void Helix(CHAIN **Chain, int Cn, HBOND **HBond, COMMAND *Cmd, float **PhiPsiMap)
{
int BondNumb, i;
float *Prob, CONST;
RESIDUE **r;
CONST = 1+Cmd->C1_H;
Prob = (float *)ckalloc(MAX_RES*sizeof(float));
for( i=0; i<Chain[Cn]->NRes; i++ )
Prob[i] = 0.0;
for( i=0; i<Chain[Cn]->NRes-5; i++ ) {
r = &Chain[Cn]->Rsd[i];
if( r[0]->Prop->PhiZn != ERR && r[0]->Prop->PsiZn != ERR &&
r[1]->Prop->PhiZn != ERR && r[1]->Prop->PsiZn != ERR &&
r[2]->Prop->PhiZn != ERR && r[2]->Prop->PsiZn != ERR &&
r[3]->Prop->PhiZn != ERR && r[3]->Prop->PsiZn != ERR &&
r[4]->Prop->PhiZn != ERR && r[4]->Prop->PsiZn != ERR ) {
if( (BondNumb = FindPolInt(HBond,r[4],r[0])) != ERR ) {
Prob[i] = HBond[BondNumb]->Energy*(CONST+Cmd->C2_H*
0.5*(PhiPsiMap[r[0]->Prop->PhiZn][r[0]->Prop->PsiZn]+
PhiPsiMap[r[4]->Prop->PhiZn][r[4]->Prop->PsiZn]));
}
}
}
for( i=0; i<Chain[Cn]->NRes-5; i++ ) {
if( Prob[i] < Cmd->Treshold_H1 && Prob[i+1] < Cmd->Treshold_H1 ) {
r = &Chain[Cn]->Rsd[i];
r[1]->Prop->Asn = 'H';
r[2]->Prop->Asn = 'H';
r[3]->Prop->Asn = 'H';
r[4]->Prop->Asn = 'H';
if( r[0]->Prop->PhiZn!= ERR && r[0]->Prop->PsiZn != ERR &&
PhiPsiMap[r[0]->Prop->PhiZn][r[0]->Prop->PsiZn] > Cmd->Treshold_H3 )
r[0]->Prop->Asn = 'H';
if( r[5]->Prop->PhiZn != ERR && r[5]->Prop->PsiZn != ERR &&
PhiPsiMap[r[5]->Prop->PhiZn][r[5]->Prop->PsiZn] > Cmd->Treshold_H4 )
r[5]->Prop->Asn = 'H';
}
}
for( i=0; i<Chain[Cn]->NRes-4; i++ ) {
r = &Chain[Cn]->Rsd[i];
if( FindBnd(HBond,r[3],r[0]) != ERR && FindBnd(HBond,r[4],r[1]) != ERR &&
/*************************** This should be improved **************************/
( (r[1]->Prop->Asn != 'H' && r[2]->Prop->Asn != 'H') ||
(r[2]->Prop->Asn != 'H' && r[3]->Prop->Asn != 'H') ) )
/******************************************************************************/
{
r[1]->Prop->Asn = 'G';
r[2]->Prop->Asn = 'G';
r[3]->Prop->Asn = 'G';
}
}
for( i=0; i<Chain[Cn]->NRes-6; i++ ) {
r = &Chain[Cn]->Rsd[i];
if( FindBnd(HBond,r[5],r[0]) != ERR && FindBnd(HBond,r[6],r[1]) != ERR &&
r[1]->Prop->Asn == 'C' && r[2]->Prop->Asn == 'C' &&
r[3]->Prop->Asn == 'C' && r[4]->Prop->Asn == 'C' &&
r[5]->Prop->Asn == 'C' ) {
r[1]->Prop->Asn = 'I';
r[2]->Prop->Asn = 'I';
r[3]->Prop->Asn = 'I';
r[4]->Prop->Asn = 'I';
r[5]->Prop->Asn = 'I';
}
}
if( Cmd->Info ) {
fprintf(stdout,"%s%c\n",Chain[Cn]->File,Chain[Cn]->Id);
for( i=0; i<Chain[Cn]->NRes-4; i++ ) {
r = &Chain[Cn]->Rsd[i];
if( r[0]->Prop->PhiZn != ERR && r[0]->Prop->PsiZn != ERR &&
r[4]->Prop->PhiZn != ERR && r[4]->Prop->PsiZn != ERR ) {
fprintf(stdout,"%s (%d) %c %10.7f %8.5f %8.5f | %4d %4d\n",
r[0]->PDB_ResNumb,i,r[0]->Prop->Asn,Prob[i],
PhiPsiMap[r[0]->Prop->PhiZn][r[0]->Prop->PsiZn],
PhiPsiMap[r[4]->Prop->PhiZn][r[4]->Prop->PsiZn],
r[4]->Prop->PhiZn,r[4]->Prop->PsiZn);
}
}
}
free(Prob);
}
int Link(HBOND **HBond, CHAIN **Chain, int Cn1, int Cn2, RESIDUE *Res1_1,
RESIDUE *Res1_2, RESIDUE *Res2_2, RESIDUE *Res2_1, RESIDUE *CRes1,
RESIDUE *CRes2, float **PhiPsiMap, PATTERN **Pattern, int *NumPat,
char *Text, float Treshold, COMMAND *Cmd, int Test)
{
int BondNumber1, BondNumber2, Flag = 0;
static char *Result[2] = {" NO \n"," YES \n"};
float Prob1, Prob2, Conf, Coeff;
if( (BondNumber1 = FindPolInt(HBond,Res1_1,Res1_2)) == ERR )
return(FAILURE);
if( (BondNumber2 = FindPolInt(HBond,Res2_2,Res2_1)) == ERR )
return(FAILURE);
if( CRes1 == NULL ) {
if( CRes2->Prop->PhiZn == ERR || CRes2->Prop->PsiZn == ERR )
return(FAILURE);
Conf = PhiPsiMap[CRes2->Prop->PhiZn][CRes2->Prop->PsiZn];
}
else
if( CRes2 == NULL ) {
if( CRes1->Prop->PhiZn == ERR || CRes1->Prop->PsiZn == ERR )
return(FAILURE);
Conf = PhiPsiMap[CRes1->Prop->PhiZn][CRes1->Prop->PsiZn];
}
else {
if( CRes2->Prop->PhiZn == ERR || CRes2->Prop->PsiZn == ERR ||
CRes1->Prop->PhiZn == ERR || CRes1->Prop->PsiZn == ERR )
return(FAILURE);
Conf =
0.5*(PhiPsiMap[CRes1->Prop->PhiZn][CRes1->Prop->PsiZn]+
PhiPsiMap[CRes2->Prop->PhiZn][CRes2->Prop->PsiZn]);
}
Coeff = 1+Cmd->C1_E+Cmd->C2_E*Conf;
Prob1 = HBond[BondNumber1]->Energy*Coeff;
Prob2 = HBond[BondNumber2]->Energy*Coeff;
if( Prob1 < Treshold && Prob2 < Treshold ) {
if( !Test ) {
Pattern[*NumPat] = (PATTERN *)ckalloc(sizeof(PATTERN));
Pattern[*NumPat]->ExistPattern = YES;
Pattern[*NumPat]->Hb1 = HBond[BondNumber1];
Pattern[*NumPat]->Hb2 = HBond[BondNumber2];
Pattern[*NumPat]->Nei1 = NULL;
Pattern[*NumPat]->Nei2 = NULL;
strcpy(Pattern[*NumPat]->Type,Text);
(*NumPat)++;
}
Flag = 1;
}
if( Cmd->Info && Flag ) {
fprintf(stdout,"%s %c: %3s %c: %3s | %c: %3s %c: %3s | ",
Text,
Chain[Cn1]->Id,Res1_1->PDB_ResNumb,
Chain[Cn2]->Id,Res1_2->PDB_ResNumb,
Chain[Cn2]->Id,Res2_2->PDB_ResNumb,
Chain[Cn1]->Id,Res2_1->PDB_ResNumb);
fprintf(stdout,"%8.6f %6.4f | ", Prob1,HBond[BondNumber1]->Energy);
fprintf(stdout,"%8.6f %6.4f | ", Prob2,HBond[BondNumber2]->Energy);
if( CRes1 != NULL &&
CRes1->Prop->PhiZn != ERR && CRes1->Prop->PsiZn != ERR )
fprintf(stdout,"%6.4f %2d %2d | ",
PhiPsiMap[CRes1->Prop->PhiZn][CRes1->Prop->PsiZn],
CRes1->Prop->PhiZn,CRes1->Prop->PsiZn);
else
fprintf(stdout,"000000 00 00 | ");
if( CRes2 != NULL &&
CRes2->Prop->PhiZn != ERR && CRes2->Prop->PsiZn != ERR )
fprintf(stdout,"%6.4f %2d %2d | ",
PhiPsiMap[CRes2->Prop->PhiZn][CRes2->Prop->PsiZn],
CRes2->Prop->PhiZn,CRes2->Prop->PsiZn);
else
fprintf(stdout,"000000 00 00 | ");
fprintf(stdout,"%s",Result[Flag]);
}
return(Flag);
}
