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INTBuilder
Commit 89573389 by Chloé Dequeker
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Adding a contact file feature

parent faa6f2d0
Showing with 246 additions and 18 deletions
src/INTBuilder.c
......@@ -95,6 +95,22 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
}
}
int check_ledger(int* ledger, int ledger_size, int entry) {
/* Checks the ledger array for the entry value.
* Returns 1 if present, else 0
*/
int i = 0;
for (i = 0; i < ledger_size; i++) {
if(ledger[i] == entry){
return 1;
}
}
return 0;
}
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
......@@ -122,6 +138,28 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
struct residue** t_candidateR = NULL;
int nbCandR = pdbR->nbRes, nbCandL = pdbL->nbRes;
/* Contacts are stored in the following way for each array.
* First is the ID of the particle for the receptor protein, then
* one or more ID for the particles in contact from the ligand protein.
* We go to the next ID of the receptor protein when
* we encounter the -1 value
*
* In the case of residue resolution, only residue ID is added.
* In atom resolution, two values are added every time, first residue
* then atom.
*/
int* pdbR_contacts_id = NULL;
int allocate_contacts_cpt = pdbR->nbAtom, contact_iter = 0, new_resi_check = 1;
pdbR_contacts_id = calloc(allocate_contacts_cpt, sizeof(int));
if (pdbR_contacts_id == NULL) {
perror("calloc");
exit(EXIT_FAILURE);
}
/* Keeps in memory for the current resi the ones already in contact on the lig */
int t_res_contact_ledger[pdbL->nbRes], ledger_size = 0;
/** Here we reset the number of clashes as this is a new interface computation **/
clash = 0;
......@@ -199,11 +237,28 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
/* For each candidate residue of the receptor */
for(i=0;i<nbCandR;i++){
isClashed = 0;
if (!atom_res && !new_resi_check){
new_resi_check = 1;
pdbR_contacts_id[contact_iter] = -1;
contact_iter++;
ledger_size = 0;
check_size_contacts(&pdbR_contacts_id, &allocate_contacts_cpt, contact_iter);
}
for(j=0;j<t_candidateR[i]->nbAtom;j++){
x1 = t_candidateR[i]->x[j];
y1 = t_candidateR[i]->y[j];
z1 = t_candidateR[i]->z[j];
if (atom_res && !new_resi_check){
new_resi_check = 1;
pdbR_contacts_id[contact_iter] = -1;
contact_iter++;
check_size_contacts(&pdbR_contacts_id, &allocate_contacts_cpt, contact_iter);
}
/* For each candidate residue of the ligand */
for(k=0;k<nbCandL;k++){
for(l=0;l<t_candidateL[k]->nbAtom;l++){
......@@ -228,10 +283,40 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
t_candidateR[i]->isAtomCandidate[j] = 1;
t_candidateL[k]->isAtomCandidate[l] = 1;
if(!atom_res)
/* Check for contacts */
if(atom_res){
if(new_resi_check){
pdbR_contacts_id[contact_iter] = i;
pdbR_contacts_id[contact_iter+1] = j;
contact_iter += 2;
new_resi_check = 0;
check_size_contacts(&pdbR_contacts_id, &allocate_contacts_cpt, contact_iter);
}
pdbR_contacts_id[contact_iter] = k;
pdbR_contacts_id[contact_iter+1] = l;
contact_iter += 2;
check_size_contacts(&pdbR_contacts_id, &allocate_contacts_cpt, contact_iter);
}else{
if(new_resi_check){
pdbR_contacts_id[contact_iter] = i;
contact_iter++;
new_resi_check = 0;
check_size_contacts(&pdbR_contacts_id, &allocate_contacts_cpt, contact_iter);
}
/* Check if this contact has already been tagged for this residue */
if(!check_ledger(t_res_contact_ledger, ledger_size, k)){
pdbR_contacts_id[contact_iter] = k;
t_res_contact_ledger[ledger_size] = k;
ledger_size++;
contact_iter++;
check_size_contacts(&pdbR_contacts_id, &allocate_contacts_cpt, contact_iter);
}
break;
}
}
}
if(clash >= TOO_MANY_CLASHES){
break;
}
......@@ -246,6 +331,13 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
}
if(pdbR_contacts_id[contact_iter-1] == -1){
pdbR_contacts_id[contact_iter-1] = -2;
}else{
pdbR_contacts_id[contact_iter] = -2;
}
contact_iter++;
/* If the amount of clashes is still ok */
if(clash < TOO_MANY_CLASHES){
/* Output the ligand's interface */
......@@ -257,10 +349,16 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
fprintf(outputFile_rec,"%d ",confID);
write_candidate(t_candidateR,nbCandR,outputFile_rec);
fprintf(outputFile_rec,"\n");
/* Output the receptor's interface */
fprintf(outputFile_contacts,"%d ",confID);
write_contacts(t_candidateR,t_candidateL,pdbR_contacts_id,outputFile_contacts);
fprintf(outputFile_contacts,"\n");
}
free(t_candidateL);
free(t_candidateR);
free(pdbR_contacts_id);
}
int main(int argc, char** argv){
......
src/INTBuilder.h
......@@ -3,6 +3,7 @@
#ifndef INTB_HEADER
#define INTB_HEADER
int check_ledger(int* ledger, int ledger_size, int entry);
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, int confID);
void removeSpace(char* string);
......
src/allocate.c
......@@ -304,6 +304,19 @@ void free_argLine(){
}
}
void check_size_contacts(int** t_contacts, int* allocated_size, int nb_contacts){
/* Checks if the allocated_size for t_contacts is enough for nb_contacts
* If not, doubles the allocated size
*/
if (nb_contacts >= *allocated_size - 10) {
*allocated_size *= 2;
*t_contacts = realloc(*t_contacts, (*allocated_size)*sizeof(int));
}
}
void freeAll(struct pdb_values* pdbR, struct pdb_values* pdbL, struct docking_results* dock_res){
/* Free all the arguments passed to this function */
freePDB(pdbL);
......
src/allocate.h
......@@ -10,5 +10,6 @@ void reset_dockingResults(struct docking_results* dock_res);
struct pdb_values* allocate_pdb(int nbRes);
void free_argLine();
void freeAll(struct pdb_values* pdbR, struct pdb_values* pdbL, struct docking_results* dock_res);
void check_size_contacts(int** t_contacts, int* allocated_size, int nb_contacts);
#endif
src/fileIO.c
......@@ -857,25 +857,10 @@ void write_candidate(struct residue** t_candid, int sizeCand, FILE* output_strea
if(t_candid[i]->isAtomCandidate[j]){
/* Getting the residue name */
len = strlen(t_candid[i]->idRes);
k = 0;
for(l=0;l<len;l++){
if(t_candid[i]->idRes[l] != ' '){
buf[k] = t_candid[i]->idRes[l];
k++;
}
}
buf[k] = '\0';
get_resi_name(t_candid, i, buf);
/* Now, getting the atom name */
len = strlen(t_candid[i]->atomType[j]);
k = 0;
for(l=0;l<len;l++){
if(t_candid[i]->atomType[j][l] != ' '){
buf2[k] = t_candid[i]->atomType[j][l];
k++;
} }
buf2[k] = '\0';
get_atom_name(t_candid, i, j, buf2);
fprintf(output_stream,"'%s' '%c' '%s' ",buf,t_candid[i]->chain, buf2);
fflush(output_stream);
}
......@@ -899,3 +884,108 @@ void write_candidate(struct residue** t_candid, int sizeCand, FILE* output_strea
}
}
void get_resi_name(struct residue** t_residues, int resi_id, char* str_resi){
int len = 0, k = 0, l = 0;
/* Getting the residue name */
len = strlen(t_residues[resi_id]->idRes);
k = 0;
for(l=0;l<len;l++){
if(t_residues[resi_id]->idRes[l] != ' '){
str_resi[k] = t_residues[resi_id]->idRes[l];
k++;
}
}
str_resi[k] = '\0';
}
void get_atom_name(struct residue** t_residues, int resi_id, int atom_id, char* str_atom){
int len = 0, k = 0, l = 0;
/* Now, getting the atom name */
len = strlen(t_residues[resi_id]->atomType[atom_id]);
k = 0;
for(l=0;l<len;l++){
if(t_residues[resi_id]->atomType[atom_id][l] != ' '){
str_atom[k] = t_residues[resi_id]->atomType[atom_id][l];
k++;
} }
str_atom[k] = '\0';
}
void write_contacts(struct residue** t_candidR, struct residue** t_candidL, int* t_contacts_id, FILE* output_stream){
/* Output the residues selected as being part of the interface in the array
* t_candid
*/
int i = 0, j = 0, k= 0, l = 0, len = 0;
int resi_id = 0, atom_id = 0, new_contact = 1;
char buf[15] = "", buf2[15] = "";
if(atom_res){
while(t_contacts_id[i] != -2) {
resi_id = t_contacts_id[i];
atom_id = t_contacts_id[i+1];
/* Value is -1 if we look at a new contact group */
if(resi_id == -1){
new_contact = 1;
i++;
resi_id = t_contacts_id[i];
atom_id = t_contacts_id[i+1];
fprintf(output_stream,"-- ");
fflush(output_stream);
}
/* Getting the residue and atom name */
if(new_contact){
new_contact = 0;
get_resi_name(t_candidR, resi_id, buf);
get_atom_name(t_candidR, resi_id, atom_id, buf2);
fprintf(output_stream,"'%s' '%c' '%s' ",buf,t_candidR[resi_id]->chain, buf2);
}else{
get_resi_name(t_candidL, resi_id, buf);
get_atom_name(t_candidL, resi_id, atom_id, buf2);
fprintf(output_stream,"'%s' '%c' '%s' ",buf,t_candidL[resi_id]->chain, buf2);
}
fflush(output_stream);
/* Check next contact */
i += 2;
}
}else{
while(t_contacts_id[i] != -2) {
resi_id = t_contacts_id[i];
/* Value is -1 if we look at a new contact group */
if(resi_id == -1){
new_contact = 1;
i++;
resi_id = t_contacts_id[i];
fprintf(output_stream,"-- ");
fflush(output_stream);
}
/* Getting the residue and atom name */
if(new_contact){
new_contact = 0;
get_resi_name(t_candidR, resi_id, buf);
fprintf(output_stream,"'%s' '%c' ",buf,t_candidR[resi_id]->chain);
}else{
get_resi_name(t_candidL, resi_id, buf);
fprintf(output_stream,"'%s' '%c' ",buf,t_candidL[resi_id]->chain);
}
fflush(output_stream);
/* Check next contact */
i++;
}
}
}
src/fileIO.h
......@@ -14,5 +14,8 @@ struct docking_results* getDataForComplex_HEX();
struct docking_results* getDataForComplex_MAXDO();
struct docking_results* getDataForComplex_HCMD2();
struct docking_results* getDataForComplex_DEFAULT();
void get_resi_name(struct residue** t_residues, int resi_id, char* str_resi);
void get_atom_name(struct residue** t_residues, int resi_id, int atom_id, char* str_atom);
void write_contacts(struct residue** t_candidR, struct residue** t_candidL, int* t_contacts_id, FILE* output_stream);
#endif
src/param.c
......@@ -277,6 +277,13 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
perror("fopen");
exit(EXIT_FAILURE);
}
sprintf(buf,"%s/%s-%s_rec_%d_contacts.txt",outputDir,receptor,ligand,target_conf);
outputFile_contacts = fopen(buf,"w");
if(outputFile_contacts == NULL){
perror("fopen");
exit(EXIT_FAILURE);
}
}else if(complexPDB){
sprintf(buf,"%s/%s-%s_rec_0_dockinter.txt",outputDir,receptor,ligand);
outputFile_rec = fopen(buf,"w");
......@@ -291,6 +298,13 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
perror("fopen");
exit(EXIT_FAILURE);
}
sprintf(buf,"%s/%s-%s_rec_0_contacts.txt",outputDir,receptor,ligand);
outputFile_contacts = fopen(buf,"w");
if(outputFile_contacts == NULL){
perror("fopen");
exit(EXIT_FAILURE);
}
}else{
sprintf(buf,"%s/%s-%s_rec_dockinter.txt",outputDir,receptor,ligand);
outputFile_rec = fopen(buf,"w");
......@@ -305,6 +319,13 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
perror("fopen");
exit(EXIT_FAILURE);
}
sprintf(buf,"%s/%s-%s_rec_contacts.txt",outputDir,receptor,ligand);
outputFile_contacts = fopen(buf,"w");
if(outputFile_contacts == NULL){
perror("fopen");
exit(EXIT_FAILURE);
}
}
}
......
src/struct.h
......@@ -68,6 +68,7 @@ char* outputDir; /* Output directory for the interface files */
char* outputPDB; /* Output directory if we construct the PDB(s) */
FILE* outputFile_rec; /* Name of the interface output file for the receptor */
FILE* outputFile_lig; /* Name of the interface output file for the ligand */
FILE* outputFile_contacts;/* Name of the output file for the contacts */
/*************************************************/
......
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