Python rdkit.Chem.CombineMols() Examples
The following are 7
code examples of rdkit.Chem.CombineMols().
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Example #1
| Source File: normalize.py From MolVS with MIT License | 6 votes |
|
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
Example #2
| Source File: PyPretreatMolutil.py From PyBioMed with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
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
Example #3
| Source File: xyz2mol.py From xyz2mol with MIT License | 5 votes |
|
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
Example #4
| Source File: combinatorial.py From moses with MIT License | 5 votes |
|
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
Example #5
| Source File: xyz2mol.py From BCAI_kaggle_CHAMPS with MIT License | 5 votes |
|
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
Example #6
| Source File: mol_utils.py From DeepFMPO with MIT License | 4 votes |
|
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
Example #7
| Source File: mol_utils.py From DeepFMPO with MIT License | 4 votes |
|
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
