Index

_

__slots__ (obelix.molecular_graph.MolGraph attribute) _buried_volume_quadrant_analysis() (obelix.descriptor_calculator.Descriptors method) _calculate_c_c_distance_nbd() (obelix.descriptor_calculator.Descriptors static method) _calculate_dft_descriptors_from_log() (obelix.descriptor_calculator.Descriptors method) _calculate_dihedral_angles_nbd_and_metal_donors() (obelix.descriptor_calculator.Descriptors static method)

_calculate_steric_electronic_desc_morfeus() (obelix.descriptor_calculator.Descriptors method) _find_bidentate_ligand() (obelix.descriptor_calculator.Descriptors static method) _generate_adjacency_list() (obelix.molecular_graph.MolGraph method) _max_donor_idx (obelix.free_ligand.FreeLigand attribute) _merge_descriptor_dfs() (obelix.descriptor_calculator.Descriptors method) _min_donor_idx (obelix.free_ligand.FreeLigand attribute)

A

add_code_to_structure() (in module obelix.tools.utilities) adj_list (obelix.molecular_graph.MolGraph attribute) adj_matrix (obelix.molecular_graph.MolGraph attribute) assign_min_max_donor_dft() (obelix.free_ligand.FreeLigand method)

assign_min_max_donor_xtb() (obelix.free_ligand.FreeLigand method) atom_charges_dict (obelix.dft_extraction.DFTExtractor attribute) atomic_radii (in module obelix.molecular_graph), [1] (obelix.molecular_graph.MolGraph attribute) auxiliary_ligands (in module example_workflow)

B

bfs() (in module obelix.molecular_graph) bidentate (obelix.run_workflow.MACE attribute) bidentate_1_index (obelix.run_workflow.Workflow attribute)

bidentate_2_index (obelix.run_workflow.Workflow attribute) bidentate_cycle_idxs (in module obelix.tools.find_bidentate_atoms) bidentate_idxs (in module obelix.tools.find_bidentate_atoms) bond_lengths (obelix.molecular_graph.MolGraph attribute)

C

CA (in module obelix.tools.find_bidentate_atoms) (obelix.run_workflow.MACE attribute) calculate_descriptors() (obelix.run_workflow.Workflow method) calculate_dft_descriptors() (obelix.free_ligand.FreeLigand method) calculate_dft_descriptors_from_log() (obelix.descriptor_calculator.Descriptors method) calculate_dihedral() (in module obelix.tools.utilities) calculate_dipole_moment() (obelix.dft_extraction.DFTExtractor method) calculate_dispersion_energy() (obelix.dft_extraction.DFTExtractor method) calculate_distance() (in module obelix.tools.utilities) calculate_donor_lone_pair_occupancy() (obelix.dft_extraction.DFTExtractor method) calculate_electronic_descriptors() (obelix.dft_extraction.DFTExtractor method) calculate_max_donor_metal_anti_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_max_donor_metal_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_max_donor_other_anti_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_max_donor_other_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_min_donor_metal_anti_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_min_donor_metal_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_min_donor_other_anti_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_min_donor_other_orbital_occupation() (obelix.dft_extraction.DFTExtractor method) calculate_morfeus_descriptors() (obelix.descriptor_calculator.Descriptors method) calculate_mulliken_charges() (obelix.dft_extraction.DFTExtractor method) calculate_natural_charges() (obelix.dft_extraction.DFTExtractor method) carbon_back_nbd_idx (obelix.dft_extraction.NBDComplex attribute)

central_atom (in module example_workflow) (obelix.descriptor_calculator.Descriptors attribute) (obelix.model_structure_generator.MetalLigandComplex attribute) change_second_line_xyz() (in module obelix.tools.utilities) check_if_at_least_two_mapped_atoms_in_ring() (in module obelix.tools.find_bidentate_atoms) (in module obelix.tools.utilities) check_nbd_back_carbon() (obelix.dft_extraction.DFTExtractor method) (obelix.dft_extraction.NBDComplex method) check_normal_termination() (obelix.dft_extraction.DFTExtractor method) chemspax_directory (in module example_workflow) chemspax_input (in module example_workflow) (obelix.run_workflow.Workflow attribute) complex_xyz_bidentate_1_idx (obelix.free_ligand.FreeLigand attribute) complex_xyz_bidentate_2_idx (obelix.free_ligand.FreeLigand attribute) complexes_to_calc_descriptors (in module obelix.dft_extraction) (in module obelix.tools.find_bidentate_atoms) coordinates (obelix.dft_extraction.NBDComplex attribute) create_complex_mace() (obelix.model_structure_generator.MetalLigandComplex method) create_octahedral_structures() (obelix.model_structure_generator.MetalLigandComplex method) create_octahedral_structures_without_substrate() (obelix.model_structure_generator.MetalLigandComplex method) create_square_planar_structures() (obelix.model_structure_generator.MetalLigandComplex method) create_square_planar_structures_without_substrate() (obelix.model_structure_generator.MetalLigandComplex method) crest_input (obelix.run_workflow.Workflow attribute)

D

data (obelix.dft_extraction.DFTExtractor attribute) data_path (in module obelix.tools.mace_substrate_remover) dataframe_from_dictionary() (in module obelix.tools.utilities) dataset_name (in module obelix.model_structure_generator) descriptor_calculator (obelix.free_ligand.FreeLigand attribute) descriptor_calculator_input (obelix.run_workflow.Workflow attribute)

descriptor_df (obelix.descriptor_calculator.Descriptors attribute) Descriptors (class in obelix.descriptor_calculator) descriptors (in module obelix.descriptor_calculator) dft (obelix.free_ligand.FreeLigand attribute) dft_log_file (obelix.free_ligand.FreeLigand attribute) DFTExtractor (class in obelix.dft_extraction) donor_atoms (in module obelix.tools.find_bidentate_atoms), [1]

E

elements (in module obelix.tools.find_bidentate_atoms) (obelix.dft_extraction.DFTExtractor attribute) (obelix.dft_extraction.NBDComplex attribute) (obelix.molecular_graph.MolGraph attribute) example_workflow module extract_dipole_moment() (obelix.dft_extraction.DFTExtractor method) extract_dispersion_energies() (obelix.dft_extraction.DFTExtractor method) extract_donor_lone_pair_occupancy() (obelix.dft_extraction.DFTExtractor method) extract_donor_metal_antibonding_occupation() (obelix.dft_extraction.DFTExtractor method)

extract_donor_metal_bonding_occupation() (obelix.dft_extraction.DFTExtractor method) extract_donor_other_element_antibonding_occupation() (obelix.dft_extraction.DFTExtractor method) extract_donor_other_element_bonding_occupation() (obelix.dft_extraction.DFTExtractor method) extract_homo_lumo_gap() (obelix.dft_extraction.DFTExtractor method) extract_ligand_and_write_xyz() (in module obelix.molecular_graph) extract_mulliken_charges() (obelix.dft_extraction.DFTExtractor method) extract_natural_charges() (obelix.dft_extraction.DFTExtractor method) extract_natural_charges_cclib() (obelix.dft_extraction.DFTExtractor method) extract_thermodynamic_descriptors() (obelix.dft_extraction.DFTExtractor method) extract_time() (obelix.dft_extraction.DFTExtractor method)

F

filename (obelix.dft_extraction.NBDComplex attribute) find_bidentate() (in module obelix.tools.utilities) (obelix.run_workflow.MACE static method) find_bonds_with_neighbours() (in module obelix.tools.utilities) find_central_carbon_and_hydrogens_nbd_openbabel() (obelix.dft_extraction.NBDComplex method) find_nbd_indices_openbabel() (obelix.dft_extraction.NBDComplex method)

first_conformer (in module obelix.tools.find_bidentate_atoms) free_ligand_xyz_bidentate_1_idx (obelix.free_ligand.FreeLigand attribute) free_ligand_xyz_bidentate_2_idx (obelix.free_ligand.FreeLigand attribute) FreeLigand (class in obelix.free_ligand) freq_calculation (obelix.dft_extraction.DFTExtractor attribute) func_list (in module example_workflow)

G

generate_complex_OH_xyz() (obelix.run_workflow.MACE method) generate_complex_SP_xyz() (obelix.run_workflow.MACE method) geom (in module example_workflow) (in module obelix.tools.find_bidentate_atoms) (obelix.run_workflow.Workflow attribute) get_bonded_atoms() (in module obelix.tools.find_bidentate_atoms) (in module obelix.tools.utilities)

get_cluster_centroid_coord() (in module obelix.tools.utilities) get_hydrogens_bonded_to_carbon_back_nbd() (obelix.dft_extraction.DFTExtractor method) (obelix.dft_extraction.NBDComplex method) get_ligands_from_smiles() (in module obelix.tools.utilities) gjf_to_xyz() (in module obelix.tools.utilities)

H

header (in module obelix.tools.utilities)

I

initialize_chemspax() (obelix.run_workflow.Workflow method) initialize_crest() (obelix.run_workflow.Workflow method)

initialize_descriptor_calculator() (obelix.run_workflow.Workflow method) initialize_dft_extractor() (obelix.free_ligand.FreeLigand method) initialize_mace() (obelix.run_workflow.Workflow method)

L

ligand_df (in module example_workflow) (obelix.model_structure_generator.MetalLigandComplex attribute) ligand_excel_file (in module example_workflow) (in module obelix.run_workflow)

ligand_name (in module example_workflow) ligand_number_list (in module obelix.free_ligand) ligand_smiles (in module example_workflow) ligands (in module obelix.tools.find_bidentate_atoms) log_file (obelix.dft_extraction.DFTExtractor attribute)

M

MACE (class in obelix.run_workflow) mace_input (in module example_workflow) (obelix.run_workflow.Workflow attribute) mace_skeletons (obelix.run_workflow.Workflow attribute) make_dir() (obelix.model_structure_generator.MetalLigandComplex static method) max_donor_idx (obelix.dft_extraction.DFTExtractor attribute) (obelix.free_ligand.FreeLigand property) meta_data (obelix.dft_extraction.DFTExtractor attribute) metal_adduct (obelix.dft_extraction.DFTExtractor attribute) metal_center_idx (obelix.dft_extraction.DFTExtractor attribute) (obelix.free_ligand.FreeLigand attribute) metal_index (obelix.run_workflow.Workflow attribute) MetalLigandComplex (class in obelix.model_structure_generator) min_donor_idx (obelix.dft_extraction.DFTExtractor attribute) (obelix.free_ligand.FreeLigand property)

module example_workflow obelix obelix.descriptor_calculator obelix.dft_extraction obelix.free_ligand obelix.model_structure_generator obelix.molecular_graph obelix.run_workflow obelix.tools obelix.tools.find_bidentate_atoms obelix.tools.mace_substrate_remover obelix.tools.utilities molecular_graph() (in module obelix.molecular_graph) MolGraph (class in obelix.molecular_graph)

N

name_of_xyz (obelix.run_workflow.MACE attribute)

names (in module example_workflow) NBDComplex (class in obelix.dft_extraction)

O

obelix module obelix.descriptor_calculator module obelix.dft_extraction module obelix.free_ligand module obelix.model_structure_generator module obelix.molecular_graph module

obelix.run_workflow module obelix.tools module obelix.tools.find_bidentate_atoms module obelix.tools.mace_substrate_remover module obelix.tools.utilities module output_type (obelix.descriptor_calculator.Descriptors attribute)

P

parser (obelix.dft_extraction.DFTExtractor attribute) path_to_database (in module example_workflow) path_to_substituents (in module example_workflow) path_to_workflow (in module obelix.molecular_graph) (obelix.descriptor_calculator.Descriptors attribute) (obelix.free_ligand.FreeLigand attribute) (obelix.run_workflow.Workflow attribute)

prepare_folder_structure() (obelix.run_workflow.Workflow method)

R

read_xyz_coord_from_mf() (obelix.molecular_graph.MolGraph method) remove_substrate() (in module obelix.tools.mace_substrate_remover) run_chemspax() (obelix.run_workflow.Workflow method)

run_crest() (obelix.run_workflow.Workflow method) run_mace() (obelix.run_workflow.Workflow method) run_workflow() (obelix.run_workflow.Workflow method)

S

set_output_type() (obelix.descriptor_calculator.Descriptors method) solvent (obelix.run_workflow.Workflow attribute) substituent_df (in module example_workflow) substituent_list (in module example_workflow)

substrate (in module example_workflow) (in module obelix.tools.find_bidentate_atoms) (obelix.model_structure_generator.MetalLigandComplex attribute) supported_output_types (obelix.descriptor_calculator.Descriptors attribute)

T

test_ligand (in module obelix.tools.find_bidentate_atoms)

transform_smiles_to_mace_input() (obelix.model_structure_generator.MetalLigandComplex static method)

W

Workflow (class in obelix.run_workflow)

workflow (in module example_workflow)

X

X (in module obelix.tools.find_bidentate_atoms) x (obelix.molecular_graph.MolGraph attribute) Xs (in module obelix.tools.find_bidentate_atoms)

xyz_filename (obelix.free_ligand.FreeLigand attribute) xyz_string (obelix.dft_extraction.NBDComplex attribute) xyz_to_gjf() (in module obelix.tools.utilities)

Y

y (obelix.molecular_graph.MolGraph attribute)

Z

z (obelix.molecular_graph.MolGraph attribute)