B bJ@sVdZdddddZdddd dd Zd d d ZddddddddZdZGdddZdS)aQCalculate isoelectric points of polypeptides using methods of Bjellqvist. pK values and the methos are taken from:: * Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031. * Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539. I designed the algorithm according to a note by David L. Tabb, available at: http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf g@g$@g(@gQ@)NtermKRHgffffff @g333333@g@g"@)CtermDECYg333333@g@)rrg\(\@g@gQ@gQ @gHzG@g(\@g@)AMSPTVr)rrrrrrr c@s<eZdZdZdddZddZddZd d ZdddZdS)IsoelectricPointaA class for calculating the IEP or charge at given pH of a protein. Parameters ---------- :protein_sequence: A ``Bio.Seq`` or string object containing a protein sequence. :aa_content: A dictionary with amino acid letters as keys and its occurrences as integers, e.g. ``{"A": 3, "C": 0, ...}``. Default: ``None``. If ``None``, the dic will be calculated from the given sequence. Methods ------- :charge_at_pH(pH): Calculates the charge of the protein for a given pH :pi(): Calculates the isoelectric point Examples -------- The methods of this class can either be accessed from the class itself or from a ``ProtParam.ProteinAnalysis`` object (with partially different names): >>> from Bio.SeqUtils.IsoelectricPoint import IsoelectricPoint as IP >>> protein = IP("INGAR") >>> print(f"IEP of peptide {protein.sequence} is {protein.pi():.2f}") IEP of peptide INGAR is 9.75 >>> print(f"Its charge at pH 7 is {protein.charge_at_pH(7.0):.2f}") Its charge at pH 7 is 0.76 >>> from Bio.SeqUtils.ProtParam import ProteinAnalysis as PA >>> protein = PA("PETER") >>> print(f"IEP of {protein.sequence}: {protein.isoelectric_point():.2f}") IEP of PETER: 4.53 >>> print(f"Charge at pH 4.53: {protein.charge_at_pH(4.53):.2f}") Charge at pH 4.53: 0.00 NcCsLt||_|s,ddlm}||j}|||_|\|_ |_ dS)zInitialize the class.)ProteinAnalysisN) struppersequenceZBio.SeqUtils.ProtParamrZcount_amino_acids_select_chargedcharged_aas_content_update_pKs_tablespos_pKsneg_pKs)selfZprotein_sequence aa_contentZ_PArs