/*------------------------------------------------------------------------- * Function: parse_assignment * * Purpose: Parses an assignment statement of the form * * LVALUE = RVALUE * * Return: Success: the resulting parse tree. * * Failure: &ErrorCell * * Programmer: Robb Matzke * [email protected] * Feb 7 1997 * * Modifications: * *------------------------------------------------------------------------- */ static obj_t parse_assignment (lex_t *f, int skipnl) { obj_t rt=NIL, retval=NIL; retval = parse_selection (f, skipnl); if (&ErrorCell==retval) return &ErrorCell; if (TOK_EQ==lex_token (f, NULL, skipnl)) { lex_consume (f); rt = parse_selection (f, skipnl); if (&ErrorCell==rt) { obj_dest(retval); return &ErrorCell; } retval = obj_new (C_CONS, obj_new (C_SYM, "Assign"), obj_new (C_CONS, retval, obj_new (C_CONS, rt, NIL))); } return retval; }
int main(int argc, char* argv[])
{
int i = 0, j = 0;
// how to use this program
if ( argc != 5 )
{
printf("Please provide 4 arguments : path to CHARMM dcd file (binary) , path to reference structure "
"(CHARMM .cor text file) , atoms selection for rmsd and for centering (cf. next) . \n"
"Note that it is possible to use 2 different selections for centering and rmsd \n\n");
puts("For a selection by residue name (3rd column of CHARRMM .cor file): ");
printf("%s *.dcd *.cor rmsd=resname:GLY,LEU center=resname:GLY,LEU \n\n", argv[0]);
puts("For a selection by atom name (4th column of CHARRMM .cor file) : ");
printf("%s *.dcd *.cor rmsd=atname:C,CA,N center=atname:C,CA,N \n\n", argv[0]);
puts("For a selection by residue number (2nd column of CHARMM .cor file) : ");
printf("%s *.dcd *.cor rmsd=resnum:15,19,62,101 center=resnum:15,19,63 \n\n", argv[0]);
puts("For a selection by atom number (1st column of CHARMM .cor file) : ");
printf("%s *.dcd *.cor rmsd=atnum:1114,1123,1169,2056,6987 center=atname:C,CA,N \n\n", argv[0]);
return EXIT_SUCCESS;
}
// pointers to arguments for I/O and parsing
char *dcdname = argv[1];
char *corname = argv[2];
char *cent_selec = NULL, *rmsd_selec = NULL;
if ( determine_selection_mode(&argv[3]) == center_selec )
{
cent_selec = argv[3];
rmsd_selec = argv[4];
}
else
{
cent_selec = argv[4];
rmsd_selec = argv[3];
}
// opening files
FILE *dcdf = NULL;
dcdf = fopen(dcdname, "rb");
if ( dcdf == NULL )
{
printf("Error while opening the file '%s' with binary read mode\n", dcdname);
exit(DCD_OPEN_ERROR);
}
FILE *corf = NULL;
corf = fopen(corname, "rt");
if ( corf == NULL )
{
printf("Error while opening the file '%s' with text read mode\n", corname);
exit(CORFILE_OPEN_ERROR);
}
FILE *rmsdf = NULL;
char *out_name = ( char* ) malloc((strlen(rmsd_selec) + 20) * sizeof (char));
strcpy(out_name, "rmsd_");
strcat(out_name, rmsd_selec);
strcat(out_name, "_.dat");
rmsdf = fopen(out_name, "wt");
if ( rmsdf == NULL )
{
printf("Error while opening the file '%s' with text write mode\n", out_name);
exit(OUTFILE_OPEN_ERROR);
}
// a structure for reading header of dcd : will contain a lot of informations read from dcd
DCD dcd;
read_dcd_header(dcdf, &dcd);
printf("ATOMS : %d \t FRAMES : %d \n\n", dcd.NATOM, dcd.NFILE);
//for storing the atoms selections : one selection for centering and one for rmsd
char **sele_cent = NULL, **sele_rmsd = NULL;
int elem_cent = 0, elem_rmsd = 0;
PARSING_MODE pmode_cent, pmode_rmsd;
parse_selection(¢_selec, &elem_cent, &sele_cent, &pmode_cent);
parse_selection(&rmsd_selec, &elem_rmsd, &sele_rmsd, &pmode_rmsd);
//index to know if it is an "active atom" (i.e. if not it will not be used for centering or evaluating rmsd)
int *index_cent = NULL, *index_rmsd = NULL;
index_cent = ( int* ) calloc(dcd.NATOM, sizeof (int));
index_rmsd = ( int* ) calloc(dcd.NATOM, sizeof (int));
int nsele_cent = 0, nsele_rmsd = 0;
// NATOM*3 matrix for storing coordinates
float **tmpref = NULL;
tmpref = ( float** ) malloc(dcd.NATOM * sizeof (float*));
for ( i = 0; i < dcd.NATOM; i++ )
tmpref[i] = ( float* ) malloc(3 * sizeof (float));
// reads coordinates and obtains to indexes for knowing which atoms are active for centering or rmsd
read_charmm_cor(corf, &dcd, tmpref,
sele_cent, elem_cent, &pmode_cent, index_cent, &nsele_cent,
sele_rmsd, elem_rmsd, &pmode_rmsd, index_rmsd, &nsele_rmsd);
printf("%d atoms in centering selection.\n", nsele_cent);
if ( nsele_cent == 0 )
{
puts("Error : no atom matching this selection ! Exit ...");
exit(SELECTION_NO_ATOMS);
}
printf("%d atoms in rmsd selection.\n", nsele_rmsd);
if ( nsele_rmsd == 0 )
{
puts("Error : no atom matching this selection ! Exit ...");
exit(SELECTION_NO_ATOMS);
}
int ntot = 0;
for ( i = 0; i < dcd.NATOM; i++ )
{
if ( index_cent[i] || index_rmsd[i] )
ntot++;
}
printf("ntot : %d\n", ntot);
float **crd = NULL, **ref = NULL;
crd = ( float** ) malloc(ntot * sizeof (float*));
ref = ( float** ) malloc(ntot * sizeof (float*));
for ( i = 0; i < ntot; i++ )
crd[i] = ( float* ) malloc(3 * sizeof (float));
for ( i = 0; i < ntot; i++ )
ref[i] = ( float* ) malloc(3 * sizeof (float));
j = 0;
for ( i = 0; i < dcd.NATOM; i++ )
{
if ( index_cent[i] || index_rmsd[i] )
{
memcpy(ref[j], tmpref[i], 3 * sizeof (float));
j++;
}
}
for ( i = 0; i < dcd.NATOM; i++ )
free(tmpref[i]);
free(tmpref);
center_sys(dcd.NATOM, ref, ntot, index_cent, index_rmsd);
double rms = 0.;
for ( i = 0; i < dcd.NFILE; i++ )
{
read_dcd_traj(dcdf, &dcd, crd, index_cent, index_rmsd, ntot);
rms = rmsd(dcd.NATOM, crd, ref, ntot, index_cent, index_rmsd);
fprintf(rmsdf, "%lf\n", rms);
}
printf("\n");
for ( i = 0; i < ntot; i++ )
{
free(crd[i]);
free(ref[i]);
}
free(crd);
free(ref);
for ( i = 0; i < elem_cent; i++ )
free(sele_cent[i]);
free(sele_cent);
for ( i = 0; i < elem_rmsd; i++ )
free(sele_rmsd[i]);
free(sele_rmsd);
free(out_name);
free(index_cent);
free(index_rmsd);
fclose(dcdf);
fclose(rmsdf);
fclose(corf);
if ( (dcd.LNFREAT) != (dcd.NATOM) )
{
free(dcd.FREEAT);
}
return EXIT_SUCCESS;
}
