from copy import deepcopy
import math
from rdkit.Chem.Draw import MolsToGridImage
from rdkit.Chem.Draw.rdMolDraw2D import MolDraw2DSVG
from openpharmacophore.constants import PALETTE
[docs]def draw_ligands(ligands, n_per_row, pretty=True, legends=None):
""" Draw multiple ligands
Parameters
----------
ligands : list[Ligand]
A list with ligands.
n_per_row : int
Number of ligands to draw on each row.
pretty : bool, default=True
If true the ligands is drawn with no conformers.
legends : list[str], optional
A legend to add to each ligand. Must be of the same
length as ligands
"""
if pretty:
# Copy to avoid removing conformers from the original molecules
mols = [deepcopy(lig.to_rdkit()) for lig in ligands]
for mol in mols:
mol.RemoveAllConformers()
else:
mols = [lig.to_rdkit() for lig in ligands]
return MolsToGridImage(mols, molsPerRow=n_per_row, legends=legends)
def _atom_highlights(feat_ind):
""" Returns the atoms that will be highlighted in a drawing
along with their color and the radius of the circle.
Parameters
----------
feat_ind : list[dict[str, list[tuple[int]]]]
Indices of each chemical feature
Returns
-------
atoms : list[tuple[int]]
colors : list[dict[int, tuple[int]]
radii : list[dict[int, float]]
"""
atoms = []
colors = []
radii = []
for lig_feats in feat_ind:
lig_ind = []
lig_color = {}
lig_radii = {}
for feat_type, ind_list in lig_feats.items():
color = PALETTE[feat_type]
for ind_tup in ind_list:
for ind in ind_tup:
lig_ind.append(ind)
lig_color[ind] = color
lig_radii[ind] = 0.5
atoms.append(tuple(lig_ind))
colors.append(lig_color)
radii.append(lig_radii)
return atoms, colors, radii
def _drawing_size(mol_width, mol_height, n_mols):
""" Returns the width and height of a drawing consisting of n_mols
with the given width and height
Parameters
----------
mol_width : int
mol_height : int
n_mols : int
Returns
-------
width : int
height : int
"""
max_per_row = 4
max_width = max_per_row * mol_width
if mol_width * n_mols <= max_width:
width = mol_width * n_mols
n_rows = 1
else:
width = max_width
n_rows = math.ceil(mol_width * n_mols / width)
height = n_rows * mol_height
return width, height
[docs]def draw_ligands_chem_feats(ligands, lig_size):
""" Draw the ligands with their chemical features highlighted.
Parameters
----------
ligands : list[Ligand]
A list of ligands.
lig_size : tuple[int, int]
A tuple with the width and height of each ligand drawing.
Returns
-------
drawing
"""
molecules = [deepcopy(lig.to_rdkit()) for lig in ligands]
for mol in molecules:
mol.RemoveAllConformers()
feat_ind = []
for lig in ligands:
feat_ind.append(lig.feat_ind)
atoms, colors, radii = _atom_highlights(feat_ind)
width, height = _drawing_size(lig_size[0], lig_size[1], len(ligands))
drawing = MolDraw2DSVG(width=width, height=height,
panelWidth=lig_size[0], panelHeight=lig_size[1])
drawing.DrawMolecules(molecules,
highlightAtoms=atoms,
highlightAtomColors=colors,
highlightAtomRadii=radii
)
drawing.FinishDrawing()
return drawing
