feat: better describer and human describer

README.md

@@ -164,6 +164,32 @@ curl -X POST localhost:8000/describe -H 'content-type: application/json' \
 
 OpenAPI docs are served at `http://localhost:8000/docs`.
 
+
+## Human-like description
+
+OpenBlue can generate uncanny human-like description.
+```python
+
+from bluenamer import describe_human
+
+d = describe_human("CN1C=NC2=C1C(=O)N(C(=O)N2C)C")
+print(d.text)
+
+""" Processed SMILES: Cn1cnc2c1c(=O)n(C)c(=O)n2C
+Atom ids in that SMILES: C{0}n{1}1c{2}n{3}c{4}2c{5}1c{6}(=O{7})n{8}(C{13})c{9}(=O{10})n{11}2C{12}
+
+The molecule is named 2,4,7-trimethyl-2,4,7,9-tetraazabicyclo[4.3.0]nona-1(6),8-diene-3,5-dione.
+
+The molecule is built around a 9-membered bicyclic [4.3.0] heteroskeleton.
+Within that parent framework, there is nitrogen at positions 2 (atom id 11), 4 (atom id 8), 7 (atom id 1), and 9 (atom id 3).
+Within that parent framework, there is a double bond between position 1 (atom id 4) and position 6 (atom id 5) and a double bond between position 8 (atom id 2) and position 9 (atom id 3).
+The principal characteristic feature is oxo groups at positions 3 (atom id 9) and 5 (atom id 6).
+Attached to this framework are methyl groups at positions 2 (atom id 11), 4 (atom id 8), and 7 (atom id 1). """
+
+```
+
+
+
 ## Debugging
 
 Token binding metadata is currently available through the assembly decision trace when `include_trace=True`.

src/bluenamer/__init__.py

@@ -2,9 +2,10 @@
 
 from collections.abc import Iterable
 
-from .describer import DescribedComponent, Description, describe
+from .describer import DescribedComponent, Description, DescriptionTokenSummary, describe
 from .engine import DEFAULT_NAMING_ENGINE, NamingEngine, NamingRequest, NamingResult
 from .functional_groups import register_group_detector
+from .human_descriptor import HumanDescription, describe_human
 from .molecule import (
     AtomBinding,
     BondBinding,
@@ -71,7 +72,9 @@ def name_many(
     "DecisionTrace",
     "DescribedComponent",
     "Description",
+    "DescriptionTokenSummary",
     "FunctionalGroupMetadata",
+    "HumanDescription",
     "NameAnalysis",
     "NamingEngine",
     "NamingIntent",
@@ -87,6 +90,7 @@ def name_many(
     "__version__",
     "analyze_smiles",
     "describe",
+    "describe_human",
     "name",
     "name_many",
     "name_smiles",

src/bluenamer/assembler.py

@@ -329,6 +329,12 @@ def post_process_name(name: str) -> str:
     return _post_process_name(name)
 
 
+def post_process_rewrite_rules():
+    """Return shared post-processing rewrites for metadata-aware assembly paths."""
+
+    return (("post_process_name", _post_process_name),)
+
+
 def assemble_name_raw(parts: AssemblyParts) -> str:
     fused_ion_candidate = select_fused_ion_operation(parts)
     if fused_ion_candidate is not None:

src/bluenamer/assembly_parts.py

@@ -21,6 +21,10 @@ class NameTokenBinding:
     bond_ids: set[int] = field(default_factory=set)
     charge_atom_ids: set[int] = field(default_factory=set)
     locants: tuple[str, ...] = ()
+    render_order: int | None = None
+    match_priority: int = 0
+    left_context: str = ""
+    right_context: str = ""
 
 
 @dataclass

src/bluenamer/cli.py

@@ -86,9 +86,9 @@ def _cmd_batch(args: argparse.Namespace) -> int:
 
 
 def _cmd_describe(args: argparse.Namespace) -> int:
-    description = describe_one(args.smiles)
+    description = describe_one(args.smiles, debugging_tokens=args.debug_tokens)
     if args.json:
-        json.dump(description.to_dict(), sys.stdout, indent=2)
+        json.dump(description.to_dict(debugging_tokens=args.debug_tokens), sys.stdout, indent=2)
         sys.stdout.write("\n")
     else:
         sys.stdout.write(str(description) + "\n")
@@ -133,6 +133,7 @@ def _build_parser() -> argparse.ArgumentParser:
     )
     p_describe.add_argument("smiles")
     p_describe.add_argument("--json", action="store_true", help="emit structured Description as JSON")
+    p_describe.add_argument("--debug-tokens", action="store_true", help="include experimental token binding details")
     p_describe.set_defaults(func=_cmd_describe)
 
     return parser

src/bluenamer/component_modifiers.py

@@ -2,7 +2,7 @@
 
 from typing import Literal, Protocol, overload
 
-from .assembly_parts import AssemblyParts, SubstituentItem
+from .assembly_parts import AssemblyParts, NameTokenBinding, SubstituentItem
 from .formatting import strip_outer_parentheses
 from .group_atom_roles import ester_or_peroxy_single_oxygen
 from .locants import parse_locant
@@ -169,6 +169,12 @@ def add_component_n_substituents(
                         branch_exclude,
                         branch_namer,
                     )
+                    emitted_tokens = _with_n_substituent_locant_token(
+                        emitted_tokens,
+                        loc_prefix,
+                        single_n,
+                        bond_ids_within(mol, {single_n, n_sub}),
+                    )
                     if _use_hydrazone_suffix_modifier(parts, principal_key):
                         parts.principal_suffix_modifiers.append(
                             SubstituentItem(
@@ -205,6 +211,30 @@ def _charged_atoms(mol: Molecule, atom_ids: set[int]) -> set[int]:
     return {atom_idx for atom_idx in atom_ids if mol.atoms[atom_idx].charge != 0}
 
 
+def _with_n_substituent_locant_token(
+    emitted_tokens: tuple[NameTokenBinding, ...],
+    locant: str,
+    nitrogen_atom: int,
+    branch_bonds: set[int],
+) -> tuple[NameTokenBinding, ...]:
+    """Bind N-substituent locants to the principal nitrogen atom."""
+
+    locant_token = NameTokenBinding(
+        text=locant,
+        token_kind="locant",
+        source="n_substituent_locant",
+        grammar_role="n_substituent",
+        binding_key="prefix:n_substituent_locant",
+        atom_ids={nitrogen_atom},
+        bond_ids=set(branch_bonds),
+        locants=(locant,),
+    )
+    return (
+        locant_token,
+        *tuple(token for token in emitted_tokens if not (token.token_kind == "locant" and token.text == locant)),
+    )
+
+
 def _nitrogen_substituent_name(
     mol: Molecule,
     nitrogen: int,

src/bluenamer/component_namer.py

@@ -135,6 +135,7 @@ def collect_component_branch_substituents(
     *,
     name_subgraph: SubgraphNamer,
     name_spiro_subgraph: SpiroSubgraphNamer,
+    emit_metadata: bool = True,
 ) -> None:
     """Collect ordinary branch and spiro substituents from the component parent."""
 
@@ -167,16 +168,26 @@ def collect_component_branch_substituents(
 
         for n_idx in n_subs:
             if n_idx not in main_set and n_idx not in principal_involved_atom_ids and n_idx not in handled_prefix_atoms:
-                branch_decisions = DecisionTrace()
-                branch_name, branch_trace, branch_tree = name_subgraph(
-                    mol,
-                    n_idx,
-                    sub_exclude | main_set,
-                    upstream_atom=c_idx,
-                    return_trace=True,
-                    return_tree=True,
-                    decision_trace=branch_decisions,
-                )
+                branch_decisions = DecisionTrace() if emit_metadata else None
+                if emit_metadata:
+                    branch_name, branch_trace, branch_tree = name_subgraph(
+                        mol,
+                        n_idx,
+                        sub_exclude | main_set,
+                        upstream_atom=c_idx,
+                        return_trace=True,
+                        return_tree=True,
+                        decision_trace=branch_decisions,
+                    )
+                else:
+                    branch_name = name_subgraph(
+                        mol,
+                        n_idx,
+                        sub_exclude | main_set,
+                        upstream_atom=c_idx,
+                    )
+                    branch_trace = []
+                    branch_tree = None
                 if branch_name:
                     branch_exclude = sub_exclude | main_set
                     branch_atoms = subgraph_component(mol, n_idx, branch_exclude)
@@ -187,18 +198,22 @@ def collect_component_branch_substituents(
                             atom_ids=branch_atoms,
                             bond_ids=bond_ids_within(mol, branch_atoms | {c_idx}),
                             charge_atom_ids=_charged_atoms(mol, branch_atoms),
-                            emitted_tokens=graph_bound_substituent_tokens(
-                                mol,
-                                n_idx,
-                                branch_atoms,
-                                branch_name,
-                                c_idx,
-                                branch_exclude,
-                                name_subgraph,
+                            emitted_tokens=(
+                                graph_bound_substituent_tokens(
+                                    mol,
+                                    n_idx,
+                                    branch_atoms,
+                                    branch_name,
+                                    c_idx,
+                                    branch_exclude,
+                                    name_subgraph,
+                                )
+                                if emit_metadata
+                                else ()
                             ),
-                            trace_segments=branch_trace,
-                            nested_decisions=decision_trace_data(branch_decisions),
-                            substituent_tree=branch_tree,
+                            trace_segments=branch_trace if emit_metadata else [],
+                            nested_decisions=decision_trace_data(branch_decisions) if emit_metadata else [],
+                            substituent_tree=branch_tree if emit_metadata else None,
                         )
                     )
 
@@ -241,9 +256,12 @@ def _shortcut_component_result(
     stage: str,
     role: str,
     bindings: list[NameAtomBinding] | tuple[NameAtomBinding, ...] | None = None,
+    emit_metadata: bool = True,
 ) -> tuple[str, list[dict], list[dict], list[dict]]:
     """Build audited metadata for a component shortcut name."""
 
+    if not emit_metadata:
+        return name, [], [], []
     parts = AssemblyParts(parent_length=max(1, len(component_atoms)), parent_atom_ids=set(component_atoms))
     parts.name_atom_bindings = (
         list(bindings)
@@ -280,6 +298,8 @@ def name_component(
 ):
     """Name one connected component or recursive component of a molecule."""
 
+    emit_metadata = return_trace or return_tree or decision_trace is not None
+
     single_atom_name = single_atom_component_name(mol, component_atoms)
     if single_atom_name:
         name, bindings, token_spans, rewrite_history = _shortcut_component_result(
@@ -288,6 +308,7 @@ def name_component(
             single_atom_name,
             stage="shortcut",
             role="single_atom_component",
+            emit_metadata=emit_metadata,
         )
         trace_decision(
             decision_trace,
@@ -329,6 +350,7 @@ def name_component_again(next_mol: Molecule, next_atoms: set[int], is_substituen
             stage="shortcut",
             role=structural_parent_result.role,
             bindings=structural_parent_result.bindings,
+            emit_metadata=emit_metadata,
         )
         trace_decision(
             decision_trace,
@@ -382,6 +404,7 @@ def name_component_again(next_mol: Molecule, next_atoms: set[int], is_substituen
             stage="shortcut",
             role="anhydride_component",
             bindings=anhydride_result.bindings,
+            emit_metadata=emit_metadata,
         )
         trace_decision(
             decision_trace,
@@ -492,6 +515,7 @@ def name_component_again(next_mol: Molecule, next_atoms: set[int], is_substituen
         state.sub_exclude,
         name_subgraph=name_subgraph,
         name_spiro_subgraph=name_spiro_subgraph,
+        emit_metadata=emit_metadata,
     )
     retained_fused = production_retained_fused_parent(
         mol,
@@ -572,10 +596,11 @@ def name_component_again(next_mol: Molecule, next_atoms: set[int], is_substituen
     refresh_name_atom_bindings(parts)
     parts.stereo_audit_issues = list(audit_stereochemistry(mol, parts).issues)
     assert_component_fully_named(mol, state.component_atoms, parts, "<component>")
-    name = assemble_parent_name(mol, parts, numbered_path, get_loc)
-    final_result = NameAssemblyResult.from_final_name(name, parts.name_atom_bindings)
-    parts.name_token_spans = token_span_trace_data(final_result)
-    assert_final_name_assembly(mol, state.component_atoms, parts, final_result)
+    name = assemble_parent_name(mol, parts, numbered_path, get_loc, emit_metadata=emit_metadata)
+    if emit_metadata:
+        final_result = NameAssemblyResult.from_final_name(name, parts.name_atom_bindings)
+        parts.name_token_spans = token_span_trace_data(final_result)
+        assert_final_name_assembly(mol, state.component_atoms, parts, final_result)
     trace_decision(
         decision_trace,
         TracePhase.ASSEMBLY,