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parser.c
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parser.c
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/*
* Copyright (c) 2013 Pau Rué <[email protected]>
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
* FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
* COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
* IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
* CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "parser.h"
#define REACTION_TYPES 4
typedef enum _reaction_type2{
NOT_VALID,
MASS_ACTION,
HILL_ACTIVATION,
HILL_INHIBITION
} reaction_type;
const char reaction_types[][REACTION_TYPES] = {"\0", "MA", "HA", "HI"};
typedef enum _stoich_type{
REACTANTS,
PRODUCTS
} stoich_type;
typedef enum _parsing_section{
PARSING_NONE = 0,
PARSING_SPECIES = 1 ,
PARSING_REACTIONS = 2,
} parsing_section;
void parse_line_species(Model_t * model, List_t * lines) {
/* Species lines have the format:
* SpeciesName1 = 2312 # Some comment
* SpeciesName2 = 0
* We first create a list of species to ensure all of them are unique!
* */
int i, idx;
List_t * species_list;
iList_t * ics_list;
char * species_str, * ic_str, * saveptr;
species_list = list_new();
ics_list = ilist_new();
for(i=0; i< lines->size; i++) {
species_str = strtok_r(lines->items[i], "=", &saveptr);
trim(species_str);
/*TODO: Allow for more than one species per line
* for(p=strsep(&values, ","); p != NULL; p=strsep(&values, ",")) {
* value = atoi(p);
*/
ic_str = strtok_r (NULL, "=", &saveptr);
trim(ic_str);
idx = string_find(species_str, model->species, model->nspecies);
if(idx == -1){ /* Species not in list */
list_append(species_list, species_str);
ilist_append(ics_list, atoi(ic_str));
} else {
report_warning("Species '%s' is being redefined", species_str);
ics_list->items[idx] = atoi(ic_str);
}
}
/* Fill the model */
model->nspecies = species_list->size;
/* in case we have less species than lines (repeated species)*/
for(i=0; i< model->nspecies; i++){
strcpy(model->species[i], species_list->items[i]);
model->ics[i] = ics_list->items[i];
model->istate[i] = ics_list->items[i];
}
return;
}
void parse_stoichiometry(char * str, Model_t * model, int ireaction, stoich_type type) {
/* Format is 2*A + 3*B + C */
int coeff;
int nspecies;
int species[2000], stoichiometry[2000];
char * aux_str1, * aux_str2, *aux_str3, *saveptr1, *saveptr2;
int k;
aux_str1 = strtok_r (str, "+", &saveptr1);
nspecies = 0;
while(aux_str1 != NULL) {
trim(aux_str1);
//coeff=0;
//printf(".--.%s",aux_str1);
if(strlen(aux_str1)==0 || strcmp(aux_str1, "0")!=0){
aux_str2 = strtok_r(aux_str1, "*", &saveptr2);
aux_str3 = strtok_r(NULL, "*", &saveptr2);
if(aux_str3 == NULL) { /* Case "A" instead of "1*A"*/
coeff = 1;
} else { /* Case "3*A" */
coeff = atoi(aux_str2);
aux_str2 = aux_str3;
}
k = string_find(aux_str2, model->species, model->nspecies);
if(k == -1){
report_error("Species %s has not been defined", aux_str1);
exit(1);
} else if(type==REACTANTS){
model->rstoichiometry[ireaction][k] = coeff;
} else if(type==PRODUCTS) {
model->pstoichiometry[ireaction][k] = coeff;
}
species[nspecies] = k;
stoichiometry[nspecies] = coeff;
nspecies++;
}
aux_str1 = strtok_r (NULL, "+", &saveptr1);
}
return;
}
void parse_params(char * params_str, Model_t * model, int ireaction, char *rtype) {
char * saveptr;
char * aux_str;
int idx;
if (strcmp(rtype, "MA") == 0) {
model->params[ireaction] = (double *) malloc(sizeof(double));
model->params[ireaction][0] = atof(params_str);
} else if ((strcmp(rtype, "HA") == 0) || (strcmp(rtype, "HI") == 0) ) {
model->params[ireaction] = (double *) malloc(3 * sizeof(double)); /* rate, Ks, coop.*/
model->acting_species[ireaction] = (int *) malloc(sizeof(int));
/* Find Which species is acting */
trim(params_str);
aux_str = strtok_r(params_str, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][0] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* rate */
model->params[ireaction][0] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant */
model->params[ireaction][1] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity */
model->params[ireaction][2] = atof(aux_str);
} else if ((strcmp(rtype, "HIHA") == 0) || (strcmp(rtype, "HIHI") == 0) || (strcmp(rtype, "HAHA") == 0) || (strcmp(rtype, "CI") == 0) ) {
//printf("HIHA\n");
model->params[ireaction] = (double *) malloc(5 * sizeof(double)); /* rate, Ks1, coop1, Ks2, coop2.*/
/* for CI: rate, Ks, coop1, gamma, coop2. -> rate * (y1)^coop1 / ((y1)^coop1 + (Ks)^coop2 + (gamma*y2)^coop2) */
model->acting_species[ireaction] = (int *) malloc(2 * sizeof(int));
trim(params_str);
aux_str = strtok_r(params_str, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][0] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][1] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* rate */
model->params[ireaction][0] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant 1*/
model->params[ireaction][1] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity 1*/
model->params[ireaction][2] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant 2*/
model->params[ireaction][3] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity 2 */
model->params[ireaction][4] = atof(aux_str);
} else if ((strcmp(rtype, "MAHA") == 0) || (strcmp(rtype, "MAHI") == 0)) {
model->params[ireaction] = (double *) malloc(3 * sizeof(double)); /* rate, Ks1, coop1.*/
model->acting_species[ireaction] = (int *) malloc(2 * sizeof(int));
trim(params_str);
aux_str = strtok_r(params_str, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][0] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][1] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* rate */
model->params[ireaction][0] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant 1*/
model->params[ireaction][1] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity*/
model->params[ireaction][2] = atof(aux_str);
} else if ((strcmp(rtype, "HAHAC") == 0) ) {
model->params[ireaction] = (double *) malloc(6 * sizeof(double)); /* rate1, Ks1, coop1, rate2, Ks2, coop2.*/
/* for CI: rate, Ks, coop1, gamma, coop2. -> rate * (y1)^coop1 / ((y1)^coop1 + (Ks)^coop2 + (gamma*y2)^coop2) */
model->acting_species[ireaction] = (int *) malloc(2 * sizeof(int));
trim(params_str);
aux_str = strtok_r(params_str, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][0] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][1] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* rate 1*/
model->params[ireaction][0] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant 1*/
model->params[ireaction][1] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity 1*/
model->params[ireaction][2] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* rate 2*/
model->params[ireaction][3] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant 2*/
model->params[ireaction][4] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity 2 */
model->params[ireaction][5] = atof(aux_str);
} else if ((strcmp(rtype, "HAHAHIC") == 0) ) {
model->params[ireaction] = (double *) malloc(8 * sizeof(double)); /* rate1, Ks1, coop1, rate2, Ks2, coop2, Ksi, coopi.*/
/* for CI: rate, Ks, coop1, gamma, coop2. -> rate * (y1)^coop1 / ((y1)^coop1 + (Ks)^coop2 + (gamma*y2)^coop2) */
model->acting_species[ireaction] = (int *) malloc(3 * sizeof(int));
trim(params_str);
aux_str = strtok_r(params_str, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][0] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][1] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* Species name */
idx = string_find(aux_str, model->species, model->nspecies);
if(idx == -1) {
report_error("Species '%s' not found", aux_str);
exit(1);
} else {
model->acting_species[ireaction][2] = idx;
}
aux_str = strtok_r(NULL, " ", &saveptr); /* rate 1*/
model->params[ireaction][0] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant 1*/
model->params[ireaction][1] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity 1*/
model->params[ireaction][2] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* rate 2*/
model->params[ireaction][3] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant 2*/
model->params[ireaction][4] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity 2 */
model->params[ireaction][5] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* binding constant inhib*/
model->params[ireaction][6] = atof(aux_str);
aux_str = strtok_r(NULL, " ", &saveptr); /* cooperativity inhib */
model->params[ireaction][7] = atof(aux_str);
} else {
report_error("Reaction type '%s' not recognised", rtype);
exit(1);
}
}
void parse_line_reactions(Model_t * model, List_t * reactions_lines) {
int i;
char rtype[100];
char * aux_str;
char * saveptr1;
for(i=0; i<reactions_lines->size; i++) {
// Reactants
aux_str = strtok_r(reactions_lines->items[i], ">", &saveptr1);
trim(aux_str);
parse_stoichiometry(aux_str, model, i, REACTANTS);
// Products
aux_str = strtok_r(NULL, "|", &saveptr1);
trim(aux_str);
parse_stoichiometry(aux_str, model, i, PRODUCTS);
// Reaction types
aux_str = strtok_r(NULL, "|",&saveptr1);
strcpy(rtype, aux_str);
trim(rtype);
// printf("type: %s\n", rtype);
if(strcmp(rtype, "MA") == 0) {
model->prop[i] = prop_MA;
} else if(strcmp(rtype, "HA") == 0) {
model->prop[i] = prop_HA;
} else if(strcmp(rtype, "HI") == 0) {
model->prop[i] = prop_HI;
} else if(strcmp(rtype, "HIHA") == 0) {
model->prop[i] = prop_HIHA;
} else if(strcmp(rtype, "MAHI") == 0) {
model->prop[i] = prop_MAHI;
} else if(strcmp(rtype, "CI") == 0) {
model->prop[i] = prop_CI;
} else if(strcmp(rtype, "HAHAHIC") == 0) {
model->prop[i] = prop_HAHAHIC;
} else if(strcmp(rtype, "HAHAC") == 0) {
model->prop[i] = prop_HAHAC;
}else{
printf("Warning! Propensity type not detected\n");
model->prop[i] = prop_TEST;
}
//Parameters
aux_str = strtok_r (NULL, "|", &saveptr1);
parse_params(aux_str, model, i, rtype);
}
return;
}
Model_t * load_model_from_file(char * fname) {
FILE * in;
Model_t * model;
char line[MAX_LINE_SIZE];
char section_name[MAX_LINE_SIZE];
int lastchr; /* Last character read */
int linenum, len; /* line number and length*/
parsing_section section;
List_t * species_lines, * reactions_lines;
/* Lists initialisation */
species_lines = list_new();
reactions_lines = list_new();
/* Here we get the strings for the species (and its initial conditions),
* and the reactions.
* */
in = fopen(fname, "r");
if (!in){
report_error("cannot open file");
exit(1);
}
linenum = 0;
lastchr = 0;
section = PARSING_NONE;
while (fgets(line + lastchr, MAX_LINE_SIZE-lastchr, in) != NULL) {
linenum++;
len = (int) strlen(line)-1;
/* Avoid buffer overflows */
if(line[len]!='\n'){
report_error("line too long to be parsed in file");
fclose(in);
exit(1);
}
/* Get rid of \n and spaces at end of line */
while ((len>=0) && ((line[len]=='\n') || (isspace(line[len])))) {
line[len]='\0' ;
len-- ;
}
len = remove_comments(line, '#');
if(len < 1) { /* Skip empty line*/
} else if (line[0]=='[' && line[len]==']') {
/* Section name line
* TODO: Allow for different case and check the output from sscanf
* */
sscanf(line, "[%[^]]", section_name);
if(strcmp(section_name, "Species") == 0){
section = PARSING_SPECIES;
} else if(strcmp(section_name, "Reactions") == 0) {
if(section != PARSING_SPECIES){
report_error("In file: %s, line %d: Reactions must be specified after species", fname, linenum);
exit(1);
}
section = PARSING_REACTIONS;
} else {
report_error("In file: %s, section %s not valid", fname, section_name);
exit(1);
}
} else if(section == PARSING_SPECIES){
list_append(species_lines, line);
} else if(section == PARSING_REACTIONS){
list_append(reactions_lines, line);
} else {
report_error("Line not correctly formatted!");
exit(1);
}
}
fclose(in);
model = model_new();
model_set_allocate(model, species_lines->size, reactions_lines->size);
parse_line_species(model, species_lines);
parse_line_reactions(model, reactions_lines);
return model;
}