source: branches/help/GDE/MUSCLE/src/tomhydro.cpp

#include "muscle.h"
#include "profile.h"

// Original:
//HYDROPHILIC_CONTEXT 0 6 -0.3969495574
//HYDROPHILIC_CONTEXT 1 6 -0.9407126603
//HYDROPHILIC_CONTEXT 2 6 -0.4968150972
//HYDROPHILIC_CONTEXT 3 6 -0.271646023
//HYDROPHILIC_CONTEXT 4 6 0.006990406416
//HYDROPHILIC_CONTEXT 5 6 0.1381111256
//HYDROPHILIC_CONTEXT 6 6 0.2541439872

// Blosum62:
//HYDROPHILIC_CONTEXT 0 6 -0.2448419585
//HYDROPHILIC_CONTEXT 1 6 -0.8734889946
//HYDROPHILIC_CONTEXT 2 6 -0.5724336598
//HYDROPHILIC_CONTEXT 3 6 -0.2670439975
//HYDROPHILIC_CONTEXT 4 6 0.004844647323
//HYDROPHILIC_CONTEXT 5 6 0.1812057148
//HYDROPHILIC_CONTEXT 6 6 0.1036540864

static SCORE Factors[7] =
        {
        (SCORE) -0.2448419585,
        (SCORE) -0.8734889946,
        (SCORE) -0.5724336598,
        (SCORE) -0.2670439975,
        (SCORE) 0.004844647323,
        (SCORE) 0.1812057148,
        (SCORE) 0.1036540864
        };

static bool Hydrophilic[20] =
        {
        false,          // A
        false,          // C
        true,           // D
        true,           // E
        false,          // F
        true,           // G
        false,          // H
        false,          // I
        true,           // K
        false,          // L
        false,          // M
        true,           // N
        true,           // P
        true,           // Q
        true,           // R
        true,           // S
        false,          // T
        false,          // V
        false,          // Y
        false,          // W
        };

bool IsHydrophilic(const FCOUNT fcCounts[])
        {
        for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
                if (fcCounts[uLetter] > 0.0 && Hydrophilic[uLetter])
                        return false;
        return true;
        }

static double HydrophilicFraction(const FCOUNT fcCounts[])
        {
        double TotalAll = 0.0;
        double TotalHydrophilic = 0.0;
        for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
                {
                FCOUNT Freq = fcCounts[uLetter];
                TotalAll += Freq;
                if (Hydrophilic[uLetter])
                        TotalHydrophilic += Freq;
                }
        return TotalHydrophilic / TotalAll;
        }

void TomHydro(ProfPos *Prof, unsigned uLength)
        {
        if (ALPHA_Amino != g_Alpha)
                return;
        if (uLength < 6)
                return;

        for (unsigned uColIndex = 3; uColIndex < uLength - 2; ++uColIndex)
                {
        // 6-residue window:
        //       xxxxxx
        //      AARNCARNGTAGCATNAC
        //      AARN----------TNAC

                double dCount = 0.0;
                for (unsigned uColIndexW = uColIndex - 3; uColIndexW < uColIndex + 3;
                  ++uColIndexW)
                        {
                        const ProfPos &PP = Prof[uColIndexW];
                        dCount += HydrophilicFraction(PP.m_fcCounts);
                        }
        // Round to nearest integer
                unsigned uCount = (unsigned) (dCount + 0.5);
                if (uCount > 6)
                        uCount = 6;
                SCORE dFactor = Factors[uCount];
                ProfPos &PP = Prof[uColIndex];
                PP.m_scoreGapOpen += dFactor;
                PP.m_scoreGapClose += dFactor;
                }
        }