RNA3D_StructureData.cxx

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#include "RNA3D_GlobalHeader.hxx"
#include "RNA3D_Global.hxx"
#include "RNA3D_OpenGLGraphics.hxx"
#include "RNA3D_Graphics.hxx"
#include "RNA3D_StructureData.hxx"

#include <cerrno>
#include <string>
#include <iostream>
#include <fstream>

#include <arbdbt.h>
#include <aw_msg.hxx>
#include <aw_awars.hxx>
#include <aw_root.hxx>
#include <ed4_extern.hxx>
#include <ed4_plugins.hxx>
#include <BI_basepos.hxx>
#include <arb_global_defs.h>


#define COLORLINK (ED4_G_SBACK_0 - RNA3D_GC_SBACK_0)  // to link to the colors defined in primary editor ed4_defs.hxx
#define SAICOLORS (ED4_G_CBACK_0 - RNA3D_GC_CBACK_0)

using namespace std;

static Struct3Dinfo   *start3D                 = NULp;
static Struct2Dinfo   *start2D                 = NULp;
static Struct2Dplus3D *start2D3D               = NULp;
static HelixNrInfo    *start                   = NULp;
static CurrSpecies    *startSp                 = NULp;
static bool            bOldSpeciesDataExists   = false;
static Insertions     *startIns                = NULp;
static bool            bOldInsertionDataExists = false;
static bool            bStartPosStored         = false;
static bool            bEndPosStored           = false;

inline bool is_Gap(char c) {
    return GAP::is_std_gap(c); // @@@ use AWAR defined gaps?
}

static char *find_data_file(const char *name) {
    char *fname = GB_lib_file(false, "rna3d/", name);
    if (!fname) throw string("file not found: ")+name;
    return fname;
}

static void throw_IO_error(const char *filename) __ATTR__NORETURN;
static void throw_IO_error(const char *filename) {
    string error = string("IO-Error: ")+strerror(errno)+" ('"+filename+"')";
    throw error;
}

GBDATA *Structure3D::gb_main = NULp;

Structure3D::Structure3D(ED4_plugin_host& host_)
    : strCen(new Vector3(0.0, 0.0, 0.0)),
      iInterval(25),
      iMapSAI(0),
      iMapSearch(0),
      iMapEnable(0),
      iStartPos(0),
      iEndPos(0),
      iEColiStartPos(0),
      iEColiEndPos(0),
      iTotalSubs(0),
      iTotalDels(0),
      iTotalIns(0),
      LSU_molID(3), // default molecule to load in case of 23S rRNA : 1C2W
      HelixBase(500),
      EColiRef(NULp),
      Host(host_),
      GRAPHICS(new OpenGLGraphics)
{}

Structure3D::~Structure3D() {
    delete GRAPHICS;
    delete strCen;
}


void Structure3D::StoreCoordinates(float x, float y, float z, char base, unsigned int pos) {
    Struct3Dinfo *data, *temp;
    data = new Struct3Dinfo;
    data->x    = x;
    data->y    = y;
    data->z    = z;
    data->base = base;
    data->pos  = pos;
    data->next = NULp;

    if (!start3D)
        start3D = data;
    else {
        temp = start3D;
        // We know this is not NULp - list not empty!
        while (temp->next) {
            temp = temp->next;  // Move to next link in chain
        }
        temp->next = data;
    }
}

// ------------------Selecting rRNA type--------------------------//

int Structure3D::FindTypeOfRNA() { // @@@ should better return an enum type
    int       rnaType    = 0;
    GB_ERROR  error      = GB_push_transaction(gb_main);
    GBDATA   *gbTemplate = GBT_find_SAI(gb_main, "ECOLI");

    if (!gbTemplate) {
        error = "SAI:ECOLI not found";
    }
    else {
        char *ali_name = GBT_get_default_alignment(gb_main);
        if (!ali_name) {
            error = GB_await_error();
        }
        else {
            GBDATA *gbAlignment       = GB_entry(gbTemplate, ali_name);
            GBDATA *gbTemplateSeqData = gbAlignment ? GB_entry(gbAlignment, "data") : NULp;

            if (!gbTemplateSeqData) {
                error = "Could not find ECOLI sequence data in the database!";
            }
            else {
                const char *pTemplateSeqData  = GB_read_char_pntr(gbTemplateSeqData);
                int iSeqLen = strlen(pTemplateSeqData);
                int iBaseCount = 0;
                for (int i = 0; i<iSeqLen; i++) {
                    if (!is_Gap(pTemplateSeqData[i])) {
                        iBaseCount++;
                    }
                }

                if (iBaseCount > 2000)      rnaType = LSU_23S;
                else if (iBaseCount > 300)  rnaType = SSU_16S;
                else                        rnaType = LSU_5S;
            }
            free(ali_name);
        }
    }

    error = GB_end_transaction(gb_main, error);
    aw_message_if(error);

    return rnaType;
}

// ----------Delete old molecule data-------------------------------//
// Struct2Dinfo, Struct2Dplus3D, Struct3Dinfo, HelixNrInfo, Insertions

void Structure3D::DeleteOldMoleculeData() {
    // Struct2Dinfo -> start2D
    {
        Struct2Dinfo *tmp, *data;
        for (data = start2D; data; data = tmp) {
            tmp = data->next;
            delete data;
        }
        start2D = NULp;
    }

    // Struct2Dplus3D ->start2D3D
    {
        Struct2Dplus3D *tmp, *data;
        for (data = start2D3D; data; data = tmp) {
            tmp = data->next;
            delete data;
        }
        start2D3D = NULp;
    }

    // Struct3Dinfo ->start3D
    {
        Struct3Dinfo *tmp, *data;
        for (data = start3D; data; data = tmp) {
            tmp = data->next;
            delete data;
        }
        start3D = NULp;
    }

    // HelixNrInfo -> start
    {
        HelixNrInfo *tmp, *data;
        for (data = start; data; data = tmp) {
            tmp = data->next;
            delete data;
        }
        start = NULp;
    }

    // Delete insertions data
    DeleteOldInsertionData();

    // Delete mapped species data
    DeleteOldSpeciesData ();
}

// =========== Reading 3D Coordinates from PDB file ====================//

static char globalComment[1000];

void Structure3D::ReadCoOrdinateFile() {
    static char *DataFile = NULp;
    int          rnaType  = FindTypeOfRNA();

    RNA3D->bDisplayComments = true; // displaying comments in main window

    switch (rnaType) {
    case LSU_23S:
        switch (LSU_molID) {
        case _1PNU:
            DataFile = find_data_file("Ecoli_1PNU_23S_rRNA.pdb");
            sprintf(globalComment, "The 3D molecule rendered from PDB entry : 1PNU at 8.7 Angstrom.");
            break;
        case _1VOR:
            DataFile = find_data_file("Ecoli_1VOR_23S_rRNA.pdb");
            sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1VOR] with 11.5 Angstrom resolution.");
            break;
        case _1C2W:
            DataFile = find_data_file("Ecoli_1C2W_23S_rRNA.pdb");
            sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1C2W] with 7.5 Angstrom resolution.");
            break;
        }
        break;
    case LSU_5S:
        DataFile = find_data_file("Ecoli_1C2X_5S_rRNA.pdb");
        sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1C2X] with 7.5 Angstrom resolution.");
        break;
    case SSU_16S:
        DataFile = find_data_file("Ecoli_1M5G_16S_rRNA.pdb");
        sprintf(globalComment, "The 3D molecule is rendered from PDB entry [1M5G] with 11.5 Angstrom resolution.");
        break;
    }

    ifstream readData;
    readData.open(DataFile, ios::in);
    if (!readData.is_open()) {
        throw_IO_error(DataFile);
    }

    int          cntr                 = 0;
    unsigned int last3Dpos            = 0;
    static bool  bEColiStartPosStored = false;

    while (!readData.eof()) {
        char buf[256];
        readData.getline(buf, 100);

        string line(buf);
        if ((line.find("ATOM") != string::npos) || (line.find("HETATM") != string::npos)) {
            string atom = line.substr(77, 2);
            if (atom.find("P") != string::npos) {
                char     base = line[19];
                unsigned pos  = atoi(line.substr(22, 4).c_str());

                // special filter for 23S rRNA structure (IVOR/IPNU)
                // IVOR/IPNU contains artifacts and are not mentioned in any of the
                // remarks of PDB file
                if (last3Dpos != pos && !(pos >= 3093)) {
                    float X = atof(line.substr(31, 8).c_str());
                    float Y = atof(line.substr(39, 8).c_str());
                    float Z = atof(line.substr(47, 8).c_str());

                    StoreCoordinates(X, Y, Z, base, pos);
                    last3Dpos  = pos;
                    strCen->x += X; strCen->y += Y; strCen->z += Z;
                    cntr++;
                }
                if (!bEColiStartPosStored) {
                    iEColiStartPos = pos;
                    bEColiStartPosStored = true;
                }
                iEColiEndPos = pos;
            }
        }
    }

    cout<<"--------------------------------------------------"<<endl
        <<globalComment<<endl
        <<"Structure contains "<<iEColiEndPos-iEColiStartPos<<"( "<<iEColiStartPos<<" - "
        <<iEColiEndPos<<" ) positions."<<endl
        <<"---------------------------------------------------"<<endl;

    strCen->x = strCen->x/cntr;
    strCen->y = strCen->y/cntr;
    strCen->z = strCen->z/cntr;

    readData.close();
    free(DataFile);
}


void Structure3D::Store2Dinfo(char *info, int pos, int helixNr) {
    Struct2Dinfo *data = new Struct2Dinfo;

    data->base    = info[0];
    data->mask    = info[1];
    data->code    = info[2];
    data->pos     = pos;
    data->helixNr = helixNr;

    data->next = NULp;

    if (!start2D) {
        start2D = data;
    }
    else {
        Struct2Dinfo *temp = start2D;
        // We know this is not NULp - list not empty!
        while (temp->next) {
            temp = temp->next;  // Move to next link in chain
        }
        temp->next = data;
    }
}

// =========== Reading Secondary Structure Data from Ecoli Secondary Structure Mask file ====================//

void Structure3D::GetSecondaryStructureInfo() {
    static char *DataFile = NULp;
    int          rnaType  = FindTypeOfRNA();

    switch (rnaType) {
        case LSU_23S:
            DataFile = find_data_file("SecondaryStructureModel_23SrRNA.data");
            break;
        case LSU_5S:
            DataFile = find_data_file("SecondaryStructureModel_5SrRNA.data");
            break;
        case SSU_16S:
            DataFile = find_data_file("SecondaryStructureModel_16SrRNA.data");
            break;
    }

    char  buf[256];

    int  pos         = 0;
    int  helixNr     = 0;
    int  lastHelixNr = 0;
    char info[4];
    info[3]          = '\0';
    bool insideHelix = false;
    bool skip        = false;

    ifstream readData;
    readData.open(DataFile, ios::in);
    if (!readData.is_open()) {
        throw_IO_error(DataFile);
    }

    while (!readData.eof()) {
        readData.getline(buf, 100);
        char *tmp;
        tmp = strtok(buf, " ");
        for (int i = 0; tmp; tmp = strtok(NULp, " "), i++) {
            switch (i) {
                case 0: pos = atoi(tmp);      break;
                case 1: info[0] = tmp[0];     break;
                case 2: info[1] = tmp[0];     break;
                case 3: info[2] = tmp[0];     break;
                case 4: helixNr = atoi(tmp); break;
            }
        }

        bool is_SE = (info[2] == 'S') || (info[2] == 'E'); // 'S' = helix start 'E' = helix end
        if (is_SE) {
            if (helixNr>0) lastHelixNr = helixNr;

            if (!insideHelix) insideHelix = true;
            else {
                Store2Dinfo(info, pos, lastHelixNr);
                skip        = true;
                insideHelix = false;
            }
        }
        if (insideHelix) Store2Dinfo(info, pos, lastHelixNr);
        else {
            if (skip) skip = false;
            else Store2Dinfo(info, pos, 0);
        }
    }
    readData.close();
    free(DataFile);
}

void Structure3D::Store2D3Dinfo(Struct2Dinfo *s2D, Struct3Dinfo *s3D) {
    Struct2Dplus3D *data, *temp;
    data = new Struct2Dplus3D;
    data->base    = s2D->base;
    data->mask    = s2D->mask;
    data->code    = s2D->code;
    data->pos     = s2D->pos;
    data->helixNr = s2D->helixNr;
    data->x       = s3D->x;
    data->y       = s3D->y;
    data->z       = s3D->z;
    data->next    = NULp;

    if (!start2D3D)
        start2D3D = data;
    else {
        temp = start2D3D;
        while (temp->next) {
            temp = temp->next;
        }
        temp->next = data;
    }
}

// =========== Combining Secondary Structure Data with 3D Coordinates =======================//

void Structure3D::Combine2Dand3DstructureInfo() {
    Struct3Dinfo *temp3D;
    Struct2Dinfo *temp2D;
    int cntr = 0;

    cout<<"Missing Base Positions : "<<endl;

    temp3D = start3D;
    temp2D = start2D;
    while (temp3D && temp2D) {
        if (temp2D->pos == temp3D->pos) {
            Store2D3Dinfo(temp2D, temp3D);
        }
        else {
            while (temp2D->pos != temp3D->pos) {
                cout<<temp2D->pos<<", "; // missing base positions
                cntr++;
                temp2D = temp2D->next;
            }
            Store2D3Dinfo(temp2D, temp3D);
        }

        temp3D = temp3D->next;
        temp2D = temp2D->next;
    }
    cout<<endl<<"Total No. of bases missing = "<<cntr<<endl;

    // printing comments in the main window
    {
        RNA3D->bDisplayComments = true;
        char buf[256];
        sprintf(buf, "Total No. of bases missing = %d. See the console messages for the actual missing base positions.", cntr);
        strcat(globalComment, buf);
    }
}

void Structure3D::PointsToQuads(float x, float y, float z) {

    if (RNA3D->bPointSpritesSupported) {
        glVertex3f(x, y, z);
    }
    else {
        glBegin(GL_QUADS);
        // Front Face
        glTexCoord2f(0, 0); glVertex3f(x - 1, y + 1, z + 1);
        glTexCoord2f(1, 0); glVertex3f(x + 1, y + 1, z + 1);
        glTexCoord2f(1, 1); glVertex3f(x + 1, y - 1, z + 1);
        glTexCoord2f(0, 1); glVertex3f(x - 1, y - 1, z + 1);

        // Back Face
        glTexCoord2f(0, 0); glVertex3f(x + 1, y + 1, z - 1);
        glTexCoord2f(1, 0); glVertex3f(x - 1, y + 1, z - 1);
        glTexCoord2f(1, 1); glVertex3f(x - 1, y - 1, z - 1);
        glTexCoord2f(0, 1); glVertex3f(x + 1, y - 1, z - 1);

        // Top Face
        glTexCoord2f(0, 0); glVertex3f(x + 1, y + 1, z + 1);
        glTexCoord2f(1, 0); glVertex3f(x - 1, y + 1, z + 1);
        glTexCoord2f(1, 1); glVertex3f(x - 1, y + 1, z - 1);
        glTexCoord2f(0, 1); glVertex3f(x + 1, y + 1, z - 1);

        // Bottom Face
        glTexCoord2f(0, 0); glVertex3f(x + 1, y - 1, z - 1);
        glTexCoord2f(1, 0); glVertex3f(x - 1, y - 1, z - 1);
        glTexCoord2f(1, 1); glVertex3f(x - 1, y - 1, z + 1);
        glTexCoord2f(0, 1); glVertex3f(x + 1, y - 1, z + 1);

        // Left Face
        glTexCoord2f(0, 0); glVertex3f(x + 1, y + 1, z + 1);
        glTexCoord2f(1, 0); glVertex3f(x + 1, y + 1, z - 1);
        glTexCoord2f(1, 1); glVertex3f(x + 1, y - 1, z - 1);
        glTexCoord2f(0, 1); glVertex3f(x + 1, y - 1, z + 1);

        // Right Face
        glTexCoord2f(0, 0); glVertex3f(x - 1, y + 1, z - 1);
        glTexCoord2f(1, 0); glVertex3f(x - 1, y + 1, z + 1);
        glTexCoord2f(1, 1); glVertex3f(x - 1, y - 1, z + 1);
        glTexCoord2f(0, 1); glVertex3f(x - 1, y - 1, z - 1);

        glEnd();
    }
}

void Structure3D::PositionsToCoordinatesDispList(int listID, int *pos, int len) {
    Struct2Dplus3D *t;
    int tmpPos = 0;

    glNewList(listID, GL_COMPILE);
    {
        if (RNA3D->bPointSpritesSupported) {
            glBegin(GL_POINTS);
        }
        for (int i = 0; i < len; i++) {
            tmpPos = pos[i];
            t = start2D3D;
            while (t) {
                if (t->pos == tmpPos) {
                    PointsToQuads(t->x, t->y, t->z);
                    break;
                }
                t = t->next;
            }
        }
        if (RNA3D->bPointSpritesSupported) {
            glEnd();
        }
    }
    glEndList();
}

void Structure3D::GenerateSecStructureNonHelixRegions() {
    Struct2Dplus3D *t;
    const int MAX_BASE = 1000;
    int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE], baseU[MAX_BASE];
    int a, g, c, u; a=g=c=u=0;

    {
        t = start2D3D;
        while (t) {
            if (t->helixNr == 0) {
                switch (t->base) {
                    case 'A': baseA[a++] = t->pos; break;
                    case 'G': baseG[g++] = t->pos; break;
                    case 'C': baseC[c++] = t->pos; break;
                    case 'U': baseU[u++] = t->pos; break;
                }
            }
            t = t->next;
        }
    }

    PositionsToCoordinatesDispList(NON_HELIX_A, baseA, a);
    PositionsToCoordinatesDispList(NON_HELIX_G, baseG, g);
    PositionsToCoordinatesDispList(NON_HELIX_C, baseC, c);
    PositionsToCoordinatesDispList(NON_HELIX_U, baseU, u);
}

void Structure3D::GenerateSecStructureHelixRegions() {
    Struct2Dplus3D *t;
    const int MAX_BASE = 1000;
    int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE], baseU[MAX_BASE];
    int a, g, c, u; a=g=c=u=0;

    {
        t = start2D3D;
        while (t) {
            if (t->helixNr > 0) {
                if ((t->mask == '[') || (t->mask == ']') || (t->mask == '<') || (t->mask == '>')) {
                    switch (t->base) {
                        case 'A': baseA[a++] = t->pos; break;
                        case 'G': baseG[g++] = t->pos; break;
                        case 'C': baseC[c++] = t->pos; break;
                        case 'U': baseU[u++] = t->pos; break;
                    }
                }
            }
            t = t->next;
        }
    }

    PositionsToCoordinatesDispList(HELIX_A, baseA, a);
    PositionsToCoordinatesDispList(HELIX_G, baseG, g);
    PositionsToCoordinatesDispList(HELIX_C, baseC, c);
    PositionsToCoordinatesDispList(HELIX_U, baseU, u);
}

void Structure3D::GenerateSecStructureUnpairedHelixRegions() {
    Struct2Dplus3D *t;
    const int MAX_BASE = 500;
    int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE], baseU[MAX_BASE];
    int a, g, c, u; a=g=c=u=0;

    {
        t = start2D3D;
        while (t) {
            if (t->helixNr > 0) {
                if (t->mask == '.') {
                    switch (t->base) {
                        case 'A': baseA[a++] = t->pos; break;
                        case 'G': baseG[g++] = t->pos; break;
                        case 'C': baseC[c++] = t->pos; break;
                        case 'U': baseU[u++] = t->pos; break;
                    }
                }
            }
            t = t->next;
        }
    }

    PositionsToCoordinatesDispList(UNPAIRED_HELIX_A, baseA, a);
    PositionsToCoordinatesDispList(UNPAIRED_HELIX_G, baseG, g);
    PositionsToCoordinatesDispList(UNPAIRED_HELIX_C, baseC, c);
    PositionsToCoordinatesDispList(UNPAIRED_HELIX_U, baseU, u);
}

// ==============================================================================
// Tertiary Interactions of 16S ribosomal RNA model of E.coli.
// Reference : http://www.rna.icmb.utexas.edu/
// Year of Last Update : 2001.
// Pseudoknots and Triple Base pairs are extracted and displayed in
// the 3D model.
// ==============================================================================

void Structure3D::GenerateTertiaryInteractionsDispLists() {
    Struct2Dplus3D *t;
    static char    *DataFile = NULp;
    int             rnaType  = FindTypeOfRNA();

    switch (rnaType) {
        case LSU_23S:
            DataFile = find_data_file("TertiaryInteractions_23SrRNA.data");
            break;
        case LSU_5S:
            cout<<"There are no tertiary interactions observed in 5S rRNA model!"<<endl;
            return;
        case SSU_16S:
            DataFile = find_data_file("TertiaryInteractions_16SrRNA.data");
            break;
    }

    cout<<"Tertiary Interactions are fetched from comparative RNA website [http://www.rna.icmb.utexas.edu]."<<endl
        <<"The same are located in the file \""<<DataFile<<"\"."<<endl;

    char  buf[256];

    ifstream readData;
    readData.open(DataFile, ios::in);
    if (!readData.is_open()) {
        throw_IO_error(DataFile);
    }

    int K[100];
    int R[100];
    int k, r; k = r = 0;

    while (!readData.eof()) {
        readData.getline(buf, 100);
        char *tmp;
        tmp = strtok(buf, " ");
        if (tmp) {
            if (strcmp(tmp, "KNOT") == 0) {
                tmp = strtok(NULp, ":");
                while (tmp) {
                    K[k++] = atoi(tmp);
                    tmp = strtok(NULp, ":");
                }
            }
            else if (strcmp(tmp, "TRIPLE") == 0) {
                tmp = strtok(NULp, ":");
                while (tmp) {
                    R[r++] = atoi(tmp);
                    tmp = strtok(NULp, ":");
                }
            }
        }
    }
    readData.close();

    glNewList(ECOLI_TERTIARY_INTRACTION_PSEUDOKNOTS, GL_COMPILE);
    {
        for (int i = 0; i < k;) {
            glBegin(GL_LINES);
            for (int j = 0; j < 2; j++) {
                t = start2D3D;
                while (t) {
                    if (t->pos == K[i]) {
                        glVertex3f(t->x, t->y, t->z);
                        i++;
                        break;
                    }
                    t = t->next;
                }
            }
            glEnd();
        }
    }
    glEndList();

    glNewList(ECOLI_TERTIARY_INTRACTION_TRIPLE_BASES, GL_COMPILE);
    {
        for (int i = 0; i < r;) {
            glBegin(GL_LINE_STRIP);
            for (int j = 0; j < 3; j++) {
                t = start2D3D;
                while (t) {
                    if (t->pos == R[i]) {
                        glVertex3f(t->x, t->y, t->z);
                        i++;
                        break;
                    }
                    t = t->next;
                }
            }
            glEnd();
        }
    }
    glEndList();
    free(DataFile);
}

// ==============================================================================

void Structure3D::StoreHelixNrInfo(float x, float y, float z, int helixNr) {
    HelixNrInfo *data, *temp;
    data = new HelixNrInfo;
    data->helixNr = helixNr;
    data->x       = x;
    data->y       = y;
    data->z       = z;
    data->next    = NULp;

    if (!start)
        start = data;
    else {
        temp = start;
        while (temp->next) {
            temp = temp->next;
        }
        temp->next = data;
    }
}

void Structure3D::GenerateHelixDispLists(int HELIX_NR_ID, int HELIX_NR) {
    Struct2Dinfo *temp2D;
    Struct2Dplus3D *temp2D3D;

    const int MAX = 500;

    int thisStrandPos[MAX], otherStrandPos[MAX];
    int i, j; i = j = 0;
    {
        temp2D = start2D;
        while (temp2D) {
            if (temp2D->helixNr == HELIX_NR) {
                if ((temp2D->mask == '[') || (temp2D->mask == '<'))
                    thisStrandPos[i++]  = temp2D->pos;
                if ((temp2D->mask == ']') || (temp2D->mask == '>'))
                    otherStrandPos[j++] = temp2D->pos;
            }
            temp2D = temp2D->next;
        }
    }

    int tempPos = 0;
    float x1, x2, y1, y2, z1, z2; x1=x2=y1=y2=z1=z2=0.0;

    bool bThisStrand, bOtherStrand;
    bThisStrand = bOtherStrand = false;

    bool bMissingBasePair = false;

    glNewList(HELIX_NR_ID, GL_COMPILE);
    {
        for (int k = 0, l = j-1; k < i && l >= 0; k++, l--) {
            tempPos = thisStrandPos[k];
            {
                temp2D3D = start2D3D;
                while (temp2D3D) {
                    if (temp2D3D->pos == tempPos) {
                        bThisStrand = true;
                        x1=temp2D3D->x; y1=temp2D3D->y; z1=temp2D3D->z;
                        break;
                    }
                    temp2D3D = temp2D3D->next;
                }
            }
            tempPos = otherStrandPos[l];
            {
                temp2D3D = start2D3D;
                while (temp2D3D) {
                    if (temp2D3D->pos == tempPos) {
                        bOtherStrand = true;
                        x2=temp2D3D->x; y2=temp2D3D->y; z2=temp2D3D->z;
                        break;
                    }
                    temp2D3D = temp2D3D->next;
                }
            }
            // if bases present in both the strands then draw a bond
            // and store the helix number information
            if (bThisStrand && bOtherStrand) {
                glVertex3f(x1, y1, z1);
                glVertex3f(x2, y2, z2);

                x1 = (x1+x2)/2; y1 = (y1+y2)/2; z1 = (z1+z2)/2;
                StoreHelixNrInfo(x1, y1, z1, HELIX_NR);

                bThisStrand = bOtherStrand = false;
            }
            else {
                bMissingBasePair = true;
                cout<<thisStrandPos[k]<<"-"<<tempPos<<"("<<HELIX_NR_ID<<"), ";
            }
        }
        if (bMissingBasePair) cout<<endl;
    }
    glEndList();
}

void Structure3D::GenerateHelixNrDispList(int startHx, int endHx) {
    HelixNrInfo *t;

    glNewList(HELIX_NUMBERS, GL_COMPILE);
    {
        char POS[50];
        for (int i = startHx; i <= endHx; i++) {
            t = start;
            while (t) {
                if (t->helixNr == i) {
                    sprintf(POS, "%d", t->helixNr);
                    GRAPHICS->PrintString(t->x, t->y, t->z, POS, GLUT_BITMAP_8_BY_13);
                }
                t = t->next;
            }
        }
    }
    glEndList();

    glNewList(HELIX_NUMBERS_POINTS, GL_COMPILE);
    {
        if (RNA3D->bPointSpritesSupported) {
            glBegin(GL_POINTS);
        }
        for (int i = startHx; i <= endHx; i++) {
            t = start;
            while (t) {
                if (t->helixNr == i) {
                    PointsToQuads(t->x, t->y, t->z);
                }
                t = t->next;
            }
        }
        if (RNA3D->bPointSpritesSupported) {
            glEnd();
        }
    }
    glEndList();
}

void Structure3D::GenerateDisplayLists() {

    GenerateMoleculeSkeleton();
    ComputeBasePositions();

    int rnaType = FindTypeOfRNA();
    switch (rnaType) {
    case SSU_16S:
        if (glIsList(HelixBase) != GL_TRUE) {
            for (int i = 1; i <= 50; i++) {
                GenerateHelixDispLists(HelixBase+i, i);
            }
        }
        break;
    case LSU_23S:
        cout<<"=========================================================="<<endl
            <<"Missing base pairs (bracket number indicates helix number) "<<endl;
        if (glIsList(HelixBase) != GL_TRUE) {
            for (int i = 1; i <= 101; i++) {
                GenerateHelixDispLists(HelixBase+i, i);
            }
        }
        cout<<"=========================================================="<<endl;
        break;
    case LSU_5S:
        if (glIsList(HelixBase) != GL_TRUE) {
            for (int i = 1; i <= 5; i++) {
                GenerateHelixDispLists(HelixBase+i, i);
            }
        }
        break;
    }

    GenerateSecStructureHelixRegions();
    GenerateSecStructureNonHelixRegions();
    GenerateSecStructureUnpairedHelixRegions();

    GenerateTertiaryInteractionsDispLists();
}

void Structure3D::GenerateMoleculeSkeleton() {
    Struct2Dplus3D *t;

    glNewList(STRUCTURE_BACKBONE, GL_COMPILE);
    {
        glBegin(GL_LINE_STRIP);
        t = start2D3D;
        while (t) {
            glVertex3f(t->x, t->y, t->z);
            t = t->next;
        }
        glEnd();
    }
    glEndList();

    glNewList(STRUCTURE_BACKBONE_CLR, GL_COMPILE);
    {
        glBegin(GL_LINE_STRIP);
        t = start2D3D;
        while (t) {
            if (t->helixNr > 0) {
                if ((t->mask == '[') || (t->mask == ']') || (t->mask == '<') || (t->mask == '>')) {
                    GRAPHICS->SetColor(RNA3D_GC_BASES_HELIX);
                    glVertex3f(t->x, t->y, t->z);
                }
                if (t->mask == '.') {
                    GRAPHICS->SetColor(RNA3D_GC_BASES_UNPAIRED_HELIX);
                    glVertex3f(t->x, t->y, t->z);
                }
            }
            if (t->helixNr == 0) {
                GRAPHICS->SetColor(RNA3D_GC_BASES_NON_HELIX);
                glVertex3f(t->x, t->y, t->z);
            }
            t = t->next;
        }
        glEnd();
    }
    glEndList();
}

void Structure3D::GenerateCursorPositionDispList(long pos) {
    Struct3Dinfo *temp;

    glNewList(ECOLI_CURSOR_POSITION, GL_COMPILE);
    {
        glBegin(GL_POINTS);
        temp = start3D;
        while (temp) {
            if (temp->pos == pos) {
#ifdef DEBUG
                cout<<"Cursor Position : "<<pos<<endl;
#endif
                glVertex3f(temp->x, temp->y, temp->z);
                break;
            }
            temp = temp->next;
        }
        glEnd();
    }
    glEndList();
}

void Structure3D::ComputeBasePositions() {
    Struct3Dinfo *temp;

    char POS[50];
    float spacer = 1.5;
    int posSkip = iInterval;
    if (posSkip <= 0) posSkip = 25; // default interval value

    glNewList(STRUCTURE_POS, GL_COMPILE);
    {
        temp = start3D;
        while (temp) {
            if (temp->pos%posSkip == 0) {
                sprintf(POS, "%d", temp->pos);
                GRAPHICS->PrintString(temp->x-spacer, temp->y, temp->z-spacer, POS, GLUT_BITMAP_HELVETICA_10);
            }
            temp = temp->next;
        }
    }
    glEndList();

    glNewList(STRUCTURE_POS_ANCHOR, GL_COMPILE);
    {
        glLineWidth(0.5);
        glBegin(GL_LINES);
        temp = start3D;
        while (temp) {
            if (temp->pos%posSkip == 0) {
                glVertex3f(temp->x, temp->y, temp->z);
                glVertex3f(temp->x-spacer, temp->y, temp->z-spacer);
            }
            temp = temp->next;
        }
        glEnd();
    }
    glEndList();
}

// [
// removed function Structure3D::PrepareSecondaryStructureData()
// - did read data from files in Yadhus account
// - was unused
// (stored in VC.. :)
// ]

void Structure3D::StoreCurrSpeciesDifference(char base, int pos) {
    Struct2Dplus3D *st;
    st = start2D3D;
    while (st) {
        if (st->pos == pos) {
            CurrSpecies *data, *temp;
            data = new CurrSpecies;
            data->base = base;
            data->pos  = pos;
            data->x = st->x;
            data->y = st->y;
            data->z = st->z;
            data->next = NULp;

            if (!startSp) {
                startSp = data;
                bOldSpeciesDataExists = true;
            }
            else {
                temp = startSp;
                while (temp->next) {
                    temp = temp->next;
                }
                temp->next = data;
            }
            break;
        }
        st = st->next;
    }
}

void Structure3D::DeleteOldSpeciesData() {
    CurrSpecies *tmp, *data;

    for (data = startSp; data; data = tmp) {
        tmp = data->next;
        delete data;
    }
    startSp = NULp;

    bOldSpeciesDataExists = false;
}

void Structure3D::GenerateBaseDifferencePositionDisplayList() {
    CurrSpecies *t;
    Struct3Dinfo *temp;

    char POS[50];
    float spacer = 1.5;

    glNewList(MAP_SPECIES_BASE_DIFFERENCE_POS, GL_COMPILE);
    {
        for (t = startSp; t; t = t->next) {
            for (temp = start3D; temp; temp = temp->next) {
                if (temp->pos == t->pos) {
                    sprintf(POS, "%d", temp->pos);
                    GRAPHICS->PrintString(temp->x-spacer, temp->y, temp->z-spacer, POS, GLUT_BITMAP_8_BY_13);
                }
            }
        }
    }
    glEndList();

    glNewList(MAP_SPECIES_BASE_DIFFERENCE_POS_ANCHOR, GL_COMPILE);
    {
        glLineWidth(1.0);
        glBegin(GL_LINES);

        for (t = startSp; t; t = t->next) {
            for (temp = start3D; temp; temp = temp->next) {
                if (temp->pos == t->pos) {
                    glVertex3f(temp->x, temp->y, temp->z);
                    glVertex3f(temp->x-spacer, temp->y, temp->z-spacer);
                }
            }
        }
        glEnd();
    }
    glEndList();
}

void Structure3D::BuildDisplayList(int listID, int *pos, int len) {
    CurrSpecies *t;
    int tmpPos = 0;

    glNewList(listID, GL_COMPILE);
    {
        if (RNA3D->bPointSpritesSupported) {
            glBegin(GL_POINTS);
        }
        for (int i = 0; i < len; i++) {
            tmpPos = pos[i];
            t = startSp;
            while (t) {
                if (t->pos == tmpPos) {
                    PointsToQuads(t->x, t->y, t->z);
                    break;
                }
                t = t->next;
            }
        }
        if (RNA3D->bPointSpritesSupported) {
            glEnd();
        }
    }
    glEndList();
}

void Structure3D::GenerateBaseDifferenceDisplayList() {
    CurrSpecies *t;

    glNewList(MAP_SPECIES_BASE_DIFFERENCE, GL_COMPILE);
    {
        if (RNA3D->bPointSpritesSupported) {
            glBegin(GL_POINTS);
        }
        t = startSp;
        while (t) {
            PointsToQuads(t->x, t->y, t->z);
            t = t->next;
        }
        if (RNA3D->bPointSpritesSupported) {
            glEnd();
        }
    }
    glEndList();

    const int MAX_BASE = 400;
    int baseA[MAX_BASE], baseG[MAX_BASE], baseC[MAX_BASE],
        baseU[MAX_BASE], deletion[MAX_BASE], miss[MAX_BASE];
    int a, g, c, u, d, m; a=g=c=u=d=m=0;

    {
        t = startSp;
        while (t) {
            switch (t->base) {
                case 'A': baseA[a++]     = t->pos; break;
                case 'G': baseG[g++]     = t->pos; break;
                case 'C': baseC[c++]     = t->pos; break;
                case 'U': baseU[u++]     = t->pos; break;
                case '-': deletion[d++] = t->pos; break;
                case '.': miss[m++] = t->pos; break;
            }
            t = t->next;
        }
        BuildDisplayList(MAP_SPECIES_BASE_A, baseA, a);
        BuildDisplayList(MAP_SPECIES_BASE_U, baseU, u);
        BuildDisplayList(MAP_SPECIES_BASE_G, baseG, g);
        BuildDisplayList(MAP_SPECIES_BASE_C, baseC, c);
        BuildDisplayList(MAP_SPECIES_DELETION, deletion, d);
        BuildDisplayList(MAP_SPECIES_MISSING, miss, m);
        GenerateBaseDifferencePositionDisplayList();

        iTotalSubs = a+g+c+u;  // Summing up the substitutions/mutations
        iTotalDels = d;        // Storing total number of deletions
#ifdef DEBUG
        cout<<"Substitutions = "<<iTotalSubs<<endl;
        cout<<"Deletions     = "<<iTotalDels<<endl;
#endif
    }
}

void Structure3D::StoreInsertions(char base, int pos) {
    Insertions *data, *temp;
    data = new Insertions;
    data->base = base;
    data->pos  = pos;
    data->next = NULp;

    if (!startIns) {
        startIns = data;
        bOldInsertionDataExists = true;
    }
    else {
        temp = startIns;
        while (temp->next) {
            temp = temp->next;
        }
        temp->next = data;
    }
}

void Structure3D::DeleteOldInsertionData() {
    Insertions *tmp, *data;

    for (data = startIns; data; data = tmp) {
        tmp = data->next;
        delete data;
    }
    startIns = NULp;

    bOldInsertionDataExists = false;
}

void Structure3D::GenerateInsertionDisplayList() {
    Insertions   *ins;
    Struct3Dinfo *str;
    char inserts[500];
    int i, cntr;
    float spacer = 2.0;
    iTotalIns = 0;

    glNewList(MAP_SPECIES_INSERTION_BASES, GL_COMPILE);
    {
        for (str = start3D; str; str = str->next) {
            i = cntr = 0;
            for (ins = startIns; ins; ins = ins->next) {
                if (str->pos == ins->pos) {
                    inserts[i++] = ins->base;
                    cntr++;
                }
            }
            if (cntr>0) {
                inserts[i] = '\0';
                char buffer[strlen(inserts) + 10];
                sprintf(buffer, "%d:%s", cntr, inserts);
                GRAPHICS->PrintString(str->x, str->y+spacer, str->z,
                                      buffer, GLUT_BITMAP_8_BY_13);

                iTotalIns += cntr; // Summing up the insertions
            }
        }
    }
    glEndList();

#ifdef DEBUG
    cout<<"Insertions = "<<iTotalIns<<endl;
#endif

    glNewList(MAP_SPECIES_INSERTION_BASES_ANCHOR, GL_COMPILE);
    {
        glLineWidth(1.0);
        glBegin(GL_LINES);

        for (str = start3D; str; str = str->next) {
            for (ins = startIns; ins; ins = ins->next) {
                if (str->pos == ins->pos) {
                    glVertex3f(str->x, str->y, str->z);
                    glVertex3f(str->x, str->y+spacer, str->z);
                }
            }
        }
        glEnd();
    }
    glEndList();

    glNewList(MAP_SPECIES_INSERTION_POINTS, GL_COMPILE);
    {
        if (RNA3D->bPointSpritesSupported) {
            glBegin(GL_POINTS);
        }
        for (str = start3D; str; str = str->next) {
            for (ins = startIns; ins; ins = ins->next) {
                if (str->pos == ins->pos) {
                    PointsToQuads(str->x, str->y, str->z);
                    break;
                }
            }
        }
        if (RNA3D->bPointSpritesSupported) {
            glEnd();
        }
    }
    glEndList();
}

void Structure3D::MapCurrentSpeciesToEcoliTemplate(AW_root *awr) {
    GB_ERROR error = GB_push_transaction(gb_main);

    if (!error) {
        GBDATA *gbTemplate = GBT_find_SAI(gb_main, "ECOLI");

        if (!gbTemplate) {
            error = "SAI:ECOLI not found";
        }
        else {
            char *pSpeciesName = awr->awar(AWAR_SPECIES_NAME)->read_string();
            if (pSpeciesName) {
                Host.announce_current_species(pSpeciesName);
                GBDATA *gbSpecies = GBT_find_species(gb_main, pSpeciesName);
                if (gbSpecies) {
                    char *ali_name = GBT_get_default_alignment(gb_main);
                    if (!ali_name) {
                        error = GB_await_error();
                    }
                    else {
                        GBDATA *gbAlignment       = GB_entry(gbTemplate, ali_name);
                        GBDATA *gbTemplateSeqData = gbAlignment ? GB_entry(gbAlignment, "data") : NULp;

                        if (!gbTemplateSeqData) {
                            error = GBS_global_string("Mapping impossible, since SAI:ECOLI has no data in alignment '%s'", ali_name);
                        }
                        else {
                            const char *pTemplateSeqData  = GB_read_char_pntr(gbTemplateSeqData);

                            if (!RNA3D->bEColiRefInitialized) {
                                EColiRef = new BI_ecoli_ref;
                                EColiRef->init(gb_main);
                                RNA3D->bEColiRefInitialized = true;
                            }

                            char buf[100];
                            char *pSpFullName = GB_read_string(GB_entry(gbSpecies, "full_name"));
                            sprintf(buf, "%s : %s", pSpeciesName, pSpFullName);
                            awr->awar(AWAR_3D_SELECTED_SPECIES)->write_string(buf);

                            GBDATA *gbSeqData    = GBT_find_sequence(gbSpecies, ali_name);
                            const char *pSeqData = GB_read_char_pntr(gbSeqData);

                            if (pSeqData && pTemplateSeqData) {
                                int iSeqLen = strlen(pTemplateSeqData);

                                if (bOldSpeciesDataExists) {
                                    DeleteOldSpeciesData();
                                }

                                for (int i = 0, iSeqCount = 0; i<iSeqLen; i++) {
                                    if (!is_Gap(pTemplateSeqData[i])) {
                                        if (!bStartPosStored) {
                                            iStartPos = i;
                                            bStartPosStored = true;
                                        }
                                        if (pTemplateSeqData[i] != pSeqData[i]) {
                                            StoreCurrSpeciesDifference(pSeqData[i], iSeqCount);
                                        }
                                        iSeqCount++;
                                    }
                                }

                                for (int i = iSeqLen; i>0; i--) {
                                    if (!is_Gap(pTemplateSeqData[i])) {
                                        if (!bEndPosStored) {
                                            iEndPos = i;
                                            bEndPosStored = true;
                                            break;
                                        }
                                    }
                                }

                                if (bOldInsertionDataExists) {
                                    DeleteOldInsertionData();
                                }

                                for (int i = iStartPos, iSeqCount = 0; i < iEndPos; i++) {
                                    if (!is_Gap(pTemplateSeqData[i])) {
                                        // Store EColi base positions : Insertion point!
                                        iSeqCount++;
                                    }

                                    if ((pTemplateSeqData[i] == '-') && !is_Gap(pSeqData[i])) {
                                        StoreInsertions(pSeqData[i], iSeqCount);
                                    }
                                }
                            }
                            free(pSpFullName);
                        }
                        free(ali_name);
                    }
                }
                GenerateBaseDifferenceDisplayList();
                GenerateInsertionDisplayList();
            }
            free(pSpeciesName);
        }
    }

    error = GB_end_transaction(gb_main, error);
    aw_message_if(error);
}

static bool ValidSearchColor(int iColor, int mode) {
    bool isValid = false;

    switch (mode) {
        case SAI:    isValid = (iColor >= RNA3D_GC_CBACK_0) && (iColor < RNA3D_GC_MAX); break;
        case SEARCH: isValid = (iColor >= RNA3D_GC_SBACK_0) && (iColor < RNA3D_GC_MAX); break;
    }
    return isValid;
}

void Structure3D::MapSearchStringsToEcoliTemplate(AW_root * /* awr */) {
    const char *pSearchColResults = NULp;

    if (iMapSearch) pSearchColResults = Host.get_search_background(iStartPos, iEndPos);

    if (pSearchColResults) {
        int iColor = 0;

        glNewList(MAP_SEARCH_STRINGS_TO_STRUCTURE, GL_COMPILE);
        {
            if (RNA3D->bPointSpritesSupported) glBegin(GL_POINTS);
            for (int i = iStartPos; i < iEndPos; i++) {
                if (RNA3D->bEColiRefInitialized) {
                    long absPos   = (long) i;
                    long EColiPos = EColiRef->abs_2_rel(absPos);

                    for (Struct3Dinfo *t = start3D; t; t = t->next) {
                        if ((t->pos == EColiPos) && (pSearchColResults[i] >= 0)) {
                            iColor = pSearchColResults[i] - COLORLINK;

                            if (ValidSearchColor(iColor, SEARCH)) {
                                RNA3D->cGraphics->SetColor(iColor);
                                PointsToQuads(t->x, t->y, t->z);
                            }
                            break;
                        }
                    }
                }
            }
            if (RNA3D->bPointSpritesSupported) glEnd();
        }
        glEndList();

        glNewList(MAP_SEARCH_STRINGS_BACKBONE, GL_COMPILE);
        {
            int iLastClr = 0; int iLastPos = 0; Vector3 vLastPt;
            glBegin(GL_LINES);
            for (int i = iStartPos; i < iEndPos; i++) {
                if (RNA3D->bEColiRefInitialized) {
                    long absPos   = (long) i;
                    long EColiPos = EColiRef->abs_2_rel(absPos);

                    for (Struct3Dinfo *t = start3D; t; t = t->next) {
                        if ((t->pos == EColiPos) && (pSearchColResults[i] >= 0)) {
                            iColor = pSearchColResults[i] - COLORLINK;

                            if (ValidSearchColor(iColor, SEARCH)) {
                                if ((iLastClr == iColor) && (iLastPos == EColiPos-1)) {
                                    RNA3D->cGraphics->SetColor(iColor);
                                    glVertex3f(vLastPt.x, vLastPt.y, vLastPt.z);
                                    glVertex3f(t->x, t->y, t->z);
                                }
                                iLastPos = EColiPos;
                                iLastClr = iColor;
                                vLastPt.x = t->x; vLastPt.y = t->y; vLastPt.z = t->z;
                            }
                            break;
                        }
                    }
                }
            }
            glEnd();
        }
        glEndList();

        RNA3D->bMapSearchStringsDispListCreated = true;
    }
    else cout<<"BuildColorString did not get the colors : SAI cannot be Visualized!"<<endl;
}

void Structure3D::MapSaiToEcoliTemplate() {
    const char *pSearchColResults = NULp;

    if (iMapSAI && Host.SAIs_visualized()) {
        pSearchColResults = Host.get_SAI_background(iStartPos, iEndPos); // returns 0 if sth went wrong
    }

    if (pSearchColResults) {
        int iColor = 0;

        glNewList(MAP_SAI_TO_STRUCTURE, GL_COMPILE);
        {
            if (RNA3D->bPointSpritesSupported) glBegin(GL_POINTS);

            for (int i = iStartPos; i < iEndPos; i++) {
                if (RNA3D->bEColiRefInitialized) {
                    long absPos   = (long) i;
                    long EColiPos = EColiRef->abs_2_rel(absPos);

                    for (Struct3Dinfo *t = start3D; t; t = t->next) {
                        if ((t->pos == EColiPos) && (pSearchColResults[i] >= 0)) {
                            iColor = pSearchColResults[i-1] - SAICOLORS;

                            if (ValidSearchColor(iColor, SAI)) {
                                RNA3D->cGraphics->SetColor(iColor);
                                PointsToQuads(t->x, t->y, t->z);
                            }
                            break;
                        }
                    }
                }
            }

            if (RNA3D->bPointSpritesSupported) glEnd();
        }
        glEndList();

        RNA3D->bMapSaiDispListCreated = true;
    }
    else cout<<"ED4_getSaiColorString did not get the colors : SAI cannot be Visualized!"<<endl;
}