void print_cs(int p)
{
str_number t= cs_text(p);
if(p<hash_base){
if(p==null_cs){
tprint_esc("csname");
tprint_esc("endcsname");
print_char(' ');
}else{
tprint_esc("IMPOSSIBLE.");
}
}else if((p>=undefined_control_sequence)&&
((p<=eqtb_size)||p> eqtb_size+hash_extra)){
tprint_esc("IMPOSSIBLE.");
}else if(t>=str_ptr){
tprint_esc("NONEXISTENT.");
}else{
if(is_active_cs(t)){
print(active_cs_value(t));
}else{
print_esc(t);
if(single_letter(t)){
if(get_cat_code(cat_code_table_par,pool_to_unichar(str_string(t)))==letter_cmd)
print_char(' ');
}else{
print_char(' ');
}
}
}
}
int read_pdb ( char * pdbname, Protein * protein, char chain) {
Residue * sequence;
FILE * fptr = NULL;
char line[BUFFLEN];
char oldresno[PDB_ATOM_RES_NO_LEN+2]; /* res name: 4 digits + insertion code + \0 */
char oldrestype [PDB_ATOM_RES_NAME_LEN+2];
char tmp[PDB_ATOM_X_LEN+1], *auxptr;
int atomctr, resctr, no_res, ctr, nonblank;
char single_letter ( char code[]);
/* open file */
fptr = fopen ( pdbname, "r");
if ( !fptr ) {
fprintf (stderr, "Cno %s.\n", pdbname);
return 1;
}
/* warn if no chain given */
if ( !chain) fprintf ( stderr,"No chain specified. Using the first one.\n");
/* count residues */
memset (line, 0, BUFFLEN);
memset (oldresno, 0, PDB_ATOM_RES_NO_LEN+2);
resctr = 0;
while(fgets(line, BUFFLEN, fptr)!=NULL){
if ( chain && line[PDB_ATOM_CHAINID] != chain ) continue;
if ( ! strncmp(line,"TER", 3) || ! strncmp(line,"END", 3) ) break;
if( ! strncmp(line,"ATOM", 4) || ! strncmp(line,"HETATM", 6)){
if ( strncmp (line+PDB_ATOM_RES_NO, oldresno, PDB_ATOM_RES_NO_LEN+1) ) {
strncpy (oldresno, line+PDB_ATOM_RES_NO, PDB_ATOM_RES_NO_LEN+1);
oldresno[PDB_ATOM_RES_NO_LEN+1] = '\0';
/* printf ( "New residue number: %s \n", oldresno); */
resctr ++;
}
}
}
no_res = resctr;
/* printf ("no residues: %d\n", no_res); */
/* allocate space */
sequence = NULL;
sequence = emalloc ( no_res*sizeof (Residue));
/* read in the atom */
rewind ( fptr);
memset (line, 0, BUFFLEN);
memset (oldresno, 0, PDB_ATOM_RES_NO_LEN+2);
/* tyring to account for the insertion code */
memset (oldrestype, 0, PDB_ATOM_RES_NAME_LEN+2);
resctr= -1;
atomctr = 0;
while(fgets(line, BUFFLEN, fptr)!=NULL){
if ( chain && line[PDB_ATOM_CHAINID] != chain ) continue;
if ( ! strncmp(line,"TER", 3) || ! strncmp(line,"END", 3) ) break;
if( ! strncmp(line,"ATOM", 4) || ! strncmp(line,"HETATM", 6)){
/* if it's a hydrogen - skip */
if ( line[PDB_ATOM_ATOM_NAME] == 'H'
|| line[PDB_ATOM_ATOM_NAME+1] == 'H') continue;
/* adjust the counters */
if ( strncmp (line+PDB_ATOM_RES_NO, oldresno, PDB_ATOM_RES_NO_LEN+1) ) {
strncpy (oldresno, line+PDB_ATOM_RES_NO, PDB_ATOM_RES_NO_LEN+1);
strncpy (oldrestype, line+PDB_ATOM_RES_NAME, PDB_ATOM_RES_NAME_LEN);
oldresno[PDB_ATOM_RES_NO_LEN+1] = '\0';
oldrestype[PDB_ATOM_RES_NAME_LEN] = '\0';
resctr ++;
atomctr = 0;
sequence[resctr].no_atoms = 1;
strncpy ( sequence[resctr].pdb_id, oldresno, PDB_ATOM_RES_NO_LEN+2);
sequence[resctr].pdb_id[PDB_ATOM_RES_NO_LEN+1] = '\0';
strncpy ( sequence[resctr].res_type, oldrestype, PDB_ATOM_RES_NAME_LEN+1);
sequence[resctr].res_type[PDB_ATOM_RES_NAME_LEN] = '\0';
sequence[resctr].res_type_short = single_letter ( sequence[resctr].res_type );
if ( !sequence[resctr].res_type_short ) return 1;
} else {
atomctr ++;
sequence[resctr].no_atoms = atomctr + 1;
if ( atomctr >= MAX_NO_ATOMS ) {
fprintf ( stderr, "Error: I thought every aa has < %d atoms.\n",
MAX_NO_ATOMS );
return 1;
}
}
/* read in atom info */
auxptr = line+ PDB_ATOM_ATOM_NAME;
memset ( tmp, 0, PDB_ATOM_ATOM_NAME_LEN+1);
/* skip initial blanks*/
ctr = 0;
while ( !(isalpha (*(auxptr + ctr))) && (ctr <= PDB_ATOM_ATOM_NAME_LEN) ) ctr++;
/* copy alphanum info */
nonblank = 0;
while ( isalpha (*(auxptr +ctr)) && (ctr <= PDB_ATOM_ATOM_NAME_LEN) ) {
tmp[nonblank] = *(auxptr +ctr);
nonblank ++;
ctr++;
}
strncpy ( sequence[resctr].atom[atomctr].type, tmp, PDB_ATOM_ATOM_NAME_LEN );
/* is this a backbone atom?*/
sequence[resctr].atom[atomctr].backbone = 0;
if ( nonblank == 1) {
sequence[resctr].atom[atomctr].backbone =
!( strcmp ( tmp, "N") && strcmp ( tmp, "C") && strcmp ( tmp, "O") );
} else if ( nonblank == 2) {
sequence[resctr].atom[atomctr].backbone = ! strcmp ( tmp, "CA" );
}
/* printf ( " %4d %4d %4s is backbone: %1d \n", resctr, atomctr, */
/* sequence[resctr].atom[atomctr].type, sequence[resctr].atom[atomctr].backbone); */
strncpy ( tmp, line+PDB_ATOM_X, PDB_ATOM_X_LEN);
tmp[PDB_ATOM_X_LEN] = '\0';
sequence[resctr].atom[atomctr].x=atof(tmp);
strncpy ( tmp, line+PDB_ATOM_Y, PDB_ATOM_Y_LEN);
tmp[PDB_ATOM_Y_LEN] = '\0';
sequence[resctr].atom[atomctr].y=atof(tmp);
strncpy ( tmp, line+PDB_ATOM_Z, PDB_ATOM_Z_LEN);
tmp[PDB_ATOM_Z_LEN] = '\0';
sequence[resctr].atom[atomctr].z=atof(tmp);
}
}
/* close file */
fclose (fptr);
/* clean PDB id tags from spaces */
for (resctr=0; resctr < no_res; resctr ++ ) {
string_clean (sequence[resctr].pdb_id, PDB_ATOM_RES_NO_LEN+2);
}
/*return values: */
protein->sequence= sequence;
protein->length = no_res;
return 0;
}
int fill_protein_info ( FILE * fptr, char chain, Protein * protein) {
/* TODO for the moment we rely on PDB annotation
to extract structural elements - that should be changed */
Residue * sequence = NULL;
char line[BUFFLEN];
char oldresno[PDB_ATOM_RES_NO_LEN+2];
/* res name: 4 digits + insertion code + \0 */
char oldrestype [PDB_ATOM_RES_NAME_LEN+2];
char tmp[BUFFLEN], *auxptr;
char atomtypes_read_in[BUFFLEN];
char old_chain;
int atomctr, resctr, no_res,ctr, nonblank;
int retval;
int chain_found;
int ca_trace;
char single_letter ( char code[]);
int has_backbone (Residue * sequence, int from, int to);
/********************************************/
/********************************************/
/* cleanup */
memset (protein, 0, sizeof(Protein) );
/********************************************/
/********************************************/
/* count residues */
memset (line, 0, BUFFLEN);
memset (oldresno, 0, PDB_ATOM_RES_NO_LEN+2);
resctr = 0;
chain_found = 0;
old_chain = '\0';
while(fgets(line, BUFFLEN, fptr)!=NULL){
if (resctr) {
if ( ! strncmp(line,"END", 3) || (chain && line[PDB_ATOM_CHAINID] != old_chain) )
break;
}
if (chain && line[PDB_ATOM_CHAINID] != chain) continue;
chain_found = 1;
if( ! strncmp(line,"ATOM", 4)){
if ( strncmp (line+PDB_ATOM_RES_NO, oldresno, PDB_ATOM_RES_NO_LEN+1) ) {
strncpy (oldresno, line+PDB_ATOM_RES_NO, PDB_ATOM_RES_NO_LEN+1);
oldresno[PDB_ATOM_RES_NO_LEN+1] = '\0';
/* handling the case when the chain is not given, meaning: "take the first chain" */
old_chain = line[PDB_ATOM_CHAINID];
resctr ++;
}
}
}
/* sanity: */
if ( chain && ! chain_found) {
fprintf (stderr, "Chain %c not found.\n", chain);
return ERR_NO_FILE_OR_CHAIN;
}
no_res = resctr;
if ( !no_res ) return -1; /* take it as the end of the read */
/* allocate space */
sequence = emalloc ( no_res*sizeof (Residue));
if ( ! sequence ) return 1;
/*********************************************/
/*********************************************/
/* read in residue numbers and atom coords */
rewind ( fptr);
memset (line, 0, BUFFLEN);
old_chain = '\0';
memset (oldresno, 0, PDB_ATOM_RES_NO_LEN+2);
memset (oldrestype, 0, PDB_ATOM_RES_NAME_LEN+2);
resctr= -1;
atomctr = 0;
ca_trace = 1;
while(fgets(line, BUFFLEN, fptr)!=NULL){
if ( resctr > -1) {
if (! strncmp(line,"END", 3) || (chain && line[PDB_ATOM_CHAINID] != old_chain))
break;
}
if ( chain && line[PDB_ATOM_CHAINID] != chain ) continue;
if( ! strncmp(line,"ATOM", 4) ){
/* if it's a hydrogen - skip */
if ( line[PDB_ATOM_ATOM_NAME] == 'H'
|| line[PDB_ATOM_ATOM_NAME+1] == 'H') continue;
/* adjust the counters */
if ( strncmp (line+PDB_ATOM_RES_NO, oldresno, PDB_ATOM_RES_NO_LEN+1) ) {
/*+1 in PDB_ATOM_RES_NO_LEN+1 means I am including the insertion code
in the identifier */
strncpy (oldresno, line+PDB_ATOM_RES_NO, PDB_ATOM_RES_NO_LEN+1);
strncpy (oldrestype, line+PDB_ATOM_RES_NAME, PDB_ATOM_RES_NAME_LEN);
oldresno[PDB_ATOM_RES_NO_LEN+1] = '\0';
oldrestype[PDB_ATOM_RES_NAME_LEN] = '\0';
/* handling the case when the chain is not given, meaning: "take the first chain" */
old_chain = line[PDB_ATOM_CHAINID];
resctr ++;
if ( resctr >= no_res ) {
fprintf (stderr, "Error reading pdb: resctr:%d no res: %d\n",
resctr, no_res);
return ERR_NONSENSE;
}
atomctr = 0;
/* keep track of atom types we have read in */
memset (atomtypes_read_in, 0, BUFFLEN*sizeof(char));
atomtypes_read_in[0] = '_';
sequence[resctr].no_atoms = 1;
strncpy ( sequence[resctr].pdb_id, oldresno, PDB_ATOM_RES_NO_LEN+2);
sequence[resctr].pdb_id[PDB_ATOM_RES_NO_LEN+1] = '\0';
strncpy ( sequence[resctr].res_type, oldrestype, PDB_ATOM_RES_NAME_LEN+1);
sequence[resctr].res_type[PDB_ATOM_RES_NAME_LEN] = '\0';
sequence[resctr].res_type_short =
single_letter ( sequence[resctr].res_type );
/* modified residues are ok for the purposes here */
/* unless they are sugars or some such - deal with it below */
/* by checking the backbone atoms */
///if ( !sequence[resctr].res_type_short ) return 1;
} else {
atomctr ++;
sequence[resctr].no_atoms = atomctr + 1;
if ( atomctr >= MAX_NO_ATOMS ) {
fprintf ( stderr,
"Error parsing pdb: I thought every aa has < %d atoms.\n",
MAX_NO_ATOMS );
return ERR_MAX_ATOMS;
}
}
/* read in atom info */
auxptr = line+ PDB_ATOM_ATOM_NAME;
memset ( tmp, 0, PDB_ATOM_ATOM_NAME_LEN+1);
/* skip initial blanks*/
ctr = 0;
while ( !(isalpha (*(auxptr + ctr))) &&
(ctr <= PDB_ATOM_ATOM_NAME_LEN) ) ctr++;
/* copy alphanum info */
nonblank = 0;
while ( isalnum (*(auxptr +ctr)) && (ctr <= PDB_ATOM_ATOM_NAME_LEN) ) {
tmp[nonblank] = *(auxptr +ctr);
nonblank ++;
ctr++;
}
/* have we already seen this atom type by any chance? */
tmp[nonblank] = '_';
if ( strstr (atomtypes_read_in, tmp) ) {
/* ahould I check for an alt location code, or just move on? */
//printf ( " %s >> %s //// %s\n", sequence[resctr].pdb_id, atomtypes_read_in, tmp);
continue;
} else {
sprintf (atomtypes_read_in, "%s%s", atomtypes_read_in, tmp);
}
tmp[nonblank] = '\0';
strncpy ( sequence[resctr].atom[atomctr].type, tmp, PDB_ATOM_ATOM_NAME_LEN );
/* is this a backbone atom?*/
sequence[resctr].atom[atomctr].backbone = 0;
if ( nonblank == 1) {
sequence[resctr].atom[atomctr].backbone =
!( strcmp ( tmp, "N") && strcmp ( tmp, "C") && strcmp ( tmp, "O") );
} else if ( nonblank == 2) {
if ( ! strcmp ( tmp, "CA" )) {
sequence[resctr].atom[atomctr].backbone = 1;
sequence[resctr].Ca = sequence[resctr].atom+atomctr;
} else {
sequence[resctr].atom[atomctr].backbone = 0;
}
}
/* check if this is Ca trace */
if ( strcmp ( tmp, "CA" ) ) ca_trace = 0;
strncpy ( tmp, line+PDB_ATOM_X, PDB_ATOM_X_LEN);
tmp[PDB_ATOM_X_LEN] = '\0';
sequence[resctr].atom[atomctr].x=atof(tmp);
strncpy ( tmp, line+PDB_ATOM_Y, PDB_ATOM_Y_LEN);
tmp[PDB_ATOM_Y_LEN] = '\0';
sequence[resctr].atom[atomctr].y=atof(tmp);
strncpy ( tmp, line+PDB_ATOM_Z, PDB_ATOM_Z_LEN);
tmp[PDB_ATOM_Z_LEN] = '\0';
sequence[resctr].atom[atomctr].z=atof(tmp);
}
}
if ( ca_trace) return ERR_SSE_NONE|ERR_CA_TRACE;
/* clean PDB id tags from spaces */
for (resctr=0; resctr < no_res; resctr ++ ) {
retval = string_clean (sequence[resctr].pdb_id, PDB_ATOM_RES_NO_LEN+1);
if ( retval ) {
fprintf (stderr, "Error in read_pdb(): empty id string for residue with sequential no %d.\n", resctr);
return ERR_NONSENSE;
}
}
/* store the sequence and its length */
protein->sequence = sequence;
protein->length = no_res;
return 0;
}
