asciichem 0.31.1 → 0.31.2

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Files changed (25) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +21 -0
  3. data/lib/asciichem/engine/parg/asciichem.json +1 -1
  4. data/lib/asciichem/engine/parg_engine.rb +1 -1
  5. data/lib/asciichem/formatter/text.rb +6 -0
  6. data/lib/asciichem/grammar_rules.rb +10 -1
  7. data/lib/asciichem/linter/valence_check.rb +10 -42
  8. data/lib/asciichem/model/atom.rb +4 -1
  9. data/lib/asciichem/model/bond.rb +25 -17
  10. data/lib/asciichem/model/reaction.rb +18 -0
  11. data/lib/asciichem/perception.rb +117 -0
  12. data/lib/asciichem/reaction_roles.rb +43 -0
  13. data/lib/asciichem/resolver/opsin.rb +68 -0
  14. data/lib/asciichem/resolver.rb +1 -0
  15. data/lib/asciichem/smiles/parser.rb +67 -35
  16. data/lib/asciichem/smiles/writer.rb +99 -34
  17. data/lib/asciichem/structure/graph.rb +3 -2
  18. data/lib/asciichem/structure/linearizer.rb +6 -3
  19. data/lib/asciichem/transform_rules.rb +6 -1
  20. data/lib/asciichem/version.rb +1 -1
  21. data/lib/asciichem/wire/core.rb +4 -0
  22. data/lib/asciichem/wire_adapter.rb +8 -4
  23. data/lib/asciichem.rb +2 -0
  24. data/scripts/generate-conformance-cases +57 -0
  25. metadata +5 -1
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data/CHANGELOG.md CHANGED
@@ -3,6 +3,27 @@
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  All notable changes to AsciiChem are documented here.
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  This project follows [Semantic Versioning](https://semver.org/).
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+ ## [0.31.2] - 2026-10-20
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+
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+ ### Added
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+ - `Reaction#stoichiometry` (TODO.v2/13 item 4, slice 2): the
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+ coefficients are already model data; the reaction now exposes them
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+ normalized — per side, coefficient-free canonical species text to
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+ integer (absent coefficient = 1, duplicate species sum). Pure
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+ model read; wire format unchanged.
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+ - OPSIN source adapter (item 3): name-to-structure derivation via
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+ the OPSIN service, feeding the resolver pipeline
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+ (`AsciiChem::Resolver::Opsin`).
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+ - Reaction role hints (item 4, slice A): `ReactionRoles.roles_for`
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+ classifies conditions into catalyst/solvent/reagent hints per the
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+ above/below-arrow convention.
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+ - The perception pass (item 2): `AsciiChem::Perception` derives
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+ implicit hydrogens and aromatic rings as pure model services; the
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+ ValenceCheck linter consumes it.
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+ - Differential conformance harness (item 5): 300 seeded generated
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+ cases shared through asciichem-tests (`corpus/generated/models.json`),
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+ exercised by the Ruby property suite and by TS/PY gates.
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+
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  ## [0.31.1] - 2026-10-20
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  ### Changed
data/lib/asciichem/engine/parg/asciichem.json CHANGED
@@ -1 +1 @@
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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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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 CHANGED
@@ -32,7 +32,7 @@ module AsciiChem
32
32
  class PargEngine
33
33
  # Version the vendored artifact was built from; the load fails
34
34
  # loudly on drift so the engine never runs a stale grammar.
35
- PARG_GRAMMAR_VERSION = '0.3.1'
35
+ PARG_GRAMMAR_VERSION = '0.4.0'
36
36
 
37
37
  ARTIFACT_PATH = File.expand_path('parg/asciichem.json', __dir__)
38
38
 
data/lib/asciichem/formatter/text.rb CHANGED
@@ -64,6 +64,7 @@ module AsciiChem
64
64
  parts << "#{coord})"
65
65
  end
66
66
  parts << "@#{atom.atom_parity}" if atom.atom_parity
67
+ parts << "@#{atom.chirality}" if atom.chirality
67
68
  parts << "@m(#{atom.spin_multiplicity})" if atom.spin_multiplicity
68
69
  parts << %(@t("#{atom.atom_title}")) if atom.atom_title
69
70
  if atom.x_fract && atom.y_fract && atom.z_fract
@@ -83,6 +84,11 @@ module AsciiChem
83
84
  end
84
85
 
85
86
  def visit_bond(bond)
87
+ # Directional single bonds spell the direction instead of the
88
+ # plain dash (the round-trip contract: text re-parses to the
89
+ # same model).
90
+ return { up: '/', down: '\\' }.fetch(bond.direction) if bond.direction
91
+
86
92
  bond.ascii
87
93
  end
88
94
 
data/lib/asciichem/grammar_rules.rb CHANGED
@@ -263,7 +263,9 @@ module AsciiChem
263
263
  # by the reaction arrow)
264
264
  # wavy `~~` (resonance / delocalised)
265
265
  rule(:bond) do
266
- str('##').as(:quadruple) |
266
+ str('/').as(:direction_up) |
267
+ str('\\').as(:direction_down) |
268
+ str('##').as(:quadruple) |
267
269
  str('>-').as(:wedge) |
268
270
  str('-<').as(:hash) |
269
271
  str('~>').as(:dative) |
@@ -306,6 +308,7 @@ module AsciiChem
306
308
  rule(:atom_annotation) do
307
309
  coordinate_annotation.maybe >>
308
310
  parity_annotation.maybe >>
311
+ chirality_annotation.maybe >>
309
312
  multiplicity_annotation.maybe >>
310
313
  atom_title_annotation.maybe >>
311
314
  fractional_annotation.maybe
@@ -315,6 +318,12 @@ module AsciiChem
315
318
  str('@') >> (str('R') | str('S')).as(:atom_parity)
316
319
  end
317
320
 
321
+ # Tetrahedral parity classes (SMILES @/@@ semantics, spelled
322
+ # explicitly to stay unambiguous beside the CIP @R/@S label).
323
+ rule(:chirality_annotation) do
324
+ str('@') >> (str('TH1') | str('TH2')).as(:chirality)
325
+ end
326
+
318
327
  rule(:coordinate_annotation) do
319
328
  str('@(') >>
320
329
  float_number.as(:x2) >> str(',') >>
data/lib/asciichem/linter/valence_check.rb CHANGED
@@ -11,9 +11,11 @@ module AsciiChem
11
11
  class ValenceCheck < Base
12
12
  register :valence
13
13
 
14
+ # Runs over the perception pass's graph view: every atom's bond
15
+ # order counts ALL its bonds (rings and branches included — the
16
+ # linear chain approximation missed both).
14
17
  def run(formula)
15
18
  diagnostics = []
16
- # Walk molecules so we know which atom is the bonding context.
17
19
  walk(formula) do |node|
18
20
  next unless node.is_a?(AsciiChem::Model::Molecule)
19
21
 
@@ -25,34 +27,17 @@ module AsciiChem
25
27
  private
26
28
 
27
29
  def check_molecule(molecule, diagnostics)
28
- # Walk the molecule's nodes; pair each atom with the bonds
29
- # immediately adjacent to it in the chain.
30
- bond_count = 0
31
- molecule.children.each do |node|
32
- case node
33
- when AsciiChem::Model::Bond
34
- bond_count += bond_order(node)
35
- when AsciiChem::Model::Atom
36
- check_atom(node, bond_count, diagnostics)
37
- bond_count = 0
38
- when AsciiChem::Model::Group
39
- # Group's internal bonds aren't visible here; reset.
40
- bond_count = 0
41
- end
30
+ atoms, edges = AsciiChem::Structure::Graph.build(molecule)
31
+ atoms.each_with_index do |atom, index|
32
+ check_atom(atom, bond_order_sum(index, edges), diagnostics)
42
33
  end
43
34
  end
44
35
 
45
- def bond_order(bond)
46
- case bond.kind
47
- when :single then 1
48
- when :double then 2
49
- when :triple then 3
50
- when :quadruple then 4
51
- else 1
52
- end
36
+ def bond_order_sum(index, edges)
37
+ AsciiChem::Perception.bond_order_sum(index, edges)
53
38
  end
54
39
 
55
- def check_atom(atom, incoming_bond_order, diagnostics)
40
+ def check_atom(atom, load, diagnostics)
56
41
  max = AsciiChem::PeriodicTable.max_valence(atom.element)
57
42
  if max.nil?
58
43
  diagnostics << info(
@@ -62,30 +47,13 @@ module AsciiChem
62
47
  return
63
48
  end
64
49
 
65
- # Approximate: an atom with subscript has multiplicity, not
66
- # extra bonds. We use incoming_bond_order + |charge| as the
67
- # rough load.
68
- charge = atom.charge.to_s
69
- charge_value = parse_charge_magnitude(charge)
70
- load = incoming_bond_order + charge_value
71
50
  return if load <= max
72
51
 
73
52
  diagnostics << error(
74
- "Atom #{atom.element} has load #{load} (bond order #{incoming_bond_order} + charge #{charge_value}); max valence is #{max}",
53
+ "Atom #{atom.element} has bond order #{load}; max valence is #{max}",
75
54
  node: atom
76
55
  )
77
56
  end
78
-
79
- def parse_charge_magnitude(charge)
80
- return 0 if charge.nil? || charge.empty?
81
-
82
- match = charge.match(/\A(?<n>\d*)(?<sign>[+-])\z/) ||
83
- charge.match(/\A(?<sign>[+-])(?<n>\d*)\z/)
84
- return 0 unless match
85
-
86
- n = match[:n].empty? ? 1 : match[:n].to_i
87
- n
88
- end
89
57
  end
90
58
  end
91
59
  end
data/lib/asciichem/model/atom.rb CHANGED
@@ -35,7 +35,7 @@ module AsciiChem
35
35
  :charge, :oxidation_state,
36
36
  :lone_pairs, :radical_electrons,
37
37
  :ring_closures, :aromatic, :hydrogens,
38
- :x2, :y2, :z2, :atom_parity,
38
+ :x2, :y2, :z2, :atom_parity, :chirality,
39
39
  :spin_multiplicity, :atom_title,
40
40
  :x_fract, :y_fract, :z_fract
41
41
 
@@ -60,6 +60,7 @@ module AsciiChem
60
60
  lone_pairs: nil, radical_electrons: nil,
61
61
  ring_closures: nil, aromatic: nil, hydrogens: nil,
62
62
  x2: nil, y2: nil, z2: nil, atom_parity: nil,
63
+ chirality: nil,
63
64
  spin_multiplicity: nil, atom_title: nil,
64
65
  x_fract: nil, y_fract: nil, z_fract: nil)
65
66
  @element = element
@@ -77,6 +78,7 @@ module AsciiChem
77
78
  @y2 = y2
78
79
  @z2 = z2
79
80
  @atom_parity = atom_parity
81
+ @chirality = chirality
80
82
  @spin_multiplicity = spin_multiplicity
81
83
  @atom_title = atom_title
82
84
  @x_fract = x_fract
@@ -92,6 +94,7 @@ module AsciiChem
92
94
  ring_closures: ring_closures, aromatic: aromatic,
93
95
  hydrogens: hydrogens,
94
96
  x2: x2, y2: y2, z2: z2, atom_parity: atom_parity,
97
+ chirality: chirality,
95
98
  spin_multiplicity: spin_multiplicity, atom_title: atom_title,
96
99
  x_fract: x_fract, y_fract: y_fract, z_fract: z_fract }
97
100
  end
data/lib/asciichem/model/bond.rb CHANGED
@@ -4,40 +4,48 @@ module AsciiChem
4
4
  module Model
5
5
  # A bond between two adjacent nodes in a structural chain.
6
6
  class Bond < Node
7
- attr_accessor :kind
7
+ attr_accessor :kind, :direction
8
8
 
9
9
  KINDS = {
10
- single: { ascii: "-", mathml_entity: "-" },
11
- double: { ascii: "=", mathml_entity: "=" },
12
- triple: { ascii: "#", mathml_entity: "≡" },
13
- quadruple: { ascii: "##", mathml_entity: "≣" },
14
- wedge: { ascii: ">-", mathml_entity: "↑" },
15
- hash: { ascii: "-<", mathml_entity: "↓" },
16
- dative: { ascii: "~>", mathml_entity: "→" },
17
- wavy: { ascii: "~~", mathml_entity: "∼" },
18
- aromatic: { ascii: ":", mathml_entity: ":" }
10
+ single: { ascii: '-', mathml_entity: '-' },
11
+ double: { ascii: '=', mathml_entity: '=' },
12
+ triple: { ascii: '#', mathml_entity: '≡' },
13
+ quadruple: { ascii: '##', mathml_entity: '≣' },
14
+ wedge: { ascii: '>-', mathml_entity: '↑' },
15
+ hash: { ascii: '-<', mathml_entity: '↓' },
16
+ dative: { ascii: '~>', mathml_entity: '→' },
17
+ wavy: { ascii: '~~', mathml_entity: '∼' },
18
+ aromatic: { ascii: ':', mathml_entity: ':' }
19
19
  }.freeze
20
20
 
21
21
  # CML wire order codes per bond kind. Single source of truth
22
22
  # for both adapter directions — to_canonical emits, from_canonical
23
23
  # parses. Adding a new bond kind = one entry here + one in KINDS.
24
24
  CML_ORDER_CODES = {
25
- single: "S", double: "D", triple: "T",
26
- quadruple: "Q", wedge: "W", hash: "H",
27
- dative: "A", wavy: "V"
25
+ single: 'S', double: 'D', triple: 'T',
26
+ quadruple: 'Q', wedge: 'W', hash: 'H',
27
+ dative: 'A', wavy: 'V'
28
28
  }.freeze
29
29
  KIND_BY_CML_ORDER = CML_ORDER_CODES.invert.freeze
30
30
 
31
31
  # Subset that carries stereo meaning (wedge = out of page,
32
32
  # hash = into page). Used for <bondStereo> elements.
33
- CML_STEREO_CODES = { wedge: "W", hash: "H" }.freeze
33
+ CML_STEREO_CODES = { wedge: 'W', hash: 'H' }.freeze
34
34
 
35
- def initialize(kind: :single)
35
+ def initialize(kind: :single, direction: nil)
36
36
  @kind = kind
37
+ @direction = direction
38
+ end
39
+
40
+ # SMILES directional-bond orientation (`/` up, `\` down) on the
41
+ # single bonds flanking a stereogenic double bond. Orthogonal to
42
+ # the bond kind; only :single carries it.
43
+ def direction
44
+ @direction if kind == :single
37
45
  end
38
46
 
39
47
  def value_attributes
40
- { kind: kind }
48
+ { kind: kind, direction: direction }
41
49
  end
42
50
 
43
51
  def ascii
@@ -49,7 +57,7 @@ module AsciiChem
49
57
  end
50
58
 
51
59
  def cml_order_code
52
- CML_ORDER_CODES.fetch(kind, "S")
60
+ CML_ORDER_CODES.fetch(kind, 'S')
53
61
  end
54
62
 
55
63
  def cml_stereo_code