GetMorganFingerprintAsBitVect() Method in RDKit

Cheminformatics Tutorials - Herong's Tutorial Examples

∟GetMorganFingerprintAsBitVect() Method in RDKit

This section provides a quick introduction on the rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect() Method in the RDKit library.

GetMorganFingerprintAsBitVect(mol, radius) method is located in the rdkit.Chem.rdMolDescriptors module of the RDKit library. The same method is also packaged as rdkit.Chem.AllChem.GetMorganFingerprintAsBitVect() for easier access.

GetMorganFingerprintAsBitVect() method provides the same functionality as the GetMorganFingerprint() method, except that it returns the fingerprint as a bit string.

Here is the full description of the method:

rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect((Mol)mol, 
  (int)radius[, 
  (int)nBits=2048[, 
  (AtomPairsParameters)invariants=[][, 
  (AtomPairsParameters)fromAtoms=[][, 
  (bool)useChirality=False[, 
  (bool)useBondTypes=True[, 
  (bool)useFeatures=False[, 
  (AtomPairsParameters)bitInfo=None[, 
  (bool)includeRedundantEnvironments=False]]]]]]]]) 
-> ExplicitBitVect

Descriptions of all arguments:

mol: the molecule to use.
radius: the bond radius of the local substructure.
nBits (optional): number of bits in the fingerprint.
invariants (optional): a list of initial identifiers for each atom node in the molecule. This will override identifiers hashed from those predefined invariants on each atom node. Basically, you are providing the Morgan fingerprint for radius=0.
fromAtoms (optional): a sequence of atom node indices. If provided, only those atom nodes are encoded.
useChirality (optional): if set, node chirality will be encoded.
useBondTypes (optional): if set, bond types will be considered when updating identifiers with neighboring atom nodes.
useFeatures (optional): if set, feature invariants will be used instead of atom node invariants. This flags the generator to return FCFP fingerprints instead of ECFP fingerprints.
bitInfo (optional): an empty dict. If provided, the result will contain a dict with identifiers as keys and corresponding atom with radius as values.
includeRedundantEnvironments (optional):

By default, GetMorganFingerprintAsBitVect() uses the "useFeatures=False" option to provide an implementation of the ECFP (Extended Connectivity Fingerprint) method as described in the "ECFP (Extended Connectivity Fingerprint) Method - 2000" section in this book.

Note that GetMorganFingerprintAsBitVect() returns the fingerprint as a bit string, representing identifiers of all atom nodes generated at different radiuses.

If you want the fingerprint to be returned as a collection of identifiers, you can call the GetMorganFingerprint() method, as described in the "GetMorganFingerprint() Method in RDKit" section in this chapter.

Now let's verify its ECFP implementation with some simple tests.

1. Molecule "C" has a single non-hydrogen atom. So a single identifier will be generated at radius=0.

from rdkit.Chem import AllChem
from rdkit.DataStructs.cDataStructs import UIntSparseIntVect
mol = AllChem.MolFromSmiles('C')
fp = AllChem.GetMorganFingerprint(mol, 0)
display(UIntSparseIntVect.GetNonzeroElements(fp))

bitInfo = {}
fp = AllChem.GetMorganFingerprintAsBitVect(mol, 0, nBits=64,
  bitInfo=bitInfo)
display(fp.ToBitString())
print(bitInfo)

# output: 
{2246733040: 1}
'0000000000000000000000000000000000000000000000001000000000000000'
{48: ((0, 0),)}

As you can see, GetMorganFingerprintAsBitVect() encodes the only identifier 2246733040 into a 64 long bit string with value 1 at location 48, which is the remainder of 2246733040 divided by 64: 2246733040 % 64 = 48.

2. Molecule with a 2 identical atoms: "CC", expressed in SMILES.

mol = AllChem.MolFromSmiles('CC')
fp = AllChem.GetMorganFingerprint(mol, 0)
display(UIntSparseIntVect.GetNonzeroElements(fp))

bitInfo = {}
fp = AllChem.GetMorganFingerprintAsBitVect(mol, 0, nBits=64,
  bitInfo=bitInfo)
display(fp.ToBitString())
print(bitInfo)

# output: 
{2246728737: 2}
'0000000000000000000000000000000001000000000000000000000000000000'
{33: ((0, 0), (1, 0))}

GetMorganFingerprint() returns 2 identical identifiers: 2246728737. GetMorganFingerprintAsBitVect() encodes both into a single value 1 at location 33, which is the remainder of 2246728737 divided by 64: 2246728737 % 64 = 33.

3. Same molecule "CC" with radius=1.

mol = AllChem.MolFromSmiles('CC')
fp = AllChem.GetMorganFingerprint(mol, 1)
display(UIntSparseIntVect.GetNonzeroElements(fp))

bitInfo = {}
fp = AllChem.GetMorganFingerprintAsBitVect(mol, 1, nBits=64,
  bitInfo=bitInfo)
display(fp.ToBitString())
print(bitInfo)

# output:
{2246728737: 2, 3545175291: 1}
'0000000000000000000000000000000001000000000000000000000000010000'
{33: ((0, 0), (1, 0)), 59: ((0, 1),)}

Now GetMorganFingerprint() returns 3 identifiers: 2246728737 for 2 times and 3545175291 once. GetMorganFingerprintAsBitVect() encodes them into value 1 at location 33 and 59.

Notice that when duplicated identifiers are encoded into a bit string, the number of duplications is lost. So the fingerprint generated by GetMorganFingerprintAsBitVect() carry less information than GetMorganFingerprint().