def testGithub3101(self):
m = Chem.MolFromSmiles('CCCC')
IPythonConsole.ipython_useSVG = True
IPythonConsole.drawOptions.addAtomIndices = True
res = Draw.MolsToGridImage((m, m))
self.assertIn('class="note"', res.data)
dopts = rdMolDraw2D.MolDrawOptions()
res = Draw.MolsToGridImage((m, m), drawOptions=dopts)
self.assertNotIn('class="note"', res.data)
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 test_smiles_to_svg():
smi = 'Cc1ccc(NC(=O)c2ccc(CN3CCN(C)CC3)cc2)cc1Nc1nccc(-c2cccnc2)n1'
img = vis_utils.smiles_to_svg(smi) # smiles to SVG
assert img is not None
assert naive_svg_check(img) is True
# Check size updates.
dims = (450, 400)
img = vis_utils.smiles_to_svg(smi, size=dims)
assert svg_dimensions(img) == dims
# Check drawing options (clear background).
drawOpts = rdMolDraw2D.MolDrawOptions()
drawOpts.clearBackground = True
img = vis_utils.smiles_to_svg(smi, draw_options=drawOpts)
assert '</rect>' in img # <rect> exists with background
drawOpts.clearBackground = False
img = vis_utils.smiles_to_svg(smi, draw_options=drawOpts)
assert '</rect>' not in img
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
try:
import Image
except ImportError:
from PIL import Image
molSize = (450, 150)
highlightSubstructs = True
kekulizeStructures = True
highlightByReactant = False
ipython_useSVG = False
ipython_3d = False
molSize_3d = (400, 400)
drawing_type_3d = 'stick' # default drawing type for 3d structures
bgcolor_3d = '0xeeeeee'
drawOptions = rdMolDraw2D.MolDrawOptions()
# expose RDLogs to Python StdErr so they are shown
# in the IPythonConsole not the server logs.
Chem.WrapLogs()
def addMolToView(mol, view, confId=-1, drawAs=None):
if mol.GetNumAtoms() >= 999 or drawAs == 'cartoon':
# py3DMol is happier with TER and MASTER records present
pdb = Chem.MolToPDBBlock(mol, flavor=0x20 | 0x10)
view.addModel(pdb, 'pdb')
else:
# py3Dmol does not currently support v3k mol files, so
# we can only provide those with "smaller" molecules
mb = Chem.MolToMolBlock(mol, confId=confId)
