rdkit.Chem.rdchem.Mol - The Molecule Class

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.rdchem.Mol - The Molecule Class

This section provides a quick introduction of the rdkit.Chem.rdchem.Mol class, which represents a molecule with its properties, child objcts, and operation methods.

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

rdkit.Chem.rdchem.Mol represents a molecule with the following main properties, child objects, and methods.

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

m.Compute2DCoords() or rdkit.Chem.rdchem.Mol.Compute2DCoords(m) - Compute 2 dimensional coordinates of atoms and bonds of a given molecule to depict it as a 2-D structure.

m.GetNumAtoms() or rdkit.Chem.rdchem.Mol.GetNumAtoms(m) - Returns the number of atoms of the given molecule.

m.GetNumBonds() or rdkit.Chem.rdchem.Mol.GetNumBonds(m) - Returns the number of bonds of the given molecule.

m.SetProp(key, value) or rdkit.Chem.rdchem.Mol.SetProp(m, key, value) - Adds or updates a custom property in the given molecule.

m.GetProp(key) or rdkit.Chem.rdchem.Mol.SetProp(m, key) - Returns the value of a given custom property from the given molecule.

m.GetPropsAsDict() or rdkit.Chem.rdchem.Mol.GetPropsAsDict(m) - Returns all custom properties as a dictionary from the given molecule.

m.Debug() or rdkit.Chem.rdchem.Mol.Debug(m) - Prints debug information of the given molecule.

m.GetAtomWithIdx(i) or rdkit.Chem.rdchem.Mol.GetAtomWithIdx(m, i) - Returns the Atom object at a given index from the given molecule.

m.GetAtoms() or rdkit.Chem.rdchem.Mol.GetAtoms(m) - Returns a sequence that represents all child atoms of the given molecule.

m.GetBondWithIdx(i) or rdkit.Chem.rdchem.Mol.GetBondWithIdx(m, i) - Returns the Bond object at a given index from the given molecule.

m.GetBonds() or rdkit.Chem.rdchem.Mol.GetBonds(m) - Returns a sequence that represents all child bonds of the given molecule.

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

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

>>> m.GetNumAtoms()
7
>>> m.GetNumBonds()
7
>>> rdkit.Chem.rdchem.Mol.GetNumAtoms(m)
7
>>> rdkit.Chem.rdchem.Mol.GetNumBonds(m)
7

>>> m.getProp("Tag", "MyMolecule")
>>> rdkit.Chem.rdchem.Mol.SetProp(m, "Note", "First Molecule")

>>> m.GetProp("Tag")
'MyMolecule'
>>> m.GetPropsAsDict()
{'Tag': 'MyMolecule', 'Note': 'First Molecule'}