def depictMultipleMols(mols_list,
filename=None,
ipython=False,
legends=None,
highlightAtoms=None,
mols_perrow=3):
"""
Returns the image or the ipython rendering.
Parameters
----------
mols_list: list
The list of the rdkit molecules to depict
filename: str
The filename of the image
ipython: bool
If True, the SVG rendering for jupiter-nootebook are returned
legends: list
List of titles subfigure for each molecule
highlightAtoms: list
List of list of atom index to highlight.
mols_perrow: int
The number of subfigures per row
Returns
-------
svg: SVG
If ipython set as True, the SVG rendering is returned
"""
import rdkit
from rdkit.Chem.Draw import MolsToGridImage
from IPython.display import SVG
from os.path import splitext
sel_atoms = []
sel_colors = []
if highlightAtoms is not None:
if isinstance(highlightAtoms[0][0], list):
sel_atoms = [[a for a in subset] for mol_set in highlightAtoms
for subset in mol_set]
sel_colors = [{
aIdx: _highlight_colors[n % len(_highlight_colors)]
for aIdx in subset
} for mol_set in highlightAtoms
for n, subset in enumerate(mol_set)]
else:
sel_atoms = highlightAtoms
sel_colors = [{aIdx: _highlight_colors[0]
for aIdx in subset} for subset in highlightAtoms]
from rdkit.Chem.Draw import IPythonConsole as CDIPythonConsole
if MolsToGridImage == CDIPythonConsole.ShowMols:
CDIPythonConsole.UninstallIPythonRenderer()
from rdkit.Chem.Draw import MolsToGridImage
svg = MolsToGridImage(mols_list,
highlightAtomLists=sel_atoms,
highlightBondLists=[],
highlightAtomColors=sel_colors,
legends=legends,
molsPerRow=mols_perrow,
useSVG=True)
if filename:
ext = splitext(filename)[-1]
filename = filename if ext != '' else filename + '.svg'
f = open(filename, 'w')
f.write(svg)
f.close()
if ipython:
_svg = SVG(svg)
return _svg
else:
return None
def setUp(self):
if IPythonConsole is not None and Draw.MolsToGridImage == IPythonConsole.ShowMols:
IPythonConsole.UninstallIPythonRenderer()
self.mol = Chem.MolFromSmiles(
'c1c(C[15NH3+])ccnc1[C@](Cl)(Br)[C@](Cl)(Br)F')
def tearDown(self):
if IPythonConsole is not None:
IPythonConsole.UninstallIPythonRenderer()