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