vibesketch.document.formats¶

Import and export: SMILES, MOL, SDF, RXN, CDXML, InChI, names, KET and XYZ.

Import turns a file into molecules (and a reaction, when the format carries one), writes them onto the canvas as KET and derives the document from it, so an imported structure is drawn exactly like a drawn one. An XYZ file, as vibe-view exports one, keeps its coordinates as each species’ 3D structure. Export reads the document: structures keep the coordinates they have on the canvas.

Formats a document cannot be expressed in are refused with the reason, never approximated: an RXN file needs a reaction, PNG of a reaction scheme needs a renderer this version does not have.

Module Attributes

`EXPORT_FORMATS`	the format of every file in the vibe family.
`WHOLE_DOCUMENTS`	Formats that carry a whole document, not just structures.

Functions

`export`(document, fmt, *[, style])	`document` in `fmt`; raises `ExportRefused`.
`format_for_path`(path)	The import format a file name implies; raises `ImportFailed`.
`import_into`(document, data, fmt, *[, mode])	Read `data` and draw it on `document`'s canvas (a new document if `None`).
`read_structures`(data, fmt)	Read structures in `fmt`; raises `ImportFailed`.
`species_mols`(document)	An RDKit molecule per species: with canvas coordinates when drawn.

Classes

`Imported`(molecules, reaction, conditions, ket)
`Payload`(content, media_type, extension)

Exceptions

`ExportRefused`	The document cannot be expressed in the requested format.
`ImportFailed`	The data could not be read in the stated format.

vibesketch.document.formats.EXPORT_FORMATS: tuple[str, ...] = ('qvf', 'vsk', 'ket', 'mol', 'sdf', 'rxn', 'smiles', 'inchi', 'svg', 'png')¶

the format of every file in the vibe family.

Type:: QVF first

exception vibesketch.document.formats.ExportRefused¶

Bases: ValueError

The document cannot be expressed in the requested format.

exception vibesketch.document.formats.ImportFailed¶

Bases: ValueError

The data could not be read in the stated format.

class vibesketch.document.formats.Imported(molecules: 'list[Any]' = <factory>, reaction: 'tuple[list[Any], list[Any], list[Any]] | None' = None, conditions: 'list[str]' = <factory>, ket: 'dict[str, Any] | None' = None)¶

Bases: object

Parameters:

molecules (list[Any])
reaction (tuple[list[Any], list[Any], list[Any]] | None)
conditions (list[str])
ket (dict[str, Any] | None)

molecules: list[Any]¶

reaction: tuple[list[Any], list[Any], list[Any]] | None = None¶

conditions: list[str]¶

ket: dict[str, Any] | None = None¶: A whole canvas (KET or a .vsk’s), used as it is.

class vibesketch.document.formats.Payload(content: 'bytes', media_type: 'str', extension: 'str')¶

Bases: object

Parameters:

content (bytes)
media_type (str)
extension (str)

content: bytes¶

media_type: str¶

extension: str¶

vibesketch.document.formats.export(document, fmt, *, style=None)¶

document in fmt; raises ExportRefused.

Parameters:

document (Document)
fmt (str)
style (str | None)

Return type:

Payload

vibesketch.document.formats.format_for_path(path)¶

The import format a file name implies; raises ImportFailed.

Parameters:: path (str | Path)
Return type:: str

vibesketch.document.formats.import_into(document, data, fmt, *, mode='append')¶

Read data and draw it on document’s canvas (a new document if None).

Parameters:

document (Document | None)
data (str | bytes)
fmt (str)
mode (Literal['append', 'replace'])

Return type:

Derivation

vibesketch.document.formats.read_structures(data, fmt)¶

Read structures in fmt; raises ImportFailed.

Parameters:

data (str | bytes)
fmt (str)

Return type:

Imported

vibesketch.document.formats.species_mols(document)¶

An RDKit molecule per species: with canvas coordinates when drawn.

Parameters:: document (Document)
Return type:: dict[str, Any]