Identify peptides and derivatives from small molecule datasets
Project description
PepSift
Summary
Identify peptides and their derivatives from small molecule datasets.
Installation
pip install pepsift
Usage
First instantiate a PepSift
by defining a level of filtering.
There are currently 5 different levels available:
level | description | comment |
---|---|---|
SiftLevel.NaturalLAminoAcids |
natural L-amino acids and peptides thereof | e.g. identify L-Alanine or the sequence ACDEFGHIKLMNPQRSTVWY |
SiftLevel.NaturalLDAminoAcids |
natural L- and D-amino acid and peptides thereof | e.g. identify L-Alanine or the sequences D-A L-W , L-H D-Q , D-M D-K |
SiftLevel.NaturalAminoAcidDerivatives |
derivatives of natural L- and D-amino acid and peptides thereof | i.e. any compound containing a canonical amino acid/peptide backbone |
SiftLevel.NonNaturalAminoAcidDerivatives |
non-natural amino acid derivatives and peptides thereof | e.g. identify beta-homo-alanine or alpha-methyl-Tyr |
SiftLevel.AllAmineAndAcid |
compounds containing amine and carboxylic acid moeities | e.g. 3-[3-(2-Aminoethyl)cyclohexyl]propionic acid |
These levels allow for granular selection of different types amino acids/peptides.
Let's instantiate a sift for each level to see the difference:
from pepsift import PepSift, SiftLevel
from rdkit import Chem
ps1 = PepSift(SiftLevel.NaturalLAminoAcids)
ps2 = PepSift(SiftLevel.NaturalLDAminoAcids)
ps3 = PepSift(SiftLevel.NaturalAminoAcidDerivatives)
ps4 = PepSift(SiftLevel.NonNaturalAminoAcidDerivatives)
ps5 = PepSift(SiftLevel.AllAmineAndAcid)
mols = [Chem.MolFromSmiles('C[C@@H](C(=O)O)N'), # L-Ala
Chem.MolFromSmiles('C[C@H](C(=O)O)N'), # D-Ala
Chem.MolFromSmiles('C[C@@H](CN)C(=O)O'), # Beta-homo-Ala
Chem.MolFromSmiles('CC(C)(C(=O)O)N'), # Alpha-methyl-Ala
Chem.MolFromSmiles('NCCCCCCCCCCCCCCCC(=O)O'), # Amino-hexadecanoic acid
Chem.MolFromSmiles('c1cccc1'), # Benzene
]
for mol in mols:
print((ps1.is_peptide(mol),
ps2.is_peptide(mol),
ps3.is_peptide(mol),
ps4.is_peptide(mol),
ps5.is_peptide(mol)
)
)
# L-Ala
# (True, True, True, True, True)
# D-Ala
# (False, True, True, True, True)
# Beta-homo-Ala
# (False, False, True, True, True)
# Alpha-methyl-Ala
# (False, False, False, True, True)
# Amino-hexadecanoic acid
# (False, False, False, False, True)
# Benzene
# (False, False, False, False, False)
:warning: Any peptide containing a natural amino acid is considered a derivative of natural amino acids (even if it also contains non natural amino acids)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
pepsift-0.0.1.tar.gz
(9.1 kB
view hashes)