RNAlib-2.1.1: /mount/gensoft2/src/ViennaRNA/ViennaRNA-2.1.1/H/data

00001 #ifndef __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__
00002 #define __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__
00003 
00004 #include "energy_const.h"
00010 /* to use floats instead of doubles in pf_fold() comment next line */
00011 #define LARGE_PF
00012 #ifdef  LARGE_PF
00013 #define FLT_OR_DBL double
00014 #else
00015 #define FLT_OR_DBL float
00016 #endif
00017 
00018 #ifndef NBASES
00019 #define NBASES 8
00020 #endif
00021 
00022 #ifndef MAXALPHA
00023 
00026 #define MAXALPHA              20
00027 #endif
00028 
00032 #define MAXDOS                1000
00033 
00034 #define   VRNA_GQUAD_MAX_STACK_SIZE     7
00035 #define   VRNA_GQUAD_MIN_STACK_SIZE     2
00036 #define   VRNA_GQUAD_MAX_LINKER_LENGTH  15
00037 #define   VRNA_GQUAD_MIN_LINKER_LENGTH  1
00038 #define   VRNA_GQUAD_MIN_BOX_SIZE       ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))
00039 #define   VRNA_GQUAD_MAX_BOX_SIZE       ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))
00040 
00041 
00042 /*
00043 * ############################################################
00044 * Here are the type definitions of various datastructures
00045 * shared among the Vienna RNA Package
00046 * ############################################################
00047 */
00048 
00052 typedef struct plist {
00053   int i;
00054   int j;
00055   float p;
00056   int type;
00057 } plist;
00058 
00062 typedef struct cpair {
00063   int i,j,mfe;
00064   float p, hue, sat;
00065 } cpair;
00066 
00071 typedef struct {
00072   float X; /* X coords */
00073   float Y; /* Y coords */
00074 } COORDINATE;
00075 
00079 typedef struct sect {
00080   int  i;
00081   int  j;
00082   int ml;
00083 } sect;
00084 
00088 typedef struct bondT {
00089    unsigned int i;
00090    unsigned int j;
00091 } bondT;
00092 
00096 typedef struct bondTEn {
00097    int i;
00098    int j;
00099    int energy;
00100 } bondTEn;
00101 
00106 typedef struct{
00107   int     dangles;      
00113   int     special_hp;   
00114   int     noLP;         
00115   int     noGU;         
00116   int     noGUclosure;  
00117   int     logML;        
00118   int     circ;         
00119   int     gquad;        
00120 } model_detailsT;
00121 
00125 typedef struct{
00126   int id;
00127   int stack[NBPAIRS+1][NBPAIRS+1];
00128   int hairpin[31];
00129   int bulge[MAXLOOP+1];
00130   int internal_loop[MAXLOOP+1];
00131   int mismatchExt[NBPAIRS+1][5][5];
00132   int mismatchI[NBPAIRS+1][5][5];
00133   int mismatch1nI[NBPAIRS+1][5][5];
00134   int mismatch23I[NBPAIRS+1][5][5];
00135   int mismatchH[NBPAIRS+1][5][5];
00136   int mismatchM[NBPAIRS+1][5][5];
00137   int dangle5[NBPAIRS+1][5];
00138   int dangle3[NBPAIRS+1][5];
00139   int int11[NBPAIRS+1][NBPAIRS+1][5][5];
00140   int int21[NBPAIRS+1][NBPAIRS+1][5][5][5];
00141   int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
00142   int ninio[5];
00143   double  lxc;
00144   int     MLbase;
00145   int     MLintern[NBPAIRS+1];
00146   int     MLclosing;
00147   int     TerminalAU;
00148   int     DuplexInit;
00149   int     Tetraloop_E[200];
00150   char    Tetraloops[1401];
00151   int     Triloop_E[40];
00152   char    Triloops[241];
00153   int     Hexaloop_E[40];
00154   char    Hexaloops[1801];
00155   int     TripleC;
00156   int     MultipleCA;
00157   int     MultipleCB;
00158   int     gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
00159                 [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
00160 
00161   double  temperature;            
00163   model_detailsT model_details;   
00165 }  paramT;
00166 
00170 typedef struct{
00171   int     id;
00172   double  expstack[NBPAIRS+1][NBPAIRS+1];
00173   double  exphairpin[31];
00174   double  expbulge[MAXLOOP+1];
00175   double  expinternal[MAXLOOP+1];
00176   double  expmismatchExt[NBPAIRS+1][5][5];
00177   double  expmismatchI[NBPAIRS+1][5][5];
00178   double  expmismatch23I[NBPAIRS+1][5][5];
00179   double  expmismatch1nI[NBPAIRS+1][5][5];
00180   double  expmismatchH[NBPAIRS+1][5][5];
00181   double  expmismatchM[NBPAIRS+1][5][5];
00182   double  expdangle5[NBPAIRS+1][5];
00183   double  expdangle3[NBPAIRS+1][5];
00184   double  expint11[NBPAIRS+1][NBPAIRS+1][5][5];
00185   double  expint21[NBPAIRS+1][NBPAIRS+1][5][5][5];
00186   double  expint22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
00187   double  expninio[5][MAXLOOP+1];
00188   double  lxc;
00189   double  expMLbase;
00190   double  expMLintern[NBPAIRS+1];
00191   double  expMLclosing;
00192   double  expTermAU;
00193   double  expDuplexInit;
00194   double  exptetra[40];
00195   double  exptri[40];
00196   double  exphex[40];
00197   char    Tetraloops[1401];
00198   double  expTriloop[40];
00199   char    Triloops[241];
00200   char    Hexaloops[1801];
00201   double  expTripleC;
00202   double  expMultipleCA;
00203   double  expMultipleCB;
00204   double  expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
00205                   [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
00206 
00207   double  kT;
00208   double  pf_scale;     
00210   double  temperature;  
00211   double  alpha;        
00218   model_detailsT model_details; 
00220 }  pf_paramT;
00221 
00222 
00223 
00224 /*
00225 * ############################################################
00226 * SUBOPT data structures
00227 * ############################################################
00228 */
00229 
00230 
00234 typedef struct {
00235   int i;
00236   int j;
00237 } PAIR;
00238 
00242 typedef struct {
00243     int i;
00244     int j;
00245     int array_flag;
00246 } INTERVAL;
00247 
00251 typedef struct {
00252   float energy;       
00253   char *structure;    
00254 } SOLUTION;
00255 
00256 /*
00257 * ############################################################
00258 * COFOLD data structures
00259 * ############################################################
00260 */
00261 
00265 typedef struct cofoldF {
00266   /* free energies for: */
00267   double F0AB;  
00268   double FAB;   
00269   double FcAB;  
00270   double FA;    
00271   double FB;    
00272 } cofoldF;
00273 
00277 typedef struct ConcEnt {
00278   double A0;    
00279   double B0;    
00280   double ABc;   
00281   double AAc;
00282   double BBc;
00283   double Ac;
00284   double Bc;
00285 } ConcEnt;
00286 
00290 typedef struct pairpro{
00291   struct plist *AB;
00292   struct plist *AA;
00293   struct plist *A;
00294   struct plist *B;
00295   struct plist *BB;
00296 }pairpro;
00297 
00308 typedef struct {
00309    unsigned i;    
00310    unsigned j;    
00311    float p;       
00312    float ent;     
00313    short bp[8];   
00314    char comp;     
00315 } pair_info;
00316 
00317 
00318 /*
00319 * ############################################################
00320 * FINDPATH data structures
00321 * ############################################################
00322 */
00323 
00327 typedef struct move {
00328   int i;  /* i,j>0 insert; i,j<0 delete */
00329   int j;
00330   int when;  /* 0 if still available, else resulting distance from start */
00331   int E;
00332 } move_t;
00333 
00337 typedef struct intermediate {
00338   short *pt;      
00339   int Sen;        
00340   int curr_en;    
00341   move_t *moves;  
00342 } intermediate_t;
00343 
00347 typedef struct path {
00348   double en;
00349   char *s;
00350 } path_t;
00351 
00352 /*
00353 * ############################################################
00354 * RNAup data structures
00355 * ############################################################
00356 */
00357 
00361 typedef struct pu_contrib {
00362   double **H; 
00363   double **I; 
00364   double **M; 
00365   double **E; 
00366   int length; 
00367   int w;      
00368 } pu_contrib;
00369 
00373 typedef struct interact {
00374   double *Pi;       
00375   double *Gi;       
00376   double Gikjl;     
00378   double Gikjl_wo;  
00379   int i;            
00380   int k;            
00381   int j;            
00382   int l;            
00383   int length;       
00384 } interact;
00385 
00389 typedef struct pu_out {
00390   int len;            
00391   int u_vals;         
00392   int contribs;       
00393   char **header;      
00394   double **u_values;  
00395 } pu_out;
00396 
00400 typedef struct constrain{
00401   int *indx;
00402   char *ptype;
00403 } constrain;
00404 
00405 /*
00406 * ############################################################
00407 * RNAduplex data structures
00408 * ############################################################
00409 */
00410 
00414 typedef struct {
00415   int i;
00416   int j;
00417   int end;
00418   char *structure;
00419   double energy;
00420   double energy_backtrack;
00421   double opening_backtrack_x;
00422   double opening_backtrack_y;
00423   int offset;
00424   double dG1;
00425   double dG2;
00426   double ddG;
00427   int tb;
00428   int te;
00429   int qb;
00430   int qe;
00431 } duplexT;
00432 
00433 /*
00434 * ############################################################
00435 * RNAsnoop data structures
00436 * ############################################################
00437 */
00438 
00442 typedef struct node {
00443   int k;
00444   int energy;
00445   struct node *next;
00446 } folden;
00447 
00451 typedef struct {
00452   int i;
00453   int j;
00454   int u;
00455   char *structure;
00456   float energy;
00457   float Duplex_El;
00458   float Duplex_Er;
00459   float Loop_E;
00460   float Loop_D;
00461   float pscd;
00462   float psct;
00463   float pscg;
00464   float Duplex_Ol;
00465   float Duplex_Or;
00466   float Duplex_Ot;
00467   float fullStemEnergy;
00468 } snoopT;
00469 
00470 
00471 
00472 
00473 
00474 
00475 
00476 /*
00477 * ############################################################
00478 * PKplex data structures
00479 * ############################################################
00480 */
00481 
00485 typedef struct dupVar{
00486   int i;
00487   int j;
00488   int end;
00489   char *pk_helix;
00490   char *structure;
00491   double energy;
00492   int offset;
00493   double dG1;
00494   double dG2;
00495   double ddG;
00496   int tb;
00497   int te;
00498   int qb;
00499   int qe;
00500   int inactive;
00501   int processed;
00502 } dupVar;
00503 
00504 
00505 
00506 /*
00507 * ############################################################
00508 * 2Dfold data structures
00509 * ############################################################
00510 */
00511 
00526 typedef struct{
00527   int k;          
00528   int l;          
00529   float en;       
00530   char *s;        
00531 } TwoDfold_solution;
00532 
00538 typedef struct{
00539   paramT          *P;             
00540   int             do_backtrack;   
00541   char            *ptype;         
00542   char            *sequence;      
00543   short           *S, *S1;        
00544   unsigned int    maxD1;          
00545   unsigned int    maxD2;          
00548   unsigned int    *mm1;           
00549   unsigned int    *mm2;           
00551   int             *my_iindx;      
00553   double          temperature;
00554 
00555   unsigned int    *referenceBPs1; 
00556   unsigned int    *referenceBPs2; 
00557   unsigned int    *bpdist;        
00559   short           *reference_pt1;
00560   short           *reference_pt2;
00561   int             circ;
00562   int             dangles;
00563   unsigned int    seq_length;
00564 
00565   int             ***E_F5;
00566   int             ***E_F3;
00567   int             ***E_C;
00568   int             ***E_M;
00569   int             ***E_M1;
00570   int             ***E_M2;
00571 
00572   int             **E_Fc;
00573   int             **E_FcH;
00574   int             **E_FcI;
00575   int             **E_FcM;
00576 
00577   int             **l_min_values;
00578   int             **l_max_values;
00579   int             *k_min_values;
00580   int             *k_max_values;
00581 
00582   int             **l_min_values_m;
00583   int             **l_max_values_m;
00584   int             *k_min_values_m;
00585   int             *k_max_values_m;
00586 
00587   int             **l_min_values_m1;
00588   int             **l_max_values_m1;
00589   int             *k_min_values_m1;
00590   int             *k_max_values_m1;
00591 
00592   int             **l_min_values_f;
00593   int             **l_max_values_f;
00594   int             *k_min_values_f;
00595   int             *k_max_values_f;
00596 
00597   int             **l_min_values_f3;
00598   int             **l_max_values_f3;
00599   int             *k_min_values_f3;
00600   int             *k_max_values_f3;
00601 
00602   int             **l_min_values_m2;
00603   int             **l_max_values_m2;
00604   int             *k_min_values_m2;
00605   int             *k_max_values_m2;
00606 
00607   int             *l_min_values_fc;
00608   int             *l_max_values_fc;
00609   int             k_min_values_fc;
00610   int             k_max_values_fc;
00611 
00612   int             *l_min_values_fcH;
00613   int             *l_max_values_fcH;
00614   int             k_min_values_fcH;
00615   int             k_max_values_fcH;
00616 
00617   int             *l_min_values_fcI;
00618   int             *l_max_values_fcI;
00619   int             k_min_values_fcI;
00620   int             k_max_values_fcI;
00621 
00622   int             *l_min_values_fcM;
00623   int             *l_max_values_fcM;
00624   int             k_min_values_fcM;
00625   int             k_max_values_fcM;
00626 
00627   /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */
00628   int             *E_F5_rem;
00629   int             *E_F3_rem;
00630   int             *E_C_rem;
00631   int             *E_M_rem;
00632   int             *E_M1_rem;
00633   int             *E_M2_rem;
00634 
00635   int             E_Fc_rem;
00636   int             E_FcH_rem;
00637   int             E_FcI_rem;
00638   int             E_FcM_rem;
00639 
00640 #ifdef COUNT_STATES
00641   unsigned long             ***N_F5;
00642   unsigned long             ***N_C;
00643   unsigned long             ***N_M;
00644   unsigned long             ***N_M1;
00645 #endif
00646 } TwoDfold_vars;
00647 
00660 typedef struct{
00661   int k;          
00662   int l;          
00663   FLT_OR_DBL  q;  
00664 } TwoDpfold_solution;
00665 
00672 typedef struct{
00673 
00674   unsigned int    alloc;
00675   char            *ptype;         
00676   char            *sequence;      
00677   short           *S, *S1;        
00678   unsigned int    maxD1;          
00679   unsigned int    maxD2;          
00681   double          temperature;    /* temperature in last call to scale_pf_params */
00682   double          init_temp;      /* temperature in last call to scale_pf_params */
00683   FLT_OR_DBL      *scale;
00684   FLT_OR_DBL      pf_scale;
00685   pf_paramT       *pf_params;     /* holds all [unscaled] pf parameters */
00686 
00687   int             *my_iindx;      
00688   int             *jindx;         
00690   short           *reference_pt1;
00691   short           *reference_pt2;
00692 
00693   unsigned int    *referenceBPs1; 
00694   unsigned int    *referenceBPs2; 
00695   unsigned int    *bpdist;        
00697   unsigned int    *mm1;           
00698   unsigned int    *mm2;           
00700   int             circ;
00701   int             dangles;
00702   unsigned int    seq_length;
00703 
00704   FLT_OR_DBL      ***Q;
00705   FLT_OR_DBL      ***Q_B;
00706   FLT_OR_DBL      ***Q_M;
00707   FLT_OR_DBL      ***Q_M1;
00708   FLT_OR_DBL      ***Q_M2;
00709 
00710   FLT_OR_DBL      **Q_c;
00711   FLT_OR_DBL      **Q_cH;
00712   FLT_OR_DBL      **Q_cI;
00713   FLT_OR_DBL      **Q_cM;
00714 
00715   int             **l_min_values;
00716   int             **l_max_values;
00717   int             *k_min_values;
00718   int             *k_max_values;
00719 
00720   int             **l_min_values_b;
00721   int             **l_max_values_b;
00722   int             *k_min_values_b;
00723   int             *k_max_values_b;
00724 
00725   int             **l_min_values_m;
00726   int             **l_max_values_m;
00727   int             *k_min_values_m;
00728   int             *k_max_values_m;
00729 
00730   int             **l_min_values_m1;
00731   int             **l_max_values_m1;
00732   int             *k_min_values_m1;
00733   int             *k_max_values_m1;
00734 
00735   int             **l_min_values_m2;
00736   int             **l_max_values_m2;
00737   int             *k_min_values_m2;
00738   int             *k_max_values_m2;
00739 
00740   int             *l_min_values_qc;
00741   int             *l_max_values_qc;
00742   int             k_min_values_qc;
00743   int             k_max_values_qc;
00744 
00745   int             *l_min_values_qcH;
00746   int             *l_max_values_qcH;
00747   int             k_min_values_qcH;
00748   int             k_max_values_qcH;
00749 
00750   int             *l_min_values_qcI;
00751   int             *l_max_values_qcI;
00752   int             k_min_values_qcI;
00753   int             k_max_values_qcI;
00754 
00755   int             *l_min_values_qcM;
00756   int             *l_max_values_qcM;
00757   int             k_min_values_qcM;
00758   int             k_max_values_qcM;
00759 
00760   /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */
00761   FLT_OR_DBL      *Q_rem;
00762   FLT_OR_DBL      *Q_B_rem;
00763   FLT_OR_DBL      *Q_M_rem;
00764   FLT_OR_DBL      *Q_M1_rem;
00765   FLT_OR_DBL      *Q_M2_rem;
00766 
00767   FLT_OR_DBL      Q_c_rem;
00768   FLT_OR_DBL      Q_cH_rem;
00769   FLT_OR_DBL      Q_cI_rem;
00770   FLT_OR_DBL      Q_cM_rem;
00771 
00772 } TwoDpfold_vars;
00773 
00774 #endif
/mount/gensoft2/src/ViennaRNA/ViennaRNA-2.1.1/H/data_structures.h
