rdkit.Chem.rdchem.Atom - The Atom Class

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.rdchem.Atom - The Atom Class

This section provides a quick introduction of the rdkit.Chem.rdchem.Atom class, which represents an atom with its properties, associated objcts, and operation methods.

What Is rdkit.Chem.rdchem.Atom? - rdkit.Chem.rdchem.Atom is the Atom class located in the rdkit.Chem.rdchem module of the RDKit library.

rdkit.Chem.rdchem.Atom represents an atom, which is usually included in a molecule as a child object. An Atom object has the following main properties, associated objects, and methods.

m = rdkit.Chem.rdmolfiles.MolFromSmiles('Cc1ccccc1') - Creates rdkit.Chem.rdchem.Mol object from the given SMILES.

a = m.GetAtomWithIdx(0) - Returns the first rdkit.Chem.rdchem.Atom object from the given molecule.

a.GetSymbol() or rdkit.Chem.rdchem.Atom.GetSymbol(a) - Returns the atomic symbol of the given atom.

a.GetAtomicNum() or rdkit.Chem.rdchem.Atom.GetAtomicNum(a) - Returns the atomic number of the given atom.

a.GetMass() or rdkit.Chem.rdchem.Atom.GetMass(a) - Returns the atomic mass of the given atom.

a.GetOwningMol() or rdkit.Chem.rdchem.Atom.GetOwningMol(a) - Returns the molecule object that owns the given atom.

a.GetNeighbors() or rdkit.Chem.rdchem.Atom.GetNeighbors(a) - Returns a sequence that represents neighboring atom objects of the given atom.

a.GetBonds() or rdkit.Chem.rdchem.Atom.GetBonds(a) - Returns a sequence that represents bond objects connected to the given atom.

a.GetFormalCharge() or rdkit.Chem.rdchem.Atom.GetFormalCharge(a) - Returns the formal charge at the given atom within the owning molecule.

Here is an example session of using rdkit.Chem.rdchem.Atom class:

>>> import rdkit
>>> m = rdkit.Chem.rdmolfiles.MolFromSmiles('Cc1ccccc1')
>>> a = m.GetAtomWithIdx(0)

>>> a.GetSymbol()
'C'
>>> a.GetAtomicNum()
6

>>> a.GetMass()
12.011
>>> rdkit.Chem.rdchem.Atom.GetMass(a)
12.011

>>> a.GetFormalCharge()
0