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asngener.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"
/*************************************************************************
** **
** Remove short stretches of secondary structure from the assignment **
** **
** INPUT: *Asn String with one letter secondary structure **
** assignment **
** Length Length of the string **
** SecStrType Type of the secondary structure to which this **
** operation should be applied **
** EditChar Character to be used instead of removed symbols **
** MaxLength Maximal length of secondary struture segments to **
** be removed **
** **
** OUTPUT: *Asn Edited secondary structure assignment **
** **
*************************************************************************/
void CorrectAsn(char *Asn, int Length, char SecStrType, char EditChar, int MaxLength)
{
int NStr = 0, Res, Flag = 0, Bound[MAX_ASSIGN][2], i;
for( Res=0; Res<Length; Res++ ) {
if( Asn[Res] == SecStrType && Flag == 0 ) {
Flag = 1;
Bound[NStr][0] = Res;
}
else
if( Asn[Res] != SecStrType && Flag == 1 ) {
Flag = 0;
Bound[NStr++][1] = Res-1;
}
}
for( i=0; i<NStr; i++ )
if( Bound[i][1]-Bound[i][0]+1 <= MaxLength )
for( Res=Bound[i][0]; Res<=Bound[i][1]; Res++ )
Asn[Res] = EditChar;
}
void CorrectAsnDouble(char *Asn1, char *Asn2, char *KnownAsn, int Length,
char SecStrType, char EditChar)
{
register int Res;
for( Res=0; Res<Length; Res++ )
if( (Asn1[Res] == SecStrType || Asn2[Res] == SecStrType) && KnownAsn[Res] != SecStrType &&
( (Res == 0 && Asn1[Res+1] != SecStrType && Asn2[Res+1] != SecStrType) ||
(Res == Length-1 && Asn1[Res-1] != SecStrType && Asn2[Res-1] != SecStrType) ||
(Res > 0 && Res < Length-1 &&
Asn1[Res-1] != SecStrType && Asn2[Res-1] != SecStrType &&
Asn1[Res+1] != SecStrType && Asn2[Res+1] != SecStrType) ) )
Asn1[Res] = Asn2[Res] = EditChar;
}
/*************************************************************************
** **
** Calculate the number of true positives, true negatives, false **
** negatives and false positives resulting from comparison of test and **
** known secondary structure assignments for a particular secondary **
** structure type **
** **
** INPUT: *TestAsn String with one letter test secondary structure **
** assignment **
** *KnownAsn String with one letter known secondary structure **
** assignment **
** Length Length of the assignment **
** SecStrType Type of the secondary structure to which this **
** operation should be applied **
** **
** OUTPUT: *Quality Pointer to the structure with quality assessment **
** **
*************************************************************************/
int Difference(char *TestAsn, char *KnownAsn, int Length, char SecStrType, QUALITY *Qual)
{
register int Res;
Qual->TP = Qual->TN = Qual->FP = Qual->FN = 0;
for( Res=0; Res<Length; Res++ ) {
if( KnownAsn[Res] != 'X' ) {
if( KnownAsn[Res] == SecStrType && TestAsn[Res] == SecStrType ) Qual->TP++;
else
if( KnownAsn[Res] != SecStrType && TestAsn[Res] != SecStrType ) Qual->TN++;
else
if( KnownAsn[Res] != SecStrType && TestAsn[Res] == SecStrType ) Qual->FP++;
else
if( KnownAsn[Res] == SecStrType && TestAsn[Res] != SecStrType ) Qual->FN++;
}
}
if( Qual->TP == 0 && Qual->TN == 0 && Qual->FP == 0 && Qual->FN == 0 ) {
Qual->Perc = 0.0;
return(FAILURE);
}
Qual->Perc =
((float)Qual->TP+(float)Qual->TN)/
((float)Qual->TP+(float)Qual->TN+(float)Qual->FP+(float)Qual->FN);
return(SUCCESS);
}
/*************************************************************************
** **
** Calculate percent of the correctly assigned residues **
** **
** INPUT: *TestAsn String with one letter test secondary structure **
** assignment **
** *KnownAsn String with one letter known secondary structure **
** assignment **
** Length Length of the assignment **
** **
** RETURNS: Percent correct **
** **
*************************************************************************/
float PercentCorrect(char *TestAsn, char *KnownAsn, int Length)
{
int Res, Count=0;;
for( Res=0; Res<Length; Res++ )
if( KnownAsn[Res] == TestAsn[Res] )
Count++;
return( ((float)Count/(float)Length) );
}
/*************************************************************************
** **
** Calculate measures of secondary structure assignment quality based **
** on the number of true positives, true negatives, false negatives and **
** false positives resulting from comparison of test and known **
** assignments **
** **
** INPUT: *Quality Pointer to the structure with quality assessment **
** assignment **
** OUTPUT: Quality->Corr Correlation coefficient between the two **
** assignments as suggested by B.Matthews **
** (1975) Biochim. Biophys. Acta, 405, 442-451 **
** Quality->Perc Percent correct **
** **
*************************************************************************/
int AssessCorr(QUALITY *Qual)
{
float TP, TN, FP, FN;
if( (Qual->TP == 0 && Qual->FN == 0) || (Qual->TP == 0 && Qual->FP == 0) ) return(FAILURE);
else {
TP = (float)Qual->TP;
TN = (float)Qual->TN;
FP = (float)Qual->FP;
FN =(float)Qual->FN;
Qual->Corr = (TP*TN - FN*FP)/sqrt((TN+FN)*(TN+FP)*(TP+FN)*(TP+FP));
return(SUCCESS);
}
}
int AssessPerc(QUALITY *Qual)
{
float TP, TN, FP, FN;
TP = (float)Qual->TP;
TN = (float)Qual->TN;
FP = (float)Qual->FP;
FN =(float)Qual->FN;
Qual->Perc = (TP+TN)/(TP+TN+FP+FN);
return(SUCCESS);
}
void ExcludeObvious(char *Asn1, char *Asn2, char *KnownAsn, int Length)
{
register int i;
for( i=0; i<Length; i++ )
if( Asn1[i] == Asn2[i] ) {
KnownAsn[i] = 'X';
Asn1[i] = 'X';
Asn2[i] = 'X';
}
}