schrodinger.livedesign.draw module

class schrodinger.livedesign.draw.Format(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

PNG = 1
SVG = 2
class schrodinger.livedesign.draw.AromaticBondDisplay(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

KEKULE = 1
AROMATIC = 2
class schrodinger.livedesign.draw.ImageGenOptions(img_format: schrodinger.livedesign.draw.Format = Format.SVG, width: int = 400, height: int = 400, background_color: PyQt6.QtGui.QColor = <PyQt6.QtGui.QColor object>, show_stereo_annotation: bool = True, show_simplified_stereo_annotation: bool = True, show_terminal_methyl: bool = False, show_wiggly_bonds: bool = False, aromatic_bond_display: schrodinger.livedesign.draw.AromaticBondDisplay = AromaticBondDisplay.KEKULE, highlight_atoms: typing.Optional[typing.List[int]] = None, highlight_bonds: typing.Optional[typing.List[int]] = None, highlight_atom_colors: typing.Optional[typing.List[typing.Dict]] = None, highlight_bond_colors: typing.Optional[typing.List[typing.Dict]] = None, fallback_entity_class: typing.Optional[schrodinger.livedesign.entity_type.EntityClass] = None)

Bases: NamedTuple

Variables

  • img_format – image format to be returned

  • aromatic_bond_display – how aromatic bonds should be drawn

  • background_color – background QColor

  • width – width of the image

  • height – height of the image

  • show_stereo_annotation – whether to label stereochemistry

  • show_simplified_stereo_annotation – whether to use molecular labels

  • show_wiggly_bonds – whether to render wiggly bonds instead of crossed

  • show_terminal_methyl – whether to render terminal methyl groups

  • highlight_atoms – indices of atoms to highlight

  • highlight_bonds – indices of bonds to highlight

  • highlight_atom_colors – colors to assign to each atom highlight

  • highlight_bond_colors – colors to assign to each bond highlight

img_format: schrodinger.livedesign.draw.Format

Alias for field number 0

width: int

Alias for field number 1

height: int

Alias for field number 2

background_color: PyQt6.QtGui.QColor

Alias for field number 3

show_stereo_annotation: bool

Alias for field number 4

show_simplified_stereo_annotation: bool

Alias for field number 5

show_terminal_methyl: bool

Alias for field number 6

show_wiggly_bonds: bool

Alias for field number 7

aromatic_bond_display: schrodinger.livedesign.draw.AromaticBondDisplay

Alias for field number 8

highlight_atoms: Optional[List[int]]

Alias for field number 9

highlight_bonds: Optional[List[int]]

Alias for field number 10

highlight_atom_colors: Optional[List[Dict]]

Alias for field number 11

highlight_bond_colors: Optional[List[Dict]]

Alias for field number 12

fallback_entity_class: Optional[schrodinger.livedesign.entity_type.EntityClass]

Alias for field number 13

schrodinger.livedesign.draw.set_rgroup_highlight(match_mol: rdkit.Chem.rdchem.Mol, rgroup_decomp: Dict[str, rdkit.Chem.rdchem.Mol], options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → schrodinger.livedesign.draw.ImageGenOptions

Sets the highlighting to use for each atom and bond according to which of the rgroups or core the atom/bond belongs to.

Parameters

  • mol – molecule to highlight rgroup decoposition of

  • rgroup_decomp – core and rgroups from rgroup decomposition

  • options – image generation options to update

Returns

options with updated atoms/bonds to highlight

schrodinger.livedesign.draw.set_highlight(mol: rdkit.Chem.rdchem.Mol, highlight_mol: rdkit.Chem.rdchem.Mol, substructure_options: Optional[schrodinger.rdkit.substructure.QueryOptions] = None, options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → schrodinger.livedesign.draw.ImageGenOptions

Sets the atoms and bonds that match a specified highlight core.

Parameters

  • mol – query molecule

  • highlight_mol – core to highlight matches of

  • substructure_options – substructure matching options

  • options – image generation options to update

Returns

options with updated atoms/bonds to highlight

schrodinger.livedesign.draw.assign_highlight_options(draw_opts: schrodinger.livedesign.draw.ImageGenOptions, sk_opts: schrodinger.ui._sketcher.RenderOptions)

Maps the colors set on the ImageGenOptions object to a RenderOptions object

schrodinger.livedesign.draw.to_RenderOptions(draw_options: schrodinger.livedesign.draw.ImageGenOptions) → schrodinger.ui._sketcher.RenderOptions
Parameters

draw_options – input options defined in this module

Returns

translated sketcher compatible RenderOptions

schrodinger.livedesign.draw.draw_image(mol: Union[rdkit.Chem.rdchem.Mol, rdkit.Chem.rdChemReactions.ChemicalReaction], options: Optional[schrodinger.livedesign.draw.ImageGenOptions] = None) → bytes

Generates an image from an RDKit molecule or reaction

Parameters

  • mol – molecule or reaction to get image of

  • options – image generation options

Returns

generated image as a string (SVG) or as bytes (PNG)

schrodinger.livedesign.draw.get_entity_stock_image_bytes(options: schrodinger.livedesign.draw.ImageGenOptions) → bytes
Parameters

entity_class – the entity class to get the stock image for

Returns

bytes for the entity specific stock image