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)