vibesketch.document.ket

The KET bridge: between the canvas engine’s JSON and RDKit molecules.

KET is Ketcher’s document format. Reading goes KET to a molfile to RDKit, so wedge bonds become stereo centres and double-bond geometry becomes E/Z exactly as a molfile reader would see them. KET coordinates have the same orientation as a molfile’s, so no axis flips. Writing goes RDKit to KET with a bond length of 1.0, the length Ketcher draws with.

Anything the reader cannot turn into a well-defined molecule is reported, never guessed: query atoms and bonds, R-groups, polymer brackets and valence errors make a fragment unsupported with the reason.

Module Attributes

BOND_LENGTH

The bond length Ketcher draws with, in KET units.

GAP

Horizontal gap between laid-out items, in bond lengths.

ARROW_MODES

The KET arrow mode that draws each of the document's arrow kinds.

ROW_GAP

Vertical gap between the rows of a scheme, in bond lengths.

Functions

molecule_reason(molecule)

Why a KET molecule cannot be read as a plain structure, or None.

molfile(atoms, bonds)

A molfile for KET atoms and bonds, in their order; callers check molecule_reason() first.

read_scene(ket)

The molecules, arrows, plus signs and text on a KET canvas.

write_scene(molecules, *[, reaction, ...])

A KET document laying molecules out in a row, or a reaction scheme.

Classes

KetArrow(tail, head, mode)

KetFragment(mol, node, centre, bounds[, ...])

One connected molecule on the canvas.

KetScene([fragments, arrows, pluses, texts])

What the canvas holds, in chemical terms.

KetText(text, centre)

SceneStep(tail, head[, reagents, arrow, ...])

One reaction row: the molecules at the arrow's tail and head, and what is at it.
vibesketch.document.ket.ARROW_MODES = {'equilibrium': 'equilibrium-open-angle', 'forward': 'open-angle', 'resonance': 'both-ends-filled-triangle', 'retrosynthetic': 'retrosynthetic'}

The KET arrow mode that draws each of the document’s arrow kinds.

vibesketch.document.ket.BOND_LENGTH = 1.0

The bond length Ketcher draws with, in KET units.

class vibesketch.document.ket.KetArrow(tail: 'tuple[float, float]', head: 'tuple[float, float]', mode: 'str')

Bases: object

Parameters:
tail: tuple[float, float]
head: tuple[float, float]
mode: str
class vibesketch.document.ket.KetFragment(mol, node, centre, bounds, unsupported=None)

Bases: object

One connected molecule on the canvas.

Parameters:
mol: Any

The RDKit molecule with the canvas coordinates, or None if unsupported.

node: str

The KET node it came from, for example mol0.

centre: tuple[float, float]

Centre of its atoms, in KET coordinates.

bounds: tuple[float, float, float, float]

Bounding box (xmin, ymin, xmax, ymax).

unsupported: str | None = None

Why the fragment cannot be used as a species, or None.

class vibesketch.document.ket.KetScene(fragments=<factory>, arrows=<factory>, pluses=<factory>, texts=<factory>)

Bases: object

What the canvas holds, in chemical terms.

Parameters:
fragments: list[KetFragment]
arrows: list[KetArrow]
pluses: list[tuple[float, float]]
texts: list[KetText]
class vibesketch.document.ket.KetText(text: 'str', centre: 'tuple[float, float]')

Bases: object

Parameters:
text: str
centre: tuple[float, float]
class vibesketch.document.ket.SceneStep(tail, head, reagents=<factory>, arrow='forward', conditions=<factory>)

Bases: object

One reaction row: the molecules at the arrow’s tail and head, and what is at it.

Parameters:
tail: list[Any]
head: list[Any]
reagents: list[Any]
arrow: str = 'forward'
conditions: list[str]
vibesketch.document.ket.molecule_reason(molecule)

Why a KET molecule cannot be read as a plain structure, or None.

Parameters:

molecule (dict[str, Any])

Return type:

str | None

vibesketch.document.ket.molfile(atoms, bonds)

A molfile for KET atoms and bonds, in their order; callers check molecule_reason() first.

Parameters:
Return type:

str

vibesketch.document.ket.read_scene(ket)

The molecules, arrows, plus signs and text on a KET canvas.

Parameters:

ket (dict[str, Any])

Return type:

KetScene

vibesketch.document.ket.write_scene(molecules, *, reaction=None, conditions=None, steps=None)

A KET document laying molecules out in a row, or a reaction scheme.

With reaction=(reactants, reagents, products) the row is the reactants joined by plus signs, an arrow with the reagents above it and the conditions below, then the products. With steps each step is such a row, the rows one below the other, a species that takes part in several steps drawn in each, and molecules in a last row.

Parameters:
Return type:

dict[str, Any]