Source code for seqme.models.amino_acid_descriptors
from typing import Literal
import numpy as np
from .exceptions import OptionalDependencyError
[docs]
class AliphaticIndex:
"""Aliphatic index of amino acid sequences.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute aliphatic index.
Args:
sequences: Amino acid sequences.
Returns:
Aliphatic index for each sequence.
"""
try:
from modlamp.descriptors import GlobalDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = GlobalDescriptor(sequences)
d.aliphatic_index()
return d.descriptor.squeeze(axis=-1)
[docs]
class Aromaticity:
"""Aromaticity of amino acid sequences.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute aromaticity.
Args:
sequences: Amino acid sequences.
Returns:
Aromaticity value for each sequence.
"""
try:
from modlamp.descriptors import GlobalDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = GlobalDescriptor(sequences)
d.aromaticity()
return d.descriptor.squeeze(axis=-1)
[docs]
class BomanIndex:
"""Boman index, estimating binding potential to proteins.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute Boman index.
Args:
sequences: Amino acid sequences.
Returns:
Boman index value for each sequence.
"""
try:
from modlamp.descriptors import GlobalDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = GlobalDescriptor(sequences)
d.boman_index()
return d.descriptor.squeeze(axis=-1)
[docs]
class Charge:
"""Net charge of amino acid sequences at a given pH.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __init__(self, ph: float = 7.0):
"""Initialize model.
Args:
ph: pH value at which to calculate the charge.
"""
self.ph = ph
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def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute net charge.
Args:
sequences: List of amino acid sequences.
Returns:
Net charge for each sequence.
"""
try:
from modlamp.descriptors import GlobalDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = GlobalDescriptor(sequences)
d.calculate_charge(ph=self.ph)
return d.descriptor.squeeze(axis=-1)
[docs]
class Gravy:
"""GRAVY (hydropathy) score for amino acid sequences.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute GRAVY.
Args:
sequences: Amino acid sequences.
Returns:
GRAVY score for each sequence.
"""
try:
from modlamp.descriptors import PeptideDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = PeptideDescriptor(sequences)
d.load_scale("gravy")
d.calculate_global()
return d.descriptor.squeeze(axis=-1)
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class Hydrophobicity:
"""Hydrophobicity using a selected scale.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
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def __init__(self, scale: Literal["eisenberg", "hopp-woods", "janin", "kytedoolittle"] = "eisenberg"):
"""Initialize the hydrophobicity.
Args:
scale: Name of the hydrophobicity scale to use.
"""
self.scale = scale
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def __call__(self, sequences: list[str]) -> np.ndarray:
"""
Compute hydrophobicity.
Args:
sequences: Amino acid sequences.
Returns:
Hydrophobicity score for each sequence.
"""
try:
from modlamp.descriptors import PeptideDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = PeptideDescriptor(sequences)
d.load_scale(self.scale)
d.calculate_global()
return d.descriptor.squeeze(axis=-1)
[docs]
class HydrophobicMoment:
"""Hydrophobic moment (i.e., amphiphilicity) for one or more amino acid sequences using a sliding-window approach.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __init__(
self,
scale: Literal["eisenberg", "hopp-woods", "janin", "kytedoolittle"] = "eisenberg",
window: int = 11,
angle: int = 100,
modality: Literal["max", "mean"] = "mean",
):
"""Initialize the hydrophobic moment.
Args:
scale: Name of the hydrophobicity scale to use.
window: Size of window
angle: Angle in which to calculate the moment. 100 for alpha helices, 180 for beta sheets.
modality: Method to compute statistic
"""
self.scale = scale
self.window = window
self.angle = angle
self.modality = modality
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def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute hydrophobic moment.
Args:
sequences: List of amino acid sequences.
Returns:
hydrophobic moment for each sequence.
"""
try:
from modlamp.descriptors import PeptideDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = PeptideDescriptor(sequences)
d.load_scale(self.scale)
d.calculate_moment(window=self.window, angle=self.angle, modality=self.modality)
return d.descriptor.squeeze(axis=-1)
[docs]
class InstabilityIndex:
"""Instability index, predicting in vitro protein stability.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute instability index.
Args:
sequences: Amino acid sequences.
Returns:
Instability index for each sequence.
"""
try:
from modlamp.descriptors import GlobalDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = GlobalDescriptor(sequences)
d.instability_index()
return d.descriptor.squeeze(axis=-1)
[docs]
class IsoelectricPoint:
"""Isoelectric point of amino acid sequences.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute isoelectric point.
Args:
sequences: Amino acid sequences.
Returns:
Isoelectric point for each sequence.
"""
try:
from modlamp.descriptors import GlobalDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = GlobalDescriptor(sequences)
d.isoelectric_point()
return d.descriptor.squeeze(axis=-1)
[docs]
class ProteinWeight:
"""Molecular weight of amino acid sequences.
Installation: ``pip install "seqme[aa_descriptors]"``
"""
[docs]
def __call__(self, sequences: list[str]) -> np.ndarray:
"""Compute molecular weight of amino acid sequences.
Args:
sequences: Amino acid sequences.
Returns:
Molecular weight for each sequence.
"""
try:
from modlamp.descriptors import GlobalDescriptor
except ModuleNotFoundError:
raise OptionalDependencyError("aa_descriptors") from None
d = GlobalDescriptor(sequences)
d.calculate_MW()
return d.descriptor.squeeze(axis=-1)
