# PepSift
## Summary
***Identify peptides and their derivatives from small molecule datasets.***
## Installation
```commandline
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` <br/><img src="images/L-Ala.png" alt="L-Ala" width=200> |
| `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` <br/><img src="images/D-Ala.png" alt="D-Ala" width=200> |
| `SiftLevel.NaturalAminoAcidDerivatives` | derivatives of natural L- and D-amino acid and peptides thereof | i.e. any compound containing a canonical amino acid/peptide backbone <br/><img src="images/AA.png" alt="AA" width=200> |
| `SiftLevel.NonNaturalAminoAcidDerivatives` | non-natural amino acid derivatives and peptides thereof | e.g. identify beta-homo-alanine or alpha-methyl-Tyr <br/><img src="images/beta-homo-Ala.png" alt="BH-Ala" width=200> <img src="images/alpha-methyl-Tyr.png" alt="AM-Tyr" width=200> |
| `SiftLevel.AllAmineAndAcid` | compounds containing amine and carboxylic acid moieties | e.g. 3-[3-(2-Aminoethyl)cyclohexyl]propionic acid <br/><img src="images/5N1NAPHT.png" alt="5N1NAPHT" width=200> |
These levels allow for granular selection of different types amino acids/peptides.
<br/>
The decreasing stringency of `SiftLevel` criteria is exemplified below.
```python
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)
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"description": "# PepSift\r\n\r\n\r\n## Summary\r\n\r\n***Identify peptides and their derivatives from small molecule datasets.***\r\n\r\n## Installation\r\n\r\n```commandline\r\npip install pepsift\r\n```\r\n\r\n## Usage\r\n\r\n`PepSift` relies on multiple criteria defining different types od amino acids and polymers thereof.\r\n\r\nThere are currently 5 different levels available from most to least stringent:\r\n\r\n| level | description | comment |\r\n|--------------------------------------------|-------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\r\n| `SiftLevel.NaturalLAminoAcids` | natural L-amino acids and peptides thereof | e.g. identify L-Alanine or the sequence `ACDEFGHIKLMNPQRSTVWY` <br/><img src=\"images/L-Ala.png\" alt=\"L-Ala\" width=200> |\r\n| `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` <br/><img src=\"images/D-Ala.png\" alt=\"D-Ala\" width=200> |\r\n| `SiftLevel.NaturalAminoAcidDerivatives` | derivatives of natural L- and D-amino acid and peptides thereof | i.e. any compound containing a canonical amino acid/peptide backbone <br/><img src=\"images/AA.png\" alt=\"AA\" width=200> |\r\n| `SiftLevel.NonNaturalAminoAcidDerivatives` | non-natural amino acid derivatives and peptides thereof | e.g. identify beta-homo-alanine or alpha-methyl-Tyr <br/><img src=\"images/beta-homo-Ala.png\" alt=\"BH-Ala\" width=200> <img src=\"images/alpha-methyl-Tyr.png\" alt=\"AM-Tyr\" width=200> |\r\n| `SiftLevel.AllAmineAndAcid` | compounds containing amine and carboxylic acid moieties | e.g. 3-[3-(2-Aminoethyl)cyclohexyl]propionic acid <br/><img src=\"images/5N1NAPHT.png\" alt=\"5N1NAPHT\" width=200> |\r\n\r\nThese levels allow for granular selection of different types amino acids/peptides.\r\n\r\n<br/>\r\nThe decreasing stringency of `SiftLevel` criteria is exemplified below.\r\n\r\n```python\r\nfrom pepsift import PepSift, SiftLevel\r\n\r\nfrom rdkit import Chem\r\n\r\nps1 = PepSift(SiftLevel.NaturalLAminoAcids)\r\nps2 = PepSift(SiftLevel.NaturalLDAminoAcids)\r\nps3 = PepSift(SiftLevel.NaturalAminoAcidDerivatives)\r\nps4 = PepSift(SiftLevel.NonNaturalAminoAcidDerivatives)\r\nps5 = PepSift(SiftLevel.AllAmineAndAcid)\r\n\r\nmols = [Chem.MolFromSmiles('C[C@@H](C(=O)O)N'), # L-Ala\r\n Chem.MolFromSmiles('C[C@H](C(=O)O)N'), # D-Ala\r\n Chem.MolFromSmiles('C[C@@H](CN)C(=O)O'), # Beta-homo-Ala\r\n Chem.MolFromSmiles('CC(C)(C(=O)O)N'), # Alpha-methyl-Ala\r\n Chem.MolFromSmiles('NCCCCCCCCCCCCCCCC(=O)O'), # Amino-hexadecanoic acid\r\n Chem.MolFromSmiles('c1ccccc1'), # Benzene\r\n ]\r\n\r\nfor mol in mols:\r\n print((ps1.is_peptide(mol),\r\n ps2.is_peptide(mol),\r\n ps3.is_peptide(mol),\r\n ps4.is_peptide(mol),\r\n ps5.is_peptide(mol)\r\n )\r\n )\r\n\r\n# L-Ala\r\n# (True, True, True, True, True)\r\n# D-Ala\r\n# (False, True, True, True, True)\r\n# Beta-homo-Ala\r\n# (False, False, True, True, True)\r\n# Alpha-methyl-Ala\r\n# (False, False, False, True, True)\r\n# Amino-hexadecanoic acid\r\n# (False, False, False, False, True)\r\n# Benzene\r\n# (False, False, False, False, False)\r\n```\r\n\r\n\r\n\r\n: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)\r\n",
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