josch/stride
1
0
Fork 0
Code Issues Pull requests Projects Releases Wiki Activity
stride/report.c
josch 79d3138e97 initial commit
2013-09-18 16:12:31 +02:00

419 lines
10 KiB
C
Raw Blame History

#include "stride.h"
void Report(CHAIN **Chain, int NChain, HBOND **HBond, COMMAND *Cmd)
{
FILE *Out;
if( !strlen(Cmd->OutFile) )
Out = stdout;
else
if( !(Out = fopen(Cmd->OutFile,"w")) )
die("Can not open output file %s\n",Cmd->OutFile);
if( !Cmd->ReportSummaryOnly )
ReportGeneral(Chain,Out);
ReportSummary(Chain,NChain,Out,Cmd);
ReportShort(Chain,NChain,Out,Cmd);
ReportTurnTypes(Chain,NChain,Out,Cmd);
ReportSSBonds(Chain,Out);
if( !Cmd->ReportSummaryOnly )
ReportDetailed(Chain,NChain,Out,Cmd);
if( Cmd->ReportBonds )
ReportHydrBonds(Chain,NChain,HBond,Out,Cmd);
if( Cmd->Measure ) {
Measure(Chain,NChain,0,Cmd,Out);
Measure(Chain,NChain,1,Cmd,Out);
}
if( Out != stdout )
fclose(Out);
}
void ReportGeneral(CHAIN **Chain, FILE *Out)
{
register int i;
BUFFER Bf, Tmp;
if( !Chain[0]->NInfo )
return;
PrepareBuffer(Bf,Chain);
Glue(Bf,"REM --------------------------------------------------------------------",Out);
Glue(Bf,"REM",Out);
Glue(Bf,"REM STRIDE: Knowledge-based secondary structure assignment",Out);
Glue(Bf,"REM Please cite: D.Frishman & P.Argos, Proteins XX, XXX-XXX, 1995",Out);
Glue(Bf,"REM",Out);
Glue(Bf,"REM Residue accessible surface area calculation",Out);
Glue(Bf,"REM Please cite: F.Eisenhaber & P.Argos, J.Comp.Chem. 14, 1272-1280, 1993 ",Out);
Glue(Bf,"REM F.Eisenhaber et al., J.Comp.Chem., 1994, submitted",Out);
Glue(Bf,"REM",Out);
sprintf(Tmp,"REM ------------------------ ");
strcat(Tmp,"General information");
strcat(Tmp," -----------------------");
Glue(Bf,Tmp,Out);
Glue(Bf,"REM",Out);
for( i=0; i<Chain[0]->NInfo; i++ ) {
strcpy(Tmp,Chain[0]->Info[i]);
Tmp[66] = '\0';
Replace(Tmp,'\n',' ');
Glue(Bf,Tmp,Out);
}
Glue(Bf,"REM",Out);
}
void ReportSummary(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
{
int Cn, Width, CurrWidth, NBlocks, Tail, i, j, From, To;
BUFFER Bf, Tmp, Tmp1;
PrepareBuffer(Bf,Chain);
sprintf(Tmp,"REM -------------------- ");
strcat(Tmp,"Secondary structure summary");
strcat(Tmp," -------------------");
Glue(Bf,Tmp,Out);
for( Cn=0; Cn<NChain; Cn++ ) {
if( !Chain[Cn]->Valid )
continue;
Width = 50;
Glue(Bf,"REM",Out);
strncpy(Tmp1,Chain[Cn]->File,40);
Tmp1[40] = '\0';
sprintf(Tmp,"CHN %s %c",Tmp1,SpaceToDash(Chain[Cn]->Id));
Glue(Bf,Tmp,Out);
NBlocks = Chain[Cn]->NRes/Width;
Tail = Chain[Cn]->NRes % Width;
if( Tail ) NBlocks++;
for( i=0; i<NBlocks; i++ ) {
Glue(Bf,"REM",Out);
From = i*Width;
if( i == NBlocks-1 && Tail )
CurrWidth = Tail;
else
CurrWidth = Width;
To = From+CurrWidth;
sprintf(Tmp,"REM ");
for( j=0; j<CurrWidth; j++ )
if( j && (j+1)%10 == 0 )
strcat(Tmp,".");
else
strcat(Tmp," ");
Glue(Bf,Tmp,Out);
sprintf(Tmp,"SEQ %-4d ",From+1);
for( j=From; j<From+Width; j++ ) {
if( j < To )
sprintf(Tmp1,"%c",ThreeToOne(Chain[Cn]->Rsd[j]->ResType));
else
sprintf(Tmp1," ");
strcat(Tmp,Tmp1);
}
sprintf(Tmp1," %4d",To);
strcat(Tmp,Tmp1);
Glue(Bf,Tmp,Out);
sprintf(Tmp,"STR ");
for( j=From; j<To; j++ ) {
if( Chain[Cn]->Rsd[j]->Prop->Asn == 'C' )
sprintf(Tmp1," ");
else
sprintf(Tmp1,"%c",Chain[Cn]->Rsd[j]->Prop->Asn);
strcat(Tmp,Tmp1);
}
strcat(Tmp," ");
Glue(Bf,Tmp,Out);
}
}
}
void ReportDetailed(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
{
register int i, Cn;
RESIDUE *p;
BUFFER Bf, Tmp, Tmp1;
PrepareBuffer(Bf,Chain);
Glue(Bf,"REM",Out);
sprintf(Tmp,"REM --------------- ");
strcat(Tmp,"Detailed secondary structure assignment");
strcat(Tmp,"-------------");
Glue(Bf,Tmp,Out);
Glue(Bf,"REM",Out);
Glue(Bf,"REM |---Residue---| |--Structure--| |-Phi-| |-Psi-| |-Area-| ",Out);
for( Cn=0; Cn<NChain; Cn++ ) {
if( !Chain[Cn]->Valid )
continue;
for( i=0; i<Chain[Cn]->NRes; i++ ) {
p = Chain[Cn]->Rsd[i];
sprintf(Tmp,"ASG %3s %c %4s %4d %c %11s %7.2f %7.2f %7.1f",
p->ResType,SpaceToDash(Chain[Cn]->Id),p->PDB_ResNumb,i+1,
p->Prop->Asn,Translate(p->Prop->Asn),p->Prop->Phi,
p->Prop->Psi,p->Prop->Solv);
if( Cmd->BrookhavenAsn ) {
Tmp[26] = p->Prop->PdbAsn;
Tmp[25] = ' ';
Tmp[27] = ' ';
}
if( Cmd->DsspAsn ) {
Tmp[28] = p->Prop->DsspAsn;
Tmp[27] = ' ';
Tmp[29] = ' ';
sprintf(Tmp1," %6.1f ",p->Prop->DsspSolv);
strcat(Tmp,Tmp1);
}
Glue(Bf,Tmp,Out);
}
}
}
void ReportHydrBonds(CHAIN **Chain, int NChain, HBOND **HBond, FILE *Out,
COMMAND *Cmd)
{
register int i, k, Cn;
int Cnt, Res;
BUFFER Bf, Tmp, Tmp1;
HBOND *p;
RESIDUE *r;
PrepareBuffer(Bf,Chain);
Glue(Bf,"REM",Out);
sprintf(Tmp,"REM ------------------ ");
strcat(Tmp,"Mainchain hydrogen bonds");
strcat(Tmp," ------------------------");
Glue(Bf,Tmp,Out);
Glue(Bf,"REM",Out);
Glue(Bf,"REM Definition of Stickle et al., J.Mol.Biol. 226:1143-1159, 1992",Out);
Glue(Bf,"REM A1 is the angle between the planes of donor complex and O..N-C",Out);
Glue(Bf,"REM A2 is the angle between the planes of acceptor complex and N..O=C",Out);
Glue(Bf,"REM",Out);
sprintf(Tmp,"HBT %-6d",Chain[0]->NHydrBondTotal);
Glue(Bf,Tmp,Out);
sprintf(Tmp,"HBI %-6d",Chain[0]->NHydrBondInterchain);
Glue(Bf,Tmp,Out);
for( Cn=0; Cn<NChain; Cn++ )
if( Chain[Cn]->Valid ) {
sprintf(Tmp,"HBC %-6d %s %c %4d",
Chain[Cn]->NHydrBond,Chain[Cn]->File,SpaceToDash(Chain[Cn]->Id),Chain[Cn]->NRes);
Glue(Bf,Tmp,Out);
}
Glue(Bf,"REM",Out);
Glue(Bf,"REM |--Residue 1--| |--Residue 2--| N-O N..O=C O..N-C A1 A2",Out);
for( Cn=0; Cn<NChain; Cn++ ) {
if( !Chain[Cn]->Valid )
continue;
for( i=0; i<Chain[Cn]->NRes; i++ ) {
r = Chain[Cn]->Rsd[i];
Cnt = 0;
for( k=0; k<r->Inv->NBondDnr; k++ ) {
p = HBond[r->Inv->HBondDnr[k]];
if( p->ExistHydrBondRose ) {
Res = p->Acc->A_Res;
sprintf(Tmp,"DNR %4s %c %4s %4d -> ",
r->ResType,SpaceToDash(Chain[Cn]->Id),r->PDB_ResNumb,i);
sprintf(Tmp1,"%4s %c %4s %4d %4.1f %6.1f %6.1f %6.1f %6.1f ",
p->Acc->Chain->Rsd[Res]->ResType,
/* patch replace SpaceToDash(Chain[Cn]->Id), */
SpaceToDash(p->Acc->Chain->Id),
p->Acc->Chain->Rsd[Res]->PDB_ResNumb,Res,p->AccDonDist,p->AccAng,
p->DonAng,p->AccDonAng,p->DonAccAng);
strcat(Tmp,Tmp1);
Glue(Bf,Tmp,Out);
Cnt++;
}
}
Cnt = 0;
for( k=0; k<r->Inv->NBondAcc; k++ ) {
p = HBond[r->Inv->HBondAcc[k]];
if( p->ExistHydrBondRose ) {
Res = p->Dnr->D_Res;
sprintf(Tmp,"ACC %4s %c %4s %4d -> ",
r->ResType,SpaceToDash(Chain[Cn]->Id),r->PDB_ResNumb,i);
sprintf(Tmp1,"%4s %c %4s %4d %4.1f %6.1f %6.1f %6.1f %6.1f ",
p->Dnr->Chain->Rsd[Res]->ResType,
/* patch replace SpaceToDash(Chain[Cn]->Id), */
SpaceToDash(p->Dnr->Chain->Id),
p->Dnr->Chain->Rsd[Res]->PDB_ResNumb,Res,p->AccDonDist,
p->AccAng,p->DonAng,p->AccDonAng,p->DonAccAng);
strcat(Tmp,Tmp1);
Glue(Bf,Tmp,Out);
Cnt++;
}
}
}
}
}
void ReportSSBonds(CHAIN **Chain, FILE *Out)
{
register int i;
BUFFER Bf, Tmp;
SSBOND *s;
if( !Chain[0]->NBond ) return;
PrepareBuffer(Bf,Chain);
for( i=0; i<Chain[0]->NBond; i++ ) {
s = Chain[0]->SSbond[i];
sprintf(Tmp,"LOC Disulfide CYS %4s %c CYS %4s %c ",
s->PDB_ResNumb1,SpaceToDash(s->ChainId1),
s->PDB_ResNumb2,SpaceToDash(s->ChainId2));
if( s->AsnSource == Pdb )
strcat(Tmp," PDB");
else
strcat(Tmp,"STRIDE\n");
Glue(Bf,Tmp,Out);
}
}
void ReportTurnTypes(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
{
register int Cn, Tn;
BUFFER Bf, Tmp;
TURN *t;
Tn = 0;
for( Cn=0; Cn<NChain; Cn++ )
if( Chain[Cn]->Valid )
Tn += Chain[Cn]->NAssignedTurn;
if( !Tn ) return;
PrepareBuffer(Bf,Chain);
for( Cn=0; Cn<NChain; Cn++ ) {
if( !Chain[Cn]->Valid )
continue;
for( Tn=0; Tn<Chain[Cn]->NAssignedTurn; Tn++ ) {
t = Chain[Cn]->AssignedTurn[Tn];
sprintf(Tmp,"LOC %-11s %3s %4s %c %3s %4s %c",
Translate(t->TurnType),t->Res1,t->PDB_ResNumb1,
SpaceToDash(Chain[Cn]->Id),t->Res2,
t->PDB_ResNumb2,SpaceToDash(Chain[Cn]->Id));
Glue(Bf,Tmp,Out);
}
}
}
void ReportShort(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
{
register int Cn, i;
BUFFER Bf, Tmp;
char *Asn;
static char *StrTypes = "HGIE";
int Bound[MAX_ASSIGN][2], NStr;
if( !ExistsSecStr(Chain,NChain) )
return;
PrepareBuffer(Bf,Chain);
Glue(Bf,"REM",Out);
Glue(Bf,"REM",Out);
Glue(Bf,"REM",Out);
for( ; *StrTypes!= '\0'; StrTypes++ ) {
for( Cn=0; Cn<NChain; Cn++ ) {
if( !Chain[Cn]->Valid )
continue;
Asn = (char *)ckalloc(Chain[Cn]->NRes*sizeof(char));
ExtractAsn(Chain,Cn,Asn);
NStr = Boundaries(Asn,Chain[Cn]->NRes,(*StrTypes),Bound);
for( i=0; i<NStr; i++ ) {
sprintf(Tmp,"LOC %-10s %3s %4s %c %3s %4s %c",Translate(*StrTypes),
Chain[Cn]->Rsd[Bound[i][0]]->ResType,
Chain[Cn]->Rsd[Bound[i][0]]->PDB_ResNumb,
SpaceToDash(Chain[Cn]->Id),
Chain[Cn]->Rsd[Bound[i][1]]->ResType,
Chain[Cn]->Rsd[Bound[i][1]]->PDB_ResNumb,
SpaceToDash(Chain[Cn]->Id));
Glue(Bf,Tmp,Out);
}
free(Asn);
}
}
}
void PrepareBuffer(BUFFER Bf, CHAIN **Chain)
{
memset(Bf,' ',OUTPUTWIDTH);
strcpy(Bf+OUTPUTWIDTH-5,Chain[0]->PdbIdent);
Bf[OUTPUTWIDTH] = '\0';
Bf[OUTPUTWIDTH-1] = '\n';
}
void Glue(char *String1, char *String2, FILE *Out)
{
BUFFER Bf;
strcpy(Bf,String1);
strncpy(Bf,String2,(int)strlen(String2));
fprintf(Out,"%s",Bf);
}
Reference in a new issue View git blame Copy permalink