RNAlib-2.0.7: H/loop_energies.h Source 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