void addemail4parent(char* mailid,pid_t childpid){
char domainname[80];
getdomain(mailid,domainname);
domainData newdomain;
strcpy(newdomain.domain,domainname);
newdomain.pid=childpid;
data[noDomains]=newdomain;
noDomains++;
sleep(2);
kill(childpid,SIGUSR1);
sleep(2);
}
int *NEWinserteffectlits(int *a,Seff *se,int *b) {
int *vals;
switch(se->t) {
case SEpatom: *a = fePLIT(atomindex(se->a,b)); return a+1;
case SEnatom: *a = feNLIT(atomindex(se->a,b)); return a+1;
case SEconj: return NEWinserteffectlitsL(a,se->juncts,b);
case SEwhen: return a;
case SEforall:
vals = getdomain(se->ss->t);
while(*vals != -1) {
b[-1-se->ss->v] = *vals;
a = NEWinserteffectlits(a,se->effect,b);
vals = vals + 1;
}
return a;
default: return a;
}
}
void NEWgroundoperators() {
int i,j;
int *domains[1000];
int binding[1000];
int staticrestriction[1000];
atom *al;
NEWpreprocessoperators();
initactions(); /* initialize the ground action data structure */
initatomtable(); /* initialize the tables for atoms */
for(i=0;i<nOfSActions;i++) {
typedvarlist *params = Sactions[i].params;
typedvarlist *l = params;
if(flagShowInput) {
printf("Grounding schema %i:%s\n",i,symbol(Sactions[i].name));
printSaction(&Sactions[i]);
}
/* Fetch domains of the parameters */
nOfBindings = 0;
while(l != NULL) {
staticrestriction[nOfBindings] = occursinstatic(nOfBindings,Sactions[i].precon);
#ifdef DEBUG
if(staticrestriction[nOfBindings]) {
printf("Parameter %i is static.\n",nOfBindings);
printSaction(&Sactions[i]);
} else { printf("."); }
#endif
#ifdef ASSERTS
assert(isvar(l->v));
#endif
domains[nOfBindings] = getdomain(l->t);
nOfBindings += 1;
l = l->tl;
}
#ifdef ASSERTS
assert(nOfBindings < 100);
#endif
/* Go through all parameter assignments and ground */
NEWgothrough(0,i,domains,staticrestriction);
}
goal = NEWgroundfma(Sgoal,binding);
/* Go through the initial state description to assign
indices to initial state atoms. */
al = Sinit;
while(*al != NULL) {
atomindex(*al,NULL);
al = al + 1;
}
initialstate = (int *)malloc(sizeof(int) * nOfAtoms);
for(i=0;i<nOfAtoms;i++) initialstate[i] = 0;
al = Sinit;
while(*al != NULL) {
j = atomindex(*al,NULL);
initialstate[j] = 1;
#ifdef ASSERTS
assert(j>=0); assert(j<nOfAtoms);
#endif
al = al + 1;
}
}
fma *NEWgroundfma(Sfma *sf,int *b) {
int *vals;
fma *f = (fma *)malloc(sizeof(fma));
switch(Sfmatypeof(sf)) {
case STRUE: f->t = TRUE; break;
case SFALSE: f->t = FALSE; break;
case Sconj:
f->t = conj;
f->juncts = NEWgroundfmalist(sf->juncts,b);
break;
case Sdisj:
f->t = disj;
f->juncts = NEWgroundfmalist(sf->juncts,b);
break;
case Seq:
if(bvalue(sf->p1,b) == bvalue(sf->p2,b)) {
f->t = TRUE;
} else {
f->t = FALSE;
}
break;
case Sneq:
if(bvalue(sf->p1,b) == bvalue(sf->p2,b)) {
f->t = FALSE;
} else {
f->t = TRUE;
}
break;
case Spatom:
f->t = patom;
f->a = atomindex(sf->a,b);
break;
case Snatom:
f->t = natom;
f->a = atomindex(sf->a,b);
break;
case Sforall: /* Iterate over all values of the variable. */
f->t = conj;
f->juncts = NULL;
vals = getdomain(sf->ss->t);
while(*vals != -1) {
b[-1-sf->ss->v] = *vals;
f->juncts = fmacons(NEWgroundfma(sf->f,b),f->juncts);
vals = vals + 1;
}
break;
case Sforsome: /* Iterate over all values of the variable. */
f->t = disj;
f->juncts = NULL;
vals = getdomain(sf->ss->t);
while(*vals != -1) {
b[-1-sf->ss->v] = *vals;
f->juncts = fmacons(NEWgroundfma(sf->f,b),f->juncts);
vals = vals + 1;
}
break;
}
return f;
}
eff *NEWlocateconditionals(Seff *se,int *b,eff *ac,int whennesting) {
int *vals,i,*ptr;
eff *e,*ac0;
Sefflist *ses;
switch(se->t) {
case SEconj:
ses = se->juncts;
while(ses != NULL) {
ac = NEWlocateconditionals(ses->hd,b,ac,whennesting);
ses = ses->tl;
}
return ac;
case SEwhen:
e = (eff *)malloc(sizeof(eff));
whenstack[whennesting] = se->cond;
ac0 = NEWlocateconditionals(se->effect,b,ac,whennesting+1);
if(se->cond->t == SFALSE) return ac0;
if(!someunconditional(se->effect)) return ac0;
if(whennesting == 0) { /* Non-nested when */
e->condition = NEWgroundfma(se->cond,b);
#ifdef CFMA
e->ccondition = Cgroundfma(se->cond,b);
// printcfma(e->ccondition);
#endif
} else{ /* Nesting of 2 or more whens */
fmalist *fs = NULL;
for(i=0;i<=whennesting;i++) {
fs = fmacons(NEWgroundfma(whenstack[i],b),fs);
}
e->condition = (fma *)malloc(sizeof(fma));
e->condition->t = conj;
e->condition->juncts = fs;
}
e->effectlits = (int *)malloc((NEWnOfEffectLits(se->effect)+1) * sizeof(int));
ptr = NEWinserteffectlits(e->effectlits,se->effect,b);
*ptr = -1;
e->tl = ac0;
return e;
case SEforall:
vals = getdomain(se->ss->t);
while(*vals != -1) {
b[-1-se->ss->v] = *vals;
ac = NEWlocateconditionals(se->effect,b,ac,whennesting);
vals = vals + 1;
}
return ac;
default: return ac;
}
}
void run(){
char domainname[80];
char op[20],mailid[80],temp[80];
char* add_email="add_email";
struct sigaction usr_action;
sigset_t block_mask;
printf("Enter op: ");
scanf("%s",op);
if(comparestr(op,"add_email")){
printf("Entered addition zone. Enter mailid\n");
scanf("%s",mailid);
strcpy(temp,mailid);
getdomain(temp,domainname);
int searchVal=searchDomain(domainname);
if(searchVal == -1){ //create new domain
printf("\n------------------------------------\nAdding a new process\n");
//fork a new process here
pid_t childpid; /* variable to store the child's pid */
int retval; /* child process: user-provided return code */
int status; /* parent process: child's exit status */
/* only 1 int variable is needed because each process would have its
own instance of the variable
here, 2 int variables are used for clarity */
/* now create new process */
childpid = fork();
if (childpid >= 0) /* fork succeeded */
{
if (childpid == 0){ /* fork() returns 0 to the child process */
noEmails=0;
sigfillset (&block_mask);
usr_action.sa_handler = child_handler;
usr_action.sa_mask = block_mask;
usr_action.sa_flags = 0;
sigaction (SIGUSR1, &usr_action, NULL);
struct sigaction act2;
memset (&act2, '\0', sizeof(act2));
/* Use the sa_sigaction field because the handles has two additional parameters */
act2.sa_sigaction = &child_handler_kill;
/* The SA_SIGINFO flag tells sigaction() to use the sa_sigaction field, not sa_handler. */
act2.sa_flags = SA_SIGINFO;
if (sigaction(SIGTERM, &act2, NULL) < 0) {
printf ("sigaction");
}
while(1){;}
}
// connect to (and possibly create) the segment: //
if(childpid > 0){
sigfillset (&block_mask);
usr_action.sa_handler = parent_handler;
usr_action.sa_mask = block_mask;
usr_action.sa_flags = 0;
sigaction (SIGUSR2, &usr_action, NULL);
strcpy(p2cshared->email, mailid);
strcpy(p2cshared->op, op);
addemail4parent(mailid,childpid);
}
}
else /* fork returns -1 on failure */
{
perror("fork"); /* display error message */
exit(0);
}
}
else{
strcpy(p2cshared->email, mailid);
strcpy(p2cshared->op, op);
sleep(2);
kill(data[searchVal].pid,SIGUSR1);
sleep(2);
}
}
else if(comparestr(op,"delete_email")){
printf("Entered deleting zone. Enter mailid\n");
scanf("%s",mailid);
operationp(mailid,op);
}
else if(comparestr(op,"search_email")){
printf("Entered searching zone. Enter mailid\n");
scanf("%s",mailid);
operationp(mailid,op);
}
else if(comparestr(op,"delete_domain")){
printf("Entered deleting zone. Enter mailid\n");
scanf("%s",mailid);
int id=searchDomain(mailid);
if(id==-1){
printf("Parent: Domain does not exist\n");
}
else{
kill(data[id].pid,SIGTERM);
waitpid(data[id].pid, 0, 0); //important for wait so that child doesnt become zombie
//A child that terminates, but has not been waited for becomes a "zombie".
printf("Parent process - Domain %s with PID - %d deleted\n", mailid, data[id].pid);
data[id].pid = -1;
data[id].domain[0]='\0';
}
}
else if(comparestr(op,"Quit")){
printf("Quit\n");
int i=0;
for(i=0;i<noDomains;i++){
if(data[i].pid != 0){
kill(data[i].pid, SIGTERM);
waitpid(data[i].pid, 0, 0); //important for wait so that child doesnt become zombie
}
}
printf("Parent : Killed all children, now suicide awaits\n");
//raise(SIGKILL);
}
else{
printf("Incorrect input: try again");
}
}
struct address *
verify(struct letter *let, struct domain *dom, char *p, int flags, int *reason)
{
char *e = p + strlen(p);
int bad = 0;
struct address *ret;
extern char *addr(char*,int*);
struct iplist mxes;
int i;
while ( (e > p) && (isspace(e[-1]) || e[-1] == '\r' || e[-1] == '\n') )
--e;
if (*e)
*e = 0;
if ((e > p) && (ret = mkaddress(addr(p, &bad))) ) {
if (ret->domain) {
ret->local = 0;
/* check that there is an mx (or A record) for the mail domain;
* if that fails we fail unless verify_from is off and it's
* a MAIL FROM:<> address
*/
if ( (getMXes(ret->domain, 1, &mxes) > 0) ) {
for (i=0; i < mxes.count; i++)
if ( localIP(let->env, &mxes.a[i] ) ) {
/* we are a legitimate mx for this address.
*/
ret->local = 1;
if ( (i == 0) || !(let->env->mxpool) ) {
/* If we're not mxpooling, we handle mail for
* this domain locally, but if we are mxpooling
* we only handle the mail locally if we're the
* best mx for the domain
*/
ret->deliver_here = 1;
ret->dom = getdomain(ret->domain);
}
break;
}
freeiplist(&mxes);
}
else if ( !okayanyhow(let->env,flags) ) {
if (reason) *reason = V_NOMX;
freeaddress(ret);
return 0;
}
}
else {
ret->deliver_here = ret->local = 1;
ret->dom = dom;
}
if (ret->deliver_here && (!userok(let,ret)) && (flags & VF_USER) ) {
if (reason) *reason = V_WRONG;
freeaddress(ret);
return 0;
}
return ret;
}
if (reason) { *reason = bad ? V_BOGUS : V_ERROR; }
return 0;
}
int main(int argc, char *argv[]) {
int i,j/*,k,test*/;
int ndomain,total,add;
int gottrans;
int T_FLAG;
/* char c; */
char *env;
char *deffile,*keyword,*value;
FILE *PARMS,*TRANS,*PDB;
struct parameters *parms;
struct domain_loc *domain;
if(argc<2) exit_error();
/* get environment variable */
if((env=getenv("STAMPDIR"))==NULL) {
fprintf(stderr,"error: environment variable STAMPDIR must be set\n");
exit(-1);
}
parms=(struct parameters*)malloc(sizeof(struct parameters));
strcpy(parms[0].stampdir,env);
/* read in default parameters from $STAMPDIR/stamp.defaults */
deffile=(char*)malloc(1000*sizeof(char));
#if defined(_MSC_VER)
sprintf(deffile,"%s\\stamp.defaults",env);
#else
sprintf(deffile,"%s/stamp.defaults",env);
#endif
if((PARMS=fopen(deffile,"r"))==NULL) {
fprintf(stderr,"error: default parameter file %s does not exist\n",deffile);
exit(-1);
}
if(getpars(PARMS,parms)==-1) exit(-1);
fclose(PARMS);
/* define DSSP directory file name */
sprintf(&parms[0].dsspfile[0],"%s/dssp.directories",env);
/* now search the command line for commands */
keyword=(char*)malloc(1000*sizeof(char));
value=(char*)malloc(1000*sizeof(char));
for(i=1; i<argc; ++i) {
if(argv[i][0]!='-') exit_error();
strcpy(keyword,&argv[i][1]);
if(i+1<argc) strcpy(value,argv[i+1]);
else strcpy(value,"none");
for(j=0; j<strlen(keyword); ++j)
keyword[j]=ltou(keyword[j]); /* change to upper case */
T_FLAG=(value[0]=='Y' || value[0]=='y' || value[0]=='1' ||
value[0]=='T' || value[0]=='t' || value[0]=='o' ||
value[0]=='O');
/* enables one to write '1', 'YES', 'Yes', 'yes', 'T_FLAG', 'True' or 'true' to
* set any boolean parmsiable to one */
if((strcmp(&argv[i][1],"l")==0) || (strcmp(&argv[i][1],"f")==0) || (strcmp(&argv[i][1],"p")==0)) {
if(i+1>=argc) exit_error();
/* listfile name */
strcpy(parms[0].listfile,argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"P")==0) {
/* want to read in parameter file */
if(i+1>=argc) exit_error();
if((PARMS=fopen(argv[i+1],"r"))==NULL) {
fprintf(stderr,"error opening file %s\n",argv[i+1]);
exit(-1);
}
if(getpars(PARMS,parms)==-1) exit(-1);
fclose(PARMS);
i++;
} else if(strcmp(&argv[i][1],"o")==0) {
/* output file */
if(i+1>=argc) exit_error();
strcpy(parms[0].logfile,argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"help")==0) {
help_exit_error();
} else if((strcmp(&argv[i][1],"V")==0) || (strcmp(&argv[i][1],"v")==0)) {
parms[0].verbose=1;
strcpy(parms[0].logfile,"stdout");
} else if(strcmp(&argv[i][1],"s")==0) {
parms[0].SCAN=1;
parms[0].TREEWISE=parms[0].PAIRWISE=0;
} else if(strcmp(&argv[i][1],"n")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%d",&parms[0].NPASS);
i++;
if(parms[0].NPASS!=1 && parms[0].NPASS!=2) exit_error();
} else if(strcmp(keyword,"PAIRPEN") == 0 || strcmp(keyword,"PEN")==0 || strcmp(keyword,"SECOND_PAIRPEN")==0) {
sscanf(value,"%f",&parms[0].second_PAIRPEN);
i++;
} else if(strcmp(keyword,"FIRST_PAIRPEN")==0) {
sscanf(value,"%f",&parms[0].first_PAIRPEN);
i++;
} else if(strcmp(keyword,"MAXPITER") == 0 || strcmp(keyword,"MAXSITER") == 0) {
sscanf(value,"%d",&parms[0].MAXPITER);
i++;
} else if(strcmp(keyword,"MAXTITER") == 0) {
sscanf(value,"%d",&parms[0].MAXTITER);
i++;
} else if(strcmp(keyword,"TREEPEN") == 0 || strcmp(keyword,"SECOND_TREEPEN")==0) {
sscanf(value,"%f",&parms[0].second_TREEPEN);
i++;
} else if(strcmp(keyword,"FIRST_TREEPEN")==0) {
sscanf(value,"%f",&parms[0].first_TREEPEN);
i++;
} else if(strcmp(keyword,"SCORETOL") == 0) {
sscanf(value,"%f",&parms[0].SCORETOL);
i++;
} else if(strcmp(keyword,"CLUSTMETHOD") == 0) {
sscanf(value,"%d",&parms[0].CLUSTMETHOD);
i++;
} else if(strcmp(keyword,"E1") == 0 || strcmp(keyword,"SECOND_E1")==0) {
sscanf(value,"%f",&parms[0].second_E1);
i++;
} else if(strcmp(keyword,"E2") == 0 || strcmp(keyword,"SECOND_E2")==0) {
sscanf(value,"%f",&parms[0].second_E2);
i++;
} else if(strcmp(keyword,"FIRST_E1")==0) {
sscanf(value,"%f",&parms[0].first_E1);
i++;
} else if(strcmp(keyword,"FIRST_E2")==0) {
sscanf(value,"%f",&parms[0].first_E2);
i++;
} else if(strcmp(keyword,"NPASS")==0) {
sscanf(value,"%d",&parms[0].NPASS);
i++;
if(parms[0].NPASS!=1 && parms[0].NPASS!=2) {
fprintf(stderr,"error: NPASS must be either 1 or 2\n");
return -1;
}
} else if(strcmp(keyword,"CUTOFF") == 0 || strcmp(keyword,"SECOND_CUTOFF")==0) {
sscanf(value,"%f",&parms[0].second_CUTOFF);
i++;
} else if(strcmp(keyword,"FIRST_CUTOFF")==0) {
sscanf(value,"%f",&parms[0].first_CUTOFF);
i++;
} else if(strcmp(keyword,"TREEPLOT") == 0) {
parms[0].TREEPLOT=T_FLAG;
i++;
} else if(strcmp(keyword,"PAIRPLOT") == 0) {
parms[0].PAIRPLOT=T_FLAG;
i++;
} else if(strcmp(keyword,"NALIGN") == 0) {
sscanf(value,"%d",&parms[0].NALIGN);
i++;
} else if(strcmp(keyword,"DISPALL") == 0) {
parms[0].DISPALL=T_FLAG;
i++;
} else if(strcmp(keyword,"HORIZ") ==0) {
parms[0].HORIZ=T_FLAG;
i++;
} else if(strcmp(keyword,"ADD") ==0) {
sscanf(value,"%f",&parms[0].ADD);
i++;
} else if(strcmp(keyword,"NMEAN") ==0) {
sscanf(value,"%f",&parms[0].NMEAN);
i++;
} else if(strcmp(keyword,"NSD") ==0) {
sscanf(value,"%f",&parms[0].NSD);
i++;
} else if(strcmp(keyword,"STATS") ==0) {
parms[0].STATS=T_FLAG;
i++;
} else if(strcmp(keyword,"NA") == 0) {
sscanf(value,"%f",&parms[0].NA);
i++;
} else if(strcmp(keyword,"NB") == 0) {
sscanf(value,"%f",&parms[0].NB);
i++;
} else if(strcmp(keyword,"NASD") == 0) {
sscanf(value,"%f",&parms[0].NASD);
i++;
} else if(strcmp(keyword,"NBSD") == 0) {
sscanf(value,"%f",&parms[0].NBSD);
i++;
} else if(strcmp(keyword,"PAIRWISE") == 0) {
parms[0].PAIRWISE=T_FLAG;
i++;
} else if(strcmp(keyword,"TREEWISE") == 0) {
parms[0].TREEWISE=T_FLAG;
i++;
} else if(strcmp(keyword,"ORDFILE") == 0) {
strcpy(parms[0].ordfile,value);
i++;
} else if(strcmp(keyword,"TREEFILE") == 0) {
strcpy(parms[0].treefile,value);
i++;
} else if(strcmp(keyword,"PLOTFILE") == 0) {
strcpy(parms[0].plotfile,value);
i++;
} else if(strcmp(keyword,"PREFIX") == 0 || strcmp(keyword,"TRANSPREFIX")==0 || strcmp(keyword,"STAMPPREFIX")==0) {
strcpy(parms[0].transprefix,value);
i++;
} else if(strcmp(keyword,"MATFILE") == 0) {
strcpy(parms[0].matfile,value);
i++;
} else if(strcmp(keyword,"THRESH") ==0) {
sscanf(value,"%f",&parms[0].THRESH);
i++;
} else if(strcmp(keyword,"TREEALIGN")==0) {
parms[0].TREEALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"TREEALLALIGN")==0) {
parms[0].TREEALLALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"PAIRALIGN")==0 || strcmp(keyword,"SCANALIGN")==0) {
parms[0].PAIRALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"PAIRALLALIGN")==0 || strcmp(keyword,"SCANALLALIGN")==0) {
parms[0].PAIRALLALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"PRECISION")==0) {
sscanf(value,"%d",&parms[0].PRECISION);
i++;
} else if(strcmp(keyword,"MAX_SEQ_LEN")==0) {
sscanf(value,"%d",&parms[0].MAX_SEQ_LEN);
i++;
} else if(strcmp(keyword,"ROUGHFIT")==0) {
parms[0].ROUGHFIT=T_FLAG;
i++;
} else if(strcmp(keyword,"ROUGH")==0) {
parms[0].ROUGHFIT=1;
} else if(strcmp(keyword,"ROUGHOUT")==0) {
parms[0].roughout=1;
} else if(strcmp(keyword,"ROUGHOUTFILE")==0) {
if(i+1>=argc) exit_error();
strcpy(&parms[0].roughoutfile[0],argv[i+1]);
i++;
parms[0].roughout=1;
} else if(strcmp(keyword,"BOOLCUT")==0 || strcmp(keyword,"SECOND_BOOLCUT")==0) {
sscanf(value,"%f",&parms[0].second_BOOLCUT);
i++;
} else if(strcmp(keyword,"FIRST_BOOLCUT")==0) {
sscanf(value,"%f",&parms[0].first_BOOLCUT);
i++;
} else if(strcmp(keyword,"SCANSLIDE")==0) {
sscanf(value,"%d",&parms[0].SCANSLIDE);
i++;
} else if(strcmp(keyword,"SCAN")==0) {
parms[0].SCAN=T_FLAG;
i++;
if(T_FLAG)
parms[0].PAIRWISE=parms[0].TREEWISE=0;
} else if(strcmp(keyword,"SCANMODE")==0) {
sscanf(value,"%d",&parms[0].SCANMODE);
i++;
if(parms[0].SCANMODE==1) parms[0].PAIRALIGN=1;
} else if(strcmp(keyword,"SCANCUT")==0) {
sscanf(value,"%f",&parms[0].SCANCUT);
i++;
} else if(strcmp(keyword,"SECSCREEN")==0) {
parms[0].SECSCREEN=T_FLAG;
i++;
} else if(strcmp(keyword,"SECSCREENMAX")==0) {
sscanf(value,"%f",&parms[0].SECSCREENMAX);
i++;
} else if(strcmp(keyword,"SCANTRUNC")==0) {
parms[0].SCANTRUNC=T_FLAG;
i++;
} else if(strcmp(keyword,"SCANTRUNCFACTOR")==0) {
sscanf(value,"%f",&parms[0].SCANTRUNCFACTOR);
i++;
} else if(strcmp(keyword,"DATABASE")==0) {
strcpy(&parms[0].database[0],value);
i++;
} else if(strcmp(keyword,"SCANFILE")==0) {
strcpy(&parms[0].scanfile[0],value);
i++;
} else if(strcmp(keyword,"LOGFILE")==0) {
strcpy(&parms[0].logfile[0],value);
i++;
} else if(strcmp(keyword,"SECTYPE")==0) {
sscanf(value,"%d",&parms[0].SECTYPE);
i++;
} else if(strcmp(keyword,"SCANSEC")==0) {
sscanf(value,"%d",&parms[0].SCANSEC);
i++;
} else if(strcmp(keyword,"SECFILE")==0) {
strcpy(&parms[0].secfile[0],value);
i++;
parms[0].SECTYPE=2;
} else if(strcmp(keyword,"BOOLEAN")==0) {
parms[0].BOOLEAN=T_FLAG;
i++;
} else if(strcmp(keyword,"BOOLMETHOD")==0) {
sscanf(value,"%d",&parms[0].BOOLMETHOD);
i++;
} else if(strcmp(keyword,"LISTFILE")==0) {
strcpy(&parms[0].listfile[0],value);
i++;
} else if(strcmp(keyword,"STAMPDIR")==0) {
strcpy(&parms[0].stampdir[0],value);
i++;
} else if(strcmp(keyword,"CLUST")==0) {
parms[0].CLUST=T_FLAG;
i++;
} else if(strcmp(keyword,"COLUMNS")==0) {
sscanf(value,"%d",&parms[0].COLUMNS);
i++;
} else if(strcmp(keyword,"SW")==0) {
sscanf(value,"%d",&parms[0].SW);
i++;
} else if(strcmp(keyword,"CCFACTOR")==0) {
sscanf(value,"%f",&parms[0].CCFACTOR);
i++;
} else if(strcmp(keyword,"CCADD")==0) {
parms[0].CCADD=T_FLAG;
i++;
} else if(strcmp(keyword,"MINFIT")==0) {
sscanf(value,"%d",&parms[0].MINFIT);
i++;
} else if(strcmp(keyword,"ROUGHALIGN")==0) {
strcpy(parms[0].roughalign,value);
i++;
} else if(strcmp(keyword,"FIRST_THRESH")==0) {
sscanf(value,"%f",&parms[0].first_THRESH);
i++;
} else if(strcmp(keyword,"MIN_FRAC")==0) {
sscanf(value,"%f",&parms[0].MIN_FRAC);
i++;
} else if(strcmp(keyword,"SCORERISE")==0) {
parms[0].SCORERISE=T_FLAG;
i++;
} else if(strcmp(keyword,"SKIPAHEAD")==0) {
parms[0].SKIPAHEAD=T_FLAG;
i++;
} else if(strcmp(keyword,"SCANSCORE")==0) {
sscanf(value,"%d",&parms[0].SCANSCORE);
i++;
} else if(strcmp(keyword,"PAIROUTPUT")==0) {
parms[0].PAIROUTPUT=T_FLAG;
i++;
} else if(strcmp(keyword,"ALLPAIRS")==0) {
parms[0].ALLPAIRS=T_FLAG;
i++;
} else if (strcmp(keyword,"ATOMTYPE")==0) {
parms[0].ATOMTYPE=T_FLAG;
i++;
} else if(strcmp(keyword,"DSSP")==0) {
parms[0].DSSP=T_FLAG;
i++;
} else if(strcmp(keyword,"SLOWSCAN")==0) {
parms[0].SLOWSCAN=T_FLAG;
i++;
} else if(strcmp(keyword,"SLOW")==0) {
parms[0].SLOWSCAN=1;
} else if(strcmp(keyword,"CUT")==0) {
parms[0].CO=1;
} else if(strcmp(&argv[i][1],"slide")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%d",&parms[0].SCANSLIDE);
i++;
} else if(strcmp(&argv[i][1],"d")==0) {
/* database file */
if(i+1>=argc) exit_error();
strcpy(&parms[0].database[0],argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"pen1")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%f",&parms[0].first_PAIRPEN);
i++;
} else if(strcmp(&argv[i][1],"pen2")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%f",&parms[0].second_PAIRPEN);
i++;
} else if(strcmp(&argv[i][1],"prefix")==0) {
if(i+1>=argc) exit_error();
strcpy(&parms[0].transprefix[0],argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"scancut")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%f",&parms[0].SCANCUT);
i++;
} else if(strcmp(&argv[i][1],"opd")==0) {
parms[0].opd=1;
} else {
exit_error();
}
}
free(keyword);
free(value);
/* make the names of all the output files using the prefix */
sprintf(&parms[0].ordfile[0],"%s.ord",parms[0].transprefix);
sprintf(&parms[0].treefile[0],"%s.tree",parms[0].transprefix);
sprintf(&parms[0].plotfile[0],"%s.plot",parms[0].transprefix);
sprintf(&parms[0].matfile[0],"%s.mat",parms[0].transprefix);
sprintf(&parms[0].roughalign[0],"%s_align.rough",parms[0].transprefix);
sprintf(&parms[0].scanfile[0],"%s.scan",parms[0].transprefix);
if(strcmp(parms[0].logfile,"stdout")==0 ||
strcmp(parms[0].logfile,"STDOUT")==0) {
parms[0].LOG=stdout;
} else if(strcmp(parms[0].logfile,"silent")==0 ||
strcmp(parms[0].logfile,"SILENT")==0) {
#if defined(_MSC_VER)
parms[0].LOG=stdout;
#else
parms[0].LOG=fopen("/dev/null","w");
#endif
} else {
if((parms[0].LOG=fopen(parms[0].logfile,"w"))==NULL) {
fprintf(stderr,"error opening file %s\n",parms[0].logfile);
exit(-1);
}
}
if(strcmp(parms[0].logfile,"silent")==0) {
printf("\nSTAMP Structural Alignment of Multiple Proteins\n");
printf(" by Robert B. Russell & Geoffrey J. Barton \n");
printf(" Please cite PROTEINS, v14, 309-323, 1992\n\n");
}
fprintf(parms[0].LOG,"-------------------------------------------------------------------------------\n");
fprintf(parms[0].LOG," S t A M P\n");
fprintf(parms[0].LOG," Structural Alignment of\n");
fprintf(parms[0].LOG," Multiple Proteins\n");
fprintf(parms[0].LOG," By Robert B. Russell & Geoffrey J. Barton \n");
fprintf(parms[0].LOG," Last Modified: %s\n",lastmod);
fprintf(parms[0].LOG," Please cite Ref: Russell and GJ Barton, PROTEINS, v14, 309-323, 1992\n");
fprintf(parms[0].LOG,"-------------------------------------------------------------------------------\n\n");
fprintf(parms[0].LOG,"STAMPDIR has been set to %s\n\n\n",parms[0].stampdir);
/* read in coordinate locations and initial transformations */
if((TRANS = fopen(parms[0].listfile,"r")) == NULL) {
fprintf(stderr,"error: file %s does not exist\n",parms[0].listfile);
exit(-1);
}
/* determine the number of domains specified */
ndomain=count_domain(TRANS);
domain=(struct domain_loc*)malloc(ndomain*sizeof(struct domain_loc));
rewind(TRANS);
if(getdomain(TRANS,domain,&ndomain,ndomain,&gottrans,parms[0].stampdir,parms[0].DSSP,parms[0].LOG)==-1) exit(-1);
fclose(TRANS);
fprintf(parms[0].LOG,"Details of this run:\n");
if(parms[0].PAIRWISE) fprintf(parms[0].LOG,"PAIRWISE mode specified\n");
if(parms[0].TREEWISE) fprintf(parms[0].LOG,"TREEWISE mode specified\n");
if(parms[0].SCAN) fprintf(parms[0].LOG,"SCAN mode specified\n");
if(!parms[0].SCAN) {
/* if no MINFIT has been given, then take the smallest length and divide it by two */
if(parms[0].MINFIT==-1) {
parms[0].MINFIT=parms[0].MAXLEN;
for(i=0; i<ndomain; ++i) if(domain[i].ncoords<parms[0].MINFIT) parms[0].MINFIT=domain[i].ncoords;
parms[0].MINFIT/=2;
}
fprintf(parms[0].LOG," pairwise score file: %s\n",parms[0].matfile);
if(parms[0].TREEWISE) {
fprintf(parms[0].LOG," tree order file: %s\n",parms[0].ordfile);
fprintf(parms[0].LOG," tree file: %s\n",parms[0].treefile);
fprintf(parms[0].LOG," tree plot file: %s\n",parms[0].plotfile);
}
} else {
fprintf(parms[0].LOG," SCANMODE set to %d\n",parms[0].SCANMODE);
fprintf(parms[0].LOG," SCANSCORE set to %d\n",parms[0].SCANSCORE);
fprintf(parms[0].LOG," (see documentation for an explanation)\n");
if(parms[0].opd==1) fprintf(parms[0].LOG," Domains will be skipped after the first match is found\n");
if(parms[0].SCANMODE==1) {
fprintf(parms[0].LOG," Transformations for Sc values greater than %f are to be output\n",parms[0].SCANCUT);
fprintf(parms[0].LOG," to the file %s\n",parms[0].transprefix);
} else {
fprintf(parms[0].LOG," Only the scores are to be output to the file %s\n",parms[0].scanfile);
}
fprintf(parms[0].LOG," secondary structures are ");
switch(parms[0].SCANSEC) {
case 0:
fprintf(parms[0].LOG," not to be considered\n");
break;
case 1:
fprintf(parms[0].LOG," to be from DSSP\n");
break;
case 2:
fprintf(parms[0].LOG," to be read in from %s\n",parms[0].secfile);
break;
default:
fprintf(parms[0].LOG," not to be considered\n");
}
if(parms[0].SECSCREEN) {
fprintf(parms[0].LOG," An initial screen on secondary structure content is to performed when possible\n");
fprintf(parms[0].LOG," Secondary structure summaries farther than %6.2f %% apart result in\n",parms[0].SECSCREENMAX);
fprintf(parms[0].LOG," a comparison being ignored\n");
}
fprintf(parms[0].LOG," Initial fits are to be performed by aligning the N-terminus of the query\n with every %d residue of the database sequence\n",parms[0].SCANSLIDE);
fprintf(parms[0].LOG," of the query along the database structure.\n");
if(parms[0].SCANTRUNC) {
fprintf(parms[0].LOG," If sequences in the database are > %5.3f x the query sequence length\n",parms[0].SCANTRUNCFACTOR);
fprintf(parms[0].LOG," then a fraction of the the database structure, corresponding to this\n");
fprintf(parms[0].LOG," of length %5.3f x the query, will be considered\n",parms[0].SCANTRUNCFACTOR);
fprintf(parms[0].LOG," comparisons are to be ignored if the database structure is less than\n %6.4f x the length of the query structure\n",parms[0].MIN_FRAC);
}
fprintf(parms[0].LOG," Domain database file to be scanned %s\n",parms[0].database);
}
if(parms[0].TREEWISE)
fprintf(parms[0].LOG," output files prefix: %s\n",parms[0].transprefix);
fprintf(parms[0].LOG,"\n\nParameters:\n");
fprintf(parms[0].LOG,"Rossmann and Argos parameters:\n");
if(parms[0].NPASS==2) {
fprintf(parms[0].LOG," Two fits are to be performed, the first fit with:\n");
fprintf(parms[0].LOG," E1=%7.3f,",parms[0].first_E1);
fprintf(parms[0].LOG," E2=%7.3f,",parms[0].first_E2);
fprintf(parms[0].LOG," CUT=%7.3f,",parms[0].first_CUTOFF);
fprintf(parms[0].LOG," PAIRPEN=%7.3f,",parms[0].first_PAIRPEN);
fprintf(parms[0].LOG," TREEPEN=%7.3f\n",parms[0].first_TREEPEN);
/* fprintf(parms[0].LOG," E1=%7.3f, E2=%7.3f, CUT=%7.3f, PAIRPEN=%7.3f, TREEPEN=%7.3f\n",
parms[0].first_E1,parms[0].first_E2,parms[0].first_CUTOFF,parms[0].first_PAIRPEN,parms[0].first_TREEPEN); */
fprintf(parms[0].LOG," The second fit with:\n");
} else
fprintf(parms[0].LOG," One fit is to performed with:\n");
fprintf(parms[0].LOG," E1=%7.3f, E2=%7.3f, CUT=%7.3f, PAIRPEN=%7.3f, TREEPEN=%7.3f\n",
parms[0].second_E1,parms[0].second_E2,parms[0].second_CUTOFF,parms[0].second_PAIRPEN,parms[0].second_TREEPEN);
if(parms[0].BOOLEAN) {
fprintf(parms[0].LOG," BOOLEAN mode specified\n");
fprintf(parms[0].LOG," A boolean matrix will be calculated corresponding to whether\n");
fprintf(parms[0].LOG," positions have Pij values greater than:\n");
if(parms[0].NPASS==2)
fprintf(parms[0].LOG," %7.3f, for the first fit and\n",parms[0].first_BOOLCUT);
fprintf(parms[0].LOG," %7.3f",parms[0].second_BOOLCUT);
if(parms[0].NPASS==2)
fprintf(parms[0].LOG," for the second fit.\n");
else
fprintf(parms[0].LOG,".\n");
fprintf(parms[0].LOG," In the multiple case, this criteria must be satisfied for *all*\n");
fprintf(parms[0].LOG," possible pairwise comparisons\n");
}
if(parms[0].SW==1) {
fprintf(parms[0].LOG," Corner cutting is to be performed\n");
fprintf(parms[0].LOG," Corner cutting length: %6.2f\n",parms[0].CCFACTOR);
if(parms[0].CCADD)
fprintf(parms[0].LOG," The length difference is to be added to this value\n");
} else {
fprintf(parms[0].LOG," The entire SW matrix is to be calculated and used\n");
}
fprintf(parms[0].LOG," The minimum length of alignment to be evaluated further is %3d residues\n",parms[0].MINFIT);
fprintf(parms[0].LOG,"\n");
fprintf(parms[0].LOG," Convergence tolerance SCORETOL= %f %%\n", parms[0].SCORETOL);
fprintf(parms[0].LOG," Other parameters:\n");
fprintf(parms[0].LOG," MAX_SEQ_LEN=%d, MAXPITER=%d, MAXTITER=%d\n",
parms[0].MAX_SEQ_LEN,parms[0].MAXPITER,parms[0].MAXTITER);
fprintf(parms[0].LOG," PAIRPLOT (SCANPLOT) = %d, TREEPLOT = %d, PAIRALIGN (SCANALIGN) = %d, TREEALIGN = %d\n",
parms[0].PAIRPLOT,parms[0].TREEPLOT,parms[0].PAIRALIGN,parms[0].TREEALIGN);
fprintf(parms[0].LOG," PAIRALLALIGN (SCANALLALIGN) = %d, TREEALLALIGN = %d\n",parms[0].PAIRALLALIGN,parms[0].TREEALLALIGN);
if(!parms[0].BOOLEAN) {
fprintf(parms[0].LOG,"\n\nDetails of Confidence value calculations:\n");
if(parms[0].STATS) fprintf(parms[0].LOG," actual mean and standard deviations are to be\n used for determination of Pij' values.\n");
else {
fprintf(parms[0].LOG," pre-set mean and standard deviations are to be used\n and multiple comparisons are to be corrected.\n");
fprintf(parms[0].LOG," mean Xt = %f, standard deviation SDt = %f\n", parms[0].NMEAN,parms[0].NSD);
fprintf(parms[0].LOG," for the multiple case:\n");
fprintf(parms[0].LOG," pairwise means are to be calculated from:\n Xp = exp(%6.4f * log(length) + %6.4f)\n",parms[0].NA,parms[0].NB);
fprintf(parms[0].LOG," and pairwise standard deviations from:\n SDp = exp(%6.4f * log(length) + %6.4f)\n",parms[0].NASD,parms[0].NBSD);
fprintf(parms[0].LOG," the mean to be used is calculated from: \n Xc = (Xm/Xp) * Xt).\n");
fprintf(parms[0].LOG," and the standard deviation from: \n SDc = (SDm/SDp)*SDt).\n");
} /* End of if(parms[0].STATS) */
} else {
fprintf(parms[0].LOG," Positional values will consist of one's or zeros depending on whether\n");
fprintf(parms[0].LOG," a position satisfies the BOOLEAN criterion above\n");
fprintf(parms[0].LOG," The score (Sp) for each alignment will be a sum of these positions.\n");
} /* end of if(parms[0].BOOLEAN */
if(!parms[0].SCAN && parms[0].TREEWISE) {
fprintf(parms[0].LOG,"\n\nTree is to be generated by ");
if(parms[0].CLUSTMETHOD==0) fprintf(parms[0].LOG,"1/rms values.\n");
if(parms[0].CLUSTMETHOD==1) {
fprintf(parms[0].LOG,"scores from path tracings modified as follows:\n");
fprintf(parms[0].LOG," Sc = (Sp/Lp) * ((Lp-ia)/La) * ((Lp-ib)/Lb),\n");
fprintf(parms[0].LOG," where Sp is the actual score, Lp is the path length.\n");
fprintf(parms[0].LOG," and La & Lb are the lengths of the structures considered.\n");
} /* End of if(parms[0].METHOD==2) */
}
fprintf(parms[0].LOG,"\n\n");
fprintf(parms[0].LOG,"Reading coordinates...\n");
for(i=0; i<ndomain; ++i) {
fprintf(parms[0].LOG,"Domain %3d %s %s\n ",i+1,domain[i].filename,domain[i].id);
if((PDB=openfile(domain[i].filename,"r"))==NULL) {
fprintf(stderr,"error opening file %s\n",domain[i].filename);
exit(-1);
}
domain[i].ncoords=0;
domain[i].coords=(int**)malloc(parms[0].MAX_SEQ_LEN*sizeof(int*));
domain[i].aa=(char*)malloc((parms[0].MAX_SEQ_LEN+1)*sizeof(char));
domain[i].numb=(struct brookn*)malloc((parms[0].MAX_SEQ_LEN)*sizeof(struct brookn));
total=0;
fprintf(parms[0].LOG," ");
for(j=0; j<domain[i].nobj; ++j) {
if(!parms[0].DSSP) {
if(igetca(PDB,&domain[i].coords[total],&domain[i].aa[total],&domain[i].numb[total],
&add,domain[i].start[j],domain[i].end[j],domain[i].type[j],(parms[0].MAX_SEQ_LEN-total),
domain[i].reverse[j],parms[0].PRECISION,parms[0].ATOMTYPE,parms[0].LOG)==-1) {
fprintf(stderr,"Error in domain %s object %d \n",domain[i].id,j+1);
exit(-1);
}
} else {
if(igetcadssp(PDB,&domain[i].coords[total],&domain[i].aa[total],&domain[i].numb[total],
&add,domain[i].start[j],domain[i].end[j],domain[i].type[j],(parms[0].MAX_SEQ_LEN-total),
domain[i].reverse[j],parms[0].PRECISION,parms[0].LOG)==-1) exit(-1);
}
switch(domain[i].type[j]) {
case 1:
fprintf(parms[0].LOG," all residues");
break;
case 2:
fprintf(parms[0].LOG," chain %c",domain[i].start[j].cid);
break;
case 3:
fprintf(parms[0].LOG," from %c %4d %c to %c %4d %c",
domain[i].start[j].cid,domain[i].start[j].n,domain[i].start[j].in,
domain[i].end[j].cid,domain[i].end[j].n,domain[i].end[j].in);
break;
}
fprintf(parms[0].LOG,"%4d CAs ",add);
total+=add;
closefile(PDB,domain[i].filename);
PDB=openfile(domain[i].filename,"r");
}
domain[i].ncoords=total;
fprintf(parms[0].LOG,"=> %4d CAs in total\n",domain[i].ncoords);
fprintf(parms[0].LOG,"Applying the transformation... \n");
printmat(domain[i].R,domain[i].V,3,parms[0].LOG);
fprintf(parms[0].LOG," ...to these coordinates.\n");
matmult(domain[i].R,domain[i].V,domain[i].coords,domain[i].ncoords,parms[0].PRECISION);
closefile(PDB,domain[i].filename);
}
fprintf(parms[0].LOG,"\n\n");
fprintf(parms[0].LOG,"Secondary structure...\n");
for(i=0; i<ndomain; ++i)
domain[i].sec=(char*)malloc(parms[0].MAX_SEQ_LEN*sizeof(char));
switch(parms[0].SECTYPE) {
case 0: {
fprintf(parms[0].LOG,"No secondary structure assignment will be considered\n");
for(i=0; i<ndomain; ++i) {
for(j=0; j<domain[i].ncoords; ++j) domain[i].sec[j]='?';
domain[i].sec[j]='\0';
}
parms[0].SECSCREEN=0;
}
break;
case 1: {
fprintf(parms[0].LOG,"Will try to find Kabsch and Sander DSSP assignments\n");
if(getks(domain,ndomain,parms)!=0) parms[0].SECSCREEN=0;
}
break;
case 2: {
fprintf(parms[0].LOG,"Reading in secondary structure assignments from file: %s\n",parms[0].secfile);
if(getsec(domain,ndomain,parms)!=0) parms[0].SECSCREEN=0;
}
break;
default: {
fprintf(stderr,"error: unrecognised secondary structure assignment option\n");
exit(-1);
}
}
fprintf(parms[0].LOG,"\n\n");
if(parms[0].SCAN) {
i=0;
fprintf(parms[0].LOG,"Scanning with domain %s\n",&(domain[i].id[0]));
if(strcmp(parms[0].logfile,"silent")==0) {
printf("Results of scan will be written to file %s\n",parms[0].scanfile);
printf("Fits = no. of fits performed, Sc = STAMP score, RMS = RMS deviation\n");
printf("Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues\n");
printf("Secs = no. equiv. secondary structures, %%I = seq. identity, %%S = sec. str. identity\n");
printf("P(m) = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694\n");
printf("\n");
printf(" Domain1 Domain2 Fits Sc RMS Len1 Len2 Align Fit Eq. Secs %%I %%S P(m)\n");
}
if(parms[0].SLOWSCAN==1) {
if(slow_scan(domain[i],parms)==-1) exit(-1);
} else {
if(scan(domain[i],parms)==-1) exit(-1);
}
if(strcmp(parms[0].logfile,"silent")==0)
printf("See the file %s.scan\n",parms[0].transprefix);
fprintf(parms[0].LOG,"\n");
} else {
if(parms[0].ROUGHFIT) if(roughfit(domain,ndomain,parms)==-1) exit(-1);
if(parms[0].PAIRWISE) if(pairwise(domain,ndomain,parms)==-1) exit(-1);
if(parms[0].TREEWISE) if(treewise(domain,ndomain,parms)==-1) exit(-1);
} /* end of if(parms[0].SCAN... */
/* freeing memory to keep purify happy */
/*
for(i=0; i<ndomain; ++i) {
free(domain[i].aa);
free(domain[i].sec);
free(domain[i].v); free(domain[i].V);
for(j=0; j<3; ++j) {
free(domain[i].R[j]);
free(domain[i].r[j]);
}
free(domain[i].R);
free(domain[i].r);
for(j=0; j<domain[i].ncoords; ++j)
free(domain[i].coords[j]);
free(domain[i].coords);
free(domain[i].type);
free(domain[i].start);
free(domain[i].end);
free(domain[i].reverse);
free(domain[i].numb);
}
*/
free(domain);
exit(0);
}
