def testDrawRDKit(self):
m = Chem.MolFromSmiles('c1ccccc1CC1CC1')
bi = {}
rdkfp = Chem.RDKFingerprint(m, maxPath=5, bitInfo=bi)
self.assertTrue(1553 in bi)
svg1 = Draw.DrawRDKitBit(m, 1553, bi)
path = bi[1553][0]
svg2 = Draw.DrawRDKitEnv(m, path)
self.assertEqual(svg1, svg2)
self.assertTrue("style='fill:#E5E533;" in svg1)
self.assertFalse("style='fill:#CCCCCC;" in svg1)
self.assertFalse("style='fill:#9999E5;" in svg1)
with self.assertRaises(KeyError):
Draw.DrawRDKitBit(m, 32, bi)
def draw_fragments(self, draw_tuple):
image_list = []
for tup in draw_tuple:
mol, bit_ID, fp = tup
if self.draw_all:
# one molecule can have multiple fragments
for i in range(len(fp[bit_ID])):
img = Draw.DrawRDKitBit(mol, bit_ID, fp, whichExample=i)
image_list.append(img)
else:
img = Draw.DrawRDKitBit(mol, bit_ID, fp, whichExample=0)
image_list.append(img)
imgs = Image.fromarray(np.concatenate(image_list, axis=0))
return imgs
def testDrawRDKit(self):
m = Chem.MolFromSmiles('c1ccccc1CC1CC1')
bi = {}
_ = Chem.RDKFingerprint(m, maxPath=5, bitInfo=bi)
self.assertTrue(1553 in bi)
svg1 = Draw.DrawRDKitBit(m, 1553, bi)
path = bi[1553][0]
svg2 = Draw.DrawRDKitEnv(m, path)
self.assertEqual(svg1, svg2)
self.assertTrue("style='fill:#E5E533;" in svg1)
self.assertFalse("style='fill:#CCCCCC;" in svg1)
self.assertFalse("style='fill:#9999E5;" in svg1)
with self.assertRaises(KeyError):
Draw.DrawRDKitBit(m, 32, bi)
if hasattr(Draw, 'MolDraw2DCairo'):
# Github #3796: make sure we aren't trying to generate metadata:
png = Draw.DrawRDKitBit(m, 1553, bi, useSVG=False)
self.assertIn(b'PNG', png)
self.assertIsNone(Chem.MolFromPNGString(png))
def draw_fragment(self,
fragment_id: Union[str, int],
show_zscore: bool = True) -> str:
"""Draw a specified fragmnet.
Args:
fragment_id (Union[str, int]): User-defined fragment string, or position of the
Morgan fingerprint bit to be drawn.
show_zscore (bool, optional): Annotate drawing with zscore. Defaults to True.
Returns:
str: Molecule drawing SVG.
"""
# images will be annotated with zscore
legend = f"zscore = {self.zscores[fragment_id]:.2f}" if show_zscore else ""
# handle drawing of user-defined fragments
if self.user_frags:
mol = Chem.MolFromSmarts(fragment_id)
img = Draw.MolsToGridImage([mol],
molsPerRow=1,
subImgSize=(200, 200),
legends=[legend])
# handle drawing of auto-generated fragments
mol = self._get_mol_with_frag(fragment_id)
bit_info = {}
if self.fp_type == "morgan":
_ = rdMolDescriptors.GetMorganFingerprintAsBitVect(
mol, radius=self.fp_rad, nBits=self.fp_bits, bitInfo=bit_info)
img = Draw.DrawMorganBit(mol,
fragment_id,
bit_info,
useSVG=True,
legend=legend)
if self.fp_type == "rdkit":
_ = Chem.RDKFingerprint(
mol,
minPath=self.fp_rad,
maxPath=self.fp_rad,
fpSize=self.fp_bits,
bitInfo=bit_info,
)
img = Draw.DrawRDKitBit(mol,
fragment_id,
bit_info,
useSVG=True,
legend=legend)
return img
