionConfig attribute) (qm_atlas.command_line.pipeline.PipelineSubmissionConfig attribute) CORINA_DRIVEROPT (in module qm_atlas.wrappers.corina) CorinaOptions (class in qm_atlas.tasks.conformer_generation) cosmo_to_df() (in module qm_atlas.wrappers.cosmotherm.cpsa) CosmoConfig (class in qm_atlas.tasks.cosmo_properties) CosmoDeltaGConfig (class in qm_atlas.tasks.cosmo_properties) CosmoDescriptorsConfig (class in qm_atlas.tasks.cosmo_properties) CosmoLogPConfig (class in qm_atlas.tasks.cosmo_properties) CosmoPaths (class in qm_atlas.wrappers.cosmotherm.interface) CosmoPermConfig (class in qm_atlas.tasks.cosmo_properties) CosmoPsaConfig (class in qm_atlas.tasks.cosmo_properties) CosmoSettings (class in qm_atlas.wrappers.cosmotherm.cosmo_utils) covalent_hydration (qm_atlas.wrappers.moka.moka.MokaPrediction attribute) create_calculation_config() (in module qm_atlas.tasks.calculate_properties) ctd_dir (qm_atlas.wrappers.cosmotherm.interface.CosmoPaths attribute) ctd_file (qm_atlas.wrappers.cosmotherm.interface.CosmoPaths attribute)

D

database_dir (qm_atlas.wrappers.cosmotherm.interface.CosmoPaths attribute) DEFAULT_BASIS (in module qm_atlas.wrappers.jaguar.qm_descriptors) (in module qm_atlas.wrappers.turbomole.jobex) (in module qm_atlas.wrappers.turbomole.single_point) DEFAULT_ENERGY_CONV (in module qm_atlas.wrappers.turbomole.jobex) DEFAULT_FINAL_OPTIMIZATION_CONFIG (in module qm_atlas.workflows.fast_conformers) (in module qm_atlas.workflows.rescoss_conformers) DEFAULT_FORCE_CONSTANT (in module qm_atlas.wrappers.xtb), [1] DEFAULT_FUNCTIONAL (in module qm_atlas.wrappers.jaguar.qm_descriptors) (in module qm_atlas.wrappers.turbomole.jobex) (in module qm_atlas.wrappers.turbomole.single_point) DEFAULT_GEOM_CONV (in module qm_atlas.wrappers.turbomole.jobex) DEFAULT_GRID (in module qm_atlas.wrappers.turbomole.jobex) (in module qm_atlas.wrappers.turbomole.single_point) DEFAULT_NUM_CLUSTERS (in module qm_atlas.workflows.rescoss_conformers) DEFAULT_NUM_PER_CLUSTER (in module qm_atlas.workflows.rescoss_conformers) DEFAULT_OPT_LEVEL (in module qm_atlas.wrappers.turbomole.xtb_opt) DEFAULT_OPTIMIZATION_CONFIG (in module qm_atlas.workflows.fast_conformers) (in module qm_atlas.workflows.optimize_constrained)

DEFAULT_RICORE (in module qm_atlas.wrappers.turbomole.single_point) DEFAULT_SCF_CONV (in module qm_atlas.wrappers.turbomole.jobex) (in module qm_atlas.wrappers.turbomole.single_point) DEFAULT_SCFITERLIMIT (in module qm_atlas.wrappers.turbomole.jobex) (in module qm_atlas.wrappers.turbomole.single_point) DEFAULT_SCR (in module qm_atlas.constants) DEFAULT_SECOND_FORCE_CONSTANT (in module qm_atlas.workflows.optimize_constrained) DEFAULT_SOLVENT (in module qm_atlas.wrappers.turbomole.jobex) (in module qm_atlas.wrappers.turbomole.single_point) DEFAULT_STEPS (in module qm_atlas.wrappers.turbomole.jobex) DEFAULT_XTB_TM_STEPS (in module qm_atlas.wrappers.turbomole.xtb_opt) DESCRIPTORS_SETTINGS (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) deserialize_conf_gens() (qm_atlas.tasks.conformer_generation.ConformerGenerationOptions class method) deserialize_conformer_generator_config() (in module qm_atlas.tasks.conformer_generation) deserialize_protonation_config() (in module qm_atlas.tasks.protonation) DG_SETTINGS (in module qm_atlas.wrappers.cosmotherm.cosmo_tasks) dist_mat() (in module qm_atlas.wrappers.cosmotherm.cpsa)

E

energy_conv (qm_atlas.tasks.optimize.JobexOptions attribute) energy_cutoff (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) energy_to_j_per_mol() (in module qm_atlas.tasks.boltzmann) engine (qm_atlas.command_line.base_config.SubmissionConfig attribute) ensure_local_job_server() (in module qm_atlas.wrappers.helpers) environment_variables (qm_atlas.software_environment.SoftwareEnvironment attribute) EnvironmentManager (class in qm_atlas.software_environment) eq_phases (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) extract_charges_fukui() (in module qm_atlas.wrappers.turbomole.fukui) extract_converged() (in module qm_atlas.wrappers.turbomole.utils)

extract_cosmo_output() (in module qm_atlas.tasks.calculate_properties) extract_cpd_dirs() (in module qm_atlas.command_line.base_config) extract_energies_fukui() (in module qm_atlas.wrappers.turbomole.fukui) extract_energy() (in module qm_atlas.wrappers.turbomole.utils) extract_log_file() (in module qm_atlas.wrappers.jaguar.common) extract_molar_weights() (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) extract_psa() (in module qm_atlas.wrappers.cosmotherm.cpsa) extract_psa_from_cosmo_file() (in module qm_atlas.wrappers.cosmotherm.cpsa) extract_sigma_density_and_charges() (in module qm_atlas.wrappers.cosmotherm.cpsa) extract_worker_paths() (in module qm_atlas.command_line.base_config)

F

fast_conformer_filtering() (in module qm_atlas.workflows.fast_conformers) FAST_DEFAULT_OPTIONS (in module qm_atlas.workflows.fast_conformers) filter_molobj_shapes() (in module qm_atlas.workflows.fast_conformers) find_cosmo_files() (in module qm_atlas.wrappers.cosmotherm.cosmo_utils) find_heavy_atom_torsions() (in module qm_atlas.wrappers.torsion_constraints) finish_setup() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method) fix_coordinates() (in module qm_atlas.wrappers.turbomole.utils) fix_header_line() (in module qm_atlas.wrappers.cosmotherm.interface) fix_line() (in module qm_atlas.wrappers.cosmotherm.interface) force_constant (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) force_field (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) force_rerun (qm_atlas.command_line.base_config.BaseInterfaceConfig attribute) FREEH_SETTINGS (in module qm_atlas.wrappers.turbomole.freeh) freeh_settings (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute)

from_mol() (qm_atlas.tasks.common.AtomBasedProperty class method) (qm_atlas.tasks.common.BondBasedProperty class method) (qm_atlas.tasks.common.BoolProperty class method) (qm_atlas.tasks.common.Property class method) (qm_atlas.tasks.common.ScalarProperty class method) (qm_atlas.tasks.common.StringProperty class method) (qm_atlas.tasks.common.TensorProperty class method) functional (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute)

G

generate_conformers() (in module qm_atlas.tasks.conformer_generation) (in module qm_atlas.wrappers.macromodel) (in module qm_atlas.wrappers.moe) generate_conformers_molobj() (in module qm_atlas.wrappers.corina) (in module qm_atlas.wrappers.openeye) generate_conformers_with_fallback() (in module qm_atlas.tasks.conformer_generation) generate_corina_conformers() (in module qm_atlas.tasks.conformer_generation) generate_fast_conformers() (in module qm_atlas.workflows) (in module qm_atlas.workflows.fast_conformers) generate_input_mol() (in module qm_atlas.wrappers.openeye) generate_ionic_species() (in module qm_atlas.wrappers.moka.process) generate_joint_conformer_set() (in module qm_atlas.tasks.conformer_generation) generate_macrocycle_conformers() (in module qm_atlas.tasks.conformer_generation) (in module qm_atlas.wrappers.macromodel) generate_macromodel_conformers() (in module qm_atlas.tasks.conformer_generation) generate_moe_conformers() (in module qm_atlas.tasks.conformer_generation) generate_omega_conformers() (in module qm_atlas.tasks.conformer_generation) generate_rdkit_conformers() (in module qm_atlas.tasks.conformer_generation) generate_rescoss_conformers() (in module qm_atlas.workflows) (in module qm_atlas.workflows.rescoss_conformers) generate_sdfs() (in module qm_atlas.wrappers.moka.blabber) generate_single_charge_ions() (in module qm_atlas.wrappers.moka.process) generate_tautomer_conformers() (in module qm_atlas.tasks.tautomer_generation) generate_tautomers() (in module qm_atlas.tasks.tautomer_generation) (in module qm_atlas.workflows) (in module qm_atlas.workflows.score_tautomers) geo_opt_settings (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) geom_conv (qm_atlas.tasks.optimize.JobexOptions attribute) get_all_cosmo_files() (in module qm_atlas.wrappers.cosmotherm.cosmo_utils) get_atom_indices_map() (in module qm_atlas.utils) get_atom_property_names() (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions method) get_charge_schemes() (in module qm_atlas.wrappers.turbomole.fukui) get_charge_suffix() (in module qm_atlas.wrappers.moka.process) get_command() (qm_atlas.software_environment.EnvironmentManager method) get_command_lines() (qm_atlas.wrappers.cosmotherm.cosmo_utils.CosmoSettings method) get_concentration_string() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method) get_config_file() (in module qm_atlas.software_environment) get_conformer_property_worker_paths() (in module qm_atlas.command_line.base_config) get_conformer_shapes() (in module qm_atlas.workflows.fast_conformers) get_cosmo_descriptors() (in module qm_atlas.workflows.rescoss_conformers) get_cosmo_files() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method) get_cosmo_paths() (in module qm_atlas.wrappers.cosmotherm.interface) get_cosmo_property_worker_paths() (in module qm_atlas.command_line.base_config) get_cosmo_solvents_dir_key() (in module qm_atlas.software_environment) get_cosmo_solvents_dirs() (in module qm_atlas.software_environment) get_databases() (in module qm_atlas.wrappers.cosmotherm.cosmo_utils) get_default_command_line() (in module qm_atlas.wrappers.cosmotherm.cosmo_utils) get_env_from_modules() (in module qm_atlas.software_environment) get_environment_manager() (qm_atlas.software_environment.SoftwareConfig method) get_environment_variables() (qm_atlas.software_environment.EnvironmentManager method) get_generator_function() (in module qm_atlas.tasks.conformer_generation) get_global_settings() (qm_atlas.software_environment.EnvironmentManager method) get_hydrogen_abstraction_energies() (in module qm_atlas.wrappers.jaguar.bond_dissociation) get_idx_map() (in module qm_atlas.wrappers.jaguar.bond_dissociation) get_input_worker_paths() (in module qm_atlas.command_line.base_config) get_moka_line() (qm_atlas.wrappers.moka.moka.MokaPrediction method) get_moka_model() (in module qm_atlas.software_environment) get_moka_prediction() (in module qm_atlas.wrappers.moka.moka) get_moka_prediction_on_batch() (in module qm_atlas.wrappers.moka.moka) get_moka_std() (qm_atlas.wrappers.moka.moka.PredictedPKA method) get_moka_string() (qm_atlas.wrappers.moka.moka.PredictedPKA method) get_moka_version() (in module qm_atlas.wrappers.moka.moka) get_num_unpaired_electrons() (in module qm_atlas.wrappers.xtb) get_omega_command() (in module qm_atlas.wrappers.openeye) get_optimization_converged() (in module qm_atlas.wrappers.xtb) get_pka_centers_from_arrays() (in module qm_atlas.wrappers.moka.process) get_position() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method)

get_property_names() (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions method) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions method) (qm_atlas.tasks.calculate_properties.PropertyCalculatorOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions method) (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions method) (qm_atlas.tasks.cosmo_properties.CosmoConfig method) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig method) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig method) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig method) (qm_atlas.tasks.cosmo_properties.CosmoPermConfig method) (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig method) get_property_prefix() (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions method) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions method) (qm_atlas.tasks.calculate_properties.PropertyCalculatorOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions method) (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions method) (qm_atlas.tasks.cosmo_properties.CosmoConfig method) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig method) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig method) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig method) (qm_atlas.tasks.cosmo_properties.CosmoPermConfig method) (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig method) get_property_types() (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions method) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions method) (qm_atlas.tasks.calculate_properties.PropertyCalculatorOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions method) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions method) (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions method) (qm_atlas.tasks.cosmo_properties.CosmoConfig method) (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig method) get_property_value() (qm_atlas.tasks.common.AtomBasedProperty method) (qm_atlas.tasks.common.BondBasedProperty method) (qm_atlas.tasks.common.BoolProperty method) (qm_atlas.tasks.common.Property method) (qm_atlas.tasks.common.ScalarProperty method) (qm_atlas.tasks.common.StringProperty method) (qm_atlas.tasks.common.TensorProperty method) get_protonation() (in module qm_atlas.wrappers.moka.blabber) get_protonation_from_sdf() (in module qm_atlas.wrappers.moka.blabber) get_python_activation_command() (in module qm_atlas.software_environment) get_reference_string() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method) get_reference_worker_paths() (in module qm_atlas.command_line.base_config) get_run_environment() (qm_atlas.software_environment.EnvironmentManager method) get_scalar_property_names() (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions method) get_scratch_dir() (in module qm_atlas.utils) get_solubility_action_line() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method) get_solubility_action_line_mixture() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method) get_solvent_screening_worker_paths() (in module qm_atlas.command_line.base_config) get_submission_config() (qm_atlas.software_environment.EnvironmentManager method) get_tautomers() (in module qm_atlas.wrappers.unicon) get_turbomole_version() (in module qm_atlas.wrappers.turbomole.utils) get_xtb_energies_and_weights() (in module qm_atlas.tasks.calculate_properties) grid (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute)

H

has_hydrogens() (in module qm_atlas.utils) has_macrocycle() (in module qm_atlas.utils)

heavy_atom_torsions_fixed (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute)

I

index (qm_atlas.wrappers.moka.process.PkaCenter attribute) input (qm_atlas.command_line.base_config.BaseInterfaceConfig attribute) input_file (qm_atlas.command_line.pipeline.PipelineConfig attribute) intervals_overlap() (in module qm_atlas.utils) is_contained() (qm_atlas.wrappers.moka.process.PkaCalculationInfo method)

is_in_ph_range() (qm_atlas.wrappers.moka.process.PkaCenter method) is_relevant() (qm_atlas.wrappers.moka.process.PkaCenter method) is_woctanol (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) is_zwitterion() (in module qm_atlas.utils) iterate_solvents() (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable method)

J

jaguar_options (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) JaguarHydrogenAbstractionOptions (class in qm_atlas.tasks.calculate_properties)

JaguarQmDescriptorsOptions (class in qm_atlas.tasks.calculate_properties) JobexOptions (class in qm_atlas.tasks.optimize) jobs_per_task (qm_atlas.command_line.base_config.SubmissionConfig attribute) join_conformers() (in module qm_atlas.tasks.conformer_generation)

K

klamt (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute)

L

level (qm_atlas.tasks.cosmo_properties.CosmoConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) license_buffer (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) license_dir (qm_atlas.wrappers.cosmotherm.interface.CosmoPaths attribute) license_timeout (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute)

LINEAR_ANGLE_TOLERANCE_DEG (in module qm_atlas.wrappers.torsion_constraints) load_config() (in module qm_atlas.command_line.pipeline) load_environment_manager() (in module qm_atlas.software_environment) log_debug_information() (in module qm_atlas.wrappers.turbomole.jobex) log_macromodel_errors() (in module qm_atlas.wrappers.macromodel.utils) log_output() (in module qm_atlas.wrappers.cosmotherm.interface) lower_limit (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig attribute) lower_ph_threshold (qm_atlas.tasks.protonation.MokaIonicSpeciesConfig attribute) (qm_atlas.tasks.protonation.MokaSingleChargeConfig attribute)

M

MacrocycleOptions (class in qm_atlas.tasks.conformer_generation) MacromodelOptions (class in qm_atlas.tasks.conformer_generation) main() (in module qm_atlas.command_line.pipeline) map_conformers_onto_template() (in module qm_atlas.wrappers.helpers) mass_fractions (qm_atlas.wrappers.cosmotherm.cosmo_solubility.ReferenceSolubility attribute) max_conformers (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) (qm_atlas.tasks.conformer_generation.MoeOptions attribute) (qm_atlas.tasks.conformer_generation.OmegaOptions attribute) (qm_atlas.tasks.conformer_generation.RdkitOptions attribute) max_num_steps (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) max_time (qm_atlas.command_line.base_config.SubmissionConfig attribute) (qm_atlas.command_line.pipeline.PipelineSubmissionConfig attribute) max_total_num_cores (qm_atlas.command_line.base_config.SubmissionConfig attribute) mem_per_core (qm_atlas.command_line.base_config.SubmissionConfig attribute) meta_func() (in module qm_atlas.utils) method (qm_atlas.tasks.conformer_generation.RdkitOptions attribute) (qm_atlas.tasks.optimize.XtbOptions attribute) micelle_file (qm_atlas.tasks.cosmo_properties.CosmoPermConfig attribute) micelle_name (qm_atlas.tasks.cosmo_properties.CosmoPermConfig attribute) missing_reference_optimizations() (in module qm_atlas.command_line.base_config) MLIMIT (in module qm_atlas.wrappers.cosmotherm.cpsa) mode (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) (qm_atlas.tasks.conformer_generation.MoeOptions attribute) model_config (qm_atlas.command_line.base_config.BaseInterfaceConfig attribute) (qm_atlas.command_line.base_config.CalculationInput attribute) (qm_atlas.command_line.base_config.SubmissionConfig attribute) (qm_atlas.command_line.pipeline.PipelineConfig attribute) (qm_atlas.command_line.pipeline.PipelineSubmissionConfig attribute) (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) (qm_atlas.tasks.calculate_properties.PropertyCalculatorOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute) (qm_atlas.tasks.conformer_generation.ConformerGenerationOptions attribute) (qm_atlas.tasks.conformer_generation.ConformerGeneratorOptions attribute) (qm_atlas.tasks.conformer_generation.CorinaOptions attribute) (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) (qm_atlas.tasks.conformer_generation.MoeOptions attribute) (qm_atlas.tasks.conformer_generation.OmegaOptions attribute) (qm_atlas.tasks.conformer_generation.RdkitOptions attribute) (qm_atlas.tasks.cosmo_properties.CosmoConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoPermConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.OptimizationOptions attribute) (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) (qm_atlas.tasks.protonation.MokaBlabberConfig attribute) (qm_atlas.tasks.protonation.MokaIonicSpeciesConfig attribute) (qm_atlas.tasks.protonation.MokaSingleChargeConfig attribute) (qm_atlas.tasks.protonation.ProtonationOptions attribute)

module qm_atlas qm_atlas.command_line qm_atlas.command_line.base_config qm_atlas.command_line.pipeline qm_atlas.constants qm_atlas.software_environment qm_atlas.tasks qm_atlas.tasks.boltzmann qm_atlas.tasks.calculate_properties qm_atlas.tasks.common qm_atlas.tasks.conformer_generation qm_atlas.tasks.cosmo_properties qm_atlas.tasks.optimize qm_atlas.tasks.protonation qm_atlas.tasks.tautomer_generation qm_atlas.tasks.utils qm_atlas.units qm_atlas.utils qm_atlas.workflows.fast_conformers qm_atlas.workflows.optimize_constrained qm_atlas.workflows.rescoss_conformers qm_atlas.workflows.score_tautomers qm_atlas.wrappers qm_atlas.wrappers.common qm_atlas.wrappers.corina qm_atlas.wrappers.cosmotherm.cosmo_cocrystal qm_atlas.wrappers.cosmotherm.cosmo_solubility qm_atlas.wrappers.cosmotherm.cosmo_tasks qm_atlas.wrappers.cosmotherm.cosmo_utils qm_atlas.wrappers.cosmotherm.cpsa qm_atlas.wrappers.cosmotherm.interface qm_atlas.wrappers.helpers qm_atlas.wrappers.jaguar.bond_dissociation qm_atlas.wrappers.jaguar.common qm_atlas.wrappers.jaguar.qm_descriptors qm_atlas.wrappers.macromodel qm_atlas.wrappers.macromodel.utils qm_atlas.wrappers.moe qm_atlas.wrappers.moka.blabber qm_atlas.wrappers.moka.moka qm_atlas.wrappers.moka.process qm_atlas.wrappers.openeye qm_atlas.wrappers.torsion_constraints qm_atlas.wrappers.turbomole.freeh qm_atlas.wrappers.turbomole.fukui qm_atlas.wrappers.turbomole.jobex qm_atlas.wrappers.turbomole.nmr_shielding qm_atlas.wrappers.turbomole.single_point qm_atlas.wrappers.turbomole.utils qm_atlas.wrappers.turbomole.vcd qm_atlas.wrappers.turbomole.xtb_opt qm_atlas.wrappers.unicon qm_atlas.wrappers.xtb MoeOptions (class in qm_atlas.tasks.conformer_generation) moka_version_is_v5() (in module qm_atlas.wrappers.moka.moka) MokaBlabberConfig (class in qm_atlas.tasks.protonation) MokaIonicSpeciesConfig (class in qm_atlas.tasks.protonation) MokaPrediction (class in qm_atlas.wrappers.moka.moka) MokaSingleChargeConfig (class in qm_atlas.tasks.protonation) mol (qm_atlas.tasks.protonation.ProtomerEntry attribute)

N

n_cores (qm_atlas.command_line.base_config.BaseInterfaceConfig attribute) (qm_atlas.tasks.conformer_generation.OmegaOptions attribute) name (qm_atlas.command_line.base_config.SubmissionConfig attribute) (qm_atlas.command_line.pipeline.PipelineSubmissionConfig attribute) (qm_atlas.wrappers.moka.moka.MokaPrediction attribute) name_to_cosmo_files (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable attribute)

name_to_mol (qm_atlas.wrappers.moka.process.PkaCalculationInfo attribute) name_to_position (qm_atlas.wrappers.cosmotherm.cosmo_solubility.SolventInputTable attribute) normalize_settings_key() (in module qm_atlas.workflows.optimize_constrained) num_centers (qm_atlas.wrappers.moka.moka.MokaPrediction attribute) num_cores (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) NUM_STEPS_BINARY_MIXTURE (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) NUM_STEPS_TERNARY_MIXTURE (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility)

O

OmegaOptions (class in qm_atlas.tasks.conformer_generation) on_charges (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig attribute) opt_level (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) OptimizationOptions (class in qm_atlas.tasks.optimize)

optimize_conformer() (in module qm_atlas.tasks.optimize) optimize_fixed_mol() (in module qm_atlas.workflows.optimize_constrained) optimize_geometry() (in module qm_atlas.wrappers.xtb) optimize_mol() (in module qm_atlas.tasks.optimize) optimize_mols() (in module qm_atlas.tasks.optimize) optimize_with_fallback() (in module qm_atlas.tasks.optimize)

P

parent_name (qm_atlas.wrappers.moka.process.PkaCenter attribute) parent_smiles (qm_atlas.tasks.protonation.ProtonationPkaTransition attribute) parse_coord() (in module qm_atlas.wrappers.turbomole.jobex) parse_descriptors() (in module qm_atlas.wrappers.jaguar.qm_descriptors) parse_freeh() (in module qm_atlas.wrappers.turbomole.freeh) parse_fukui() (in module qm_atlas.wrappers.turbomole.fukui) parse_h_abs_out() (in module qm_atlas.wrappers.jaguar.bond_dissociation) parse_moka_output() (in module qm_atlas.wrappers.moka.moka) parse_nmr_isotropic() (in module qm_atlas.wrappers.turbomole.nmr_shielding) parse_ridft() (in module qm_atlas.wrappers.turbomole.single_point) parse_solubility_data() (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) parse_solvent_row() (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) parse_vcd() (in module qm_atlas.wrappers.turbomole.vcd) pH (qm_atlas.tasks.cosmo_properties.CosmoPermConfig attribute) ph (qm_atlas.tasks.protonation.MokaBlabberConfig attribute) PipelineConfig (class in qm_atlas.command_line.pipeline) PipelineSubmissionConfig (class in qm_atlas.command_line.pipeline) pka_centers (qm_atlas.wrappers.moka.process.PkaCalculationInfo attribute) pka_type (qm_atlas.tasks.protonation.ProtonationPkaTransition attribute) (qm_atlas.wrappers.moka.moka.PredictedPKA attribute) pka_value (qm_atlas.tasks.protonation.ProtonationPkaTransition attribute) (qm_atlas.wrappers.moka.process.PkaCenter attribute) PkaCalculationInfo (class in qm_atlas.wrappers.moka.process) PkaCenter (class in qm_atlas.wrappers.moka.process) PkaTypes (class in qm_atlas.wrappers.moka.moka) plain_average() (in module qm_atlas.tasks.boltzmann) PLIMIT (in module qm_atlas.wrappers.cosmotherm.cpsa) predicted_pkas (qm_atlas.wrappers.moka.moka.MokaPrediction attribute) PredictedPKA (class in qm_atlas.wrappers.moka.moka) PREPARE_FREEH (in module qm_atlas.wrappers.turbomole.freeh)

PREPARE_FUKUI (in module qm_atlas.wrappers.turbomole.fukui) prepare_jaguar_input() (in module qm_atlas.wrappers.jaguar.common) PREPARE_JOBEX (in module qm_atlas.wrappers.turbomole.jobex) PREPARE_NMR (in module qm_atlas.wrappers.turbomole.nmr_shielding) PREPARE_SP (in module qm_atlas.wrappers.turbomole.single_point) prepare_turbomole_input() (in module qm_atlas.wrappers.turbomole.utils) PREPARE_VCD (in module qm_atlas.wrappers.turbomole.vcd) properties (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) Property (class in qm_atlas.tasks.common) property_prefix (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) (qm_atlas.tasks.calculate_properties.JaguarQmDescriptorsOptions attribute) (qm_atlas.tasks.calculate_properties.PropertyCalculatorOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute) (qm_atlas.tasks.cosmo_properties.CosmoConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoPermConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig attribute) PropertyCalculatorOptions (class in qm_atlas.tasks.calculate_properties) ProtomerEntry (class in qm_atlas.tasks.protonation) protomers (qm_atlas.tasks.protonation.ProtonationResult attribute) ProtonationOptions (class in qm_atlas.tasks.protonation) ProtonationPkaTransition (class in qm_atlas.tasks.protonation) ProtonationResult (class in qm_atlas.tasks.protonation)

Q

qm_atlas module qm_atlas.command_line module qm_atlas.command_line.base_config module qm_atlas.command_line.pipeline module qm_atlas.constants module qm_atlas.software_environment module qm_atlas.tasks module qm_atlas.tasks.boltzmann module qm_atlas.tasks.calculate_properties module qm_atlas.tasks.common module qm_atlas.tasks.conformer_generation module qm_atlas.tasks.cosmo_properties module qm_atlas.tasks.optimize module qm_atlas.tasks.protonation module qm_atlas.tasks.tautomer_generation module qm_atlas.tasks.utils module qm_atlas.units module qm_atlas.utils module qm_atlas.workflows.fast_conformers module qm_atlas.workflows.optimize_constrained module qm_atlas.workflows.rescoss_conformers module qm_atlas.workflows.score_tautomers module qm_atlas.wrappers module qm_atlas.wrappers.common module qm_atlas.wrappers.corina module qm_atlas.wrappers.cosmotherm.cosmo_cocrystal module qm_atlas.wrappers.cosmotherm.cosmo_solubility module

qm_atlas.wrappers.cosmotherm.cosmo_tasks module qm_atlas.wrappers.cosmotherm.cosmo_utils module qm_atlas.wrappers.cosmotherm.cpsa module qm_atlas.wrappers.cosmotherm.interface module qm_atlas.wrappers.helpers module qm_atlas.wrappers.jaguar.bond_dissociation module qm_atlas.wrappers.jaguar.common module qm_atlas.wrappers.jaguar.qm_descriptors module qm_atlas.wrappers.macromodel module qm_atlas.wrappers.macromodel.utils module qm_atlas.wrappers.moe module qm_atlas.wrappers.moka.blabber module qm_atlas.wrappers.moka.moka module qm_atlas.wrappers.moka.process module qm_atlas.wrappers.openeye module qm_atlas.wrappers.torsion_constraints module qm_atlas.wrappers.turbomole.freeh module qm_atlas.wrappers.turbomole.fukui module qm_atlas.wrappers.turbomole.jobex module qm_atlas.wrappers.turbomole.nmr_shielding module qm_atlas.wrappers.turbomole.single_point module qm_atlas.wrappers.turbomole.utils module qm_atlas.wrappers.turbomole.vcd module qm_atlas.wrappers.turbomole.xtb_opt module qm_atlas.wrappers.unicon module qm_atlas.wrappers.xtb module

R

random_seed (qm_atlas.tasks.conformer_generation.RdkitOptions attribute) RdkitOptions (class in qm_atlas.tasks.conformer_generation) read_conformers_as_mols() (in module qm_atlas.wrappers.helpers) read_cosmo_file() (in module qm_atlas.wrappers.turbomole.single_point) read_cosmotherm_output() (in module qm_atlas.wrappers.cosmotherm.interface) read_errors_output() (in module qm_atlas.wrappers.cosmotherm.interface) read_properties_from_stdout() (in module qm_atlas.wrappers.xtb) read_table() (in module qm_atlas.wrappers.cosmotherm.interface) read_xtb_output() (in module qm_atlas.wrappers.xtb) read_xyz_coordinates() (in module qm_atlas.wrappers.common) reference_input_file (qm_atlas.command_line.pipeline.PipelineConfig attribute) ReferenceSolubility (class in qm_atlas.wrappers.cosmotherm.cosmo_solubility) reindex_conformers() (in module qm_atlas.workflows.fast_conformers) reload_environment_manager() (qm_atlas.software_environment.SoftwareConfig method) remove_conformers() (in module qm_atlas.utils) remove_salt() (in module qm_atlas.utils) remove_zero_charged (qm_atlas.tasks.protonation.MokaBlabberConfig attribute) RESCOSS_DEFAULT_CONF_GENS (in module qm_atlas.workflows.rescoss_conformers) resolve_dihedral_constraints() (in module qm_atlas.wrappers.xtb) resolve_steps() (qm_atlas.command_line.pipeline.PipelineConfig method) restore_atom_indices() (in module qm_atlas.utils) results_directory (qm_atlas.command_line.base_config.CalculationInput attribute) (qm_atlas.command_line.pipeline.PipelineConfig attribute) ricore (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute)

rms_threshold (qm_atlas.tasks.conformer_generation.ConformerGenerationOptions attribute) (qm_atlas.tasks.conformer_generation.MacrocycleOptions attribute) (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) (qm_atlas.tasks.conformer_generation.MoeOptions attribute) (qm_atlas.tasks.conformer_generation.OmegaOptions attribute) (qm_atlas.tasks.conformer_generation.RdkitOptions attribute) rmsd_method (qm_atlas.tasks.conformer_generation.ConformerGenerationOptions attribute) RMSD_THRESHOLD (in module qm_atlas.workflows.rescoss_conformers) run_command() (in module qm_atlas.wrappers.common) run_constrained_optimization() (in module qm_atlas.workflows) (in module qm_atlas.workflows.optimize_constrained) run_cosmo_calculation() (in module qm_atlas.tasks.cosmo_properties) run_cosmotherm() (in module qm_atlas.wrappers.cosmotherm.interface) run_jaguar_hydrogen_abstraction() (in module qm_atlas.wrappers.jaguar.bond_dissociation) run_jobex() (in module qm_atlas.wrappers.turbomole.jobex) run_moka_sdf() (in module qm_atlas.wrappers.moka.moka) run_pipeline() (in module qm_atlas.command_line.pipeline) run_protonation() (in module qm_atlas.tasks.protonation) run_ridft() (in module qm_atlas.wrappers.turbomole.single_point) run_xtb() (in module qm_atlas.wrappers.xtb) run_xtb_tm_optimization() (in module qm_atlas.wrappers.turbomole.xtb_opt)

S

ScalarProperty (class in qm_atlas.tasks.common) scf_conv (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) scfdamp (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) scfiterlimit (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) screen_cocrystals() (in module qm_atlas.wrappers.cosmotherm.cosmo_cocrystal) seek_match() (in module qm_atlas.wrappers.turbomole.utils) select_from_clusters() (in module qm_atlas.workflows.rescoss_conformers) select_stable_tautomers() (in module qm_atlas.tasks.tautomer_generation) set_property_on_mol() (qm_atlas.tasks.common.AtomBasedProperty method) (qm_atlas.tasks.common.BondBasedProperty method) (qm_atlas.tasks.common.BoolProperty method) (qm_atlas.tasks.common.Property method) (qm_atlas.tasks.common.ScalarProperty method) (qm_atlas.tasks.common.StringProperty method) (qm_atlas.tasks.common.TensorProperty method) SETTINGS_CONSTRAINED_OPTIMIZATION_PROP (in module qm_atlas.workflows.optimize_constrained) settings_key() (in module qm_atlas.workflows.optimize_constrained) setup_cosmotherm() (in module qm_atlas.wrappers.cosmotherm.interface) setup_logging() (in module qm_atlas.command_line.base_config) single_point_settings (qm_atlas.tasks.calculate_properties.JaguarHydrogenAbstractionOptions attribute) smoothen (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig attribute) software_available() (qm_atlas.software_environment.EnvironmentManager method) software_config (qm_atlas.command_line.base_config.BaseInterfaceConfig attribute) (qm_atlas.command_line.pipeline.PipelineConfig attribute)

SoftwareConfig (class in qm_atlas.software_environment) SoftwareEnvironment (class in qm_atlas.software_environment) SOLUBILITY_SETTINGS (in module qm_atlas.wrappers.cosmotherm.cosmo_solubility) solubility_unit (qm_atlas.wrappers.cosmotherm.cosmo_solubility.ReferenceSolubility attribute) solvation_model (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute) (qm_atlas.tasks.optimize.XtbOptions attribute) solvent (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) solvent_name (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) solvent_names (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) (qm_atlas.wrappers.cosmotherm.cosmo_solubility.ReferenceSolubility attribute) solvent_num (qm_atlas.tasks.conformer_generation.MacromodelOptions attribute) SolventInputTable (class in qm_atlas.wrappers.cosmotherm.cosmo_solubility) solvents_dirs (qm_atlas.tasks.cosmo_properties.CosmoConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) split_dict() (in module qm_atlas.wrappers.jaguar.bond_dissociation) standard_deviation (qm_atlas.wrappers.moka.moka.PredictedPKA attribute) start_from_corina (qm_atlas.tasks.conformer_generation.OmegaOptions attribute) steps (qm_atlas.command_line.pipeline.PipelineConfig attribute) store_atom_indices() (in module qm_atlas.utils) store_atom_map_numbers() (in module qm_atlas.wrappers.helpers) StringProperty (class in qm_atlas.tasks.common) submission_config (qm_atlas.command_line.base_config.BaseInterfaceConfig attribute) (qm_atlas.command_line.pipeline.PipelineConfig attribute) SubmissionConfig (class in qm_atlas.command_line.base_config) submit (qm_atlas.command_line.base_config.SubmissionConfig attribute) submit() (in module qm_atlas.command_line.pipeline)

T

task_control_file (qm_atlas.command_line.base_config.CalculationInput attribute) task_id (qm_atlas.command_line.base_config.CalculationInput attribute) TAUTOMER_TM_SP_CONFIG (in module qm_atlas.workflows.score_tautomers) temperature (qm_atlas.wrappers.cosmotherm.cosmo_solubility.ReferenceSolubility attribute) temperature_Celsius (qm_atlas.tasks.cosmo_properties.CosmoConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) template_str (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute)

TensorProperty (class in qm_atlas.tasks.common) thread_control_variables (qm_atlas.software_environment.SoftwareEnvironment attribute) torsions_fixed (qm_atlas.tasks.optimize.XtbOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) transitions (qm_atlas.tasks.protonation.ProtonationResult attribute) TurbomoleFreehOptions (class in qm_atlas.tasks.calculate_properties) TurbomoleFukuiOptions (class in qm_atlas.tasks.calculate_properties) TurbomoleNmrShieldingOptions (class in qm_atlas.tasks.calculate_properties) TurbomoleSinglePointOptions (class in qm_atlas.tasks.calculate_properties) TurbomoleVcdOptions (class in qm_atlas.tasks.calculate_properties)

U

unstable_tautomer (qm_atlas.wrappers.moka.moka.MokaPrediction attribute) update_mol() (in module qm_atlas.tasks.optimize) upper_limit (qm_atlas.tasks.cosmo_properties.CosmoPsaConfig attribute) upper_ph_threshold (qm_atlas.tasks.protonation.MokaIonicSpeciesConfig attribute) (qm_atlas.tasks.protonation.MokaSingleChargeConfig attribute) use_config_cosmo_dir (qm_atlas.tasks.cosmo_properties.CosmoConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDeltaGConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoDescriptorsConfig attribute) (qm_atlas.tasks.cosmo_properties.CosmoLogPConfig attribute) use_cosmo (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute)

use_disp (qm_atlas.tasks.calculate_properties.TurbomoleFreehOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleFukuiOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleNmrShieldingOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleSinglePointOptions attribute) (qm_atlas.tasks.calculate_properties.TurbomoleVcdOptions attribute) (qm_atlas.tasks.optimize.JobexOptions attribute) (qm_atlas.tasks.optimize.XtbTurbomoleOptions attribute) user_email (qm_atlas.command_line.base_config.SubmissionConfig attribute)

V

validate_compound_directories_field() (qm_atlas.command_line.base_config.CalculationInput class method) validate_cores_configuration() (qm_atlas.command_line.base_config.SubmissionConfig method) validate_input_file() (qm_atlas.command_line.pipeline.PipelineConfig class method) validate_method() (qm_atlas.tasks.conformer_generation.RdkitOptions class method) validate_mutual_exclusivity() (qm_atlas.command_line.base_config.CalculationInput method) validate_results_dir() (in module qm_atlas.command_line.base_config) validate_results_directory_field() (qm_atlas.command_line.base_config.CalculationInput class method) (qm_atlas.command_line.pipeline.PipelineConfig class method)

validate_task_control_file() (qm_atlas.command_line.base_config.CalculationInput class method) validate_task_id_requires_task_control_file() (qm_atlas.command_line.base_config.CalculationInput method) value (qm_atlas.wrappers.cosmotherm.cosmo_solubility.ReferenceSolubility attribute) (qm_atlas.wrappers.moka.moka.PredictedPKA attribute) verbose (qm_atlas.command_line.base_config.BaseInterfaceConfig attribute) (qm_atlas.command_line.pipeline.PipelineConfig attribute)

W

wait (qm_atlas.command_line.base_config.SubmissionConfig attribute) wait_for_license() (in module qm_atlas.wrappers.helpers) weighted_average() (in module qm_atlas.tasks.boltzmann) worker_path_completed() (in module qm_atlas.command_line.base_config)

write_conformer() (in module qm_atlas.wrappers.cosmotherm.interface) write_conformers() (in module qm_atlas.wrappers.cosmotherm.interface) write_xcontrol_file() (in module qm_atlas.wrappers.xtb) write_xtb_input() (in module qm_atlas.wrappers.xtb) write_xyz() (in module qm_atlas.wrappers.common)

X

XCONTROL_TEMPLATE_CSTR (in module qm_atlas.wrappers.turbomole.xtb_opt) XCONTROL_TEMPLATE_OPT (in module qm_atlas.wrappers.xtb) XCONTROL_TEMPLATE_SP (in module qm_atlas.wrappers.xtb) xtb_command_add (qm_atlas.tasks.calculate_properties.XtbSinglePointOptions attribute)

XTB_OPTIMIZATION_CONFIG (in module qm_atlas.workflows.rescoss_conformers) XtbOptions (class in qm_atlas.tasks.optimize) XtbSinglePointOptions (class in qm_atlas.tasks.calculate_properties) XtbTurbomoleOptions (class in qm_atlas.tasks.optimize)