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from ...domains.materials import MacroMolecule
from ..utils import get_descriptor
[docs]def length(protein: MacroMolecule) -> int:
"""Retrieves the number of residues of a protein."""
desc = get_descriptor(protein)
desc.length()
return int(desc.descriptor)
[docs]def molecular_weight(protein: MacroMolecule, amide: bool = False) -> float:
"""Computes the molecular weight of a protein."""
desc = get_descriptor(protein)
desc.calculate_MW(amide=amide)
return float(desc.descriptor)
[docs]def boman_index(protein: MacroMolecule) -> float:
"""Computes the Boman index of a protein (sum of solubility values of all residues).
Boman, H. G. (2003).
Antibacterial peptides: basic facts and emerging concepts.
Journal of internal medicine, 254(3), 197-215.
"""
desc = get_descriptor(protein)
desc.boman_index()
return float(desc.descriptor)
[docs]def aliphatic_index(protein: MacroMolecule) -> float:
"""Computes the aliphatic index of a protein. Measure of thermal stability.
Ikai, A. (1980).
Thermostability and aliphatic index of globular proteins.
The Journal of Biochemistry, 88(6), 1895-1898.
"""
desc = get_descriptor(protein)
desc.aliphatic_index()
return float(desc.descriptor)
[docs]def hydrophobic_ratio(protein: MacroMolecule) -> float:
"""Computes the hydrophobicity of a protein, relative freq. of **A,C,F,I,L,M & V**."""
desc = get_descriptor(protein)
desc.hydrophobic_ratio()
return float(desc.descriptor)
[docs]def charge(protein: MacroMolecule, ph: float = 7.0, amide: bool = False) -> float:
"""Computes the charge of a protein.
Bjellqvist, B., Hughes, G. J., Pasquali, C., Paquet, N., Ravier, F., Sanchez, J. C., ... & Hochstrasser, D. (1993).
The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences.
Electrophoresis, 14(1), 1023-1031.
"""
desc = get_descriptor(protein)
desc.calculate_charge(ph=ph, amide=amide)
return float(desc.descriptor)
[docs]def charge_density(
protein: MacroMolecule, ph: float = 7.0, amide: bool = False
) -> float:
"""Computes the charge density of a protein.
Bjellqvist, B., Hughes, G. J., Pasquali, C., Paquet, N., Ravier, F., Sanchez, J. C., ... & Hochstrasser, D. (1993).
The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences.
Electrophoresis, 14(1), 1023-1031.
"""
desc = get_descriptor(protein)
desc.charge_density(ph=ph, amide=amide)
return float(desc.descriptor)
[docs]def isoelectric_point(protein: MacroMolecule, amide: bool = False) -> float:
"""Computes the isoelectric point of every residue and aggregates."""
desc = get_descriptor(protein)
desc.isoelectric_point(amide=amide)
return float(desc.descriptor)
[docs]def aromaticity(protein: MacroMolecule) -> float:
"""Computes aromaticity of the protein (relative frequency of Phe+Trp+Tyr).
Lobry, J. R., & Gautier, C. (1994).
Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage
in 999 Escherichia coli chromosome-encoded genes.
Nucleic acids research, 22(15), 3174-3180.
"""
desc = get_descriptor(protein)
desc.aromaticity()
return float(desc.descriptor)
[docs]def instability(protein: MacroMolecule) -> float:
"""Calculates the protein instability.
Guruprasad, K., Reddy, B. B., & Pandit, M. W. (1990).
Correlation between stability of a protein and its dipeptide composition: a novel
approach for predicting in vivo stability of a protein from its primary sequence.
Protein Engineering, Design and Selection, 4(2), 155-161.
"""
desc = get_descriptor(protein)
desc.instability_index()
return float(desc.descriptor)