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dssp.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"
int ReadDSSP(CHAIN **Chain, DSSP **Dssp, COMMAND *Cmd)
{
FILE *fi;
int ChainNumber = -1, Start = 0, i;
BOOLEAN DuplicateChain = NO;
BUFFER Buffer, Tmp1, Tmp2;
char *Fields[MAX_FIELD];
if( strlen(Cmd->DsspFile) == 0 ) {
strcpy(Cmd->DsspFile,DSSPPATH);
GetFileNameFromPath(Chain[0]->File,Tmp1);
StripPathFromLastExtention(Tmp1,Tmp2);
strcat(Cmd->DsspFile,Tmp2);
strcat(Cmd->DsspFile,".dssp");
}
if( (fi = fopen(Cmd->DsspFile,"r")) ) {
while( fgets(Buffer,BUFSZ,fi) != NULL && !DuplicateChain ) {
if( Buffer[2] == '#' ) Start = 1;
else
if( Start == 1 ) {
if( Buffer[13] == '!' ) continue;
if( ChainNumber > 0 ) {
for( i=0; i<ChainNumber; i++ )
if( Dssp[i]->Id == Buffer[11] ) {
DuplicateChain = YES;
fprintf(stderr,"# Duplicate chain(s) in DSSP file %s\n",Cmd->DsspFile);
break;
}
}
if( ( ChainNumber == -1 || Buffer[11] != Dssp[ChainNumber]->Id ) ) {
ChainNumber++;
Dssp[ChainNumber] = (DSSP *)ckalloc(sizeof(DSSP));
Dssp[ChainNumber]->ResType = CharMatrix(MAX_RES,RES_FIELD);
Dssp[ChainNumber]->PDB_ResNumb = CharMatrix(MAX_RES,RES_FIELD);
Dssp[ChainNumber]->SecondStr = (char *)ckalloc(MAX_RES*sizeof(char));
Dssp[ChainNumber]->Accessibility = (float *)ckalloc(MAX_RES*sizeof(float));
strcpy(Dssp[ChainNumber]->File,Cmd->DsspFile);
Dssp[ChainNumber]->Id = Buffer[11];
Dssp[ChainNumber]->NRes = 0;
}
if( islower(Buffer[13]) ) Buffer[13] = 'C';
strcpy(Dssp[ChainNumber]->ResType[ Dssp[ChainNumber]->NRes ],OneToThree(Buffer[13]));
if( Buffer[16] == ' ' )
Dssp[ChainNumber]->SecondStr[ Dssp[ChainNumber]->NRes ] = 'C';
else
Dssp[ChainNumber]->SecondStr[ Dssp[ChainNumber]->NRes ] = Buffer[16];
SplitString(Buffer+6,Fields,1);
strcpy(Dssp[ChainNumber]->PDB_ResNumb[Dssp[ChainNumber]->NRes],Fields[0]);
SplitString(Buffer+34,Fields,1);
Dssp[ChainNumber]->Accessibility[ Dssp[ChainNumber]->NRes ] = atof(Fields[0]);
Dssp[ChainNumber]->NRes++;
}
}
fclose(fi);
}
ChainNumber++;
for( i=0; i<ChainNumber; i++ )
Dssp[i]->Id = SpaceToDash(Dssp[i]->Id);
return(ChainNumber);
}
/*************************************************************************
** **
** Check whether PDB and DSSP files correspond to each other **
** **
** INPUT: *Chain Pointer to a PDB chain **
** *Dssp Pointer to a DSSP chain **
** **
*************************************************************************/
int CompPdbDssp(CHAIN *Chain, DSSP *Dssp)
{
int Res, CA;
/* If the first or the last PDB residue does not have Ca, insert one residue in
coil conformation in the beginning or in the end of the DSSP chain */
if( !FindAtom(Chain,0,"CA",&CA) )
InsertFirst(Dssp,Chain);
if( Chain->NRes-1 > 0 && !FindAtom(Chain,Chain->NRes-1,"CA",&CA) )
InsertLast(Dssp,Chain);
/* Check correspondence of residue types */
for( Res=0; Res<Chain->NRes; Res++ )
if( strcmp(Chain->Rsd[Res]->ResType,Dssp->ResType[Res]) )
return(FAILURE);
/* If DSSP chain is still longer than PDB chain, shrink it */
if( Chain->NRes != Dssp->NRes )
Dssp->NRes = Chain->NRes;
return(SUCCESS);
}
/*************************************************************************
** **
** Insert one residue in the beginning of a DSSP chain and assign coil **
** conformation to it. This is neccessary to get rid of descrepancy **
** between the DSSP and PDB protein chains resulting from the fact **
** that DSSP does not consider residues without Ca atoms. Such residues,**
** e.g. ACE, often occur as first residues in PDB files **
** **
** INPUT: *Chain Pointer to protein chain **
** *Dssp Pointer to DSSP chain **
** **
** OUTPUT: *DSSP Pointer to modified DSSP chain **
** **
*************************************************************************/
void InsertFirst(DSSP *Dssp, CHAIN *Chain)
{
int Res;
for( Res=Dssp->NRes; Res>=1; Res-- ) {
strcpy(Dssp->ResType[Res],Dssp->ResType[Res-1]);
strcpy(Dssp->PDB_ResNumb[Res],Dssp->PDB_ResNumb[Res-1]);
Dssp->SecondStr[Res] = Dssp->SecondStr[Res-1];
}
strcpy(Dssp->ResType[0],Chain->Rsd[0]->ResType);
strcpy(Dssp->PDB_ResNumb[0],Chain->Rsd[0]->PDB_ResNumb);
Dssp->SecondStr[0] = 'C';
Dssp->NRes++;
}
/*************************************************************************
** **
** Insert one residue in the end a DSSP chain and assign coil **
** conformation to it. This is neccessary to get rid of descrepancy **
** between the DSSP and PDB protein chains resulting from the fact **
** that DSSP does not consider residues without Ca atoms. Such residues,**
** often occur as last residues in PDB files **
** **
** INPUT: *Chain Pointer to protein chain **
** *Dssp Pointer to DSSP chain **
** **
** OUTPUT: *DSSP Pointer to modified DSSP chain **
** **
*************************************************************************/
void InsertLast(DSSP *Dssp, CHAIN *Chain)
{
strcpy(Dssp->ResType[Dssp->NRes],Chain->Rsd[Dssp->NRes]->ResType);
strcpy(Dssp->PDB_ResNumb[Dssp->NRes],Chain->Rsd[Dssp->NRes]->PDB_ResNumb);
Dssp->SecondStr[Dssp->NRes] = 'C';
Dssp->NRes++;
}
/*************************************************************************
** **
** Get DSSP secondary structure assignment for every residue **
** **
*************************************************************************/
void GetDsspAsn(CHAIN **Chain, int NChain, COMMAND *Cmd)
{
DSSP **Dssp;
int NDsspChain=0, DsspCn, Cn, i;
Dssp = (DSSP **)ckalloc(MAX_CHAIN*sizeof(DSSP *));
if( (NDsspChain = ReadDSSP(Chain,Dssp,Cmd)) == 0 )
die("NODSSP Dssp file for %s not found\n",Chain[0]->File);
for( Cn=0; Cn<NChain; Cn++ ) {
if( !Chain[Cn]->Valid )
continue;
for( DsspCn=0; DsspCn<NDsspChain; DsspCn++ )
if( SpaceToDash(Chain[Cn]->Id) == Dssp[DsspCn]->Id )
break;
if( DsspCn == NDsspChain ) {
fprintf(stderr,"No DSSP chain corresponding to %s%c\n",
Chain[Cn]->File,SpaceToDash(Chain[Cn]->Id));
continue;
}
if( !CompPdbDssp(Chain[Cn],Dssp[DsspCn]) )
die("PDBDSSPDIF Chain %s%c differs from %s%c\n",
Dssp[DsspCn]->File,Dssp[DsspCn]->Id,Chain[Cn]->File,SpaceToDash(Chain[Cn]->Id));
for( i=0; i<Chain[Cn]->NRes; i++ ) {
Chain[Cn]->Rsd[i]->Prop->DsspAsn = Dssp[DsspCn]->SecondStr[i];
Chain[Cn]->Rsd[i]->Prop->DsspSolv = Dssp[DsspCn]->Accessibility[i];
}
}
if( Cmd->DsspAsn ) {
for( i=0; i<NDsspChain; i++ ) free(Dssp[i]);
free(Dssp);
}
}