2013-09-18 15:09:44 +00:00
|
|
|
/*
|
|
|
|
|
* 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.
|
|
|
|
|
*/
|
|
|
|
|
|
|
|
|
|
|
2013-09-18 14:12:31 +00:00
|
|
|
#include "stride.h"
|
|
|
|
|
|
|
|
|
|
int PlaceHydrogens(CHAIN *Chain)
|
|
|
|
|
{
|
|
|
|
|
|
|
|
|
|
int Res, i, N, C, CA, H, PlacedCnt=0;
|
|
|
|
|
float Length_N_C, Length_N_CA, Length_N_H;
|
|
|
|
|
RESIDUE *r, *rr;
|
|
|
|
|
|
|
|
|
|
for( Res=1; Res<Chain->NRes; Res++ ) {
|
|
|
|
|
|
|
|
|
|
r = Chain->Rsd[Res];
|
|
|
|
|
rr = Chain->Rsd[Res-1];
|
|
|
|
|
|
|
|
|
|
if( !strcmp(r->ResType,"PRO") ) continue;
|
|
|
|
|
|
|
|
|
|
/* Replace deiterium atoms by hydrogens */
|
|
|
|
|
if( FindAtom(Chain,Res,"D",&H) )
|
|
|
|
|
strcmp(r->AtomType[H],"H");
|
|
|
|
|
|
|
|
|
|
if( !FindAtom(Chain,Res,"H",&H) && FindAtom(Chain,Res,"N",&N) &&
|
|
|
|
|
FindAtom(Chain,Res-1,"C",&C) && FindAtom(Chain,Res,"CA",&CA) ) {
|
|
|
|
|
|
|
|
|
|
H = r->NAtom;
|
|
|
|
|
|
|
|
|
|
Length_N_C = Dist(r->Coord[N],rr->Coord[C]);
|
|
|
|
|
Length_N_CA = Dist(r->Coord[N],r->Coord[CA]);
|
|
|
|
|
|
|
|
|
|
for( i=0; i<3; i++ )
|
|
|
|
|
r->Coord[H][i] = r->Coord[N][i] -
|
|
|
|
|
( (rr->Coord[C][i] - r->Coord[N][i])/Length_N_C +
|
|
|
|
|
(r->Coord[CA][i] - r->Coord[N][i])/Length_N_CA );
|
|
|
|
|
|
|
|
|
|
Length_N_H = Dist(r->Coord[N],r->Coord[H]);
|
|
|
|
|
|
|
|
|
|
for( i=0; i<3; i++ )
|
|
|
|
|
r->Coord[H][i] = r->Coord[N][i] +
|
|
|
|
|
DIST_N_H*(r->Coord[H][i]-r->Coord[N][i])/Length_N_H;
|
|
|
|
|
|
|
|
|
|
strcpy(r->AtomType[H],"H");
|
|
|
|
|
r->NAtom++;
|
|
|
|
|
PlacedCnt++;
|
|
|
|
|
}
|
|
|
|
|
}
|
|
|
|
|
return(PlacedCnt);
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
