What Is rdkit.Chem.rdmolops Module

Cheminformatics Tutorials - Herong's Tutorial Examples

∟rdkit.Chem.rdmolops - Molecule Operations

∟What Is rdkit.Chem.rdmolops Module

This section provides a quick introduction of the rdkit.Chem.rdmolops module in RDKit library, which provides many functionalities to manipulate molecules.

What Is rdkit.Chem.rdmolops Module? - rdkit.Chem.rdmolops Module is a major module of the RDKit library. It provides many functionalities to manipulate molecules.

rdkit.Chem.rdmolops contains the following main methods:

n = rdkit.Chem.rdmolops.AddHs(m) - Adds hydrogens to the graph of a molecule.

rdkit.Chem.rdmolops.Cleanup(m) - Cleans up internal data of a molecule.

n = dkit.Chem.rdmolops.CombineMols(m1, m2) - Combines two molecules to produce a new molecule, which is really a combination of 2 molecule fragments.

n = rdkit.Chem.rdmolops.DeleteSubstructs(m, s> - Removes atoms and related bonds matching a substructure from a molecule. The resulting molecule could be fragmented.

l = rdkit.Chem.rdmolops.FindAtomEnvironmentOfRadiusN((m, r, a) - Finds the bonds within a certain radius of an atom in a molecule.

ms = rdkit.Chem.rdmolops.GetMolFrags(m) - Returns the disconnected fragments from a molecule as a list of molecules.

f = rdkit.Chem.rdmolops.PatternFingerprint(m) - Returns the fingerprint using SMARTS patterns from a molecule.

f = rdkit.Chem.rdmolops.RDKFingerprint(m) - Returns the fingerprint using RDKit topological algorithm from a molecule.

n = rdkit.Chem.rdmolops.RemoveHs(m) - Removes any hydrogens from the graph of a molecule.

n = rdkit.Chem.rdmolops.ReplaceCore(m, s) - Removes a substructure as the core of a molecule and labels the sidechains with dummy atoms.

n = rdkit.Chem.rdmolops.ReplaceSidechains(m, s) - Replaces sidechains of a substructure in a molecule with dummy atoms for their attachment points.

To simplify access names, rdkit.Chem.rdmolops module members are also imported at the rdkit.Chem package level. So you can access module members at both levels: the rdkit.Chem package level and the rdkit.Chem.rdmolops module level, as shown below:

herong$ python
>>> import rdkit.Chem.rdmolops
>>> n = rdkit.Chem.rdmolops.AddHs(m)
>>> exit()

herong$ python
>>> import rdkit.Chem
>>> n = rdkit.Chem.rdmolops.AddHs()
>>> exit()

herong$ python
>>> from rdkit.Chem import rdmolops
>>> n = rdmolops.AddHs()
>>> exit()

herong$ python
>>> from rdkit import Chem
>>> n = Chem.rdmolops.AddHs()
>>> exit()