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stride/measure.c

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/*
* Copyright (C) 1992-1994 Dmitrij Frishman <d.frishman at wzw.tum.de>
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
#include "stride.h"
void Measure(CHAIN **Chain, int NChain, int El, COMMAND *Cmd, FILE *Out)
{
QUALITY QualDssp_H, QualDssp_E, Qual_H, Qual_E;
int i, Cn, Flag1, Flag2;
float Q2_, Q2_Dssp, O_, O_Dssp;
float Content, AlphaCont, BetaCont, PerCor, PerCorDssp;
int HelAlp, HelPI, Hel310, Sheet, Turn;
int YYN_H, NYY_H, YNN_H, NNY_H, YYN_E, NYY_E, YNN_E, NNY_E;
int Total_H, Better_H, Worse_H, Total_E, Better_E, Worse_E;
char Tmp[3][MAX_RES], *Asn, *PdbAsn, *DsspAsn;
CHAIN *c;
for( Cn=0; Cn<NChain; Cn++ ) {
c = Chain[Cn];
if( !c->Valid )
continue;
Asn = (char *)ckalloc(c->NRes*sizeof(char));
PdbAsn = (char *)ckalloc(c->NRes*sizeof(char));
DsspAsn = (char *)ckalloc(c->NRes*sizeof(char));
ExtractAsn(Chain,Cn,Asn);
ExtractPdbAsn(Chain,Cn,PdbAsn);
ExtractDsspAsn(Chain,Cn,DsspAsn);
for( i=0; i<c->NRes; i++ ) {
if( Asn[i] != 'H' && Asn[i] != 'E' && Asn[i] != 'B' )
Asn[i] = 'C';
if( PdbAsn[i] != 'H' && PdbAsn[i] != 'E' )
PdbAsn[i] = 'C';
if( DsspAsn[i] != 'H' && DsspAsn[i] != 'E' && DsspAsn[i] != 'B' )
DsspAsn[i] = 'C';
if( Asn[i] == 'B' )
Asn[i] = 'E';
if( DsspAsn[i] == 'B' )
DsspAsn[i] = 'E';
}
CorrectAsnDouble(Asn,DsspAsn,PdbAsn,c->NRes,'E','C');
if( El ) {
FullElement(Asn,PdbAsn,DsspAsn,c->NRes,'H',4,'z',&YYN_H,&NYY_H,&YNN_H,&NNY_H);
FullElement(Asn,PdbAsn,DsspAsn,c->NRes,'E',1,'y',&YYN_E,&NYY_E,&YNN_E,&NNY_E);
fprintf(Out,"DIFF_EL ");
}
else
fprintf(Out,"DIFF ");
Content = SecStrContent(c,&HelAlp,&HelPI,&Hel310,&Sheet,&Turn);
AlphaCont = (float)HelAlp/(float)c->NRes;
BetaCont = (float)Sheet/(float)c->NRes;
Presnell(PdbAsn,c->NRes,DsspAsn,c->NRes,'E',0.5,&Q2_Dssp,&O_Dssp);
Presnell(PdbAsn,c->NRes,Asn,c->NRes,'E',0.5,&Q2_,&O_);
Difference(DsspAsn,PdbAsn,c->NRes,'H',&QualDssp_H);
Difference(DsspAsn,PdbAsn,c->NRes,'E',&QualDssp_E);
Difference(Asn,PdbAsn,c->NRes,'H',&Qual_H);
Difference(Asn,PdbAsn,c->NRes,'E',&Qual_E);
PerCor = PercentCorrect(Asn,PdbAsn,c->NRes);
PerCorDssp = PercentCorrect(DsspAsn,PdbAsn,c->NRes);
Total_H = CompareElements(Asn,PdbAsn,DsspAsn,c->NRes,'H',&Better_H,&Worse_H);
Total_E = CompareElements(Asn,PdbAsn,DsspAsn,c->NRes,'E',&Better_E,&Worse_E);
if( (Flag1=AssessCorr(&Qual_H)) )
fprintf(Out,"%6.4f ",Qual_H.Corr);
else fprintf(Out," None ");
fprintf(Out,"%6.4f ",Qual_H.Perc);
if( (Flag2=AssessCorr(&QualDssp_H)) )
fprintf(Out,"%6.4f ",QualDssp_H.Corr);
else fprintf(Out," None ");
fprintf(Out,"%6.4f ",QualDssp_H.Perc);
if( Flag1 && Flag2 )
fprintf(Out,"%7.4f ",Qual_H.Corr-QualDssp_H.Corr);
else fprintf(Out," None ");
fprintf(Out,"%7.4f | ",Qual_H.Perc-QualDssp_H.Perc);
if( (Flag1=AssessCorr(&Qual_E)) )
fprintf(Out,"%6.4f ",Qual_E.Corr);
else fprintf(Out," None ");
fprintf(Out,"%6.4f ",Qual_E.Perc);
if( (Flag2=AssessCorr(&QualDssp_E)) )
fprintf(Out,"%6.4f ",QualDssp_E.Corr);
else fprintf(Out," None ");
fprintf(Out,"%6.4f ",QualDssp_E.Perc);
if( Flag1 && Flag2 )
fprintf(Out,"%7.4f ",Qual_E.Corr-QualDssp_E.Corr);
else fprintf(Out," None ");
fprintf(Out,"%7.4f | ",Qual_E.Perc-QualDssp_E.Perc);
fprintf(Out,"%6.4f %6.4f | %6.4f %6.4f | ",Q2_,Q2_Dssp,O_,O_Dssp);
fprintf(Out,"%4d %4d %4d %4d | %4d %4d %4d %4d |%4d %4d %4d %4d |%4d %4d %4d %4d | %s%c %4d %4.2f | %5.3f %5.3f %5.3f",
Qual_H.TP,Qual_H.TN,Qual_H.FP,Qual_H.FN,
QualDssp_H.TP,QualDssp_H.TN,QualDssp_H.FP,QualDssp_H.FN,
Qual_E.TP,Qual_E.TN,Qual_E.FP,Qual_E.FN,
QualDssp_E.TP,QualDssp_E.TN,QualDssp_E.FP,QualDssp_E.FN,
c->File,c->Id,c->NRes,c->Resolution,Content,AlphaCont,BetaCont);
if( El ) {
fprintf(Out," FullH: YYN %2d NYY %2d YNN %2d NNY %2d ",YYN_H,NYY_H,YNN_H,NNY_H);
fprintf(Out," FullE: YYN %2d NYY %2d YNN %2d NNY %2d ",YYN_E,NYY_E,YNN_E,NNY_E);
}
memset(Tmp[0],'C',c->NRes);
memset(Tmp[1],'C',c->NRes);
memset(Tmp[2],'C',c->NRes);
for( i=0; i<c->NRes; i++ ) {
if( Asn[i] == 'H' )
Tmp[0][i] = Asn[i];
if( PdbAsn[i] == 'H' )
Tmp[1][i] = PdbAsn[i];
if( DsspAsn[i] == 'H' )
Tmp[2][i] = DsspAsn[i];
}
ExcludeObvious(Tmp[0],Tmp[2],Tmp[1],c->NRes);
Difference(Tmp[0],Tmp[1],c->NRes,'H',&Qual_H);
fprintf(Out," | ResH: YYN %3d NNY %3d YNN %3d NYY %3d",
Qual_H.TP,Qual_H.TN,Qual_H.FP,Qual_H.FN);
memset(Tmp[0],'C',c->NRes);
memset(Tmp[1],'C',c->NRes);
memset(Tmp[2],'C',c->NRes);
for( i=0; i<c->NRes; i++ ) {
if( Asn[i] == 'E' )
Tmp[0][i] = Asn[i];
if( PdbAsn[i] == 'E' )
Tmp[1][i] = PdbAsn[i];
if( DsspAsn[i] == 'E' )
Tmp[2][i] = DsspAsn[i];
}
ExcludeObvious(Tmp[0],Tmp[2],Tmp[1],c->NRes);
Difference(Tmp[0],Tmp[1],c->NRes,'E',&Qual_E);
fprintf(Out," | ResE: YYN %3d NNY %3d YNN %3d NYY %3d",
Qual_E.TP,Qual_E.TN,Qual_E.FP,Qual_E.FN);
fprintf(Out," | ToH: %2d BtH: %2d WsH: %2d ",Total_H,Better_H,Worse_H);
fprintf(Out," | ToE: %2d BtE: %2d WsE: %2d ",Total_E,Better_E,Worse_E);
fprintf(Out,"PerCor %7.4f PerCorDssp %7.4f\n",PerCor,PerCorDssp);
fprintf(Out,"\n");
/* int Bound[MAX_ASSIGN][2], NElem; */
/* if( !El ) {
* NElem = Boundaries(Asn,c->NRes,'H',Bound);
* for( i=0; i<NElem; i++ )
* fprintf(Out,"HELIXSTRIDE %4d residues long in %s%c\n",
* Bound[i][1]-Bound[i][0]+1,c->File,c->Id);
*
* NElem = Boundaries(Asn,c->NRes,'E',Bound);
* for( i=0; i<NElem; i++ )
* fprintf(Out,"STRANDSTRIDE %4d residues long in %s%c\n",
* Bound[i][1]-Bound[i][0]+1,c->File,c->Id);
*
* NElem = Boundaries(PdbAsn,c->NRes,'H',Bound);
* for( i=0; i<NElem; i++ )
* fprintf(Out,"HELIXPDB %4d residues long in %s%c\n",
* Bound[i][1]-Bound[i][0]+1,c->File,c->Id);
*
* NElem = Boundaries(PdbAsn,c->NRes,'E',Bound);
* for( i=0; i<NElem; i++ )
* fprintf(Out,"STRANDPDB %4d residues long in %s%c\n",
* Bound[i][1]-Bound[i][0]+1,c->File,c->Id);
*
* NElem = Boundaries(DsspAsn,c->NRes,'H',Bound);
* for( i=0; i<NElem; i++ )
* fprintf(Out,"HELIXSDSSP %4d residues long in %s%c\n",
* Bound[i][1]-Bound[i][0]+1,c->File,c->Id);
*
* NElem = Boundaries(DsspAsn,c->NRes,'E',Bound);
* for( i=0; i<NElem; i++ )
* fprintf(Out,"STRANDDSSP %4d residues long in %s%c\n",
* Bound[i][1]-Bound[i][0]+1,c->File,c->Id);
* }
*/
free(Asn);
free(PdbAsn);
free(DsspAsn);
}
}
int Presnell(char *Asn1, int L1, char *Asn2, int L2, char SecStr, float Threshold,
float *Q2, float *O)
{
int Boundaries(char *Asn, int L, char SecondStr, int (*Bound)[2]);
int Bound1[MAX_ASSIGN][2], Bound2[MAX_ASSIGN][2], Length1[MAX_ASSIGN],
Length2[MAX_ASSIGN], NSeg1, NSeg2;
int Overlap, MaxOverlap, TP=0, FP=0, FN=0;
register int i, j;
NSeg1 = Boundaries(Asn1,L1,SecStr,Bound1);
NSeg2 = Boundaries(Asn2,L2,SecStr,Bound2);
for(i=0; i<NSeg1; i++)
Length1[i] = Bound1[i][1]-Bound1[i][0]+1;
for(j=0; j<NSeg2; j++)
Length2[j] = Bound2[j][1]-Bound2[j][0]+1;
for(i=0; i<NSeg1; i++) {
MaxOverlap = 0;
for(j=0; j<NSeg2; j++) {
Overlap = Minimum(Bound1[i][1],Bound2[j][1])-Maximum(Bound1[i][0],Bound2[j][0])+1;
if( Overlap > MaxOverlap ) MaxOverlap = Overlap;
}
if( (float)MaxOverlap/(float)Length1[i] >= Threshold )
TP++;
else
FN++;
}
for(i=0; i<NSeg2; i++) {
MaxOverlap = 0;
for(j=0; j<NSeg1; j++) {
Overlap = Minimum(Bound2[i][1],Bound1[j][1])-Maximum(Bound2[i][0],Bound1[j][0])+1;
if( Overlap > MaxOverlap ) MaxOverlap = Overlap;
}
if( (float)MaxOverlap/(float)Length2[i] < Threshold )
FP++;
}
if( TP+FN != 0 ) {
*Q2 = (float)TP/((float)TP+(float)FN);
*O = (float)FP/((float)TP+(float)FN);
}
else {
*Q2 = -1.0;
*O = -1.0;
}
return(1);
}
int Sov(char *Asn1, int L1, char *Asn2, int L2, char SecStr, float Threshold, float *Q2)
{
int Bound1[MAX_ASSIGN][2], Bound2[MAX_ASSIGN][2], Length1[MAX_ASSIGN],
Length2[MAX_ASSIGN], NSeg1, NSeg2;
int Overlap, MaxOverlap, TP=0, FN=0;
register int i, j;
NSeg1 = Boundaries(Asn1,L1,SecStr,Bound1);
NSeg2 = Boundaries(Asn2,L2,SecStr,Bound2);
for(i=0; i<NSeg1; i++)
Length1[i] = Bound1[i][1]-Bound1[i][0]+1;
for(j=0; j<NSeg2; j++)
Length2[j] = Bound2[j][1]-Bound2[j][0]+1;
for(i=0; i<NSeg1; i++) {
MaxOverlap = 0;
for(j=0; j<NSeg2; j++) {
if( Bound1[i][0] > Bound2[j][1] || Bound1[i][1] < Bound2[j][0] ) /*No overlap */
Overlap = 0;
else if ( Bound2[j][0] >= Bound1[i][0] && Bound2[j][1] <= Bound1[i][1] ) /* j inside i */
Overlap = Length2[j];
else if ( Bound1[i][0] <= Bound2[j][0] ) /* j shifted to the right with respect to i */
Overlap = Minimum(Bound2[j][1]-Bound2[j][0],Bound1[i][1]-Bound2[j][0])+1;
else if( Bound1[i][0] >= Bound2[j][0] ) /* i shifted to the right with respect to j */
Overlap = Minimum(Bound2[j][1]-Bound2[j][0],Bound2[j][1]-Bound1[i][0])+1;
else
Overlap = Length1[i]; /* i inside j */
if( Overlap > MaxOverlap ) MaxOverlap = Overlap;
}
if( (float)MaxOverlap/(float)Length1[i] >= Threshold )
TP++;
else
FN++;
}
if( TP+FN != 0 )
*Q2 = (float)TP/((float)TP+(float)FN);
else
*Q2 = -1.0;
/* O = (float)TP/((float)TP+(float)FN);*/
return(1);
}
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