def testMolContours(self):
m = Chem.MolFromSmiles("C1N[C@@H]2OCC12")
dm = Draw.PrepareMolForDrawing(m)
conf = dm.GetConformer()
gs = []
ws = []
hs = []
for i in range(conf.GetNumAtoms()):
p = conf.GetAtomPosition(i)
p2 = Geometry.Point2D(p.x, p.y)
gs.append(p2)
hs.append(0.4)
if not i % 2:
ws.append(-0.5)
else:
ws.append(1)
d = Draw.MolDraw2DSVG(300, 300)
d.ClearDrawing()
Draw.ContourAndDrawGaussians(d, gs, hs, ws, mol=dm)
d.drawOptions().clearBackground = False
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
with open("contour_from_py_1.svg", 'w+') as outf:
print(txt, file=outf)
d = Draw.MolDraw2DSVG(300, 300)
d.ClearDrawing()
ps = Draw.ContourParams()
ps.fillGrid = True
Draw.ContourAndDrawGaussians(d, gs, hs, ws, params=ps, mol=dm)
d.drawOptions().clearBackground = False
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
with open("contour_from_py_2.svg", 'w+') as outf:
print(txt, file=outf)
def GetSimilarityMapFromWeights(mol,
weights,
colorMap=None,
scale=-1,
size=(250, 250),
sigma=None,
coordScale=1.5,
step=0.01,
colors='k',
contourLines=10,
alpha=0.5,
draw2d=None,
**kwargs):
"""
Generates the similarity map for a molecule given the atomic weights.
Parameters:
mol -- the molecule of interest
colorMap -- the matplotlib color map scheme, default is custom PiWG color map
scale -- the scaling: scale < 0 -> the absolute maximum weight is used as maximum scale
scale = double -> this is the maximum scale
size -- the size of the figure
sigma -- the sigma for the Gaussians
coordScale -- scaling factor for the coordinates
step -- the step for calcAtomGaussian
colors -- color of the contour lines
contourLines -- if integer number N: N contour lines are drawn
if list(numbers): contour lines at these numbers are drawn
alpha -- the alpha blending value for the contour lines
kwargs -- additional arguments for drawing
"""
if mol.GetNumAtoms() < 2:
raise ValueError("too few atoms")
if draw2d is not None:
mol = rdMolDraw2D.PrepareMolForDrawing(mol, addChiralHs=False)
if not mol.GetNumConformers():
rdDepictor.Compute2DCoords(mol)
if sigma is None:
if mol.GetNumBonds() > 0:
bond = mol.GetBondWithIdx(0)
idx1 = bond.GetBeginAtomIdx()
idx2 = bond.GetEndAtomIdx()
sigma = 0.3 * (
mol.GetConformer().GetAtomPosition(idx1) -
mol.GetConformer().GetAtomPosition(idx2)).Length()
else:
sigma = 0.3 * (mol.GetConformer().GetAtomPosition(0) -
mol.GetConformer().GetAtomPosition(1)).Length()
sigma = round(sigma, 2)
sigmas = [sigma] * mol.GetNumAtoms()
locs = []
for i in range(mol.GetNumAtoms()):
p = mol.GetConformer().GetAtomPosition(i)
locs.append(Geometry.Point2D(p.x, p.y))
draw2d.ClearDrawing()
ps = Draw.ContourParams()
ps.fillGrid = True
ps.gridResolution = 0.1
ps.extraGridPadding = 0.5
Draw.ContourAndDrawGaussians(draw2d,
locs,
weights,
sigmas,
nContours=contourLines,
params=ps)
draw2d.drawOptions().clearBackground = False
draw2d.DrawMolecule(mol)
return draw2d
fig = Draw.MolToMPL(mol, coordScale=coordScale, size=size, **kwargs)
if sigma is None:
if mol.GetNumBonds() > 0:
bond = mol.GetBondWithIdx(0)
idx1 = bond.GetBeginAtomIdx()
idx2 = bond.GetEndAtomIdx()
sigma = 0.3 * math.sqrt(
sum([(mol._atomPs[idx1][i] - mol._atomPs[idx2][i])**2
for i in range(2)]))
else:
sigma = 0.3 * \
math.sqrt(sum([(mol._atomPs[0][i] - mol._atomPs[1][i])**2 for i in range(2)]))
sigma = round(sigma, 2)
x, y, z = Draw.calcAtomGaussians(mol, sigma, weights=weights, step=step)
# scaling
if scale <= 0.0:
maxScale = max(math.fabs(numpy.min(z)), math.fabs(numpy.max(z)))
else:
maxScale = scale
# coloring
if colorMap is None:
if cm is None:
raise RuntimeError("matplotlib failed to import")
PiYG_cmap = cm.get_cmap('PiYG', 2)
colorMap = LinearSegmentedColormap.from_list(
'PiWG',
[PiYG_cmap(0),
(1.0, 1.0, 1.0), PiYG_cmap(1)], N=255)
fig.axes[0].imshow(z,
cmap=colorMap,
interpolation='bilinear',
origin='lower',
extent=(0, 1, 0, 1),
vmin=-maxScale,
vmax=maxScale)
# contour lines
# only draw them when at least one weight is not zero
if len([w for w in weights if w != 0.0]):
contourset = fig.axes[0].contour(x,
y,
z,
contourLines,
colors=colors,
alpha=alpha,
**kwargs)
for j, c in enumerate(contourset.collections):
if contourset.levels[j] == 0.0:
c.set_linewidth(0.0)
elif contourset.levels[j] < 0:
c.set_dashes([(0, (3.0, 3.0))])
fig.axes[0].set_axis_off()
return fig
