advancements for ATTRACT, rotate rec OK

src/fileIO.c

@@ -176,9 +176,10 @@ struct docking_results* getDataForComplex_ATTRACT(){
         dock_res->pivot_X_L  = pivot[1][0];
         dock_res->pivot_Y_L  = pivot[1][1];
         dock_res->pivot_Z_L  = pivot[1][2];
-        dock_res->centered_R = centered_R;
-        dock_res->centered_L = centered_L;
     }
+    dock_res->centered_R = centered_R;
+    dock_res->centered_L = centered_L;
+    dock_res->auto_pivot = auto_pivot;
     
     int curConf = 0;
     int mode = 0;

src/param.c

@@ -43,6 +43,8 @@ void print_usage() {
     "<-HEX>.............Means that the docking file is in the HEX format\n"
     "OR\n"
     "<-ZDOCK>...........Means that the docking file is in the ZDOCK format\n"
+    "OR\n"
+    "<-ATTRACT>.........Means that the docking file is in the ATTRACT format\n"
     );
 }
 
@@ -62,6 +64,7 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
     constructPDB     = 0;
     HCMD2            = 0;
     MAXDo            = 0;
+    ATTRACT          = 0;
     HEX              = 0;
     ZDOCK            = 0;
     complexPDB       = 0;
@@ -156,6 +159,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
             HCMD2 = 1;
         }else if(strcmp(argv[i],"-MAXDo") == 0){
             MAXDo = 1;
+        }else if(strcmp(argv[i],"-ATTRACT") == 0){
+            ATTRACT = 1;
         }else if(strcmp(argv[i],"-ZDOCK") == 0){
             ZDOCK = 1;
         }else if(strcmp(argv[i],"-HEX") == 0){
@@ -179,8 +184,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
         }
     }
 
-    if(MAXDo + HCMD2 + HEX + ZDOCK > 1){
-        fprintf(stderr,"You must choose only one mode out of the three 'MAXDo', 'HCMD2' and 'HEX'\n");
+    if(ATTRACT + MAXDo + HCMD2 + HEX + ZDOCK > 1){
+        fprintf(stderr,"You must choose only one mode out of 'ATTRACT', 'MAXDo', 'HCMD2' and 'HEX'\n");
         if(!print_help)
             print_usage();
         exit(EXIT_SUCCESS);

src/rotation.c

@@ -68,6 +68,113 @@ void sphericToxyz(float *x, float *y, float *z, float x0, float y0, float z0, fl
     *z = z0 + R * cos(theta);
 }
 
+struct pdb_values* rotate_R_ATTRACT(struct pdb_values* pdb, struct pdb_values* newPDB, struct docking_results* dock_res, int target_conf){
+    int i = 0, j = 0;
+    float rot_mat[9];
+
+    float xx = 0, yy = 0, zz = 0;
+
+    float pivot_X_R, pivot_Y_R, pivot_Z_R;
+    float cp = cos(dock_res->phi_R[target_conf]);
+    float cs = cos(dock_res->ssi_R[target_conf]);
+    float cr = cos(dock_res->rot_R[target_conf]);
+    float sp = sin(dock_res->phi_R[target_conf]);
+    float ss = sin(dock_res->ssi_R[target_conf]);
+    float sr = sin(dock_res->rot_R[target_conf]);
+    float cscp = cs * cp;
+    float cssp = cs * sp;
+    float sscp = ss * cp;
+    float sssp = ss * sp;
+
+    rot_mat[0] = cr * cscp + sr * sp;
+    rot_mat[1] = sr * cscp - cr * sp;
+    rot_mat[2] = sscp;
+
+    rot_mat[3] = cr * cssp - sr * cp;
+    rot_mat[4] = sr * cssp + cr * cp;
+    rot_mat[5] = sssp;
+
+    rot_mat[6] = -cr * ss;
+    rot_mat[7] = -sr * ss;
+    rot_mat[8] = cs;
+
+    /* If the receptor is centered, we need to substract the 
+     * pivot from all of its atoms
+     */
+    if(dock_res->auto_pivot){
+        pivot_X_R = newPDB->centerX;
+        pivot_Y_R = newPDB->centerY;
+        pivot_Z_R = newPDB->centerZ;
+    }else{
+        pivot_X_R = dock_res->pivot_X_R;
+        pivot_Y_R = dock_res->pivot_Y_R;
+        pivot_Z_R = dock_res->pivot_Z_R;
+    }
+
+    if(dock_res->centered_R){
+        dock_res->trans_X_R[i] -= pivot_X_R;
+        dock_res->trans_Y_R[i] -= pivot_Y_R;
+        dock_res->trans_Z_R[i] -= pivot_Z_R;
+    }
+
+    for(i=0;i<newPDB->nbRes;i++){
+        for(j=0;i<newPDB->residues[i].nbAtom;j++){
+            xx = newPDB->residues[i].x[j];
+            yy = newPDB->residues[i].y[j];
+            zz = newPDB->residues[i].z[j];
+
+            newPDB->residues[i].x[j] = xx * rot_mat[0] + yy * rot_mat[1] + zz * rot_mat[2];
+            newPDB->residues[i].y[j] = xx * rot_mat[3] + yy * rot_mat[4] + zz * rot_mat[5];
+            newPDB->residues[i].z[j] = xx * rot_mat[6] + yy * rot_mat[7] + zz * rot_mat[8];
+
+            newPDB->residues[i].x[j] = newPDB->residues[i].x[j] + dock_res->trans_X_R[target_conf] + pivot_X_R;
+            newPDB->residues[i].y[j] = newPDB->residues[i].y[j] + dock_res->trans_Y_R[target_conf] + pivot_Y_R;
+            newPDB->residues[i].z[j] = newPDB->residues[i].z[j] + dock_res->trans_Z_R[target_conf] + pivot_Z_R;
+        }
+    }
+
+    return newPDB;
+}
+
+struct pdb_values* rotate_ATTRACT(struct pdb_values* pdb, struct pdb_values* newPDB, struct docking_results* dock_res, int target_conf, int isRec){
+    int i = 0, j = 0;
+
+    /* Copy the pdb into newPDB (which will be returned */
+    if(newPDB == NULL){
+        newPDB = allocate_pdb(pdb->nbRes);
+        newPDB->nbAtom = pdb->nbAtom;
+    }
+    memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
+    
+    if(isRec){
+        /* If the receptor is centered, we need to substract the 
+         * pivot from all of its atoms
+         */
+        if(dock_res->centered_R){
+            for(i=0;i<newPDB->nbRes;i++){
+                for(j=0;j<newPDB->residues[i].nbAtom;j++){
+                    newPDB->residues[i].x[j] -= dock_res->pivot_X_R;
+                    newPDB->residues[i].y[j] -= dock_res->pivot_Y_R;
+                    newPDB->residues[i].z[j] -= dock_res->pivot_Z_R;
+                }
+            }
+        }
+    }else{
+        /* Same thing for the ligand */
+        if(dock_res->centered_L){
+            for(i=0;i<newPDB->nbRes;i++){
+                for(j=0;j<newPDB->residues[i].nbAtom;j++){
+                    newPDB->residues[i].x[j] -= dock_res->pivot_X_R;
+                    newPDB->residues[i].y[j] -= dock_res->pivot_Y_R;
+                    newPDB->residues[i].z[j] -= dock_res->pivot_Z_R;
+                }
+            }
+        }
+    }
+    
+    return newPDB;
+}
+
 
 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){
     /* This function aims at rotating the pdb parameter and gets its new coordinates

src/struct.h

@@ -27,6 +27,7 @@ int     constructPDB;       /* 1 if we should build the PDB */
 int     target_conf;        /* 1 if we are specific to one conformation */
 int     HCMD2;              /* 1 if this is HCMD2 format */
 int     MAXDo;              /* 1 if this is MAXDo format */
+int     ATTRACT;            /* 1 if this is ATTRACT format */
 int     HEX;                /* 1 if this is HEX format */
 int     ZDOCK;              /* 1 if this is ZDOCK format */
 int     complexPDB;         /* 1 if we are computing the interface of a given complex */
@@ -135,6 +136,7 @@ struct docking_results {
     float*              trans_Z_L;
     int                 centered_R;
     int                 centered_L;
+    int                 auto_pivot;
 };
 
 #endif