static void read_int22(int use_dna_params, tab8_t *t)
{
fill8(t, NOT_A_NUMBER);
FILE *f = parfile("int22", use_dna_params);
look_for_line_containing(f, "5' ------> 3'");
char buf[MAXLINE+1];
while (fgets(buf, MAXLINE, f)) {
if (strlen(buf) >= MAXLINE)
die("read_int22: line too long");
if (is_only_whitespace(buf))
continue;
look_for_line_containing(f, "5' ------> 3'");
char a[4];
if (!(fgets(buf, MAXLINE, f) && sscanf(buf, " %c \\/ \\_/ %c", &a[0], &a[1]) == 2))
die("read_int22: couldn't read first line");
if (!(fgets(buf, MAXLINE, f) && sscanf(buf, " %c /\\ | %c", &a[2], &a[3]) == 2))
die("read_int22: couldn't read second line");
expect_line_containing(f, "3' <------ 5'");
int i, j;
base_t b[4];
for (i = 0; i < 4; i++)
b[i] = base_from_char(a[i]);
for (i = 0; i < 4; i++)
for (j = 0; j < 4; j++) {
int_t val[16];
read_next_values(f, val, 16);
int k, l;
for (k = 0; k < 4; k++)
for (l = 0; l < 4; l++)
(*t)[b[0]][b[1]][b[2]][b[3]][i][k][j][l] = val[4*k+l];
}
}
fclose(f);
}
static void read_int21(int use_dna_params, tab7_t *t)
{
fill7(t, NOT_A_NUMBER);
FILE *f = parfile("int21", use_dna_params);
look_for_line_containing(f, "5' --> 3'");
char buf[MAXLINE+1];
while (fgets(buf, MAXLINE, f)) {
if (strlen(buf) >= MAXLINE)
die("read_int21: line too long");
if (is_only_whitespace(buf))
continue;
look_for_line_containing(f, "5' --> 3'");
expect_line_containing(f, "X");
base_t b1[12], b2[12], b3[6];
read_next_line(f, buf);
read_twelve_bases(buf, b1);
read_next_line(f, buf);
read_twelve_bases(buf, b2);
read_next_line(f, buf);
read_six_bases(buf, b3);
expect_line_containing(f, "3' <-- 5'");
int i;
for (i = 0; i < 4; i++) {
int_t val[24];
read_next_values(f, val, 24);
int j, k;
for (j = 0; j < 6; j++)
for (k = 0; k < 4; k++)
(*t)[b1[2*j]][b2[2*j]][i][k][b3[j]][b1[2*j+1]][b2[2*j+1]] = val[4*j+k];
}
}
fclose(f);
}
static void read_dangle(int use_dna_params, tab3_t *d3p, tab3_t *d5p)
{
fill3(d3p, NOT_A_NUMBER);
fill3(d5p, NOT_A_NUMBER);
FILE *f = parfile("dangle", use_dna_params);
char buf[MAXLINE+1];
while (fgets(buf, MAXLINE, f)) {
if (strlen(buf) >= MAXLINE)
die("read_dangle: line too long");
if (is_only_whitespace(buf))
continue;
look_for_line_containing(f, "5' --> 3'");
read_next_line(f, buf);
tab3_t *d = strchr(buf,'X') ? d3p : d5p;
base_t a[4], b[4];
read_four_bases(buf, a);
read_next_line(f, buf);
read_four_bases(buf, b);
expect_line_containing(f, "3' <-- 5'");
int_t val[16];
read_next_values(f, val, 16);
int i, j;
for (i = 0; i < 4; i++)
for (j = 0; j < 4; j++)
(*d)[a[i]][b[i]][j] = val[4*i+j];
}
fclose(f);
}
static void read_miscloop(param_t p)
{
FILE *f = parfile("miscloop", p->use_dna_params);
p->Extrapolation_for_large_loops = next_value(f);
p->prelog = 10.79f;
p->maximum_correction = next_value(f);
p->fm_array_first_element = next_value(f);
int_t tmp[3];
look_for_arrow(f);
read_next_values(f, tmp, 3);
p->a = p->multibranched_loop_offset = tmp[0];
p->b = p->multibranched_loop_per_nuc_penalty = tmp[1];
p->c = p->multibranched_loop_helix_penalty = tmp[2];
p->a_2c = p->a + 2*p->c;
p->a_2b_2c = p->a + 2*p->b + 2*p->c;
look_for_arrow(f); /* skip efn2 params */
look_for_arrow(f); /* skip multiloop asym */
look_for_arrow(f); /* skip multiloop strain */
p->terminal_AU_penalty = next_value(f);
p->bonus_for_GGG_hairpin = next_value(f);
p->c_hairpin_slope = next_value(f);
p->c_hairpin_intercept = next_value(f);
p->c_hairpin_of_3 = next_value(f);
look_for_arrow(f); /* skip Intermolecular initiation */
p->Bonus_for_Single_C_bulges_adjacent_to_C = next_value(f);
fclose(f);
}
static void read_loop(param_t p)
{
FILE *f = parfile("loop", p->use_dna_params);
look_for_dashes(f);
char buf[MAXLINE+1];
int i;
for (i = 0; i <= LOOP_MAX; i++) {
p->internal_loop_initiation[i] = NOT_A_NUMBER;
p->bulge_loop_initiation[i] = NOT_A_NUMBER;
p->hairpin_loop_initiation[i] = NOT_A_NUMBER;
}
while (fgets(buf, MAXLINE, f)) {
if (strlen(buf) >= MAXLINE)
die("read_loop: line too long");
char fld[4][MAXLINE];
if (sscanf(buf, "%s%s%s%s", fld[0], fld[1], fld[2], fld[3]) != 4)
die("read_loop: could not find 4 fields");
const int i = atoi(fld[0]);
if (i <= 0 || i > LOOP_MAX)
die("read_loop: index out of range");
p->internal_loop_initiation[i] = value_from_string(fld[1]);
p->bulge_loop_initiation[i] = value_from_string(fld[2]);
p->hairpin_loop_initiation[i] = value_from_string(fld[3]);
}
fclose(f);
}
static void read_stack(const char *name, int use_dna_params, tab4_t *p)
{
fill4(p, NOT_A_NUMBER);
const int coaxial = !strcmp(name,"coaxial");
FILE *f = parfile(name, use_dna_params);
look_for_line_containing(f, "STACKING ENERGIES");
char buf[MAXLINE+1];
int i = 0, k = 0;
while (fgets(buf, MAXLINE, f)) {
if (strlen(buf) >= MAXLINE)
die("read_stack: line too long");
if (!strchr(buf,'.'))
continue;
int j = 0, l = 0;
char *b;
for (b = strtok(buf,whitespace); b; b = strtok(0,whitespace)) {
if (coaxial)
(*p)[j][i][k][l] = value_from_string(b);
else
(*p)[i][j][k][l] = value_from_string(b);
l++;
if (l == NBASE) {
j++;
l = 0;
}
}
k++;
if (k == NBASE) {
i++;
k = 0;
}
}
fclose(f);
}
void initial_params::save()
{
adstring extension;
if (current_phase == max_number_phases)
{
extension = "ar";
}
else if (current_phase >= 10)
{
extension = str(current_phase);
}
else
{
extension = "0" + str(current_phase);
}
{
adstring tadstring=ad_comm::adprogram_name + adstring(".p") + extension;
ofstream parfile((char*)tadstring);
if (parfile.good())
{
parfile << setshowpoint()
<< "# Number of parameters = " << initial_params::nvarcalc()
<< " Objective function value = " << *objective_function_value::pobjfun
<< " Maximum gradient component = " << objective_function_value::gmax
<< endl;
for (int i = 0; i < num_initial_params; ++i)
{
varsptr[i]->save_value(parfile);
}
}
}
{
adstring tadstring = ad_comm::adprogram_name + adstring(".b") + extension;
uostream barfile((char*)tadstring);
if (barfile.good())
{
for (int i = 0; i < num_initial_params; ++i)
{
(varsptr[i])->bsave_value(barfile);
}
}
}
}
