- Main Page
- Related Pages
- Data Structures
- Files

- File List
- Globals

# H/loop_energies.h

Go to the documentation of this file.

    00001 #ifndef __VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H__
    00002 #define __VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H__
    00003
    00004 #include <stdio.h>
    00005 #include <stdlib.h>
    00006 #include <math.h>
    00007 #include <ctype.h>
    00008 #include <string.h>
    00009 #include "params.h"
    00010 #include "fold_vars.h"
    00011 #include "energy_par.h"
    00012
    00013 #ifdef __GNUC__
    00014 # define INLINE inline
    00015 #else
    00016 # define INLINE
    00017 #endif
    00018
    00054 //#define E_MLstem(A,B,C,D)     E_Stem((A),(B),(C),0,(D))
    00055 INLINE  PRIVATE int E_MLstem( int type,
    00056                               int si1,
    00057                               int sj1,
    00058                               paramT *P);
    00059
    00066 //#define exp_E_MLstem(A,B,C,D) exp_E_Stem((A),(B),(C),0,(D))
    00067 INLINE  PRIVATE double exp_E_MLstem(int type,
    00068                                     int si1,
    00069                                     int sj1,
    00070                                     pf_paramT *P);
    00071
    00091 //#define E_ExtLoop(A,B,C,D)      E_Stem((A),(B),(C),1,(D))
    00092 INLINE  PRIVATE int E_ExtLoop(int type,
    00093                               int si1,
    00094                               int sj1,
    00095                               paramT *P);
    00096
    00103 //#define exp_E_ExtLoop(A,B,C,D)  exp_E_Stem((A),(B),(C),1,(D))
    00104 INLINE  PRIVATE double exp_E_ExtLoop( int type,
    00105                                       int si1,
    00106                                       int sj1,
    00107                                       pf_paramT *P);
    00108
    00153 INLINE  PRIVATE int E_IntLoop(int n1,
    00154                               int n2,
    00155                               int type,
    00156                               int type_2,
    00157                               int si1,
    00158                               int sj1,
    00159                               int sp1,
    00160                               int sq1,
    00161                               paramT *P);
    00162
    00163
    00195 INLINE  PRIVATE int E_Hairpin(int size,
    00196                               int type,
    00197                               int si1,
    00198                               int sj1,
    00199                               const char *string,
    00200                               paramT *P);
    00201
    00247 INLINE  PRIVATE int E_Stem( int type,
    00248                             int si1,
    00249                             int sj1,
    00250                             int extLoop,
    00251                             paramT *P);
    00252
    00261 INLINE  PRIVATE double exp_E_Stem(int type,
    00262                                   int si1,
    00263                                   int sj1,
    00264                                   int extLoop,
    00265                                   pf_paramT *P);
    00266
    00284 INLINE  PRIVATE double exp_E_Hairpin( int u,
    00285                                       int type,
    00286                                       short si1,
    00287                                       short sj1,
    00288                                       const char *string,
    00289                                       pf_paramT *P);
    00290
    00310 INLINE  PRIVATE double  exp_E_IntLoop(int u1,
    00311                                       int u2,
    00312                                       int type,
    00313                                       int type2,
    00314                                       short si1,
    00315                                       short sj1,
    00316                                       short sp1,
    00317                                       short sq1,
    00318                                       pf_paramT *P);
    00319
    00320
    00321 /*
    00322 #################################
    00323 # BEGIN OF FUNCTION DEFINITIONS #
    00324 #################################
    00325 */
    00326 INLINE  PRIVATE int E_Hairpin(int size, int type, int si1, int sj1, const char *string, paramT *P){
    00327   int energy;
    00328
    00329   energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(int)(P->lxc*log((size)/30.));
    00330   if (P->model_details.special_hp){
    00331     if (size == 4) { /* check for tetraloop bonus */
    00332       char tl[7]={0}, *ts;
    00333       strncpy(tl, string, 6);
    00334       if ((ts=strstr(P->Tetraloops, tl)))
    00335         return (P->Tetraloop_E[(ts - P->Tetraloops)/7]);
    00336     }
    00337     else if (size == 6) {
    00338       char tl[9]={0}, *ts;
    00339       strncpy(tl, string, 8);
    00340       if ((ts=strstr(P->Hexaloops, tl)))
    00341         return (energy = P->Hexaloop_E[(ts - P->Hexaloops)/9]);
    00342     }
    00343     else if (size == 3) {
    00344       char tl[6]={0,0,0,0,0,0}, *ts;
    00345       strncpy(tl, string, 5);
    00346       if ((ts=strstr(P->Triloops, tl))) {
    00347         return (P->Triloop_E[(ts - P->Triloops)/6]);
    00348       }
    00349       return (energy + (type>2 ? P->TerminalAU : 0));
    00350     }
    00351   }
    00352   energy += P->mismatchH[type][si1][sj1];
    00353
    00354   return energy;
    00355 }
    00356
    00357 INLINE  PRIVATE int E_IntLoop(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, paramT *P){
    00358   /* compute energy of degree 2 loop (stack bulge or interior) */
    00359   int nl, ns, energy;
    00360
    00361   if (n1>n2) { nl=n1; ns=n2;}
    00362   else {nl=n2; ns=n1;}
    00363
    00364   if (nl == 0)
    00365     return P->stack[type][type_2];  /* stack */
    00366
    00367   if (ns==0) {                      /* bulge */
    00368     energy = (nl<=MAXLOOP)?P->bulge[nl]:
    00369       (P->bulge[30]+(int)(P->lxc*log(nl/30.)));
    00370     if (nl==1) energy += P->stack[type][type_2];
    00371     else {
    00372       if (type>2) energy += P->TerminalAU;
    00373       if (type_2>2) energy += P->TerminalAU;
    00374     }
    00375     return energy;
    00376   }
    00377   else {                            /* interior loop */
    00378     if (ns==1) {
    00379       if (nl==1)                    /* 1x1 loop */
    00380         return P->int11[type][type_2][si1][sj1];
    00381       if (nl==2) {                  /* 2x1 loop */
    00382         if (n1==1)
    00383           energy = P->int21[type][type_2][si1][sq1][sj1];
    00384         else
    00385           energy = P->int21[type_2][type][sq1][si1][sp1];
    00386         return energy;
    00387       }
    00388       else {  /* 1xn loop */
    00389         energy = (nl+1<=MAXLOOP)?(P->internal_loop[nl+1]) : (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));
    00390         energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);
    00391         energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type_2][sq1][sp1];
    00392         return energy;
    00393       }
    00394     }
    00395     else if (ns==2) {
    00396       if(nl==2)      {              /* 2x2 loop */
    00397         return P->int22[type][type_2][si1][sp1][sq1][sj1];}
    00398       else if (nl==3){              /* 2x3 loop */
    00399         energy = P->internal_loop[5]+P->ninio[2];
    00400         energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type_2][sq1][sp1];
    00401         return energy;
    00402       }
    00403
    00404     }
    00405     { /* generic interior loop (no else here!)*/
    00406       energy = (n1+n2<=MAXLOOP)?(P->internal_loop[n1+n2]) : (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));
    00407
    00408       energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);
    00409
    00410       energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type_2][sq1][sp1];
    00411     }
    00412   }
    00413   return energy;
    00414 }
    00415
    00416 INLINE  PRIVATE int E_Stem(int type, int si1, int sj1, int extLoop, paramT *P){
    00417   int energy = 0;
    00418   int d5 = (si1 >= 0) ? P->dangle5[type][si1] : 0;
    00419   int d3 = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;
    00420
    00421   if(type > 2)
    00422     energy += P->TerminalAU;
    00423
    00424   if(si1 >= 0 && sj1 >= 0)
    00425     energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1][sj1];
    00426   else
    00427     energy += d5 + d3;
    00428
    00429   if(!extLoop) energy += P->MLintern[type];
    00430   return energy;
    00431 }
    00432
    00433 INLINE  PRIVATE int E_ExtLoop(int type, int si1, int sj1, paramT *P){
    00434   int energy = 0;
    00435   if(si1 >= 0 && sj1 >= 0){
    00436     energy += P->mismatchExt[type][si1][sj1];
    00437   }
    00438   else if (si1 >= 0){
    00439     energy += P->dangle5[type][si1];
    00440   }
    00441   else if (sj1 >= 0){
    00442     energy += P->dangle3[type][sj1];
    00443   }
    00444
    00445   if(type > 2)
    00446     energy += P->TerminalAU;
    00447
    00448   return energy;
    00449 }
    00450
    00451 INLINE  PRIVATE int E_MLstem(int type, int si1, int sj1, paramT *P){
    00452   int energy = 0;
    00453   if(si1 >= 0 && sj1 >= 0){
    00454     energy += P->mismatchM[type][si1][sj1];
    00455   }
    00456   else if (si1 >= 0){
    00457     energy += P->dangle5[type][si1];
    00458   }
    00459   else if (sj1 >= 0){
    00460     energy += P->dangle3[type][sj1];
    00461   }
    00462
    00463   if(type > 2)
    00464     energy += P->TerminalAU;
    00465
    00466   energy += P->MLintern[type];
    00467
    00468   return energy;
    00469 }
    00470
    00471 INLINE  PRIVATE double exp_E_Hairpin(int u, int type, short si1, short sj1, const char *string, pf_paramT *P){
    00472   double q, kT;
    00473   kT = P->kT;   /* kT in cal/mol  */
    00474
    00475   if(u <= 30)
    00476     q = P->exphairpin[u];
    00477   else
    00478     q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);
    00479
    00480   if(u < 3) return q; /* should only be the case when folding alignments */
    00481
    00482   if ((P->model_details.special_hp)&&(u==4)) {
    00483     char tl[7]={0,0,0,0,0,0,0}, *ts;
    00484     strncpy(tl, string, 6);
    00485     if ((ts=strstr(P->Tetraloops, tl))){
    00486       if(type != 7)
    00487         return (P->exptetra[(ts-P->Tetraloops)/7]);
    00488       else
    00489         q *= P->exptetra[(ts-P->Tetraloops)/7];
    00490     }
    00491   }
    00492   if ((tetra_loop)&&(u==6)) {
    00493     char tl[9]={0,0,0,0,0,0,0,0,0}, *ts;
    00494     strncpy(tl, string, 6);
    00495     if ((ts=strstr(P->Hexaloops, tl)))
    00496       return  (P->exphex[(ts-P->Hexaloops)/9]);
    00497   }
    00498   if (u==3) {
    00499     char tl[6]={0,0,0,0,0,0}, *ts;
    00500     strncpy(tl, string, 5);
    00501     if ((ts=strstr(P->Triloops, tl)))
    00502       return (P->exptri[(ts-P->Triloops)/6]);
    00503     if (type>2)
    00504       q *= P->expTermAU;
    00505   }
    00506   else /* no mismatches for tri-loops */
    00507     q *= P->expmismatchH[type][si1][sj1];
    00508
    00509   return q;
    00510 }
    00511
    00512 INLINE  PRIVATE double exp_E_IntLoop(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, pf_paramT *P){
    00513   int ul, us, no_close = 0;
    00514   double z;
    00515
    00516   if ((no_closingGU) && ((type2==3)||(type2==4)||(type==3)||(type==4)))
    00517     no_close = 1;
    00518
    00519   if (u1>u2) { ul=u1; us=u2;}
    00520   else {ul=u2; us=u1;}
    00521
    00522   if (ul==0) /* stack */
    00523     z = P->expstack[type][type2];
    00524   else if(!no_close){
    00525     if (us==0) {                      /* bulge */
    00526       z = P->expbulge[ul];
    00527       if (ul==1) z *= P->expstack[type][type2];
    00528       else {
    00529         if (type>2) z *= P->expTermAU;
    00530         if (type2>2) z *= P->expTermAU;
    00531       }
    00532       return z;
    00533     }
    00534     else if (us==1) {
    00535       if (ul==1){                    /* 1x1 loop */
    00536         return P->expint11[type][type2][si1][sj1];
    00537       }
    00538       if (ul==2) {                  /* 2x1 loop */
    00539         if (u1==1)
    00540           return P->expint21[type][type2][si1][sq1][sj1];
    00541         else
    00542           return P->expint21[type2][type][sq1][si1][sp1];
    00543       }
    00544       else {  /* 1xn loop */
    00545         z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];
    00546         return z * P->expninio[2][ul-us];
    00547       }
    00548     }
    00549     else if (us==2) {
    00550       if(ul==2) /* 2x2 loop */
    00551         return P->expint22[type][type2][si1][sp1][sq1][sj1];
    00552       else if(ul==3){              /* 2x3 loop */
    00553         z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];
    00554         return z * P->expninio[2][1];
    00555       }
    00556     }
    00557     /* generic interior loop (no else here!)*/
    00558     z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];
    00559     return z * P->expninio[2][ul-us];
    00560
    00561   }
    00562   return z;
    00563 }
    00564
    00565 INLINE  PRIVATE double exp_E_Stem(int type, int si1, int sj1, int extLoop, pf_paramT *P){
    00566   double energy = 1.0;
    00567   double d5 = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;
    00568   double d3 = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;
    00569
    00570   if(type > 2)
    00571     energy *= P->expTermAU;
    00572
    00573   if(si1 >= 0 && sj1 >= 0)
    00574     energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[type][si1][sj1];
    00575   else
    00576     energy *= d5 * d3;
    00577
    00578   if(!extLoop) energy *= P->expMLintern[type];
    00579   return energy;
    00580 }
    00581
    00582 INLINE  PRIVATE double exp_E_MLstem(int type, int si1, int sj1, pf_paramT *P){
    00583   double energy = 1.0;
    00584   if(si1 >= 0 && sj1 >= 0){
    00585     energy *= P->expmismatchM[type][si1][sj1];
    00586   }
    00587   else if(si1 >= 0){
    00588     energy *= P->expdangle5[type][si1];
    00589   }
    00590   else if(sj1 >= 0){
    00591     energy *= P->expdangle3[type][sj1];
    00592   }
    00593
    00594   if(type > 2)
    00595     energy *= P->expTermAU;
    00596
    00597   energy *= P->expMLintern[type];
    00598   return energy;
    00599 }
    00600
    00601 INLINE  PRIVATE double exp_E_ExtLoop(int type, int si1, int sj1, pf_paramT *P){
    00602   double energy = 1.0;
    00603   if(si1 >= 0 && sj1 >= 0){
    00604     energy *= P->expmismatchExt[type][si1][sj1];
    00605   }
    00606   else if(si1 >= 0){
    00607     energy *= P->expdangle5[type][si1];
    00608   }
    00609   else if(sj1 >= 0){
    00610     energy *= P->expdangle3[type][sj1];
    00611   }
    00612
    00613   if(type > 2)
    00614     energy *= P->expTermAU;
    00615
    00616   return energy;
    00617 }
    00618
    00619 INLINE  PRIVATE int     E_IntLoop_Co(int type, int type_2, int i, int j, int p, int q, int cutpoint, short si1, short sj1, short sp1, short sq1, int dangles, paramT *P){
    00620   int energy = 0;
    00621   if(type > 2)   energy += P->TerminalAU;
    00622   if(type_2 > 2) energy += P->TerminalAU;
    00623
    00624   if(!dangles) return energy;
    00625
    00626   int ci = (i>=cutpoint)||((i+1)<cutpoint);
    00627   int cj = ((j-1)>=cutpoint)||(j<cutpoint);
    00628   int cp = ((p-1)>=cutpoint)||(p<cutpoint);
    00629   int cq = (q>=cutpoint)||((q+1)<cutpoint);
    00630
    00631   int d3    = ci  ? P->dangle3[type][si1]   : 0;
    00632   int d5    = cj  ? P->dangle5[type][sj1]   : 0;
    00633   int d5_2  = cp  ? P->dangle5[type_2][sp1] : 0;
    00634   int d3_2  = cq  ? P->dangle3[type_2][sq1] : 0;
    00635
    00636   int tmm   = (cj && ci) ? P->mismatchExt[type][sj1][si1]   : d5 + d3;
    00637   int tmm_2 = (cp && cq) ? P->mismatchExt[type_2][sp1][sq1] : d5_2 + d3_2;
    00638
    00639   if(dangles == 2) return energy + tmm + tmm_2;
    00640
    00641   /* now we may have non-double dangles only */
    00642   if(i+2 < p){
    00643     if(q+2 < j){ energy += tmm + tmm_2;}
    00644     else if(q+2 == j){ energy += (cj && cq) ? MIN2(tmm + d5_2, tmm_2 + d3) : tmm + tmm_2;}
    00645     else energy += d3 + d5_2;
    00646   }
    00647   else if(i+2 == p){
    00648     if(q+2 < j){ energy += (ci && cp) ? MIN2(tmm + d3_2, tmm_2 + d5) : tmm + tmm_2;}
    00649     else if(q+2 == j){
    00650       energy += MIN2(tmm, MIN2(tmm_2, MIN2(d5 + d5_2, d3 + d3_2)));
    00651     }
    00652     else energy += MIN2(d3, d5_2);
    00653   }
    00654   else{
    00655     if(q+2 < j){ energy += d5 + d3_2;}
    00656     else if(q+2 == j){ energy += MIN2(d5, d3_2);}
    00657   }
    00658   return energy;
    00659 }
    00660
    00661 #endif