def get_kappa_after_phosphorylation(self):
"""
Function which recomputes kappa after complete
phosphorylation based on the currently defined
phosphosites.
OUTPUT:
--------------------------------------------------------------------------------
returns a float corresponding to the sequence's kappa value if
all the currently defined phosphosites were phosphorylated
"""
if len(self.get_phosphosites()) == 0:
status_message(
"Be aware that there are no phosphosites currently set - getting 'naked' kappa")
return self.SeqObj.kappa_at_maxPhos()
def get_full_phosphostatus_kappa_distribution(self):
"""
This function calculates the kappa value of all possible phosphorylation
states, given the defined phosphosites.
This is computationally tractable for small numbers of phosphosites, but can
rapidly become extremely expensive.
OUTPUT:
--------------------------------------------------------------------------------
Returns a list of tuples, where each tuple corresponds to a unique phosphostate
of the protein of interest. Each position within the tuple is defined as follows;
0 - kappa of sequence
1 - Fraction of positive residues (F+) (does not change)
2 - Fraction of negative residues (F-)
3 - Fraction of charged residues (FCR)
4 - Net Charge Per Residue (NCRP)
5 - Mean hydropathy
6 - phosphostatus
These are all self explanatory, with the exception of phosphostatus, which defines
a tuple with a position for each phosphorylatable site, set to 0 if not phosphorylated
and 1 if phosphorylated. As an example, if I had a protein with three phosphosites
(S4,Y43,S105), the tuple for the fully unphosphorylated would be (0,0,0) and with
Y43 phosphorylated would be (0,1,0)
"""
# determine the number of calculations needed to run
ncalcs = self.SeqObj.calculateNumberDifferentPhosphoStates()
# print status message
status_message(
"Running exaustive kappa distribution analysis based on phosphorylation states")
status_message(
"This function will now make " +
str(ncalcs) +
" independent kappa calculations\nIf this is a big number you may want to investigate a subset of possible phosphosites or\nuse a Monte Carlo approach to subsample")
return self.SeqObj.calculateKappaDistOfPhosphoStates()
!--------------------------------------------------------------------------!
! !
! MAIN AUTHOR: Alex Holehouse !
! !
!--------------------------------------------------------------------------!
File Description:
================
This is the main package import file for the localCIDER package.
"""
__all__ = ['sequenceParameters', 'plots']
from backend.config import VERSION as localCIDER_version
from backend.backendtools import status_message
import sequenceParameters as sequenceParameters
import sequencePermutants as sequencePermutants
import plots as plots
# Explicit exception importing
from backend.localciderExceptions import KeyFileException
from backend.localciderExceptions import PlottingException
from backend.localciderExceptions import SequenceException
from backend.localciderExceptions import SequenceFileParserException
from backend.localciderExceptions import ResTableException
from backend.localciderExceptions import WLException
status_message("localCIDER version " + localCIDER_version)
!--------------------------------------------------------------------------!
! !
! MAIN AUTHOR: Alex Holehouse !
! !
!--------------------------------------------------------------------------!
File Description:
================
This is the main package import file for the localCIDER package.
"""
__all__ = ['sequenceParameters', 'plots']
from backend.config import VERSION as localCIDER_version
from backend.backendtools import status_message
import sequenceParameters as sequenceParameters
import sequencePermutants as sequencePermutants
import plots as plots
# Explicit exception importing
from backend.localciderExceptions import KeyFileException
from backend.localciderExceptions import PlottingException
from backend.localciderExceptions import SequenceException
from backend.localciderExceptions import SequenceFileParserException
from backend.localciderExceptions import ResTableException
from backend.localciderExceptions import WLException
status_message("localCIDER version " + localCIDER_version)