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|
import random
import re
import unittest
from os import environ
import numpy as np
from rdkit import Chem, Geometry, RDConfig
from rdkit.Chem import AllChem, Draw, rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1(self):
m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
AllChem.Compute2DCoords(m)
d = Draw.MolDraw2DSVG(300, 300)
d.DrawMolecule(m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("<svg") != -1)
self.assertTrue(txt.find("</svg>") != -1)
def test2(self):
m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
AllChem.Compute2DCoords(m)
d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
do = d.drawOptions()
do.atomLabels[3] = 'foolabel'
d.DrawMolecule(m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find(">f</text>") != -1)
self.assertTrue(txt.find(">o</text>") != -1)
self.assertTrue(txt.find(">l</text>") != -1)
self.assertTrue(txt.find(">a</text>") != -1)
@unittest.skipUnless(hasattr(Draw, 'MolDraw2DCairo'), 'Cairo support not enabled')
def testGithubIssue571(self):
m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
AllChem.Compute2DCoords(m)
d = Draw.MolDraw2DCairo(300, 300)
d.DrawMolecule(m)
d.FinishDrawing()
txt = d.GetDrawingText()
def testPrepareForDrawing(self):
m = Chem.MolFromSmiles('c1ccccc1[C@H](F)Cl')
nm = rdMolDraw2D.PrepareMolForDrawing(m)
self.assertEqual(nm.GetNumAtoms(), 9)
self.assertEqual(nm.GetNumConformers(), 1)
m = Chem.MolFromSmiles('C1CC[C@H]2NCCCC2C1')
nm = rdMolDraw2D.PrepareMolForDrawing(m)
self.assertEqual(nm.GetNumAtoms(), 11)
self.assertEqual(nm.GetNumConformers(), 1)
nm = rdMolDraw2D.PrepareMolForDrawing(m, addChiralHs=False)
self.assertEqual(nm.GetNumAtoms(), 10)
self.assertEqual(nm.GetNumConformers(), 1)
m = Chem.MolFromSmiles('CC=CC')
m.GetBondWithIdx(1).SetStereo(Chem.BondStereo.STEREOANY)
nm = rdMolDraw2D.PrepareMolForDrawing(m)
self.assertEqual(nm.GetBondWithIdx(1).GetStereo(), Chem.BondStereo.STEREOANY)
self.assertEqual(nm.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.NONE)
nm = rdMolDraw2D.PrepareMolForDrawing(m, wavyBonds=True)
self.assertEqual(nm.GetBondWithIdx(1).GetStereo(), Chem.BondStereo.STEREONONE)
self.assertEqual(nm.GetBondWithIdx(0).GetBondDir(), Chem.BondDir.UNKNOWN)
def testRepeatedPrepareForDrawingCalls(self):
m = Chem.MolFromMolBlock("""
11280715312D 1 1.00000 0.00000 0
33 36 0 1 0 999 V2000
7.6125 -5.7917 0.0000 C 0 0 0 0 0 0 0 0 0
7.0917 -6.0917 0.0000 C 0 0 1 0 0 0 0 0 0
6.4792 -6.8917 0.0000 C 0 0 2 0 0 0 0 0 0
8.1292 -6.0792 0.0000 N 0 0 0 0 0 0 0 0 0
5.5042 -6.8917 0.0000 C 0 0 3 0 0 0 0 0 0
11.2375 -4.8542 0.0000 N 0 0 0 0 0 0 0 0 0
9.6792 -5.1667 0.0000 N 0 0 3 0 0 0 0 0 0
5.9917 -6.5417 0.0000 C 0 0 0 0 0 0 0 0 0
7.6042 -5.1917 0.0000 O 0 0 0 0 0 0 0 0 0
10.7167 -5.1625 0.0000 C 0 0 0 0 0 0 0 0 0
6.2917 -7.4667 0.0000 C 0 0 0 0 0 0 0 0 0
6.5750 -5.7917 0.0000 C 0 0 0 0 0 0 0 0 0
10.2000 -4.8667 0.0000 C 0 0 0 0 0 0 0 0 0
8.6500 -5.7792 0.0000 C 0 0 3 0 0 0 0 0 0
8.6417 -5.1792 0.0000 C 0 0 0 0 0 0 0 0 0
9.1667 -6.0750 0.0000 C 0 0 0 0 0 0 0 0 0
9.6875 -5.7667 0.0000 C 0 0 0 0 0 0 0 0 0
9.1542 -4.8750 0.0000 C 0 0 0 0 0 0 0 0 0
5.6917 -7.4667 0.0000 C 0 0 0 0 0 0 0 0 0
5.2042 -7.4042 0.0000 F 0 0 0 0 0 0 0 0 0
4.9875 -6.5917 0.0000 F 0 0 0 0 0 0 0 0 0
7.5167 -6.5167 0.0000 O 0 0 0 0 0 0 0 0 0
11.7542 -5.1500 0.0000 C 0 0 0 0 0 0 0 0 0
11.2417 -6.0542 0.0000 C 0 0 0 0 0 0 0 0 0
10.7250 -5.7625 0.0000 C 0 0 0 0 0 0 0 0 0
6.5750 -5.1917 0.0000 C 0 0 0 0 0 0 0 0 0
6.0542 -6.0917 0.0000 C 0 0 0 0 0 0 0 0 0
11.7667 -5.7542 0.0000 C 0 0 0 0 0 0 0 0 0
12.2750 -4.8417 0.0000 C 0 0 0 0 0 0 0 0 0
6.0542 -4.8917 0.0000 C 0 0 0 0 0 0 0 0 0
5.5375 -5.7917 0.0000 C 0 0 0 0 0 0 0 0 0
5.5375 -5.1917 0.0000 C 0 0 0 0 0 0 0 0 0
6.3167 -6.3042 0.0000 H 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0
3 2 1 0 0 0
4 1 1 0 0 0
5 8 1 0 0 0
6 10 1 0 0 0
7 17 1 0 0 0
8 3 1 0 0 0
9 1 2 0 0 0
10 13 1 0 0 0
11 3 1 0 0 0
12 2 1 0 0 0
13 7 1 0 0 0
14 4 1 0 0 0
15 14 1 0 0 0
16 14 1 0 0 0
17 16 1 0 0 0
18 15 1 0 0 0
19 11 1 0 0 0
20 5 1 0 0 0
21 5 1 0 0 0
2 22 1 6 0 0
23 6 2 0 0 0
24 25 1 0 0 0
25 10 2 0 0 0
26 12 1 0 0 0
27 12 2 0 0 0
28 24 2 0 0 0
29 23 1 0 0 0
30 26 2 0 0 0
31 27 1 0 0 0
32 31 2 0 0 0
3 33 1 6 0 0
7 18 1 0 0 0
19 5 1 0 0 0
32 30 1 0 0 0
28 23 1 0 0 0
M END""")
nm = Draw.PrepareMolForDrawing(m)
self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondType(), Chem.BondType.SINGLE)
self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondDir(), Chem.BondDir.NONE)
self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondType(), Chem.BondType.SINGLE)
self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondDir(), Chem.BondDir.BEGINWEDGE)
nm = Draw.PrepareMolForDrawing(nm)
self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondType(), Chem.BondType.SINGLE)
self.assertEqual(nm.GetBondBetweenAtoms(2, 1).GetBondDir(), Chem.BondDir.NONE)
self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondType(), Chem.BondType.SINGLE)
self.assertEqual(nm.GetBondBetweenAtoms(2, 7).GetBondDir(), Chem.BondDir.BEGINWEDGE)
def testDrawMoleculesArgs(self):
smis = [
'O=C1c2cccc3c(N4CCCCC4)ccc(c23)C(=O)N1c1ccccn1', 'Cc1ccc[n+](C2=Nc3ccccc3[N-]C2=C(C#N)C#N)c1',
'CC(=O)NC1=NN(C(C)=O)C(c2ccccn2)S1', 'COc1cc(Cc2nccc3cc(OC)c(OC)cc23)c(S(=O)(=O)O)cc1OC'
]
tms = [Chem.MolFromSmiles(x) for x in smis]
[rdMolDraw2D.PrepareMolForDrawing(x) for x in tms]
drawer = rdMolDraw2D.MolDraw2DSVG(600, 600, 300, 300)
p = Chem.MolFromSmarts('c1ccccn1')
matches = [x.GetSubstructMatch(p) for x in tms]
acolors = []
for mv in matches:
clrs = {}
random.seed(0xf00d)
for idx in mv:
clrs[idx] = (random.random(), random.random(), random.random())
acolors.append(clrs)
# the bonds between the matching atoms too
bnds = []
for mol, mv in zip(tms, matches):
tmp = []
for bnd in p.GetBonds():
tmp.append(
mol.GetBondBetweenAtoms(mv[bnd.GetBeginAtomIdx()], mv[bnd.GetEndAtomIdx()]).GetIdx())
bnds.append(tmp)
drawer.DrawMolecules(tms, highlightAtoms=matches, highlightBonds=bnds,
highlightAtomColors=acolors)
drawer.FinishDrawing()
svg = drawer.GetDrawingText()
# 4 molecules, 6 bonds each:
re_str = r"path class='bond-\d+ atom-\d+ atom-\d+' d='M \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+ Z' style='fill:"
patt = re.compile(re_str)
self.assertEqual(len(patt.findall(svg)), 24)
# 4 molecules, one atom each:
self.assertEqual(svg.count('fill:#DB2D2B;fill-rule:evenodd;stroke:#DB2D2B'), 4)
def testGetDrawCoords(self):
m = Chem.MolFromSmiles('c1ccc(C)c(C)c1C')
AllChem.Compute2DCoords(m)
d = Draw.MolDraw2DSVG(300, 300)
d.DrawMolecule(m)
conf = m.GetConformer()
for idx in range(m.GetNumAtoms()):
pos = conf.GetAtomPosition(idx)
pos = Geometry.Point2D(pos.x, pos.y)
dpos1 = d.GetDrawCoords(idx)
dpos2 = d.GetDrawCoords(pos)
self.assertAlmostEqual(dpos1.x, dpos2.x, 6)
self.assertAlmostEqual(dpos1.y, dpos2.y, 6)
def testReaction1(self):
rxn = AllChem.ReactionFromSmarts(
'[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
useSmiles=True)
d = Draw.MolDraw2DSVG(900, 300)
d.DrawReaction(rxn)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("<svg") != -1)
self.assertTrue(txt.find("</svg>") != -1)
# print(txt,file=open('blah1.svg','w+'))
def testReaction2(self):
rxn = AllChem.ReactionFromSmarts(
'[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
useSmiles=True)
d = Draw.MolDraw2DSVG(900, 300)
d.DrawReaction(rxn, highlightByReactant=True)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("<svg") != -1)
self.assertTrue(txt.find("</svg>") != -1)
# print(txt,file=open('blah2.svg','w+'))
def testReaction3(self):
rxn = AllChem.ReactionFromSmarts(
'[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
useSmiles=True)
colors = [(0.3, 0.7, 0.9), (0.9, 0.7, 0.9), (0.6, 0.9, 0.3), (0.9, 0.9, 0.1)]
d = Draw.MolDraw2DSVG(900, 300)
d.DrawReaction(rxn, highlightByReactant=True, highlightColorsReactants=colors)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("<svg") != -1)
self.assertTrue(txt.find("</svg>") != -1)
def testReaction4(self):
rxn = AllChem.ReactionFromSmarts(
'[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=[O:3])[NH:6][CH3:5].[OH2:4]',
useSmiles=True)
colors = [(100, 155, 245), (0, 45, 155)]
d = Draw.MolDraw2DSVG(900, 300)
self.assertRaises(ValueError, d.DrawReaction, rxn, True, colors)
def testBWDrawing(self):
m = Chem.MolFromSmiles('CCOCNCCl')
dm = Draw.PrepareMolForDrawing(m)
d = Draw.MolDraw2DSVG(300, 300)
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke:#000000") >= 0)
self.assertTrue(txt.find("stroke:#00CC00") >= 0)
d = Draw.MolDraw2DSVG(300, 300)
d.drawOptions().useBWAtomPalette()
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke:#000000") >= 0)
self.assertTrue(txt.find("stroke:#00CC00") == -1)
def testUpdatePalette(self):
m = Chem.MolFromSmiles('CCOCNCCl')
dm = Draw.PrepareMolForDrawing(m)
d = Draw.MolDraw2DSVG(300, 300)
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke:#000000") >= 0)
self.assertTrue(txt.find("stroke:#00CC00") >= 0)
d = Draw.MolDraw2DSVG(300, 300)
d.drawOptions().updateAtomPalette({6: (1, 1, 0)})
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke:#000000") == -1)
self.assertTrue(txt.find("stroke:#00CC00") >= 0)
self.assertTrue(txt.find("stroke:#FFFF00") >= 0)
def testSetPalette(self):
m = Chem.MolFromSmiles('CCOCNCCl')
dm = Draw.PrepareMolForDrawing(m)
d = Draw.MolDraw2DSVG(300, 300)
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke:#000000") >= 0)
self.assertTrue(txt.find("stroke:#00CC00") >= 0)
d = Draw.MolDraw2DSVG(300, 300)
d.drawOptions().setAtomPalette({-1: (1, 1, 0)})
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke:#000000") == -1)
self.assertTrue(txt.find("stroke:#00CC00") == -1)
self.assertTrue(txt.find("stroke:#FFFF00") >= 0)
# try a palette that doesn't have a default:
d = Draw.MolDraw2DSVG(300, 300)
d.drawOptions().setAtomPalette({0: (1, 1, 0)})
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke:#000000") >= 0)
self.assertTrue(txt.find("stroke:#00CC00") == -1)
self.assertTrue(txt.find("stroke:#FFFF00") == -1)
def testGithub1829(self):
d = Draw.MolDraw2DSVG(300, 300, 100, 100)
d.DrawMolecules(tuple())
d.FinishDrawing()
d.GetDrawingText()
def testSetLineWidth(self):
" this was github #2149 "
m = Chem.MolFromSmiles('CC')
dm = Draw.PrepareMolForDrawing(m)
d = Draw.MolDraw2DSVG(300, 300)
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke-width:2.0px") >= 0)
self.assertTrue(txt.find("stroke-width:4.0px") == -1)
d = Draw.MolDraw2DSVG(300, 300)
d.SetLineWidth(4)
d.DrawMolecule(dm)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("stroke-width:2.0px") == -1)
self.assertTrue(txt.find("stroke-width:4.0px") >= 0)
def testPrepareAndDrawMolecule(self):
m = Chem.MolFromSmiles("C1N[C@@H]2OCC12")
d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find(">H</text>") > 0)
m = Chem.MolFromSmiles("c1ccccc1")
d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertLess(txt.find("stroke-dasharray"), 0)
d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
rdMolDraw2D.PrepareAndDrawMolecule(d, m, kekulize=False)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertGreater(txt.find("stroke-dasharray"), 0)
def testAtomTagging(self):
m = Chem.MolFromSmiles("C1N[C@@H]2OCC12")
d = Draw.MolDraw2DSVG(300, 300)
dm = Draw.PrepareMolForDrawing(m)
rdMolDraw2D.PrepareAndDrawMolecule(d, dm)
d.TagAtoms(dm, events={'onclick': 'alert'})
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertTrue(txt.find("<circle") > 0)
self.assertTrue(txt.find("onclick=") > 0)
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 testGridContours(self):
grid = np.zeros((50, 100), np.double)
ycoords = list(np.arange(0, 5, 0.1))
xcoords = list(np.arange(0, 10, 0.1))
for i in range(grid.shape[1]):
gxp = xcoords[i]
for j in range(grid.shape[0]):
gyp = ycoords[j]
for v in range(1, 4):
dvx = 2 * v - gxp
dvy = v - gyp
d2 = dvx * dvx + dvy * dvy
if d2 > 0:
grid[j, i] += 1 / np.sqrt(d2)
# sg = 255 * grid / np.max(grid)
# from PIL import Image
# img = Image.fromarray(sg.astype(np.uint8))
# img.save('img.png')
d = Draw.MolDraw2DSVG(300, 300)
d.ClearDrawing()
Draw.ContourAndDrawGrid(d, np.transpose(grid), xcoords, ycoords)
d.drawOptions().clearBackground = False
d.FinishDrawing()
txt = d.GetDrawingText()
with open("contour_from_py_3.svg", 'w+') as outf:
print(txt, file=outf)
def testExtraDrawingCommands(self):
" this is another test just to make sure that things work "
m = Chem.MolFromMolBlock("""
Mrv1810 07271915232D
6 6 0 0 0 0 999 V2000
-1.5 -1.5 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5 0.0 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0 0.0 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0 -1.5 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5 1.5 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5 -1.5 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 1 1 0 0 0 0
2 5 1 0 0 0 0
4 6 1 0 0 0 0
M END
""")
d = Draw.MolDraw2DSVG(300, 300)
dm = Draw.PrepareMolForDrawing(m)
d.DrawMolecule(dm)
conf = dm.GetConformer()
ps3 = (
conf.GetAtomPosition(0),
conf.GetAtomPosition(1),
conf.GetAtomPosition(3),
)
ps = [Geometry.Point2D(p.x, p.y) for p in ps3]
d.DrawPolygon(ps)
d.DrawArrow(Geometry.Point2D(0, 0), Geometry.Point2D(0, 1.5))
d.DrawAttachmentLine(Geometry.Point2D(0, 0), Geometry.Point2D(1.5, 0), (0.5, 0.5, 0.5), len=0.5)
d.DrawLine(Geometry.Point2D(0, 0), Geometry.Point2D(1.5, 0))
d.DrawWavyLine(Geometry.Point2D(0, 0), Geometry.Point2D(1.5, 1.5), (0, 0, 0), (1, 0.2, 0.2))
d.FinishDrawing()
txt = d.GetDrawingText()
with open("extras_1.svg", "w+") as outf:
outf.write(txt)
def testSetDrawOptions(self):
m = Chem.MolFromSmiles('CCNC(=O)O')
d = rdMolDraw2D.MolDraw2DSVG(250, 200, -1, -1, True)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertNotEqual(txt.find("fill:#0000FF' >N</text>"), -1)
self.assertEqual(txt.find("fill:#000000' >N</text>"), -1)
d = rdMolDraw2D.MolDraw2DSVG(250, 200, -1, -1, True)
do = rdMolDraw2D.MolDrawOptions()
do.useBWAtomPalette()
d.SetDrawOptions(do)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertEqual(txt.find("fill:#0000FF' >N</text>"), -1)
self.assertNotEqual(txt.find("fill:#000000' >N</text>"), -1)
def testAlternativeFreetypeFont(self):
# this one, you have to look at the pictures
m = Chem.MolFromSmiles('S(=O)(=O)(O)c1c(Cl)c(Br)c(I)c(F)c(N)1')
d = rdMolDraw2D.MolDraw2DSVG(250, 200)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
with open('test_ff.svg', 'w') as f:
f.write(txt)
d = rdMolDraw2D.MolDraw2DSVG(250, 200)
do = rdMolDraw2D.MolDrawOptions()
rdbase = environ['RDBASE']
if rdbase:
do.fontFile = '{}/Code/GraphMol/MolDraw2D/Amadeus.ttf'.format(rdbase)
d.SetDrawOptions(do)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
with open('test_aff.svg', 'w') as f:
f.write(txt)
else:
pass
def testExplictMethyl(self):
m = Chem.MolFromSmiles('CC')
d = rdMolDraw2D.MolDraw2DSVG(250, 200)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertEqual(txt.find("class='atom-"), -1)
d = rdMolDraw2D.MolDraw2DSVG(250, 200)
do = rdMolDraw2D.MolDrawOptions()
do.explicitMethyl = True
d.SetDrawOptions(do)
rdMolDraw2D.PrepareAndDrawMolecule(d, m)
d.FinishDrawing()
txt = d.GetDrawingText()
self.assertNotEqual(txt.find("class='atom-"), -1)
def testDrawMoleculeWithHighlights(self):
COLS = [(1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (1.0, 0.55, 0.0)]
def get_hit_atoms_and_bonds(mol, smt):
alist = []
blist = []
q = Chem.MolFromSmarts(smt)
for match in mol.GetSubstructMatches(q):
alist.extend(match)
for ha1 in alist:
for ha2 in alist:
if ha1 > ha2:
b = mol.GetBondBetweenAtoms(ha1, ha2)
if b:
blist.append(b.GetIdx())
return alist, blist
def add_colours_to_map(els, cols, col_num):
for el in els:
if el not in cols:
cols[el] = []
if COLS[col_num] not in cols[el]:
cols[el].append(COLS[col_num])
def do_a_picture(smi, smarts, label, lasso=None):
rdDepictor.SetPreferCoordGen(False)
mol = Chem.MolFromSmiles(smi)
mol = Draw.PrepareMolForDrawing(mol)
acols = {}
bcols = {}
h_rads = {}
h_lw_mult = {}
for i, smt in enumerate(smarts):
alist, blist = get_hit_atoms_and_bonds(mol, smt)
h_rads[alist[0]] = 0.4
h_lw_mult[blist[0]] = 2
col = i % 4
add_colours_to_map(alist, acols, col)
add_colours_to_map(blist, bcols, col)
d = rdMolDraw2D.MolDraw2DSVG(500, 500)
d.drawOptions().fillHighlights = False
if lasso is not None:
if lasso == "Direct":
d.drawOptions().multiColourHighlightStyle = Draw.MultiColourHighlightStyle.Lasso
elif lasso == "ViaJSON":
print('json lasso')
Draw.UpdateDrawerParamsFromJSON(d, '{"multiColourHighlightStyle": "Lasso"}')
d.DrawMoleculeWithHighlights(mol, label, acols, bcols, h_rads, h_lw_mult, -1)
d.FinishDrawing()
return d.GetDrawingText()
smi = 'CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]'
smarts = ['CONN', 'N#CC~CO', 'C=CON', 'CONNCN']
txt = do_a_picture(smi, smarts, 'pyTest2')
self.assertGreater(txt.find('stroke:#FF8C00;stroke-width:8.0'), -1)
self.assertEqual(
txt.find("ellipse cx='244.253' cy='386.518'"
" rx='11.9872' ry='12.8346'"
" style='fill:none;stroke:#00FF00'"), -1)
txt = do_a_picture(smi, smarts, 'pyTest4', lasso="Direct")
# the lasso mode puts paths, not ellipses.
self.assertGreater(txt.find("<path class='atom-5'"), -1)
self.assertEqual(txt.find("ellipse"), -1)
txt = do_a_picture(smi, smarts, 'pyTest4', lasso="ViaJSON")
# the lasso mode puts paths, not ellipses.
self.assertGreater(txt.find("<path class='atom-5'"), -1)
self.assertEqual(txt.find("ellipse"), -1)
# test for no-longer-mysterious OSX crash.
smi = 'c1ccccc1Cl'
smarts = []
do_a_picture(smi, smarts, 'pyTest3')
@unittest.skipUnless(hasattr(Draw, 'MolDraw2DCairo'), 'Cairo support not enabled')
@unittest.skipUnless(hasattr(Chem,'MolFromPNGString'),
"RDKit not built with iostreams support")
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 testUpdateMolDrawOptionsAndDrawerParamsFromJSON(self):
m = Chem.MolFromSmiles('c1ccccc1NC(=O)C1COC1')
d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
txt = d2d.GetDrawingText()
self.assertFalse('>8</text>' in txt)
drawOptions = rdMolDraw2D.MolDrawOptions()
Draw.UpdateMolDrawOptionsFromJSON(drawOptions, '{"addAtomIndices": 1}')
self.assertTrue(drawOptions.addAtomIndices)
d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
d2d.SetDrawOptions(drawOptions)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
txt = d2d.GetDrawingText()
self.assertTrue('>8</text>' in txt)
d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
Draw.UpdateDrawerParamsFromJSON(d2d, '{"addAtomIndices": 1}')
d2d.DrawMolecule(m)
d2d.FinishDrawing()
txt = d2d.GetDrawingText()
self.assertTrue('>8</text>' in txt)
def testIsotopeLabels(self):
m = Chem.MolFromSmiles("[1*]c1cc([2*])c([3*])c[14c]1")
regex = re.compile(r"<text\s+.*>\d</text>")
self.assertIsNotNone(m)
d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
textIsoDummyIso = d2d.GetDrawingText()
nIsoDummyIso = len(regex.findall(textIsoDummyIso))
self.assertEqual(nIsoDummyIso, 5)
d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
d2d.drawOptions().isotopeLabels = False
d2d.DrawMolecule(m)
d2d.FinishDrawing()
textNoIsoDummyIso = d2d.GetDrawingText()
nNoIsoDummyIso = len(regex.findall(textNoIsoDummyIso))
self.assertEqual(nNoIsoDummyIso, 3)
d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
d2d.drawOptions().dummyIsotopeLabels = False
d2d.DrawMolecule(m)
d2d.FinishDrawing()
textIsoNoDummyIso = d2d.GetDrawingText()
nIsoNoDummyIso = len(regex.findall(textIsoNoDummyIso))
self.assertEqual(nIsoNoDummyIso, 2)
d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
d2d.drawOptions().isotopeLabels = False
d2d.drawOptions().dummyIsotopeLabels = False
d2d.DrawMolecule(m)
d2d.FinishDrawing()
textNoIsoNoDummyIso = d2d.GetDrawingText()
nNoIsoNoDummyIso = len(regex.findall(textNoIsoNoDummyIso))
self.assertEqual(nNoIsoNoDummyIso, 0)
m = Chem.MolFromSmiles("C([1H])([2H])([3H])[H]")
deuteriumTritiumRegex = re.compile(r"<text\s+.*>[DT]</text>")
d2d = Draw.MolDraw2DSVG(300, 300, -1, -1, True)
d2d.drawOptions().isotopeLabels = False
d2d.drawOptions().dummyIsotopeLabels = False
d2d.drawOptions().atomLabelDeuteriumTritium = True
d2d.DrawMolecule(m)
d2d.FinishDrawing()
textDeuteriumTritium = d2d.GetDrawingText()
nDeuteriumTritium = len(deuteriumTritiumRegex.findall(textDeuteriumTritium))
self.assertEqual(nDeuteriumTritium, 2)
def testNewDrawingModes(self):
m = Chem.MolFromSmiles("CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+] |SgD:7:note:some extra text:=:::|")
d2d = Draw.MolDraw2DSVG(300, 300)
rdMolDraw2D.SetDarkMode(d2d)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
text = d2d.GetDrawingText()
self.assertIn("<rect style='opacity:1.0;fill:#000000;stroke:none'", text)
d2d = Draw.MolDraw2DSVG(300, 300)
rdMolDraw2D.SetMonochromeMode(d2d, (1, 1, 1), (.5, .5, .5))
d2d.DrawMolecule(m)
d2d.FinishDrawing()
text = d2d.GetDrawingText()
self.assertIn("<rect style='opacity:1.0;fill:#7F7F7F;stroke:none'", text)
self.assertIn("stroke:#FFFFFF;stroke-width:2", text)
d2d = Draw.MolDraw2DSVG(300, 300)
d2d.drawOptions().useAvalonAtomPalette()
d2d.DrawMolecule(m)
d2d.FinishDrawing()
text = d2d.GetDrawingText()
self.assertIn("<rect style='opacity:1.0;fill:#FFFFFF;stroke:none'", text)
self.assertIn("stroke:#007E00;stroke-width:2", text)
d2d = Draw.MolDraw2DSVG(300, 300)
d2d.drawOptions().useCDKAtomPalette()
d2d.DrawMolecule(m)
d2d.FinishDrawing()
text = d2d.GetDrawingText()
self.assertIn("<rect style='opacity:1.0;fill:#FFFFFF;stroke:none'", text)
self.assertIn("stroke:#2F50F7;stroke-width:2", text)
def testGithub4838(self):
m = Chem.MolFromSmiles("CCCC")
d2d = Draw.MolDraw2DSVG(300, 300)
d2d.DrawMolecule(m)
d2d.DrawString("foo1", Geometry.Point2D(1, 0))
d2d.DrawString("foo0", Geometry.Point2D(1, 1), 0)
d2d.DrawString("foo2", Geometry.Point2D(1, 2), 1)
d2d.DrawString("foo3", Geometry.Point2D(1, 3), 2)
with self.assertRaises(ValueError):
d2d.DrawString("fail", Geometry.Point2D(1, 4), 3)
def testGithub5298(self):
with self.assertRaises(RuntimeError):
rdMolDraw2D.PrepareMolForDrawing(None)
def testACS1996Mode(self):
m = Chem.MolFromSmiles("CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+]")
AllChem.Compute2DCoords(m)
rdMolDraw2D.PrepareMolForDrawing(m)
svg = rdMolDraw2D.MolToACS1996SVG(m, "ACS Mode")
with open("testACSMode_1.svg", 'w') as f:
f.write(svg)
highlight_atoms = [0, 2, 4, 6, 8]
highlight_bonds = [1, 3, 5, 7, 9]
highlight_atom_cols = {
0: (1.0, 1.0, 0.0),
8: (1.0, 0.0, 1.0),
}
highlight_bond_cols = {
0: (0.0, 1.0, 1.0),
8: (0.0, 0.0, 1.0),
}
svg = rdMolDraw2D.MolToACS1996SVG(m, "Highlights", highlight_atoms, highlight_bonds,
highlight_atom_cols, highlight_bond_cols)
with open("testACSMode_2.svg", 'w') as f:
f.write(svg)
if hasattr(Draw, 'MolDraw2DCairo'):
drawer = rdMolDraw2D.MolDraw2DCairo(-1, -1)
rdMolDraw2D.DrawMoleculeACS1996(drawer, m)
drawer.FinishDrawing()
drawer.WriteDrawingText('testACSMode_1.png')
def testMolSize(self):
m = Chem.MolFromSmiles("CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+]")
AllChem.Compute2DCoords(m)
rdMolDraw2D.PrepareMolForDrawing(m)
d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
d2d.DrawMolecule(m)
sz = d2d.Width(), d2d.Height()
d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
sz2 = d2d.GetMolSize(m)
self.assertEqual(sz, sz2)
def testQueryColour(self):
m = Chem.MolFromSmarts("c1ccc2nc([*:1])nc([*:2])c2c1")
self.assertIsNotNone(m)
# Check that default queryColour is #7F7F7F.
d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
text = d2d.GetDrawingText()
self.assertTrue("#7F7F7F" in text)
# Check that queryColour can be set to black.
query_colour = (0.0, 0.0, 0.0)
d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
d2d.drawOptions().setQueryColour(query_colour)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
text = d2d.GetDrawingText()
self.assertTrue("#7F7F7F" not in text)
@unittest.skipUnless(hasattr(Draw, 'MolDraw2DCairo'), 'Cairo support not enabled')
def testGithub7409(self):
m = Chem.MolFromSmiles('CC |(-0.75,0,;0.75,0,)|')
m.GetConformer().SetId(5)
d2d = rdMolDraw2D.MolDraw2DCairo(200, 200)
# it's enough to check that this doesn't throw an exception
d2d.DrawMolecule(m)
if __name__ == "__main__":
unittest.main()
|
