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INTBuilder
Commit e1f8bd83 by Chloe Dequeker
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Adding parameters : --force or -f will allow the user to choose weither or not… 

Adding parameters : --force or -f will allow the user to choose weither or not clashes should be taken into account. Conformations with too many clashes will be skipped
parent b761cbe1
Showing with 58 additions and 22 deletions
src/INTBuilder.c
......@@ -95,7 +95,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
}
}
void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
/* This function will output the docking interface between pdbR and pdbL
* To compute the docking interface, we considered that any residue of P1 at or closer than 10A
* of a residue of P2 will represent a contact
......@@ -122,6 +122,10 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
struct residue** t_candidateR = NULL;
int nbCandR = pdbR->nbRes, nbCandL = pdbL->nbRes;
/** Here we reset the number of clashes as this is a new interface computation **/
clash = 0;
t_candidateL = malloc((2*pdbL->nbRes)*sizeof(struct residue*));
if(t_candidateL == NULL){
perror("malloc");
......@@ -192,7 +196,7 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
/* For each candidate residue of the ligand */
for(k=0;k<nbCandL;k++){
/* If both the residues we are looking at are already selected */
if(t_candidateL[k]->isCandidate && t_candidateR[i]->isCandidate){
if(force && t_candidateL[k]->isCandidate && t_candidateR[i]->isCandidate){
continue;
}
for(l=0;l<t_candidateL[k]->nbAtom;l++){
......@@ -201,20 +205,46 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL){
z2 = t_candidateL[k]->z[l];
dist = sqrt((x1-x2)*(x1-x2) + (y1-y2)*(y1-y2) + (z1-z2)*(z1-z2));
if(dist < DIST_FOR_CLASH){
clash++;
if(clash >= TOO_MUCH_CLASHES){
break;
}
continue;
}
if(dist <= DIST_FOR_CONTACT){
t_candidateR[i]->isCandidate = 1;
t_candidateL[k]->isCandidate = 1;
break;
}
}
if(clash >= TOO_MUCH_CLASHES){
break;
}
}
if(clash >= TOO_MUCH_CLASHES){
break;
}
}
if(clash >= TOO_MUCH_CLASHES){
break;
}
}
printf("number of clashes : %d \n",clash);
/* If the amount of clashes is still ok */
if(clash < TOO_MUCH_CLASHES){
/* Output the ligand's interface */
fprintf(outputFile_lig,"%d ",confID);
write_candidate(t_candidateL,nbCandL,outputFile_lig);
fprintf(outputFile_lig,"\n");
/* Output the ligand's interface */
write_candidate(t_candidateL,nbCandL,outputFile_lig);
/* Output the receptor's interface */
write_candidate(t_candidateR,nbCandR,outputFile_rec);
/* Output the receptor's interface */
fprintf(outputFile_rec,"%d ",confID);
write_candidate(t_candidateR,nbCandR,outputFile_rec);
fprintf(outputFile_rec,"\n");
}
free(t_candidateL);
free(t_candidateR);
......@@ -252,11 +282,7 @@ int main(int argc, char** argv){
if(complexPDB){ /* If we are building for a given complex, no rotation */
/* Write the number of the conformation and get the interface */
fprintf(outputFile_lig,"%d ",i);
fprintf(outputFile_rec,"%d ",i);
getInterface(pdbR,pdbL);
fprintf(outputFile_lig,"\n");
fprintf(outputFile_rec,"\n");
getInterface(pdbR,pdbL,0);
if(constructPDB){
writePDB(newPDB, ligand,target_conf);
......@@ -274,11 +300,7 @@ int main(int argc, char** argv){
/* Write the number of the conformation and get the interface */
if(!doNotOutputINT){
fprintf(outputFile_lig,"%d ",i);
fprintf(outputFile_rec,"%d ",i);
getInterface(pdbR,newPDB);
fprintf(outputFile_lig,"\n");
fprintf(outputFile_rec,"\n");
getInterface(pdbR,newPDB,target_conf);
}
if(constructPDB){
......@@ -312,11 +334,7 @@ int main(int argc, char** argv){
/* Write the number of the conformation and get the interface */
if(!doNotOutputINT){
fprintf(outputFile_lig,"%d ",i);
fprintf(outputFile_rec,"%d ",i);
getInterface(pdbR,newPDB);
fprintf(outputFile_lig,"\n");
fprintf(outputFile_rec,"\n");
getInterface(pdbR,newPDB,i);
}
if(constructPDB){
......
src/INTBuilder.h
......@@ -4,7 +4,7 @@
#define INTB_HEADER
void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, struct residue** t_candid2, int* nbCand1, int* nbCand2);
void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL);
void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID);
void removeSpace(char* string);
int main(int argc, char** argv);
......
src/fileIO.c
......@@ -61,10 +61,15 @@ struct docking_results* getDataForComplex(){
if(feof(condFile_stream)){
break;
}
/* printf("curConf : %d\n",idConf); */
rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->distCenters[idConf],&dock_res->theta[idConf],&dock_res->phi[idConf],&dock_res->alpha[idConf],&dock_res->beta[idConf],&dock_res->gamma[idConf]);
rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
if(idConf == 137)
printf("\n%f %f %f %f %f %f\n",dock_res->distCenters[idConf],dock_res->theta[idConf],dock_res->phi[idConf],dock_res->alpha[idConf],dock_res->beta[idConf],dock_res->gamma[idConf]);
/* theta and phi angles are written in Radian already
* However that is not the case for alpha, beta and gamma angles
*/
......
src/param.c
......@@ -30,6 +30,8 @@ void print_usage() {
"<-HCMD2> Means that the docking file is in the HCMD2 MAXDo format\n"
"<-noOutput> Will prevent the program to output the docking interface\n"
" Useful if you only want to use the '-outputPDB' option\n"
"<--force/-f> Will force the computation of the pause even in case of\n"
" huge number of clashes (threshold defined in struct.h)\n"
);
}
......@@ -51,6 +53,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
HCMD2 = 0;
complexPDB = 0;
doNotOutputINT = 0;
clash = 0;
force = 0;
outputDir = NULL;
outputPDB = NULL;
verbose_file = NULL;
......@@ -120,6 +124,9 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
}else if(strcmp(argv[i],"-h") == 0 ||
strcmp(argv[i],"--help") == 0){
print_help = 1;
}else if(strcmp(argv[i],"-f") == 0 ||
strcmp(argv[i],"--force") == 0){
force = 1;
}else if(strcmp(argv[i],"-v") == 0 ||
strcmp(argv[i],"--verbose") == 0){
verbose = 1;
......
src/struct.h
......@@ -11,8 +11,12 @@
#define COEF_DEGREE_TO_RADIAN 0.017453293 /* Coefficient to convert degrees to radians */
#define NB_MAX_ATOM_PER_RES 100 /* No residue has more atoms than that */
#define TOO_MUCH_CLASHES 20 /* If not forcing, program will skip conformation after
* this number of clashes */
#define DIST_FOR_CONTACT 6 /* Distance under which we consider
* two residues are in contact */
#define DIST_FOR_CLASH 2 /* Distance in Angstrom under which we consider
* the contact is a clash */
/* This is the format of a line in a PDB file */
#define FORMAT_LINE_PDB "ATOM %5d %3s %3s %c%5s %8.3f%8.3f%8.3f\n"
......@@ -23,6 +27,8 @@ int target_conf; /* 1 if we are specific to one conformation */
int HCMD2; /* 1 if this is HCMD2 format */
int complexPDB; /* 1 if we are computing the interface of a given complex */
int doNotOutputINT; /* 1 if we don't want to output the interface */
int clash; /* Maybe be incremented in case of clashes */
int force; /* Will output even if clash, may increase computation time */
FILE* verbose_file; /* If verbose mode, the output file */
char* pdbDir; /* Directory containing the PDBs */
char* receptor; /* Name of the receptor */
......
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