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