rdkit.Chem.rdchem.RWMol - The RWMol Class

Cheminformatics Tutorials - Herong's Tutorial Examples

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

This section provides a quick introduction of the rdkit.Chem.rdchem.RWMol class, which is a sub-class of rdkit.Chem.rdchem.Mol class with additional read and write functionalities.

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

rdkit.Chem.rdchem.RWMol represents a molecule class with additional read and write functionalities. Basically, you build a new molecule or modify a molecule represented by the RWMol sub-class.

Here are some useful methods provided in the RWMol sub-class.

m = rdkit.Chem.rdchem.RWMol() - Creates an empty molecule.

m.AddAtom(a) or rdkit.Chem.rdchem.RWMol.AddAtom(m, a) - Adds a given atom to the given molecule.

m.AddBond(i, j) or rdkit.Chem.rdchem.RWMol.AddBond(m, i, j) - Adds a bond from the i-th atom to the j-th atom in the given molecule.

m.RemoveAtom(i) or rdkit.Chem.rdchem.RWMol.RemoveAtom(m, i) - Removes the i-th atom from the given molecule.

m.RemoveBond(i) or rdkit.Chem.rdchem.RWMol.RemoveBond(m, i) - Removes the j-th bond from the given molecule.

m.ReplaceAtom(i, a) or rdkit.Chem.rdchem.RWMol.ReplaceAtom(m, i, a) - Replaces the i-th atom with a given atom in the given molecule.

m.ReplaceBond(i, b) or rdkit.Chem.rdchem.RWMol.ReplaceBond(m, i, b) - Replaces j-th bond with a given bond in the given molecule.

m.InsertMol(s) or rdkit.Chem.rdchem.RWMol.InsertMol(m, s) - Inserts another molecule into the given molecule.

rdkit.Chem.SanitizeMol(m) - Sanitizes the given molecule.

rdkit.Chem.MolToSmiles(m) - Returns the SMILES string of the given molecule.

rdkit.Chem.MolToMolBlock(m) - Returns the SDF string of the given molecule.

Here is an example session of using rdkit.Chem.rdchem.RWMol class to build molecules from scratch:

>>> import rdkit

>>> water = rdkit.Chem.rdchem.RWMol()
>>> O = rdkit.Chem.rdchem.Atom("O")
>>> H = rdkit.Chem.rdchem.Atom("H")
>>>
>>> water.AddAtom(O)
0
>>> water.AddAtom(H)
2
>>> water.AddBond(0, 1, rdkit.Chem.rdchem.BondType.SINGLE)
1
>>> water.AddBond(0, 2, rdkit.Chem.rdchem.BondType.SINGLE)
2

>>> rdkit.Chem.SanitizeMol(water)
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE

>>> rdkit.Chem.MolToSmiles(water)
'[H]O[H]'


>>> ring = rdkit.Chem.rdchem.RWMol()
>>> C = rdkit.Chem.rdchem.Atom("C")
>>> ring.AddAtom(C)
0
>>> ring.AddAtom(C)
1
>>> ring.AddAtom(C)
2
>>> ring.AddAtom(C)
3
>>> ring.AddAtom(C)
4
>>> ring.AddBond(0, 1, rdkit.Chem.rdchem.BondType.SINGLE)
1
>>> ring.AddBond(1, 2, rdkit.Chem.rdchem.BondType.SINGLE)
2
>>> ring.AddBond(2, 3, rdkit.Chem.rdchem.BondType.SINGLE)
3
>>> ring.AddBond(3, 4, rdkit.Chem.rdchem.BondType.SINGLE)
4
>>> ring.AddBond(4, 0, rdkit.Chem.rdchem.BondType.SINGLE)
5

>>> rdkit.Chem.SanitizeMol(ring)
rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE

>>> rdkit.Chem.MolToSmiles(ring)
'C1CCCC1'