def add_terminal_atom(mol,
condition,
newAtomicNumber,
newAtomInfo=lambda atm: Chem.AtomMonomerInfo(),
aromatic=lambda atm: False,
bondType=1): #TODO make bondType also a function?
"""create new atom(s) based on expression
Parameters:
----------
mol : rdkmol
Main moelcule one which addition is perforemd
condition : function
outputs how many atoms to add at each atom site of @mol
newAtomicNumber : function
outputs element types to add at each atom site of @mol
newAtomInfo : function
outputs the rdkit AtomInfo block information add at each atom site of @mol
aromatic : function
True/False value for atom aromaticity
bondType : float
Returns
-------
mol : rdkmol
modified molecule
Example:
--------
residue = Chem.MolFromSequence("KK", flavor = 0)
residue = add_terminal_atom(mol = residue,
condition = lambda atm: atm.GetPDBResidueInfo().GetName().strip() == "N",
newAtomName = lambda atm : "CN",
newAtomicNumber = lambda atm: 6)
print(Chem.MolToPDBBlock(residue))
"""
def mapper(condition, mol):
for idx, repeats in enumerate(map(condition, mol.GetAtoms())):
for j in range(repeats):
yield mol.GetAtomWithIdx(idx)
bondType = _bondtypes[bondType]
mol = Chem.RWMol(mol)
for atom in mapper(condition, copy.deepcopy(mol)):
newatom = Chem.Atom(newAtomicNumber(atom))
newatom.SetIsAromatic(aromatic(atom))
newatom.SetMonomerInfo(newAtomInfo(atom))
# newatom.SetMonomerInfo(Chem.AtomPDBResidueInfo(atomName = " {: <3s}".format(newAtomName(atom)),
# residueName = atom.GetPDBResidueInfo().GetResidueName(),
# residueNumber = atom.GetPDBResidueInfo().GetResidueNumber(),
# chainId = atom.GetPDBResidueInfo().GetChainId(),
# ))
mol.AddAtom(newatom)
mol.AddBond(atom.GetIdx(), mol.GetNumAtoms() - 1, bondType)
# mol.UpdatePropertyCache(strict = False)
mol.UpdatePropertyCache()
Chem.GetSSSR(mol)
return mol.GetMol()
