--- /dev/null
+\hypertarget{1_88_84__epars_8h}{\section{1.8.4\-\_\-epars.h}
+\label{1_88_84__epars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/lib/1.\-8.\-4\-\_\-epars.\-h}}
+}
+
+\begin{DoxyCode}
+00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_OLD\_EPARS\_\_}
+00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_OLD\_EPARS\_\_}
+00003 \textcolor{preprocessor}{}
+00038 \textcolor{preprocessor}{#define K0 273.15}
+00039 \textcolor{preprocessor}{}\textcolor{preprocessor}{#ifdef INF}
+00040 \textcolor{preprocessor}{}\textcolor{preprocessor}{#undef INF}
+00041 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00042 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define INF 1000000}
+00043 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NBPAIRS 7}
+00044 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define NST 0 }\textcolor{comment}{/* Energy for nonstandard stacked pairs */}\textcolor{preprocessor}{}
+00045 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEF -50 }\textcolor{comment}{/* Default terminal mismatch, used for I */}\textcolor{preprocessor}{}
+00046 \textcolor{preprocessor}{} \textcolor{comment}{/* and any non\_pairing bases */}
+00047 \textcolor{preprocessor}{#define NSM 0 }\textcolor{comment}{/* terminal mismatch for non standard pairs */}\textcolor{preprocessor}{}
+00048 \textcolor{preprocessor}{}
+00049 PRIVATE \textcolor{keywordtype}{double} Tmeasure\_184 = 37 + \hyperlink{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{K0}; \textcolor{comment}{/* temperature of param measurements */}
+00050 PRIVATE \textcolor{keywordtype}{double} lxc37\_184 = 107.856; \textcolor{comment}{/* parameter for logarithmic loop}
+00051 \textcolor{comment}{ energy extrapolation */}
+00052
+00053 PRIVATE \textcolor{keywordtype}{int} stack37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1] =
+00054 \textcolor{comment}{/* CG GC GU UG AU UA */}
+00055 \{ \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\},
+00056 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -240, -330, -210, -140, -210, -210, NST\},
+00057 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -330, -340, -250, -150, -220, -240, NST\},
+00058 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -210, -250, 130, -50, -140, -130, NST\},
+00059 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -140, -150, -50, 30, -60, -100, NST\},
+00060 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -210, -220, -140, -60, -110, -90, NST\},
+00061 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -210, -240, -130, -100, -90, -130, NST\},
+00062 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, NST, NST, NST, NST, NST, NST, NST\}\};
+00063
+00064 \textcolor{comment}{/* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */}
+00065 \textcolor{comment}{/* different from mfold-2.3, which uses values from mfold-2.2 */}
+00066 PRIVATE \textcolor{keywordtype}{int} enthalpies\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1] =
+00067 \textcolor{comment}{/* CG GC GU UG AU UA */}
+00068 \{ \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\},
+00069 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1060, -1340, -1210, -560, -1050, -1040, NST\},
+00070 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1340, -1490, -1260, -830, -1140, -1240, NST\},
+00071 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1210, -1260, -1460, -1350, -880, -1280, NST\},
+00072 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -560, -830, -1350, -930, -320, -700, NST\},
+00073 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1050, -1140, -880, -320, -940, -680, NST\},
+00074 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -1040, -1240, -1280, -700, -680, -770, NST\},
+00075 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, NST, NST, NST, NST, NST, NST, NST\}\};
+00076
+00077
+00078 \textcolor{comment}{/* old values are here just for comparison */}
+00079 PRIVATE \textcolor{keywordtype}{int} oldhairpin37\_184[31] = \{ \textcolor{comment}{/* from ViennaRNA 1.3 */}
+00080 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 410, 490, 440, 470, 500, 510, 520, 531,
+00081 542, 551, 560, 568, 575, 582, 589, 595, 601, 606,
+00082 611, 616, 621, 626, 630, 634, 638, 642, 646, 650\};
+00083
+00084 PRIVATE \textcolor{keywordtype}{int} hairpin37\_184[31] = \{
+00085 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 570, 560, 560, 540, 590, 560, 640, 650,
+00086 660, 670, 678, 686, 694, 701, 707, 713, 719, 725,
+00087 730, 735, 740, 744, 749, 753, 757, 761, 765, 769\};
+00088
+00089 PRIVATE \textcolor{keywordtype}{int} oldbulge37\_184[31] = \{
+00090 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,
+00091 565, 574, 583, 591, 598, 605, 612, 618, 624, 630,
+00092 635, 640, 645, 649, 654, 658, 662, 666, 670, 673\};
+00093
+00094 PRIVATE \textcolor{keywordtype}{int} bulge37\_184[31] = \{
+00095 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,
+00096 500, 510, 519, 527, 534, 541, 548, 554, 560, 565,
+00097 571, 576, 580, 585, 589, 594, 598, 602, 605, 609\};
+00098
+00099 PRIVATE \textcolor{keywordtype}{int} oldinternal\_loop37\_184[31] = \{
+00100 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 410, 510, 490, 530, 570, 587, 601, 614, 625,
+00101 635, 645, 653, 661, 669, 676, 682, 688, 694, 700,
+00102 705, 710, 715, 720, 724, 728, 732, 736, 740, 744\};
+00103
+00104 PRIVATE \textcolor{keywordtype}{int} internal\_loop37\_184[31] = \{
+00105 \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, 410, 510, 170, 180, 200, 220, 230, 240, 250,
+00106 260, 270, 278, 286, 294, 301, 307, 313, 319, 325,
+00107 330, 335, 340, 345, 349, 353, 357, 361, 365, 369\};
+00108
+00109 \textcolor{comment}{/* terminal mismatches */}
+00110 \textcolor{comment}{/* mismatch free energies for interior loops at 37C */}
+00111 PRIVATE \textcolor{keywordtype}{int} mismatchI37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] =
+00112 \{ \textcolor{comment}{/* @@ */}
+00113 \{\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\}\},
+00114 \{ \textcolor{comment}{/* CG */}
+00115 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00116 \{ 0, 0, 0, -110, 0\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00117 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00118 \{ 0, -110, 0, 0, 0\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00119 \{ 0, 0, 0, 0, -70\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00120 \{ \textcolor{comment}{/* GC */}
+00121 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00122 \{ 0, 0, 0, -110, 0\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00123 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00124 \{ 0, -110, 0, 0, 0\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00125 \{ 0, 0, 0, 0, -70\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00126 \{ \textcolor{comment}{/* GU */}
+00127 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00128 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00129 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00130 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00131 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00132 \{ \textcolor{comment}{/* UG */}
+00133 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00134 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00135 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00136 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00137 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00138 \{ \textcolor{comment}{/* AU */}
+00139 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00140 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00141 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00142 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00143 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00144 \{ \textcolor{comment}{/* UA */}
+00145 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00146 \{ 0, 70, 70, -40, 70\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00147 \{ 0, 70, 70, 70, 70\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00148 \{ 0, -40, 70, 70, 70\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00149 \{ 0, 70, 70, 70, 0\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00150 \{ \textcolor{comment}{/* @@ */}
+00151 \{ 90, 90, 90, 90, 90\},\{ 90, 90, 90, 90,-20\},\{ 90, 90, 90, 90, 90\},
+00152 \{ 90,-20, 90, 90, 90\},\{ 90, 90, 90, 90, 20\}\}
+00153 \};
+00154
+00155 \textcolor{comment}{/* mismatch free energies for hairpins at 37C */}
+00156 PRIVATE \textcolor{keywordtype}{int} mismatchH37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] =
+00157 \{ \textcolor{comment}{/* @@ */}
+00158 \{\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\}\},
+00159 \{ \textcolor{comment}{/* CG */}
+00160 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00161 \{ -90, -150, -150, -140, -180\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00162 \{ -90, -100, -90, -290, -80\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00163 \{ -90, -220, -200, -160, -110\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00164 \{ -90, -170, -140, -180, -200\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00165 \{ \textcolor{comment}{/* GC */}
+00166 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00167 \{ -70, -110, -150, -130, -210\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00168 \{ -70, -110, -70, -240, -50\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00169 \{ -70, -240, -290, -140, -120\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00170 \{ -70, -190, -100, -220, -150\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00171 \{ \textcolor{comment}{/* GU */}
+00172 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00173 \{ 0, 20, -50, -30, -30\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00174 \{ 0, -10, -20, -150, -20\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00175 \{ 0, -90, -110, -30, 0\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00176 \{ 0, -30, -30, -40, -110\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00177 \{ \textcolor{comment}{/* UG */}
+00178 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00179 \{ 0, -50, -30, -60, -50\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00180 \{ 0, -20, -10, -170, 0\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00181 \{ 0, -80, -120, -30, -70\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00182 \{ 0, -60, -10, -60, -80\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00183 \{ \textcolor{comment}{/* AU */}
+00184 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00185 \{ 0, -30, -50, -30, -30\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00186 \{ 0, -10, -20, -150, -20\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00187 \{ 0, -110, -120, -20, 20\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00188 \{ 0, -30, -30, -60, -110\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00189 \{ \textcolor{comment}{/* UA */}
+00190 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00191 \{ 0, -50, -30, -60, -50\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00192 \{ 0, -20, -10, -120, -0\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00193 \{ 0, -140, -120, -70, -20\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00194 \{ 0, -30, -10, -50, -80\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00195 \{ \textcolor{comment}{/* @@ */}
+00196 \{ 0, 0, 0, 0, 0\},\{ 0, 0, 0, 0, 0\},\{ 0, 0, 0, 0, 0\},
+00197 \{ 0, 0, 0, 0, 0\},\{ 0, 0, 0, 0, 0\}\}
+00198 \};
+00199
+00200 \textcolor{comment}{/* mismatch energies in multiloops */}
+00201 PRIVATE \textcolor{keywordtype}{int} mismatchM37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5];
+00202
+00203 \textcolor{comment}{/* these are probably junk */}
+00204 \textcolor{comment}{/* mismatch enthalpies for temperature scaling */}
+00205 PRIVATE \textcolor{keywordtype}{int} mism\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5][5] =
+00206 \{ \textcolor{comment}{/* no pair */}
+00207 \{\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\},\{0,0,0,0,0\}\},
+00208 \{ \textcolor{comment}{/* CG */}
+00209 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00210 \{ DEF,-1030, -950,-1030,-1030\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00211 \{ DEF, -520, -450, -520, -670\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00212 \{ DEF, -940, -940, -940, -940\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00213 \{ DEF, -810, -740, -810, -860\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00214 \{ \textcolor{comment}{/* GC */}
+00215 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00216 \{ DEF, -520, -880, -560, -880\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00217 \{ DEF, -720, -310, -310, -390\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00218 \{ DEF, -710, -740, -620, -740\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00219 \{ DEF, -500, -500, -500, -570\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00220 \{ \textcolor{comment}{/* GU */}
+00221 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00222 \{ DEF, -430, -600, -600, -600\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00223 \{ DEF, -260, -240, -240, -240\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00224 \{ DEF, -340, -690, -690, -690\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00225 \{ DEF, -330, -330, -330, -330\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00226 \{ \textcolor{comment}{/* UG */}
+00227 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00228 \{ DEF, -720, -790, -960, -810\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00229 \{ DEF, -480, -480, -360, -480\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00230 \{ DEF, -660, -810, -920, -810\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00231 \{ DEF, -550, -440, -550, -360\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00232 \{ \textcolor{comment}{/* AU */}
+00233 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00234 \{ DEF, -430, -600, -600, -600\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00235 \{ DEF, -260, -240, -240, -240\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00236 \{ DEF, -340, -690, -690, -690\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00237 \{ DEF, -330, -330, -330, -330\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00238 \{ \textcolor{comment}{/* UA */}
+00239 \{ 0, 0, 0, 0, 0\}, \textcolor{comment}{/* @@ @A @C @G @U */}
+00240 \{ DEF, -400, -630, -890, -590\}, \textcolor{comment}{/* A@ AA AC AG AU */}
+00241 \{ DEF, -430, -510, -200, -180\}, \textcolor{comment}{/* C@ CA CC CG CU */}
+00242 \{ DEF, -380, -680, -890, -680\}, \textcolor{comment}{/* G@ GA GC GG GU */}
+00243 \{ DEF, -280, -140, -280, -140\}\},\textcolor{comment}{/* U@ UA UC UG UU */}
+00244 \{ \textcolor{comment}{/* nonstandard pair */}
+00245 \{DEF,DEF,DEF,DEF,DEF\},\{DEF,DEF,DEF,DEF,DEF\},\{DEF,DEF,DEF,DEF,DEF\},
+00246 \{DEF,DEF,DEF,DEF,DEF\},\{DEF,DEF,DEF,DEF,DEF\}\}
+00247 \};
+00248
+00249 \textcolor{comment}{/* 5' dangling ends (unpaird base stacks on first paired base) */}
+00250 PRIVATE \textcolor{keywordtype}{int} dangle5\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]=
+00251 \{\textcolor{comment}{/* @ A C G U */}
+00252 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */}
+00253 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -50, -30, -20, -10\}, \textcolor{comment}{/* CG (stacks on C) */}
+00254 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -20, -30, -0, -0\}, \textcolor{comment}{/* GC (stacks on G) */}
+00255 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -30, -40, -20\}, \textcolor{comment}{/* GU */}
+00256 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -10, -20, -20\}, \textcolor{comment}{/* UG */}
+00257 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -30, -40, -20\}, \textcolor{comment}{/* AU */}
+00258 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -30, -10, -20, -20\}, \textcolor{comment}{/* UA */}
+00259 \{ 0, 0, 0, 0, 0\} \textcolor{comment}{/* @ */}
+00260 \};
+00261
+00262 \textcolor{comment}{/* 3' dangling ends (unpaired base stacks on second paired base */}
+00263 PRIVATE \textcolor{keywordtype}{int} dangle3\_37\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5]=
+00264 \{\textcolor{comment}{/* @ A C G U */}
+00265 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */}
+00266 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -110, -40, -130, -60\}, \textcolor{comment}{/* CG (stacks on G) */}
+00267 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -170, -80, -170, -120\}, \textcolor{comment}{/* GC */}
+00268 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -70, -10, -70, -10\}, \textcolor{comment}{/* GU */}
+00269 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -80, -50, -80, -60\}, \textcolor{comment}{/* UG */}
+00270 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -70, -10, -70, -10\}, \textcolor{comment}{/* AU */}
+00271 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, -80, -50, -80, -60\}, \textcolor{comment}{/* UA */}
+00272 \{ 0, 0, 0, 0, 0\} \textcolor{comment}{/* @ */}
+00273 \};
+00274
+00275 \textcolor{comment}{/* enthalpies for temperature scaling */}
+00276 PRIVATE \textcolor{keywordtype}{int} dangle3\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5] =
+00277 \{\textcolor{comment}{/* @ A C G U */}
+00278 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */}
+00279 \{ 0, -740, -280, -640, -360\},
+00280 \{ 0, -900, -410, -860, -750\},
+00281 \{ 0, -740, -240, -720, -490\},
+00282 \{ 0, -490, -90, -550, -230\},
+00283 \{ 0, -570, -70, -580, -220\},
+00284 \{ 0, -490, -90, -550, -230\},
+00285 \{ 0, 0, 0, 0, 0\}
+00286 \};
+00287
+00288 PRIVATE \textcolor{keywordtype}{int} dangle5\_H\_184[\hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}+1][5] =
+00289 \{\textcolor{comment}{/* @ A C G U */}
+00290 \{ \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, INF\}, \textcolor{comment}{/* no pair */}
+00291 \{ 0, -240, 330, 80, -140\},
+00292 \{ 0, -160, 70, -460, -40\},
+00293 \{ 0, 160, 220, 70, 310\},
+00294 \{ 0, -150, 510, 10, 100\},
+00295 \{ 0, 160, 220, 70, 310\},
+00296 \{ 0, -50, 690, -60, -60\},
+00297 \{ 0, 0, 0, 0, 0\}
+00298 \};
+00299
+00300
+00301 \textcolor{comment}{/* constants for linearly destabilizing contributions for multi-loops}
+00302 \textcolor{comment}{ F = ML\_closing + ML\_intern*k + ML\_BASE*u */}
+00303 \textcolor{comment}{/* old versions erroneously used ML\_intern*(k-1) */}
+00304 PRIVATE \textcolor{keywordtype}{int} ML\_BASE37\_184 = 0;
+00305 PRIVATE \textcolor{keywordtype}{int} ML\_closing37\_184 = 340;
+00306 PRIVATE \textcolor{keywordtype}{int} ML\_intern37\_184 = 40;
+00307
+00308 \textcolor{comment}{/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */}
+00309 \textcolor{comment}{/* ninio\_energy = min\{max\_ninio, |n1-n2|*F\_ninio[min\{4.0, n1, n2\}] \} */}
+00310 PRIVATE \textcolor{keywordtype}{int} MAX\_NINIO\_184 = 300; \textcolor{comment}{/* maximum correction */}
+00311 PRIVATE \textcolor{keywordtype}{int} F\_ninio37\_184[5] = \{ 0, 40, 50, 20, 10 \}; \textcolor{comment}{/* only F[2] used */}
+00312
+00313 \textcolor{comment}{/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */}
+00314
+00315 PRIVATE \textcolor{keywordtype}{char} Tetraloops\_184[1400] = \textcolor{comment}{/* place for up to 200 tetra loops */}
+00316 \textcolor{stringliteral}{"GGGGAC "}
+00317 \textcolor{stringliteral}{"GGUGAC "}
+00318 \textcolor{stringliteral}{"CGAAAG "}
+00319 \textcolor{stringliteral}{"GGAGAC "}
+00320 \textcolor{stringliteral}{"CGCAAG "}
+00321 \textcolor{stringliteral}{"GGAAAC "}
+00322 \textcolor{stringliteral}{"CGGAAG "}
+00323 \textcolor{stringliteral}{"CUUCGG "}
+00324 \textcolor{stringliteral}{"CGUGAG "}
+00325 \textcolor{stringliteral}{"CGAAGG "}
+00326 \textcolor{stringliteral}{"CUACGG "}
+00327 \textcolor{stringliteral}{"GGCAAC "}
+00328 \textcolor{stringliteral}{"CGCGAG "}
+00329 \textcolor{stringliteral}{"UGAGAG "}
+00330 \textcolor{stringliteral}{"CGAGAG "}
+00331 \textcolor{stringliteral}{"AGAAAU "}
+00332 \textcolor{stringliteral}{"CGUAAG "}
+00333 \textcolor{stringliteral}{"CUAACG "}
+00334 \textcolor{stringliteral}{"UGAAAG "}
+00335 \textcolor{stringliteral}{"GGAAGC "}
+00336 \textcolor{stringliteral}{"GGGAAC "}
+00337 \textcolor{stringliteral}{"UGAAAA "}
+00338 \textcolor{stringliteral}{"AGCAAU "}
+00339 \textcolor{stringliteral}{"AGUAAU "}
+00340 \textcolor{stringliteral}{"CGGGAG "}
+00341 \textcolor{stringliteral}{"AGUGAU "}
+00342 \textcolor{stringliteral}{"GGCGAC "}
+00343 \textcolor{stringliteral}{"GGGAGC "}
+00344 \textcolor{stringliteral}{"GUGAAC "}
+00345 \textcolor{stringliteral}{"UGGAAA "}
+00346 ;
+00347
+00348 PRIVATE \textcolor{keywordtype}{int} TETRA\_ENERGY37\_184[200] = \{
+00349 -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,
+00350 -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,
+00351 -150, -150, -150, -150, -150, -150\};
+00352
+00353 PRIVATE \textcolor{keywordtype}{int} TETRA\_ENTH37\_184 = -400;
+00354
+00355 PRIVATE \textcolor{keywordtype}{char} Triloops\_184[241] = \textcolor{stringliteral}{""};
+00356
+00357 PRIVATE \textcolor{keywordtype}{int} Triloop\_E37\_184[40];
+00358
+00359 \textcolor{comment}{/* penalty for AU (or GU) terminating helix) */}
+00360 \textcolor{comment}{/* mismatches already contain these */}
+00361 PRIVATE \textcolor{keywordtype}{int} TerminalAU\_184 = 50;
+00362
+00363 \textcolor{comment}{/* penalty for forming a bi-molecular duplex */}
+00364 PRIVATE \textcolor{keywordtype}{int} DuplexInit\_184 = 410;
+00365
+00366 \textcolor{preprocessor}{#endif}
+\end{DoxyCode}
git://source.jalview.org / jabaws.git / blobdiff