/*********************************************************************************/ /*Program: cut_sequence.c */ /* */ /* Stefan Henrich */ /* cut_sequence.c */ /* Date: 18.05.2005 version 4 */ /* 15.09.2005 v5: MAXPOINT 60,foutpdb, stdout */ /* */ /* Purpose: */ /* cutting pdb files for ANAL/GOLPE based on sequence alignment of CLUSTAL W */ /* */ /* */ /* argv[1] sequence file created by prep_interaction.sh */ /* argv[2] number of components of protein (extracting from alignment, phylib) */ /* argv[3] number of components of ligand (extracting from alignment, phylib) */ /* */ /* output file: .cut.pdb */ /* */ /*COMPILATION: cc -o cut_sequence cut_sequence.c */ /*USAGE: >cut_sequence sequence.pir $(head -n1 sequence.phylib) */ /*********************************************************************************/ /* Das Programm soll die Anzahl der Sequenzen und deren Laenge von sequence.phy lesen und sequence.pir lesen und in eine Matrix schreiben. Ueberall wo ein "-" steht wird der Sequenzbereich auf 0 gesetzt. Danach erfolgt das Lesen der PDB files und es werden nur die Reste rausgeschrieben, bei denen die Matrix an der Stelle !=0 ist.*/ #include #include #include #define MAXPOINT 60 /* the sequence alignment (pir) has 50 characters in each line */ int mod_and_remainder(int i) /* return i/MAXPOINT */ { int mod=0; while(i>=MAXPOINT){i-=MAXPOINT; mod++;} return(mod); } struct pdbdata { char *filename; char *sequencestr; char *inpdb; char *outpdb; }; int main (int argc, char **argv) { FILE *fpirseq,*finpdb,*foutpdb; int number=atoi(argv[2]),residue=atoi(argv[3]); int i,j,k,mod,length,resinumb=0; char line[120],templine[120],strnumber[10],strresidues[10],pdb[1000],tmppdb[MAXPOINT]; char matrix[number+14][residue+1],character; //keine Ahnung warum das nur mit number+14 funktioniert char *filename,*sequencestr,*inpdb,*outpdb; struct pdbdata pdbfiles[number+1]; char strseq[residue]; char resinew[]=" ",resiold[]=" ",fill[]=" ",buffer[]=" "; if((fpirseq = fopen(argv[1] , "r"))==NULL) {printf("pirseq\n");exit(2);} mod=mod_and_remainder(residue); printf("mod %i\n",mod); printf("Number of sequences %i\n",number); printf("Number of residue %i\n",residue); printf("Number of MAXPOINTS %i\n",MAXPOINT); //writing '0' into first row filename = malloc(1); *filename='\0'; pdbfiles[0].filename = filename; for(j=1;j<=residue;j++) matrix[0][j]='1'; // reading sequence.pir for(i=1;i<=number;i++) // number of pdb files { // read file name // line 1 fscanf(fpirseq,"%s\n",line); //reads first line with sequence name length=strlen(line+4); filename = malloc(length+1); strcpy(filename,line+4); pdbfiles[i].filename = filename; pdbfiles[i].filename[length] = '\0'; printf("%i 1 line %s\n%s\n",i,line,pdbfiles[i].filename); // read sequence for(j=0;j<=mod;j++) // lines of sequence { for(k=1;k<=MAXPOINT;k++) // characters of line { if((j*MAXPOINT+k)<=residue) { fscanf(fpirseq,"%c",); printf("%c",character); matrix[i][j*MAXPOINT+k]=character; if( character=='-' ) matrix[0][j*MAXPOINT+k]='0'; } } fgets(line,MAXPOINT+2,fpirseq); printf("\n"); } fgets(line,MAXPOINT+2,fpirseq); // read * } /////////////// // write /////////////// for(j=1;j<=residue;j++) printf("%c",matrix[0][j]); printf("\n"); //write sequence 0 for(i=1;i<=number;i++) { printf("\n%s\n",pdbfiles[i].filename); length=strlen(pdbfiles[i].filename); finpdb=fopen(pdbfiles[i].filename,"r"); outpdb = malloc(length+50); pdbfiles[i].outpdb=pdbfiles[i].filename; // strncat(pdbfiles[i].outpdb,".pdb",4); strncpy(pdbfiles[i].outpdb+(length-3),"cut.pdb",8); // finpdb=fopen(pdbfiles[i].inpdb,"r"); foutpdb=fopen(pdbfiles[i].outpdb,"w"); //write sequences to stdout for(j=1;j<=residue;j++) { if(matrix[0][j]=='1') {printf("%c",matrix[i][j]);} else {printf("-");} } printf("\n"); //write lines in pdb files j=1; while(fgets(line,100,finpdb)) { strncpy (templine,line,100); //get string of residue number and extension if(strncmp(line,"ATOM ",6)==0) strncpy(resinew,line+22,5); //jump over - if((strncmp(line,"ATOM ",6)==0) && strcmp(resinew,resiold)!=0 && j<=residue) { // fprintf(foutpdb,"0) j %i\n0) %s",j,line); while(matrix[i][j]=='-' && j<=residue+1) {j++;} // j++; // fprintf(foutpdb,"1) %c %c residue %s j %i\n1) %s",matrix[0][j],matrix[i][j],resinew,j,line); // fprintf(foutpdb,"1) j %i\n1) %s",j,line); } //print ATOM lines of protein if((strncmp(line,"ATOM ",6)==0) && j<=residue && matrix[0][j]=='1' && strcmp(resinew,resiold)!=0) { fprintf(foutpdb,"%s",line); // fprintf(foutpdb,"2) %c %c residue %s j %i\n2) %s",matrix[0][j],matrix[i][j],resinew,j,line); } if((strncmp(line,"ATOM ",6)==0) && j<=residue && matrix[0][j-1]=='1' && strcmp(resinew,resiold)==0) { fprintf(foutpdb,"%s",line); // fprintf(foutpdb,"2) %c %c residue %s j %i\n2) %s",matrix[0][j],matrix[i][j],resinew,j,line); } //print non-ATOM lines if(strncmp(line,"ATOM ",6)!=0) { fprintf(foutpdb,"%s",line); // fprintf(foutpdb,"3) %c %c residue %s j %i\n3) %s",matrix[0][j],matrix[i][j],resinew,j,line); } if((strncmp(line,"ATOM ",6)==0) && strcmp(resinew,resiold)!=0) { j++; } //print ATOM lines, but not protein if((strncmp(line,"ATOM ",6)==0) && j>residue+1) { fprintf(foutpdb,"%s",line); // fprintf(foutpdb,"4) %c %c resinew %s residue %i j %i\n4)%s",matrix[0][j],matrix[i][j],resinew,residue,j,line); } strcpy(resiold,resinew); //store residue number for next cycle } // fclose(finpdb); strcpy(resinew," "); strcpy(resiold," "); } // for(j=1;j<=residue;j++) printf("%c",matrix[0][j]); printf("\n"); //write sequence 0 fclose(fpirseq); return(0); }