asciichem-model 0.3.2

data/schemas/v1/examples/07-spectrum.yaml

@@ -0,0 +1,18 @@
+# 07 — Spectrum with peaks (negative example files follow in 99-*)
+
+# An NMR record: technique, acquisition parameters, peaks with
+# assignments.
+type: spectrum
+technique: nmr
+params:
+  solvent: CDCl3
+  frequency: "400 MHz"
+peaks:
+  - position: "2.1"
+    intensity: "3H"
+    multiplicity: s
+    assignment: CH3
+  - position: "7.3"
+    intensity: "1H"
+    multiplicity: t
+    assignment: ArH

data/schemas/v1/examples/99-01-negative-atom-bad-element.yaml

@@ -0,0 +1,5 @@
+# NEGATIVE 99-01 — atom with a malformed element symbol.
+# Must FAIL validation against atom.yaml (pattern ^[A-Z][a-z]?$;
+# "HX" has an uppercase second letter, which no element symbol has).
+type: atom
+element: HX

data/schemas/v1/examples/99-02-negative-identifier-bad-convention.yaml

@@ -0,0 +1,5 @@
+# NEGATIVE 99-02 — identifier with an unregistered convention.
+# Must FAIL validation against identifier.yaml (convention enum).
+type: identifier
+value: "xyz"
+convention: smarts

data/schemas/v1/examples/99-03-negative-group-empty.yaml

@@ -0,0 +1,4 @@
+# NEGATIVE 99-03 — group with no children.
+# Must FAIL validation against group.yaml (nodes minItems 1).
+type: group
+nodes: []

data/schemas/v1/formula.yaml

@@ -0,0 +1,30 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/formula"
+title: AsciiChem Formula node (document root)
+description: |
+  The root of a parsed AsciiChem document: an ordered sequence of
+  top-level nodes. This is the canonical wire form every
+  implementation emits under the envelope's `root` key.
+type: object
+required: [type, nodes]
+properties:
+  type:
+    const: formula
+  nodes:
+    type: array
+    description: |
+      Top-level nodes. Items reference the shipped node schemas;
+      node types not yet shipped (electron-configuration,
+      embedded-math, text, name, mechanism, spectrum, crystal,
+      zmatrix, calculation) are TODO.impl/30 and referenced loosely
+      until their schemas land.
+    items:
+      anyOf:
+        - $ref: "atom.yaml"
+        - $ref: "molecule.yaml"
+        - $ref: "group.yaml"
+        - $ref: "reaction.yaml"
+        - $ref: "reaction-cascade.yaml"
+        - $ref: "identifier.yaml"
+additionalProperties: false

data/schemas/v1/group.yaml

@@ -0,0 +1,29 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/group"
+title: AsciiChem Group node
+description: |
+  A bracketed sub-formula with an optional multiplier that applies to
+  the whole group (`(OH)_2`).
+type: object
+required: [type, nodes]
+properties:
+  type:
+    const: group
+  nodes:
+    type: array
+    minItems: 1
+    items:
+      anyOf:
+        - $ref: "atom.yaml"
+        - $ref: "molecule.yaml"
+        - $ref: "group.yaml"
+  multiplicity:
+    type: string
+    pattern: "^\\d+$"
+    description: Multiplier applied to the group ("2" in (OH)_2).
+  bracket:
+    default: paren
+    enum: [paren, square, brace]
+    description: Bracket kind — paren (), square [], brace {}.
+additionalProperties: false

data/schemas/v1/identifier.yaml

@@ -0,0 +1,32 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/identifier"
+title: AsciiChem Identifier node
+description: |
+  A substance identifier with its convention. Maps to CML
+  `<identifier convention="...">`. Format constraints live with the
+  implementations' offline validators; this schema pins the shape and
+  the convention registry.
+type: object
+required: [type, value, convention]
+properties:
+  type:
+    const: identifier
+  value:
+    type: string
+    minLength: 1
+    description: The identifier value (e.g. "50-78-2").
+  convention:
+    enum: [cas, inchi, inchikey, smiles, canonical-smiles, iupac-name, pubchem-cid, chebi]
+    description: The identifier convention registry value.
+  dictRef:
+    type: string
+    description: Optional dictionary reference for CML round-trip.
+additionalProperties: false
+examples:
+  - type: identifier
+    value: "50-78-2"
+    convention: cas
+  - type: identifier
+    value: "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"
+    convention: inchikey

data/schemas/v1/mechanism.yaml

@@ -0,0 +1,30 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/mechanism"
+title: AsciiChem Mechanism node
+description: |
+  A reaction mechanism: labelled reaction steps plus spectator
+  species.
+type: object
+required: [type]
+properties:
+  type:
+    const: mechanism
+  steps:
+    type: array
+    items:
+      type: object
+      required: [reaction]
+      properties:
+        label:
+          type: string
+          description: Step label, e.g. "initiation".
+        reaction:
+          $ref: "reaction.yaml"
+      additionalProperties: false
+  spectators:
+    type: array
+    description: Species present but not transformed.
+    items:
+      $ref: "molecule.yaml"
+additionalProperties: false

data/schemas/v1/molecule.yaml

@@ -0,0 +1,28 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/molecule"
+title: AsciiChem Molecule node
+description: |
+  An ordered sequence of atoms/groups with optional coefficient and
+  attached substance identifiers (CML-level annotations).
+type: object
+required: [type, nodes]
+properties:
+  type:
+    const: molecule
+  nodes:
+    type: array
+    description: Ordered child nodes (atoms, groups, nested molecules).
+    items:
+      $ref: "atom.yaml"
+    minItems: 1
+  coefficient:
+    type: string
+    pattern: "^\\d+$"
+    description: Stoichiometric coefficient ("2" in 2H_2O).
+  identifiers:
+    type: array
+    description: Substance identifiers attached to this molecule.
+    items:
+      $ref: "identifier.yaml"
+additionalProperties: false

data/schemas/v1/name.yaml

@@ -0,0 +1,22 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/name"
+title: AsciiChem Name node
+description: |
+  A molecule name. Maps to CML `<name>`; convention distinguishes
+  IUPAC, CAS, trivial, trade names.
+type: object
+required: [type, content]
+properties:
+  type:
+    const: name
+  content:
+    type: string
+    description: The name text.
+  convention:
+    type: string
+    description: Naming convention (e.g. "iupac", "cas", "trivial").
+  dictRef:
+    type: string
+    description: Optional dictionary reference for CML round-trip.
+additionalProperties: false

data/schemas/v1/provenance.yaml

@@ -0,0 +1,28 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/provenance"
+title: AsciiChem Provenance node
+description: |
+  Where a piece of identity data came from — which source asserted
+  it, when it was retrieved, which source version, and the
+  attribution line licensing requires (e.g. CAS Common Chemistry's
+  CC BY-NC 4.0). Modelled after how the chemicals library attributes
+  databanks and how Relaton models bibliographic retrieval.
+type: object
+required: [type, source, retrievedAt]
+properties:
+  type:
+    const: provenance
+  source:
+    type: string
+    description: Source adapter name (e.g. "pubchem", "commonchemistry").
+  retrievedAt:
+    type: string
+    format: date-time
+  sourceVersion:
+    type: string
+    description: Source release or accessed-date pin where versionless.
+  attribution:
+    type: string
+    description: Attribution string emitted with NC-licensed data.
+additionalProperties: false

data/schemas/v1/reaction-cascade.yaml

@@ -0,0 +1,17 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/reaction-cascade"
+title: AsciiChem ReactionCascade node
+description: |
+  Two or more reactions chained together (A -> B -> C).
+type: object
+required: [type, steps]
+properties:
+  type:
+    const: reaction-cascade
+  steps:
+    type: array
+    minItems: 2
+    items:
+      $ref: "reaction.yaml"
+additionalProperties: false

data/schemas/v1/reaction.yaml

@@ -0,0 +1,34 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/reaction"
+title: AsciiChem Reaction node
+description: |
+  A chemical reaction: reactants, an arrow (with optional conditions
+  above/below), and products.
+type: object
+required: [type, reactants, products]
+properties:
+  type:
+    const: reaction
+  reactants:
+    type: array
+    items:
+      $ref: "molecule.yaml"
+  products:
+    type: array
+    items:
+      $ref: "molecule.yaml"
+  arrow:
+    default: forward
+    enum: [forward, reverse, equilibrium, resonance]
+    description: forward (->), reverse (<-), equilibrium (<=>), resonance (<->).
+  conditions:
+    type: object
+    description: Text carried above/below the arrow.
+    properties:
+      above:
+        type: string
+      below:
+        type: string
+    additionalProperties: false
+additionalProperties: false

data/schemas/v1/spectrum.yaml

@@ -0,0 +1,39 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/spectrum"
+title: AsciiChem Spectrum node
+description: |
+  A spectroscopy record: technique type, acquisition parameters, and
+  peaks.
+type: object
+required: [type]
+properties:
+  type:
+    const: spectrum
+  technique:
+    type: string
+    description: Technique type, e.g. "nmr", "ir", "mass".
+  params:
+    type: object
+    description: Acquisition parameters (solvent, frequency, ...).
+    additionalProperties:
+      type: string
+  peaks:
+    type: array
+    items:
+      type: object
+      required: [position]
+      properties:
+        position:
+          type: string
+          description: Peak position (ppm, cm^-1, m/z, ...).
+        intensity:
+          type: string
+        multiplicity:
+          type: string
+          description: Splitting pattern (s, d, t, q, m).
+        assignment:
+          type: string
+          description: Structural assignment of the peak.
+      additionalProperties: false
+additionalProperties: false

data/schemas/v1/substance-record.yaml

@@ -0,0 +1,57 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/substance-record"
+title: AsciiChem SubstanceRecord node
+description: |
+  The resolved view of a substance produced by a resolver source —
+  shaped after the CAS Common Chemistry detail payload so resolver
+  output maps onto it 1:1. Every identifier and property carries its
+  own provenance.
+type: object
+required: [type, identifiers]
+properties:
+  type:
+    const: substance-record
+  preferredName:
+    type: string
+    description: The source's preferred chemical name.
+  synonyms:
+    type: array
+    items:
+      type: string
+    description: Systematic, common, and trade names.
+  formula:
+    type: string
+    description: Molecular formula as the source states it (e.g. "C9H8O4").
+  molecularWeight:
+    type: number
+    description: Molecular weight in g/mol as the source states it.
+  identifiers:
+    type: array
+    minItems: 1
+    items:
+      type: object
+      required: [identifier, provenance]
+      properties:
+        identifier:
+          $ref: "identifier.yaml"
+        provenance:
+          $ref: "provenance.yaml"
+      additionalProperties: false
+  properties:
+    type: array
+    items:
+      type: object
+      required: [name, value, provenance]
+      properties:
+        name:
+          type: string
+          description: e.g. "boiling point", "melting point", "density".
+        value:
+          type: string
+        units:
+          type: string
+        provenance:
+          $ref: "provenance.yaml"
+      additionalProperties: false
+additionalProperties: false

data/schemas/v1/text.yaml

@@ -0,0 +1,16 @@
+%YAML 1.2
+---
+$id: "https://github.com/asciichem/asciichem-model/v1/text"
+title: AsciiChem Text node
+description: |
+  Free-form text in double quotes (matching AsciiMath convention).
+  Unquoted prose is a parse error by design.
+type: object
+required: [type, content]
+properties:
+  type:
+    const: text
+  content:
+    type: string
+    description: The text content without the quote delimiters.
+additionalProperties: false

data/schemas/v1/types/atom.ts

@@ -0,0 +1,12 @@
+// Generated from schemas/v1/atom.yaml — do not edit; regenerate.
+export interface Atom {
+  readonly type: "atom";
+  readonly element: string;
+  readonly isotope?: string;
+  readonly charge?: string;
+  readonly subscript?: string;
+  readonly oxidationState?: string;
+  readonly lonePairs?: number;
+  readonly radicalElectrons?: number;
+  readonly ringClosures?: string;
+}

data/schemas/v1/types/bond.ts

@@ -0,0 +1,5 @@
+// Generated from schemas/v1/bond.yaml — do not edit; regenerate.
+export interface Bond {
+  readonly type: "bond";
+  readonly kind?: "single" | "double" | "triple" | "quadruple" | "wedge" | "hash" | "dative" | "wavy";
+}

data/schemas/v1/types/calculation.ts

@@ -0,0 +1,13 @@
+// Generated from schemas/v1/calculation.yaml — do not edit; regenerate.
+export interface Calculation {
+  readonly type: "calculation";
+  readonly method?: string;
+  readonly basis?: string;
+  readonly properties?: {
+    title: string;
+    value: string;
+    units?: string;
+    dictRef?: string;
+    convention?: string;
+  }[];
+}

data/schemas/v1/types/crystal.ts

@@ -0,0 +1,13 @@
+// Generated from schemas/v1/crystal.yaml — do not edit; regenerate.
+export interface Crystal {
+  readonly type: "crystal";
+  readonly name?: string;
+  readonly a?: number;
+  readonly b?: number;
+  readonly c?: number;
+  readonly alpha?: number;
+  readonly beta?: number;
+  readonly gamma?: number;
+  readonly spacegroup?: string;
+  readonly atoms?: Atom[];
+}

data/schemas/v1/types/electron-configuration.ts

@@ -0,0 +1,13 @@
+// Generated from schemas/v1/electron-configuration.yaml — do not edit; regenerate.
+export interface ElectronConfiguration {
+  readonly type: "electron-configuration";
+  readonly orbitals: {
+    orbital: string;
+    occupancy: string;
+  }[];
+  readonly termSymbol?: {
+    multiplicity?: string;
+    letter?: string;
+    jValue?: string;
+  };
+}

data/schemas/v1/types/embedded-math.ts

@@ -0,0 +1,5 @@
+// Generated from schemas/v1/embedded-math.yaml — do not edit; regenerate.
+export interface EmbeddedMath {
+  readonly type: "embedded-math";
+  readonly source: string;
+}

data/schemas/v1/types/formula.ts

@@ -0,0 +1,5 @@
+// Generated from schemas/v1/formula.yaml — do not edit; regenerate.
+export interface Formula {
+  readonly type: "formula";
+  readonly nodes: (Atom | Molecule | Group | Reaction | ReactionCascade | Identifier)[];
+}

data/schemas/v1/types/group.ts

@@ -0,0 +1,7 @@
+// Generated from schemas/v1/group.yaml — do not edit; regenerate.
+export interface Group {
+  readonly type: "group";
+  readonly nodes: (Atom | Molecule | Group)[];
+  readonly multiplicity?: string;
+  readonly bracket?: "paren" | "square" | "brace";
+}

data/schemas/v1/types/identifier.ts

@@ -0,0 +1,7 @@
+// Generated from schemas/v1/identifier.yaml — do not edit; regenerate.
+export interface Identifier {
+  readonly type: "identifier";
+  readonly value: string;
+  readonly convention: "cas" | "inchi" | "inchikey" | "smiles" | "canonical-smiles" | "iupac-name" | "pubchem-cid" | "chebi";
+  readonly dictRef?: string;
+}

data/schemas/v1/types/index.ts

@@ -0,0 +1,21 @@
+// Union of every node type in the v1 model.
+export type Node =
+  | Atom
+  | Bond
+  | Calculation
+  | Crystal
+  | ElectronConfiguration
+  | EmbeddedMath
+  | Formula
+  | Group
+  | Identifier
+  | Mechanism
+  | Molecule
+  | Name
+  | Provenance
+  | ReactionCascade
+  | Reaction
+  | Spectrum
+  | SubstanceRecord
+  | Text
+  | ZMatrix;

data/schemas/v1/types/mechanism.ts

@@ -0,0 +1,9 @@
+// Generated from schemas/v1/mechanism.yaml — do not edit; regenerate.
+export interface Mechanism {
+  readonly type: "mechanism";
+  readonly steps?: {
+    label?: string;
+    reaction: Reaction;
+  }[];
+  readonly spectators?: Molecule[];
+}

data/schemas/v1/types/molecule.ts

@@ -0,0 +1,7 @@
+// Generated from schemas/v1/molecule.yaml — do not edit; regenerate.
+export interface Molecule {
+  readonly type: "molecule";
+  readonly nodes: Atom[];
+  readonly coefficient?: string;
+  readonly identifiers?: Identifier[];
+}

data/schemas/v1/types/name.ts

@@ -0,0 +1,7 @@
+// Generated from schemas/v1/name.yaml — do not edit; regenerate.
+export interface Name {
+  readonly type: "name";
+  readonly content: string;
+  readonly convention?: string;
+  readonly dictRef?: string;
+}

data/schemas/v1/types/provenance.ts

@@ -0,0 +1,8 @@
+// Generated from schemas/v1/provenance.yaml — do not edit; regenerate.
+export interface Provenance {
+  readonly type: "provenance";
+  readonly source: string;
+  readonly retrievedAt: string;
+  readonly sourceVersion?: string;
+  readonly attribution?: string;
+}

data/schemas/v1/types/reaction-cascade.ts

@@ -0,0 +1,5 @@
+// Generated from schemas/v1/reaction-cascade.yaml — do not edit; regenerate.
+export interface ReactionCascade {
+  readonly type: "reaction-cascade";
+  readonly steps: Reaction[];
+}

data/schemas/v1/types/reaction.ts

@@ -0,0 +1,11 @@
+// Generated from schemas/v1/reaction.yaml — do not edit; regenerate.
+export interface Reaction {
+  readonly type: "reaction";
+  readonly reactants: Molecule[];
+  readonly products: Molecule[];
+  readonly arrow?: "forward" | "reverse" | "equilibrium" | "resonance";
+  readonly conditions?: {
+    above?: string;
+    below?: string;
+  };
+}

data/schemas/v1/types/spectrum.ts

@@ -0,0 +1,14 @@
+// Generated from schemas/v1/spectrum.yaml — do not edit; regenerate.
+export interface Spectrum {
+  readonly type: "spectrum";
+  readonly technique?: string;
+  readonly params?: {
+
+  };
+  readonly peaks?: {
+    position: string;
+    intensity?: string;
+    multiplicity?: string;
+    assignment?: string;
+  }[];
+}

data/schemas/v1/types/substance-record.ts

@@ -0,0 +1,18 @@
+// Generated from schemas/v1/substance-record.yaml — do not edit; regenerate.
+export interface SubstanceRecord {
+  readonly type: "substance-record";
+  readonly preferredName?: string;
+  readonly synonyms?: string[];
+  readonly formula?: string;
+  readonly molecularWeight?: number;
+  readonly identifiers: {
+    identifier: Identifier;
+    provenance: Provenance;
+  }[];
+  readonly properties?: {
+    name: string;
+    value: string;
+    units?: string;
+    provenance: Provenance;
+  }[];
+}

data/schemas/v1/types/text.ts

@@ -0,0 +1,5 @@
+// Generated from schemas/v1/text.yaml — do not edit; regenerate.
+export interface Text {
+  readonly type: "text";
+  readonly content: string;
+}

data/schemas/v1/types/zmatrix.ts

@@ -0,0 +1,13 @@
+// Generated from schemas/v1/zmatrix.yaml — do not edit; regenerate.
+export interface ZMatrix {
+  readonly type: "zmatrix";
+  readonly rows?: {
+    atom: string;
+    ref1?: string;
+    distance?: string;
+    ref2?: string;
+    angle?: string;
+    ref3?: string;
+    dihedral?: string;
+  }[];
+}