File size: 7,785 Bytes
80a72c3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 | #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);
}
}
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