pepsift 0.0.2.post1

Description:

pepsift 0.0.2.post1

PepSift
Summary
Identify peptides and their derivatives from small molecule datasets.
Installation
pip install pepsift

Usage
PepSift relies on multiple criteria defining different types od amino acids and polymers thereof.
There are currently 5 different levels available from most to least stringent:



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 moieties
e.g. 3-[3-(2-Aminoethyl)cyclohexyl]propionic acid



These levels allow for granular selection of different types amino acids/peptides.

The decreasing stringency of `SiftLevel` criteria is exemplified below.
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('c1ccccc1'), # 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)