# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
A class used for computing different types of protein descriptors!
You can freely use and distribute it. If you have any problem,
you could contact with us timely.
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com
"""
from AAComposition import CalculateAAComposition, CalculateDipeptideComposition, GetSpectrumDict
from Autocorrelation import CalculateNormalizedMoreauBrotoAutoTotal, CalculateMoranAutoTotal, CalculateGearyAutoTotal
from Autocorrelation import CalculateEachGearyAuto, CalculateEachMoranAuto, CalculateEachNormalizedMoreauBrotoAuto
from CTD import CalculateCTD
from QuasiSequenceOrder import GetSequenceOrderCouplingNumberTotal, GetQuasiSequenceOrder, \
GetSequenceOrderCouplingNumberp, GetQuasiSequenceOrderp
from PseudoAAC import _GetPseudoAAC, GetAPseudoAAC, GetPseudoAAC
from GetSubSeq import GetSubSequence
from AAIndex import GetAAIndex1, GetAAIndex23
from ConjointTriad import CalculateConjointTriad
[docs]class PyProtein():
"""
This GetProDes class aims at collecting all descriptor calcualtion modules into a simple class.
"""
AALetter = ["A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"]
Version = 1.0
def __init__(self, ProteinSequence=''):
"""
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):
"""
amino acid compositon descriptors (20)
Usage:
result = GetAAComp()
"""
res = CalculateAAComposition(self.ProteinSequence)
return res
[docs] def GetDPComp(self):
"""
dipeptide composition descriptors (400)
Usage:
result = GetDPComp()
"""
res = CalculateDipeptideComposition(self.ProteinSequence)
return res
[docs] def GetTPComp(self):
"""
tri-peptide composition descriptors (8000)
Usage:
result = GetTPComp()
"""
res = GetSpectrumDict(self.ProteinSequence)
return res
[docs] def GetMoreauBrotoAuto(self):
"""
Normalized Moreau-Broto autocorrelation descriptors (240)
Usage:
result = GetMoreauBrotoAuto()
"""
res = CalculateNormalizedMoreauBrotoAutoTotal(self.ProteinSequence)
return res
[docs] def GetMoranAuto(self):
"""
Moran autocorrelation descriptors (240)
Usage:
result = GetMoranAuto()
"""
res = CalculateMoranAutoTotal(self.ProteinSequence)
return res
[docs] def GetGearyAuto(self):
"""
Geary autocorrelation descriptors (240)
Usage:
result = GetGearyAuto()
"""
res = CalculateGearyAutoTotal(self.ProteinSequence)
return res
[docs] def GetCTD(self):
"""
Composition Transition Distribution descriptors (147)
Usage:
result = GetCTD()
"""
res = CalculateCTD(self.ProteinSequence)
return res
[docs] def GetPAAC(self, lamda=10, weight=0.05):
"""
Type I Pseudo amino acid composition descriptors (default is 30)
Usage:
result = GetPAAC(lamda=10,weight=0.05)
lamda factor 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 factor 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.
"""
res = _GetPseudoAAC(self.ProteinSequence, lamda=lamda, weight=weight)
return res
[docs] def GetPAACp(self, lamda=10, weight=0.05, AAP=[]):
"""
Type I Pseudo amino acid composition descriptors for the given properties (default is 30)
Usage:
result = GetPAACp(lamda=10,weight=0.05,AAP=[])
lamda factor 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 factor 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 is a list form containing the properties, each of which is a dict form.
"""
res = GetPseudoAAC(self.ProteinSequence, lamda=lamda, weight=weight, AAP=AAP)
return res
[docs] def GetAPAAC(self, lamda=10, weight=0.5):
"""
Amphiphilic (Type II) Pseudo amino acid composition descriptors
default is 30
Usage:
result = GetAPAAC(lamda=10,weight=0.5)
lamda factor 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 factor 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.
"""
res = GetAPseudoAAC(self.ProteinSequence, lamda=lamda, weight=weight)
return res
[docs] def GetSOCN(self, maxlag=45):
"""
Sequence order coupling numbers default is 45
Usage:
result = GetSOCN(maxlag=45)
maxlag is the maximum lag and the length of the protein should be larger
than maxlag. default is 45.
"""
res = GetSequenceOrderCouplingNumberTotal(self.ProteinSequence, maxlag=maxlag)
return res
[docs] def GetSOCNp(self, maxlag=45, distancematrix={}):
"""
Sequence order coupling numbers default is 45
Usage:
result = GetSOCN(maxlag=45)
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
"""
res = GetSequenceOrderCouplingNumberp(self.ProteinSequence, maxlag=maxlag, distancematrix=distancematrix)
return res
[docs] def GetQSO(self, maxlag=30, weight=0.1):
"""
Quasi sequence order descriptors default is 50
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=30, weight=0.1, distancematrix={}):
"""
Quasi sequence order descriptors default is 50
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
"""
res = GetQuasiSequenceOrderp(self.ProteinSequence, maxlag=maxlag, weight=weight, distancematrix=distancematrix)
return res
[docs] def GetMoreauBrotoAutop(self, AAP={}, AAPName='p'):
"""
Normalized Moreau-Broto autocorrelation descriptors for the given property (30)
Usage:
result = GetMoreauBrotoAutop(AAP={},AAPName='p')
AAP is a dict containing physicochemical properities of 20 amino acids
"""
res = CalculateEachNormalizedMoreauBrotoAuto(self.ProteinSequence, AAP=AAP, AAPName=AAPName)
return res
[docs] def GetMoranAutop(self, AAP={}, AAPName='p'):
"""
Moran autocorrelation descriptors for the given property (30)
Usage:
result = GetMoranAutop(AAP={},AAPName='p')
AAP is a dict containing physicochemical properities of 20 amino acids
"""
res = CalculateEachMoranAuto(self.ProteinSequence, AAP=AAP, AAPName=AAPName)
return res
[docs] def GetGearyAutop(self, AAP={}, AAPName='p'):
"""
Geary autocorrelation descriptors for the given property (30)
Usage:
result = GetGearyAutop(AAP={},AAPName='p')
AAP is a dict containing physicochemical properities of 20 amino acids
"""
res = CalculateEachGearyAuto(self.ProteinSequence, AAP=AAP, AAPName=AAPName)
return res
[docs] def GetSubSeq(self, ToAA='S', window=3):
"""
obtain the sub sequences wit length 2*window+1, whose central point is ToAA
Usage:
result = GetSubSeq(ToAA='S',window=3)
ToAA is the central (query point) amino acid in the sub-sequence.
window is the span.
"""
res = GetSubSequence(self.ProteinSequence, ToAA=ToAA, window=window)
return res
[docs] def GetTriad(self):
"""
Calculate the conjoint triad features from protein sequence.
Useage:
res = GetTriad()
Output is a dict form containing all 343 conjoint triad features.
"""
res = CalculateConjointTriad(self.ProteinSequence)
return res
[docs] def GetALL(self):
"""
Calcualte all descriptors except tri-peptide descriptors
"""
res = {}
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())
res.update(self.GetAPAAC())
res.update(self.GetSOCN())
res.update(self.GetQSO())
res.update(self.GetTriad())
return res
[docs] def GetAAindex1(self, name, path='.'):
"""
Get the amino acid property values from aaindex1
Usage:
result=GetAAIndex1(name)
Input: name is the name of amino acid property (e.g., KRIW790103)
Output: result is a dict form containing the properties of 20 amino acids
"""
return GetAAIndex1(name, path=path)
[docs] def GetAAindex23(self, name, path='.'):
"""
Get the amino acid property values from aaindex2 and aaindex3
Usage:
result=GetAAIndex23(name)
Input: name is the name of amino acid property (e.g.,TANS760101,GRAR740104)
Output: result is a dict form containing the properties of 400 amino acid pairs
"""
return GetAAIndex23(name, path=path)
#####################################################################################################
if __name__ == "__main__":
import os
from Autocorrelation import _Steric
from PseudoAAC import _Hydrophobicity, _hydrophilicity, _residuemass
protein = "ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"
cds = PyProtein(protein)
print cds.GetAAComp()
print cds.GetDPComp()
print cds.GetTPComp()
print cds.GetCTD()
print cds.GetPAAC(lamda=5)
print cds.GetALL()
print cds.GetMoreauBrotoAutop(AAP=_Steric, AAPName='Steric')
print cds.GetMoranAutop(AAP=_Steric, AAPName='Steric')
print cds.GetGearyAutop(AAP=_Steric, AAPName='Steric')
print cds.GetPAACp(lamda=5, weight=0.05, AAP=[_Hydrophobicity, _hydrophilicity])
print cds.GetSubSeq(ToAA='D', window=5)
print cds.GetTriad()
proper = cds.GetAAindex23('GRAR740104')
print cds.GetAAindex1('KRIW790103')
print cds.GetQSOp(maxlag=30, weight=0.1, distancematrix=proper)
print cds.GetSOCNp(maxlag=30, distancematrix=proper)
