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h_common.cpp
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h_common.cpp
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#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <iostream>
#include "constants.h"
#include "externs.h"
#include "h_externs.h"
#include "common.h"
#include "h_struct.h"
#include "h_common.h"
#include "params.h"
#include "simfold.h"
// Hosna feb 12, 2008
#include "W_final.h"
#include "hfold.h"
// Hosna, May 3rd, 2012
//#include "hfold_pkonly.h"
// Hosna, November 16, 2015
#include "dinoknot.hh"
//kevin
#include <vector>
#include <utility>
#include "init.h"
/*
* This function is just the same as detect_original_pairs
* but it also calculates the arcs for each base and saves them in arc_table
*
* The algorithm for finding the arcs is as follows:
* When checking each base in the input structure,
*
* case 1) if (structure[i] == '.' or ' ' or '_')
* 1-a) if stack is not empty, then put arc_table[i] = top element on the stack
* 1-b) otherwise arc_table[i] = -1
*
* case 2) if (structure[i] == '(')
* 2-a) if stack is not empty, then put arc_table[i] = top element on the stack and push i in the stack
* 2-b) otherwise arc_table[i] = -1 and push i in the stack
*
* case 3) if (strcuture[i] == ')'), pop the stack and match it with j
* 3-a) if stack is not empty, then put arc_table[i] = top element on the stack
* 3-b) otherwise put arc_table[i] = -1
*
*/
void detect_original_pairs_arcs(char *structure, int *p_table, int *arc_table)
// PRE: structure contains the desired structure
// POST: pairs will contain the index of each base pair
// or -1 if it does not pair
//
{
//printf("structure: %s\n", structure);
int i, j, struct_len;
stack_ds st;
h_init (&st);
remove_space (structure);
//printf("The given structure is: \n %s\n", structure);
struct_len = strlen (structure);
// Hosna March 8, 2012
// since index i starts at 0 and stack top is also set to 0 to show stack is empty, if i=0 is paired then we have incorrect arc values!
// So I am introducing STACK_EMPTY = -1 to h_common.h and change h_init and h_pop accordingly
for (i=0; i < struct_len; i++)
{
// Hosna March 8, 2012
// changing nested ifs to switch for optimality
switch (structure[i])
{
case '.':
{
p_table[i] = RESTRICTED_UNPAIR;
if (st.top > STACK_EMPTY){//0){
// if (debug)
// printf("base %d: stack has %d elements in it and its top element is %d \n",i, st.top, st.elem[st.top]);
arc_table[i] = st.elem[st.top];
}else{
arc_table[i] = NOT_COVERED;
}
}
break;
case ' ':
case '_':
{
p_table[i] = FREE_TO_PAIR;
if (st.top > STACK_EMPTY){//0){
// if (debug)
// printf("base %d: stack has %d elements in it and its top element is %d \n",i, st.top, st.elem[st.top]);
arc_table[i] = st.elem[st.top];
}else{
arc_table[i] = NOT_COVERED;
}
}
break;
case '(':
{
if (st.top > STACK_EMPTY){//0){
// if (debug)
// printf("base %d: stack has %d elements in it and its top element is %d \n",i, st.top, st.elem[st.top]);
arc_table[i] = st.elem[st.top];
}else{
arc_table[i] = NOT_COVERED;
}
h_push (&st, i);
}
break;
case ')':
//else if (structure[i] == ')')
{
j = h_pop (&st);
p_table[i] = j;
p_table[j] = i;
if (st.top > STACK_EMPTY){//0){
// if (debug)
// printf("base %d: stack has %d elements in it and its top element is %d \n",i, st.top, st.elem[st.top]);
arc_table[i] = st.elem[st.top];
}else{
arc_table[i] = NOT_COVERED;
}
}
break;
}
}
/* for (i=137; i<struct_len; i++){
printf("p_table[%d] = %d AND arc_table[%d]=%d \n\n",i,p_table[i],i,arc_table[i]);
}
printf(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n"); */
if (st.top != STACK_EMPTY)//0)
{
fprintf (stderr, "The given structure is not valid: %d more left parentheses than right parentheses\n", st.top);
exit (1);
}
}
/**
* This function is just like the above function except the case that
* it can handle the pseudoknotted structures of at most density 2
*
* the density 2 structures can be presented with ( and [ in dot parenthesis format
* so we need at most 2 stacks to keep track of the base pairings
* we call the stacks st and st_brack for ( and [ respectively.
*
*
*/
void detect_original_PKed_pairs(char *structure, int *p_table)
// PRE: structure contains the desired structure
// POST: pairs will contain the index of each base pair
// or -1 if it does not pair
{
int i, j, struct_len;
stack_ds st; //stach used for (
stack_ds st_brack; // stack used for [
h_init (&st);
h_init (&st_brack);
remove_space (structure);
struct_len = strlen (structure);
for (i=0; i < struct_len; i++)
{
// Hosna March 8, 2012
// changing nested ifs to switch for optimality
switch (structure[i])
{
case '.':
//if (structure[i] == '.')
{
p_table[i] = -1;
}
break;
case ' ':
case '_':
//else if (structure[i] == ' ' || structure[i] == '_')
{
p_table[i] = -2;
}
break;
case '(':
//else if (structure[i] == '(')
{
h_push (&st, i);
}
break;
case '[':
//else if (structure[i] == '[')
{
h_push (&st_brack, i);
}
break;
case ')':
//else if (structure[i] == ')')
{
j = h_pop (&st);
p_table[i] = j;
p_table[j] = i;
}
break;
case ']':
// else if (structure[i] == ']')
{
j = h_pop (&st_brack);
p_table[i] = j;
p_table[j] = i;
}
break;
}
}
if (st.top != STACK_EMPTY || st_brack.top != STACK_EMPTY) //0 || st_brack.top != 0)
{
fprintf (stderr, "The given structure is not valid: %d more left parenthesis than right parentheses\n", st.top);
exit (1);
}
}
/*
* The algorithm for finding the weakly closed regions for a given pseudoknot free structure is as follows
*
* initialization:
* open = -1;
* weakly_closed array initialized to 0
*
*
* case 1) if the region is of the form [i,i] and i is not paired,
* then it is considered as a weakly closed region and we put weakly_closed[ii] = 1
* otherwise we put open = i
*
* case 2) if we are considering region [i,j] where i!=j and we know region [i, j-1] is weakly closed
* 2-a) if j is not paired, then [i,j] is also weakly closed and we put weakly_closed[ij] = 1
* 2-b) if j is paired and we have i <= bp(j) < j then [i,j] is weakly_closed and we put weakly_closed[ij] = 1
* THIS CASE CAN NEVER HAPPERN ==> REMOVE FROM CODE
* 2-c) otherwise [i,j] is NOT weakly closed
* if (open == -1) then open = j
*
* case 3) if we are considering region [i,j] where i!=j and we know region [i,j-1] is NOT weakly closed
* 3-a) if j is paired and bp(j) == open then [i,j] is weakly closed and we put weakly_closed[ij] = 1 and open = -1
* 3-b) otherwise the region is still NOT weakly closed
*
*/
void detect_weakly_closed(h_str_features *fres, int *weakly_closed, int nb_nucleotides, int *index){
int i,j;
int open = -1;
for (i = 0; i < nb_nucleotides; i++){
open = -1;
for (j = i; j < nb_nucleotides; j++){
int ij = index[i]+j-i; // index[i]+j-i gives the index ij
// if ( i == 7 && j == 27){
// printf("weakly_closed[%d,%d] = %d and open = %d \n", i,j-1,weakly_closed[ij-1], open);
// }
if (i == j ){
if (fres[j].pair < 0){ // j is not paired
weakly_closed[ij]= 1;
// if (debug ){//_weakly_closed){
// printf("%d==%d and %d is not paired => weakly closed\n",i,j,j);
// }
}else{
open = j;
// if (debug){//_weakly_closed){
// printf("%d==%d and %d is paired => not weakly closed, and open = %d\n",i,j,j,open);
// }
}
}else if (weakly_closed[ij-1]){
if (fres[j].pair < 0){ // j is not paired
weakly_closed[ij] = 1;
// if (debug ){//_weakly_closed){
// printf("[%d,%d] is weakly closed and %d is not paired => weakly closed\n",i,j-1,j);
// }
}else if (open == -1){
open = j;
// if (debug ){//_weakly_closed){
// printf("[%d,%d] is weakly closed but %d is paired => not weakly closed, and open = %d\n",i,j-1,j,open);
// }
}
}else if(fres[j].pair >= 0 && open == fres[j].pair){
weakly_closed[ij] = 1;
open = -1;
// if (debug && i == 27 && j == 68){//_weakly_closed){
// printf("[%d,%d] is not weakly closed but %d is paired with %d => weakly closed\n",i,j-1,j,fres[j].pair);
// }
}
//if (debug){//_weakly_closed){
// if (i == 27 && j == 68){//_weakly_closed){
// printf("weakly_closed[%d,%d] = %d\n",i,j,weakly_closed[ij]);
// }
// if (weakly_closed[ij] == 1)
// printf("Region [%d,%d] is Weakly closed\n",i,j);
//}
}
}
}
/*
* Hosna: Feb 12, 2007
* algorithm for finding if region [i,j] is an empty region
* We define an empty region as follows:
* region [i,j] is an empty region if for all k i<k<j, k is unpaired
*
* in our program we only need to know empty regions based on the original structure
*
* for every base i and j, such that i <= j
* 1) if (i == j && i is not paired in G)
* then region [i,i] is an empty region and
* we put not_paired_all[i,j] = 1
*
* 2) else if j is not paired in G and we know that region[i,j-1] is an empty region
* then region [i,j] is an empty region and we put
* not_paired_all[i,j] = 1
*
* 3) otherwise region[i,j] is not an empty region and we put
* not_paired_all[i,j] = 0
*
*/
void detect_not_paired_all(h_str_features *fres, int *not_paired_all, int nb_nucleotides, int *index){
int i, j;
for(i = 0; i < nb_nucleotides; i++){
for(j = i; j < nb_nucleotides; j++){
int ij = index[i]+j-i;
if (i == j){
if (fres[i].pair < 0){
not_paired_all[ij]=1;
// if (debug){//_empty){
// printf("region [%d,%d] is empty \n",i,j);
// }
}else{
not_paired_all[ij] = 0;
// if (debug){//_empty){
// printf("region [%d,%d] is NOT empty \n",i,j);
// }
}
}else if (not_paired_all[ij-1] == 1 && fres[j].pair < 0){
not_paired_all[ij] = 1;
// if (debug){//_empty){
// printf("region [%d,%d] is empty \n",i,j);
// }
}
else{
not_paired_all[ij] = 0;
// if (debug){//_empty){
// printf("region [%d,%d] is NOT empty \n",i,j);
// }
}
}
}
}
/* Hosna:
* The algorithm for finding b(i,l) and B(l,j) is as follows:
*
* for every base l, if l is in an arc and l is not paired (i.e. f[l].arc != -1)
* and every i (0 < i < nb_nucleotides)
*
* 1) if (i <= arc(l)) then we are finding b(i,l):
* 1-a) temp = arc(arc(l))
* 1-b) if (temp == -1 || temp <= i) then we put
* b(i,l) = b'(i,l) (i.e. border_bs[l][i] = arc(l))
* 1-c) otherwise
* 1-c-i) while (arc(temp) ! = -1 && arc(temp) > i)
* temp = arc(temp)
* 1-c-ii) b(i,l) = temp and we put border_bs[l][i] = temp
*
* 2) if (i >= pair(arc(l))) then we are finding B(l,j):
* 1-a) temp = arc(arc(l))
* 1-b) if (temp == -1 || pair(temp) >= i) then we put
* B(l,i) = B'(l,i) (i.e. border_bs[l][i] = pair(arc(l)))
* 1-c) otherwise
* 1-c-i) while (arc(temp) ! = -1 && pair(arc(temp)) < i)
* temp = arc(temp)
* 1-c-ii) B(l,i) = pair(temp) and we put border_bs[l][i] = pair(temp)
*
* 3) if (i > arc(l) && i < pair(arc(l))) then border_bs[l][i] = -1
*/
void detect_border_bs(h_str_features *fres, int** border_bs, int nb_nucleotides){
int l,i;
for (l = 0; l < nb_nucleotides; l++){
for (i = 0; i < nb_nucleotides; i++){
int cover_l = fres[l].arc, pair_l=fres[l].pair; // Hosna March 8, 2012, using local varibales for optimality
if (cover_l == -1 || pair_l >= 0){
border_bs[l][i] = -2;
// if (debug_border_bs){
// printf("fres[%d].arc = %d, fres[%d].pair = %d \n",l, fres[l].arc,l,fres[l].pair);
// printf("border_bs[%d][%d] = %d \n",l,i,border_bs[l][i]);
// }
}else{
if (i <= cover_l){
int temp = fres[cover_l].arc;
if (temp == -1 || temp < i){ // Hosna: Jan 31, 2007: temp <= i changed to < to include i itself too
border_bs[l][i] = cover_l;
}else{
while(fres[temp].arc != -1 && fres[temp].arc >= i){ // Hosna: Jan 31, 2007: fres[temp].arc > i changed to >= to include i itself too
temp = fres[temp].arc;
}
border_bs[l][i] = temp;
}
}
if (i >= fres[cover_l].pair){
int temp = fres[cover_l].arc;
if (temp == -1 || fres[temp].pair > i){ //Hosna: Jan 31, 2007: fres[temp].pair >= i changed to > to include i itself too
border_bs[l][i] = fres[cover_l].pair;
}else{
while(fres[temp].arc != -1 && fres[fres[temp].arc].pair <= i){ //Hosna: Jan 31, 2007: fres[fres[temp].arc].pair < i changed to <= to include i itself too
temp = fres[temp].arc;
}
border_bs[l][i] = fres[temp].pair;
}
}
if (i > cover_l && i < fres[cover_l].pair){
border_bs[l][i] = -1;
}
// if (debug_border_bs){
// printf("fres[%d].arc = %d, fres[%d].pair = %d \n",l, fres[l].arc,l,fres[l].pair);
// printf("border_bs[%d][%d] = %d \n",l,i,border_bs[l][i]);
// }
}
}
}
}
/* Hosna:
* The algorithm for finding b'(i,l) and B'(l,j) is as follows:
*
* for every base l, if l is in an arc and l is not paired (i.e. f[l].arc != -1)
* and every i (0 < i < nb_nucleotides)
*
* 1) if (i < arc(l)) then b'(i,l) = arc(l)
* and we put the corresponding value in border_bps[l][i]
*
* 2) if (i > pair(arc(l))) then B'(l,i) = pair(arc(l))
* and we put the corresponding value in border_bps[l][i]
*
* 3) if (i >= arc(l) && i<= pair(arc(l))) then border[l][i] = -1
*
*/
void detect_border_bps(h_str_features *fres, int** border_bps, int nb_nucleotides){
// TODO ian should these be different if the i,l they are at is at linker (X) ?
int l, i;
for (l = 0; l < nb_nucleotides; l++){
for (i = 0; i < nb_nucleotides ; i++){
int cover_l = fres[l].arc, pair_l=fres[l].pair; // Hosna March 8, 2012, using local varibales for optimality
if (cover_l == -1 || pair_l >= 0){
border_bps[l][i] = -2;//INF;//-2;
// if (debug_border_bps){
// printf("fres[%d].arc = %d, fres[%d].pair = %d \n",l, fres[l].arc,l,fres[l].pair);
// printf("border_bps[%d][%d] = %d \n",l,i,border_bps[l][i]);
// }
//break;
}else{
if (i <= cover_l ){ //Hosna: Jan 31, 2007: < changed to <= to include i itself too
border_bps[l][i] = cover_l ;
}
if (i >= fres[cover_l ].pair){ //Hosna: Jan 31, 2007: > changed to >= to include i itself too
border_bps[l][i] = fres[fres[l].arc].pair;
}
if ( i > cover_l && i < fres[cover_l].pair){ //Hosna: Jan 31, 2007: >= and <= changed to > and < to include i itself too
border_bps[l][i] = -1;
}
// if (debug_border_bps){
// printf("fres[%d].arc = %d, fres[%d].pair = %d \n",l, fres[l].arc,l,fres[l].pair);
// printf("border_bps[%d][%d] = %d \n",l,i,border_bps[l][i]);
// }
}
}
}
}
void h_init (stack_ds *st)
// PRE: None
// POST: Initialize the stack st
{
st->top = STACK_EMPTY;//0;
}
void h_push (stack_ds *st, int el)
// PRE: st is a valid stack
// POST: Push an element to the stack
{
st->top = st->top +1;
st->elem[st->top] = el;
}
int h_pop (stack_ds *st)
// PRE: st is a valid stack, that is not empty
// POST: pop an element from the stack and return it
{
if (st->top <= STACK_EMPTY)//0)
{
fprintf (stderr, "The given structure is not valid: more right parentheses than left parentheses\n");
exit (1);
}
int result = st->elem[st->top];
st->top = st->top -1 ;
return result;
}
h_str_features *convert_str_features_to_h_str_features(str_features *f){
h_str_features *fres;
fres->arc = -1;
fres->num_branches = f->num_branches;
fres->pair = f->pair;
fres->type = f->type;
int i;
for (i = 0; i < fres->num_branches; i++){
fres->bri[i] = f->bri[i];
}
return fres;
}
str_features *convert_h_str_features_to_str_features(h_str_features *f){
str_features *fres;
fres->num_branches = f->num_branches;
fres->pair = f->pair;
fres->type = f->type;
int i;
for (i = 0; i < fres->num_branches; i++){
fres->bri[i] = f->bri[i];
}
return fres;
}
void detect_h_structure_features (char *structure, h_str_features *f)
// PRE: None
// POST: The variable f is filled with structure features, i.e. what type of elementary structure
// this base is closing (such as stacked pair, hairpin loop etc.)
{
int num_branches, i, j;
int p_table[MAXSLEN];
int arc_table[MAXSLEN];
int bri[MAX_BRANCHES];
int nb_nucleotides;
nb_nucleotides = strlen(structure);
detect_original_pairs_arcs (structure, p_table, arc_table);
for (i=0; i < nb_nucleotides; i++)
{
// Hosna, March 8, 2012
// use local variables instead of getting array values all the time
int i_pair = p_table[i];
f[i].pair = i_pair;//p_table[i];
f[i].arc = arc_table[i];
if (i_pair>i)//p_table[i] > i)
{
//f[i].pair = p_table[i]; //Hosna March 8, 2012, this statement seemed redundant! so removed
f[i_pair].pair = i;//f[p_table[i]].pair = i;
// check if it is stacked pair
int i_pair_plus1 = p_table[i+1];
if (i_pair_plus1 == i_pair-1 && i_pair_plus1 > i+1)//(p_table[i+1] == p_table[i]-1 && p_table[i+1] > i+1)
{
f[i].type = STACK;
f[i_pair].type = STACK;//f[p_table[i]].type = STACK;
/* if (i>=136){
printf("END OF THE LOOP \n");
printf("p_table[%d]=%d \n",i,p_table[i]);
printf("f[%d].pair = %d, f[%d].type = %c, f[%d].arc = %d \n",i,f[i].pair,i,f[i].type,i,f[i].arc);
} */
continue;
}
// check if it is hairpin, internal loop or multi-loop
num_branches = 0;
for (j=i+1; j<i_pair; j++)//(j=i+1; j < p_table[i]; j++)
{
if (p_table[j] > j)
{
bri[num_branches] = j;
num_branches++;
j = p_table[j];
}
}
if (num_branches == 0) // hairpin
{
f[i].type = HAIRP;
f[i_pair].type = HAIRP; //f[p_table[i]].type = HAIRP;
}
else if (num_branches == 1) // internal loop
{
f[i].type = INTER;
f[i_pair].type = INTER; //f[p_table[i]].type = INTER;
f[i].num_branches = 1;
f[i].bri[0] = bri[0];
}
else // multi loop
{
f[i].type = MULTI;
f[i_pair].type = MULTI; //f[p_table[i]].type = MULTI;
f[i].num_branches = num_branches;
for (j=0; j < num_branches; j++)
f[i].bri[j] = bri[j];
}
}
/* if (i>=136){
printf("END OF THE LOOP \n");
printf("p_table[%d]=%d \n",i,p_table[i]);
printf("f[%d].pair = %d, f[%d].type = %c, f[%d].arc = %d \n",i,f[i].pair,i,f[i].type,i,f[i].arc);
} */
}
if (debug){
printf("h_str_features was successful! \n");
}
}
/*
* Hosna: January 10, 2008
* The following two functions are modified versions of
* the functions found in simfold/src/common/common.cpp
* the modifications are to make them work for density-2 structures
*
*/
double compute_h_sensitivity (char *ref_structure, char *pred_structure)
// returns 0 if undefined (denominator is 0)
{
int ptable_ref[MAXSLEN];
int ptable_pred[MAXSLEN];
int distance;
int len, i;
double sens;
int num_correct_bp;
int num_true_bp;
len = strlen(ref_structure);
detect_original_PKed_pairs (ref_structure, ptable_ref);
detect_original_PKed_pairs (pred_structure, ptable_pred);
num_correct_bp = 0;
num_true_bp = 0;
for (i=0; i < len; i++)
{
if (ptable_ref[i] > -1) // paired base
{
num_true_bp++;
if (ptable_pred[i] == ptable_ref[i])
num_correct_bp++;
}
}
if (num_true_bp == 0)
return -1.0;
sens = num_correct_bp*1.0/num_true_bp;
return sens;
}
double compute_h_ppv (char *ref_structure, char *pred_structure)
// returns 0 if undefined (denominator is 0)
{
int ptable_ref[MAXSLEN];
int ptable_pred[MAXSLEN];
int distance;
int len, i;
double ppv;
int num_correct_bp;
int num_pred_bp;
len = strlen(ref_structure);
detect_original_PKed_pairs (ref_structure, ptable_ref);
detect_original_PKed_pairs (pred_structure, ptable_pred);
num_correct_bp = 0;
num_pred_bp = 0;
for (i=0; i < len; i++)
{
if (ptable_ref[i] > -1 && ptable_pred[i] == ptable_ref[i]) // paired base
num_correct_bp++;
if (ptable_pred[i] > -1) // paired base
num_pred_bp++;
}
if (num_pred_bp == 0)
return -1.0;
ppv = num_correct_bp*1.0/num_pred_bp;
return ppv;
}
/*
* Hosna Jan 10, 2008
* The following function is used to tune the parameters
* using Andronescu's GC program
* This function is supposed to reset the pseudoknotted parameters
*/
void h_fill_data_structures_with_new_parameters (char *filename){
FILE *file;
char buffer[100];
double param;
int line = 0;
//printf ("FILENAME: %s\n", filename);
if ((file = fopen (filename, "r")) == NULL)
{
giveup ("Cannot open file", filename);
}
// PS_penalty: exterior pseudoloop initiation penalty (originally 9.6 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
PS_penalty = (int) param;
//PSM_penalty: penalty for introducing pseudoknot inside a multiloop (originally 15 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
PSM_penalty = (int) param;
//PSP_penalty: penalty for introducing pseudoknot inside a pseudoloop (originally 15 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
PSP_penalty = (int) param;
//PB_penalty: band penalty (originally 0.2 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
PB_penalty = (int) param;
//PUP_penalty: penalty for an un-paired base in a pseudoloop or a band (originally 0.1 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
PUP_penalty = (int) param;
//PPS_penalty: penalty for nested closed region inside either a pseudoloop or a multiloop that spans a band(originally 0.1 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
PPS_penalty = (int) param;
//a_penalty: penalty for introducing a multiloop (originally 3.4 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
a_penalty = (int) param;
//b_penalty: penalty for base pair in a multiloop (originally 0.4 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
b_penalty = (int) param;
//c_penalty: penalty for un-paired base in a multi-loop (originally 0)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
c_penalty = (int) param;
// e_stP = 0.83 * e_s
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
e_stP_penalty = param;
// e_intP = 0.83 * e_int
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
e_intP_penalty = param;
//ap_penalty: penalty for introducing a multiloop that spans a band (originally 3.4 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
ap_penalty = (int) param;
//bp_penalty: base pair penalty for a multiloop that spans a band (originally 0.4 Kcal/mol)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
bp_penalty = (int) param;
//cp_penalty: penalty for unpaired base in a multiloop that spans a band (originally 0)
fgets (buffer, sizeof(buffer), file);
line++;
sscanf (buffer, "%lf", ¶m);
param *= 100;
cp_penalty = (int) param;
fclose (file);
//printf ("****** we must have 14 lines by now: LINES = %d\n", line);
}
void h_fill_data_structures_with_new_parameters (double *param)
{
if (param == NULL){
giveup ("Incorrect parameter length", "h_fill_data_structure_with_new_parameters");
}
// PS_penalty: exterior pseudoloop initiation penalty (originally 9.6 Kcal/mol)
param[0] *= 100;
PS_penalty = (int) param[0];
//PSM_penalty: penalty for introducing pseudoknot inside a multiloop (originally 15 Kcal/mol)
param[1] *= 100;
PSM_penalty = (int) param[1];
//PSP_penalty: penalty for introducing pseudoknot inside a pseudoloop (originally 15 Kcal/mol)
param[2] *= 100;
PSP_penalty = (int) param[2];
//PB_penalty: band penalty (originally 0.2 Kcal/mol)
param[3] *= 100;
PB_penalty = (int) param[3];
//PUP_penalty: penalty for an un-paired base in a pseudoloop or a band (originally 0.1 Kcal/mol)
param[4] *= 100;
PUP_penalty = (int) param[4];
//PPS_penalty: penalty for nested closed region inside either a pseudoloop or a multiloop that spans a band(originally 0.1 Kcal/mol)
param[5] *= 100;
PPS_penalty = (int) param[5];
//a_penalty: penalty for introducing a multiloop (originally 3.4 Kcal/mol)
param[6] *= 100;
a_penalty = (int) param[6];
//b_penalty: penalty for base pair in a multiloop (originally 0.4 Kcal/mol)
param[7] *= 100;
b_penalty = (int) param[7];
//c_penalty: penalty for un-paired base in a multi-loop (originally 0)
param[8] *= 100;
c_penalty = (int) param[8];
// e_stP = 0.83 * e_s
e_stP_penalty = param[9];
// e_intP = 0.83 * e_int
e_intP_penalty = param[10];
//ap_penalty: penalty for introducing a multiloop that spans a band (originally 3.4 Kcal/mol)
param[11] *= 100;
ap_penalty = (int) param[11];
//bp_penalty: base pair penalty for a multiloop that spans a band (originally 0.4 Kcal/mol)
param[12] *= 100;
bp_penalty = (int) param[12];
//cp_penalty: penalty for unpaired base in a multiloop that spans a band (originally 0)
param[13] *= 100;
cp_penalty = (int) param[13];
}
int h_create_string_params(){
int index = create_string_params();
sprintf (string_params[index++], "PS_penalty");
sprintf (string_params[index++], "PSM_penalty");
sprintf (string_params[index++], "PSP_penalty");
sprintf (string_params[index++], "PB_penalty");
sprintf (string_params[index++], "PUP_penalty");
sprintf (string_params[index++], "PPS_penalty");
sprintf (string_params[index++], "a_penalty");
sprintf (string_params[index++], "b_penalty");
sprintf (string_params[index++], "c_penalty");
sprintf (string_params[index++], "e_stP_penalty");
sprintf (string_params[index++], "e_intP_penalty");
sprintf (string_params[index++], "ap_penalty");
sprintf (string_params[index++], "bp_penalty");
sprintf (string_params[index++], "cp_penalty");
return index;
}
double hfold(char *sequence, char *restricted, char *structure){
W_final *min_fold = new W_final (sequence, restricted);
if (min_fold == NULL) giveup ("Cannot allocate memory", "HFold");
double energy = min_fold->hfold();
min_fold->return_structure (structure);
delete min_fold;
return energy;
}
//AP. HFold_Emodel is used by HFold and HFold_interacting. The only difference is the passed in energy model vector.
/*
double hfold_emodel(char *sequence, char *restricted, char *structure, std::vector<energy_model> *energy_models){
W_final *min_fold = new W_final (sequence, restricted, energy_models);
if (min_fold == NULL) giveup ("Cannot allocate memory", "HFold");
double energy = min_fold->hfold_emodel();
min_fold->return_structure (structure);
return energy;
}
*/
//---------------------------------------this function is suppose to be the same as the one in Hfold_iterative, if any changes are made, please change that one too--------------------
//kevin 19 july (verified by Mahyar 19 july 2017)
//count+1 when open bracket, count-1 when close bracket
//whgen count is 0, we have a substructure
//assume valid structure
void find_disjoint_substructure(char* structure, std::vector< std::pair<int,int> > &pair_vector){
int length = strlen(structure);
int count = 0;
int first_time = 1; //flag for first time getting a open bracket for substructure
int i = 0;
int j = 0;
for(int k=0; k<length;k++){
if(structure[k] == '(' || structure[k] == '['){
if(first_time && count == 0){
first_time = 0;
i = k;
}
count += 1;
}else if(structure[k] == ')' || structure[k] == ']'){
count -= 1;
j = k;
if(count == 0){
std::pair <int,int> ij_pair (i,j);
pair_vector.push_back(ij_pair);
first_time = 1;
}
}
}
}
//---------------------------------------this function is suppose to be the same as the one in Hfold_iterative, if any changes are made, please change that one too--------------------
//31 Aug 2017 kevin and Mahyar
//input[i] is _ or . and it did not turn into a . in the output structure, then it is not empty
int is_empty_structure(char* input_structure, char* output_structure){
for(int i=0; i<strlen(input_structure);i++){
if(input_structure[i] != output_structure[i]){
if((input_structure[i] == '_' || input_structure[i] == '.' ) && output_structure[i] != '.'){
return 0;
}
}
}
return 1;
}
//---------------------------------------this function is suppose to be the same as the one in Hfold_iterative, if any changes are made, please change that one too--------------------
//kevin 18 July
int paired_structure(int i, int j, int *pair_index, int length){
if(i >= 0 && j < length && (pair_index[i] == j) && (pair_index[j] == i) ){
return 1;
}
return 0;
}
//---------------------------------------this function is suppose to be the same as the one in Hfold_iterative, if any changes are made, please change that one too--------------------
//kevin 18 July
void obtainRelaxedStems(char* G1, char* G2, char* Gresult){
int length = strlen(G1);
int G1_pair[length];
int G2_pair[length];
//Gresult <- G1