static int readline_intrinsic_internal (Slsh_Readline_Type *sri, char *prompt, int noecho)
{
char *line;
if (sri == NULL)
sri = Intrinsic_Rline_Info;
#if USE_SLANG_READLINE
if ((sri == NULL) && Use_Readline)
{
Intrinsic_Rline_Info = open_slsh_readline (NULL, SL_RLINE_BLINK_MATCH);
if (Intrinsic_Rline_Info == NULL)
return -1;
(void) SLang_add_cleanup_function (close_intrinsic_readline);
sri = Intrinsic_Rline_Info;
}
#endif
enable_keyboard_interrupt ();
line = read_input_line (sri, prompt, noecho);
if (noecho == 0)
(void) save_input_line (sri, line);
(void) SLang_push_malloced_string (line);
return 0;
}
void compile_file(const char *src, const char *dest){
printf("Compiling file: %s into %s\n", src, dest);
printf("Initializing compiler...\n");
compile_init();
open_input_m4(src);
codelist_entry *entry;
while(is_input_open()){
while(read_input_line()){
entry = process_line();
if(entry != NULL){
printf("Adding codelist entry...\n");
add_codelist_entry(entry);
}
}
close_input();
}
close_input();
compile_cleanup();
}
/* Returns a malloced value */
static char *get_input_line (SLang_Load_Type *x)
{
char *line;
int parse_level;
int free_prompt = 0;
char *prompt;
parse_level = x->parse_level;
if (Prompt_Hook != NULL)
{
if ((-1 == SLang_start_arg_list ())
|| (-1 == SLang_push_int (parse_level))
|| (-1 == SLang_end_arg_list ())
|| (-1 == SLexecute_function (Prompt_Hook))
|| (-1 == SLang_pop_slstring (&prompt)))
{
SLang_verror (SL_RunTime_Error, "Disabling prompt hook");
SLang_free_function (Prompt_Hook);
Prompt_Hook = NULL;
return NULL;
}
free_prompt = 1;
}
else if (parse_level == 0)
prompt = (char *) "slsh> ";
else
prompt = (char *) " ";
if (parse_level == 0)
{
if (-1 == SLang_run_hooks ("slsh_interactive_before_hook", 0))
{
if (free_prompt)
SLang_free_slstring (prompt);
return NULL;
}
}
line = read_input_line (Default_Readline_Info, prompt, 0);
if (free_prompt)
SLang_free_slstring (prompt);
if ((line == NULL)
&& (parse_level == 0)
&& (SLang_get_error() == 0))
{
Slsh_Quit = 1;
return NULL;
}
if (line == NULL)
{
return NULL;
}
/* This hook is used mainly for logging input */
(void) SLang_run_hooks ("slsh_interactive_after_hook", 1, line);
(void) save_input_line (Default_Readline_Info, line);
return line;
}
static int ReadQuotas(int i)
{
#ifdef _WINDOWS
HANDLE hin;
DWORD savemode, newmode;
hin = GetStdHandle(STD_INPUT_HANDLE);
GetConsoleMode(hin, &savemode);
newmode = savemode | ENABLE_PROCESSED_INPUT | ENABLE_LINE_INPUT;
newmode &= ~ENABLE_ECHO_INPUT;
SetConsoleMode(hin, newmode);
while (bytesAvailable[i] == 0)
{
DWORD read;
BOOL r;
char buffer[21];
r = ReadFile(hin, buffer, 20, &read, 0);
if (!r || read == 0)
fatalbox("ReadFile failed in ReadQuotas");
buffer[read] = 0;
if (buffer[0] != '-')
{
if (input_pushback != 0)
fatalbox("input_pushback not null!");
else
input_pushback = strdup(buffer);
}
else
ProcessQuotaCmd(buffer);
}
SetConsoleMode(hin, savemode);
#else
char* line;
while (bytesAvailable[i] == 0)
{
int error = 0;
line = read_input_line(1, &error);
if (line == NULL || error)
{
fatalbox("read_input_line failed in ReadQuotas");
break;
}
if (line[0] != '-')
{
if (input_pushback != 0)
fatalbox("input_pushback not null!");
else
input_pushback = strdup(line);
}
else
ProcessQuotaCmd(line);
sfree(line);
}
#endif //_WINDOWS
return 1;
}
ErrorCode init_dsa(const char* cfg)
{
ErrorCode error = NO_ERROR;
char *linehead = NULL;
char *energyname = NULL;
char *energycfg = NULL;
char *rbasinsname = NULL;
char *rbasinscfg = NULL;
printf(" Initializing DSA sampler...\n");
if (open_input_text_file(cfg) == NO_ERROR)
{
while (read_input_line())
{
get_input_strval(&linehead, "=", 0);
if (strcmp(linehead, "ENERGY FUNCTION") == 0)
{
get_input_strval(&energyname, "=", 1);
}
else if (strcmp(linehead, "ENERGY CONFIG") == 0)
{
get_input_strval(&energycfg, "=", 1);
}
else if (strcmp(linehead, "RB CALCULATOR") == 0)
{
get_input_strval(&rbasinsname, "=", 1);
}
else if (strcmp(linehead, "RB CONFIG") == 0)
{
get_input_strval(&rbasinscfg, "=", 1);
}
else
{
print_error(UNKNOWN_PARAMETER_ERROR, "init_oops", 2, "header ", linehead);
}
free(linehead);
linehead = NULL; // Make sure of set this string pointer to NULL, beacause it will be used again when reading the next line.
}
close_input_file();
}
error = get_energy_module(&energymod, energyname);
if (error != NO_ERROR)
{
print_error(error, "init_dsa", 1, " when getting energy module");
}
free(energyname);
error = get_custom_module(&rbasinsmod, rbasinsname);
if (error != NO_ERROR)
{
print_error(error, "init_dsa", 1, " when getting rbasins module");
}
free(rbasinsname);
// Initializing energy module.
execute_init_func_energy_module(energymod, energycfg);
free(energycfg);
// Initializing rbasins module.
execute_init_func_custom_module(rbasinsmod, rbasinscfg);
free(rbasinscfg);
// Calculating initial assignement of torsional angles for the whole system.
update_all_torsional_angles(residues, chains, nchains, coords);
// Initializing global variables..
T = 350.0;
create_bool_array(&flags, nres);
printf(" Done.\n");
return error;
}
ErrorCode init_dopecb(const char* cfg)
{
debug=0;
nactivepairs=0;
natoms2=natoms*natoms;
create_float_array(&pairenergies,natoms2);
create_index_array(&pairrows,natoms2);
create_index_array(&updatepairs,natoms2);
create_index_array(&activepairs,natoms2);
BINSIZE=DISTANCECUTOFF/NUMBINS;
printf(" Initializing DOPE function...\n");
printf(" Loading Parameter file...\n");
char *linehead = NULL;
char *parfilename = NULL;
if (open_input_text_file(cfg) == NO_ERROR)
{
while (read_input_line())
{
get_input_strval(&linehead, "=", 0);
char firstchar=linehead[0];
if (firstchar=='#') {
free(linehead);
linehead = NULL;
continue;
}
if (strcmp(linehead, "PARFILE") == 0)
{
get_input_strval(&parfilename, "=,", 1);
}
else if (strcmp(linehead, "DEBUG") == 0)
{
get_input_ival(&debug, "=,", 1);
}
else
{
print_error(UNKNOWN_PARAMETER_ERROR, "init_debug", 0);
printf("...line: %s\n",linehead);
}
free(linehead);
linehead = NULL; // Make sure of set this string pointer to NULL, beacause it will be used again when reading the next line.
}
close_input_file();
}
load_dopecb_parfile(parfilename);
free(parfilename);
//check to make sure dope is loaded correctly
IndexValue i,j,k,l,m;
if (debug){
for (i=0;i<MAXAACODE;i++)
for(j=0;j<MAXATCODE;j++)
for(k=0;k<MAXAACODE;k++)
for(l=0;l<MAXATCODE;l++){
//printf("%i %i %i %i ",i,j,k,l);
printf("%s(%i) %s(%i) %s(%i) %s(%i)",aacodetoonelet[i+1],i,dopecodetolet[j],j,aacodetoonelet[k+1],k,dopecodetolet[l],l);
for(m=0;m<=MAXBINNUM;m++){
printf(" %4.2f ",dopeenergies[convert_to_dopecb_row(i,j,k,l)+m]);
}
printf("\n");
}
}
IndexValue resi,typei,restypei,resj,typej,restypej;
for (i=0;i<natoms;i++){
IndexValue dopeattypei=convtodope[atoms[i].type];
typei=atoms[i].niprop=dopeattypei;
resi=atoms[i].res; // starts from 0
restypei=residues[resi].type-1; //starts from 1
//atoms[i].niprop=0;
//if (debug) printf("%i) Atom: %i, Type: %i,Residue type: %i\n",resi,i,typei,restypei);
for (j=0;j<natoms;j++){
IndexValue dopeattypej=convtodope[atoms[j].type];
typej=atoms[j].niprop=dopeattypej;
resj=atoms[j].res; // starts from 0
restypej=residues[resj].type-1; //starts from 1
pairrows[natoms*i+j]=pairrows[natoms*j+i]=convert_to_dopecb_row(restypei,typei,restypej,typej);
//printf("Dope Row: %i,idx1: %i, idx2: %i\n",row,idx1,idx2);
if (resj>resi+0) { //change this to reflect ii+n only
activepairs[2*nactivepairs]=i;
activepairs[2*nactivepairs+1]=j;
nactivepairs+=1;
}
pairenergies[natoms*i+j]=0;
}
}
printf(" Done.\n");
return NO_ERROR;
}