def testDrawMorgan(self):
from rdkit.Chem import rdMolDescriptors
m = Chem.MolFromSmiles('c1ccccc1CC1CC1')
bi = {}
fp = rdMolDescriptors.GetMorganFingerprintAsBitVect(m,
radius=2,
bitInfo=bi)
self.assertTrue(872 in bi)
svg1 = Draw.DrawMorganBit(m, 872, bi)
aid, r = bi[872][0]
svg2 = Draw.DrawMorganEnv(m, aid, r)
self.assertEqual(svg1, svg2)
self.assertTrue("style='fill:#CCCCCC;" in svg1)
self.assertTrue("style='fill:#E5E533;" in svg1)
self.assertTrue("style='fill:#9999E5;" in svg1)
svg1 = Draw.DrawMorganBit(m, 872, bi, centerColor=None)
aid, r = bi[872][0]
svg2 = Draw.DrawMorganEnv(m, aid, r, centerColor=None)
self.assertEqual(svg1, svg2)
self.assertTrue("style='fill:#CCCCCC;" in svg1)
self.assertTrue("style='fill:#E5E533;" in svg1)
self.assertFalse("style='fill:#9999E5;" in svg1)
with self.assertRaises(KeyError):
Draw.DrawMorganBit(m, 32, bi)
def testDrawMorgan(self):
m = Chem.MolFromSmiles('c1ccccc1CC1CC1')
bi = {}
_ = rdMolDescriptors.GetMorganFingerprintAsBitVect(m,
radius=2,
bitInfo=bi)
self.assertTrue(872 in bi)
svg1 = Draw.DrawMorganBit(m, 872, bi)
aid, r = bi[872][0]
svg2 = Draw.DrawMorganEnv(m, aid, r)
self.assertEqual(svg1, svg2)
self.assertTrue("style='fill:#CCCCCC;" in svg1)
self.assertTrue("style='fill:#E5E533;" in svg1)
self.assertTrue("style='fill:#9999E5;" in svg1)
svg1 = Draw.DrawMorganBit(m, 872, bi, centerColor=None)
aid, r = bi[872][0]
svg2 = Draw.DrawMorganEnv(m, aid, r, centerColor=None)
self.assertEqual(svg1, svg2)
self.assertTrue("style='fill:#CCCCCC;" in svg1)
self.assertTrue("style='fill:#E5E533;" in svg1)
self.assertFalse("style='fill:#9999E5;" in svg1)
with self.assertRaises(KeyError):
Draw.DrawMorganBit(m, 32, bi)
if hasattr(Draw, 'MolDraw2DCairo'):
# Github #3796: make sure we aren't trying to generate metadata:
png = Draw.DrawMorganBit(m, 872, bi, useSVG=False)
self.assertIn(b'PNG', png)
self.assertIsNone(Chem.MolFromPNGString(png))
def draw_fp_bit(fp_func,base_path,mol,idx=None,**kwargs):
info = {}
Mol_add_atomSymbol(mol)
fp = fp_func(mol,bitInfo=info,**kwargs)
if not os.path.exists(base_path):
os.mkdir(base_path)
if idx is None:
for key in info.keys():
print("Bit {} : \n".format(key))
sub_svg=Draw.DrawMorganBit(mol,key,info,useSVG=True)
key = str(key)
full_path = join(base_path,key)
Draw_from_svg(sub_svg,full_path)
else:
sub_svg=Draw.DrawMorganBit(mol,idx,info,useSVG=True)
Draw_from_svg(sub_svg,join(base_path,idx))
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
def DrawBitFromSmiles(smiles, fp_choice, weboutput=True):
fp_choice = int(fp_choice)
mol = Chem.MolFromSmiles(smiles)
bitInfo = {}
fp = AllChem.GetMorganFingerprint(mol,
3,
bitInfo=bitInfo,
useChirality=True)
if fp_choice in bitInfo:
svg = Draw.DrawMorganBit(mol, fp_choice, bitInfo, useSVG=True)
if weboutput:
svg = svg.replace("\n", "")
return (svg)
else:
return (None)
# 64: ((1, 1), (2, 1)), 74: ((3, 1),),
# 81: ((0, 0), (1, 0), (2, 0), (3, 0)), 100: ((5, 0),),
# 121: ((4, 2),), 122: ((4, 0),),
# 131: ((2, 2),), 172: ((4, 1),),
# 175: ((1, 2),), 179: ((0, 2),),
# 186: ((6, 1),), 192: ((3, 2),),
# 195: ((5, 1),), 214: ((0, 1),)
# }
# 对bit进行可视化
bits = list(bi.keys())
print(bits)
[19, 33, 64, 74, 81, 100, 121, 122, 131, 172, 175, 179, 186, 192, 195, 214]
bits = [19, 64, 81]
imgs = []
for bit in bits:
mfp2_svg = Draw.DrawMorganBit(mol, bit, bi)
imgs.append(mfp2_svg)
def displayingsinrow(imgs, col=4):
plt.figure(figsize=(20, 20))
columns = col
for i, image in enumerate(imgs):
ax = plt.subplot(len(imgs) / columns, columns, i)
ax.set_axis_off()
plt.imshow(image)
displayingsinrow(imgs)
bi_tuple = [(mol, bit, bi) for bit in list(bi.keys())]
continue
# remove 3D info for Draw Bits, may fail for Kekulize
m = Chem.MolFromSmiles(Chem.MolToSmiles(m))
if m is None:
continue
info = {}
fp = AllChem.GetMorganFingerprintAsBitVect(m,
2,
nBits=nBits,
bitInfo=info)
if bit in set(fp.GetOnBits()):
bit_examples.append((m, bit, info))
example_count += 1
break
# http://rdkit.blogspot.com/2018/10/using-new-fingerprint-bit-rendering-code.html
examples_svg = [Draw.DrawMorganBit(*i) for i in bit_examples]
# remove two '\n' at the start and end of svg
examples_svg = [i.strip() for i in examples_svg]
examples_svg = [i.replace('\n<svg', '<svg') for i in examples_svg]
for list_, svg in zip(bits_examples, examples_svg):
list_.append(svg)
svg_cols = [f'example_{i+1}' for i in range(4)]
for col, list_ in zip(svg_cols, bits_examples):
df[col] = list_
df = df.sort_values(by='zinc_freq', ascending=False)
df = df.reset_index(drop=True)
df.index += 1
df['bit'] = [f'bit:<br>{i}' for i in df['bit']]
df['log2_FC'] = [f'log2(FC):<br>{i:.2f}' for i in df['log2_FC']]
for col in ['active_freq', 'decoy_freq', 'mean_freq', 'zinc_freq']:
