# propy3, formerly protpy, is a Python package to compute protein descriptors
# Copyright (C) 2012 Dongsheng Cao and Yizeng Liang, oriental-cds@163.com
# Copyright (C) 2020-2022 Martin Thoma
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; in version 2
# of the License.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor,
# Boston, MA 02110-1301, USA.
"""Computing different types of protein descriptors."""
# Core Library
from typing import Any, Dict, List, Optional
# Local
from .AAComposition import (
CalculateAAComposition,
CalculateDipeptideComposition,
GetSpectrumDict,
)
from .AAIndex import GetAAIndex1, GetAAIndex23
from .Autocorrelation import (
CalculateEachGearyAuto,
CalculateEachMoranAuto,
CalculateEachNormalizedMoreauBrotoAuto,
CalculateGearyAutoTotal,
CalculateMoranAutoTotal,
CalculateNormalizedMoreauBrotoAutoTotal,
)
from .CTD import CalculateCTD
from .GetSubSeq import GetSubSequence
from .PseudoAAC import GetAPseudoAAC, GetPseudoAAC, _GetPseudoAAC
from .QuasiSequenceOrder import (
GetQuasiSequenceOrder,
GetQuasiSequenceOrderp,
GetSequenceOrderCouplingNumberp,
GetSequenceOrderCouplingNumberTotal,
)
[docs]class GetProDes:
"""Collect all descriptor calcualtion modules."""
AALetter = list("ARNDCEQGHILKMFPSTWYV")
Version = 1.0
def __init__(self, ProteinSequence: str = "") -> None:
"""Input a protein sequence."""
if len(ProteinSequence) == 0:
print(
"You must input a protein sequence "
"when constructing a object. It is a string!"
)
else:
self.ProteinSequence = ProteinSequence
[docs] def GetAAComp(self) -> Dict[str, float]:
"""
Amino acid compositon descriptors (20).
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetAAComp()
"""
res = CalculateAAComposition(self.ProteinSequence)
return res
[docs] def GetDPComp(self) -> Dict[str, float]:
"""
Dipeptide composition descriptors (400).
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetDPComp()
"""
res = CalculateDipeptideComposition(self.ProteinSequence)
return res
[docs] def GetTPComp(self) -> Dict[str, int]:
"""
Tri-peptide composition descriptors (8000).
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetTPComp()
"""
res = GetSpectrumDict(self.ProteinSequence)
return res
[docs] def GetMoreauBrotoAuto(self) -> Dict[Any, Any]:
"""
Normalized Moreau-Broto autocorrelation descriptors (240).
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetMoreauBrotoAuto()
"""
res = CalculateNormalizedMoreauBrotoAutoTotal(self.ProteinSequence)
return res
[docs] def GetMoranAuto(self) -> Dict[Any, Any]:
"""
Moran autocorrelation descriptors (240).
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetMoranAuto()
"""
res = CalculateMoranAutoTotal(self.ProteinSequence)
return res
[docs] def GetGearyAuto(self) -> Dict[Any, Any]:
"""
Geary autocorrelation descriptors (240).
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetGearyAuto()
"""
res = CalculateGearyAutoTotal(self.ProteinSequence)
return res
[docs] def GetCTD(self) -> Dict[Any, Any]:
"""
Composition Transition Distribution descriptors (147).
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetCTD()
"""
res = CalculateCTD(self.ProteinSequence)
return res
[docs] def GetPAAC(self, lamda: int = 10, weight: float = 0.05) -> Dict[Any, Any]:
"""
Type I Pseudo amino acid composition descriptors (default is 30).
Parameters
----------
lamda : int, optional (default: 10)
reflects the rank of correlation and is a non-Negative integer,
such as 15. Note that (1)lamda should NOT be larger than the length
of input protein sequence; (2) lamda must be non-Negative integer,
such as 0, 1, 2, ...; (3) when lamda =0, the output of PseAA server
is the 20-D amino acid composition.
weight : float, optional (default: 0.05)
is designed for the users to put weight on the additional PseAA
components with respect to the conventional AA components. The user
can select any value within the region from 0.05 to 0.7 for the
weight factor.
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetPAAC(lamda=10, weight=0.05)
"""
res = _GetPseudoAAC(self.ProteinSequence, lamda=lamda, weight=weight)
return res
[docs] def GetPAACp(
self, lamda: int = 10, weight: float = 0.05, AAP: Optional[List[Any]] = None
) -> Dict[Any, Any]:
"""
Type I Pseudo amino acid composition descriptors for the given properties
Default is 30.
Parameters
----------
lamda : int, optional (default: 10)
reflects the rank of correlation and is a non-Negative integer,
such as 15. Note that (1)lamda should NOT be larger than the length
of input protein sequence; (2) lamda must be non-Negative integer,
such as 0, 1, 2, ...; (3) when lamda =0, the output of PseAA server
is the 20-D amino acid composition.
weight : float, optional (default: 0.05)
is designed for the users to put weight on the additional PseAA
components with respect to the conventional AA components. The user
can select any value within the region from 0.05 to 0.7 for the
weight factor.
AAP : List
contains the properties, each of which is a dict form.
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetPAACp(lamda=10, weight=0.05, AAP=[])
"""
if AAP is None:
AAP = []
res = GetPseudoAAC(self.ProteinSequence, lamda=lamda, weight=weight, AAP=AAP)
return res
[docs] def GetAPAAC(self, lamda: int = 10, weight: float = 0.5) -> Dict[Any, Any]:
"""
Amphiphilic (Type II) Pseudo amino acid composition descriptors.
default is 30
Parameters
----------
lamda : int, optional (default: 10)
reflects the rank of correlation and is a non-Negative integer,
such as 15. Note that (1)lamda should NOT be larger than the length
of input protein sequence; (2) lamda must be non-Negative integer,
such as 0, 1, 2, ...; (3) when lamda =0, the output of PseAA server
is the 20-D amino acid composition.
weight : float, optional (default: 0.05)
is designed for the users to put weight on the additional PseAA
components with respect to the conventional AA components. The user
can select any value within the region from 0.05 to 0.7 for the
weight factor.
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetAPAAC(lamda=10, weight=0.5)
"""
res = GetAPseudoAAC(self.ProteinSequence, lamda=lamda, weight=weight)
return res
[docs] def GetSOCN(self, maxlag: int = 45) -> Dict[Any, Any]:
"""
Sequence order coupling numbers default is 45.
Parameters
----------
maxlag : int
is the maximum lag and the length of the protein should be larger
than maxlag
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetSOCN(maxlag=45)
"""
res = GetSequenceOrderCouplingNumberTotal(self.ProteinSequence, maxlag=maxlag)
return res
[docs] def GetSOCNp(
self, maxlag: int = 45, distancematrix: Optional[Dict[Any, Any]] = None
) -> Dict[Any, Any]:
"""
Sequence order coupling numbers default is 45.
Parameters
----------
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 45.
distancematrix is a dict form containing 400 distance values
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetSOCN(maxlag=45)
"""
if distancematrix is None:
distancematrix = {}
res = GetSequenceOrderCouplingNumberp(
self.ProteinSequence, maxlag=maxlag, distancematrix=distancematrix
)
return res
[docs] def GetQSO(self, maxlag: int = 30, weight: float = 0.1) -> Dict[Any, Any]:
"""
Quasi sequence order descriptors default is 50.
Parameters
----------
result = GetQSO(maxlag=30, weight=0.1)
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 45.
"""
res = GetQuasiSequenceOrder(self.ProteinSequence, maxlag=maxlag, weight=weight)
return res
[docs] def GetQSOp(
self,
maxlag: int = 30,
weight: float = 0.1,
distancematrix: Optional[Dict[Any, Any]] = None,
) -> Dict[Any, Any]:
"""
Quasi sequence order descriptors default is 50.
Parameters
----------
result = GetQSO(maxlag=30, weight=0.1)
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 45.
distancematrix is a dict form containing 400 distance values
"""
if distancematrix is None:
distancematrix = {}
res = GetQuasiSequenceOrderp(
self.ProteinSequence,
maxlag=maxlag,
weight=weight,
distancematrix=distancematrix,
)
return res
[docs] def GetMoreauBrotoAutop(
self, AAP: Optional[Dict[Any, Any]] = None, AAPName: str = "p"
) -> Dict[str, float]:
"""
Normalized Moreau-Broto autocorrelation descriptors for the given property (30).
Parameters
----------
AAP : Dict[Any, Any]
contains physicochemical properities of 20 amino acids
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetMoreauBrotoAutop(AAP={}, AAPName='p')
"""
if AAP is None:
AAP = {}
res = CalculateEachNormalizedMoreauBrotoAuto(
self.ProteinSequence, AAP=AAP, AAPName=AAPName
)
return res
[docs] def GetMoranAutop(
self, AAP: Optional[Dict[Any, Any]] = None, AAPName: str = "p"
) -> Dict[Any, Any]:
"""
Moran autocorrelation descriptors for the given property (30).
Parameters
----------
AAP : Dict[Any, Any]
contains physicochemical properities of 20 amino acids
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetMoranAutop(AAP={}, AAPName='p')
"""
if AAP is None:
AAP = {}
res = CalculateEachMoranAuto(self.ProteinSequence, AAP=AAP, AAPName=AAPName)
return res
[docs] def GetGearyAutop(
self, AAP: Optional[Dict[Any, Any]] = None, AAPName: str = "p"
) -> Dict[Any, Any]:
"""
Geary autocorrelation descriptors for the given property (30).
Parameters
----------
AAP : Dict[Any, Any]
contains physicochemical properities of 20 amino acids
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetGearyAutop(AAP={}, AAPName='p')
"""
if AAP is None:
AAP = {}
res = CalculateEachGearyAuto(self.ProteinSequence, AAP=AAP, AAPName=AAPName)
return res
[docs] def GetSubSeq(self, ToAA: str = "S", window: int = 3) -> List[str]:
"""
Obtain the sub sequences wit length 2*window+1, whose central point is ToAA.
ToAA is the central (query point) amino acid in the sub-sequence.
window is the span.
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetSubSeq(ToAA='S', window=3)
"""
res = GetSubSequence(self.ProteinSequence, ToAA=ToAA, window=window)
return res
[docs] def GetALL(
self,
paac_lamda: int = 10,
paac_weight: float = 0.05,
apaac_lamda: int = 10,
apaac_weight: float = 0.5,
socn_maxlag: int = 45,
qso_maxlag: int = 30,
qso_weight: float = 0.1,
) -> Dict[Any, Any]:
"""
Calcualte all descriptors except tri-peptide descriptors.
Parameters
----------
paac_lamda : int, optional (default: 10)
used by GetPAAC()
reflects the rank of correlation and is a non-Negative integer,
such as 15. Note that (1)lamda should NOT be larger than the length
of input protein sequence; (2) lamda must be non-Negative integer,
such as 0, 1, 2, ...; (3) when lamda =0, the output of PseAA server
is the 20-D amino acid composition.
paac_weight : float, optional (default: 0.05)
used by GetPAAC()
is designed for the users to put weight on the additional PseAA
components with respect to the conventional AA components. The user
can select any value within the region from 0.05 to 0.7 for the
weight factor.
apaac_lamda : int, optional (default: 10)
Same as "paac_lambda" but for APAAC()
apaac_weight : float, optional (default: 0.5)
Same as "paac_weight" but for APAAC()
socn_maxlag : int, optional (default: 45)
Used by GetSOCN()
is the maximum lag and the length of the protein should be larger
than maxlag.
qso_maxlag : int, optional (default: 30)
Used by GetQSO()
is the maximum lag and the length of the protein should be larger
than maxlag.
qso_weight : float, optional (default: 0.1)
Used by GetQSO()
"""
res: Dict[Any, Any] = {}
res.update(self.GetAAComp())
res.update(self.GetDPComp())
# res.update(self.GetTPComp())
res.update(self.GetMoreauBrotoAuto())
res.update(self.GetMoranAuto())
res.update(self.GetGearyAuto())
res.update(self.GetCTD())
res.update(self.GetPAAC(lamda=paac_lamda, weight=paac_weight))
res.update(self.GetAPAAC(lamda=apaac_lamda, weight=apaac_weight))
res.update(self.GetSOCN(maxlag=socn_maxlag))
res.update(self.GetQSO(maxlag=qso_maxlag, weight=qso_weight))
return res
[docs] def GetAAindex1(self, name: str, path: Optional[str] = ".") -> Dict[str, float]:
"""
Get the amino acid property values from aaindex1.
Parameters
----------
name : str
is the name of amino acid property (e.g., KRIW790103)
Returns
-------
result is a dict form containing the properties of 20 amino acids
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetAAindex1(name="KRIW790103")
"""
return GetAAIndex1(name, path=path)
[docs] def GetAAindex23(self, name: str, path: Optional[str] = ".") -> Dict[str, float]:
"""
Get the amino acid property values from aaindex2 and aaindex3.
Parameters
----------
name is the name of amino acid property (e.g. TANS760101, GRAR740104)
Returns
-------
result is a dict form containing the properties of 400 amino acid pairs
Examples
--------
>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetProDes(protein).GetAAindex23(name="KRIW790103")
"""
return GetAAIndex23(name, path=path)