schrodinger.livedesign.draw module

class schrodinger.livedesign.draw.Format(value)

Bases: enum.Enum

An enumeration.

PNG = 1
SVG = 2
class schrodinger.livedesign.draw.AromaticBondDisplay(value)

Bases: enum.Enum

An enumeration.

KEKULE = 1
AROMATIC = 2
class schrodinger.livedesign.draw.ImageGenOptions(img_format: schrodinger.livedesign.draw.Format = Format.SVG, aromatic_bond_display: schrodinger.livedesign.draw.AromaticBondDisplay = AromaticBondDisplay.KEKULE, background_color: str = '#ff', width: int = 400, height: int = 400, show_stereo_annotation: bool = True, show_simplified_stereo_annotation: bool = True, show_absolute_stereo_groups: bool = False, show_wiggly_bonds: bool = False, show_terminal_methyl: bool = False, highlight_atoms: Optional[List[int]] = None, highlight_bonds: Optional[List[int]] = None, highlight_atom_colors: Optional[List[Dict]] = None, highlight_bond_colors: Optional[List[Dict]] = None)

Bases: tuple

Variables

  • img_format – image format to be returned

  • aromatic_bond_display – how aromatic bonds should be drawn

  • background_color – background color

  • 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_absolute_stereo_groups – whether to show absolute enhanced stereo label

  • 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

aromatic_bond_display: schrodinger.livedesign.draw.AromaticBondDisplay

Alias for field number 1

background_color: str

Alias for field number 2

width: int

Alias for field number 3

height: int

Alias for field number 4

show_stereo_annotation: bool

Alias for field number 5

show_simplified_stereo_annotation: bool

Alias for field number 6

show_absolute_stereo_groups: bool

Alias for field number 7

show_wiggly_bonds: bool

Alias for field number 8

show_terminal_methyl: bool

Alias for field number 9

highlight_atoms: Optional[List[int]]

Alias for field number 10

highlight_bonds: Optional[List[int]]

Alias for field number 11

highlight_atom_colors: Optional[List[Dict]]

Alias for field number 12

highlight_bond_colors: Optional[List[Dict]]

Alias for field number 13

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

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.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)