void destroy_eval__safe() {
prim_container *c = all_prims;
while (c != NULL) {
prim_container *t;
free_malloced(c->prim);
t = c;
c = c->next;
free_malloced(t);
}
/* Frees containers and non heap values (?) held in
environments. */
destroy_env(&special_forms);
destroy_env(&toplevel);
destroy_env(&primitives);
destroy_env(&lib);
destroy_env(&internal);
//orig_sexpr == NULL;
//*live_root;
/* This will free resources held by symbol representation. */
free_symtab(global_symtab);
global_symtab = NULL;
__gs.head = NULL;
}
static void
write_resolution (void)
{
unsigned int i;
FILE *f;
check (resolution_file, LDPL_FATAL, "resolution file not specified");
f = fopen (resolution_file, "w");
check (f, LDPL_FATAL, "could not open file");
fprintf (f, "%d\n", num_claimed_files);
for (i = 0; i < num_claimed_files; i++)
{
struct plugin_file_info *info = &claimed_files[i];
struct plugin_symtab *symtab = &info->symtab;
struct ld_plugin_symbol *syms = symtab->syms;
get_symbols (info->handle, symtab->nsyms, syms);
finish_conflict_resolution (symtab, &info->conflicts);
fprintf (f, "%s %d\n", info->name, symtab->nsyms + info->conflicts.nsyms);
dump_symtab (f, symtab);
if (info->conflicts.nsyms)
{
dump_symtab (f, &info->conflicts);
free_symtab (&info->conflicts);
}
}
fclose (f);
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time, *step;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = nullptr;
atoms.pdbinfo = nullptr;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
fr->step = 0;
step = std::strstr(title, " step= ");
fr->bStep = ((step != nullptr) && sscanf(step+7, "%" SCNd64, &fr->step) == 1);
dbl = 0.0;
time = std::strstr(title, " t= ");
fr->bTime = ((time != nullptr) && sscanf(time+4, "%lf", &dbl) == 1);
fr->time = dbl;
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
void
clear_profiler()
{
if (!newprofile) {
newprofile = true;
profile = false;
traversed = false;
free_tree(calltree);
calltree = NULL;
free_symtab();
symtab = NULL;
}
}
void Estimator_Destroy(Estimator_type * est)
{
prng_Destroy(est->prng);
for(int i=0; i < est->c; i++)
{
Sample_Destroy(est->samplers[i]);
}
free(est->samplers);
Freq_Destroy(est->freq);
free_bheap(est->bheap);
free_heap(est->prim_heap);
free_symtab(est->hashtable);
free(est);
}
static void read_whole_conf(const char *infile, char *title,
t_atoms *atoms, rvec x[], rvec *v, matrix box)
{
FILE *in;
int ndec;
t_symtab symtab;
/* open file */
in = gmx_fio_fopen(infile, "r");
open_symtab(&symtab);
get_w_conf(in, infile, title, &symtab, atoms, &ndec, x, v, box);
/* We can't free the symbols, as they are still used in atoms, so
* the only choice is to leak them. */
free_symtab(&symtab);
gmx_fio_fclose(in);
}
static void
write_resolution (void)
{
unsigned int i;
FILE *f;
check (resolution_file, LDPL_FATAL, "resolution file not specified");
f = fopen (resolution_file, "w");
check (f, LDPL_FATAL, "could not open file");
fprintf (f, "%d\n", num_claimed_files);
for (i = 0; i < num_claimed_files; i++)
{
struct plugin_file_info *info = &claimed_files[i];
struct plugin_symtab *symtab = &info->symtab;
struct ld_plugin_symbol *syms = symtab->syms;
/* Version 2 of API supports IRONLY_EXP resolution that is
accepted by GCC-4.7 and newer. */
if (get_symbols_v2)
get_symbols_v2 (info->handle, symtab->nsyms, syms);
else
get_symbols (info->handle, symtab->nsyms, syms);
finish_conflict_resolution (symtab, &info->conflicts);
fprintf (f, "%s %d\n", info->name, symtab->nsyms + info->conflicts.nsyms);
dump_symtab (f, symtab);
if (info->conflicts.nsyms)
{
dump_symtab (f, &info->conflicts);
free_symtab (&info->conflicts);
}
}
fclose (f);
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = NULL;
atoms.pdbinfo = NULL;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, NULL);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
if (model_nr != -1)
{
fr->bStep = TRUE;
fr->step = model_nr;
}
time = std::strstr(title, " t= ");
if (time)
{
fr->bTime = TRUE;
sscanf(time+4, "%lf", &dbl);
fr->time = (real)dbl;
}
else
{
fr->bTime = FALSE;
/* this is a bit dirty, but it will work: if no time is read from
comment line in pdb file, set time to current frame number */
if (fr->bStep)
{
fr->time = (real)fr->step;
}
else
{
fr->time = (real)nframes_read(status);
}
}
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
void decode(char *read_line,ssize_t read_len,char **label,char **pneumonic,char **operand,char *int_filename,FILE *inp_file,FILE *int_file,FILE *out_file,char ***optab,int num_ops,sym_tab *symtab,long int LOCCTR,char *read_raw_line)
{
(*label)=NULL;
(*pneumonic)=NULL;
(*operand)=NULL;
char *work_string;
if( (work_string=malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
if(inp_file)
fclose(inp_file);
if(int_file)
fclose(int_file);
if(out_file)
fclose(out_file);
if(int_filename)
free(int_filename);
if(read_raw_line)
free(read_raw_line);
else
free(read_line);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(12);
}
sscanf(read_line,"%s",work_string);
if( work_string[strlen(work_string)-1] == ':' )
(*label)=work_string;
else
free(work_string);
work_string=NULL;
if( (work_string=malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
if(inp_file)
fclose(inp_file);
if(int_file)
fclose(int_file);
if(out_file)
fclose(out_file);
if(int_filename)
free(int_filename);
if(read_raw_line)
free(read_raw_line);
else
free(read_line);
if((*pneumonic))
free((*pneumonic));
else
free((*label));
free_optab(optab,num_ops);
free_symtab(symtab);
exit(12);
}
if((*label))
{
strcpy(work_string,"");
sscanf(strstr(read_line,(*label))+strlen((*label)),"%s",work_string);
if((*work_string)=='\0')
{
printf("Bad Assembly coding...\n");
printf("No peumonic corresponding to label at %lX\n",LOCCTR);
if(inp_file)
fclose(inp_file);
if(int_file)
fclose(int_file);
if(out_file)
fclose(out_file);
if(int_filename)
free(int_filename);
if(read_raw_line)
free(read_raw_line);
else
free(read_line);
free((*label));
free(work_string);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(12);
}
(*pneumonic)=work_string;
work_string=NULL;
if( (work_string=malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
if(inp_file)
fclose(inp_file);
if(int_file)
fclose(int_file);
if(out_file)
fclose(out_file);
if(int_filename)
free(int_filename);
if(read_raw_line)
free(read_raw_line);
else
free(read_line);
free((*label));
free((*pneumonic));
free_optab(optab,num_ops);
free_symtab(symtab);
exit(14);
}
strcpy(work_string,"");
sscanf(strstr(read_line,(*pneumonic))+strlen((*pneumonic)),"%s",work_string);
if((*work_string)!='\0')
(*operand)=work_string;
else
free(work_string);
}
else
{
sscanf(read_line,"%s",work_string);
(*pneumonic)=work_string;
work_string=NULL;
if( (work_string=malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
if(inp_file)
fclose(inp_file);
if(int_file)
fclose(int_file);
if(out_file)
fclose(out_file);
if(int_filename)
free(int_filename);
if(read_raw_line)
free(read_raw_line);
else
free(read_line);
free((*pneumonic));
free_optab(optab,num_ops);
free_symtab(symtab);
exit(14);
}
strcpy(work_string,"");
sscanf(strstr(read_line,(*pneumonic))+strlen((*pneumonic)),"%s",work_string);
if((*work_string)=='\0')
free(work_string);
else
{
(*operand)=work_string;
work_string=NULL;
}
}
}
int main(int argc,char *argv[])
{
if(argc!=2)
{
printf("Usage: %s <input file>\n",argv[0]);
exit(1);
}
/* Load Optab */
char ***optab=NULL;
int num_ops;
if( (optab=load_optab("opfile",&num_ops)) == NULL)
{
printf("Optab generation failed\n");
exit(2);
}
/* Now let us load and initialize the symtab */
sym_tab *symtab=NULL;
if( (symtab=init_symtab())==NULL )
{
printf("Failed to initiate symtab\n");
free_optab(optab,num_ops);
exit(3);
}
FILE *inp_file=NULL;
if( (inp_file=fopen(argv[1],"r")) == NULL )
{
printf("Failed to open input file\n");
free_optab(optab,num_ops);
free_symtab(symtab);
exit(4);
}
FILE *out_file=NULL;
char *int_filename=NULL;
if( (int_filename=(char *)malloc(strlen(argv[1])+5)) == NULL )
{
printf("Out of memory\n");
free_optab(optab,num_ops);
free_symtab(symtab);
exit(5);
}
strcpy(int_filename,argv[1]);
strcat(int_filename,"_INT");
FILE *int_file=NULL;
if( (int_file=fopen(int_filename,"w+")) == NULL )
{
printf("Failed to open intermediate file\n");
free_optab(optab,num_ops);
free_symtab(symtab);
free(int_filename);
fclose(inp_file);
exit(6);
}
/* And Here We Go */
long int LOCCTR=0;
long int start_addr;
char *read_line=NULL;
size_t to_read = 0;
ssize_t read_len;
char *work_string=NULL;
char *work_string2=NULL;
char *prog_name=NULL;
char *search_space=NULL;
int start_loop=0;
while( (read_len=getline(&read_line,&to_read,inp_file)) != -1 )
{
if( (search_space=(char *)malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(10);
}
strcpy(search_space,"");
sscanf(read_line,"%s",search_space);
if(((*search_space)=='\0')||((*search_space)==';'))
{
free(search_space);
search_space=NULL;
free(read_line);
read_line=NULL;
continue;
}
free(search_space);
search_space=NULL;
if( (prog_name=malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(7);
}
if( (work_string=malloc( (read_len-strlen(prog_name)) +1) ) == NULL)
{
printf("Out of memory\n");
fclose(inp_file);
fclose(int_file);
free(prog_name);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(7);
}
sscanf(read_line,"%s%s",prog_name,work_string);
if(!strcmp(work_string,"START"))
{
if( (work_string2=malloc((read_len-strlen(work_string))+1)) == NULL )
{
free(work_string);
free(prog_name);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
printf("Out of memory\n");
exit(8);
}
char *searched=strstr(read_line,work_string);
sscanf(searched+strlen(work_string),"%s",work_string2);
if((*work_string2)=='\0')
{
printf("START directive requires an argument\n");
free(work_string);
free(prog_name);
free(work_string2);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(9);
}
char *waste;
LOCCTR=strtol(work_string2,&waste,16);
if(waste == work_string2)
{
printf("Bad Assembly coding...\n");
printf("No suitable value for operand for START directive\n");
free(work_string);
free(prog_name);
free(work_string2);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(9);
}
start_addr=LOCCTR;
fprintf(int_file,"%lX\t%s\t%s\t%lX\n",LOCCTR,prog_name,work_string,start_addr);
free(work_string2);
free(prog_name);
prog_name=NULL;
free(work_string);
work_string=NULL;
free(read_line);
read_line=NULL;
to_read=0;
while( (read_len=getline(&read_line,&to_read,inp_file)) != -1)
{
if( (search_space=(char *)malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(10);
}
strcpy(search_space,"");
sscanf(read_line,"%s",search_space);
if(((*search_space)=='\0')||((*search_space)==';'))
{
free(search_space);
search_space=NULL;
free(read_line);
read_line=NULL;
continue;
}
free(search_space);
search_space=NULL;
break;
}
start_loop=1;
}
else
{
LOCCTR=start_addr=0;
start_loop=1;
}
if(start_loop)
break;
}
// Check if the loop exited becuase the EOF was reached. If so exit...
if(read_len == -1)
{
if(read_line)
free(read_line);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(0);
}
if( (work_string=malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(11);
}
char *label=NULL;
char *pneumonic=NULL;
char *operand=NULL;
decode(read_line,read_len,&label,&pneumonic,&operand,int_filename,inp_file,int_file,NULL,optab,num_ops,symtab,LOCCTR,NULL);
if(label)
label[strlen(label)-1]='\0';
while(strcmp(pneumonic,"END"))
{
if(label)
fprintf(int_file,"%lX\t%s\t%s\t%s\n",LOCCTR,label,pneumonic,operand);
else
{
if(operand)
fprintf(int_file,"%lX\t%s\t%s\n",LOCCTR,pneumonic,operand);
else
fprintf(int_file,"%lX\t%s\n",LOCCTR,pneumonic);
}
if(label)
{
label[strlen(label)-1]='\0';
if(search_symtab(symtab,label)>0)
{
printf("Duplicate symbol at %lX\n",LOCCTR);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(12);
}
else
{
if(insert_symtab(label,symtab,LOCCTR)!=0)
{
printf("Failed to insert into symtab\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(13);
}
}
}
char *opcode,*waste;
if( (opcode=search_optab(optab,pneumonic,num_ops)) != NULL)
{
LOCCTR+=3;
}
else if(!strcmp(pneumonic,"WORD"))
{
LOCCTR+=3;
}
else if(!strcmp(pneumonic,"RESW"))
{
if(operand == NULL)
{
printf("Bad assembly coding...\n");
printf("No value given for operand near RESW directive at %lX\n",LOCCTR);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(23);
}
else
{
LOCCTR+=(3*strtol(operand,&waste,10));
if(waste == operand)
{
printf("Bad assembly coding...\n");
printf("No suitable value was found for allocating memory for RESW directive at %lX\n",LOCCTR);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(21);
}
}
}
else if(!strcmp(pneumonic,"RESB"))
{
if(operand == NULL)
{
printf("Bad assembly coding...\n");
printf("No value given for operand near RESB directive at %lX\n",LOCCTR);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(23);
}
else
{
LOCCTR+=(strtol(operand,&waste,10));
if(waste == operand)
{
printf("Bad assembly coding...\n");
printf("No suitable value was found for allocating memory for RESB directive at %lX\n",LOCCTR);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(22);
}
}
}
else if(!strcmp(pneumonic,"BYTE"))
{
long int old_locctr=LOCCTR;
if(!operand)
{
printf("Bad assembly coding...\n");
printf("No operand corresponding to BYTE directive at %lX\n",LOCCTR);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(52);
}
if( ((*operand)=='c')|| ((*operand)=='C'))
LOCCTR+=(strlen(operand)-3);
else if( ((*operand)=='x')|| ((*operand)=='X'))
{
LOCCTR+=(strlen(operand)-3)/2;
if( (strlen(operand)-3)%2)
LOCCTR+=1;
}
else
{
printf("Bad assembly coding...\n");
printf("Wrong format for constant\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(14);
}
if( (LOCCTR-old_locctr)>MC_SIZE )
{
printf("Constant value too long...\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(50);
}
if( !( (strlen(operand)>=4)&&(operand[1]=='\'')&&(operand[strlen(operand)-1]=='\'') ) )
{
printf("Format for constant is convoluted at %lX...\n",old_locctr);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(51);
}
}
else
{
printf("Opcode not found at %lX...\n",LOCCTR);
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(15);
}
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
read_line=NULL;
to_read=0;
while( (read_len=getline(&read_line,&to_read,inp_file)) != -1)
{
if( (search_space=(char *)malloc(read_len+1)) == NULL )
{
printf("Out of memory\n");
fclose(inp_file);
fclose(int_file);
free(int_filename);
free(read_line);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(10);
}
strcpy(search_space,"");
sscanf(read_line,"%s",search_space);
if(((*search_space)=='\0')||((*search_space)==';'))
{
free(search_space);
search_space=NULL;
free(read_line);
read_line=NULL;
continue;
}
free(search_space);
search_space=NULL;
break;
}
if(read_len == -1)
{
printf("Bad assembly coding...\n");
printf("End of file was reached before END directive\n");
fclose(int_file);
fclose(inp_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(16);
}
label=NULL;
pneumonic=NULL;
operand=NULL;
decode(read_line,read_len,&label,&pneumonic,&operand,int_filename,inp_file,int_file,NULL,optab,num_ops,symtab,LOCCTR,NULL);
}
//First Pass finished... Beginning second pass
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
fprintf(int_file,"%lX\t%s",LOCCTR,read_line);
free(read_line);
label=NULL;
operand=NULL;
pneumonic=NULL;
read_line=NULL;
fclose(inp_file);
out_file=fopen("a.out","w+");
if( out_file == NULL)
{
printf("Failed to open output file...\n");
fclose(int_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(30);
}
//Write out the intermediate file and re-open it for second pass
fclose(int_file);
int_file=fopen(int_filename,"r");
if( int_file == NULL)
{
printf("Failed to open intermediate file...\n");
fclose(out_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(31);
}
int_file=fopen(int_filename,"r");
if( int_file == NULL)
{
printf("Failed to open intermediate file...\n");
fclose(out_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(31);
}
char *read_raw_line=NULL;
char string_loc[35];
while( (read_len=getline(&read_raw_line,&to_read,int_file)) != -1)
{
read_raw_line[strlen(read_raw_line)-1]='\0';
fprintf(out_file,"%s",read_raw_line);
read_raw_line[strlen(read_raw_line)]='\n';
memset(mc,0,MC_SIZE);
//We dont have to worry about about newlines spaces etc
sscanf(read_raw_line,"%s",string_loc);
read_line=read_raw_line+strlen(string_loc)+1;
decode(read_line,read_len,&label,&pneumonic,&operand,int_filename,NULL,int_file,out_file,optab,num_ops,symtab,LOCCTR,read_raw_line);
if(!label)
fprintf(out_file,"\t");
if(!operand)
fprintf(out_file,"\t");
char *opcode;
long int add;
if( (opcode=search_optab(optab,pneumonic,num_ops)) != NULL )
{
sprintf(mc,"%s",opcode);
if(operand)
{
if( (add=search_symtab(symtab,operand)) > 0 )
{
sprintf(mc+strlen(mc),"%lX",add);
}
else
{
printf("Operand not available in symbol table\n");
fclose(int_file);
fclose(out_file);
free(int_filename);
free(read_raw_line);
free_optab(optab,num_ops);
free_symtab(symtab);
exit(35);
}
}
}
else if(!strcmp(pneumonic,"BYTE"))
{
convert_const(&operand);
}
read_raw_line[strlen(read_raw_line)-1]='\0';
fprintf(out_file,"\t\t%s\n",mc);
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
label=pneumonic=operand=NULL;
free(read_raw_line);
read_raw_line=NULL;
}
if(label)
free(label);
if(operand)
free(operand);
if(pneumonic)
free(pneumonic);
fclose(int_file);
fclose(out_file);
free(int_filename);
free_optab(optab,num_ops);
free_symtab(symtab);
return 0;
}
void
iprofiletable()
{
nialptr result; /* result to be returned */
int c1,
c2;
int num_funs = 0; /* total number of used functions */
int pos = 0; /* current count of used fucntions */
if (newprofile) {
buildfault("no profile available");
return;
}
#ifndef OLD_BUILD_SYMBOL_TABLE
if (symtab)
free_symtab();
symtab = NULL;
build_symbol_table();
#endif
/* If profiling is still on, then turn it off */
if (profile == true) {
apush(createbool(0));
isetprofile();
apop();
}
/* traverse the call tree placing nodes in the symbol table entries */
if (!traversed) {
traverse_tree(calltree);
traversed = true;
}
/* count the number of called functions so we know how big to
make the container array. Funcitons in the symbol table that
are not called at all are excluded */
for (c1 = 0; c1 < symtabsize; c1++)
if ((symtab[c1]->num_locs > 0) || (symtab[c1]->num_rcalls > 0))
num_funs++;
/* create the outer most container to hold the table */
result = new_create_array(atype, 1, 0, &num_funs);
for (c1 = 0; c1 < symtabsize; c1++) {
if ((symtab[c1]->num_locs > 0) || (symtab[c1]->num_rcalls > 0)) {
double totaloptime = 0;
int totalopcalls = 0;
int totalropcalls;
int len = 5;
/* create the table entry */
nialptr table_entry = new_create_array(atype, 1, 0, &len);
/* store it in the outer table */
store_array(result, pos, table_entry);
for (c2 = 0; c2 < symtab[c1]->num_locs; c2++) {
if (symtab[c1]->id != symtab[c1]->locations[c2]->parent->opid)
/* omit adding calls and time for direct recursions */
{
totaloptime += symtab[c1]->locations[c2]->total_time;
totalopcalls += symtab[c1]->locations[c2]->total_calls;
}
}
totalropcalls = symtab[c1]->num_rcalls;
/* fill in the cells in the table entry */
store_array(table_entry, 0, makephrase(symtab[c1]->name));
store_array(table_entry, 1, createint(totalopcalls));
store_array(table_entry, 2, createint(totalropcalls));
store_array(table_entry, 3, createreal(totaloptime));
{
struct node **chlist;
nialptr child_array;
int c,
used,
cpos = 0;
int children = 0;
chlist = merge_children(symtab[c1], &used);
for (c = 0; c < used; c++)
if (chlist[c]->opid != symtab[c1]->id) /* recursions only counted */
children++;
child_array = new_create_array(atype, 1, 0, &children);
store_array(table_entry, 4, child_array);
for (c = 0; c < used; c++) {
nialptr child_entry;
int len = 5;
if (chlist[c]->opid == symtab[c1]->id) /* recursions only counted */
break;
/* create each child entry and place it in the child list */
child_entry = new_create_array(atype, 1, 0, &len);
store_array(child_array, cpos, child_entry);
/* fill in the information about the child entry */
store_array(child_entry, 0, makephrase(num_to_name(chlist[c]->opid)));
store_array(child_entry, 1, createint(chlist[c]->total_calls));
store_array(child_entry, 2, createint(0));
store_array(child_entry, 3, createreal(chlist[c]->total_time));
store_array(child_entry, 4, Null);
cpos++;
}
free_merge_list(chlist, used);
}
}
pos++;
}
apush(result);
}
void
iprofile()
{
char sbuf[1000];
nialptr z;
FILE *prf = STDOUT;
int c1,
c2;
int i;
double real_total_time = 0;
double profile_duration_time;
int NMWIDTH = 30;
/* grab the argument */
z = apop();
if (newprofile) {
buildfault("no profile available");
freeup(z);
return;
}
/* handle input argument */
if (kind(z) == phrasetype) {
apush(z);
istring();
z = apop();
}
if (tally(z) != 0) {
if (!istext(z)) {
buildfault("profile file name arg is not text");
freeup(z);
return;
}
else {
prf = openfile(pfirstchar(z), 'w', 't');
if (prf == OPENFAILED) {
buildfault("unable to open specified file to write profile to");
freeup(z);
return;
/* exit_cover(NC_PROFILE_FILE_W); removed Nov 22/95 because this
* cleared profile information */
}
}
}
freeup(z);
/* If profiling is still on, then turn it off */
if (profile == true) {
apush(createbool(0));
isetprofile();
apop();
}
#ifndef OLD_BUILD_SYMBOL_TABLE
if (symtab)
free_symtab();
symtab = NULL;
build_symbol_table();
#endif
profile_duration_time = (calltree->total_time);
for (i = 0;i <calltree->num_children;i++) {
real_total_time += calltree->children[i]->total_time;
}
/* traverse the call tree placing nodes in the symbol table entries */
if (!traversed) {
traverse_tree(calltree);
traversed = true;
}
/* generate the output and place it in the output file or stdout */
/* if a filename has been specified then write that out */
if (tally(z)) {
sprintf(sbuf,"Profile output file: \"%s\"\n\n",pfirstchar(z));
writechars(prf, sbuf, strlen(sbuf), false);
}
sprintf(sbuf, "\nTotal execution time of profile session: \t%f\n", profile_duration_time);
writechars(prf, sbuf, strlen(sbuf), false);
sprintf(sbuf, "Total execution time in top level calls: \t%f\n\n",real_total_time);
writechars(prf, sbuf, strlen(sbuf), false);
/* header line for all data */
sprintf(sbuf, "op name[.tr arg] calls[rec] ");
writechars(prf, sbuf, strlen(sbuf), false);
sprintf(sbuf, "time time/call %% time\n");
writechars(prf, sbuf, strlen(sbuf), false);
for (c1 = 0; c1 < symtabsize; c1++) {
if ((symtab[c1]->num_locs > 0) || (symtab[c1]->num_rcalls > 0)) {
double totaloptime = 0;
int totalopcalls = 0;
int totalropcalls;
char *tmp;
for (c2 = 0; c2 < symtab[c1]->num_locs; c2++) {
if (symtab[c1]->id != symtab[c1]->locations[c2]->parent->opid)
/* omit adding calls and time for direct recursions */
{
totaloptime += symtab[c1]->locations[c2]->total_time;
totalopcalls += symtab[c1]->locations[c2]->total_calls;
}
}
totalropcalls = symtab[c1]->num_rcalls;
sprintf(sbuf, "%s%5d", (tmp = padright(NMWIDTH, (char *) symtab[c1]->name)),
totalopcalls);
writechars(prf, sbuf, strlen(sbuf), false);
free(tmp);
if (totalropcalls != 0) {
sprintf(sbuf, "[%5d]", totalropcalls);
writechars(prf, sbuf, strlen(sbuf), false);
}
else {
sprintf(sbuf, " ");
writechars(prf, sbuf, strlen(sbuf), false);
}
/* details for each definition */
sprintf(sbuf, "%8.2f %8.4f %8.1f%s\n",
totaloptime,
(totaloptime / totalopcalls),
100 * (totaloptime / real_total_time),
((symtab[c1]->toplevel_call == true)?"<":""));
writechars(prf, sbuf, strlen(sbuf), false);
{
struct node **chlist;
int c,
used;
char tname[40];
chlist = merge_children(symtab[c1], &used);
for (c = 0; c < used; c++) {
char *tmp;
if (chlist[c]->opid == symtab[c1]->id) /* recursions only counted */
break;
strcpy(tname, num_to_name(chlist[c]->opid));
/* details for each definition it calls */
if (chlist[c]->total_time > 0.0)
sprintf(sbuf, " %s%5d %8.2f %8.4f %8.2f\n",
(tmp = padright(NMWIDTH - 1, tname)),
chlist[c]->total_calls,
chlist[c]->total_time,
chlist[c]->total_time / chlist[c]->total_calls,
100 * (chlist[c]->total_time / totaloptime));
else
sprintf(sbuf, " %s%5d %8.2f %8.4f %8.2f\n",
(tmp = padright(NMWIDTH - 1, tname)),
chlist[c]->total_calls,
chlist[c]->total_time,
0.0, 0.0);
writechars(prf, sbuf, strlen(sbuf), false);
free(tmp);
}
free_merge_list(chlist, used);
}
sprintf(sbuf, "\n");
writechars(prf, sbuf, strlen(sbuf), false);
}
}
if (prf != STDOUT)
closefile(prf);
apush(Nullexpr);
return;
}
int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
{
t_symtab *symtab = NULL;
gmx_bool bAtStart, bTime, bAtoms, bPos, bVel, bBox, bEnd, bFinished;
int natoms, nbp;
double db1, db2, db3, db4, db5, db6, db7, db8, db9;
bAtStart = (ftell(fp) == 0);
clear_trxframe(fr, FALSE);
if (!symtab)
{
snew(symtab, 1);
open_symtab(symtab);
}
natoms = 0;
if (bAtStart)
{
while (!fr->bTitle && fgets2(line, STRLEN, fp))
{
fr->bTitle = (strcmp(line, "TITLE") == 0);
}
if (fr->title == NULL)
{
fgets2(line, STRLEN, fp);
fr->title = gmx_strdup(line);
}
bEnd = FALSE;
while (!bEnd && fgets2(line, STRLEN, fp))
{
bEnd = (strcmp(line, "END") == 0);
}
fgets2(line, STRLEN, fp);
}
/* Do not get a line if we are not at the start of the file, *
* because without a parameter file we don't know what is in *
* the trajectory and we have already read the line in the *
* previous call (VERY DIRTY). */
bFinished = FALSE;
do
{
bTime = (strcmp(line, "TIMESTEP") == 0);
bAtoms = (strcmp(line, "POSITION") == 0);
bPos = (bAtoms || (strcmp(line, "POSITIONRED") == 0));
bVel = (strncmp(line, "VELOCITY", 8) == 0);
bBox = (strcmp(line, "BOX") == 0);
if (bTime)
{
if (!fr->bTime && !fr->bX)
{
fr->bStep = bTime;
fr->bTime = bTime;
do
{
bFinished = (fgets2(line, STRLEN, fp) == NULL);
}
while (!bFinished && (line[0] == '#'));
sscanf(line, "%15d%15lf", &(fr->step), &db1);
fr->time = db1;
}
else
{
bFinished = TRUE;
}
}
if (bPos)
{
if (!fr->bX)
{
fr->bAtoms = bAtoms;
fr->bX = bPos;
natoms = read_g96_pos(line, symtab, fp, infile, fr);
}
else
{
bFinished = TRUE;
}
}
if (fr->v && bVel)
{
fr->bV = bVel;
natoms = read_g96_vel(line, fp, infile, fr);
}
if (bBox)
{
fr->bBox = bBox;
clear_mat(fr->box);
bEnd = FALSE;
while (!bEnd && fgets2(line, STRLEN, fp))
{
bEnd = (strncmp(line, "END", 3) == 0);
if (!bEnd && (line[0] != '#'))
{
nbp = sscanf(line, "%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf",
&db1, &db2, &db3, &db4, &db5, &db6, &db7, &db8, &db9);
if (nbp < 3)
{
gmx_fatal(FARGS, "Found a BOX line, but no box in %s", infile);
}
fr->box[XX][XX] = db1;
fr->box[YY][YY] = db2;
fr->box[ZZ][ZZ] = db3;
if (nbp == 9)
{
fr->box[XX][YY] = db4;
fr->box[XX][ZZ] = db5;
fr->box[YY][XX] = db6;
fr->box[YY][ZZ] = db7;
fr->box[ZZ][XX] = db8;
fr->box[ZZ][YY] = db9;
}
}
}
bFinished = TRUE;
}
}
while (!bFinished && fgets2(line, STRLEN, fp));
free_symtab(symtab);
fr->natoms = natoms;
return natoms;
}
void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
t_topology top;
t_trxframe fr;
int i, ftp, natoms;
real d;
char g96_line[STRLEN+1];
if (atoms->nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
else if (atoms->atom == NULL)
{
gmx_mem("Uninitialized array atom");
}
if (ePBC)
{
*ePBC = -1;
}
ftp = fn2ftp(infile);
switch (ftp)
{
case efGRO:
read_whole_conf(infile, title, atoms, x, v, box);
break;
case efG96:
fr.title = NULL;
fr.natoms = atoms->nr;
fr.atoms = atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile, "r");
read_g96_conf(in, infile, &fr, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
strncpy(title, fr.title, STRLEN);
break;
case efPDB:
case efBRK:
case efENT:
read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
break;
case efESP:
read_espresso_conf(infile, atoms, x, v, box);
break;
case efTPR:
case efTPB:
case efTPA:
snew(mtop, 1);
i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
if (ePBC)
{
*ePBC = i;
}
strcpy(title, *(mtop->name));
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
top = gmx_mtop_t_to_t_topology(mtop);
tpx_make_chain_identifiers(atoms, &top.mols);
sfree(mtop);
/* The strings in the symtab are still in use in the returned t_atoms
* structure, so we should not free them. But there is no place to put the
* symbols; the only choice is to leak the memory...
* So we clear the symbol table before freeing the topology structure. */
free_symtab(&top.symtab);
done_top(&top);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
gmx_bool read_next_frame(const gmx_output_env_t *oenv, t_trxstatus *status, t_trxframe *fr)
{
real pt;
int ct;
gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
int ftp;
bRet = FALSE;
pt = fr->tf;
do
{
clear_trxframe(fr, FALSE);
fr->tppf = fr->tpf;
fr->tpf = fr->tf;
if (status->tng)
{
/* Special treatment for TNG files */
ftp = efTNG;
}
else
{
ftp = gmx_fio_getftp(status->fio);
}
switch (ftp)
{
case efTRR:
bRet = gmx_next_frame(status, fr);
break;
case efCPT:
/* Checkpoint files can not contain mulitple frames */
break;
case efG96:
{
t_symtab *symtab;
snew(symtab, 1);
open_symtab(symtab);
read_g96_conf(gmx_fio_getfp(status->fio), NULL, fr,
symtab, status->persistent_line);
free_symtab(symtab);
bRet = (fr->natoms > 0);
break;
}
case efXTC:
/* B. Hess 2005-4-20
* Sometimes is off by one frame
* and sometimes reports frame not present/file not seekable
*/
/* DvdS 2005-05-31: this has been fixed along with the increased
* accuracy of the control over -b and -e options.
*/
if (bTimeSet(TBEGIN) && (fr->tf < rTimeValue(TBEGIN)))
{
if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
{
gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
rTimeValue(TBEGIN));
}
initcount(status);
}
bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
fr->x, &fr->prec, &bOK);
fr->bPrec = (bRet && fr->prec > 0);
fr->bStep = bRet;
fr->bTime = bRet;
fr->bX = bRet;
fr->bBox = bRet;
if (!bOK)
{
/* Actually the header could also be not ok,
but from bOK from read_next_xtc this can't be distinguished */
fr->not_ok = DATA_NOT_OK;
}
break;
case efTNG:
bRet = gmx_read_next_tng_frame(status->tng, fr, NULL, 0);
break;
case efPDB:
bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
break;
case efGRO:
bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
break;
default:
#ifdef GMX_USE_PLUGINS
bRet = read_next_vmd_frame(fr);
#else
gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
ftp2ext(gmx_fio_getftp(status->fio)),
gmx_fio_getname(status->fio));
#endif
}
fr->tf = fr->time;
if (bRet)
{
bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
((fr->flags & TRX_NEED_V) && !fr->bV) ||
((fr->flags & TRX_NEED_F) && !fr->bF));
bSkip = FALSE;
if (!bMissingData)
{
ct = check_times2(fr->time, fr->t0, fr->bDouble);
if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct < 0))
{
printcount(status, oenv, fr->time, FALSE);
}
else if (ct > 0)
{
bRet = FALSE;
}
else
{
printcount(status, oenv, fr->time, TRUE);
bSkip = TRUE;
}
}
}
}
while (bRet && (bMissingData || bSkip));
if (!bRet)
{
printlast(status, oenv, pt);
if (fr->not_ok)
{
printincomp(status, fr);
}
}
return bRet;
}
int read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio;
gmx_bool bFirst, bOK;
int ftp = fn2ftp(fn);
clear_trxframe(fr, TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe = 1;
initcount(*status);
if (efTNG == ftp)
{
/* Special treatment for TNG files */
gmx_tng_open(fn, 'r', &(*status)->tng);
}
else
{
fio = (*status)->fio = gmx_fio_open(fn, "r");
}
switch (ftp)
{
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
break;
case efG96:
{
/* Can not rewind a compressed file, so open it twice */
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
t_symtab *symtab;
snew(symtab, 1);
open_symtab(symtab);
read_g96_conf(gmx_fio_getfp(fio), fn, fr, symtab, (*status)->persistent_line);
free_symtab(symtab);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
{
snew(fr->x, fr->natoms);
}
if (flags & (TRX_READ_V | TRX_NEED_V))
{
snew(fr->v, fr->natoms);
}
(*status)->fio = gmx_fio_open(fn, "r");
break;
}
case efXTC:
if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
&fr->prec, &bOK) == 0)
{
GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
fr->not_ok = DATA_NOT_OK;
}
if (fr->not_ok)
{
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efTNG:
fr->step = -1;
if (!gmx_read_next_tng_frame((*status)->tng, fr, NULL, 0))
{
fr->not_ok = DATA_NOT_OK;
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
default:
#ifdef GMX_USE_PLUGINS
fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
"GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
"This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
"GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
"Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
break;
}
fr->tf = fr->time;
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
{
fr->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
{
return FALSE;
}
}
fr->t0 = fr->time;
/* We need the number of atoms for random-access XTC searching, even when
* we don't have access to the actual frame data.
*/
(*status)->natoms = fr->natoms;
return (fr->natoms > 0);
}
int read_pdbfile(FILE *in, char *title, int *model_nr,
t_atoms *atoms, rvec x[], int *ePBC, matrix box, gmx_bool bChange,
gmx_conect conect)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
t_symtab symtab;
gmx_bool bCOMPND;
gmx_bool bConnWarn = FALSE;
char line[STRLEN+1];
int line_type;
char *c, *d;
int natom, chainnum, nres_ter_prev = 0;
char chidmax = ' ';
gmx_bool bStop = FALSE;
if (ePBC)
{
/* Only assume pbc when there is a CRYST1 entry */
*ePBC = epbcNONE;
}
if (box != NULL)
{
clear_mat(box);
}
open_symtab(&symtab);
bCOMPND = FALSE;
title[0] = '\0';
natom = 0;
chainnum = 0;
while (!bStop && (fgets2(line, STRLEN, in) != NULL))
{
line_type = line2type(line);
switch (line_type)
{
case epdbATOM:
case epdbHETATM:
natom = read_atom(&symtab, line, line_type, natom, atoms, x, chainnum, bChange);
break;
case epdbANISOU:
if (atoms->pdbinfo)
{
read_anisou(line, natom, atoms);
}
break;
case epdbCRYST1:
read_cryst1(line, ePBC, box);
break;
case epdbTITLE:
case epdbHEADER:
if (strlen(line) > 6)
{
c = line+6;
/* skip HEADER or TITLE and spaces */
while (c[0] != ' ')
{
c++;
}
while (c[0] == ' ')
{
c++;
}
/* truncate after title */
d = strstr(c, " ");
if (d)
{
d[0] = '\0';
}
if (strlen(c) > 0)
{
strcpy(title, c);
}
}
break;
case epdbCOMPND:
if ((!strstr(line, ": ")) || (strstr(line+6, "MOLECULE:")))
{
if (!(c = strstr(line+6, "MOLECULE:")) )
{
c = line;
}
/* skip 'MOLECULE:' and spaces */
while (c[0] != ' ')
{
c++;
}
while (c[0] == ' ')
{
c++;
}
/* truncate after title */
d = strstr(c, " ");
if (d)
{
while ( (d[-1] == ';') && d > c)
{
d--;
}
d[0] = '\0';
}
if (strlen(c) > 0)
{
if (bCOMPND)
{
strcat(title, "; ");
strcat(title, c);
}
else
{
strcpy(title, c);
}
}
bCOMPND = TRUE;
}
break;
case epdbTER:
chainnum++;
break;
case epdbMODEL:
if (model_nr)
{
sscanf(line, "%*s%d", model_nr);
}
break;
case epdbENDMDL:
bStop = TRUE;
break;
case epdbCONECT:
if (gc)
{
gmx_conect_addline(gc, line);
}
else if (!bConnWarn)
{
fprintf(stderr, "WARNING: all CONECT records are ignored\n");
bConnWarn = TRUE;
}
break;
default:
break;
}
}
free_symtab(&symtab);
return natom;
}
