Index

A

all_ferrocene_metals() (in module mofstructure.mofdeconstructor) analyse() (in module mofstructure.topology) analyse_many() (in module mofstructure.topology) analyse_methods() (in module mofstructure.topology) angle_tolerance_to_rad() (in module mofstructure.mofdeconstructor)

as_atoms() (in module mofstructure.topology) ase_2_pybel() (in module mofstructure.mofdeconstructor) ase_2_xyz() (in module mofstructure.mofdeconstructor) ase_atoms (mofstructure.generate_cgd.TopologyExtractor attribute) ase_to_zeoobject() (in module mofstructure.porosity) atoms (mofstructure.generate_cgd.TopologyExtractor property)

B

base_edges_with_shifts() (in module mofstructure.generate_cgd) build() (mofstructure.graph_net.PeriodicGraph class method)

build_argparser() (in module mofstructure.generate_cgd) build_cgd() (mofstructure.generate_cgd.TopologyExtractor method)

C

canonical_form() (in module mofstructure.graph_net) canonical_key() (in module mofstructure.graph_net) cgd_all_nodes() (in module mofstructure.generate_cgd) cgd_from_region_targets() (in module mofstructure.generate_cgd) cgd_ligand_cluster() (in module mofstructure.generate_cgd) cgd_single_nodes() (in module mofstructure.generate_cgd) cgd_zeolite() (in module mofstructure.generate_cgd) check_planarity() (in module mofstructure.mofdeconstructor) cheminformatics_backend() (in module mofstructure.mofdeconstructor) classify() (in module mofstructure.topology) component_atom_images() (in module mofstructure.generate_cgd) component_has_transition_metal_not_in_porphyrin() (in module mofstructure.generate_cgd) component_self_translations() (in module mofstructure.generate_cgd) components() (mofstructure.graph_net.PeriodicGraph method)

compute_ase_neighbour() (in module mofstructure.mofdeconstructor) compute_ase_neighbour_with_offsets() (in module mofstructure.mofdeconstructor) compute_cheminformatic() (in module mofstructure.mofdeconstructor) compute_cheminformatic_from_rdkit() (in module mofstructure.mofdeconstructor) compute_cof_stacking() (in module mofstructure.cof_stacking) compute_inchis() (in module mofstructure.mofdeconstructor) compute_openbabel_cheminformatic() (in module mofstructure.mofdeconstructor) compute_smi() (in module mofstructure.mofdeconstructor) compute_zeo_parameters() (in module mofstructure.porosity) connected_components() (in module mofstructure.mofdeconstructor) connected_components_iterative() (in module mofstructure.mofdeconstructor) connected_components_recursive() (in module mofstructure.mofdeconstructor) coordination_contacts() (in module mofstructure.generate_cgd) covalent_radius() (in module mofstructure.mofdeconstructor) covering_multiplicity() (mofstructure.graph_net.PeriodicGraph method)

D

dedup_periodic_edges() (in module mofstructure.generate_cgd) DEFAULT_METHOD (in module mofstructure.topology) degrees() (mofstructure.graph_net.PeriodicGraph method) describe() (in module mofstructure.graph_net) describe_key() (in module mofstructure.graph_net)

dfs_iterative() (in module mofstructure.mofdeconstructor) dfsutil_graph_method() (in module mofstructure.mofdeconstructor) dim (mofstructure.graph_net.PeriodicGraph attribute) draw_topology() (mofstructure.structure.MOFstructure method) drawing_periodic_edges() (in module mofstructure.generate_cgd)

E

edges (mofstructure.graph_net.PeriodicGraph attribute)

empty_porosity_record() (in module mofstructure.porosity)

F

filename (mofstructure.generate_cgd.TopologyExtractor attribute) find_carbonyl_sulphate() (in module mofstructure.mofdeconstructor) find_carboxylates() (in module mofstructure.mofdeconstructor) find_COS() (in module mofstructure.mofdeconstructor) find_key_or_value() (in module mofstructure.mofdeconstructor)

find_nitroxylates() (in module mofstructure.mofdeconstructor) find_phosphate() (in module mofstructure.mofdeconstructor) find_phosphite() (in module mofstructure.mofdeconstructor) find_sulfides() (in module mofstructure.mofdeconstructor) find_unique_building_units() (in module mofstructure.mofdeconstructor) from_key_string() (mofstructure.graph_net.PeriodicGraph class method)

G

genus() (mofstructure.graph_net.PeriodicGraph method) get_bond_shift() (in module mofstructure.mofdeconstructor) get_coordination_environment() (in module mofstructure.structure) get_ligand_cluster_fingerprint() (mofstructure.structure.MOFstructure method) get_ligands() (mofstructure.structure.MOFstructure method)

get_neighbour_bond_matrix() (in module mofstructure.mofdeconstructor) get_oms() (mofstructure.structure.MOFstructure method) get_porosity() (mofstructure.structure.MOFstructure method) get_sbu() (mofstructure.structure.MOFstructure method) get_topology() (mofstructure.structure.MOFstructure method)

I

ideal_embedding() (in module mofstructure.graph_net) identify() (in module mofstructure.graph_net) incidences() (mofstructure.graph_net.PeriodicGraph method) inter_atomic_distance_check() (in module mofstructure.mofdeconstructor) inter_atomic_distance_check2() (in module mofstructure.mofdeconstructor) inter_atomic_distance_iterative() (in module mofstructure.mofdeconstructor) is_alkali() (in module mofstructure.mofdeconstructor) is_atom_in_ring() (in module mofstructure.mofdeconstructor) is_cgd() (in module mofstructure.topology)

is_ferrocene() (in module mofstructure.mofdeconstructor) is_irmof() (in module mofstructure.mofdeconstructor) is_metal() (in module mofstructure.mofdeconstructor) is_mof32() (in module mofstructure.mofdeconstructor) is_paddlewheel() (in module mofstructure.mofdeconstructor) is_paddlewheel_with_water() (in module mofstructure.mofdeconstructor) is_quotient_connected() (mofstructure.graph_net.PeriodicGraph method) is_rodlike() (in module mofstructure.mofdeconstructor) is_uio66() (in module mofstructure.mofdeconstructor)

K

kept_bond_graph() (in module mofstructure.generate_cgd)

key_hash() (in module mofstructure.graph_net) key_string() (mofstructure.graph_net.PeriodicGraph method)

L

ligand_cluster_fingerprint() (in module mofstructure.generate_cgd) ligand_cluster_graph() (in module mofstructure.generate_cgd) ligand_cluster_incidences() (in module mofstructure.generate_cgd)

ligands_and_metal_clusters() (in module mofstructure.mofdeconstructor) longest_list() (in module mofstructure.mofdeconstructor) lookup() (in module mofstructure.graph_net) lookup_iupac_name() (in module mofstructure.mofdeconstructor)

M

Main() (in module mofstructure.cof_stacking) main() (in module mofstructure.generate_cgd) matrix2dict() (in module mofstructure.mofdeconstructor) max_index() (in module mofstructure.mofdeconstructor) metal_coordination_enviroment() (in module mofstructure.mofdeconstructor) metal_coordination_number() (in module mofstructure.mofdeconstructor) metal_in_porphyrin() (in module mofstructure.mofdeconstructor) metal_in_porphyrin2() (in module mofstructure.mofdeconstructor) module mofstructure.cof_stacking mofstructure.generate_cgd mofstructure.graph_net mofstructure.mofdeconstructor mofstructure.porosity mofstructure.structure mofstructure.topology MOF_METHODS (in module mofstructure.topology)

mof_regions() (in module mofstructure.mofdeconstructor) MOFstructure (class in mofstructure.structure) mofstructure.cof_stacking module mofstructure.generate_cgd module mofstructure.graph_net module mofstructure.mofdeconstructor module mofstructure.porosity module mofstructure.structure module mofstructure.topology module move2front() (in module mofstructure.mofdeconstructor)

N

n_edges (mofstructure.graph_net.PeriodicGraph property) n_vertices (mofstructure.graph_net.PeriodicGraph attribute)

name (mofstructure.graph_net.PeriodicGraph attribute) name_lookup_keys() (in module mofstructure.mofdeconstructor) net_geometry() (in module mofstructure.generate_cgd)

O

obmol_2_rdkit() (in module mofstructure.mofdeconstructor)

P

periodic_graph_cgd() (in module mofstructure.generate_cgd) PeriodicGraph (class in mofstructure.graph_net)

periodicity() (mofstructure.graph_net.PeriodicGraph method) primitive() (in module mofstructure.graph_net)

Q

quotient_graph() (in module mofstructure.topology)

R

reduced() (mofstructure.graph_net.PeriodicGraph method) regions_with_metal() (in module mofstructure.generate_cgd) relabelled() (mofstructure.graph_net.PeriodicGraph method) remove_broken_bonds_from_breaking_pairs() (in module mofstructure.generate_cgd) remove_guest() (mofstructure.generate_cgd.TopologyExtractor method) (mofstructure.structure.MOFstructure method)

remove_unbound_guest() (in module mofstructure.mofdeconstructor) remove_unbound_guest_and_return_unique() (in module mofstructure.mofdeconstructor) rings_and_atom_ring_lookup() (in module mofstructure.mofdeconstructor) rod_manipulation() (in module mofstructure.mofdeconstructor)

S

saturate_open_valences() (in module mofstructure.mofdeconstructor) sbu_drawing_graph() (in module mofstructure.generate_cgd) secondary_building_units() (in module mofstructure.mofdeconstructor)

space_group() (in module mofstructure.graph_net) spanning_tree() (mofstructure.graph_net.PeriodicGraph method) splice_two_connected_nodes() (in module mofstructure.generate_cgd)

T

to_cgd() (in module mofstructure.graph_net) TopologyExtractor (class in mofstructure.generate_cgd) transformed() (mofstructure.graph_net.PeriodicGraph method)

transition_metals() (in module mofstructure.mofdeconstructor) translated() (mofstructure.graph_net.PeriodicGraph method) translation_lattice() (mofstructure.graph_net.PeriodicGraph method)

U

UnstableNetError

W

wrap_systems_in_unit_cell() (in module mofstructure.mofdeconstructor)

write_cgd() (mofstructure.generate_cgd.TopologyExtractor static method)

Z

zeo_calculation() (in module mofstructure.porosity)

zeolite_t_edges() (in module mofstructure.generate_cgd) ZEOLITE_T_ELEMENTS (in module mofstructure.generate_cgd)