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. CDXML is read and written as a whole drawing by vibesketch.document.cdxml; binary CDX is read through it (vibesketch.document.cdx).

Module Attributes

TEXT_FORMATS	Formats whose data is short text, which the CLI and the browser take as typed.
CALCULATIONS	atoms and coordinates, whose bonds are inferred (#86).
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, dpi, ...])	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, ...)
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', 'pdf', 'eps', 'emf', 'cdxml', 'chemfig', 'helm', 'fasta')

the format of every file in the vibe family.

Type:

QVF first

vibesketch.document.formats.TEXT_FORMATS: tuple[str, ...] = ('smiles', 'inchi', 'name', 'peptide', 'dna', 'rna', 'helm')

Formats whose data is short text, which the CLI and the browser take as typed.

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, warnings: 'list[str]' = <factory>, sequenced: 'bool' = False, rgroups: 'list[Any]' = <factory>)

Bases: object

Parameters:

• molecules (list[Any])

• reaction (tuple[list[Any], list[Any], list[Any]] | None)

• conditions (list[str])

• ket (dict[str, Any] | None)

• warnings (list[str])

• sequenced (bool)

• rgroups (list[Any])

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.

warnings: list[str]

What did not carry over from the file.

sequenced: bool = False

Whether the molecules were built from sequences, which their species record (#98).

rgroups: list[Any]

R-group definitions read from an R-group file, drawn beside the molecules (#90).

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, dpi=300, stereo_labels=False, sequences=False)

document in fmt; raises ExportRefused.

stereo_labels prints CIP descriptors in SVG, PNG and PDF figures; sequences prints a species built from a sequence as it (#98).

Parameters:

• document (Document)

• fmt (str)

• style (str | None)

• dpi (int)

• stereo_labels (bool)

• sequences (bool)

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).

Input beyond vibesketch.limits is refused with ImportFailed.

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]