binaries/src/muscle/tomhydro.cpp

   1 #include "muscle.h"\r
   2 #include "profile.h"\r
   3 \r
   4 // Original:\r
   5 //HYDROPHILIC_CONTEXT 0 6 -0.3969495574
   6 //HYDROPHILIC_CONTEXT 1 6 -0.9407126603
   7 //HYDROPHILIC_CONTEXT 2 6 -0.4968150972
   8 //HYDROPHILIC_CONTEXT 3 6 -0.271646023
   9 //HYDROPHILIC_CONTEXT 4 6 0.006990406416
  10 //HYDROPHILIC_CONTEXT 5 6 0.1381111256
  11 //HYDROPHILIC_CONTEXT 6 6 0.2541439872
  12 \r
  13 // Blosum62:\r
  14 //HYDROPHILIC_CONTEXT 0 6 -0.2448419585
  15 //HYDROPHILIC_CONTEXT 1 6 -0.8734889946
  16 //HYDROPHILIC_CONTEXT 2 6 -0.5724336598
  17 //HYDROPHILIC_CONTEXT 3 6 -0.2670439975
  18 //HYDROPHILIC_CONTEXT 4 6 0.004844647323
  19 //HYDROPHILIC_CONTEXT 5 6 0.1812057148
  20 //HYDROPHILIC_CONTEXT 6 6 0.1036540864
  21
  22 static SCORE Factors[7] =\r
  23         {\r
  24         (SCORE) -0.2448419585,
  25         (SCORE) -0.8734889946,
  26         (SCORE) -0.5724336598,
  27         (SCORE) -0.2670439975,
  28         (SCORE) 0.004844647323,
  29         (SCORE) 0.1812057148,
  30         (SCORE) 0.1036540864
  31         };\r
  32 \r
  33 static bool Hydrophilic[20] =\r
  34         {\r
  35         false,          // A\r
  36         false,          // C\r
  37         true,           // D\r
  38         true,           // E\r
  39         false,          // F\r
  40         true,           // G\r
  41         false,          // H\r
  42         false,          // I\r
  43         true,           // K\r
  44         false,          // L\r
  45         false,          // M\r
  46         true,           // N\r
  47         true,           // P\r
  48         true,           // Q\r
  49         true,           // R\r
  50         true,           // S\r
  51         false,          // T\r
  52         false,          // V\r
  53         false,          // Y\r
  54         false,          // W\r
  55         };\r
  56 \r
  57 bool IsHydrophilic(const FCOUNT fcCounts[])\r
  58         {\r
  59         for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
  60                 if (fcCounts[uLetter] > 0.0 && Hydrophilic[uLetter])\r
  61                         return false;\r
  62         return true;\r
  63         }\r
  64 \r
  65 static double HydrophilicFraction(const FCOUNT fcCounts[])\r
  66         {\r
  67         double TotalAll = 0.0;\r
  68         double TotalHydrophilic = 0.0;\r
  69         for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
  70                 {\r
  71                 FCOUNT Freq = fcCounts[uLetter];\r
  72                 TotalAll += Freq;\r
  73                 if (Hydrophilic[uLetter])\r
  74                         TotalHydrophilic += Freq;\r
  75                 }\r
  76         return TotalHydrophilic / TotalAll;\r
  77         }\r
  78 \r
  79 void TomHydro(ProfPos *Prof, unsigned uLength)\r
  80         {\r
  81         if (ALPHA_Amino != g_Alpha)\r
  82                 return;\r
  83         if (uLength < 6)\r
  84                 return;\r
  85 \r
  86         for (unsigned uColIndex = 3; uColIndex < uLength - 2; ++uColIndex)\r
  87                 {\r
  88         // 6-residue window:\r
  89         //       xxxxxx\r
  90         //      AARNCARNGTAGCATNAC\r
  91         //      AARN----------TNAC\r
  92 \r
  93                 double dCount = 0.0;\r
  94                 for (unsigned uColIndexW = uColIndex - 3; uColIndexW < uColIndex + 3;\r
  95                   ++uColIndexW)\r
  96                         {\r
  97                         const ProfPos &PP = Prof[uColIndexW];\r
  98                         dCount += HydrophilicFraction(PP.m_fcCounts);\r
  99                         }\r
 100         // Round to nearest integer\r
 101                 unsigned uCount = (unsigned) (dCount + 0.5);\r
 102                 if (uCount > 6)\r
 103                         uCount = 6;\r
 104                 SCORE dFactor = Factors[uCount];\r
 105                 ProfPos &PP = Prof[uColIndex];\r
 106                 PP.m_scoreGapOpen += dFactor;\r
 107                 PP.m_scoreGapClose += dFactor;\r
 108                 }\r
 109         }\r