def get_rotatable_bonds(mol):
"""
https://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/GraphMol/Descriptors/Lipinski.cpp#L107
Taken from rdkit source to find which bonds are rotatable store
rotatable bonds in (from_atom, to_atom)
Parameters
----------
mol: rdkit Mol
Ligand molecule
Returns
-------
rotatable_bonds: list
List of rotatable bonds in molecule
"""
from rdkit import Chem
from rdkit.Chem import rdmolops
pattern = Chem.MolFromSmarts(
"[!$(*#*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])("
"[CH3])[CH3])&!$([CD3](=[N,O,S])-!@[#7,O,S!D1])&!$([#7,O,S!D1]-!@[CD3]="
"[N,O,S])&!$([CD3](=[N+])-!@[#7!D1])&!$([#7!D1]-!@[CD3]=[N+])]-!@[!$(*#"
"*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])([CH3])"
"[CH3])]")
rdmolops.FastFindRings(mol)
rotatable_bonds = mol.GetSubstructMatches(pattern)
return rotatable_bonds
def _get_rotatable_bonds(self):
"""
https://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/GraphMol/Descriptors/Lipinski.cpp#L107
Taken from rdkit source to find which bonds are rotatable
store rotatable bonds in (from_atom, to_atom)
"""
pattern = Chem.MolFromSmarts(
"[!$(*#*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])("
"[CH3])[CH3])&!$([CD3](=[N,O,S])-!@[#7,O,S!D1])&!$([#7,O,S!D1]-!@[CD3]="
"[N,O,S])&!$([CD3](=[N+])-!@[#7!D1])&!$([#7!D1]-!@[CD3]=[N+])]-!@[!$(*#"
"*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])([CH3])"
"[CH3])]")
rdmolops.FastFindRings(self.mol)
def get_rotatable_bonds(mol: RDKitMol) -> List[Tuple[int, int]]:
"""
https://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/GraphMol/Descriptors/Lipinski.cpp#L107
Taken from rdkit source to find which bonds are rotatable store
rotatable bonds in (from_atom, to_atom)
Parameters
----------
mol: RDKit Mol
Ligand molecule
Returns
-------
rotatable_bonds: List[List[int, int]]
List of rotatable bonds in molecule
Note
----
This function requires RDKit to be installed.
"""
try:
from rdkit import Chem
from rdkit.Chem import rdmolops
except ModuleNotFoundError:
raise ValueError("This function requires RDKit to be installed.")
pattern = Chem.MolFromSmarts(
"[!$(*#*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])("
"[CH3])[CH3])&!$([CD3](=[N,O,S])-!@[#7,O,S!D1])&!$([#7,O,S!D1]-!@[CD3]="
"[N,O,S])&!$([CD3](=[N+])-!@[#7!D1])&!$([#7!D1]-!@[CD3]=[N+])]-!@[!$(*#"
"*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])([CH3])"
"[CH3])]")
rdmolops.FastFindRings(mol)
rotatable_bonds = mol.GetSubstructMatches(pattern)
return rotatable_bonds
