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import os
import sys
import logging
from typing import Optional
from rdkit import Chem
from rdkit.Chem import Draw
if 'ipykernel' in sys.modules:
from IPython.display import SVG
from .chemoinformatics import get_atom_idx_at_attachment, canonize
def safe_display(*args):
"""Displays content only if running in a Jupyter notebook."""
if 'ipykernel' in sys.modules:
display(*args)
else:
logging.warning(*args)
def display_mol(
mol: Chem.Mol,
w: int = 800,
h: int = 300,
legend: Optional[str] = None,
use_smiles_as_legend: bool = True,
display_svg: bool = True,
):
""" Display a molecule in a Jupyter notebook. Useful for having """
if mol is None:
logging.warning('Molecule is None')
return None
if use_smiles_as_legend and legend is None:
legend = Chem.MolToSmiles(mol)
if display_svg:
mol.SetProp("_Name", Chem.MolToSmiles(mol, canonical=True))
d = Draw.rdMolDraw2D.MolDraw2DSVG(w, h, noFreetype=True)
font_path = '/System/Library/Fonts/Supplemental/Arial.ttf'
if os.path.exists(font_path):
d.fontFile = font_path
d.DrawMolecule(mol, legend=legend)
d.FinishDrawing()
svg = d.GetDrawingText()
# Check if in Jupyter notebook
if sys.modules.get('ipykernel', None):
from IPython.display import SVG
safe_display(SVG(svg))
else:
img = Draw.MolToImage(mol, size=(w, h))
safe_display(img)
def get_mapped_protac_img(
protac_smiles: str,
poi_smiles: str,
linker_smiles: str,
e3_smiles: str,
w: int = 1000,
h: int = 1000,
useSVG: bool = False,
display_image: bool = False,
legend: Optional[str] = None,
show_bond_indices: bool = False,
):
""" Display a PROTAC molecule with the POI, linker, and E3 ligase highlighted.
If `useSVG` is True, then the POI-Linker bond is highlighted in purple, whereas the E3-Linker bond is highlighted in green.
If `useSVG` is False, then both splitting points are highlighted in purple.
Args:
protac_smiles: The SMILES string of the PROTAC.
poi_smiles: The SMILES string of the POI.
linker_smiles: The SMILES string of the linker.
e3_smiles: The SMILES string of the E3 ligase.
w: The width of the image.
h: The height of the image.
useSVG: Whether to use SVG format.
display_image: Whether to display the image.
legend: The legend to display.
show_bond_indices: Whether to show bond indices in the image.
"""
protac_smiles = canonize(protac_smiles)
e3_smiles = canonize(e3_smiles)
poi_smiles = canonize(poi_smiles)
linker_smiles = canonize(linker_smiles)
# Check if any of the canonicalized SMILES is None
if None in [protac_smiles, e3_smiles, poi_smiles, linker_smiles]:
return None
protac_mol = Chem.MolFromSmiles(protac_smiles)
e3_mol = Chem.MolFromSmiles(e3_smiles)
poi_mol = Chem.MolFromSmiles(poi_smiles)
linker_mol = Chem.MolFromSmiles(linker_smiles)
if None in [protac_mol, e3_mol, poi_mol, linker_mol]:
return None
if linker_smiles in ['[*:1][*:2]', '[*:2][*:1]']:
logging.warning('WARNING. Linker is empty.')
poi_attachment_idx = get_atom_idx_at_attachment(protac_mol, poi_mol, e3_mol)
e3_attachment_idx = get_atom_idx_at_attachment(protac_mol, e3_mol, poi_mol)
else:
poi_attachment_idx = get_atom_idx_at_attachment(protac_mol, poi_mol, linker_mol)
e3_attachment_idx = get_atom_idx_at_attachment(protac_mol, e3_mol, linker_mol)
cyan = (0, 1, 1, 0.5)
red = (1, 0, 0, 0.5)
green = (0, 1, 0, 0.5)
blue = (0, 0, 1, 0.5)
purple = (1, 0, 1, 0.3)
highlight_atoms = []
highlight_bonds = []
atom_colors = {}
bond_colors = {}
if poi_attachment_idx is not None:
if len(poi_attachment_idx) != 2:
if linker_smiles in ['[*:1][*:2]', '[*:2][*:1]']:
logging.warning(f'WARNING. Linker is empty, no highlighting will be showed for the POI.')
else:
logging.warning(f'WARNING. POI attachment points must be only two, got instead: {poi_attachment_idx}')
else:
poi_bond_idx = protac_mol.GetBondBetweenAtoms(*poi_attachment_idx).GetIdx()
highlight_atoms += poi_attachment_idx
highlight_bonds.append(poi_bond_idx)
atom_colors[poi_attachment_idx[0]] = purple
atom_colors[poi_attachment_idx[1]] = purple
bond_colors[poi_bond_idx] = purple
if e3_attachment_idx is not None:
if len(e3_attachment_idx) != 2:
if linker_smiles in ['[*:1][*:2]', '[*:2][*:1]']:
logging.warning(f'WARNING. Linker is empty, no highlighting will be showed for the E3.')
else:
logging.warning(f'WARNING. E3 attachment points must be only two, got instead: {e3_attachment_idx}')
else:
e3_bond_idx = protac_mol.GetBondBetweenAtoms(*e3_attachment_idx).GetIdx()
highlight_atoms += e3_attachment_idx
highlight_bonds.append(e3_bond_idx)
atom_colors[e3_attachment_idx[0]] = green
atom_colors[e3_attachment_idx[1]] = green
bond_colors[e3_bond_idx] = green
if useSVG:
drawer = Draw.rdMolDraw2D.MolDraw2DSVG(w, h, noFreetype=True)
options = drawer.drawOptions()
options.fontFile = '/System/Library/Fonts/Supplemental/Arial.ttf'
if legend is None:
# legend = '.'.join([e3_smiles, linker_smiles, poi_smiles])
legend = ""
drawer.DrawMolecule(
protac_mol,
legend=legend,
highlightAtoms=highlight_atoms,
highlightBonds=highlight_bonds,
highlightAtomColors=atom_colors,
highlightBondColors=bond_colors,
)
# Add bond indices as text in the center of each bond
if show_bond_indices:
# Needs coordinates; ensure 2D coords present
Chem.rdDepictor.Compute2DCoords(protac_mol)
for bond in protac_mol.GetBonds():
idx = bond.GetIdx()
begin = bond.GetBeginAtomIdx()
end = bond.GetEndAtomIdx()
begin_pos = drawer.GetDrawCoords(begin)
end_pos = drawer.GetDrawCoords(end)
mid_y = (begin_pos.y + end_pos.y) / 2
mid_x = (begin_pos.x + end_pos.x) / 2
drawer.DrawString(f"{idx}", Chem.rdGeometry.Point2D(mid_x, mid_y), rawCoords=True)
drawer.FinishDrawing()
svg_text = drawer.GetDrawingText()
if display_image:
safe_display(SVG(svg_text))
return svg_text
else:
img = Draw.MolToImage(
protac_mol,
size=(w, h),
highlightColor=purple,
highlightAtoms=highlight_atoms,
highlightBonds=highlight_bonds,
highlightAtomColors=atom_colors,
highlightBondColors=bond_colors,
)
if display_image:
safe_display(img)
return img |