1 | #include "RNA3D_GlobalHeader.hxx" |
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2 | #include "RNA3D_Global.hxx" |
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3 | #include "RNA3D_OpenGLGraphics.hxx" |
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4 | #include "RNA3D_Graphics.hxx" |
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5 | #include "RNA3D_StructureData.hxx" |
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6 | |
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7 | #include <cerrno> |
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8 | #include <string> |
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9 | #include <iostream> |
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10 | #include <fstream> |
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11 | |
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12 | #include <arbdbt.h> |
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13 | #include <aw_msg.hxx> |
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14 | #include <aw_awars.hxx> |
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15 | #include <aw_root.hxx> |
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16 | #include <ed4_extern.hxx> |
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17 | #include <ed4_plugins.hxx> |
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18 | #include <BI_basepos.hxx> |
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19 | |
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20 | |
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21 | #define COLORLINK (ED4_G_SBACK_0 - RNA3D_GC_SBACK_0) // to link to the colors defined in primary editor ed4_defs.hxx |
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22 | #define SAICOLORS (ED4_G_CBACK_0 - RNA3D_GC_CBACK_0) |
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23 | |
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24 | using namespace std; |
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25 | |
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26 | static Struct3Dinfo *start3D = NULp; |
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27 | static Struct2Dinfo *start2D = NULp; |
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28 | static Struct2Dplus3D *start2D3D = NULp; |
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29 | static HelixNrInfo *start = NULp; |
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30 | static CurrSpecies *startSp = NULp; |
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31 | static bool bOldSpeciesDataExists = false; |
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32 | static Insertions *startIns = NULp; |
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33 | static bool bOldInsertionDataExists = false; |
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34 | static bool bStartPosStored = false; |
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35 | static bool bEndPosStored = false; |
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36 | |
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37 | static char *find_data_file(const char *name) { |
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38 | char *fname = GB_lib_file(false, "rna3d/", name); |
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39 | if (!fname) throw string("file not found: ")+name; |
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40 | return fname; |
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41 | } |
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42 | |
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43 | static void throw_IO_error(const char *filename) __ATTR__NORETURN; |
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44 | static void throw_IO_error(const char *filename) { |
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45 | string error = string("IO-Error: ")+strerror(errno)+" ('"+filename+"')"; |
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46 | throw error; |
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47 | } |
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48 | |
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49 | GBDATA *Structure3D::gb_main = NULp; |
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50 | |
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51 | Structure3D::Structure3D(ED4_plugin_host& host_) |
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52 | : strCen(new Vector3(0.0, 0.0, 0.0)), |
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53 | iInterval(25), |
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54 | iMapSAI(0), |
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55 | iMapSearch(0), |
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56 | iMapEnable(0), |
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57 | iStartPos(0), |
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58 | iEndPos(0), |
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59 | iEColiStartPos(0), |
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60 | iEColiEndPos(0), |
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61 | iTotalSubs(0), |
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62 | iTotalDels(0), |
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63 | iTotalIns(0), |
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64 | LSU_molID(3), // default molecule to load in case of 23S rRNA : 1C2W |
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65 | HelixBase(500), |
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66 | EColiRef(NULp), |
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67 | Host(host_), |
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68 | GRAPHICS(new OpenGLGraphics) |
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69 | {} |
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70 | |
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71 | Structure3D::~Structure3D() { |
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72 | delete GRAPHICS; |
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73 | delete strCen; |
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74 | } |
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75 | |
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76 | |
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77 | void Structure3D::StoreCoordinates(float x, float y, float z, char base, unsigned int pos) { |
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78 | Struct3Dinfo *data, *temp; |
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79 | data = new Struct3Dinfo; |
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80 | data->x = x; |
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81 | data->y = y; |
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82 | data->z = z; |
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83 | data->base = base; |
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84 | data->pos = pos; |
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85 | data->next = NULp; |
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86 | |
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87 | if (!start3D) |
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88 | start3D = data; |
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89 | else { |
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90 | temp = start3D; |
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91 | // We know this is not NULp - list not empty! |
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92 | while (temp->next) { |
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93 | temp = temp->next; // Move to next link in chain |
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94 | } |
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95 | temp->next = data; |
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96 | } |
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97 | } |
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98 | |
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99 | // ------------------Selecting rRNA type--------------------------// |
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100 | |
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101 | int Structure3D::FindTypeOfRNA() { // @@@ should better return an enum type |
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102 | int rnaType = 0; |
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103 | GB_push_transaction(gb_main); // opening a transaction |
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104 | |
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105 | GBDATA *gbTemplate = GBT_find_SAI(gb_main, "ECOLI"); |
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106 | if (!gbTemplate) { |
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107 | aw_message("SAI:ECOLI not found"); |
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108 | } |
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109 | else { |
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110 | char *ali_name = GBT_get_default_alignment(gb_main); |
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111 | GBDATA *gbAlignment = GB_entry(gbTemplate, ali_name); |
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112 | GBDATA *gbTemplateSeqData = gbAlignment ? GB_entry(gbAlignment, "data") : NULp; |
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113 | |
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114 | if (!gbTemplateSeqData) { |
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115 | aw_message("Could not find species in the database!"); |
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116 | } |
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117 | else { |
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118 | const char *pTemplateSeqData = GB_read_char_pntr(gbTemplateSeqData); |
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119 | int iSeqLen = strlen(pTemplateSeqData); |
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120 | int iBaseCount = 0; |
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121 | for (int i = 0; i<iSeqLen; i++) { |
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122 | if ((pTemplateSeqData[i] != '.') && (pTemplateSeqData[i] != '-')) { |
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123 | iBaseCount++; |
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124 | } |
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125 | } |
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126 | |
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127 | if (iBaseCount > 2000) rnaType = LSU_23S; |
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128 | else if (iBaseCount > 300) rnaType = SSU_16S; |
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129 | else rnaType = LSU_5S; |
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130 | } |
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131 | } |
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132 | GB_pop_transaction(gb_main); |
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133 | |
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134 | return rnaType; |
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135 | } |
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136 | |
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137 | // ----------Delete old molecule data-------------------------------// |
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138 | // Struct2Dinfo, Struct2Dplus3D, Struct3Dinfo, HelixNrInfo, Insertions |
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139 | |
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140 | void Structure3D::DeleteOldMoleculeData() { |
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141 | // Struct2Dinfo -> start2D |
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142 | { |
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143 | Struct2Dinfo *tmp, *data; |
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144 | for (data = start2D; data; data = tmp) { |
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145 | tmp = data->next; |
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146 | delete data; |
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147 | } |
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148 | start2D = NULp; |
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149 | } |
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150 | |
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151 | // Struct2Dplus3D ->start2D3D |
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152 | { |
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153 | Struct2Dplus3D *tmp, *data; |
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154 | for (data = start2D3D; data; data = tmp) { |
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155 | tmp = data->next; |
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156 | delete data; |
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157 | } |
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158 | start2D3D = NULp; |
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159 | } |
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160 | |
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161 | // Struct3Dinfo ->start3D |
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162 | { |
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163 | Struct3Dinfo *tmp, *data; |
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164 | for (data = start3D; data; data = tmp) { |
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165 | tmp = data->next; |
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166 | delete data; |
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167 | } |
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168 | start3D = NULp; |
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169 | } |
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170 | |
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171 | // HelixNrInfo -> start |
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172 | { |
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173 | HelixNrInfo *tmp, *data; |
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174 | for (data = start; data; data = tmp) { |
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175 | tmp = data->next; |
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176 | delete data; |
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177 | } |
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178 | start = NULp; |
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179 | } |
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180 | |
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181 | // Delete insertions data |
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182 | DeleteOldInsertionData(); |
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183 | |
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184 | // Delete mapped species data |
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185 | DeleteOldSpeciesData (); |
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186 | } |
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187 | |
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188 | // =========== Reading 3D Coordinates from PDB file ====================// |
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189 | |
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190 | static char globalComment[1000]; |
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191 | |
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192 | void Structure3D::ReadCoOrdinateFile() { |
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193 | static char *DataFile = NULp; |
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194 | int rnaType = FindTypeOfRNA(); |
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195 | |
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196 | RNA3D->bDisplayComments = true; // displaying comments in main window |
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197 | |
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198 | switch (rnaType) { |
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199 | case LSU_23S: |
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200 | switch (LSU_molID) { |
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201 | case _1PNU: |
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202 | DataFile = find_data_file("Ecoli_1PNU_23S_rRNA.pdb"); |
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203 | sprintf(globalComment, "The 3D molecule rendered from PDB entry : 1PNU at 8.7 Angstrom."); |
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204 | break; |
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205 | case _1VOR: |
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206 | DataFile = find_data_file("Ecoli_1VOR_23S_rRNA.pdb"); |
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207 | sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1VOR] with 11.5 Angstrom resolution."); |
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208 | break; |
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209 | case _1C2W: |
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210 | DataFile = find_data_file("Ecoli_1C2W_23S_rRNA.pdb"); |
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211 | sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1C2W] with 7.5 Angstrom resolution."); |
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212 | break; |
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213 | } |
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214 | break; |
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215 | case LSU_5S: |
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216 | DataFile = find_data_file("Ecoli_1C2X_5S_rRNA.pdb"); |
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217 | sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1C2X] with 7.5 Angstrom resolution."); |
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218 | break; |
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219 | case SSU_16S: |
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220 | DataFile = find_data_file("Ecoli_1M5G_16S_rRNA.pdb"); |
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221 | sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1M5G] with 11.5 Angstrom resolution."); |
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222 | break; |
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223 | } |
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224 | |
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225 | ifstream readData; |
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226 | readData.open(DataFile, ios::in); |
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227 | if (!readData.is_open()) { |
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228 | throw_IO_error(DataFile); |
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229 | } |
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230 | |
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231 | int cntr = 0; |
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232 | unsigned int last3Dpos = 0; |
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233 | static bool bEColiStartPosStored = false; |
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234 | |
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235 | while (!readData.eof()) { |
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236 | char buf[256]; |
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237 | readData.getline(buf, 100); |
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238 | |
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239 | string line(buf); |
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240 | if ((line.find("ATOM") != string::npos) || (line.find("HETATM") != string::npos)) { |
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241 | string atom = line.substr(77, 2); |
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242 | if (atom.find("P") != string::npos) { |
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243 | char base = line[19]; |
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244 | unsigned pos = atoi(line.substr(22, 4).c_str()); |
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245 | |
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246 | // special filter for 23S rRNA structure (IVOR/IPNU) |
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247 | // IVOR/IPNU contains artifacts and are not mentioned in any of the |
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248 | // remarks of PDB file |
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249 | if (last3Dpos != pos && !(pos >= 3093)) { |
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250 | float X = atof(line.substr(31, 8).c_str()); |
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251 | float Y = atof(line.substr(39, 8).c_str()); |
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252 | float Z = atof(line.substr(47, 8).c_str()); |
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253 | |
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254 | StoreCoordinates(X, Y, Z, base, pos); |
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255 | last3Dpos = pos; |
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256 | strCen->x += X; strCen->y += Y; strCen->z += Z; |
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257 | cntr++; |
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258 | } |
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259 | if (!bEColiStartPosStored) { |
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260 | iEColiStartPos = pos; |
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261 | bEColiStartPosStored = true; |
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262 | } |
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263 | iEColiEndPos = pos; |
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264 | } |
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265 | } |
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266 | } |
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267 | |
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268 | cout<<"--------------------------------------------------"<<endl |
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269 | <<globalComment<<endl |
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270 | <<"Structure contains "<<iEColiEndPos-iEColiStartPos<<"( "<<iEColiStartPos<<" - " |
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271 | <<iEColiEndPos<<" ) positions."<<endl |
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272 | <<"---------------------------------------------------"<<endl; |
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273 | |
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274 | strCen->x = strCen->x/cntr; |
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275 | strCen->y = strCen->y/cntr; |
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276 | strCen->z = strCen->z/cntr; |
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277 | |
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278 | readData.close(); |
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279 | free(DataFile); |
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280 | } |
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281 | |
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282 | |
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283 | void Structure3D::Store2Dinfo(char *info, int pos, int helixNr) { |
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284 | Struct2Dinfo *data = new Struct2Dinfo; |
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285 | |
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286 | data->base = info[0]; |
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287 | data->mask = info[1]; |
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288 | data->code = info[2]; |
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289 | data->pos = pos; |
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290 | data->helixNr = helixNr; |
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291 | |
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292 | data->next = NULp; |
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293 | |
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294 | if (!start2D) { |
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295 | start2D = data; |
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296 | } |
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297 | else { |
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298 | Struct2Dinfo *temp = start2D; |
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299 | // We know this is not NULp - list not empty! |
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300 | while (temp->next) { |
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301 | temp = temp->next; // Move to next link in chain |
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302 | } |
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303 | temp->next = data; |
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304 | } |
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305 | } |
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306 | |
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307 | // =========== Reading Secondary Structure Data from Ecoli Secondary Structure Mask file ====================// |
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308 | |
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309 | void Structure3D::GetSecondaryStructureInfo() { |
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310 | static char *DataFile = NULp; |
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311 | int rnaType = FindTypeOfRNA(); |
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312 | |
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313 | switch (rnaType) { |
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314 | case LSU_23S: |
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315 | DataFile = find_data_file("SecondaryStructureModel_23SrRNA.data"); |
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316 | break; |
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317 | case LSU_5S: |
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318 | DataFile = find_data_file("SecondaryStructureModel_5SrRNA.data"); |
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319 | break; |
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320 | case SSU_16S: |
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321 | DataFile = find_data_file("SecondaryStructureModel_16SrRNA.data"); |
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322 | break; |
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323 | } |
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324 | |
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325 | char buf[256]; |
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326 | |
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327 | int pos = 0; |
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328 | int helixNr = 0; |
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329 | int lastHelixNr = 0; |
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330 | char info[4]; |
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331 | info[3] = '\0'; |
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332 | bool insideHelix = false; |
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333 | bool skip = false; |
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334 | |
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335 | ifstream readData; |
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336 | readData.open(DataFile, ios::in); |
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337 | if (!readData.is_open()) { |
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338 | throw_IO_error(DataFile); |
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339 | } |
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340 | |
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341 | while (!readData.eof()) { |
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342 | readData.getline(buf, 100); |
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343 | char *tmp; |
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344 | tmp = strtok(buf, " "); |
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345 | for (int i = 0; tmp; tmp = strtok(NULp, " "), i++) { |
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346 | switch (i) { |
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347 | case 0: pos = atoi(tmp); break; |
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348 | case 1: info[0] = tmp[0]; break; |
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349 | case 2: info[1] = tmp[0]; break; |
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350 | case 3: info[2] = tmp[0]; break; |
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351 | case 4: helixNr = atoi(tmp); break; |
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352 | } |
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353 | } |
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354 | |
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355 | bool is_SE = (info[2] == 'S') || (info[2] == 'E'); // 'S' = helix start 'E' = helix end |
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356 | if (is_SE) { |
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357 | if (helixNr>0) lastHelixNr = helixNr; |
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358 | |
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359 | if (!insideHelix) insideHelix = true; |
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360 | else { |
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361 | Store2Dinfo(info, pos, lastHelixNr); |
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362 | skip = true; |
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363 | insideHelix = false; |
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364 | } |
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365 | } |
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366 | if (insideHelix) Store2Dinfo(info, pos, lastHelixNr); |
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367 | else { |
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368 | if (skip) skip = false; |
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369 | else Store2Dinfo(info, pos, 0); |
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370 | } |
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371 | } |
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372 | readData.close(); |
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373 | free(DataFile); |
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374 | } |
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375 | |
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376 | void Structure3D::Store2D3Dinfo(Struct2Dinfo *s2D, Struct3Dinfo *s3D) { |
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377 | Struct2Dplus3D *data, *temp; |
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378 | data = new Struct2Dplus3D; |
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379 | data->base = s2D->base; |
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380 | data->mask = s2D->mask; |
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381 | data->code = s2D->code; |
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382 | data->pos = s2D->pos; |
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383 | data->helixNr = s2D->helixNr; |
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384 | data->x = s3D->x; |
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385 | data->y = s3D->y; |
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386 | data->z = s3D->z; |
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387 | data->next = NULp; |
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388 | |
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389 | if (!start2D3D) |
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390 | start2D3D = data; |
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391 | else { |
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392 | temp = start2D3D; |
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393 | while (temp->next) { |
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394 | temp = temp->next; |
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395 | } |
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396 | temp->next = data; |
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397 | } |
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398 | } |
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399 | |
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400 | // =========== Combining Secondary Structure Data with 3D Coordinates =======================// |
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401 | |
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402 | void Structure3D::Combine2Dand3DstructureInfo() { |
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403 | Struct3Dinfo *temp3D; |
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404 | Struct2Dinfo *temp2D; |
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405 | int cntr = 0; |
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406 | |
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407 | cout<<"Missing Base Positions : "<<endl; |
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408 | |
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409 | temp3D = start3D; |
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410 | temp2D = start2D; |
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411 | while (temp3D && temp2D) { |
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412 | if (temp2D->pos == temp3D->pos) { |
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413 | Store2D3Dinfo(temp2D, temp3D); |
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414 | } |
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415 | else { |
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416 | while (temp2D->pos != temp3D->pos) { |
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417 | cout<<temp2D->pos<<", "; // missing base positions |
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418 | cntr++; |
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419 | temp2D = temp2D->next; |
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420 | } |
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421 | Store2D3Dinfo(temp2D, temp3D); |
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422 | } |
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423 | |
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424 | temp3D = temp3D->next; |
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425 | temp2D = temp2D->next; |
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426 | } |
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427 | cout<<endl<<"Total No. of bases missing = "<<cntr<<endl; |
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428 | |
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429 | // printing comments in the main window |
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430 | { |
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431 | RNA3D->bDisplayComments = true; |
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432 | char buf[256]; |
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433 | sprintf(buf, "Total No. of bases missing = %d. See the console messages for the actual missing base positions.", cntr); |
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434 | strcat(globalComment, buf); |
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435 | } |
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436 | } |
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437 | |
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438 | void Structure3D::PointsToQuads(float x, float y, float z) { |
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439 | |
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440 | if (RNA3D->bPointSpritesSupported) { |
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441 | glVertex3f(x, y, z); |
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442 | } |
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443 | else { |
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444 | glBegin(GL_QUADS); |
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445 | // Front Face |
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446 | glTexCoord2f(0, 0); glVertex3f(x - 1, y + 1, z + 1); |
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447 | glTexCoord2f(1, 0); glVertex3f(x + 1, y + 1, z + 1); |
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448 | glTexCoord2f(1, 1); glVertex3f(x + 1, y - 1, z + 1); |
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449 | glTexCoord2f(0, 1); glVertex3f(x - 1, y - 1, z + 1); |
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450 | |
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451 | // Back Face |
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452 | glTexCoord2f(0, 0); glVertex3f(x + 1, y + 1, z - 1); |
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453 | glTexCoord2f(1, 0); glVertex3f(x - 1, y + 1, z - 1); |
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454 | glTexCoord2f(1, 1); glVertex3f(x - 1, y - 1, z - 1); |
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455 | glTexCoord2f(0, 1); glVertex3f(x + 1, y - 1, z - 1); |
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456 | |
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457 | // Top Face |
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458 | glTexCoord2f(0, 0); glVertex3f(x + 1, y + 1, z + 1); |
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459 | glTexCoord2f(1, 0); glVertex3f(x - 1, y + 1, z + 1); |
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460 | glTexCoord2f(1, 1); glVertex3f(x - 1, y + 1, z - 1); |
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461 | glTexCoord2f(0, 1); glVertex3f(x + 1, y + 1, z - 1); |
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462 | |
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463 | // Bottom Face |
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464 | glTexCoord2f(0, 0); glVertex3f(x + 1, y - 1, z - 1); |
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465 | glTexCoord2f(1, 0); glVertex3f(x - 1, y - 1, z - 1); |
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466 | glTexCoord2f(1, 1); glVertex3f(x - 1, y - 1, z + 1); |
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467 | glTexCoord2f(0, 1); glVertex3f(x + 1, y - 1, z + 1); |
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468 | |
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469 | // Left Face |
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470 | glTexCoord2f(0, 0); glVertex3f(x + 1, y + 1, z + 1); |
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471 | glTexCoord2f(1, 0); glVertex3f(x + 1, y + 1, z - 1); |
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472 | glTexCoord2f(1, 1); glVertex3f(x + 1, y - 1, z - 1); |
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473 | glTexCoord2f(0, 1); glVertex3f(x + 1, y - 1, z + 1); |
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474 | |
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475 | // Right Face |
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476 | glTexCoord2f(0, 0); glVertex3f(x - 1, y + 1, z - 1); |
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477 | glTexCoord2f(1, 0); glVertex3f(x - 1, y + 1, z + 1); |
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478 | glTexCoord2f(1, 1); glVertex3f(x - 1, y - 1, z + 1); |
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479 | glTexCoord2f(0, 1); glVertex3f(x - 1, y - 1, z - 1); |
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480 | |
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481 | glEnd(); |
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482 | } |
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483 | } |
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484 | |
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485 | void Structure3D::PositionsToCoordinatesDispList(int listID, int *pos, int len) { |
---|
486 | Struct2Dplus3D *t; |
---|
487 | int tmpPos = 0; |
---|
488 | |
---|
489 | glNewList(listID, GL_COMPILE); |
---|
490 | { |
---|
491 | if (RNA3D->bPointSpritesSupported) { |
---|
492 | glBegin(GL_POINTS); |
---|
493 | } |
---|
494 | for (int i = 0; i < len; i++) { |
---|
495 | tmpPos = pos[i]; |
---|
496 | t = start2D3D; |
---|
497 | while (t) { |
---|
498 | if (t->pos == tmpPos) { |
---|
499 | PointsToQuads(t->x, t->y, t->z); |
---|
500 | break; |
---|
501 | } |
---|
502 | t = t->next; |
---|
503 | } |
---|
504 | } |
---|
505 | if (RNA3D->bPointSpritesSupported) { |
---|
506 | glEnd(); |
---|
507 | } |
---|
508 | } |
---|
509 | glEndList(); |
---|
510 | } |
---|
511 | |
---|
512 | void Structure3D::GenerateSecStructureNonHelixRegions() { |
---|
513 | Struct2Dplus3D *t; |
---|
514 | const int MAX_BASE = 1000; |
---|
515 | int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE], baseU[MAX_BASE]; |
---|
516 | int a, g, c, u; a=g=c=u=0; |
---|
517 | |
---|
518 | { |
---|
519 | t = start2D3D; |
---|
520 | while (t) { |
---|
521 | if (t->helixNr == 0) { |
---|
522 | switch (t->base) { |
---|
523 | case 'A': baseA[a++] = t->pos; break; |
---|
524 | case 'G': baseG[g++] = t->pos; break; |
---|
525 | case 'C': baseC[c++] = t->pos; break; |
---|
526 | case 'U': baseU[u++] = t->pos; break; |
---|
527 | } |
---|
528 | } |
---|
529 | t = t->next; |
---|
530 | } |
---|
531 | } |
---|
532 | |
---|
533 | PositionsToCoordinatesDispList(NON_HELIX_A, baseA, a); |
---|
534 | PositionsToCoordinatesDispList(NON_HELIX_G, baseG, g); |
---|
535 | PositionsToCoordinatesDispList(NON_HELIX_C, baseC, c); |
---|
536 | PositionsToCoordinatesDispList(NON_HELIX_U, baseU, u); |
---|
537 | } |
---|
538 | |
---|
539 | void Structure3D::GenerateSecStructureHelixRegions() { |
---|
540 | Struct2Dplus3D *t; |
---|
541 | const int MAX_BASE = 1000; |
---|
542 | int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE], baseU[MAX_BASE]; |
---|
543 | int a, g, c, u; a=g=c=u=0; |
---|
544 | |
---|
545 | { |
---|
546 | t = start2D3D; |
---|
547 | while (t) { |
---|
548 | if (t->helixNr > 0) { |
---|
549 | if ((t->mask == '[') || (t->mask == ']') || (t->mask == '<') || (t->mask == '>')) { |
---|
550 | switch (t->base) { |
---|
551 | case 'A': baseA[a++] = t->pos; break; |
---|
552 | case 'G': baseG[g++] = t->pos; break; |
---|
553 | case 'C': baseC[c++] = t->pos; break; |
---|
554 | case 'U': baseU[u++] = t->pos; break; |
---|
555 | } |
---|
556 | } |
---|
557 | } |
---|
558 | t = t->next; |
---|
559 | } |
---|
560 | } |
---|
561 | |
---|
562 | PositionsToCoordinatesDispList(HELIX_A, baseA, a); |
---|
563 | PositionsToCoordinatesDispList(HELIX_G, baseG, g); |
---|
564 | PositionsToCoordinatesDispList(HELIX_C, baseC, c); |
---|
565 | PositionsToCoordinatesDispList(HELIX_U, baseU, u); |
---|
566 | } |
---|
567 | |
---|
568 | void Structure3D::GenerateSecStructureUnpairedHelixRegions() { |
---|
569 | Struct2Dplus3D *t; |
---|
570 | const int MAX_BASE = 500; |
---|
571 | int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE], baseU[MAX_BASE]; |
---|
572 | int a, g, c, u; a=g=c=u=0; |
---|
573 | |
---|
574 | { |
---|
575 | t = start2D3D; |
---|
576 | while (t) { |
---|
577 | if (t->helixNr > 0) { |
---|
578 | if (t->mask == '.') { |
---|
579 | switch (t->base) { |
---|
580 | case 'A': baseA[a++] = t->pos; break; |
---|
581 | case 'G': baseG[g++] = t->pos; break; |
---|
582 | case 'C': baseC[c++] = t->pos; break; |
---|
583 | case 'U': baseU[u++] = t->pos; break; |
---|
584 | } |
---|
585 | } |
---|
586 | } |
---|
587 | t = t->next; |
---|
588 | } |
---|
589 | } |
---|
590 | |
---|
591 | PositionsToCoordinatesDispList(UNPAIRED_HELIX_A, baseA, a); |
---|
592 | PositionsToCoordinatesDispList(UNPAIRED_HELIX_G, baseG, g); |
---|
593 | PositionsToCoordinatesDispList(UNPAIRED_HELIX_C, baseC, c); |
---|
594 | PositionsToCoordinatesDispList(UNPAIRED_HELIX_U, baseU, u); |
---|
595 | } |
---|
596 | |
---|
597 | // ============================================================================== |
---|
598 | // Tertiary Interactions of 16S ribosomal RNA model of E.coli. |
---|
599 | // Reference : http://www.rna.icmb.utexas.edu/ |
---|
600 | // Year of Last Update : 2001. |
---|
601 | // Pseudoknots and Triple Base pairs are extracted and displayed in |
---|
602 | // the 3D model. |
---|
603 | // ============================================================================== |
---|
604 | |
---|
605 | void Structure3D::GenerateTertiaryInteractionsDispLists() { |
---|
606 | Struct2Dplus3D *t; |
---|
607 | static char *DataFile = NULp; |
---|
608 | int rnaType = FindTypeOfRNA(); |
---|
609 | |
---|
610 | switch (rnaType) { |
---|
611 | case LSU_23S: |
---|
612 | DataFile = find_data_file("TertiaryInteractions_23SrRNA.data"); |
---|
613 | break; |
---|
614 | case LSU_5S: |
---|
615 | cout<<"There are no tertiary interactions observed in 5S rRNA model!"<<endl; |
---|
616 | return; |
---|
617 | case SSU_16S: |
---|
618 | DataFile = find_data_file("TertiaryInteractions_16SrRNA.data"); |
---|
619 | break; |
---|
620 | } |
---|
621 | |
---|
622 | cout<<"Tertiary Interactions are fetched from comparative RNA website [http://www.rna.icmb.utexas.edu]."<<endl |
---|
623 | <<"The same are located in the file \""<<DataFile<<"\"."<<endl; |
---|
624 | |
---|
625 | char buf[256]; |
---|
626 | |
---|
627 | ifstream readData; |
---|
628 | readData.open(DataFile, ios::in); |
---|
629 | if (!readData.is_open()) { |
---|
630 | throw_IO_error(DataFile); |
---|
631 | } |
---|
632 | |
---|
633 | int K[100]; |
---|
634 | int R[100]; |
---|
635 | int k, r; k = r = 0; |
---|
636 | |
---|
637 | while (!readData.eof()) { |
---|
638 | readData.getline(buf, 100); |
---|
639 | char *tmp; |
---|
640 | tmp = strtok(buf, " "); |
---|
641 | if (tmp) { |
---|
642 | if (strcmp(tmp, "KNOT") == 0) { |
---|
643 | tmp = strtok(NULp, ":"); |
---|
644 | while (tmp) { |
---|
645 | K[k++] = atoi(tmp); |
---|
646 | tmp = strtok(NULp, ":"); |
---|
647 | } |
---|
648 | } |
---|
649 | else if (strcmp(tmp, "TRIPLE") == 0) { |
---|
650 | tmp = strtok(NULp, ":"); |
---|
651 | while (tmp) { |
---|
652 | R[r++] = atoi(tmp); |
---|
653 | tmp = strtok(NULp, ":"); |
---|
654 | } |
---|
655 | } |
---|
656 | } |
---|
657 | } |
---|
658 | readData.close(); |
---|
659 | |
---|
660 | glNewList(ECOLI_TERTIARY_INTRACTION_PSEUDOKNOTS, GL_COMPILE); |
---|
661 | { |
---|
662 | for (int i = 0; i < k;) { |
---|
663 | glBegin(GL_LINES); |
---|
664 | for (int j = 0; j < 2; j++) { |
---|
665 | t = start2D3D; |
---|
666 | while (t) { |
---|
667 | if (t->pos == K[i]) { |
---|
668 | glVertex3f(t->x, t->y, t->z); |
---|
669 | i++; |
---|
670 | break; |
---|
671 | } |
---|
672 | t = t->next; |
---|
673 | } |
---|
674 | } |
---|
675 | glEnd(); |
---|
676 | } |
---|
677 | } |
---|
678 | glEndList(); |
---|
679 | |
---|
680 | glNewList(ECOLI_TERTIARY_INTRACTION_TRIPLE_BASES, GL_COMPILE); |
---|
681 | { |
---|
682 | for (int i = 0; i < r;) { |
---|
683 | glBegin(GL_LINE_STRIP); |
---|
684 | for (int j = 0; j < 3; j++) { |
---|
685 | t = start2D3D; |
---|
686 | while (t) { |
---|
687 | if (t->pos == R[i]) { |
---|
688 | glVertex3f(t->x, t->y, t->z); |
---|
689 | i++; |
---|
690 | break; |
---|
691 | } |
---|
692 | t = t->next; |
---|
693 | } |
---|
694 | } |
---|
695 | glEnd(); |
---|
696 | } |
---|
697 | } |
---|
698 | glEndList(); |
---|
699 | free(DataFile); |
---|
700 | } |
---|
701 | |
---|
702 | // ============================================================================== |
---|
703 | |
---|
704 | void Structure3D::StoreHelixNrInfo(float x, float y, float z, int helixNr) { |
---|
705 | HelixNrInfo *data, *temp; |
---|
706 | data = new HelixNrInfo; |
---|
707 | data->helixNr = helixNr; |
---|
708 | data->x = x; |
---|
709 | data->y = y; |
---|
710 | data->z = z; |
---|
711 | data->next = NULp; |
---|
712 | |
---|
713 | if (!start) |
---|
714 | start = data; |
---|
715 | else { |
---|
716 | temp = start; |
---|
717 | while (temp->next) { |
---|
718 | temp = temp->next; |
---|
719 | } |
---|
720 | temp->next = data; |
---|
721 | } |
---|
722 | } |
---|
723 | |
---|
724 | void Structure3D::GenerateHelixDispLists(int HELIX_NR_ID, int HELIX_NR) { |
---|
725 | Struct2Dinfo *temp2D; |
---|
726 | Struct2Dplus3D *temp2D3D; |
---|
727 | |
---|
728 | const int MAX = 500; |
---|
729 | |
---|
730 | int thisStrandPos[MAX], otherStrandPos[MAX]; |
---|
731 | int i, j; i = j = 0; |
---|
732 | { |
---|
733 | temp2D = start2D; |
---|
734 | while (temp2D) { |
---|
735 | if (temp2D->helixNr == HELIX_NR) { |
---|
736 | if ((temp2D->mask == '[') || (temp2D->mask == '<')) |
---|
737 | thisStrandPos[i++] = temp2D->pos; |
---|
738 | if ((temp2D->mask == ']') || (temp2D->mask == '>')) |
---|
739 | otherStrandPos[j++] = temp2D->pos; |
---|
740 | } |
---|
741 | temp2D = temp2D->next; |
---|
742 | } |
---|
743 | } |
---|
744 | |
---|
745 | int tempPos = 0; |
---|
746 | float x1, x2, y1, y2, z1, z2; x1=x2=y1=y2=z1=z2=0.0; |
---|
747 | |
---|
748 | bool bThisStrand, bOtherStrand; |
---|
749 | bThisStrand = bOtherStrand = false; |
---|
750 | |
---|
751 | bool bMissingBasePair = false; |
---|
752 | |
---|
753 | glNewList(HELIX_NR_ID, GL_COMPILE); |
---|
754 | { |
---|
755 | for (int k = 0, l = j-1; k < i && l >= 0; k++, l--) { |
---|
756 | tempPos = thisStrandPos[k]; |
---|
757 | { |
---|
758 | temp2D3D = start2D3D; |
---|
759 | while (temp2D3D) { |
---|
760 | if (temp2D3D->pos == tempPos) { |
---|
761 | bThisStrand = true; |
---|
762 | x1=temp2D3D->x; y1=temp2D3D->y; z1=temp2D3D->z; |
---|
763 | break; |
---|
764 | } |
---|
765 | temp2D3D = temp2D3D->next; |
---|
766 | } |
---|
767 | } |
---|
768 | tempPos = otherStrandPos[l]; |
---|
769 | { |
---|
770 | temp2D3D = start2D3D; |
---|
771 | while (temp2D3D) { |
---|
772 | if (temp2D3D->pos == tempPos) { |
---|
773 | bOtherStrand = true; |
---|
774 | x2=temp2D3D->x; y2=temp2D3D->y; z2=temp2D3D->z; |
---|
775 | break; |
---|
776 | } |
---|
777 | temp2D3D = temp2D3D->next; |
---|
778 | } |
---|
779 | } |
---|
780 | // if bases present in both the strands then draw a bond |
---|
781 | // and store the helix number information |
---|
782 | if (bThisStrand && bOtherStrand) { |
---|
783 | glVertex3f(x1, y1, z1); |
---|
784 | glVertex3f(x2, y2, z2); |
---|
785 | |
---|
786 | x1 = (x1+x2)/2; y1 = (y1+y2)/2; z1 = (z1+z2)/2; |
---|
787 | StoreHelixNrInfo(x1, y1, z1, HELIX_NR); |
---|
788 | |
---|
789 | bThisStrand = bOtherStrand = false; |
---|
790 | } |
---|
791 | else { |
---|
792 | bMissingBasePair = true; |
---|
793 | cout<<thisStrandPos[k]<<"-"<<tempPos<<"("<<HELIX_NR_ID<<"), "; |
---|
794 | } |
---|
795 | } |
---|
796 | if (bMissingBasePair) cout<<endl; |
---|
797 | } |
---|
798 | glEndList(); |
---|
799 | } |
---|
800 | |
---|
801 | void Structure3D::GenerateHelixNrDispList(int startHx, int endHx) { |
---|
802 | HelixNrInfo *t; |
---|
803 | |
---|
804 | glNewList(HELIX_NUMBERS, GL_COMPILE); |
---|
805 | { |
---|
806 | char POS[50]; |
---|
807 | for (int i = startHx; i <= endHx; i++) { |
---|
808 | t = start; |
---|
809 | while (t) { |
---|
810 | if (t->helixNr == i) { |
---|
811 | sprintf(POS, "%d", t->helixNr); |
---|
812 | GRAPHICS->PrintString(t->x, t->y, t->z, POS, GLUT_BITMAP_8_BY_13); |
---|
813 | } |
---|
814 | t = t->next; |
---|
815 | } |
---|
816 | } |
---|
817 | } |
---|
818 | glEndList(); |
---|
819 | |
---|
820 | glNewList(HELIX_NUMBERS_POINTS, GL_COMPILE); |
---|
821 | { |
---|
822 | if (RNA3D->bPointSpritesSupported) { |
---|
823 | glBegin(GL_POINTS); |
---|
824 | } |
---|
825 | for (int i = startHx; i <= endHx; i++) { |
---|
826 | t = start; |
---|
827 | while (t) { |
---|
828 | if (t->helixNr == i) { |
---|
829 | PointsToQuads(t->x, t->y, t->z); |
---|
830 | } |
---|
831 | t = t->next; |
---|
832 | } |
---|
833 | } |
---|
834 | if (RNA3D->bPointSpritesSupported) { |
---|
835 | glEnd(); |
---|
836 | } |
---|
837 | } |
---|
838 | glEndList(); |
---|
839 | } |
---|
840 | |
---|
841 | void Structure3D::GenerateDisplayLists() { |
---|
842 | |
---|
843 | GenerateMoleculeSkeleton(); |
---|
844 | ComputeBasePositions(); |
---|
845 | |
---|
846 | int rnaType = FindTypeOfRNA(); |
---|
847 | switch (rnaType) { |
---|
848 | case SSU_16S: |
---|
849 | if (glIsList(HelixBase) != GL_TRUE) { |
---|
850 | for (int i = 1; i <= 50; i++) { |
---|
851 | GenerateHelixDispLists(HelixBase+i, i); |
---|
852 | } |
---|
853 | } |
---|
854 | break; |
---|
855 | case LSU_23S: |
---|
856 | cout<<"=========================================================="<<endl |
---|
857 | <<"Missing base pairs (bracket number indicates helix number) "<<endl; |
---|
858 | if (glIsList(HelixBase) != GL_TRUE) { |
---|
859 | for (int i = 1; i <= 101; i++) { |
---|
860 | GenerateHelixDispLists(HelixBase+i, i); |
---|
861 | } |
---|
862 | } |
---|
863 | cout<<"=========================================================="<<endl; |
---|
864 | break; |
---|
865 | case LSU_5S: |
---|
866 | if (glIsList(HelixBase) != GL_TRUE) { |
---|
867 | for (int i = 1; i <= 5; i++) { |
---|
868 | GenerateHelixDispLists(HelixBase+i, i); |
---|
869 | } |
---|
870 | } |
---|
871 | break; |
---|
872 | } |
---|
873 | |
---|
874 | GenerateSecStructureHelixRegions(); |
---|
875 | GenerateSecStructureNonHelixRegions(); |
---|
876 | GenerateSecStructureUnpairedHelixRegions(); |
---|
877 | |
---|
878 | GenerateTertiaryInteractionsDispLists(); |
---|
879 | } |
---|
880 | |
---|
881 | void Structure3D::GenerateMoleculeSkeleton() { |
---|
882 | Struct2Dplus3D *t; |
---|
883 | |
---|
884 | glNewList(STRUCTURE_BACKBONE, GL_COMPILE); |
---|
885 | { |
---|
886 | glBegin(GL_LINE_STRIP); |
---|
887 | t = start2D3D; |
---|
888 | while (t) { |
---|
889 | glVertex3f(t->x, t->y, t->z); |
---|
890 | t = t->next; |
---|
891 | } |
---|
892 | glEnd(); |
---|
893 | } |
---|
894 | glEndList(); |
---|
895 | |
---|
896 | glNewList(STRUCTURE_BACKBONE_CLR, GL_COMPILE); |
---|
897 | { |
---|
898 | glBegin(GL_LINE_STRIP); |
---|
899 | t = start2D3D; |
---|
900 | while (t) { |
---|
901 | if (t->helixNr > 0) { |
---|
902 | if ((t->mask == '[') || (t->mask == ']') || (t->mask == '<') || (t->mask == '>')) { |
---|
903 | GRAPHICS->SetColor(RNA3D_GC_BASES_HELIX); |
---|
904 | glVertex3f(t->x, t->y, t->z); |
---|
905 | } |
---|
906 | if (t->mask == '.') { |
---|
907 | GRAPHICS->SetColor(RNA3D_GC_BASES_UNPAIRED_HELIX); |
---|
908 | glVertex3f(t->x, t->y, t->z); |
---|
909 | } |
---|
910 | } |
---|
911 | if (t->helixNr == 0) { |
---|
912 | GRAPHICS->SetColor(RNA3D_GC_BASES_NON_HELIX); |
---|
913 | glVertex3f(t->x, t->y, t->z); |
---|
914 | } |
---|
915 | t = t->next; |
---|
916 | } |
---|
917 | glEnd(); |
---|
918 | } |
---|
919 | glEndList(); |
---|
920 | } |
---|
921 | |
---|
922 | void Structure3D::GenerateCursorPositionDispList(long pos) { |
---|
923 | Struct3Dinfo *temp; |
---|
924 | |
---|
925 | glNewList(ECOLI_CURSOR_POSITION, GL_COMPILE); |
---|
926 | { |
---|
927 | glBegin(GL_POINTS); |
---|
928 | temp = start3D; |
---|
929 | while (temp) { |
---|
930 | if (temp->pos == pos) { |
---|
931 | #ifdef DEBUG |
---|
932 | cout<<"Cursor Position : "<<pos<<endl; |
---|
933 | #endif |
---|
934 | glVertex3f(temp->x, temp->y, temp->z); |
---|
935 | break; |
---|
936 | } |
---|
937 | temp = temp->next; |
---|
938 | } |
---|
939 | glEnd(); |
---|
940 | } |
---|
941 | glEndList(); |
---|
942 | } |
---|
943 | |
---|
944 | void Structure3D::ComputeBasePositions() { |
---|
945 | Struct3Dinfo *temp; |
---|
946 | |
---|
947 | char POS[50]; |
---|
948 | float spacer = 1.5; |
---|
949 | int posSkip = iInterval; |
---|
950 | if (posSkip <= 0) posSkip = 25; // default interval value |
---|
951 | |
---|
952 | glNewList(STRUCTURE_POS, GL_COMPILE); |
---|
953 | { |
---|
954 | temp = start3D; |
---|
955 | while (temp) { |
---|
956 | if (temp->pos%posSkip == 0) { |
---|
957 | sprintf(POS, "%d", temp->pos); |
---|
958 | GRAPHICS->PrintString(temp->x-spacer, temp->y, temp->z-spacer, POS, GLUT_BITMAP_HELVETICA_10); |
---|
959 | } |
---|
960 | temp = temp->next; |
---|
961 | } |
---|
962 | } |
---|
963 | glEndList(); |
---|
964 | |
---|
965 | glNewList(STRUCTURE_POS_ANCHOR, GL_COMPILE); |
---|
966 | { |
---|
967 | glLineWidth(0.5); |
---|
968 | glBegin(GL_LINES); |
---|
969 | temp = start3D; |
---|
970 | while (temp) { |
---|
971 | if (temp->pos%posSkip == 0) { |
---|
972 | glVertex3f(temp->x, temp->y, temp->z); |
---|
973 | glVertex3f(temp->x-spacer, temp->y, temp->z-spacer); |
---|
974 | } |
---|
975 | temp = temp->next; |
---|
976 | } |
---|
977 | glEnd(); |
---|
978 | } |
---|
979 | glEndList(); |
---|
980 | } |
---|
981 | |
---|
982 | void Structure3D::PrepareSecondaryStructureData() { |
---|
983 | // const char |
---|
984 | // outFile[] = "/nfshome/yadhu/DataBase/Struct3D/model16SrRNA/test.data", |
---|
985 | // EcoliFile[] = "/nfshome/yadhu/DataBase/Struct3D/model16SrRNA/ECOLI_GAPS", |
---|
986 | // HelixNrFile[] = "/nfshome/yadhu/DataBase/Struct3D/model16SrRNA/HELIX_NR", |
---|
987 | // HelixGapFile[] = "/nfshome/yadhu/DataBase/Struct3D/model16SrRNA/HELIX_GAP", |
---|
988 | // ErrorMsg[] = "\n *** Error Opening File : "; |
---|
989 | |
---|
990 | const char |
---|
991 | outFile[] = "/home/Yadhu/DataBase/Struct3D/model23SrRNA/test.data", |
---|
992 | EcoliFile[] = "/home/Yadhu/DataBase/Struct3D/model23SrRNA/Ecoli_23SrRNA_with_gaps.seq", |
---|
993 | HelixNrFile[] = "/home/Yadhu/DataBase/Struct3D/model23SrRNA/HelixNumbers.msk", |
---|
994 | HelixGapFile[] = "/home/Yadhu/DataBase/Struct3D/model23SrRNA/SecStructureMask_with_gaps.msk", |
---|
995 | ErrorMsg[] = "\n *** Error Opening File : "; |
---|
996 | |
---|
997 | // const char |
---|
998 | // outFile[] = "/home/Yadhu/DataBase/Struct3D/model5SrRNA/test.data", |
---|
999 | // EcoliFile[] = "/home/Yadhu/DataBase/Struct3D/model5SrRNA/Ecoli_5SrRNA_with_gaps.seq", |
---|
1000 | // HelixNrFile[] = "/home/Yadhu/DataBase/Struct3D/model5SrRNA/HelixNumbers.msk", |
---|
1001 | // HelixGapFile[] = "/home/Yadhu/DataBase/Struct3D/model5SrRNA/SecStructureMask_with_gaps.msk", |
---|
1002 | // ErrorMsg[] = "\n *** Error Opening File : "; |
---|
1003 | |
---|
1004 | int fileLen = 0; |
---|
1005 | char *helixNrBuf, *helixGapBuf, *ecoliBuf; |
---|
1006 | |
---|
1007 | ofstream out; |
---|
1008 | out.open(outFile, ios::out); |
---|
1009 | if (!out.is_open()) cerr<<ErrorMsg<<outFile<<endl; |
---|
1010 | |
---|
1011 | ifstream inFile; |
---|
1012 | { |
---|
1013 | { |
---|
1014 | inFile.open(EcoliFile, ios::binary); |
---|
1015 | if (!inFile.is_open()) cerr<<ErrorMsg<<HelixGapFile<<endl; |
---|
1016 | |
---|
1017 | inFile.seekg (0, ios::end); // get length of file |
---|
1018 | fileLen = inFile.tellg(); |
---|
1019 | inFile.seekg (0, ios::beg); |
---|
1020 | |
---|
1021 | ecoliBuf = new char[fileLen]; // allocate memory: |
---|
1022 | |
---|
1023 | inFile.read (ecoliBuf, fileLen); // read data as a block: |
---|
1024 | inFile.close(); |
---|
1025 | } |
---|
1026 | |
---|
1027 | { |
---|
1028 | inFile.open(HelixNrFile, ios::binary); |
---|
1029 | if (!inFile.is_open()) cerr<<ErrorMsg<<HelixGapFile<<endl; |
---|
1030 | |
---|
1031 | inFile.seekg (0, ios::end); // get length of file |
---|
1032 | fileLen = inFile.tellg(); |
---|
1033 | inFile.seekg (0, ios::beg); |
---|
1034 | |
---|
1035 | helixNrBuf = new char[fileLen]; // allocate memory: |
---|
1036 | |
---|
1037 | inFile.read (helixNrBuf, fileLen); // read data as a block: |
---|
1038 | inFile.close(); |
---|
1039 | } |
---|
1040 | |
---|
1041 | { |
---|
1042 | inFile.open(HelixGapFile, ios::binary); |
---|
1043 | if (!inFile.is_open()) cerr<<ErrorMsg<<HelixNrFile<<endl; |
---|
1044 | |
---|
1045 | inFile.seekg (0, ios::end); // get length of file |
---|
1046 | fileLen = inFile.tellg(); |
---|
1047 | inFile.seekg (0, ios::beg); |
---|
1048 | |
---|
1049 | helixGapBuf = new char[fileLen]; // allocate memory: |
---|
1050 | |
---|
1051 | inFile.read (helixGapBuf, fileLen); // read data as a block: |
---|
1052 | inFile.close(); |
---|
1053 | } |
---|
1054 | |
---|
1055 | char helixNr[4]; helixNr[3] = '\0'; |
---|
1056 | int skip, gaps, k; |
---|
1057 | skip = gaps = k = 0; |
---|
1058 | |
---|
1059 | for (unsigned int i = 0; i < strlen(ecoliBuf); i++) { |
---|
1060 | if (ecoliBuf[i] == '\n') skip++; |
---|
1061 | else { |
---|
1062 | if ((ecoliBuf[i] == '.') || (ecoliBuf[i] == '-')) gaps++; |
---|
1063 | else { |
---|
1064 | int pos = (i - (skip + gaps)) + 1; |
---|
1065 | out<<pos<<" "<<ecoliBuf[i]<<" "<<helixGapBuf[i]<<" "; |
---|
1066 | switch (helixGapBuf[i]) { |
---|
1067 | case '.': out<<"N "; break; |
---|
1068 | case '[': out<<"S "; break; |
---|
1069 | case ']': out<<"E "; break; |
---|
1070 | case '<': out<<"H "; break; |
---|
1071 | case '>': out<<"H "; break; |
---|
1072 | } |
---|
1073 | for (unsigned int j = i; helixNrBuf[j] != '.'; j++) { |
---|
1074 | helixNr[k++] = helixNrBuf[j]; |
---|
1075 | } |
---|
1076 | for (int l = k; l < 4; l++) helixNr[l] = '\0'; |
---|
1077 | k = 0; |
---|
1078 | if ((helixGapBuf[i] == '[') || (helixGapBuf[i] == ']')) { |
---|
1079 | out<<helixNr; |
---|
1080 | } |
---|
1081 | out<<endl; |
---|
1082 | } |
---|
1083 | } |
---|
1084 | } |
---|
1085 | delete [] helixNrBuf; |
---|
1086 | delete [] ecoliBuf; |
---|
1087 | delete [] helixGapBuf; |
---|
1088 | out.close(); |
---|
1089 | } |
---|
1090 | } |
---|
1091 | |
---|
1092 | void Structure3D::StoreCurrSpeciesDifference(char base, int pos) { |
---|
1093 | Struct2Dplus3D *st; |
---|
1094 | st = start2D3D; |
---|
1095 | while (st) { |
---|
1096 | if (st->pos == pos) { |
---|
1097 | CurrSpecies *data, *temp; |
---|
1098 | data = new CurrSpecies; |
---|
1099 | data->base = base; |
---|
1100 | data->pos = pos; |
---|
1101 | data->x = st->x; |
---|
1102 | data->y = st->y; |
---|
1103 | data->z = st->z; |
---|
1104 | data->next = NULp; |
---|
1105 | |
---|
1106 | if (!startSp) { |
---|
1107 | startSp = data; |
---|
1108 | bOldSpeciesDataExists = true; |
---|
1109 | } |
---|
1110 | else { |
---|
1111 | temp = startSp; |
---|
1112 | while (temp->next) { |
---|
1113 | temp = temp->next; |
---|
1114 | } |
---|
1115 | temp->next = data; |
---|
1116 | } |
---|
1117 | break; |
---|
1118 | } |
---|
1119 | st = st->next; |
---|
1120 | } |
---|
1121 | } |
---|
1122 | |
---|
1123 | void Structure3D::DeleteOldSpeciesData() { |
---|
1124 | CurrSpecies *tmp, *data; |
---|
1125 | |
---|
1126 | for (data = startSp; data; data = tmp) { |
---|
1127 | tmp = data->next; |
---|
1128 | delete data; |
---|
1129 | } |
---|
1130 | startSp = NULp; |
---|
1131 | |
---|
1132 | bOldSpeciesDataExists = false; |
---|
1133 | } |
---|
1134 | |
---|
1135 | void Structure3D::GenerateBaseDifferencePositionDisplayList() { |
---|
1136 | CurrSpecies *t; |
---|
1137 | Struct3Dinfo *temp; |
---|
1138 | |
---|
1139 | char POS[50]; |
---|
1140 | float spacer = 1.5; |
---|
1141 | |
---|
1142 | glNewList(MAP_SPECIES_BASE_DIFFERENCE_POS, GL_COMPILE); |
---|
1143 | { |
---|
1144 | for (t = startSp; t; t = t->next) { |
---|
1145 | for (temp = start3D; temp; temp = temp->next) { |
---|
1146 | if (temp->pos == t->pos) { |
---|
1147 | sprintf(POS, "%d", temp->pos); |
---|
1148 | GRAPHICS->PrintString(temp->x-spacer, temp->y, temp->z-spacer, POS, GLUT_BITMAP_8_BY_13); |
---|
1149 | } |
---|
1150 | } |
---|
1151 | } |
---|
1152 | } |
---|
1153 | glEndList(); |
---|
1154 | |
---|
1155 | glNewList(MAP_SPECIES_BASE_DIFFERENCE_POS_ANCHOR, GL_COMPILE); |
---|
1156 | { |
---|
1157 | glLineWidth(1.0); |
---|
1158 | glBegin(GL_LINES); |
---|
1159 | |
---|
1160 | for (t = startSp; t; t = t->next) { |
---|
1161 | for (temp = start3D; temp; temp = temp->next) { |
---|
1162 | if (temp->pos == t->pos) { |
---|
1163 | glVertex3f(temp->x, temp->y, temp->z); |
---|
1164 | glVertex3f(temp->x-spacer, temp->y, temp->z-spacer); |
---|
1165 | } |
---|
1166 | } |
---|
1167 | } |
---|
1168 | glEnd(); |
---|
1169 | } |
---|
1170 | glEndList(); |
---|
1171 | } |
---|
1172 | |
---|
1173 | void Structure3D::BuildDisplayList(int listID, int *pos, int len) { |
---|
1174 | CurrSpecies *t; |
---|
1175 | int tmpPos = 0; |
---|
1176 | |
---|
1177 | glNewList(listID, GL_COMPILE); |
---|
1178 | { |
---|
1179 | if (RNA3D->bPointSpritesSupported) { |
---|
1180 | glBegin(GL_POINTS); |
---|
1181 | } |
---|
1182 | for (int i = 0; i < len; i++) { |
---|
1183 | tmpPos = pos[i]; |
---|
1184 | t = startSp; |
---|
1185 | while (t) { |
---|
1186 | if (t->pos == tmpPos) { |
---|
1187 | PointsToQuads(t->x, t->y, t->z); |
---|
1188 | break; |
---|
1189 | } |
---|
1190 | t = t->next; |
---|
1191 | } |
---|
1192 | } |
---|
1193 | if (RNA3D->bPointSpritesSupported) { |
---|
1194 | glEnd(); |
---|
1195 | } |
---|
1196 | } |
---|
1197 | glEndList(); |
---|
1198 | } |
---|
1199 | |
---|
1200 | void Structure3D::GenerateBaseDifferenceDisplayList() { |
---|
1201 | CurrSpecies *t; |
---|
1202 | |
---|
1203 | glNewList(MAP_SPECIES_BASE_DIFFERENCE, GL_COMPILE); |
---|
1204 | { |
---|
1205 | if (RNA3D->bPointSpritesSupported) { |
---|
1206 | glBegin(GL_POINTS); |
---|
1207 | } |
---|
1208 | t = startSp; |
---|
1209 | while (t) { |
---|
1210 | PointsToQuads(t->x, t->y, t->z); |
---|
1211 | t = t->next; |
---|
1212 | } |
---|
1213 | if (RNA3D->bPointSpritesSupported) { |
---|
1214 | glEnd(); |
---|
1215 | } |
---|
1216 | } |
---|
1217 | glEndList(); |
---|
1218 | |
---|
1219 | const int MAX_BASE = 400; |
---|
1220 | int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE], |
---|
1221 | baseU[MAX_BASE], deletion[MAX_BASE], miss[MAX_BASE]; |
---|
1222 | int a, g, c, u, d, m; a=g=c=u=d=m=0; |
---|
1223 | |
---|
1224 | { |
---|
1225 | t = startSp; |
---|
1226 | while (t) { |
---|
1227 | switch (t->base) { |
---|
1228 | case 'A': baseA[a++] = t->pos; break; |
---|
1229 | case 'G': baseG[g++] = t->pos; break; |
---|
1230 | case 'C': baseC[c++] = t->pos; break; |
---|
1231 | case 'U': baseU[u++] = t->pos; break; |
---|
1232 | case '-': deletion[d++] = t->pos; break; |
---|
1233 | case '.': miss[m++] = t->pos; break; |
---|
1234 | } |
---|
1235 | t = t->next; |
---|
1236 | } |
---|
1237 | BuildDisplayList(MAP_SPECIES_BASE_A, baseA, a); |
---|
1238 | BuildDisplayList(MAP_SPECIES_BASE_U, baseU, u); |
---|
1239 | BuildDisplayList(MAP_SPECIES_BASE_G, baseG, g); |
---|
1240 | BuildDisplayList(MAP_SPECIES_BASE_C, baseC, c); |
---|
1241 | BuildDisplayList(MAP_SPECIES_DELETION, deletion, d); |
---|
1242 | BuildDisplayList(MAP_SPECIES_MISSING, miss, m); |
---|
1243 | GenerateBaseDifferencePositionDisplayList(); |
---|
1244 | |
---|
1245 | iTotalSubs = a+g+c+u; // Summing up the substitutions/mutations |
---|
1246 | iTotalDels = d; // Storing total number of deletions |
---|
1247 | #ifdef DEBUG |
---|
1248 | cout<<"Substitutions = "<<iTotalSubs<<endl; |
---|
1249 | cout<<"Deletions = "<<iTotalDels<<endl; |
---|
1250 | #endif |
---|
1251 | } |
---|
1252 | } |
---|
1253 | |
---|
1254 | void Structure3D::StoreInsertions(char base, int pos) { |
---|
1255 | Insertions *data, *temp; |
---|
1256 | data = new Insertions; |
---|
1257 | data->base = base; |
---|
1258 | data->pos = pos; |
---|
1259 | data->next = NULp; |
---|
1260 | |
---|
1261 | if (!startIns) { |
---|
1262 | startIns = data; |
---|
1263 | bOldInsertionDataExists = true; |
---|
1264 | } |
---|
1265 | else { |
---|
1266 | temp = startIns; |
---|
1267 | while (temp->next) { |
---|
1268 | temp = temp->next; |
---|
1269 | } |
---|
1270 | temp->next = data; |
---|
1271 | } |
---|
1272 | } |
---|
1273 | |
---|
1274 | void Structure3D::DeleteOldInsertionData() { |
---|
1275 | Insertions *tmp, *data; |
---|
1276 | |
---|
1277 | for (data = startIns; data; data = tmp) { |
---|
1278 | tmp = data->next; |
---|
1279 | delete data; |
---|
1280 | } |
---|
1281 | startIns = NULp; |
---|
1282 | |
---|
1283 | bOldInsertionDataExists = false; |
---|
1284 | } |
---|
1285 | |
---|
1286 | void Structure3D::GenerateInsertionDisplayList() { |
---|
1287 | Insertions *ins; |
---|
1288 | Struct3Dinfo *str; |
---|
1289 | char inserts[500]; |
---|
1290 | int i, cntr; |
---|
1291 | float spacer = 2.0; |
---|
1292 | iTotalIns = 0; |
---|
1293 | |
---|
1294 | glNewList(MAP_SPECIES_INSERTION_BASES, GL_COMPILE); |
---|
1295 | { |
---|
1296 | for (str = start3D; str; str = str->next) { |
---|
1297 | i = cntr = 0; |
---|
1298 | for (ins = startIns; ins; ins = ins->next) { |
---|
1299 | if (str->pos == ins->pos) { |
---|
1300 | inserts[i++] = ins->base; |
---|
1301 | cntr++; |
---|
1302 | } |
---|
1303 | } |
---|
1304 | if (cntr>0) { |
---|
1305 | inserts[i] = '\0'; |
---|
1306 | char buffer[strlen(inserts) + 10]; |
---|
1307 | sprintf(buffer, "%d:%s", cntr, inserts); |
---|
1308 | GRAPHICS->PrintString(str->x, str->y+spacer, str->z, |
---|
1309 | buffer, GLUT_BITMAP_8_BY_13); |
---|
1310 | |
---|
1311 | iTotalIns += cntr; // Summing up the insertions |
---|
1312 | } |
---|
1313 | } |
---|
1314 | } |
---|
1315 | glEndList(); |
---|
1316 | |
---|
1317 | #ifdef DEBUG |
---|
1318 | cout<<"Insertions = "<<iTotalIns<<endl; |
---|
1319 | #endif |
---|
1320 | |
---|
1321 | glNewList(MAP_SPECIES_INSERTION_BASES_ANCHOR, GL_COMPILE); |
---|
1322 | { |
---|
1323 | glLineWidth(1.0); |
---|
1324 | glBegin(GL_LINES); |
---|
1325 | |
---|
1326 | for (str = start3D; str; str = str->next) { |
---|
1327 | for (ins = startIns; ins; ins = ins->next) { |
---|
1328 | if (str->pos == ins->pos) { |
---|
1329 | glVertex3f(str->x, str->y, str->z); |
---|
1330 | glVertex3f(str->x, str->y+spacer, str->z); |
---|
1331 | } |
---|
1332 | } |
---|
1333 | } |
---|
1334 | glEnd(); |
---|
1335 | } |
---|
1336 | glEndList(); |
---|
1337 | |
---|
1338 | glNewList(MAP_SPECIES_INSERTION_POINTS, GL_COMPILE); |
---|
1339 | { |
---|
1340 | if (RNA3D->bPointSpritesSupported) { |
---|
1341 | glBegin(GL_POINTS); |
---|
1342 | } |
---|
1343 | for (str = start3D; str; str = str->next) { |
---|
1344 | for (ins = startIns; ins; ins = ins->next) { |
---|
1345 | if (str->pos == ins->pos) { |
---|
1346 | PointsToQuads(str->x, str->y, str->z); |
---|
1347 | break; |
---|
1348 | } |
---|
1349 | } |
---|
1350 | } |
---|
1351 | if (RNA3D->bPointSpritesSupported) { |
---|
1352 | glEnd(); |
---|
1353 | } |
---|
1354 | } |
---|
1355 | glEndList(); |
---|
1356 | } |
---|
1357 | |
---|
1358 | void Structure3D::MapCurrentSpeciesToEcoliTemplate(AW_root *awr) { |
---|
1359 | |
---|
1360 | GB_push_transaction(gb_main); |
---|
1361 | |
---|
1362 | GBDATA *gbTemplate = GBT_find_SAI(gb_main, "ECOLI"); |
---|
1363 | |
---|
1364 | if (!gbTemplate) { |
---|
1365 | aw_message("SAI:ECOLI not found"); |
---|
1366 | } |
---|
1367 | else { |
---|
1368 | char *pSpeciesName = awr->awar(AWAR_SPECIES_NAME)->read_string(); |
---|
1369 | if (pSpeciesName) { |
---|
1370 | Host.announce_current_species(pSpeciesName); |
---|
1371 | GBDATA *gbSpecies = GBT_find_species(gb_main, pSpeciesName); |
---|
1372 | if (gbSpecies) { |
---|
1373 | char *ali_name = GBT_get_default_alignment(gb_main); |
---|
1374 | GBDATA *gbAlignment = GB_entry(gbTemplate, ali_name); |
---|
1375 | GBDATA *gbTemplateSeqData = gbAlignment ? GB_entry(gbAlignment, "data") : NULp; |
---|
1376 | |
---|
1377 | if (!gbTemplateSeqData) { |
---|
1378 | aw_message(GBS_global_string("Mapping impossible, since SAI:ECOLI has no data in alignment '%s'", ali_name)); |
---|
1379 | } |
---|
1380 | else { |
---|
1381 | const char *pTemplateSeqData = GB_read_char_pntr(gbTemplateSeqData); |
---|
1382 | |
---|
1383 | if (!RNA3D->bEColiRefInitialized) { |
---|
1384 | EColiRef = new BI_ecoli_ref; |
---|
1385 | EColiRef->init(gb_main); |
---|
1386 | RNA3D->bEColiRefInitialized = true; |
---|
1387 | } |
---|
1388 | |
---|
1389 | char buf[100]; |
---|
1390 | char *pSpFullName = GB_read_string(GB_entry(gbSpecies, "full_name")); |
---|
1391 | sprintf(buf, "%s : %s", pSpeciesName, pSpFullName); |
---|
1392 | awr->awar(AWAR_3D_SELECTED_SPECIES)->write_string(buf); |
---|
1393 | |
---|
1394 | GBDATA *gbSeqData = GBT_find_sequence(gbSpecies, ali_name); |
---|
1395 | const char *pSeqData = GB_read_char_pntr(gbSeqData); |
---|
1396 | |
---|
1397 | if (pSeqData && pTemplateSeqData) { |
---|
1398 | int iSeqLen = strlen(pTemplateSeqData); |
---|
1399 | |
---|
1400 | if (bOldSpeciesDataExists) { |
---|
1401 | DeleteOldSpeciesData(); |
---|
1402 | } |
---|
1403 | |
---|
1404 | for (int i = 0, iSeqCount = 0; i<iSeqLen; i++) { |
---|
1405 | if ((pTemplateSeqData[i] != '.') && (pTemplateSeqData[i] != '-')) { |
---|
1406 | if (!bStartPosStored) { |
---|
1407 | iStartPos = i; |
---|
1408 | bStartPosStored = true; |
---|
1409 | } |
---|
1410 | if (pTemplateSeqData[i] != pSeqData[i]) { |
---|
1411 | StoreCurrSpeciesDifference(pSeqData[i], iSeqCount); |
---|
1412 | } |
---|
1413 | iSeqCount++; |
---|
1414 | } |
---|
1415 | } |
---|
1416 | |
---|
1417 | for (int i = iSeqLen; i>0; i--) { |
---|
1418 | if ((pTemplateSeqData[i] != '.') && (pTemplateSeqData[i] != '-')) { |
---|
1419 | if (!bEndPosStored) { |
---|
1420 | iEndPos = i; |
---|
1421 | bEndPosStored = true; |
---|
1422 | break; |
---|
1423 | } |
---|
1424 | } |
---|
1425 | } |
---|
1426 | |
---|
1427 | if (bOldInsertionDataExists) { |
---|
1428 | DeleteOldInsertionData(); |
---|
1429 | } |
---|
1430 | |
---|
1431 | for (int i = iStartPos, iSeqCount = 0; i < iEndPos; i++) { |
---|
1432 | if ((pTemplateSeqData[i] != '.') && (pTemplateSeqData[i] != '-')) { |
---|
1433 | // Store EColi base positions : Insertion point! |
---|
1434 | iSeqCount++; |
---|
1435 | } |
---|
1436 | |
---|
1437 | if ((pTemplateSeqData[i] == '-') && |
---|
1438 | (pSeqData[i] != '-') && |
---|
1439 | (pSeqData[i] != '.')) |
---|
1440 | { |
---|
1441 | StoreInsertions(pSeqData[i], iSeqCount); |
---|
1442 | } |
---|
1443 | } |
---|
1444 | } |
---|
1445 | free(pSpFullName); |
---|
1446 | } |
---|
1447 | free(ali_name); |
---|
1448 | } |
---|
1449 | GenerateBaseDifferenceDisplayList(); |
---|
1450 | GenerateInsertionDisplayList(); |
---|
1451 | } |
---|
1452 | free(pSpeciesName); |
---|
1453 | } |
---|
1454 | GB_pop_transaction(gb_main); |
---|
1455 | } |
---|
1456 | |
---|
1457 | static bool ValidSearchColor(int iColor, int mode) { |
---|
1458 | bool isValid = false; |
---|
1459 | |
---|
1460 | switch (mode) { |
---|
1461 | case SAI: isValid = (iColor >= RNA3D_GC_CBACK_0) && (iColor < RNA3D_GC_MAX); break; |
---|
1462 | case SEARCH: isValid = (iColor >= RNA3D_GC_SBACK_0) && (iColor < RNA3D_GC_MAX); break; |
---|
1463 | } |
---|
1464 | return isValid; |
---|
1465 | } |
---|
1466 | |
---|
1467 | void Structure3D::MapSearchStringsToEcoliTemplate(AW_root * /* awr */) { |
---|
1468 | const char *pSearchColResults = NULp; |
---|
1469 | |
---|
1470 | if (iMapSearch) pSearchColResults = Host.get_search_background(iStartPos, iEndPos); |
---|
1471 | |
---|
1472 | if (pSearchColResults) { |
---|
1473 | int iColor = 0; |
---|
1474 | |
---|
1475 | glNewList(MAP_SEARCH_STRINGS_TO_STRUCTURE, GL_COMPILE); |
---|
1476 | { |
---|
1477 | if (RNA3D->bPointSpritesSupported) glBegin(GL_POINTS); |
---|
1478 | for (int i = iStartPos; i < iEndPos; i++) { |
---|
1479 | if (RNA3D->bEColiRefInitialized) { |
---|
1480 | long absPos = (long) i; |
---|
1481 | long EColiPos = EColiRef->abs_2_rel(absPos); |
---|
1482 | |
---|
1483 | for (Struct3Dinfo *t = start3D; t; t = t->next) { |
---|
1484 | if ((t->pos == EColiPos) && (pSearchColResults[i] >= 0)) { |
---|
1485 | iColor = pSearchColResults[i] - COLORLINK; |
---|
1486 | |
---|
1487 | if (ValidSearchColor(iColor, SEARCH)) { |
---|
1488 | RNA3D->cGraphics->SetColor(iColor); |
---|
1489 | PointsToQuads(t->x, t->y, t->z); |
---|
1490 | } |
---|
1491 | break; |
---|
1492 | } |
---|
1493 | } |
---|
1494 | } |
---|
1495 | } |
---|
1496 | if (RNA3D->bPointSpritesSupported) glEnd(); |
---|
1497 | } |
---|
1498 | glEndList(); |
---|
1499 | |
---|
1500 | glNewList(MAP_SEARCH_STRINGS_BACKBONE, GL_COMPILE); |
---|
1501 | { |
---|
1502 | int iLastClr = 0; int iLastPos = 0; Vector3 vLastPt; |
---|
1503 | glBegin(GL_LINES); |
---|
1504 | for (int i = iStartPos; i < iEndPos; i++) { |
---|
1505 | if (RNA3D->bEColiRefInitialized) { |
---|
1506 | long absPos = (long) i; |
---|
1507 | long EColiPos = EColiRef->abs_2_rel(absPos); |
---|
1508 | |
---|
1509 | for (Struct3Dinfo *t = start3D; t; t = t->next) { |
---|
1510 | if ((t->pos == EColiPos) && (pSearchColResults[i] >= 0)) { |
---|
1511 | iColor = pSearchColResults[i] - COLORLINK; |
---|
1512 | |
---|
1513 | if (ValidSearchColor(iColor, SEARCH)) { |
---|
1514 | if ((iLastClr == iColor) && (iLastPos == EColiPos-1)) { |
---|
1515 | RNA3D->cGraphics->SetColor(iColor); |
---|
1516 | glVertex3f(vLastPt.x, vLastPt.y, vLastPt.z); |
---|
1517 | glVertex3f(t->x, t->y, t->z); |
---|
1518 | } |
---|
1519 | iLastPos = EColiPos; |
---|
1520 | iLastClr = iColor; |
---|
1521 | vLastPt.x = t->x; vLastPt.y = t->y; vLastPt.z = t->z; |
---|
1522 | } |
---|
1523 | break; |
---|
1524 | } |
---|
1525 | } |
---|
1526 | } |
---|
1527 | } |
---|
1528 | glEnd(); |
---|
1529 | } |
---|
1530 | glEndList(); |
---|
1531 | |
---|
1532 | RNA3D->bMapSearchStringsDispListCreated = true; |
---|
1533 | } |
---|
1534 | else cout<<"BuildColorString did not get the colors : SAI cannot be Visualized!"<<endl; |
---|
1535 | } |
---|
1536 | |
---|
1537 | void Structure3D::MapSaiToEcoliTemplate() { |
---|
1538 | const char *pSearchColResults = NULp; |
---|
1539 | |
---|
1540 | if (iMapSAI && Host.SAIs_visualized()) { |
---|
1541 | pSearchColResults = Host.get_SAI_background(iStartPos, iEndPos); // returns 0 if sth went wrong |
---|
1542 | } |
---|
1543 | |
---|
1544 | if (pSearchColResults) { |
---|
1545 | int iColor = 0; |
---|
1546 | |
---|
1547 | glNewList(MAP_SAI_TO_STRUCTURE, GL_COMPILE); |
---|
1548 | { |
---|
1549 | if (RNA3D->bPointSpritesSupported) glBegin(GL_POINTS); |
---|
1550 | |
---|
1551 | for (int i = iStartPos; i < iEndPos; i++) { |
---|
1552 | if (RNA3D->bEColiRefInitialized) { |
---|
1553 | long absPos = (long) i; |
---|
1554 | long EColiPos = EColiRef->abs_2_rel(absPos); |
---|
1555 | |
---|
1556 | for (Struct3Dinfo *t = start3D; t; t = t->next) { |
---|
1557 | if ((t->pos == EColiPos) && (pSearchColResults[i] >= 0)) { |
---|
1558 | iColor = pSearchColResults[i-1] - SAICOLORS; |
---|
1559 | |
---|
1560 | if (ValidSearchColor(iColor, SAI)) { |
---|
1561 | RNA3D->cGraphics->SetColor(iColor); |
---|
1562 | PointsToQuads(t->x, t->y, t->z); |
---|
1563 | } |
---|
1564 | break; |
---|
1565 | } |
---|
1566 | } |
---|
1567 | } |
---|
1568 | } |
---|
1569 | |
---|
1570 | if (RNA3D->bPointSpritesSupported) glEnd(); |
---|
1571 | } |
---|
1572 | glEndList(); |
---|
1573 | |
---|
1574 | RNA3D->bMapSaiDispListCreated = true; |
---|
1575 | } |
---|
1576 | else cout<<"ED4_getSaiColorString did not get the colors : SAI cannot be Visualized!"<<endl; |
---|
1577 | } |
---|