how to use atom pair fingerprint?
时间: 2023-11-27 14:04:22 浏览: 44
Atom pair fingerprint is a type of molecular fingerprint that encodes the presence or absence of pairs of atoms in a molecule. It is commonly used in cheminformatics to compare molecules and predict their properties.
To compute atom pair fingerprint, you can use software packages such as RDKit, Open Babel, or CDK. Here is an example of computing atom pair fingerprint using RDKit in Python:
```python
from rdkit import Chem
from rdkit.Chem.AtomPairs import Pairs
from rdkit.Chem import AllChem
# create a molecule object from a SMILES string
mol = Chem.MolFromSmiles('CCO')
# compute atom pair fingerprint
atom_pairs = Pairs.GetAtomPairFingerprint(mol)
# convert the fingerprint to a numpy array
fp_array = AllChem.DataStructs.ConvertToNumpyArray(atom_pairs)
print(fp_array)
```
This will print a numpy array representing the atom pair fingerprint of the molecule 'CCO'. You can then use this fingerprint to compare with other molecules using similarity metrics such as Tanimoto coefficient or cosine similarity.
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