/* parse_param_line reads a line in the given parameter sets buffer and stores it in the given array of doubles
parameters:
params: the array of doubles to store the parameters in
buffer_line: the buffer with the line to read
index_buffer: the index of the buffer to start from
returns: true if a line was found, false if the end of the file was reached without finding a valid line
notes:
The buffer should contain one parameter set per line, each set containing comma-separated floating point parameters.
Blank lines and lines starting with # will be ignored.
Each line must contain the correct number of parameters or the program will exit.
index_buffer is a reference, allowing this function to store where it finished parsing.
todo:
*/
bool parse_param_line (double* params, char* buffer_line, int& index_buffer) {
static const char* usage_message = "There was an error reading the given parameter sets file.";
int index_params = 0; // Current index in params
int index_digits = index_buffer; // Index of the start of the digits to read
int i = index_buffer; // Current index in buffer_line
int line_start = i; // The start of the line, used to tell whether or not a line is empty
for (; not_EOL(buffer_line[i]); i++) {
if (buffer_line[i] == '#') { // Skip any lines starting with #
for(; not_EOL(buffer_line[i]); i++);
i++;
} else if (buffer_line[i] == ',') { // Indicates the end of the digits to read
if (sscanf(buffer_line + index_digits, "%lf", &(params[index_params++])) < 1) { // Convert the string of digits to a double when storing it in params
usage(usage_message);
}
index_digits = i + 1;
}
}
index_buffer = i + 1;
if (i - line_start > 0) { // This line has content
if (sscanf(buffer_line + index_digits, "%lf", &(params[index_params++])) < 1) {
usage(usage_message);
}
if (index_params != NUM_PARS) {
cout << term->red << "The given parameter sets file contains sets with an incorrect number of rates! This simulation requires " << NUM_PARS << " per set but at least one line contains " << index_params << " per set." << term->reset << endl;
exit(EXIT_INPUT_ERROR);
}
return true;
} else if (buffer_line[index_buffer] != '\0') { // There are more lines to try to parse
return parse_param_line(params, buffer_line, index_buffer);
} else { // The end of the buffer was found
return false;
}
}
void parse_params( char *env, char *cfgfile, char *argv[], int argc ) {
int i;
if ( env ) {
char *val = getenv( env );
if ( val )
parse_param_line( val );
}
if ( cfgfile ) {
char *cfg = xfind( cfgfile, getrundir());
#if DEBUG
printf( "*** ConfigFile '%s'\n", cfg );
#endif
parse_param_file( cfg );
}
for (i = 1; i < argc; i++)
parse_param( argv[i] );
}
void parse_param_file( char *file ) {
static char line1[ LINE_MAX ];
static char line[ LINE_MAX ] ;
FILE *fp;
assert( file != NULL );
fp = fopen( file, "rt" );
if (fp) {
while( fgets( line, LINE_MAX-1, fp ) ) {
int len = strlen( line );
if ( len > 0 && line[len-1] == '\n' )
line[len-1] = '\0';
scan_env(line1, line) ;
parse_param_line( line1 );
}
fclose( fp );
} else {
perror( file );
}
}
/*
load a default set of parameters from a file
*/
void Replay::load_param_file(const char *pfilename)
{
FILE *f = fopen(pfilename, "r");
if (f == NULL) {
printf("Failed to open parameter file: %s\n", pfilename);
exit(1);
}
char line[100];
while (fgets(line, sizeof(line)-1, f)) {
char *pname;
float value;
if (!parse_param_line(line, &pname, value)) {
continue;
}
struct user_parameter *u = new user_parameter;
strncpy(u->name, pname, sizeof(u->name));
u->value = value;
u->next = user_parameters;
user_parameters = u;
}
fclose(f);
}
/*
load a default set of parameters from a file
*/
bool AP_Param::load_defaults_file(const char *filename)
{
FILE *f = fopen(filename, "r");
if (f == NULL) {
return false;
}
char line[100];
/*
work out how many parameter default structures to allocate
*/
uint16_t num_defaults = 0;
while (fgets(line, sizeof(line)-1, f)) {
char *pname;
float value;
if (!parse_param_line(line, &pname, value)) {
continue;
}
if (!find_def_value_ptr(pname)) {
fclose(f);
return false;
}
num_defaults++;
}
fclose(f);
if (param_overrides != NULL) {
free(param_overrides);
}
num_param_overrides = 0;
param_overrides = new param_override[num_defaults];
if (param_overrides == NULL) {
return false;
}
/*
re-open to avoid possible seek issues with NuttX
*/
f = fopen(filename, "r");
if (f == NULL) {
return false;
}
uint16_t idx = 0;
while (fgets(line, sizeof(line)-1, f)) {
char *pname;
float value;
if (!parse_param_line(line, &pname, value)) {
continue;
}
const float *def_value_ptr = find_def_value_ptr(pname);
if (!def_value_ptr) {
fclose(f);
return false;
}
param_overrides[idx].def_value_ptr = def_value_ptr;
param_overrides[idx].value = value;
idx++;
enum ap_var_type var_type;
AP_Param *vp = AP_Param::find(pname, &var_type);
if (!vp) {
fclose(f);
return false;
}
vp->set_float(value, var_type);
}
fclose(f);
num_param_overrides = num_defaults;
return true;
}
void read_parameter_library(
char FN_parameter_library[MAX_CHARS],
int outlev
)
{
static ParameterEntry thisParameter;
FILE *parameter_library_file;
char parameter_library_line[MAX_CHARS];
int nfields;
int param_keyword = -1;
int int_hbond_type = 0;
pr(logFile, "Using read_parameter_library\n");
// Open and read the parameter library
//
if ((parameter_library_file = ag_fopen(FN_parameter_library, "r")) == NULL) {
fprintf(stderr,"Sorry, I can't find or open %s\n", FN_parameter_library);
exit(-1);
}
while (fgets(parameter_library_line, sizeof(parameter_library_line), parameter_library_file) != NULL) {
param_keyword = parse_param_line( parameter_library_line );
if (debug > 0) {
pr(logFile, "DEBUG: parameter_library_line = %sDEBUG: param_keyword = %d\n", parameter_library_line, param_keyword);
}
switch (param_keyword) {
case PAR_:
case PAR_NULL:
case PAR_COMMENT:
break;
case PAR_VDW:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_vdW);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the van der Waals term = \t%.4lf\n\n", AD4.coeff_vdW);
break;
case PAR_HBOND:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_hbond);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the H-bonding term = \t%.4lf\n\n", AD4.coeff_hbond);
break;
case PAR_ESTAT:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_estat);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the electrostatic term = \t%.4lf\n\n", AD4.coeff_estat);
break;
case PAR_DESOLV:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_desolv);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the desolvation term = \t%.4lf\n\n", AD4.coeff_desolv);
break;
case PAR_TORS:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_tors);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the torsional term = \t%.4lf\n\n", AD4.coeff_tors);
break;
case PAR_ATOM_PAR:
// Read in one line of atom parameters;
// NB: scanf doesn't try to write missing fields
nfields = sscanf(parameter_library_line, "%*s %s %lf %lf %lf %lf %lf %lf %d %d %d %d",
thisParameter.autogrid_type,
&thisParameter.Rij,
&thisParameter.epsij,
&thisParameter.vol,
&thisParameter.solpar,
&thisParameter.Rij_hb,
&thisParameter.epsij_hb,
&int_hbond_type,
&thisParameter.rec_index,
&thisParameter.map_index,
&thisParameter.bond_index);
if (nfields < 2) {
continue; // skip any parameter_library_line without enough info
}
if (int_hbond_type == 0) {
thisParameter.hbond = NON;
} else if (int_hbond_type == 1) {
thisParameter.hbond = DS;
} else if (int_hbond_type == 2) {
thisParameter.hbond = D1;
} else if (int_hbond_type == 3) {
thisParameter.hbond = AS;
} else if (int_hbond_type == 4) {
thisParameter.hbond = A1;
} else if (int_hbond_type == 5) {
thisParameter.hbond = A2;
} else {
thisParameter.hbond = NON;
}
thisParameter.epsij *= AD4.coeff_vdW;
thisParameter.epsij_hb *= AD4.coeff_hbond;
apm_enter(thisParameter.autogrid_type, thisParameter);
pr(logFile, "Parameters for the atom type named \"%s\" were read in from the parameter library as follows:\n", thisParameter.autogrid_type);
if (outlev > 2) {
pr(logFile, "\tR-eqm = %5.2f Angstrom\n\tweighted epsilon = %5.3f\n\tAtomic fragmental volume = %5.3f\n\tAtomic solvation parameter = %5.3f\n\tH-bonding R-eqm = %5.3f\n\tweighted H-bonding epsilon = %5.3f\n\tH-bonding type = %d, bond index = %d\n\n",
thisParameter.Rij, thisParameter.epsij, thisParameter.vol, thisParameter.solpar,
thisParameter.Rij_hb, thisParameter.epsij_hb, thisParameter.hbond, thisParameter.bond_index );
} else {
pr(logFile, "\tR-eqm = %.2f Angstrom, weighted epsilon = %.3f, At.frag.vol. = %.3f, At.solv.par. = %.3f, \n\tHb R-eqm = %.3f, weighted Hb epsilon = %.3f, Hb type = %d, bond index = %d\n\n",
thisParameter.Rij, thisParameter.epsij, thisParameter.vol, thisParameter.solpar,
thisParameter.Rij_hb, thisParameter.epsij_hb, thisParameter.hbond, thisParameter.bond_index );
}
break;
default:
break;
} // switch
} // while there is another line of parameters to read in
}
void setup_parameter_library( int outlev )
{
static ParameterEntry thisParameter;
char parameter_library_line[MAX_CHARS];
int nfields;
int param_keyword = -1;
int int_hbond_type = 0;
register int counter = 0;
pr(logFile, "Setting up parameter library with factory defaults.\n\n\n");
// Default parameters
//
// These are set up in "default_parameters.h"
// and stored in the param_string[MAX_LINES] array
while ( param_string[counter] != NULL) {
param_keyword = parse_param_line( param_string[counter] );
(void)strcpy(parameter_library_line, param_string[counter]);
counter++;
if (debug > 0) {
pr(logFile, "DEBUG: parameter_library_line = %sDEBUG: param_keyword = %d\n", parameter_library_line, param_keyword);
}
switch (param_keyword) {
case PAR_:
case PAR_NULL:
case PAR_COMMENT:
break;
case PAR_VDW:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_vdW);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the van der Waals term = \t%.4lf\n\n", AD4.coeff_vdW);
break;
case PAR_HBOND:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_hbond);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the H-bonding term = \t%.4lf\n\n", AD4.coeff_hbond);
break;
case PAR_ESTAT:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_estat);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the electrostatic term = \t%.4lf\n\n", AD4.coeff_estat);
break;
case PAR_DESOLV:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_desolv);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the desolvation term = \t%.4lf\n\n", AD4.coeff_desolv);
break;
case PAR_TORS:
nfields = sscanf(parameter_library_line, "%*s %lf", &AD4.coeff_tors);
if (nfields < 1) {
pr( logFile, "%s: WARNING: Please supply a coefficient as a floating point number.\n\n", programname);
continue; // skip any parameter_library_line without enough info
}
pr( logFile, "Free energy coefficient for the torsional term = \t%.4lf\n\n", AD4.coeff_tors);
break;
case PAR_ATOM_PAR:
// Read in one line of atom parameters;
// NB: scanf doesn't try to write missing fields
nfields = sscanf(parameter_library_line, "%*s %s %lf %lf %lf %lf %lf %lf %d %d %d %d",
thisParameter.autogrid_type,
&thisParameter.Rij,
&thisParameter.epsij,
&thisParameter.vol,
&thisParameter.solpar,
&thisParameter.Rij_hb,
&thisParameter.epsij_hb,
&int_hbond_type,
&thisParameter.rec_index,
&thisParameter.map_index,
&thisParameter.bond_index);
if (nfields < 2) {
continue; // skip any parameter_library_line without enough info
}
if (int_hbond_type == 0) {
thisParameter.hbond = NON;
} else if (int_hbond_type == 1) {
thisParameter.hbond = DS;
} else if (int_hbond_type == 2) {
thisParameter.hbond = D1;
} else if (int_hbond_type == 3) {
thisParameter.hbond = AS;
} else if (int_hbond_type == 4) {
thisParameter.hbond = A1;
} else if (int_hbond_type == 5) {
thisParameter.hbond = A2;
} else {
thisParameter.hbond = NON;
}
thisParameter.epsij *= AD4.coeff_vdW;
thisParameter.epsij_hb *= AD4.coeff_hbond;
apm_enter(thisParameter.autogrid_type, thisParameter);
pr(logFile, "Parameters for the atom type named \"%s\" were read in from the parameter library as follows:\n", thisParameter.autogrid_type);
if (outlev > 2) {
pr(logFile, "\tR-eqm = %5.2f Angstrom\n\tweighted epsilon = %5.3f\n\tAtomic fragmental volume = %5.3f\n\tAtomic solvation parameter = %5.3f\n\tH-bonding R-eqm = %5.3f\n\tweighted H-bonding epsilon = %5.3f\n\tH-bonding type = %d, bond index = %d\n\n",
thisParameter.Rij, thisParameter.epsij, thisParameter.vol, thisParameter.solpar,
thisParameter.Rij_hb, thisParameter.epsij_hb, thisParameter.hbond, thisParameter.bond_index );
} else {
pr(logFile, "\tR-eqm = %.2f Angstrom, weighted epsilon = %.3f, At.frag.vol. = %.3f, At.solv.par. = %.3f, \n\tHb R-eqm = %.3f, weighted Hb epsilon = %.3f, Hb type = %d, bond index = %d\n\n",
thisParameter.Rij, thisParameter.epsij, thisParameter.vol, thisParameter.solpar,
thisParameter.Rij_hb, thisParameter.epsij_hb, thisParameter.hbond, thisParameter.bond_index );
}
break;
default:
break;
} // switch
} // while there is another line of parameters to read in
}