本文整理匯總了Python中rdkit.Chem.CombineMols方法的典型用法代碼示例。如果您正苦於以下問題：Python Chem.CombineMols方法的具體用法？Python Chem.CombineMols怎麽用？Python Chem.CombineMols使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類rdkit.Chem的用法示例。
在下文中一共展示了Chem.CombineMols方法的7個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: normalize
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import CombineMols [as 別名]
def normalize(self, mol):
"""Apply a series of Normalization transforms to correct functional groups and recombine charges.
A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
until no further changes occur. If any changes occurred, we go back and start from the first Normalization
again, in case the changes mean an earlier transform is now applicable. The molecule is returned once the entire
series of Normalizations cause no further changes or if max_restarts (default 200) is reached.
:param mol: The molecule to normalize.
:type mol: rdkit.Chem.rdchem.Mol
:return: The normalized fragment.
:rtype: rdkit.Chem.rdchem.Mol
"""
log.debug('Running Normalizer')
# Normalize each fragment separately to get around quirky RunReactants behaviour
fragments = []
for fragment in Chem.GetMolFrags(mol, asMols=True):
fragments.append(self._normalize_fragment(fragment))
# Join normalized fragments into a single molecule again
outmol = fragments.pop()
for fragment in fragments:
outmol = Chem.CombineMols(outmol, fragment)
Chem.SanitizeMol(outmol)
return outmol 示例2: normalize
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import CombineMols [as 別名]
def normalize(self, mol):
"""Apply a series of Normalization transforms to correct functional groups and recombine charges.
A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
until no further changes occur. If any changes occurred, we go back and start from the first Normalization
again, in case the changes mean an earlier transform is now applicable. The molecule is returned once the entire
series of Normalizations cause no further changes or if max_restarts (default 200) is reached.
:param mol: The molecule to normalize.
:type mol: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
:return: The normalized fragment.
:rtype: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
"""
log.debug("Running Normalizer")
# Normalize each fragment separately to get around quirky RunReactants behaviour
fragments = []
for fragment in Chem.GetMolFrags(mol, asMols=True):
fragments.append(self._normalize_fragment(fragment))
# Join normalized fragments into a single molecule again
outmol = fragments.pop()
for fragment in fragments:
outmol = Chem.CombineMols(outmol, fragment)
Chem.SanitizeMol(outmol)
return outmol 示例3: clean_charges
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import CombineMols [as 別名]
def clean_charges(mol):
"""
This hack should not be needed anymore, but is kept just in case
"""
Chem.SanitizeMol(mol)
#rxn_smarts = ['[N+:1]=[*:2]-[C-:3]>>[N+0:1]-[*:2]=[C-0:3]',
# '[N+:1]=[*:2]-[O-:3]>>[N+0:1]-[*:2]=[O-0:3]',
# '[N+:1]=[*:2]-[*:3]=[*:4]-[O-:5]>>[N+0:1]-[*:2]=[*:3]-[*:4]=[O-0:5]',
# '[#8:1]=[#6:2]([!-:6])[*:3]=[*:4][#6-:5]>>[*-:1][*:2]([*:6])=[*:3][*:4]=[*+0:5]',
# '[O:1]=[c:2][c-:3]>>[*-:1][*:2][*+0:3]',
# '[O:1]=[C:2][C-:3]>>[*-:1][*:2]=[*+0:3]']
rxn_smarts = ['[#6,#7:1]1=[#6,#7:2][#6,#7:3]=[#6,#7:4][CX3-,NX3-:5][#6,#7:6]1=[#6,#7:7]>>'
'[#6,#7:1]1=[#6,#7:2][#6,#7:3]=[#6,#7:4][-0,-0:5]=[#6,#7:6]1[#6-,#7-:7]',
'[#6,#7:1]1=[#6,#7:2][#6,#7:3](=[#6,#7:4])[#6,#7:5]=[#6,#7:6][CX3-,NX3-:7]1>>'
'[#6,#7:1]1=[#6,#7:2][#6,#7:3]([#6-,#7-:4])=[#6,#7:5][#6,#7:6]=[-0,-0:7]1']
fragments = Chem.GetMolFrags(mol,asMols=True,sanitizeFrags=False)
for i, fragment in enumerate(fragments):
for smarts in rxn_smarts:
patt = Chem.MolFromSmarts(smarts.split(">>")[0])
while fragment.HasSubstructMatch(patt):
rxn = AllChem.ReactionFromSmarts(smarts)
ps = rxn.RunReactants((fragment,))
fragment = ps[0][0]
Chem.SanitizeMol(fragment)
if i == 0:
mol = fragment
else:
mol = Chem.CombineMols(mol, fragment)
return mol 示例4: connect_mols
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import CombineMols [as 別名]
def connect_mols(mol1, mol2, atom1, atom2):
combined = Chem.CombineMols(mol1, mol2)
emol = Chem.EditableMol(combined)
neighbor1_idx = atom1.GetNeighbors()[0].GetIdx()
neighbor2_idx = atom2.GetNeighbors()[0].GetIdx()
atom1_idx = atom1.GetIdx()
atom2_idx = atom2.GetIdx()
bond_order = atom2.GetBonds()[0].GetBondType()
emol.AddBond(neighbor1_idx,
neighbor2_idx + mol1.GetNumAtoms(),
order=bond_order)
emol.RemoveAtom(atom2_idx + mol1.GetNumAtoms())
emol.RemoveAtom(atom1_idx)
mol = emol.GetMol()
return mol 示例5: clean_charges
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import CombineMols [as 別名]
def clean_charges(mol):
# this hack should not be needed any more but is kept just in case
#
rxn_smarts = ['[N+:1]=[*:2]-[C-:3]>>[N+0:1]-[*:2]=[C-0:3]',
'[N+:1]=[*:2]-[O-:3]>>[N+0:1]-[*:2]=[O-0:3]',
'[N+:1]=[*:2]-[*:3]=[*:4]-[O-:5]>>[N+0:1]-[*:2]=[*:3]-[*:4]=[O-0:5]',
'[#8:1]=[#6:2]([!-:6])[*:3]=[*:4][#6-:5]>>[*-:1][*:2]([*:6])=[*:3][*:4]=[*+0:5]',
'[O:1]=[c:2][c-:3]>>[*-:1][*:2][*+0:3]',
'[O:1]=[C:2][C-:3]>>[*-:1][*:2]=[*+0:3]']
fragments = Chem.GetMolFrags(mol,asMols=True,sanitizeFrags=False)
for i,fragment in enumerate(fragments):
for smarts in rxn_smarts:
patt = Chem.MolFromSmarts(smarts.split(">>")[0])
while fragment.HasSubstructMatch(patt):
rxn = AllChem.ReactionFromSmarts(smarts)
ps = rxn.RunReactants((fragment,))
fragment = ps[0][0]
if i == 0:
mol = fragment
else:
mol = Chem.CombineMols(mol,fragment)
return mol 示例6: join_fragments
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import CombineMols [as 別名]
def join_fragments(fragments):
to_join = []
bonds = []
pairs = []
del_atoms = []
new_mol = fragments[0]
j,b,r = get_join_list(fragments[0])
to_join += j
del_atoms += r
bonds += b
offset = fragments[0].GetNumAtoms()
for f in fragments[1:]:
j,b,r = get_join_list(f)
p = to_join.pop()
pb = bonds.pop()
# Check bond types if b[:-1] == pb
if b[:-1] != pb:
assert("Can't connect bonds")
pairs.append((p, j[-1] + offset,pb))
for x in j[:-1]:
to_join.append(x + offset)
for x in r:
del_atoms.append(x + offset)
bonds += b[:-1]
offset += f.GetNumAtoms()
new_mol = Chem.CombineMols(new_mol, f)
new_mol = Chem.EditableMol(new_mol)
for a1,a2,b in pairs:
new_mol.AddBond(a1,a2, order=b)
# Remove atom with greatest number first:
for s in sorted(del_atoms, reverse=True):
new_mol.RemoveAtom(s)
return new_mol.GetMol()
# Decide the class of a fragment
# Either R-group, Linker or Scaffold 示例7: join_fragments
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import CombineMols [as 別名]
def join_fragments(fragments):
to_join = []
bonds = []
pairs = []
del_atoms = []
new_mol = fragments[0]
j,b,r = get_join_list(fragments[0])
to_join += j
del_atoms += r
bonds += b
offset = fragments[0].GetNumAtoms()
for f in fragments[1:]:
j,b,r = get_join_list(f)
p = to_join.pop()
pb = bonds.pop()
# Check bond types if b[:-1] == pb
if b[:-1] != pb:
assert("Can't connect bonds")
pairs.append((p, j[-1] + offset,pb))
for x in j[:-1]:
to_join.append(x + offset)
for x in r:
del_atoms.append(x + offset)
bonds += b[:-1]
offset += f.GetNumAtoms()
new_mol = Chem.CombineMols(new_mol, f)
new_mol = Chem.EditableMol(new_mol)
for a1,a2,b in pairs:
new_mol.AddBond(a1,a2, order=b)
# Remove atom with greatest number first:
for s in sorted(del_atoms, reverse=True):
new_mol.RemoveAtom(s)
return new_mol.GetMol()
# Decide the class of a fragment
# Either R-group, Linker or Scaffold