Index

A

all_ferrocene_metals() (in module mofstructure.mofdeconstructor) angle_tolerance_to_rad() (in module mofstructure.mofdeconstructor) 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) best_component() (mofstructure.systre.SystreTopology method)

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

C

cell (mofstructure.systre.RelaxedComponent attribute) cgd_from_region_targets() (in module mofstructure.generate_cgd) cgd_path (mofstructure.systre.SystreResult attribute) check_planarity() (in module mofstructure.mofdeconstructor) component_atom_images() (in module mofstructure.generate_cgd) component_has_transition_metal_not_in_porphyrin() (in module mofstructure.generate_cgd) component_index (mofstructure.systre.RelaxedComponent attribute) compute_ase_neighbour() (in module mofstructure.mofdeconstructor) compute_ase_neighbour_with_offsets() (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) connected_components() (in module mofstructure.mofdeconstructor) connected_components_iterative() (in module mofstructure.mofdeconstructor) connected_components_recursive() (in module mofstructure.mofdeconstructor) coordination_number (mofstructure.systre.RelaxedComponent attribute) covalent_radius() (in module mofstructure.mofdeconstructor) crystal2_fallback_from_periodic_graph() (in module mofstructure.systre) crystal2_hash() (mofstructure.systre.RelaxedComponent method) (mofstructure.systre.SystreTopology method) crystal2_text() (mofstructure.systre.RelaxedComponent method) (mofstructure.systre.SystreTopology method) crystal2_text_from_component() (in module mofstructure.systre)

D

dfs_iterative() (in module mofstructure.mofdeconstructor)

dfsutil_graph_method() (in module mofstructure.mofdeconstructor) dimension (mofstructure.systre.RelaxedComponent attribute)

E

edge_centers (mofstructure.systre.RelaxedComponent attribute) edges (mofstructure.systre.RelaxedComponent attribute)

extract_relaxed_components() (in module mofstructure.systre) (mofstructure.systre.SystreTopology method)

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_java() (in module mofstructure.systre)

find_key_or_value() (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)

G

get_bond_shift() (in module mofstructure.mofdeconstructor) get_coordination_environment() (in module mofstructure.structure) 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) given_space_group (mofstructure.systre.RelaxedComponent attribute)

H

hashes_for_unnamed_components() (mofstructure.systre.SystreTopology method)

I

ideal_space_group (mofstructure.systre.RelaxedComponent attribute) identify() (mofstructure.systre.SystreTopology method) identify_topology() (in module mofstructure.systre) identify_topology_batch() (in module mofstructure.systre) 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_ferrocene() (in module mofstructure.mofdeconstructor) is_irmof() (in module mofstructure.mofdeconstructor) is_metal() (in module mofstructure.mofdeconstructor) is_mof32() (in module mofstructure.mofdeconstructor) is_named_net (mofstructure.systre.RelaxedComponent property) is_paddlewheel() (in module mofstructure.mofdeconstructor) is_paddlewheel_with_water() (in module mofstructure.mofdeconstructor) is_rodlike() (in module mofstructure.mofdeconstructor) is_uio66() (in module mofstructure.mofdeconstructor)

L

ligands_and_metal_clusters() (in module mofstructure.mofdeconstructor)

longest_list() (in module mofstructure.mofdeconstructor)

M

Main() (in module mofstructure.cof_stacking) main() (in module mofstructure.generate_cgd) (in module mofstructure.systre) 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.mofdeconstructor mofstructure.porosity mofstructure.structure mofstructure.systre

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

N

n_edges (mofstructure.systre.RelaxedComponent property) n_nodes (mofstructure.systre.RelaxedComponent property)

named_components() (mofstructure.systre.SystreTopology method) nodes (mofstructure.systre.RelaxedComponent attribute) normalized_payload() (mofstructure.systre.RelaxedComponent method)

O

obmol_2_rdkit() (in module mofstructure.mofdeconstructor)

P

parse_relaxed_component() (in module mofstructure.systre)

parse_systre_topology() (in module mofstructure.systre)

R

rcsr_name (mofstructure.systre.RelaxedComponent attribute) regions_with_metal() (in module mofstructure.generate_cgd) RelaxedComponent (class in mofstructure.systre) 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) run_systre_on_cgd_path() (in module mofstructure.systre)

S

secondary_building_units() (in module mofstructure.mofdeconstructor) stderr (mofstructure.systre.SystreResult attribute) stdout (mofstructure.systre.SystreResult attribute)

systre_command() (in module mofstructure.systre) SystreResult (class in mofstructure.systre) SystreTopology (class in mofstructure.systre)

T

td10 (mofstructure.systre.RelaxedComponent attribute) topology (mofstructure.systre.SystreResult attribute) topology_hash() (mofstructure.systre.RelaxedComponent method) (mofstructure.systre.SystreTopology method)

topology_key() (mofstructure.systre.RelaxedComponent method) topology_summary() (mofstructure.systre.SystreTopology method) TopologyExtractor (class in mofstructure.generate_cgd) transition_metals() (in module mofstructure.mofdeconstructor)

U

unnamed_components() (mofstructure.systre.SystreTopology method)

W

wrap_systems_in_unit_cell() (in module mofstructure.mofdeconstructor)

write_cgd() (mofstructure.generate_cgd.TopologyExtractor static method) write_crystal2() (mofstructure.systre.SystreTopology method)

Z

zeo_calculation() (in module mofstructure.porosity)