def draw_mol(self, mol, size=(160, 120), **kwargs):
"""Draw a molecule
Parameters
----------
mol : rdkit.Chem.rdchem.Mol
The molecule to draw
size : tuple
The size of the drawing canvas
**kwargs : object
Attributes of the rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions class
like `fixedBondLength=35, bondLineWidth=2`
Notes
-----
The list of supported MolDrawOptions attributes are available in
https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html#rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions
"""
if self.useSVG:
d2d = Draw.MolDraw2DSVG(*size)
else:
d2d = Draw.MolDraw2DCairo(*size)
opts = Draw.MolDrawOptions()
for key, value in kwargs.items():
setattr(opts, key, value)
d2d.SetDrawOptions(opts)
d2d.DrawMolecule(mol)
d2d.FinishDrawing()
return d2d.GetDrawingText()
def draw_mol(self,
mol,
size=(160, 120),
use_coords=True,
MolDrawOptions=None,
**kwargs):
"""Draw a molecule
Parameters
----------
mol : rdkit.Chem.rdchem.Mol
The molecule to draw
size : tuple
The size of the drawing canvas
use_coords : bool
Use the 2D or 3D coordinates of the molecule
MolDrawOptions : rdkit.Chem.Draw.MolDrawOptions or None
Directly set the drawing options. Useful for making highly
customized drawings
**kwargs : object
Attributes of the rdkit.Chem.Draw.MolDrawOptions class like
`fixedBondLength=35, bondLineWidth=2`
Notes
-----
The list of supported MolDrawOptions attributes are available in
https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html#rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions
"""
if self.useSVG:
d2d = Draw.MolDraw2DSVG(*size)
else:
d2d = Draw.MolDraw2DCairo(*size)
MolDrawOptions = MolDrawOptions or Draw.MolDrawOptions()
for key, value in kwargs.items():
setattr(MolDrawOptions, key, value)
d2d.SetDrawOptions(MolDrawOptions)
if not use_coords:
mol = deepcopy(mol)
mol.RemoveAllConformers()
hl_atoms = getattr(mol, "__sssAtoms", [])
d2d.DrawMolecule(mol, highlightAtoms=hl_atoms)
d2d.FinishDrawing()
return d2d.GetDrawingText()
"""
__all__ = ["plot_pathway"]
from collections import Iterable
import numpy as np
import matplotlib.pyplot as plt
import networkx as nx
from rdkit import Chem
from rdkit.Chem import Draw
# Remove white background and highlight atoms/bonds with white circles/lines, respectively
_DRAWING_OPTIONS = Draw.MolDrawOptions()
_DRAWING_OPTIONS.clearBackground = False
_DRAWING_OPTIONS.setHighlightColour((1, 1, 1))
_DRAWING_OPTIONS.highlightBondWidthMultiplier = 20
def _get_image(inchi, size):
# Returns a PIL image from an InChI string
mol = Chem.MolFromInchi(inchi)
return Draw.MolToImage(
mol,
size=size,
options=_DRAWING_OPTIONS,
highlightAtoms=[atom.GetIdx() for atom in mol.GetAtoms()],
highlightBonds=[bond.GetIdx() for bond in mol.GetBonds()],
)
