asciichem 0.31.1 → 0.31.3

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data/CHANGELOG.md

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 All notable changes to AsciiChem are documented here.
 This project follows [Semantic Versioning](https://semver.org/).
 
+## [0.31.3] - 2026-10-20
+
+### Added
+- Perception in the shared corpus (TODO.v2/13 item 2, slice C):
+  implicit hydrogens order aromatic bonds at 1.5 (Hückel) and declare
+  a value only when a default valence fits integrally — so
+  `c1ccccc1` and `C1=CC=CC=C1` perceive identically, and
+  aromatic-schematic fusion atoms decline rather than invent. Gated
+  by `fixtures/perception.json` in all three implementations.
+- Structured condition entries (item 4, slice 1):
+  `Conditions#entries` derives typed `cat:`/`solv:`/`reag:` entries
+  (semicolon-separated) from the verbatim bracket text; free text and
+  unknown prefixes stay lossless, and the wire form is unchanged.
+  `ReactionRoles` prefers explicit roles over the above/below
+  heuristic.
+- Reaction stoichiometry as model data (slice 2):
+  `Reaction#stoichiometry` and `Molecule#stoichiometric_coefficient`
+  — one coefficient rule shared by the reaction, `BalanceCheck`, and
+  composition counting.
+- Mechanism step graph (slice 4a): `MechanismGraph.for` derives
+  parsed steps, catalysts (species on both sides), and inter-step
+  links from the verbatim `mechanism{}` entries.
+- Reaction identity via RInChI (slice 4b): `Rxn::Writer` emits MDL
+  RXN V2000 and `Rinchi::BinaryEngine` wraps the opt-in `rinchi-1`
+  binary (install guidance, `EngineMissingError`, nothing vendored).
+- Molfile stereo (L3 slice 6): `Atom#chirality` crosses as MDL atom
+  parity and stated hydrogens as the H-count field, so the identity
+  pipe derives stereoisomer-distinct InChIs; `IdentityCrossCheck`
+  covers stereo-layer mismatches.
+
+### Fixed
+- SMILES writer ring-closure emission (#103): a closure-bearing
+  child continues the chain, so the digit lands at the end of the
+  traversal — `parse(write(parse(s))) == parse(s)` and writer
+  stability now hold for ring structures such as `C1=CCC(C)C(C)C1`.
+- SMILES writer rendered stated zero hydrogens as a bare `H` (one);
+  it now emits `H0`.
+
+## [0.31.2] - 2026-10-20
+
+### Added
+- `Reaction#stoichiometry` (TODO.v2/13 item 4, slice 2): the
+  coefficients are already model data; the reaction now exposes them
+  normalized — per side, coefficient-free canonical species text to
+  integer (absent coefficient = 1, duplicate species sum). Pure
+  model read; wire format unchanged.
+- OPSIN source adapter (item 3): name-to-structure derivation via
+  the OPSIN service, feeding the resolver pipeline
+  (`AsciiChem::Resolver::Opsin`).
+- Reaction role hints (item 4, slice A): `ReactionRoles.roles_for`
+  classifies conditions into catalyst/solvent/reagent hints per the
+  above/below-arrow convention.
+- The perception pass (item 2): `AsciiChem::Perception` derives
+  implicit hydrogens and aromatic rings as pure model services; the
+  ValenceCheck linter consumes it.
+- Differential conformance harness (item 5): 300 seeded generated
+  cases shared through asciichem-tests (`corpus/generated/models.json`),
+  exercised by the Ruby property suite and by TS/PY gates.
+
 ## [0.31.1] - 2026-10-20
 
 ### Changed

data/lib/asciichem/engine/parg/asciichem.json

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Captured with the marker.","group":"Bracket group: ( ... ) [ ... ] { ... } with optional multiplicity.","group_unit":"Inside a group: reactions, molecules, electron configs, embedded\nmath and quoted text recurse (DSL group_node set).","hydrogen_atom":"Hydrogen: bare digits after H are subscripts (H cannot ring-\nclose), but H must not steal the H of He, Hf...","atom_suffix":"Suffix markers consume `_` / `^` but capture marker + value\n(AtomBuilder strips the marker).","charge":"Charges: 2+, +2, 2 (bare digits fall through to the same capture).","oxidation_state":"Oxidation state: (IV), (II)...","lewis_prefix":"Lewis markers: leading colons = lone pairs; trailing dots =\nradical electrons.","atom_annotation":"Atom annotations, DSL order: coordinates, parity, multiplicity,\ntitle, fractional coordinates.","bond":"Bonds capture under their kind name (transform contract), longest\nfirst so `##` beats `#`; `->` is reserved for reactions.","crystal":"crystal[Name](a=X,b=Y,sg=SG){atoms with @f(x,y,z)}","spectrum":"spectrum[type](params){peak data}","calculation":"calc(method/basis){key: value units}","zmatrix":"zmatrix{lines}","mechanism":"mechanism{steps}","electron_config":"`1s2 2s2 2p6` — at least two orbital terms (DSL repeat(2)).","embedded_math":"Backtick-delimited Plurimath/AsciiMath source (delimiters stripped\nby the transform).","annotated_molecule":"Free-form text uses \"...\" delimiters, matching AsciiMath; the\ncapture includes the quotes (TextNormaliser strips them).\n@name(\"aspirin\") @cas(\"50-78-2\") @meta(\"k\",\"v\") — the annotation\nvocabulary rides the molecule.","metadata_annotation":"Two quoted args, comma-separated; keys distinguish metadata from\nregular annotations.","simple_annotation":"Known types (name, inchi, ...) handled specially by the transform;\nany other lowercase word becomes a property."},"source":"grammar AsciiChemCore version \"0.3.1\" {\n  ## The AsciiChem syntax — full grammar, DSL-shaped captures\n  ## (P1b, asciichem-ruby#96). Capture names and nesting mirror\n  ## GrammarRules exactly so the PARG tree adapts to the same shape\n  ## TransformRules consumes: sequence captures merge into one hash\n  ## (parens to attach `as`), repetitions stay arrays, unwrapped\n  ## rules let their captures ride into the parent context. Absent\n  ## optionals omit their key (the tree adapter reinstates the ones\n  ## transform patterns require, e.g. group multiplicity). Structural\n  ## rules (molecule/reaction/group/annotated_molecule) are captured\n  ## and the adapter unwraps them: PARG merge semantics for captured\n  ## sequences with embedded repetitions yield arrays, and uncaptured\n  ## sequence rules drop captures non-deterministically in reps\n  ## (parsanol findings).\n  ##\n  ## Language notes (P0 findings): entries reference rules; sequences\n  ## take no trailing capture (wrap in parens); [ ] is the option\n  ## syntax so literal brackets are strings; until is exclusive\n  ## (restate the closer); strict PEG — no repetition backtracking.\n\n  entry formula: formula\n\n  ## spaces? >> nodes.as(:formula) >> spaces?\n  formula = [ 1*( ws ) ] ( formula_node 0*( [ 1*( ws ) ] formula_node ) ) as formula [ 1*( ws ) ]\n\n  ws = ( \" \" / %x09 / %x0A / %x0D )\n\n  ## Top-level nodes, DSL ordered-choice order (cascade before plain\n  ## reaction, annotations before bare molecule).\n  formula_node = cascade / reaction / electron_config / crystal / spectrum / calculation / zmatrix / mechanism / annotated_molecule / molecule / embedded_math / ( \"\\\"\" until \"\\\"\" \"\\\"\" ) as text_run\n\n  # -- reactions ---------------------------------------------------------\n\n  ## Two or more chained reactions: the transform promotes the chain\n  ## to a ReactionCascade (first leg + arrow/products segments).\n  cascade = ( ( reaction ) as first ( 1*( cascade_segment ) ) as segments ) as cascade\n\n  cascade_segment = ( arrow [ 1*( ws ) ] ( terms as products ) ) as segment\n\n  ## Reactants, arrow (with optional above/below conditions), products.\n  reaction = ( ( terms as reactants ) arrow [ 1*( ws ) ] ( terms as products ) ) as reaction\n\n  terms = molecule 0*( plus_term )\n\n  plus_term = ( [ 1*( ws ) ] \"+\" [ 1*( ws ) ] molecule ) as plus_term\n\n  ## arrow.as(:arrow) {kind, above?, below?} — leading spaces ride the\n  ## arrow, conditions attach with no gap.\n  arrow = ( [ 1*( ws ) ] ( arrow_kind ) as kind [ condition as above ] [ condition as below ] ) as arrow\n\n  arrow_kind = ( \"<=>\" / \"<->\" / \"->\" / \"<-\" )\n\n  condition = ( \"[\" ( until \"]\" ) as text ( \"]\" ) as condition_close ) as condition\n\n  ## A molecule: stereochemistry prefix, optional coefficient, units.\n  molecule = ( [ stereo_prefix ] [ coefficient ] ( 1*( unit / bond ) ) as units ) as molecule\n\n  ## `(R)-` style prefixes; a/b are the alpha/beta shorthand.\n  stereo_prefix = \"(\" ( stereo_letter ) as stereo \")\" \"-\"\n\n  stereo_letter = ( \"alpha\" / \"beta\" / \"R\" / \"S\" / \"E\" / \"Z\" / \"α\" / \"β\" / \"a\" / \"b\" )\n\n  ## Coefficient: digits only when an element or bracket follows (else\n  ## the digits are subscripts/rings). Captured as {value}.\n  coefficient = ( ( 1*(%x30-39) &( \"(\" / \"[\" / \"{\" / %x41-5A ) ) as value ) as coefficient\n\n  ## Units: prefixed (isotope) atoms, bracket groups, hydrogen\n  ## (bare-digit subscripts allowed), plain atoms.\n  unit = prefixed_atom / group / hydrogen_atom / plain_atom\n\n  ## Prefix isotope: ^14C or _14C — the marker binds to the atom, the\n  ## core semantic fix over AsciiMath. Captured with the marker.\n  prefixed_atom = ( [ lewis_prefix ] ( ( \"^\" / \"_\" ) 1*(%x30-39) ) as isotope ( %x41-5A [ %x61-7A ] ) as element atom_suffix [ lewis_radicals ] [ ( 1*(%x30-39) ) as ring_closures ] atom_annotation ) as atom\n\n  ## Bracket group: ( ... ) [ ... ] { ... } with optional multiplicity.\n  group = ( group_open ( 1*( group_unit ) ) as group_nodes group_close [ ( \"_\" 1*(%x30-39) ) as multiplicity ] ) as group\n\n  group_open = ( \"(\" / \"[\" / \"{\" ) as open_bracket\n\n  group_close = ( \")\" / \"]\" / \"}\" ) as close_bracket\n\n  ## Inside a group: reactions, molecules, electron configs, embedded\n  ## math and quoted text recurse (DSL group_node set).\n  group_unit = reaction / electron_config / molecule / group / embedded_math / ( \"\\\"\" until \"\\\"\" \"\\\"\" ) as group_text_run\n\n  ## Hydrogen: bare digits after H are subscripts (H cannot ring-\n  ## close), but H must not steal the H of He, Hf...\n  hydrogen_atom = ( [ lewis_prefix ] ( \"H\" ) as element !( %x61-7A ) [ ( \"_\" subscript_value / 1*(%x30-39) ) as subscript ] [ ( \"^\" superscript_value ) as superscript ] [ lewis_radicals ] atom_annotation ) as atom\n\n  plain_atom = ( [ lewis_prefix ] ( %x41-5A [ %x61-7A ] ) as element atom_suffix [ lewis_radicals ] [ ( 1*(%x30-39) ) as ring_closures ] atom_annotation ) as atom\n\n  ## Suffix markers consume `_` / `^` but capture marker + value\n  ## (AtomBuilder strips the marker).\n  atom_suffix = [ ( \"_\" subscript_value ) as subscript ] [ ( \"^\" superscript_value ) as superscript ]\n\n  subscript_value = ( \"{\" until \"}\" \"}\" ) / 1*(%x30-39)\n\n  superscript_value = ( \"{\" until \"}\" \"}\" ) / ( oxidation_state / charge )\n\n  ## Charges: 2+, +2, 2 (bare digits fall through to the same capture).\n  charge = ( 1*(%x30-39) [ \"+\" / \"-\" ] ) / ( ( \"+\" / \"-\" ) [ 1*(%x30-39) ] )\n\n  ## Oxidation state: (IV), (II)...\n  oxidation_state = \"(\" 1*( %x49 / %x56 / %x58 / %x4C / %x43 / %x44 ) \")\"\n\n  ## Lewis markers: leading colons = lone pairs; trailing dots =\n  ## radical electrons.\n  lewis_prefix = 1*( \":\" ) as lone_pairs\n\n  lewis_radicals = 1*( \".\" ) as radical_electrons\n\n  ## Atom annotations, DSL order: coordinates, parity, multiplicity,\n  ## title, fractional coordinates.\n  atom_annotation = [ coordinate_annotation ] [ parity_annotation ] [ multiplicity_annotation ] [ title_annotation ] [ fractional_annotation ]\n\n  coordinate_annotation = \"@(\" ( float_number ) as x2 \",\" ( float_number ) as y2 [ \",\" ( float_number ) as z2 ] ( \")\" ) as coord_close\n\n  parity_annotation = \"@\" ( \"R\" / \"S\" ) as atom_parity\n\n  multiplicity_annotation = \"@m(\" ( 1*(%x30-39) ) as spin_multiplicity ( \")\" ) as spin_close\n\n  title_annotation = \"@t(\" \"\\\"\" ( until \"\\\"\" ) as atom_title ( \"\\\"\" ) as title_quote ( \")\" ) as title_close\n\n  fractional_annotation = \"@f(\" ( float_number ) as x_fract \",\" ( float_number ) as y_fract \",\" ( float_number ) as z_fract ( \")\" ) as fract_close\n\n  float_number = [ \"-\" ] 1*(%x30-39) [ \".\" 0*(%x30-39) ]\n\n  # -- bonds ---------------------------------------------------------------\n\n  ## Bonds capture under their kind name (transform contract), longest\n  ## first so `##` beats `#`; `->` is reserved for reactions.\n  bond = ( \"##\" as quadruple ) / ( \">-\" as wedge ) / ( \"-<\" as hash ) / ( \"~>\" as dative ) / ( \"~~\" as wavy ) / ( \"#\" as triple ) / ( \"=\" as double ) / ( \"-\" as single )\n\n  # -- beyond-formulas constructs -----------------------------------------\n\n  ## crystal[Name](a=X,b=Y,sg=SG){atoms with @f(x,y,z)}\n  crystal = ( \"crystal\" [ ( \"[\" ( until \"]\" ) as crystal_name ( \"]\" ) as crystal_name_close ) ] [ ( \"(\" ( until \")\" ) as crystal_params ( \")\" ) as crystal_params_close ) ] [ ( \"{\" ( until \"}\" ) as crystal_body ( \"}\" ) as crystal_body_close ) ] ) as crystal_node\n\n  ## spectrum[type](params){peak data}\n  spectrum = ( \"spectrum\" [ ( \"[\" ( until \"]\" ) as spectrum_type ( \"]\" ) as spectrum_type_close ) ] [ ( \"(\" ( until \")\" ) as spectrum_params ( \")\" ) as spectrum_params_close ) ] [ ( \"{\" ( until \"}\" ) as spectrum_body ( \"}\" ) as spectrum_body_close ) ] ) as spectrum_node\n\n  ## calc(method/basis){key: value units}\n  calculation = ( \"calc\" [ ( \"(\" ( until \")\" ) as calc_params ( \")\" ) as calc_params_close ) ] [ ( \"{\" ( until \"}\" ) as calc_body ( \"}\" ) as calc_body_close ) ] ) as calc_node\n\n  ## zmatrix{lines}\n  zmatrix = ( \"zmatrix\" [ ( \"{\" ( until \"}\" ) as zmatrix_body ( \"}\" ) as zmatrix_body_close ) ] ) as zmatrix_node\n\n  ## mechanism{steps}\n  mechanism = ( \"mechanism\" [ ( \"{\" ( until \"}\" ) as mechanism_body ( \"}\" ) as mechanism_body_close ) ] ) as mechanism_node\n\n  # -- electron configuration ----------------------------------------------\n\n  ## `1s2 2s2 2p6` — at least two orbital terms (DSL repeat(2)).\n  electron_config = 2*( orbital \"^\" ( 1*(%x30-39) ) as occupancy [ 1*( ws ) ] ) as electron_config\n\n  orbital = ( 1*(%x30-39) ( \"s\" / \"p\" / \"d\" / \"f\" / \"g\" / \"h\" ) ) as orbital\n\n  # -- embedded math and text ------------------------------------------------\n\n  ## Backtick-delimited Plurimath/AsciiMath source (delimiters stripped\n  ## by the transform).\n  embedded_math = ( \"`\" ( until \"`\" ) as math_source ( \"`\" ) as math_close ) as embedded_math\n\n  ## Free-form text uses \"...\" delimiters, matching AsciiMath; the\n  ## capture includes the quotes (TextNormaliser strips them).\n\n  # -- molecule annotations ---------------------------------------------------\n\n  ## @name(\"aspirin\") @cas(\"50-78-2\") @meta(\"k\",\"v\") — the annotation\n  ## vocabulary rides the molecule.\n  annotated_molecule = ( ( molecule ) as mol ( 1*( annotation_item ) ) as annotations ) as annotated_molecule\n\n  annotation_item = ( [ 1*( ws ) ] ( metadata_annotation / simple_annotation ) ) as annotation_item\n\n  ## Two quoted args, comma-separated; keys distinguish metadata from\n  ## regular annotations.\n  metadata_annotation = \"@meta(\" \"\\\"\" ( until \"\\\"\" ) as meta_key \"\\\"\" \",\" \"\\\"\" ( until \"\\\"\" ) as meta_value ( \"\\\"\" ) as meta_value_close ( \")\" ) as meta_close\n\n  ## Known types (name, inchi, ...) handled specially by the transform;\n  ## any other lowercase word becomes a property.\n  simple_annotation = \"@\" ( ( known_annotation_type / property_name ) as ann_type \"(\" \"\\\"\" ( until \"\\\"\" ) as ann_value ( \"\\\"\" ) as ann_value_close ( \")\" ) as ann_close )\n\n  known_annotation_type = ( \"name\" / \"title\" / \"formula\" / \"label\" / \"inchi\" / \"smiles\" / \"cas\" / \"iupac\" / \"cid\" / \"chebi\" )\n\n  property_name = 1*( %x61-7A )\n\n  test formula {\n    accept \"H_2O\"\n    accept \"H2O\"\n    accept \"Ca^2+\"\n    accept \"SO_4^2-\"\n    accept \"C1-C-C-C-C-C1\"\n    accept \"C12-C-C1-C2\"\n    accept \"CH_3-CH_2-OH\"\n    accept \"2H_2 + O_2 -> 2H_2O\"\n    accept \"N_2 + 3H_2 <=>[Fe][400C] 2NH_3\"\n    accept \"A ->[heat] B ->[cool] C\"\n    accept \"A -> B -> C -> D\"\n    accept \"Ca(OH)_2\"\n    accept \"Fe(IV)\"\n    accept \"_14C\"\n    accept \"^14C\"\n    accept \"CC(=O)OC1=CC=CC=C1C(=O)O\"\n    accept \"Ca^2+ + CO_3^2- -> CaCO_3\"\n    accept \"(R)-CH_3CH(OH)COOH\"\n    accept \":O\"\n    accept \"1s^2 2s^2 2p^6\"\n    accept \"`x^2`\"\n    accept \"\\\"nitrogen gas\\\"\"\n    accept \"crystal[NaCl](a=5.64,sg=Fm-3m){Na@f(0,0,0)}\"\n    accept \"spectrum[nmr](type=1H){1.2: 3H s \\\"CH3\\\"}\"\n    accept \"calc(b3lyp){energy: -234.5}\"\n    accept \"zmatrix{ C1 H2 C1 1.09 }\"\n    accept \"mechanism{ step1: A -> B }\"\n    accept \"H_2O @name(\\\"water\\\") @cas(\\\"7732-18-5\\\")\"\n    accept \"H_2O @meta(\\\"source\\\",\\\"handbook\\\")\"\n    accept \"  H_2O  \"\n    accept \"C@(10,20)@R@m(2)@t(\\\"C1\\\")\"\n    reject \"\"\n    reject \"???\"\n    reject \"H_\"\n    reject \"C(=O\"\n    reject \"+ H_2O\"\n    reject \"crystal[NaCl\"\n    reject \"zmatrix{ C1 \"\n    reject \"@name(\\\"x\\\") H_2O\"\n  }\n}\n","source_hash":"bb8a13d71e196f3294318305cc157f60781c14e212802d6afb27b91d20237d56","compiler_version":"1.3.94","checksum":"sha256:4b042741d854fdd52375ffbb1fc980159855716b3a88b4f4ec6431b546eff343"}
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(shared first bytes; ordered choice is decisive)","rule known_annotation_type: branches 7 and 9 are order-dependent (shared first bytes; ordered choice is decisive)","rule known_annotation_type: branches 7 and 10 are order-dependent (shared first bytes; ordered choice is decisive)","rule known_annotation_type: branches 9 and 10 are order-dependent (shared first bytes; ordered choice is decisive)"]},"default_entry":"formula","render":{},"derive":{},"tests":[],"docs":{"formula":"spaces? >> nodes.as(:formula) >> spaces?","formula_node":"Top-level nodes, DSL ordered-choice order (cascade before plain\nreaction, annotations before bare molecule).","cascade":"Two or more chained reactions: the transform promotes the chain\nto a ReactionCascade (first leg + arrow/products segments).","reaction":"Reactants, arrow (with optional above/below conditions), products.","arrow":"arrow.as(:arrow) {kind, above?, below?} — leading spaces ride the\narrow, conditions attach with no gap.","molecule":"A molecule: stereochemistry prefix, optional coefficient, units.","stereo_prefix":"`(R)-` style prefixes; a/b are the alpha/beta shorthand.","coefficient":"Coefficient: digits only when an element or bracket follows (else\nthe digits are subscripts/rings). 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Captured with the marker.","group":"Bracket group: ( ... ) [ ... ] { ... } with optional multiplicity.","group_unit":"Inside a group: reactions, molecules, electron configs, embedded\nmath and quoted text recurse (DSL group_node set).","hydrogen_atom":"Hydrogen: bare digits after H are subscripts (H cannot ring-\nclose), but H must not steal the H of He, Hf...","atom_suffix":"Suffix markers consume `_` / `^` but capture marker + value\n(AtomBuilder strips the marker).","charge":"Charges: 2+, +2, 2 (bare digits fall through to the same capture).","oxidation_state":"Oxidation state: (IV), (II)...","lewis_prefix":"Lewis markers: leading colons = lone pairs; trailing dots =\nradical electrons.","atom_annotation":"Atom annotations, DSL order: coordinates, parity, multiplicity,\ntitle, fractional coordinates.","chirality_annotation":"Tetrahedral parity classes (SMILES @/@@ semantics, spelled\nexplicitly beside the CIP @R/@S label).","bond":"Bonds capture under their kind name (transform contract), longest\nfirst so `##` beats `#`; `->` is reserved for reactions.","crystal":"crystal[Name](a=X,b=Y,sg=SG){atoms with @f(x,y,z)}","spectrum":"spectrum[type](params){peak data}","calculation":"calc(method/basis){key: value units}","zmatrix":"zmatrix{lines}","mechanism":"mechanism{steps}","electron_config":"`1s2 2s2 2p6` — at least two orbital terms (DSL repeat(2)).","embedded_math":"Backtick-delimited Plurimath/AsciiMath source (delimiters stripped\nby the transform).","annotated_molecule":"Free-form text uses \"...\" delimiters, matching AsciiMath; the\ncapture includes the quotes (TextNormaliser strips them).\n@name(\"aspirin\") @cas(\"50-78-2\") @meta(\"k\",\"v\") — the annotation\nvocabulary rides the molecule.","metadata_annotation":"Two quoted args, comma-separated; keys distinguish metadata from\nregular annotations.","simple_annotation":"Known types (name, inchi, ...) handled specially by the transform;\nany other lowercase word becomes a property."},"source":"grammar AsciiChemCore version \"0.4.0\" {\n  ## The AsciiChem syntax — full grammar, DSL-shaped captures\n  ## (P1b, asciichem-ruby#96). Capture names and nesting mirror\n  ## GrammarRules exactly so the PARG tree adapts to the same shape\n  ## TransformRules consumes: sequence captures merge into one hash\n  ## (parens to attach `as`), repetitions stay arrays, unwrapped\n  ## rules let their captures ride into the parent context. Absent\n  ## optionals omit their key (the tree adapter reinstates the ones\n  ## transform patterns require, e.g. group multiplicity). Structural\n  ## rules (molecule/reaction/group/annotated_molecule) are captured\n  ## and the adapter unwraps them: PARG merge semantics for captured\n  ## sequences with embedded repetitions yield arrays, and uncaptured\n  ## sequence rules drop captures non-deterministically in reps\n  ## (parsanol findings).\n  ##\n  ## Language notes (P0 findings): entries reference rules; sequences\n  ## take no trailing capture (wrap in parens); [ ] is the option\n  ## syntax so literal brackets are strings; until is exclusive\n  ## (restate the closer); strict PEG — no repetition backtracking.\n\n  entry formula: formula\n\n  ## spaces? >> nodes.as(:formula) >> spaces?\n  formula = [ 1*( ws ) ] ( formula_node 0*( [ 1*( ws ) ] formula_node ) ) as formula [ 1*( ws ) ]\n\n  ws = ( \" \" / %x09 / %x0A / %x0D )\n\n  ## Top-level nodes, DSL ordered-choice order (cascade before plain\n  ## reaction, annotations before bare molecule).\n  formula_node = cascade / reaction / electron_config / crystal / spectrum / calculation / zmatrix / mechanism / annotated_molecule / molecule / embedded_math / ( \"\\\"\" until \"\\\"\" \"\\\"\" ) as text_run\n\n  # -- reactions ---------------------------------------------------------\n\n  ## Two or more chained reactions: the transform promotes the chain\n  ## to a ReactionCascade (first leg + arrow/products segments).\n  cascade = ( ( reaction ) as first ( 1*( cascade_segment ) ) as segments ) as cascade\n\n  cascade_segment = ( arrow [ 1*( ws ) ] ( terms as products ) ) as segment\n\n  ## Reactants, arrow (with optional above/below conditions), products.\n  reaction = ( ( terms as reactants ) arrow [ 1*( ws ) ] ( terms as products ) ) as reaction\n\n  terms = molecule 0*( plus_term )\n\n  plus_term = ( [ 1*( ws ) ] \"+\" [ 1*( ws ) ] molecule ) as plus_term\n\n  ## arrow.as(:arrow) {kind, above?, below?} — leading spaces ride the\n  ## arrow, conditions attach with no gap.\n  arrow = ( [ 1*( ws ) ] ( arrow_kind ) as kind [ condition as above ] [ condition as below ] ) as arrow\n\n  arrow_kind = ( \"<=>\" / \"<->\" / \"->\" / \"<-\" )\n\n  condition = ( \"[\" ( until \"]\" ) as text ( \"]\" ) as condition_close ) as condition\n\n  ## A molecule: stereochemistry prefix, optional coefficient, units.\n  molecule = ( [ stereo_prefix ] [ coefficient ] ( 1*( unit / bond ) ) as units ) as molecule\n\n  ## `(R)-` style prefixes; a/b are the alpha/beta shorthand.\n  stereo_prefix = \"(\" ( stereo_letter ) as stereo \")\" \"-\"\n\n  stereo_letter = ( \"alpha\" / \"beta\" / \"R\" / \"S\" / \"E\" / \"Z\" / \"α\" / \"β\" / \"a\" / \"b\" )\n\n  ## Coefficient: digits only when an element or bracket follows (else\n  ## the digits are subscripts/rings). Captured as {value}.\n  coefficient = ( ( 1*(%x30-39) &( \"(\" / \"[\" / \"{\" / %x41-5A ) ) as value ) as coefficient\n\n  ## Units: prefixed (isotope) atoms, bracket groups, hydrogen\n  ## (bare-digit subscripts allowed), plain atoms.\n  unit = prefixed_atom / group / hydrogen_atom / plain_atom\n\n  ## Prefix isotope: ^14C or _14C — the marker binds to the atom, the\n  ## core semantic fix over AsciiMath. Captured with the marker.\n  prefixed_atom = ( [ lewis_prefix ] ( ( \"^\" / \"_\" ) 1*(%x30-39) ) as isotope ( %x41-5A [ %x61-7A ] ) as element atom_suffix [ lewis_radicals ] [ ( 1*(%x30-39) ) as ring_closures ] atom_annotation ) as atom\n\n  ## Bracket group: ( ... ) [ ... ] { ... } with optional multiplicity.\n  group = ( group_open ( 1*( group_unit ) ) as group_nodes group_close [ ( \"_\" 1*(%x30-39) ) as multiplicity ] ) as group\n\n  group_open = ( \"(\" / \"[\" / \"{\" ) as open_bracket\n\n  group_close = ( \")\" / \"]\" / \"}\" ) as close_bracket\n\n  ## Inside a group: reactions, molecules, electron configs, embedded\n  ## math and quoted text recurse (DSL group_node set).\n  group_unit = reaction / electron_config / molecule / group / embedded_math / ( \"\\\"\" until \"\\\"\" \"\\\"\" ) as group_text_run\n\n  ## Hydrogen: bare digits after H are subscripts (H cannot ring-\n  ## close), but H must not steal the H of He, Hf...\n  hydrogen_atom = ( [ lewis_prefix ] ( \"H\" ) as element !( %x61-7A ) [ ( \"_\" subscript_value / 1*(%x30-39) ) as subscript ] [ ( \"^\" superscript_value ) as superscript ] [ lewis_radicals ] atom_annotation ) as atom\n\n  plain_atom = ( [ lewis_prefix ] ( %x41-5A [ %x61-7A ] ) as element atom_suffix [ lewis_radicals ] [ ( 1*(%x30-39) ) as ring_closures ] atom_annotation ) as atom\n\n  ## Suffix markers consume `_` / `^` but capture marker + value\n  ## (AtomBuilder strips the marker).\n  atom_suffix = [ ( \"_\" subscript_value ) as subscript ] [ ( \"^\" superscript_value ) as superscript ]\n\n  subscript_value = ( \"{\" until \"}\" \"}\" ) / 1*(%x30-39)\n\n  superscript_value = ( \"{\" until \"}\" \"}\" ) / ( oxidation_state / charge )\n\n  ## Charges: 2+, +2, 2 (bare digits fall through to the same capture).\n  charge = ( 1*(%x30-39) [ \"+\" / \"-\" ] ) / ( ( \"+\" / \"-\" ) [ 1*(%x30-39) ] )\n\n  ## Oxidation state: (IV), (II)...\n  oxidation_state = \"(\" 1*( %x49 / %x56 / %x58 / %x4C / %x43 / %x44 ) \")\"\n\n  ## Lewis markers: leading colons = lone pairs; trailing dots =\n  ## radical electrons.\n  lewis_prefix = 1*( \":\" ) as lone_pairs\n\n  lewis_radicals = 1*( \".\" ) as radical_electrons\n\n  ## Atom annotations, DSL order: coordinates, parity, multiplicity,\n  ## title, fractional coordinates.\n  atom_annotation = [ coordinate_annotation ] [ parity_annotation ] [ chirality_annotation ] [ multiplicity_annotation ] [ title_annotation ] [ fractional_annotation ]\n\n  coordinate_annotation = \"@(\" ( float_number ) as x2 \",\" ( float_number ) as y2 [ \",\" ( float_number ) as z2 ] ( \")\" ) as coord_close\n\n  parity_annotation = \"@\" ( \"R\" / \"S\" ) as atom_parity\n\n  ## Tetrahedral parity classes (SMILES @/@@ semantics, spelled\n  ## explicitly beside the CIP @R/@S label).\n  chirality_annotation = \"@\" ( \"TH1\" / \"TH2\" ) as chirality\n\n  multiplicity_annotation = \"@m(\" ( 1*(%x30-39) ) as spin_multiplicity ( \")\" ) as spin_close\n\n  title_annotation = \"@t(\" \"\\\"\" ( until \"\\\"\" ) as atom_title ( \"\\\"\" ) as title_quote ( \")\" ) as title_close\n\n  fractional_annotation = \"@f(\" ( float_number ) as x_fract \",\" ( float_number ) as y_fract \",\" ( float_number ) as z_fract ( \")\" ) as fract_close\n\n  float_number = [ \"-\" ] 1*(%x30-39) [ \".\" 0*(%x30-39) ]\n\n  # -- bonds ---------------------------------------------------------------\n\n  ## Bonds capture under their kind name (transform contract), longest\n  ## first so `##` beats `#`; `->` is reserved for reactions.\n  bond = ( \"/\" as direction_up ) / ( \"\\\\\" as direction_down ) / ( \"##\" as quadruple ) / ( \">-\" as wedge ) / ( \"-<\" as hash ) / ( \"~>\" as dative ) / ( \"~~\" as wavy ) / ( \"#\" as triple ) / ( \"=\" as double ) / ( \"-\" as single )\n\n  # -- beyond-formulas constructs -----------------------------------------\n\n  ## crystal[Name](a=X,b=Y,sg=SG){atoms with @f(x,y,z)}\n  crystal = ( \"crystal\" [ ( \"[\" ( until \"]\" ) as crystal_name ( \"]\" ) as crystal_name_close ) ] [ ( \"(\" ( until \")\" ) as crystal_params ( \")\" ) as crystal_params_close ) ] [ ( \"{\" ( until \"}\" ) as crystal_body ( \"}\" ) as crystal_body_close ) ] ) as crystal_node\n\n  ## spectrum[type](params){peak data}\n  spectrum = ( \"spectrum\" [ ( \"[\" ( until \"]\" ) as spectrum_type ( \"]\" ) as spectrum_type_close ) ] [ ( \"(\" ( until \")\" ) as spectrum_params ( \")\" ) as spectrum_params_close ) ] [ ( \"{\" ( until \"}\" ) as spectrum_body ( \"}\" ) as spectrum_body_close ) ] ) as spectrum_node\n\n  ## calc(method/basis){key: value units}\n  calculation = ( \"calc\" [ ( \"(\" ( until \")\" ) as calc_params ( \")\" ) as calc_params_close ) ] [ ( \"{\" ( until \"}\" ) as calc_body ( \"}\" ) as calc_body_close ) ] ) as calc_node\n\n  ## zmatrix{lines}\n  zmatrix = ( \"zmatrix\" [ ( \"{\" ( until \"}\" ) as zmatrix_body ( \"}\" ) as zmatrix_body_close ) ] ) as zmatrix_node\n\n  ## mechanism{steps}\n  mechanism = ( \"mechanism\" [ ( \"{\" ( until \"}\" ) as mechanism_body ( \"}\" ) as mechanism_body_close ) ] ) as mechanism_node\n\n  # -- electron configuration ----------------------------------------------\n\n  ## `1s2 2s2 2p6` — at least two orbital terms (DSL repeat(2)).\n  electron_config = 2*( orbital \"^\" ( 1*(%x30-39) ) as occupancy [ 1*( ws ) ] ) as electron_config\n\n  orbital = ( 1*(%x30-39) ( \"s\" / \"p\" / \"d\" / \"f\" / \"g\" / \"h\" ) ) as orbital\n\n  # -- embedded math and text ------------------------------------------------\n\n  ## Backtick-delimited Plurimath/AsciiMath source (delimiters stripped\n  ## by the transform).\n  embedded_math = ( \"`\" ( until \"`\" ) as math_source ( \"`\" ) as math_close ) as embedded_math\n\n  ## Free-form text uses \"...\" delimiters, matching AsciiMath; the\n  ## capture includes the quotes (TextNormaliser strips them).\n\n  # -- molecule annotations ---------------------------------------------------\n\n  ## @name(\"aspirin\") @cas(\"50-78-2\") @meta(\"k\",\"v\") — the annotation\n  ## vocabulary rides the molecule.\n  annotated_molecule = ( ( molecule ) as mol ( 1*( annotation_item ) ) as annotations ) as annotated_molecule\n\n  annotation_item = ( [ 1*( ws ) ] ( metadata_annotation / simple_annotation ) ) as annotation_item\n\n  ## Two quoted args, comma-separated; keys distinguish metadata from\n  ## regular annotations.\n  metadata_annotation = \"@meta(\" \"\\\"\" ( until \"\\\"\" ) as meta_key \"\\\"\" \",\" \"\\\"\" ( until \"\\\"\" ) as meta_value ( \"\\\"\" ) as meta_value_close ( \")\" ) as meta_close\n\n  ## Known types (name, inchi, ...) handled specially by the transform;\n  ## any other lowercase word becomes a property.\n  simple_annotation = \"@\" ( ( known_annotation_type / property_name ) as ann_type \"(\" \"\\\"\" ( until \"\\\"\" ) as ann_value ( \"\\\"\" ) as ann_value_close ( \")\" ) as ann_close )\n\n  known_annotation_type = ( \"name\" / \"title\" / \"formula\" / \"label\" / \"inchi\" / \"smiles\" / \"cas\" / \"iupac\" / \"cid\" / \"chebi\" )\n\n  property_name = 1*( %x61-7A )\n\n  test formula {\n    accept \"H_2O\"\n    accept \"H2O\"\n    accept \"Ca^2+\"\n    accept \"SO_4^2-\"\n    accept \"C1-C-C-C-C-C1\"\n    accept \"C12-C-C1-C2\"\n    accept \"CH_3-CH_2-OH\"\n    accept \"2H_2 + O_2 -> 2H_2O\"\n    accept \"N_2 + 3H_2 <=>[Fe][400C] 2NH_3\"\n    accept \"A ->[heat] B ->[cool] C\"\n    accept \"A -> B -> C -> D\"\n    accept \"Ca(OH)_2\"\n    accept \"Fe(IV)\"\n    accept \"_14C\"\n    accept \"^14C\"\n    accept \"CC(=O)OC1=CC=CC=C1C(=O)O\"\n    accept \"Ca^2+ + CO_3^2- -> CaCO_3\"\n    accept \"(R)-CH_3CH(OH)COOH\"\n    accept \":O\"\n    accept \"1s^2 2s^2 2p^6\"\n    accept \"`x^2`\"\n    accept \"\\\"nitrogen gas\\\"\"\n    accept \"crystal[NaCl](a=5.64,sg=Fm-3m){Na@f(0,0,0)}\"\n    accept \"spectrum[nmr](type=1H){1.2: 3H s \\\"CH3\\\"}\"\n    accept \"calc(b3lyp){energy: -234.5}\"\n    accept \"zmatrix{ C1 H2 C1 1.09 }\"\n    accept \"mechanism{ step1: A -> B }\"\n    accept \"H_2O @name(\\\"water\\\") @cas(\\\"7732-18-5\\\")\"\n    accept \"H_2O @meta(\\\"source\\\",\\\"handbook\\\")\"\n    accept \"  H_2O  \"\n    accept \"C@(10,20)@R@m(2)@t(\\\"C1\\\")\"\n    reject \"\"\n    reject \"???\"\n    reject \"H_\"\n    reject \"C(=O\"\n    reject \"+ H_2O\"\n    reject \"crystal[NaCl\"\n    reject \"zmatrix{ C1 \"\n    reject \"@name(\\\"x\\\") H_2O\"\n  }\n}\n","source_hash":"a94cfb4f59936a381e9974e8c141c661e56a25babe46d64b0a288bfd0b4b3e3d","compiler_version":"1.3.94","checksum":"sha256:2891ce4d795e13bdbfe556f50174e2575fa5798f13e8300e402b2a05f68c05e5"}

data/lib/asciichem/engine/parg_engine.rb

@@ -32,7 +32,7 @@ module AsciiChem
     class PargEngine
       # Version the vendored artifact was built from; the load fails
       # loudly on drift so the engine never runs a stale grammar.
-      PARG_GRAMMAR_VERSION = '0.3.1'
+      PARG_GRAMMAR_VERSION = '0.4.0'
 
       ARTIFACT_PATH = File.expand_path('parg/asciichem.json', __dir__)
 

data/lib/asciichem/formatter/text.rb

@@ -64,6 +64,7 @@ module AsciiChem
           parts << "#{coord})"
         end
         parts << "@#{atom.atom_parity}" if atom.atom_parity
+        parts << "@#{atom.chirality}" if atom.chirality
         parts << "@m(#{atom.spin_multiplicity})" if atom.spin_multiplicity
         parts << %(@t("#{atom.atom_title}")) if atom.atom_title
         if atom.x_fract && atom.y_fract && atom.z_fract
@@ -83,6 +84,11 @@ module AsciiChem
       end
 
       def visit_bond(bond)
+        # Directional single bonds spell the direction instead of the
+        # plain dash (the round-trip contract: text re-parses to the
+        # same model).
+        return { up: '/', down: '\\' }.fetch(bond.direction) if bond.direction
+
         bond.ascii
       end
 

data/lib/asciichem/grammar_rules.rb

@@ -263,7 +263,9 @@ module AsciiChem
         #                    by the reaction arrow)
         #   wavy      `~~`  (resonance / delocalised)
         rule(:bond) do
-          str('##').as(:quadruple) |
+          str('/').as(:direction_up) |
+            str('\\').as(:direction_down) |
+            str('##').as(:quadruple) |
             str('>-').as(:wedge) |
             str('-<').as(:hash) |
             str('~>').as(:dative) |
@@ -306,6 +308,7 @@ module AsciiChem
         rule(:atom_annotation) do
           coordinate_annotation.maybe >>
             parity_annotation.maybe >>
+            chirality_annotation.maybe >>
             multiplicity_annotation.maybe >>
             atom_title_annotation.maybe >>
             fractional_annotation.maybe
@@ -315,6 +318,12 @@ module AsciiChem
           str('@') >> (str('R') | str('S')).as(:atom_parity)
         end
 
+        # Tetrahedral parity classes (SMILES @/@@ semantics, spelled
+        # explicitly to stay unambiguous beside the CIP @R/@S label).
+        rule(:chirality_annotation) do
+          str('@') >> (str('TH1') | str('TH2')).as(:chirality)
+        end
+
         rule(:coordinate_annotation) do
           str('@(') >>
             float_number.as(:x2) >> str(',') >>

data/lib/asciichem/linter/balance_check.rb

@@ -51,11 +51,10 @@ module AsciiChem
       end
 
       def count_molecule(molecule)
-        coefficient = molecule.coefficient.to_i
-        coefficient = 1 if coefficient.zero?
         raw = enumerate(molecule, 1)
         return nil if raw.nil?
 
+        coefficient = molecule.stoichiometric_coefficient
         raw.transform_values { |v| v * coefficient }
       end
 

data/lib/asciichem/linter/valence_check.rb

@@ -11,9 +11,11 @@ module AsciiChem
     class ValenceCheck < Base
       register :valence
 
+      # Runs over the perception pass's graph view: every atom's bond
+      # order counts ALL its bonds (rings and branches included — the
+      # linear chain approximation missed both).
       def run(formula)
         diagnostics = []
-        # Walk molecules so we know which atom is the bonding context.
         walk(formula) do |node|
           next unless node.is_a?(AsciiChem::Model::Molecule)
 
@@ -25,34 +27,17 @@ module AsciiChem
       private
 
       def check_molecule(molecule, diagnostics)
-        # Walk the molecule's nodes; pair each atom with the bonds
-        # immediately adjacent to it in the chain.
-        bond_count = 0
-        molecule.children.each do |node|
-          case node
-          when AsciiChem::Model::Bond
-            bond_count += bond_order(node)
-          when AsciiChem::Model::Atom
-            check_atom(node, bond_count, diagnostics)
-            bond_count = 0
-          when AsciiChem::Model::Group
-            # Group's internal bonds aren't visible here; reset.
-            bond_count = 0
-          end
+        atoms, edges = AsciiChem::Structure::Graph.build(molecule)
+        atoms.each_with_index do |atom, index|
+          check_atom(atom, bond_order_sum(index, edges), diagnostics)
         end
       end
 
-      def bond_order(bond)
-        case bond.kind
-        when :single then 1
-        when :double then 2
-        when :triple then 3
-        when :quadruple then 4
-        else 1
-        end
+      def bond_order_sum(index, edges)
+        AsciiChem::Perception.bond_order_sum(index, edges)
       end
 
-      def check_atom(atom, incoming_bond_order, diagnostics)
+      def check_atom(atom, load, diagnostics)
         max = AsciiChem::PeriodicTable.max_valence(atom.element)
         if max.nil?
           diagnostics << info(
@@ -62,30 +47,13 @@ module AsciiChem
           return
         end
 
-        # Approximate: an atom with subscript has multiplicity, not
-        # extra bonds. We use incoming_bond_order + |charge| as the
-        # rough load.
-        charge = atom.charge.to_s
-        charge_value = parse_charge_magnitude(charge)
-        load = incoming_bond_order + charge_value
         return if load <= max
 
         diagnostics << error(
-          "Atom #{atom.element} has load #{load} (bond order #{incoming_bond_order} + charge #{charge_value}); max valence is #{max}",
+          "Atom #{atom.element} has bond order #{load}; max valence is #{max}",
           node: atom
         )
       end
-
-      def parse_charge_magnitude(charge)
-        return 0 if charge.nil? || charge.empty?
-
-        match = charge.match(/\A(?<n>\d*)(?<sign>[+-])\z/) ||
-                charge.match(/\A(?<sign>[+-])(?<n>\d*)\z/)
-        return 0 unless match
-
-        n = match[:n].empty? ? 1 : match[:n].to_i
-        n
-      end
     end
   end
 end