xenopict.drawer module

Core drawing functionality for xenopict.

class xenopict.drawer.Xenopict(input_mol, **kwargs)

Bases: object

This class draws an RDK molecule with sensible defaults, cleaning up the output SVG for easier modification and reduced size.

>>> from rdkit import Chem
>>> import rdkit.Chem.rdPartialCharges
>>> diclofenac = mol = Chem.MolFromSmiles('O=C(O)Cc1ccccc1Nc1c(Cl)cccc1Cl')
>>> rdkit.Chem.rdPartialCharges.ComputeGasteigerCharges(mol)

Partial charge (scaled to be in [-1, 1])

>>> shading = np.array([a.GetDoubleProp("_GasteigerCharge")  for a in mol.GetAtoms()])
>>> shading = shading / abs(shading).max()

SVG of molecule shaded by partial charge,

>>> drawer = Xenopict(mol)
>>> drawer.shade(shading)
<xenopict.drawer.Xenopict ...>
>>> str(drawer)
'<...>'

Atoms can also be annotated with a circle,

>>> drawer.mark_atoms([1, 2])
<xenopict.drawer.Xenopict ...>

The underlying svg dom (xml.dom.minidom) is accessible:

>>> drawer.svgdom
<xml.dom.minidom.Document ...>

add_atom_indices: bool = False

add_bond_indices: bool = False

align_to(template)

Align this molecule to a template molecule using MCS.

This method aligns the current molecule to match the orientation of the template molecule by finding their maximum common substructure. The alignment is done in-place, modifying the current molecule’s coordinates.

Parameters:

template (Union[str, Mol, Xenopict]) – Template molecule to align to. Can be: - SMILES string - RDKit Mol object - Another Xenopict object

Return type:

Xenopict

Returns:

self for method chaining

Examples

>>> from rdkit import Chem
>>> # Create ethanol and align propanol to it
>>> ethanol = Xenopict("CCO")
>>> propanol = Xenopict("CCCO")
>>> propanol.align_to(ethanol)  # Aligns by OH group
<xenopict.drawer.Xenopict ...>

cmap: Union[str, Colormap] = 'xenosite'

color_map(color)

copy()

Return type:

Xenopict

diverging_cmap: bool = False

down_scale: float = 0.7

draw_mol(mol=None)

dummies_are_attachments: bool = False

embed_script: bool = False

filter(atoms, bonds)

Filter the molecule to show only the specified atoms and bonds.

Return type:

Xenopict

classmethod from_smarts(smarts, **kwargs)

Create a Xenopict object from a SMARTS pattern.

Parameters:

• smarts (str) – SMARTS pattern string

• **kwargs – Additional arguments passed to Xenopict constructor

Return type:

Xenopict

Returns:

Xenopict object initialized with the SMARTS pattern

get_cmap()

Return type:

Colormap

groups: dict[str, Element]

halo()

Return type:

Xenopict

mark_atoms(atoms)

Return type:

Xenopict

mark_down_scale: float = 1.0

mark_substructure(atoms, substr_bonds=None)

Return type:

Xenopict

mol: Mol

optimize_svg: bool = True

plot_dot: PlotDot = <xenopict.plotdot.PlotDot object>

reframe(padding=1.5, atoms=None)

Return type:

Xenopict

scale: float = 20

set_backbone_color(color)

Set the color of the molecule’s backbone and atom labels.

Parameters:

color (str) – Hex color code (e.g. ‘#FF0000’ for red)

Return type:

Xenopict

Returns:

self for method chaining

shade(atom_shading=None, bond_shading=None)

Return type:

Xenopict

shade_substructure(substrs_by_atoms, shading, substrs_bonds=None)

shade_substructure shades a list of substruture, each one defined as a list of atom idxs.

By default, all the bonds connecting these structures are included. Optionally, a list of bonds can be provided instead.

Parameters:

• substrs_by_atoms (Sequence[Sequence[AtomIdx]]) – A list of substructures, each one defined as a list of atoms.

• shading (Sequence[float]) – A list of shading intensities, one for each substructure.

• substrs_bonds (Optional[Sequence[Sequence[AtomIdx]]], optional) – Optionally specify the bonds

• None. (to include for each substructure. Defaults to)

Returns:

Modifies object in place, but returns copy of self to enable chaining.

Return type:

Xenopict

shapely_resolution: int = 6

substructure_focus(atoms, substr_bonds=None)

Focus on a substructure by dimming the rest of the molecule.

Return type:

Xenopict

to_html(svg_datauri=False)

Return the HTML string depicting the molecule, embedding the SVG element within a white-background styled div. Optionally, the SVG can be placed into an img tag’s datauri isntead.

Return type:

str

to_svg(uniquify_internal_refs=True, hash_length=10, svg_attributes={})

Convert Xenopict into an svg. By default, this function will uniquify all id/hrefs int the svg with the same md5 hash. This prevents id clashes in any documents into which svgs are embedded.