ZDOCK finished

src/INTBuilder.c

@@ -34,6 +34,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
     centerZ = pdb2->centerZ;
 
     for(i=0;i<nbCandInit1;i++){
+        if(t_candid1[i]->isHET) continue;
         for(j=0;j<t_candid1[i]->nbAtom;j++){
             x = t_candid1[i]->x[j];
             y = t_candid1[i]->y[j];
@@ -55,6 +56,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
     farthestY = t_candid1[idxCand]->y[idxAtom];
     farthestZ = t_candid1[idxCand]->z[idxAtom];
     for(i=0;i<nbCandInit2;i++){
+        if(t_candid2[i]->isHET) continue;
         for(j=0;j<t_candid2[i]->nbAtom;j++){
             x = t_candid2[i]->x[j];
             y = t_candid2[i]->y[j];
@@ -78,6 +80,7 @@ void getCandidatesForP1(struct pdb_values* pdb2, struct residue** t_candid1, str
     *nbCand1 = 0;
 
     for(i=0;i<nbCandInit1;i++){
+        if(t_candid1[i]->isHET) continue;
         for(j=0;j<t_candid1[i]->nbAtom;j++){
 
             x = t_candid1[i]->x[j];
@@ -144,8 +147,9 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
     for(i=0;i<pdbR->nbRes;i++)
         t_candidateR[i] = &pdbR->residues[i];
 
-    int totR = pdbR->nbRes, totL = pdbL->nbRes, step = 0;
-    printf("RSTEP 0 1.0\n");printf("LSTEP 0 1.0\n");
+    /* int totR = pdbR->nbRes, totL = pdbL->nbRes, step = 0;
+    printf("RSTEP 0 1.0\n");printf("LSTEP 0 1.0\n"); */
+
     /* Start removing candidates */
     while(oldCandL != nbCandL && oldCandR != nbCandR){
         oldCandL = nbCandL;
@@ -167,16 +171,16 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
             nbCandR = 0;
             break;
         }
-        step++;
-        printf("RSTEP %d %d %d -- %f\n",step,nbCandR,totR,(float)(1-((float)(totR-nbCandR)/totR)));
-        printf("LSTEP %d %d %d -- %f\n",step,nbCandL,totL,(float)(1-((float)(totL-nbCandL)/totL)));
+        /* step++; */
+        /* printf("RSTEP %d %d %d -- %f\n",step,nbCandR,totR,(float)(1-((float)(totR-nbCandR)/totR))); */
+        /* printf("LSTEP %d %d %d -- %f\n",step,nbCandL,totL,(float)(1-((float)(totL-nbCandL)/totL))); */
 
     }
-    while(step < 15){
+    /* while(step < 15){
         step++;
-        printf("RSTEP %d %d %d -- %f\n",step,nbCandR,totR,(float)(1-((float)(totR-nbCandR)/totR)));
-        printf("LSTEP %d %d %d -- %f\n",step,nbCandL,totL,(float)(1-((float)(totL-nbCandL)/totL)));
-    }
+         printf("RSTEP %d %d %d -- %f\n",step,nbCandR,totR,(float)(1-((float)(totR-nbCandR)/totR)));
+         printf("LSTEP %d %d %d -- %f\n",step,nbCandL,totL,(float)(1-((float)(totL-nbCandL)/totL)));
+    }*/
 
     /* The first nbCandR values of t_candidateR correspond to the possible candidates
      * for the receptor
@@ -206,6 +210,7 @@ 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(t_candidateR[i]->isHET) continue;
         for(j=0;j<t_candidateR[i]->nbAtom;j++){
             x1 = t_candidateR[i]->x[j];
             y1 = t_candidateR[i]->y[j];
@@ -213,6 +218,7 @@ void getInterface(struct pdb_values* pdbR, struct pdb_values* pdbL, int confID){
 
             /* For each candidate residue of the ligand */
             for(k=0;k<nbCandL;k++){
+                if(t_candidateL[k]->isHET) continue;
                 for(l=0;l<t_candidateL[k]->nbAtom;l++){
                     x2 = t_candidateL[k]->x[l];
                     y2 = t_candidateL[k]->y[l];
@@ -299,7 +305,11 @@ int main(int argc, char** argv){
         /* Compute the angles for the first and fifth CA of the protein
          * This is essential to compute the rotation angles
          */
-        getAnglesFromCA1andCA5_sophie(pdbL,&alpha,&beta,&gamma);
+        getAnglesFromCA1andCA5_MAXDo(pdbL,&alpha,&beta,&gamma);
+    }
+
+    if(ZDOCK){
+        init_ZDOCK(&pdbL);
     }
 
     if(complexPDB){    /* If we are building for a given complex, no rotation */
@@ -317,7 +327,7 @@ int main(int argc, char** argv){
             dgamma = dock_res->gamma[target_conf] - gamma;
 
 
-            newPDB = rotate_sophie(pdbL,pdbR,newPDB,dock_res->distCenters[target_conf],
+            newPDB = rotate_MAXDo(pdbL,pdbR,newPDB,dock_res->distCenters[target_conf],
                                 dock_res->theta[target_conf],dock_res->phi[target_conf],
                                 dalpha,dbeta,dgamma,dock_res,target_conf);
         }else if(HEX){
@@ -326,16 +336,6 @@ int main(int argc, char** argv){
                                 dock_res->alpha[target_conf],dock_res->beta[target_conf],
                                 dock_res->gamma[target_conf]);
         }else if(ZDOCK){
-            printf("R %f %f %f\n",pdbR->centerX,pdbR->centerY,pdbR->centerZ);
-            printf("L %f %f %f\n",pdbL->centerX,pdbL->centerY,pdbL->centerZ);
-            init_ZDOCK(&pdbR,&pdbL);
-            printf("R %f %f %f\n",pdbR->centerX,pdbR->centerY,pdbR->centerZ);
-            printf("L %f %f %f\n",pdbL->centerX,pdbL->centerY,pdbL->centerZ);
-        if(constructPDB){
-            writePDB(pdbL, ligand,target_conf);
-            writePDB(pdbR, receptor,target_conf);
-        }
-
             newPDB = rotate_ZDOCK(pdbL,newPDB,dock_res->trans_X[target_conf],
                                 dock_res->trans_Y[target_conf],dock_res->trans_Z[target_conf],
                                 dock_res->alpha[target_conf],dock_res->beta[target_conf],
@@ -377,7 +377,7 @@ int main(int argc, char** argv){
                 /* This is the rotated PDB
                  * pdbL doesn't change throughout the program
                  */
-                newPDB = rotate_sophie(pdbL, pdbR, newPDB, dock_res->distCenters[i],
+                newPDB = rotate_MAXDo(pdbL, pdbR, newPDB, dock_res->distCenters[i],
                                     dock_res->theta[i], dock_res->phi[i],
                                     dalpha, dbeta, dgamma, dock_res, i);
             }else if(HEX){
@@ -386,11 +386,6 @@ int main(int argc, char** argv){
                                     dock_res->alpha[i],dock_res->beta[i],
                                     dock_res->gamma[i]);
             }else if(ZDOCK){
-                printf("%f %f %f\n",pdbR->centerX,pdbR->centerY,pdbR->centerZ);
-                init_ZDOCK(&pdbR,&pdbL);
-                printf("%f %f %f\n",pdbR->centerX,pdbR->centerY,pdbR->centerZ);
-                exit(1);
-
                 newPDB = rotate_ZDOCK(pdbL,newPDB,dock_res->trans_X[i],
                                     dock_res->trans_Y[i],dock_res->trans_Z[i],
                                     dock_res->alpha[i],dock_res->beta[i],

src/allocate.c

@@ -6,7 +6,7 @@
 void freePDB(struct pdb_values* pdb){
     free(pdb->residues);
     free(pdb);
-    pdb = NULL; /* Has not effect since the adress passed as argument 
+    pdb = NULL; /* Has not effect since the adress passed as argument
                  * won't change
                  */
 }
@@ -15,7 +15,7 @@ void freePDB(struct pdb_values* pdb){
 void freeDock(struct docking_results* dock_res){
     /* Free the docking interface */
     free(dock_res->listEner);
-    if(HEX){
+    if(HEX || ZDOCK){
         free(dock_res->trans_X);
         free(dock_res->trans_Y);
         free(dock_res->trans_Z);
@@ -97,7 +97,7 @@ struct docking_results* allocate_dockingResults(int nbConf){
             perror("malloc");
             exit(EXIT_FAILURE);
         }
-        
+
         dock_res->trans_Z = malloc((2*nbConf)*sizeof(int));
         if(dock_res->trans_Z == NULL){
             perror("malloc");

src/fileIO.c

@@ -3,8 +3,28 @@
 #include <unistd.h>
 #include <string.h>
 #include "struct.h"
+#include "fileIO.h"
 #include "allocate.h"
 
+/* Remove blank spaces */
+char* deblank(char* input){
+    int i = 0, j = 0;
+    size_t len = 0;
+    char* output = NULL;
+
+    output = input;
+    len = strlen(input);
+    for (i = 0; i<(int)len; i++){
+        if (input[i]!=' '){
+            output[j]=input[i];
+            j++;
+        }
+
+    }
+    output[j]=0;
+    return output;
+}
+
 struct docking_results* getDataForComplex(){
     char* buf = NULL;
     char buf2[100] = "";
@@ -183,9 +203,10 @@ struct pdb_values* readPDB(char* protein) {
     strcpy(buf3,"\0");
     while(!feof(pdbFile_stream)){
         rc = getline(&buf,&len,pdbFile_stream);
-        strncpy(buf2,buf,4);
-        buf2[4] = '\0';
-        if(strcmp("ATOM",buf2) == 0){
+        strncpy(buf2,buf,6);
+        buf2[6] = '\0';
+        deblank(buf2);
+        if(strcmp("ATOM",buf2) == 0 || strcmp("HETATM",buf2) == 0){
             /* get the residue ID */
             strncpy(buf2,buf+22,5);
             buf2[5] = '\0';
@@ -209,9 +230,10 @@ struct pdb_values* readPDB(char* protein) {
         rc = getline(&buf,&len,pdbFile_stream);
         if(feof(pdbFile_stream)) break; /* else the last line is read twice */
 
-        strncpy(buf2,buf,4);
-        buf2[4] = '\0';
-        if(strcmp("ATOM",buf2) != 0){
+        strncpy(buf2,buf,6);
+        buf2[6] = '\0';
+        deblank(buf2);
+        if(strcmp("ATOM",buf2) != 0 && strcmp("HETATM",buf2) != 0){
             continue;
         }
         strncpy(bufID,buf+22,5);
@@ -237,6 +259,10 @@ struct pdb_values* readPDB(char* protein) {
 
             /* atom chain */
             pdb_prot->residues[curRes].chain = buf[21];
+
+            /* if it is an HETATM */
+            if(strcmp("HETATM",buf2) == 0)
+                pdb_prot->residues[curRes].isHET = 1;
         }
 
         /* atom type */
@@ -316,10 +342,18 @@ void writePDB(struct pdb_values* pdb, char* protName, int nConf){
         exit(EXIT_FAILURE);
     }
     for(i=0;i<pdb->nbRes;i++){
-        for(j=0;j<pdb->residues[i].nbAtom;j++){
-            fprintf(fw,FORMAT_LINE_PDB,pdb->residues[i].idAtom[j],
-            pdb->residues[i].atomType[j],pdb->residues[i].resName,pdb->residues[i].chain,
-            pdb->residues[i].idRes,pdb->residues[i].x[j],pdb->residues[i].y[j],pdb->residues[i].z[j]);
+        if(pdb->residues[i].isHET){
+            for(j=0;j<pdb->residues[i].nbAtom;j++){
+                fprintf(fw,FORMAT_LINE_PDB_HET,pdb->residues[i].idAtom[j],
+                pdb->residues[i].atomType[j],pdb->residues[i].resName,pdb->residues[i].chain,
+                pdb->residues[i].idRes,pdb->residues[i].x[j],pdb->residues[i].y[j],pdb->residues[i].z[j]);
+            }
+        }else{
+            for(j=0;j<pdb->residues[i].nbAtom;j++){
+                fprintf(fw,FORMAT_LINE_PDB_ATM,pdb->residues[i].idAtom[j],
+                pdb->residues[i].atomType[j],pdb->residues[i].resName,pdb->residues[i].chain,
+                pdb->residues[i].idRes,pdb->residues[i].x[j],pdb->residues[i].y[j],pdb->residues[i].z[j]);
+            }
         }
     }
     fclose(fw);

src/rotation.c

@@ -5,30 +5,23 @@
 #include "allocate.h"
 #include "rotation.h"
 
-void init_ZDOCK(struct pdb_values** pdbR_addr, struct pdb_values** pdbL_addr){
-    struct pdb_values* pdbR = *pdbR_addr;
+void init_ZDOCK(struct pdb_values** pdbL_addr){
     struct pdb_values* pdbL = *pdbL_addr;
     struct pdb_values* newPDB = NULL;
-    
-//    newPDB = rotate_ZDOCK_init(pdbR,newPDB);
-//    (*pdbR_addr) = newPDB;
-//    newPDB = NULL;
-    // TODO : free pdbR
 
     newPDB = rotate_ZDOCK_init(pdbL,newPDB);
     (*pdbL_addr) = newPDB;
-    newPDB = NULL;
-    // TODO : free pdbL
+    freePDB(pdbL);
 }
 
-
-/**********************************************/
-/* Function rotateAtom  */
-/*  rotates around 3 euler angles  */
-/**********************************************/
 void rotateAtom (float oldX, float oldY, float oldZ,
                  float *newX, float *newY, float *newZ,
                  float alpha, float beta, float gamma, int rev) {
+    /* This function rotates an atom with the 3 Euler angles,
+     * according to the center (0,0,0)
+     * The rev option indicates if the matrix has to be transposed or not
+     */
+
     float c_a = cos(alpha), s_a = sin(alpha);
     float c_b = cos(beta), s_b = sin(beta);
     float c_g = cos(gamma), s_g = sin(gamma);
@@ -37,7 +30,7 @@ void rotateAtom (float oldX, float oldY, float oldZ,
         r11 = c_a*c_g  -  s_a*c_b*s_g;
         r21 = s_a*c_g  +  c_a*c_b*s_g;
         r31 = s_b*s_g;
-        
+
         r12 = -c_a*s_g  -  s_a*c_b*c_g;
         r22 = -s_a*s_g  +  c_a*c_b*c_g;
         r32 = s_b*c_g;
@@ -49,7 +42,7 @@ void rotateAtom (float oldX, float oldY, float oldZ,
         r11 = c_a*c_g  -  s_a*c_b*s_g;
         r12 = s_a*c_g  +  c_a*c_b*s_g;
         r13 = s_b*s_g;
-        
+
         r21 = -c_a*s_g  -  s_a*c_b*c_g;
         r22 = -s_a*s_g  +  c_a*c_b*c_g;
         r23 = s_b*c_g;
@@ -89,8 +82,6 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
      * https://upload.wikimedia.org/wikipedia/commons/thumb/a/a1/Eulerangles.svg/300px-Eulerangles.svg.png
      */
 
-    printf("rotate : T X/Y/Z : %f _%f _%f\nR A/B/G : %f %f %f\n",trans_X,trans_Y,trans_Z,alpha,beta,gamma);
-
     float xi = 0, yi = 0, zi = 0;
     float x1i = 0, y1i = 0, z1i = 0;
     float x2i = 0, y2i = 0, z2i = 0;
@@ -169,7 +160,6 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
     newPDB->centerX = newX;
     newPDB->centerY = newY;
     newPDB->centerZ = newZ;
-    printf("NEW : %f %f %f\n",newPDB->centerX,newPDB->centerY,newPDB->centerZ);
 
     return newPDB;
 }
@@ -224,7 +214,7 @@ struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values*
                 zi -= ZDOCK_LIG_Z_TRANS;
                 rotateAtom(xi, yi, zi, &x1i, &y1i, &z1i, ZDOCK_LIG_A_ROT, ZDOCK_LIG_B_ROT, ZDOCK_LIG_G_ROT, 0);
             }
-            
+
             newPDB->residues[i].x[j] = x1i;
             newPDB->residues[i].y[j] = y1i;
             newPDB->residues[i].z[j] = z1i;
@@ -330,7 +320,7 @@ struct pdb_values* rotate_global(struct pdb_values* pdb, struct pdb_values* pdbR
     /* Coordinates of the N axis */
     float xN = c_a;
     float yN = s_a;
-    float zN = 0;
+    /* float zN = 0; */
 
     /* The coordinates of the unit vector for the axis Z can be computed as such :
      */
@@ -407,7 +397,7 @@ struct pdb_values* rotate_global(struct pdb_values* pdb, struct pdb_values* pdbR
 }
 
 
-struct pdb_values* rotate_sophie(struct pdb_values* pdb, struct pdb_values* pdbR, struct pdb_values* newPDB, float R, float theta, float phi, float alpha,float beta,float gamma, struct docking_results* dock_res, int nConf){
+struct pdb_values* rotate_MAXDo(struct pdb_values* pdb, struct pdb_values* pdbR, struct pdb_values* newPDB, float R, float theta, float phi, float alpha,float beta,float gamma, struct docking_results* dock_res, int nConf){
     /* This function rotates the PDB pdb given in argument and sets the new coordinates in newPDB.
      * The final center of the xyz system is the geometric center of the PDB pdbR.
      * The angles alpha, beta, gamma in arguments correspond to the rotation angles that have to be applied to
@@ -453,7 +443,7 @@ struct pdb_values* rotate_sophie(struct pdb_values* pdb, struct pdb_values* pdbR
 
     float xN = c_a0;
     float yN = s_a0;
-    float zN = 0;
+    /* float zN = 0; */
 
     /* The coordinates of the unit vector for the axis Z can be computed as such :
      *  xZ : -s_a0 * c_b0
@@ -528,7 +518,7 @@ struct pdb_values* rotate_sophie(struct pdb_values* pdb, struct pdb_values* pdbR
 
 
 
-void getAnglesFromCA1andCA5_sophie(struct pdb_values* pdb, float* alpha, float* beta, float* gamma){
+void getAnglesFromCA1andCA5_MAXDo(struct pdb_values* pdb, float* alpha, float* beta, float* gamma){
     /* In this function, we first need to find the initial angles alpha and beta that correspond
      * to the angles alpha and beta for the first CA of the protein.
      * Then, we need to apply a rotation alpha about the axis Z, then a rotation beta

src/rotation.h

@@ -3,9 +3,9 @@
 #ifndef ROTAT_HEADER
 #define ROTAT_HEADER
 
-struct pdb_values* rotate_sophie(struct pdb_values* pdb, struct pdb_values* pdbR, struct pdb_values* newPDB, float R, float theta, float phi, float alpha,float beta,float gamma, struct docking_results* dock_res, int nConf);
+struct pdb_values* rotate_MAXDo(struct pdb_values* pdb, struct pdb_values* pdbR, struct pdb_values* newPDB, float R, float theta, float phi, float alpha,float beta,float gamma, struct docking_results* dock_res, int nConf);
 
-void getAnglesFromCA1andCA5_sophie(struct pdb_values* pdb, float* alpha, float* beta, float* gamma);
+void getAnglesFromCA1andCA5_MAXDo(struct pdb_values* pdb, float* alpha, float* beta, float* gamma);
 
 void sphericToxyz(float *x, float *y, float *z, float x0, float y0, float z0, float R, float theta, float phi);
 
@@ -17,7 +17,7 @@ struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values*
 
 struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPDB, float trans_X, float trans_Y, float trans_Z, float alpha, float beta, float gamma);
 
-void init_ZDOCK(struct pdb_values** pdbR_addr, struct pdb_values** pdbL_addr);
+void init_ZDOCK(struct pdb_values** pdbL_addr);
 
 void rotateAtom (float oldX, float oldY, float oldZ,
                  float *newX, float *newY, float *newZ,

src/struct.h

@@ -10,15 +10,17 @@
  */
 
 #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_MANY_CLASHES 20                /* If not forcing, program will skip conformation after
-                                            * this number of clashes */
+#define NB_MAX_ATOM_PER_RES 100             /* No residue has more atoms than that */
+#define TOO_MANY_CLASHES 20                 /* If not forcing, program will skip conformation after
+                                             * this number of clashes */
 #define DIST_FOR_CLASH 2           /* Distance in Angstrom under which we consider
                                     * the contact is a clash */
-#define NB_HEADER_LINE_HEX 12        /* Number of header lines at the top of a hex docking file */
-#define NB_HEADER_LINE_ZDOCK 5        /* Number of header lines at the top of a ZDOCK docking file */
+#define NB_HEADER_LINE_HEX 12      /* Number of header lines at the top of a hex docking file */
+#define NB_HEADER_LINE_ZDOCK 5     /* Number of header lines at the top of a ZDOCK docking file */
+
 /* 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"
+#define FORMAT_LINE_PDB_ATM "ATOM  %5d  %3s %3s %c%5s   %8.3f%8.3f%8.3f\n"
+#define FORMAT_LINE_PDB_HET "HETATM%5d  %3s %3s %c%5s   %8.3f%8.3f%8.3f\n"
 
 int     verbose;            /* 1 if we are in verbose mode */
 int     constructPDB;       /* 1 if we should build the PDB */
@@ -33,7 +35,10 @@ int     atom_res;           /* 1 if we want a resolution at atom's level */
 int     clash;              /* Maybe be incremented in case of clashes */
 int     force;              /* Will output even if clash, may increase computation time */
 float   DIST_FOR_CONTACT;   /* Distance under which we consider two residues are in contact */
-float   ZDOCK_LIG_A_ROT;    /* Initial rotations and translations if using ZDOCK */
+
+/* Initial rotations and translations if using ZDOCK */
+/*****************************************************/
+float   ZDOCK_LIG_A_ROT;
 float   ZDOCK_LIG_B_ROT;
 float   ZDOCK_LIG_G_ROT;
 float   ZDOCK_REC_A_ROT;
@@ -45,9 +50,13 @@ float   ZDOCK_LIG_Z_TRANS;
 float   ZDOCK_REC_X_TRANS;
 float   ZDOCK_REC_Y_TRANS;
 float   ZDOCK_REC_Z_TRANS;
-float   ZDOCK_GRID_UNIT;
-int     ZDOCK_GRID_SIZE;
-int     ZDOCK_PROT_FIXED;
+/*****************************************************/
+float   ZDOCK_GRID_UNIT;    /* The unit value for the grid used in ZDOCK */
+int     ZDOCK_GRID_SIZE;    /* Number of unit for the grid (UNITxUNITxUNIT) */
+int     ZDOCK_PROT_FIXED;   /* 1 if the receptor is fixed, 0 if the ligand is fixed.
+                             * This is set from ZDOCK docking file, but the user should
+                             * specify the right ligand and receptor in the command line
+                             * of INTBuilder */
 FILE*   verbose_file;       /* If verbose mode, the output file */
 char*   pdbDir;             /* Directory containing the PDBs */
 char*   receptor;           /* Name of the receptor */
@@ -85,6 +94,7 @@ struct residue {
     float   z[NB_MAX_ATOM_PER_RES];               /* Array containing the z for each of its atom */
     char    atomType[NB_MAX_ATOM_PER_RES][10];    /* Array containing the type of atom */
     int     idAtom[NB_MAX_ATOM_PER_RES];          /* ID of the atom */
+    int     isHET;
     int     nbAtom;                               /* Number of atom for this residue */
     int     isCandidate;                          /* 1 if this residue belongs to the docking interface */
     int     isAtomCandidate[NB_MAX_ATOM_PER_RES]; /* 1 if the atom belongs to the docking interface */