def testPNGMetadata(self):
m = Chem.MolFromMolBlock('''
Mrv2014 08172015242D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 C 2.31 -1.3337 0 0
M V30 2 C 3.6437 -2.1037 0 0
M V30 3 O 4.9774 -1.3337 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
M END''')
d = Draw.MolDraw2DCairo(200, 200)
d.DrawMolecule(m)
txt = d.GetDrawingText()
nm = Chem.MolFromPNGString(txt)
self.assertEqual(Chem.MolToSmiles(m), Chem.MolToSmiles(nm))
def _smiles_to_im(smiles: str) -> np.array:
"""
Generate a molecule figure from its SMILES representation.
Parameters
----------
smiles : str
The SMILES representation of the molecule to be converted to a figure.
Returns
-------
np.array
The molecule figure as an [N, M, 3] NumPy RGB array. N and M are
defined by `_mol_size` with empty lines cropped.
"""
# Draw the molecule.
# https://sourceforge.net/p/rdkit/mailman/message/36735785/
d2d = Draw.MolDraw2DCairo(_mol_size, _mol_size)
d2d.SetFontSize(_mol_font_size)
d2d.drawOptions().bondLineWidth = _mol_line_width
Draw.PrepareAndDrawMolecule(d2d, Chem.MolFromSmiles(smiles))
d2d.FinishDrawing()
im = plt.imread(io.BytesIO(d2d.GetDrawingText()))
# Make white pixels transparent.
im = np.dstack((im, (~im.all(2)).astype(np.float32)))
# Crop the image by removing empty (white) lines.
bottom, top, left, right = 0, im.shape[0] - 1, 0, im.shape[1] - 1
while bottom < im.shape[0] and np.isclose(im[bottom, :, 3].sum(), 0):
bottom += 1
while top > 0 and np.isclose(im[top, :, 3].sum(), 0):
top -= 1
while left < im.shape[1] and np.isclose(im[:, left, 3].sum(), 0):
left += 1
while right > 0 and np.isclose(im[:, right, 3].sum(), 0):
right -= 1
return im[bottom:top + 1:, left:right + 1, :]
def draw(reaction, save_reaction_path):
d2d = Draw.MolDraw2DCairo(6000, 2000)
d2d.DrawReaction(reaction)
png = d2d.GetDrawingText()
# 'D:/test/image/output.png'
open(save_reaction_path, 'wb+').write(png)
def draw_mol_with_property(mol, property, **kwargs):
"""
http://rdkit.blogspot.com/2015/02/new-drawing-code.html
Parameters
---------
property : dict
key atom idx, val the property (need to be stringfiable)
"""
import copy
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
def run_from_ipython():
try:
__IPYTHON__
return True
except NameError:
return False
AllChem.Compute2DCoords(mol)
mol = copy.deepcopy(mol) #FIXME do I really need deepcopy?
for idx in property:
# opts.atomLabels[idx] =
mol.GetAtomWithIdx(idx).SetProp('molAtomMapNumber',
"({})".format(str(property[idx])))
mol = Draw.PrepareMolForDrawing(mol,
kekulize=False) #enable adding stereochem
if run_from_ipython():
from IPython.display import SVG, display
if "width" in kwargs and type(
kwargs["width"]) is int and "height" in kwargs and type(
kwargs["height"]) is int:
drawer = Draw.MolDraw2DSVG(kwargs["width"], kwargs["height"])
else:
drawer = Draw.MolDraw2DSVG(500, 250)
drawer.DrawMolecule(mol)
drawer.FinishDrawing()
display(SVG(drawer.GetDrawingText().replace("svg:", "")))
else:
if "width" in kwargs and type(
kwargs["width"]) is int and "height" in kwargs and type(
kwargs["height"]) is int:
drawer = Draw.MolDraw2DCairo(kwargs["width"], kwargs["height"])
else:
drawer = Draw.MolDraw2DCairo(500,
250) #cairo requires anaconda rdkit
# opts = drawer.drawOptions()
drawer.DrawMolecule(mol)
drawer.FinishDrawing()
#
# with open("/home/shuwang/sandbox/tmp.png","wb") as f:
# f.write(drawer.GetDrawingText())
import io
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
buff = io.BytesIO()
buff.write(drawer.GetDrawingText())
buff.seek(0)
plt.figure()
i = mpimg.imread(buff)
plt.imshow(i)
plt.show()
# open('reaction3.png', 'wb+').write(png)
# rxn = AllChem.ReactionFromSmarts('C[O:1][c:2]1[cH:3][c:4]([c:5]([cH:6][c:7]1[Cl:8])[CH:9]=[O:10])[Cl:11]>CN(C)C=O.Cl[Li]>[O:10]=[CH:9][c:5]1[cH:6][c:7]([c:2]([cH:3][c:4]1[Cl:11])[OH:1])[Cl:8]')
# d2d = Draw.MolDraw2DCairo(800, 300)
# d2d.DrawReaction(rxn, highlightByReactant=True)
# png = d2d.GetDrawingText()
# open('reaction3.png', 'wb+').write(png)
rxn = AllChem.ReactionFromSmarts(
'[CH3:1][CH2:2][O:3][C:4](=[O:5])[c:6]1[cH:7][c:8]([cH:9][c:10]([cH:11]1)[C:12](=[O:13])O)-[c:14]1[cH:15][cH:16][c:17]([cH:18][c:19]1[C:20]#[N:21])[CH3:22].[OH:23][CH:24]1[CH2:25][NH:26][CH2:27]1.Cl>CCN=C=NCCCN(C)C.On1nnc2ccccc21.CC(C)N(CC)C(C)C.ClCCl.O.Cl>[CH3:1][CH2:2][O:3][C:4](=[O:5])[c:6]1[cH:7][c:8]([cH:9][c:10]([cH:11]1)[C:12](=[O:13])[N:26]1[CH2:27][CH:24]([CH2:25]1)[OH:23])-[c:14]1[cH:15][cH:16][c:17]([cH:18][c:19]1[C:20]#[N:21])[CH3:22]'
)
# d2d = Draw.MolDraw2DCairo(800, 300)
# d2d.DrawReaction(rxn, highlightByReactant=True)
# png = d2d.GetDrawingText()
# open('reaction4.png', 'wb+').write(png)')
d2d = Draw.MolDraw2DCairo(800, 300)
d2d.DrawReaction(rxn, highlightByReactant=True)
png = d2d.GetDrawingText()
open('reaction6.png', 'wb+').write(png)
rxn = AllChem.ReactionFromSmarts(
'([C:13]-[N;H0;D3;+0:14](-[C:15])-[C;H0;D3;+0:1](=[O;D1;H0:2])-[c:3]1:[c:4]:[c:5](-[C:6](=[O;D1;H0:7])-[#8:8]-[C:9]):[c:10]:[c:11]:[c:12]:1)>>(O-[C;H0;D3;+0:1](=[O;D1;H0:2])-[c:3]1:[c:4]:[c:5](-[C:6](=[O;D1;H0:7])-[#8:8]-[C:9]):[c:10]:[c:11]:[c:12]:1).([C:13]-[NH;D2;+0:14]-[C:15])'
)
# d2d = Draw.MolDraw2DCairo(800, 300)
# d2d.DrawReaction(rxn, highlightByReactant=True)
# png = d2d.GetDrawingText()
# open('reaction4.png', 'wb+').write(png)')
d2d = Draw.MolDraw2DCairo(800, 300)
d2d.DrawReaction(rxn, highlightByReactant=True)
png = d2d.GetDrawingText()
open('reaction7.png', 'wb+').write(png)