NCBI C++ Toolkit Cross Reference

  C++/include/algo/sequence/prot_prop.hpp


/* $Id: prot_prop.hpp 33815 2007-05-04 17:18:18Z kazimird $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Authors: Josh Cherry * * File Description: * */ #ifndef ALGO_SEQUENCE___PROT_PROP__HPP #define ALGO_SEQUENCE___PROT_PROP__HPP #include <objmgr/seq_vector.hpp> #include <math.h> BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) /// This class defines functions for calculating /// properties of amino acid sequences. class NCBI_XALGOSEQ_EXPORT CProtProp { public: /// Counts the numbers of occurrences of each residue type. static TSeqPos AACount(CSeqVector& v, vector<TSeqPos>& aacount); /// Estimates the isoelectric point (pI) of a protein. static double GetProteinPI(CSeqVector& v); /// Estimates the charge on a protein /// at a given pH. static double GetProteinCharge(const vector<TSeqPos>& aacount, CSeqVector::TResidue nter, CSeqVector::TResidue cter, double pH); private: static double exp10(double x) { return pow(double(10), x); } }; END_SCOPE(objects) END_NCBI_SCOPE #endif // ALGO_SEQUENCE___PROT_PROP__HPP

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