Module doc

Expand description

Declarative document — plan (pass 1) + paint (pass 2) + scheme compose.

Wire types live in [spec] (opts cascade + DepictSpec collocated). Hosts call plan_edge → process the EdgePlan with RDKit → render_doc with the EdgeResult → compose_scheme for reaction schemes. No RDKit in this module.

Structs§

AlignToSpec: Object form of document align_to (template ref + EdgePlan-style opts).
CommonOpts: Universal cascading keys (any node kind).
DocPaint: One painted molecule from render_doc (pass 2).
EdgeNode: Edge node — a reaction / network link between mol ids.
ForTypesPatch: Multi-kind patch: { "for_types": ["mol","group"], …common opts }.
LabelLanes: Lane bag: { "above": [...], "below": [...], "left": [...], "right": [...] }.
LabelPlacement: Placed label: { "id": "adh", "pos": "below" } (pos optional → above).
LayoutOpts: Layout for DepictSpec::ReactionScheme.
MolNode: Mol node — MolOpts fields + non-cascading identity / scores / align.
MolOpts: Mol cascading paint opts — what a mol leaf consumes from the cascade.
ShadeSpec: Per-atom / per-bond colormap scores (+ legacy window fields on the mol).
ShadeStyle: Cascading shade window / LUT (not per-atom scores).
TextNode: Text node — caption / chrome referenced by mols and edges via id.

AlignTo: Document align target: id string or { "ref", "atom_map"?, "min_atoms"? }.
DepictSpec: Declarative document (mol, group, or reaction_scheme root).
EdgeArrow: Arrow head / shaft style for diagram edges.
EdgeNodeKind: Discriminator for edge nodes ("type": "edge").
EdgeRouting: How edge shafts are drawn between nodes.
Label: Unified label: string id, list, placed object, or lane object.
LabelItem: One entry in a label list: bare id or { id, pos? }.
LabelPos: Side of an edge shaft (or mol caption) for a label placement.
LayoutAlgorithm: Placement algorithm for scheme layout.
LayoutDirection: Flow axis for scheme layout.
MolIds: One or more mol ids (reactants / products).
MolNodeKind: Discriminator for mol nodes ("type": "mol").
Node: Document node: mol, edge, or text.
NodeType: Document node kinds opts may target (matches wire "type" discriminants).
Opts: Cascade bag: singleton patch or list of patches.
OptsPatch: One cascade rule. Untagged order: typed → for_types → universal.
TextNodeKind: Discriminator for text nodes ("type": "text").
TypedOptsPatch: Discriminated opts patch: { "type": "mol"|"group"|"reaction_scheme"|"edge"|"text", …opts }.

apply_star_labels: Apply star_labels onto * atoms in layout encounter order.
assign_mol_ids: Assign stable unique ids (user id or m_<i>) in document order.
compose_scheme: Compose a DepictSpec::ReactionScheme from per-mol DocPaint rows.
plan_edge: Pass 1: build an EdgePlan for every mol that needs host coord gen.
render_doc: Pass 2: stitch host EdgeResult coords onto the document and paint.
resolve_mol_opts: Apply a chain of opts bags (ancestor → … → leaf) for a mol.
validate_edges: Ensure edge endpoints and label refs resolve to the right node kinds.