int Process_HELIX(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd)
{
int CC, HC;
char *Field[MAX_FIELD];
BUFFER Tmp;
if( Cmd->NActive && !ChInStr(Cmd->Active,SpaceToDash(Buffer[19])) )
return(SUCCESS);
for( CC=0; CC < *ChainNumber && Chain[CC]->Id != Buffer[19]; CC++ );
if( CC == *ChainNumber ) {
InitChain(&Chain[CC]);
Chain[CC]->Id = Buffer[19];
(*ChainNumber)++;
}
HC = Chain[CC]->NHelix;
Chain[CC]->Helix[HC] = (HELIX *)ckalloc(sizeof(HELIX));
SplitString(Buffer+15,Field,1);
strcpy(Chain[CC]->Helix[HC]->Res1,Field[0]);
SplitString(Buffer+27,Field,1);
strcpy(Chain[CC]->Helix[HC]->Res2,Field[0]);
strcpy(Tmp,Buffer);
Tmp[25] = ' ';
Tmp[37] = ' ';
SplitString(Tmp+21,Field,1);
strcpy(Chain[CC]->Helix[HC]->PDB_ResNumb1,Field[0]);
SplitString(Tmp+33,Field,1);
strcpy(Chain[CC]->Helix[HC]->PDB_ResNumb2,Field[0]);
Chain[CC]->Helix[HC]->InsCode1 = Buffer[25];
Chain[CC]->Helix[HC]->InsCode2 = Buffer[37];
Tmp[40] = ' ';
SplitString(Tmp+38,Field,1);
Chain[CC]->Helix[HC]->Class = atoi(Field[0]);
Chain[CC]->NHelix++;
return(SUCCESS);
}
static int Process_ATOM(BUFFER Buffer, CHAIN **Chain, int *ChainNumber,
BOOLEAN *First_ATOM, StrideCmd *Cmd) {
char *Field[MAX_FIELD];
BUFFER Tmp;
int CC, NR, NA;
static char LastRes[MAX_CHAIN][RES_FIELD];
RESIDUE *r;
if( Cmd->NActive && !ChInStr(Cmd->Active,SpaceToDash(Buffer[21])) )
return(SUCCESS);
if( Buffer[16] != 'A' && Buffer[16] != ' ' && Buffer[16] != '1' )
return(SUCCESS);
if( *First_ATOM ) {
for( CC=0; CC<MAX_CHAIN; CC++ )
strcpy(LastRes[CC],"XXXX");
*First_ATOM = NO;
}
for( CC=0; CC < *ChainNumber && Chain[CC]->Id != Buffer[21] ; CC++ );
if( CC == *ChainNumber ) {
InitChain(&Chain[CC]);
Chain[CC]->Id = Buffer[21];
(*ChainNumber)++;
}
else
if( Chain[CC]->Ter == 1 )
return(SUCCESS);
if( Buffer[34] != '.' || Buffer[42] != '.' || Buffer[50] != '.' )
return(escape(FAILURE,"File %s has no coordinates\n",Cmd->InputFile));
if( Cmd->Stringent && Buffer[63] != '.')
return(escape(FAILURE,"File %s has no temperature factor\n",Cmd->InputFile));
SplitString(Buffer+22,Field,1);
if( strcmp(Field[0],LastRes[CC]) ) {
if( strcmp(LastRes[CC],"XXXX") && !FindAtom(Chain[CC],Chain[CC]->NRes,"CA",&NA) ) {
free(Chain[CC]->Rsd[Chain[CC]->NRes]);
Chain[CC]->NRes--;
}
if( strcmp(LastRes[CC],"XXXX") ) Chain[CC]->NRes++;
NR = Chain[CC]->NRes;
strcpy(LastRes[CC],Field[0]);
Chain[CC]->Rsd[NR] = (RESIDUE *)ckalloc(sizeof(RESIDUE));
strcpy(Chain[CC]->Rsd[NR]->PDB_ResNumb,LastRes[CC]);
Chain[CC]->Rsd[NR]->NAtom = 0;
SplitString(Buffer+17,Field,1);
strcpy(Chain[CC]->Rsd[NR]->ResType,Field[0]);
}
else
NR = Chain[CC]->NRes;
NA = Chain[CC]->Rsd[NR]->NAtom;
if( Buffer[16] != ' ' ) {
strcpy(Tmp,Buffer);
Tmp[16] = ' ';
SplitString(Tmp+12,Field,1);
}
else
SplitString(Buffer+12,Field,1);
r = Chain[CC]->Rsd[NR];
strcpy(r->AtomType[NA],Field[0]);
strcpy(Tmp,Buffer);
Buffer[38] = ' ';
SplitString(Tmp+30,Field,1);
r->Coord[NA][0] = atof(Field[0]);
strcpy(Tmp,Buffer);
Buffer[46] = ' ';
SplitString(Tmp+38,Field,1);
r->Coord[NA][1] = atof(Field[0]);
strcpy(Tmp,Buffer);
Buffer[54] = ' ';
SplitString(Tmp+46,Field,1);
r->Coord[NA][2] = atof(Field[0]);
if( Buffer[57] == '.' ) {
strcpy(Tmp,Buffer);
Tmp[60] = ' ';
SplitString(Tmp+54,Field,1);
r->Occupancy[NA] = atof(Field[0]);
}
else
r->Occupancy[NA] = -1.00;
SplitString(Buffer+63,Field,1);
r->TempFactor[NA] = atof(Field[0]);
r->NAtom++;
if( r->NAtom > MAX_AT_IN_RES-1 )
return(escape(FAILURE,"File %s has too many atoms in residue %s %s %c\n",
Cmd->InputFile,r->ResType,r->PDB_ResNumb,Chain[CC]->Id));
return(SUCCESS);
}
int Process_SHEET(BUFFER Buffer, CHAIN **Chain, int *ChainNumber, COMMAND *Cmd)
{
int CC, SC, STC;
char *Field[MAX_FIELD];
BUFFER Tmp;
static char PreviousChain, PreviousSheetId[RES_FIELD];
if( Cmd->NActive && !ChInStr(Cmd->Active,SpaceToDash(Buffer[21])) )
return(SUCCESS);
for( CC=0; CC < *ChainNumber && Chain[CC]->Id != Buffer[21]; CC++ );
if( CC == *ChainNumber ) {
InitChain(&Chain[CC]);
Chain[CC]->Id = Buffer[21];
(*ChainNumber)++;
}
if( Chain[CC]->NSheet == -1 ) {
PreviousChain = '*';
strcpy(PreviousSheetId,"*");
}
SplitString(Buffer+7,Field,2);
if( atoi(Field[0]) == 1 || Buffer[21] != PreviousChain ) {
if( Buffer[21] == PreviousChain && !strcmp(PreviousSheetId,Field[1]) )
return(FAILURE);
/* die("Here it is! -> %s%c\n", Chain[CC]->File,Chain[CC]->Id);*/
Chain[CC]->NSheet++;
SC = Chain[CC]->NSheet;
Chain[CC]->Sheet[SC] = (SHEET *)ckalloc(sizeof(SHEET));
Chain[CC]->Sheet[SC]->NStrand = 0;
STC = Chain[CC]->Sheet[SC]->NStrand;
strcpy(Chain[CC]->Sheet[SC]->SheetId,Field[1]);
}
else
{
SC = Chain[CC]->NSheet;
STC = Chain[CC]->Sheet[SC]->NStrand;
}
SplitString(Buffer+17,Field,1);
strcpy(Chain[CC]->Sheet[SC]->ResType1[STC],Field[0]);
SplitString(Buffer+28,Field,1);
strcpy(Chain[CC]->Sheet[SC]->ResType2[STC],Field[0]);
strcpy(Tmp,Buffer);
Tmp[27] = ' ';
Tmp[38] = ' ';
SplitString(Tmp+22,Field,1);
strcpy(Chain[CC]->Sheet[SC]->PDB_ResNumb1[STC],Field[0]);
SplitString(Tmp+33,Field,1);
strcpy(Chain[CC]->Sheet[SC]->PDB_ResNumb2[STC],Field[0]);
Chain[CC]->Sheet[SC]->InsCode1[STC] = Buffer[26];
Chain[CC]->Sheet[SC]->InsCode2[STC] = Buffer[37];
SplitString(Buffer+38,Field,1);
Chain[CC]->Sheet[SC]->Sence[STC] = atoi(Field[0]);
if( Buffer[45] != ' ' ) {
Chain[CC]->Sheet[SC]->RegYN[STC] = 1;
SplitString(Buffer+45,Field,1);
strcpy(Chain[CC]->Sheet[SC]->ResTypeReg1[STC],Field[0]);
SplitString(Buffer+60,Field,1);
strcpy(Chain[CC]->Sheet[SC]->ResTypeReg2[STC],Field[0]);
Tmp[55] = ' ';
Tmp[70] = ' ';
SplitString(Tmp+50,Field,1);
strcpy(Chain[CC]->Sheet[SC]->PDB_ResNumbReg1[STC],Field[0]);
SplitString(Tmp+66,Field,1);
strcpy(Chain[CC]->Sheet[SC]->PDB_ResNumbReg2[STC],Field[0]);
Chain[CC]->Sheet[SC]->InsCodeReg1[STC] = Buffer[54];
Chain[CC]->Sheet[SC]->InsCodeReg2[STC] = Buffer[69];
Tmp[45] = ' ';
Tmp[60] = ' ';
SplitString(Tmp+41,Field,1);
strcpy(Chain[CC]->Sheet[SC]->AtomNameReg1[STC],Field[0]);
SplitString(Tmp+56,Field,1);
strcpy(Chain[CC]->Sheet[SC]->AtomNameReg2[STC],Field[0]);
}
else Chain[CC]->Sheet[SC]->RegYN[STC] = 0;
strcpy(PreviousSheetId,Chain[CC]->Sheet[SC]->SheetId);
PreviousChain = Buffer[21];
Chain[CC]->Sheet[SC]->NStrand++;
return(SUCCESS);
}
int CheckChain(CHAIN *Chain, StrideCmd *Cmd) {
int Res, /*HelAlp, HelPI, Hel310, Sheet, Turn,*/ Bound[300][2];
int i, j, AsnNumb=0, At, /*SuspCnt,*/ Beg, End;
/*float Content;*/
if( Cmd->NProcessed && !ChInStr(Cmd->Processed,SpaceToDash(Chain->Id)) ) {
Chain->Valid = NO;
return(FAILURE);
}
if( Chain->NRes < 5 )
return(NotValid(Chain,"less than 5 residues"));
if( !Cmd->Stringent )
return(SUCCESS);
for( Res=0; Res<Chain->NRes; Res++ ){
if( !CheckRes(Chain->Rsd[Res]->ResType) )
Chain->NonStandRes++;
for( At=0; At<Chain->Rsd[Res]->NAtom; At++) {
if( !CheckAtom(Chain->Rsd[Res]->AtomType[At]) )
Chain->NonStandAtom++;
if(Chain->Rsd[Res]->Coord[At][0] < MIN_X || Chain->Rsd[Res]->Coord[At][0] > MAX_X ||
Chain->Rsd[Res]->Coord[At][1] < MIN_Y || Chain->Rsd[Res]->Coord[At][1] > MAX_Y ||
Chain->Rsd[Res]->Coord[At][2] < MIN_Z || Chain->Rsd[Res]->Coord[At][2] > MAX_Z ||
Chain->Rsd[Res]->Occupancy[At] < MIN_Occupancy ||
Chain->Rsd[Res]->Occupancy[At] > MAX_Occupancy ||
Chain->Rsd[Res]->TempFactor[At] < MIN_TempFactor ||
Chain->Rsd[Res]->TempFactor[At] > MAX_TempFactor )
break;
}
if( At < Chain->Rsd[Res]->NAtom )
break;
}
if( Res < Chain->NRes )
return(NotValid(Chain,"suspicious coordinates, occupancy or temperature factor"));
if( 100.0*(float)Chain->NonStandRes/(float)Chain->NRes > MAXNONSTAND )
return(NotValid(Chain,"too many non-standard residues"));
if( Chain->NRes < Cmd->MinLength )
return(NotValid(Chain,"Short chain"));
if( Chain->NRes > Cmd->MaxLength )
return(NotValid(Chain,"Long chain"));
if( Chain->Method == XRay &&
(Chain->Resolution < Cmd->MinResolution || Chain->Resolution > Cmd->MaxResolution ) )
return(NotValid(Chain,"Resolution out of range"));
if( (int)strlen(Cmd->Cond) != 0 ) {
if( ChInStr(Cmd->Cond,'c') ) {
for( Res=0; Res<Chain->NRes; Res++ )
if( FindAtom(Chain,Res,"N",&At) ||
FindAtom(Chain,Res,"O",&At) ||
FindAtom(Chain,Res,"C",&At) )
break;
if( Res == Chain->NRes )
return(NotValid(Chain,"only CA"));
}
if( Chain->Method == NMR && !ChInStr(Cmd->Cond,'n') )
return(NotValid(Chain,"NMR chain"));
if( Chain->Method == XRay && !ChInStr(Cmd->Cond,'x') )
return(NotValid(Chain,"XRay chain"));
if( Chain->Method == Model && !ChInStr(Cmd->Cond,'m') )
return(NotValid(Chain,"Model chain"));
if( Chain->Published == NO && ChInStr(Cmd->Cond,'p') )
return(NotValid(Chain,"Not published"));
if( Chain->DsspAssigned == YES && ChInStr(Cmd->Cond,'d') )
return(NotValid(Chain,"Assigned according to DSSP"));
if( ChInStr(Cmd->Cond,'a') ) {
fprintf(stderr,
"WARNING: stride: CheckChain(): "
"Cmd->Cond == 'a': some functionality has been commented out");
if( Chain->Valid && Chain->NHelix == 0 && Chain->NSheet == -1 && Chain->NTurn == 0 )
return(NotValid(Chain,"No assignment"));
/* Not sure what these do but eliminating them */
/* allows removal of the Prop->PdbAsn field. */
/*
if( (Content = SecStrContent(Chain,&HelAlp,&HelPI,&Hel310,&Sheet,&Turn)) < 0.4 ||
Content > 0.9 )
return(NotValid(Chain,"Suspicious content"));
SuspCnt = 0;
for( Res=1; Res<Chain->NRes-1; Res++ ) {
if( ( Chain->Rsd[Res]->Prop->PdbAsn != 'H' && Chain->Rsd[Res]->Prop->PdbAsn != 'T' &&
Chain->Rsd[Res]->Prop->Phi > -150.0 && Chain->Rsd[Res]->Prop->Phi < 0.0 &&
Chain->Rsd[Res]->Prop->Psi > -100.0 && Chain->Rsd[Res]->Prop->Psi < 10.0) )
SuspCnt++;
}
if( (float)SuspCnt/(float)Chain->NRes > 0.4 )
return(NotValid(Chain,"Suspicious assignment"));
*/
for( i=0; i<Chain->NHelix; i++ ) {
if( !PdbN2SeqN(Chain,Chain->Helix[i]->PDB_ResNumb1,&Beg) ||
!PdbN2SeqN(Chain,Chain->Helix[i]->PDB_ResNumb2,&End) ||
/* !CheckRes(Chain->Helix[i]->PDB_ResNumb1) ||
!CheckRes(Chain->Helix[i]->PDB_ResNumb2) || */
Chain->Helix[i]->Class > 10 ||
Chain->Helix[i]->Class < 1 ||
End-Beg > 100 || End-Beg < 0 )
break;
else
if( Chain->Helix[i]->Class == 1 ) {
Bound[AsnNumb][0] = Beg;
Bound[AsnNumb][1] = End;
AsnNumb++;
}
}
if( i < Chain->NHelix )
return(NotValid(Chain,"Erraneous helix assignment"));
for( i=0; i<Chain->NSheet; i++ )
for( j=0; j<Chain->Sheet[i]->NStrand; j++ ) {
if( !PdbN2SeqN(Chain,Chain->Sheet[i]->PDB_ResNumb1[j],&Beg) ||
!PdbN2SeqN(Chain,Chain->Sheet[i]->PDB_ResNumb2[j],&End) ||
/* !CheckRes(Chain->Sheet[i]->PDB_ResNumb1[j]) ||
!CheckRes(Chain->Sheet[i]->PDB_ResNumb2[j]) || */
End-Beg > 100 || End-Beg < 0 )
break;
else
if( Chain->Sheet[i]->Sence[j] != 0 ) {
Bound[AsnNumb][0] = Beg;
Bound[AsnNumb][1] = End;
AsnNumb++;
}
if( j < Chain->Sheet[i]->NStrand )
break;
}
if( i < Chain->NSheet )
return(NotValid(Chain,"Erraneous sheet assignment"));
for( i=0; i<Chain->NTurn; i++ )
if( !PdbN2SeqN(Chain,Chain->Turn[i]->PDB_ResNumb1,&Beg) ||
!PdbN2SeqN(Chain,Chain->Turn[i]->PDB_ResNumb2,&End) ||
End-Beg > 100 || End-Beg < 0 )
break;
if( i < Chain->NTurn )
NotValid(Chain,"Erraneous turn assignment");
for( i=0; i<AsnNumb-1; i++ ) {
for( j=i+1; j<AsnNumb; j++ ) {
if( Bound[i][0] == Bound[j][0] && Bound[i][1] == Bound[j][1] ) continue;
if( (Bound[j][0] > Bound[i][0] && Bound[j][0] < Bound[i][1]) ||
(Bound[j][1] > Bound[i][0] && Bound[j][1] < Bound[i][1]) ||
(Bound[i][0] > Bound[j][0] && Bound[i][0] < Bound[j][1]) ||
(Bound[i][1] > Bound[j][0] && Bound[i][1] < Bound[j][1]) )
break;
}
if( j < AsnNumb )
break;
}
if( i < AsnNumb-1 )
return(NotValid(Chain,"Assignment overlap"));
}
}
fprintf(stderr,"ACCEPTED %s %c %4d %7.3f\n",
Chain->File,Chain->Id,Chain->NRes,Chain->Resolution);
return(SUCCESS);
}
