chemical_order: list
ring_type_dispatch: dict
functional_groups: dict
atom_identifier: atom_identifier
light_atoms: set

get_rings(self): 

LLM Docstring

Use RDKit cycle perception on a carbon-labeled graph with dummy coordinates.

• :returns: list

  A list of ordered ring vertex sequences.

categorize_ring(self, ring): 

LLM Docstring

Match a ring and its external valencies against known ring templates, accounting for cyclic rotations.

• ring: object

  Ordered atom indices forming the ring to categorize.

• :returns: object

  A pair (ring_category, ordered_ring_indices).

match_functional_group(self, root, neighbor_lists, cache=None): 

LLM Docstring

Test a root atom’s nested neighbor pattern against known functional-group templates with optional caching.

• root: object

  Starting node; None is passed through, while dev.default selects the first child where implemented.

• neighbor_lists: object

  Observed nested neighbor patterns.

• cache: object

  Optional dictionary caching functional-group matches.

• :returns: object

  A (group_name, matched_pattern) pair, or None.

find_functional_groups(self): 

LLM Docstring

Locate known functional groups and collect the atom indices consumed by each matched pattern.

• :returns: object

  A list of [group_name, atom_indices] records.

get_label_types(self, label_constructor=None, use_ring_identifiers=True, use_functional_group_identifiers=True): 

LLM Docstring

Generate structured chemical identifiers for every node using optional ring and functional-group annotations.

• label_constructor: object

  The value supplied for label_constructor, interpreted according to the algorithm described above.

• use_ring_identifiers: object

  Whether ring categories are included in atom identifiers.

• use_functional_group_identifiers: object

  Whether functional-group names are included in atom identifiers.

• :returns: object

  One atom_identifier per graph node.

get_heavy_atom_framework_graph(self, heavy_atoms=None, light_atoms=None, included_atoms=None): 

LLM Docstring

Extract a subgraph containing selected heavy atoms and return its original node indices.

• heavy_atoms: object

  Optional set of element symbols to retain as heavy atoms.

• light_atoms: object

  Element symbols to remove when constructing the heavy-atom framework.

• included_atoms: object

  Additional original indices that should remain in the framework.

• :returns: object

  A pair (subgraph, original_indices).

find_longest_chain(self, rings=None, root=None, use_highest_valencies=True, heavy_atoms=True, light_atoms=None): 

LLM Docstring

Find a longest chain in the heavy-atom framework and map it back to original indices.

• rings: object

  Previously detected cycles, used to avoid recomputation.

• root: object

  Starting node; None is passed through, while dev.default selects the first child where implemented.

• use_highest_valencies: object

  Whether candidate ring cuts are restricted to the most central or highest-valence ring nodes.

• heavy_atoms: object

  Optional set of element symbols to retain as heavy atoms.

• light_atoms: object

  Element symbols to remove when constructing the heavy-atom framework.

• :returns: object

  Original atom indices along the selected heavy-atom chain.

segment_by_chains(self, root=None, rings=None, use_highest_valencies=True, heavy_atoms=True, light_atoms=None, backbone=None, validate=True): 

LLM Docstring

Segment the heavy-atom framework into chains and restore original atom indices.

• root: object

  Starting node; None is passed through, while dev.default selects the first child where implemented.

• rings: object

  Previously detected cycles, used to avoid recomputation.

• use_highest_valencies: object

  Whether candidate ring cuts are restricted to the most central or highest-valence ring nodes.

• heavy_atoms: object

  Optional set of element symbols to retain as heavy atoms.

• light_atoms: object

  Element symbols to remove when constructing the heavy-atom framework.

• backbone: object

  Optional preselected backbone chain.

• validate: object

  Whether to run duplicate and attachment consistency checks.

• :returns: object

  Nested node-index groups describing the resulting graph decomposition.