File size: 7,801 Bytes
80a72c3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 | #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';
}
}
|