class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='png', path=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def __drawLabel(self, configuration, cr, x0, y0, format='pdf'):
boundingRect = self.__getLabelSize(configuration, format=format)
padding = 2
useStructures = self.__useStructureForLabel(configuration)
y = y0
for i, spec in enumerate(configuration.species):
if i > 0:
rect = self.__getTextSize('+', padding=padding, format=format)
x = x0 - 0.5 * (rect[2] - boundingRect[2]) + 2 * padding
self.__drawText('+', cr, x, y)
y += rect[3]
if useStructures:
moleculeDrawer = MoleculeDrawer()
cr.save()
surf, c, rect = moleculeDrawer.draw(spec.molecule[0], format=format)
cr.restore()
x = x0 - 0.5 * (rect[2] - boundingRect[2])
cr.save()
moleculeDrawer.render(cr, offset=(x, y))
cr.restore()
y += rect[3]
else:
rect = self.__getTextSize(spec.label, padding=padding, format=format)
x = x0 - 0.5 * (rect[2] - boundingRect[2]) + 2 * padding
self.__drawText(spec.label, cr, x, y)
y += rect[3]
return boundingRect
def _draw_label(self, configuration, cr, x0, y0, file_format='pdf'):
bounding_rect = self._get_label_size(configuration, file_format=file_format)
padding = 2
use_structures = self._use_structure_for_label(configuration)
y = y0
for i, spec in enumerate(configuration.species_list):
if i > 0:
rect = self._get_text_size('+', padding=padding, file_format=file_format)
x = x0 - 0.5 * (rect[2] - bounding_rect[2]) + 2 * padding
self._draw_text('+', cr, x, y)
y += rect[3]
if use_structures:
molecule_drawer = MoleculeDrawer()
cr.save()
rect = molecule_drawer.draw(spec.molecule[0], file_format=file_format)[2]
cr.restore()
x = x0 - 0.5 * (rect[2] - bounding_rect[2])
cr.save()
molecule_drawer.render(cr, offset=(x, y))
cr.restore()
y += rect[3]
else:
rect = self._get_text_size(spec.label, padding=padding, file_format=file_format)
x = x0 - 0.5 * (rect[2] - bounding_rect[2]) + 2 * padding
self._draw_text(spec.label, cr, x, y)
y += rect[3]
return bounding_rect
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
try:
from cairocffi import ImageSurface
except ImportError:
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='png',
target=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def testDrawNonStandardBonds(self):
spec = Species().fromSMILES('[CH2]C=C[CH2]')
hybrid = spec.getResonanceHybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(hybrid, format='pdf')
self.assertIsInstance(surface, PDFSurface)
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(smiles='CC(=O)CC')
def test_draw_png(self):
"""
Test we can create PNG files from molecules.
"""
try:
from cairocffi import ImageSurface
except ImportError:
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(self.molecule, file_format='png', target=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
self.assertGreater(width, height)
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def test_draw_pdf(self):
"""
Test we can create PDF files from molecules.
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(self.molecule, file_format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def test_draw_polycycle(self):
"""
Test we can draw a polycyclic molecule
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(smiles="C123CC4CC1COCC2CCC34")
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(polycycle, file_format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def test_draw_pdf_without_file(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(self.molecule, file_format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def test_draw_non_standard_bonds(self):
spec = Species().from_smiles('[CH2]C=C[CH2]')
hybrid = spec.get_resonance_hybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(hybrid, file_format='pdf')
self.assertGreater(width, height)
self.assertIsInstance(surface, PDFSurface)
def test_draw_hydrogen_bond_adsorbate(self):
molecule = Molecule().from_adjacency_list("""
1 O u0 p3 c-1 {2,S} {10,H}
2 N u0 p0 c+1 {1,S} {3,D} {4,S}
3 O u0 p2 c0 {2,D}
4 O u0 p2 c0 {2,S} {7,S}
5 N u0 p1 c0 {6,S} {8,S} {9,S} {7,H}
6 O u0 p2 c0 {5,S} {10,S}
7 H u0 p0 c0 {4,S} {5,H}
8 H u0 p0 c0 {5,S}
9 H u0 p0 c0 {5,S}
10 H u0 p0 c0 {6,S} {1,H}
11 X u0 p0 c0
"""
)
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, _cr, (_xoff, _yoff, _width, _height) = self.drawer.draw(molecule, file_format='pdf')
self.assertIsInstance(surface, PDFSurface)
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
try:
from cairocffi import ImageSurface
except ImportError:
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='png', target=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf', target=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
def testDrawNonStandardBonds(self):
spec = Species().fromSMILES('[CH2]C=C[CH2]')
hybrid = spec.getResonanceHybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(hybrid, format='pdf')
self.assertIsInstance(surface, PDFSurface)
class TestMoleculeDrawer(unittest.TestCase):
"""
Contains unit tests of the MoleculeDrawer class.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
self.drawer = MoleculeDrawer()
self.molecule = Molecule(SMILES='CC(=O)CC')
def testDrawPNG(self):
"""
Test we can create PNG files from molecules.
"""
from cairo import ImageSurface
path = 'test_molecule.png'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='png',
path=path)
self.assertTrue(os.path.exists(path), "File doesn't exist")
os.unlink(path)
self.assertIsInstance(surface, ImageSurface)
def testDrawPDF(self):
"""
Test we can create PDF files from molecules.
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPolycycle(self):
"""
Test we can draw a polycyclic molecule
"""
from cairo import PDFSurface
path = 'test_molecule.pdf'
if os.path.exists(path):
os.unlink(path)
polycycle = Molecule(SMILES="C123CC4CC1COCC2CCC34")
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule,
format='pdf',
path=path)
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
os.unlink(path)
def testDrawPDFwithoutFile(self):
"""
Test we can create PDF surface without a temporary file (newer versions of PyCairo?)
"""
from cairo import PDFSurface
surface, cr, (xoff, yoff, width,
height) = self.drawer.draw(self.molecule, format='pdf')
self.assertIsInstance(surface, PDFSurface)
self.assertGreater(width, height)
