You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
138 lines
4.2 KiB
C
138 lines
4.2 KiB
C
/*
|
|
* 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 Helix(CHAIN **Chain, int Cn, HBOND **HBond, COMMAND *Cmd, float **PhiPsiMap)
|
|
{
|
|
|
|
int BondNumb, i;
|
|
float *Prob, CONST;
|
|
RESIDUE **r;
|
|
|
|
CONST = 1+Cmd->C1_H;
|
|
|
|
Prob = (float *)ckalloc(MAX_RES*sizeof(float));
|
|
|
|
for( i=0; i<Chain[Cn]->NRes; i++ )
|
|
Prob[i] = 0.0;
|
|
|
|
|
|
for( i=0; i<Chain[Cn]->NRes-5; i++ ) {
|
|
|
|
r = &Chain[Cn]->Rsd[i];
|
|
|
|
if( r[0]->Prop->PhiZn != ERR && r[0]->Prop->PsiZn != ERR &&
|
|
r[1]->Prop->PhiZn != ERR && r[1]->Prop->PsiZn != ERR &&
|
|
r[2]->Prop->PhiZn != ERR && r[2]->Prop->PsiZn != ERR &&
|
|
r[3]->Prop->PhiZn != ERR && r[3]->Prop->PsiZn != ERR &&
|
|
r[4]->Prop->PhiZn != ERR && r[4]->Prop->PsiZn != ERR ) {
|
|
|
|
if( (BondNumb = FindPolInt(HBond,r[4],r[0])) != ERR ) {
|
|
Prob[i] = HBond[BondNumb]->Energy*(CONST+Cmd->C2_H*
|
|
0.5*(PhiPsiMap[r[0]->Prop->PhiZn][r[0]->Prop->PsiZn]+
|
|
PhiPsiMap[r[4]->Prop->PhiZn][r[4]->Prop->PsiZn]));
|
|
|
|
}
|
|
}
|
|
}
|
|
|
|
for( i=0; i<Chain[Cn]->NRes-5; i++ ) {
|
|
|
|
if( Prob[i] < Cmd->Treshold_H1 && Prob[i+1] < Cmd->Treshold_H1 ) {
|
|
|
|
r = &Chain[Cn]->Rsd[i];
|
|
|
|
r[1]->Prop->Asn = 'H';
|
|
r[2]->Prop->Asn = 'H';
|
|
r[3]->Prop->Asn = 'H';
|
|
r[4]->Prop->Asn = 'H';
|
|
if( r[0]->Prop->PhiZn!= ERR && r[0]->Prop->PsiZn != ERR &&
|
|
PhiPsiMap[r[0]->Prop->PhiZn][r[0]->Prop->PsiZn] > Cmd->Treshold_H3 )
|
|
r[0]->Prop->Asn = 'H';
|
|
if( r[5]->Prop->PhiZn != ERR && r[5]->Prop->PsiZn != ERR &&
|
|
PhiPsiMap[r[5]->Prop->PhiZn][r[5]->Prop->PsiZn] > Cmd->Treshold_H4 )
|
|
r[5]->Prop->Asn = 'H';
|
|
}
|
|
}
|
|
|
|
for( i=0; i<Chain[Cn]->NRes-4; i++ ) {
|
|
|
|
r = &Chain[Cn]->Rsd[i];
|
|
|
|
if( FindBnd(HBond,r[3],r[0]) != ERR && FindBnd(HBond,r[4],r[1]) != ERR &&
|
|
/*************************** This should be improved **************************/
|
|
( (r[1]->Prop->Asn != 'H' && r[2]->Prop->Asn != 'H') ||
|
|
(r[2]->Prop->Asn != 'H' && r[3]->Prop->Asn != 'H') ) )
|
|
/******************************************************************************/
|
|
{
|
|
r[1]->Prop->Asn = 'G';
|
|
r[2]->Prop->Asn = 'G';
|
|
r[3]->Prop->Asn = 'G';
|
|
}
|
|
}
|
|
|
|
for( i=0; i<Chain[Cn]->NRes-6; i++ ) {
|
|
|
|
r = &Chain[Cn]->Rsd[i];
|
|
|
|
if( FindBnd(HBond,r[5],r[0]) != ERR && FindBnd(HBond,r[6],r[1]) != ERR &&
|
|
r[1]->Prop->Asn == 'C' && r[2]->Prop->Asn == 'C' &&
|
|
r[3]->Prop->Asn == 'C' && r[4]->Prop->Asn == 'C' &&
|
|
r[5]->Prop->Asn == 'C' ) {
|
|
r[1]->Prop->Asn = 'I';
|
|
r[2]->Prop->Asn = 'I';
|
|
r[3]->Prop->Asn = 'I';
|
|
r[4]->Prop->Asn = 'I';
|
|
r[5]->Prop->Asn = 'I';
|
|
}
|
|
}
|
|
|
|
if( Cmd->Info ) {
|
|
fprintf(stdout,"%s%c\n",Chain[Cn]->File,Chain[Cn]->Id);
|
|
|
|
for( i=0; i<Chain[Cn]->NRes-4; i++ ) {
|
|
|
|
r = &Chain[Cn]->Rsd[i];
|
|
|
|
if( r[0]->Prop->PhiZn != ERR && r[0]->Prop->PsiZn != ERR &&
|
|
r[4]->Prop->PhiZn != ERR && r[4]->Prop->PsiZn != ERR ) {
|
|
|
|
fprintf(stdout,"%s (%d) %c %10.7f %8.5f %8.5f | %4d %4d\n",
|
|
r[0]->PDB_ResNumb,i,r[0]->Prop->Asn,Prob[i],
|
|
PhiPsiMap[r[0]->Prop->PhiZn][r[0]->Prop->PsiZn],
|
|
PhiPsiMap[r[4]->Prop->PhiZn][r[4]->Prop->PsiZn],
|
|
r[4]->Prop->PhiZn,r[4]->Prop->PsiZn);
|
|
}
|
|
}
|
|
}
|
|
free(Prob);
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|