2013-09-18 15:09:44 +00:00
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/*
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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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2013-09-18 14:12:31 +00:00
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#include "stride.h"
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/*************************************************************************
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** **
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** Find sequential residue number for a PDB residue number **
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** **
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** INPUT: *Chain Pointer to a protein chain **
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** *PdbN String containing PDB residue number **
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** **
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** OUTPUT: *SeqN Pointer to the sequential residue number **
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** **
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*************************************************************************/
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int PdbN2SeqN(CHAIN *Chain, char *PdbN, int *SeqN)
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{
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for( (*SeqN)=0; (*SeqN)<Chain->NRes; (*SeqN)++ )
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if( !strcmp(Chain->Rsd[(*SeqN)]->PDB_ResNumb,PdbN) )
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return(SUCCESS);
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return(FAILURE);
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}
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/*************************************************************************
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** **
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** Find atom of specified type in a residue **
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** **
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** INPUT: *Chain Pointer to a protein chain **
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** ResNumb Number of residue in the protein chain **
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** *Atom String containing atom name **
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** **
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** OUTPUT: *AtNumb Pointer to the atom number in the residue **
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** **
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*************************************************************************/
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int FindAtom(CHAIN *Chain, int ResNumb, char *Atom, int *AtNumb)
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{
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for( (*AtNumb)=0; (*AtNumb)<Chain->Rsd[ResNumb]->NAtom; (*AtNumb)++ )
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if( !strcmp(Atom,Chain->Rsd[ResNumb]->AtomType[(*AtNumb)]) )
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return(SUCCESS);
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*AtNumb = ERR;
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return(FAILURE);
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}
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/*************************************************************************
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** **
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** Find beginning and end residues of each secondary structure element **
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** in a secondary structure assignment **
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** **
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** INPUT: *Asn One letter secondary structure assignment **
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** L Length of the protein chain **
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** SecondStr Secondary structure type **
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** **
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** OUTPUT: *(Bound)[2] Two dimensional array containing numbers of **
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** first and last residue of each secondary **
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** structure element **
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** **
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** RETURNS: Number of the Secondary structure elements **
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** **
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*************************************************************************/
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int Boundaries(char *Asn, int L, char SecondStr, int (*Bound)[2])
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{
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register int Res;
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int NStr = 0, Flag = 0;
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for( Res=0; Res<L; Res++ ) {
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if( Asn[Res] == SecondStr && Flag == 0 ) {
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Flag = 1;
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Bound[NStr][0] = Res;
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}
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else
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if( Asn[Res] != SecondStr && Flag == 1 ) {
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Flag = 0;
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Bound[NStr++][1] = Res-1;
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}
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}
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return(NStr);
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}
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/*************************************************************************
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** **
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** Find protein chain with a given chain identifier number **
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** **
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** INPUT: **Chain Array of protein chains **
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** NChain Number of chains **
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** ChainId Chain identifier **
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** **
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** RETURNS: Number of the protein chain with identifier ChainId **
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** **
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*************************************************************************/
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int FindChain(CHAIN **Chain, int NChain, char ChainId)
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{
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register int i;
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for( i=0; i<NChain; i++ )
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if( Chain[i]->Id == ChainId )
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return(i);
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return(ERR);
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}
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BOOLEAN IsHydrogen(char *AtomName)
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{
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if( ( isdigit(AtomName[0]) &&
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( AtomName[1] == 'H' || AtomName[1] == 'D' ||
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AtomName[1] == 'T' || AtomName[1] == 'Q' ) ) ||
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AtomName[0] == 'H' || AtomName[0] == 'D' ||
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AtomName[0] == 'T' || AtomName[0] == 'Q' )
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return(SUCCESS);
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else
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return(FAILURE);
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}
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char *Translate(char Code)
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{
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static char *Dictionary[18] = {
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"AlphaHelix","310Helix","PiHelix","Strand","Bridge","Coil","TurnI","TurnI'",
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"TurnII","TurnII'","TurnVIa","TurnVIb","TurnVIII","TurnIV","GammaClassic",
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"GammaInv","Turn","Unknown" };
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switch(Code) {
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case 'H': return(Dictionary[0]);
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case 'G': return(Dictionary[1]);
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case 'I': return(Dictionary[2]);
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case 'E': return(Dictionary[3]);
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case 'B':
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case 'b':
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return(Dictionary[4]);
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case 'C': return(Dictionary[5]);
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case '1': return(Dictionary[6]);
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case '2': return(Dictionary[7]);
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case '3': return(Dictionary[8]);
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case '4': return(Dictionary[9]);
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case '5': return(Dictionary[10]);
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case '6': return(Dictionary[11]);
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case '7': return(Dictionary[12]);
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case '8': return(Dictionary[13]);
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case '@': return(Dictionary[14]);
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case '&': return(Dictionary[15]);
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case 'T': return(Dictionary[16]);
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default: return(Dictionary[17]);
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}
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}
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char SpaceToDash(char Id)
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{
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static char NewId;
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if( Id == ' ' )
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NewId = '-';
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else
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NewId = Id;
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return(NewId);
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}
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BOOLEAN ChInStr(char *String, char Char)
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{
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if( strchr(String,toupper(Char)) ||
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strchr(String,Char) ||
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strchr(String,tolower(Char)) )
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return(YES);
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return(NO);
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}
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void ExtractAsn(CHAIN **Chain, int Cn, char *Asn)
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{
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register int Res;
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for( Res=0; Res<Chain[Cn]->NRes; Res++ )
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Asn[Res] = Chain[Cn]->Rsd[Res]->Prop->Asn;
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}
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void ExtractPdbAsn(CHAIN **Chain, int Cn, char *Asn)
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{
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register int Res;
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for( Res=0; Res<Chain[Cn]->NRes; Res++ )
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Asn[Res] = Chain[Cn]->Rsd[Res]->Prop->PdbAsn;
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}
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void ExtractDsspAsn(CHAIN **Chain, int Cn, char *Asn)
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{
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register int Res;
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for( Res=0; Res<Chain[Cn]->NRes; Res++ )
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Asn[Res] = Chain[Cn]->Rsd[Res]->Prop->DsspAsn;
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}
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BOOLEAN ExistsSecStr(CHAIN **Chain, int NChain)
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{
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register int i, Cn;
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for( Cn=0; Cn<NChain; Cn++ )
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for( i=0; i<Chain[Cn]->NRes; i++ )
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if( Chain[Cn]->Rsd[i]->Prop->Asn != 'C' )
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return(YES);
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return(NO);
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}
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/*************************************************************************
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** **
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** Calculate the number of residues in helical or beta sheet state and **
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** what percent they constitute from the total number of residues in a **
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** protein chain **
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** **
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** INPUT: *Chain Pointer to a protein chain **
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** **
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** OUTPUT: *HelAlp Number of alpha-helical residues **
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** *HelPI Number of residues in pi-helices **
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** *Hel310 Number of residues in 3-10 helices **
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** *Sheet Number of residues in beta sheet **
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** **
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** RETURNS: Secondary structure content **
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** **
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*************************************************************************/
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float SecStrContent(CHAIN *Chain, int *HelAlp, int *HelPI, int *Hel310, int *Sheet, int *Turn)
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{
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int Res;
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float Content = 0.0;
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*HelAlp = 0; *HelPI = 0; *Hel310 = 0; *Sheet = 0; *Turn = 0;
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for( Res=0; Res<Chain->NRes; Res++ ) {
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switch( Chain->Rsd[Res]->Prop->PdbAsn ) {
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case 'H' : (*HelAlp)++;
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break;
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case 'G' : (*Hel310)++;
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break;
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case 'I' : (*HelPI)++;
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break;
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case 'E' : (*Sheet)++;
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break;
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case 'T' : (*Turn)++;
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break;
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}
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}
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Content = ( (float)( (*HelAlp)+(*HelPI)+(*Hel310)+(*Sheet)+(*Turn) ) )/(float)Chain->NRes;
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return(Content);
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}
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