Index

A

add_fragment() (cgsmiles.sample.MoleculeSampler method) angle_between() (in module cgsmiles.drawing_utils) angle_of_interest() (in module cgsmiles.drawing_utils) annotate_ez_isomers_cgsmiles() (in module cgsmiles.pysmiles_utils)

annotate_fragments() (in module cgsmiles.graph_utils) assign_angles() (in module cgsmiles.graph_layout_utils) assign_bonds() (in module cgsmiles.graph_layout_utils) assing_dihedral_angles() (in module cgsmiles.graph_layout_utils)

C

cgsmiles module cgsmiles.cgsmiles_utils module cgsmiles.coordinates module cgsmiles.dialects module cgsmiles.drawing module cgsmiles.drawing_utils module cgsmiles.graph_layout module cgsmiles.graph_layout_utils module cgsmiles.graph_utils module cgsmiles.linalg_functions module cgsmiles.pysmiles_utils module

cgsmiles.rdkit module cgsmiles.read_cgsmiles module cgsmiles.read_fragments module cgsmiles.resolve module cgsmiles.sample module cgsmiles.test_utils module cgsmiles.write_cgsmiles module check_and_cast_types() (in module cgsmiles.dialects) check_and_fix_cis_trans() (in module cgsmiles.graph_layout_utils) circular_layout() (in module cgsmiles.graph_layout) collect_ring_number() (in module cgsmiles.read_fragments) compatible() (in module cgsmiles.resolve) compute_mass() (in module cgsmiles.pysmiles_utils) create_dialect() (in module cgsmiles.dialects)

D

dihedral_angle_between() (in module cgsmiles.linalg_functions)

draw_molecule() (in module cgsmiles.drawing)

E

edges_from_bonding_descrpt() (cgsmiles.resolve.MoleculeResolver method)

embed_3d_via_rdkit() (in module cgsmiles.rdkit) embedd_cg_molecule_via_rdkit() (in module cgsmiles.coordinates)

F

find_complementary_bonding_descriptor() (in module cgsmiles.cgsmiles_utils) find_open_bonds() (in module cgsmiles.cgsmiles_utils) find_triplets() (in module cgsmiles.graph_layout_utils) format_bonding() (in module cgsmiles.write_cgsmiles) format_node() (in module cgsmiles.write_cgsmiles)

forward_map_molecule() (in module cgsmiles.coordinates) fragment_iter() (in module cgsmiles.read_fragments) from_fragment_dicts() (cgsmiles.resolve.MoleculeResolver class method) from_fragment_string() (cgsmiles.sample.MoleculeSampler class method) from_graph() (cgsmiles.resolve.MoleculeResolver class method) from_string() (cgsmiles.resolve.MoleculeResolver class method)

M

make_edge() (in module cgsmiles.drawing_utils) make_graph_edges() (in module cgsmiles.drawing_utils) make_mapped_edges() (in module cgsmiles.drawing_utils) make_node_pies() (in module cgsmiles.drawing_utils) match_bonding_descriptors() (in module cgsmiles.resolve) merge_graphs() (in module cgsmiles.graph_utils) module cgsmiles cgsmiles.cgsmiles_utils cgsmiles.coordinates cgsmiles.dialects cgsmiles.drawing cgsmiles.drawing_utils cgsmiles.graph_layout cgsmiles.graph_layout_utils cgsmiles.graph_utils cgsmiles.linalg_functions cgsmiles.pysmiles_utils cgsmiles.rdkit cgsmiles.read_cgsmiles cgsmiles.read_fragments cgsmiles.resolve cgsmiles.sample cgsmiles.test_utils cgsmiles.write_cgsmiles

MoleculeResolver (class in cgsmiles.resolve) MoleculeSampler (class in cgsmiles.sample)

N

networkx_to_rdkit() (in module cgsmiles.rdkit)

P

parse_graph_base_node() (in module cgsmiles.dialects)

peek() (cgsmiles.read_fragments.PeekIter method) PeekIter (class in cgsmiles.read_fragments)

R

rdkit_to_networkx() (in module cgsmiles.rdkit) read_cgsmiles() (in module cgsmiles.read_cgsmiles) read_fragment_cgsmiles() (in module cgsmiles.cgsmiles_utils) read_fragment_smiles() (in module cgsmiles.pysmiles_utils) read_fragment_strings() (cgsmiles.resolve.MoleculeResolver static method) read_fragments() (in module cgsmiles.read_fragments) rebuild_h_atoms() (in module cgsmiles.pysmiles_utils) resolve() (cgsmiles.resolve.MoleculeResolver method)

resolve_all() (cgsmiles.resolve.MoleculeResolver method) resolve_disconnected_molecule() (cgsmiles.resolve.MoleculeResolver method) resolve_iter() (cgsmiles.resolve.MoleculeResolver method) rotate() (in module cgsmiles.linalg_functions) rotate_2D() (in module cgsmiles.drawing_utils) rotate_degrees() (in module cgsmiles.linalg_functions) rotate_subgraph() (in module cgsmiles.graph_layout_utils) rotate_to_axis() (in module cgsmiles.linalg_functions) rotation_from_x_axis() (in module cgsmiles.drawing_utils)

S

sample() (cgsmiles.sample.MoleculeSampler method) set_atom_names_atomistic() (in module cgsmiles.graph_utils)

sort_nodes_by_attr() (in module cgsmiles.graph_utils) squash_atoms() (cgsmiles.resolve.MoleculeResolver method) strip_bonding_descriptors() (in module cgsmiles.read_fragments)

U

u_vect() (in module cgsmiles.linalg_functions)

V

vector_angle_degrees() (in module cgsmiles.linalg_functions)

vespr_layout() (in module cgsmiles.graph_layout) vespr_refined_layout() (in module cgsmiles.graph_layout)

W

write_cgsmiles() (in module cgsmiles.write_cgsmiles) write_cgsmiles_fragments() (in module cgsmiles.write_cgsmiles)

write_cgsmiles_graph() (in module cgsmiles.write_cgsmiles) write_graph() (in module cgsmiles.write_cgsmiles)