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Commit 36ae572f by Chloe Dequeker
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finishing ZDOCK implementation

parent 7ae24af0
Showing with 127 additions and 104 deletions
src/rotation.c
......@@ -10,18 +10,61 @@ void init_ZDOCK(struct pdb_values** pdbR_addr, struct pdb_values** pdbL_addr){
struct pdb_values* pdbL = *pdbL_addr;
struct pdb_values* newPDB = NULL;
newPDB = rotate_ZDOCK_init(pdbR,newPDB,ZDOCK_REC_X_TRANS,ZDOCK_REC_Y_TRANS,ZDOCK_REC_Z_TRANS,ZDOCK_REC_A_ROT,ZDOCK_REC_B_ROT,ZDOCK_REC_G_ROT);
(*pdbR_addr) = newPDB;
newPDB = NULL;
// newPDB = rotate_ZDOCK_init(pdbR,newPDB);
// (*pdbR_addr) = newPDB;
// newPDB = NULL;
// TODO : free pdbR
newPDB = rotate_ZDOCK_init(pdbL,newPDB,ZDOCK_LIG_X_TRANS,ZDOCK_LIG_Y_TRANS,ZDOCK_LIG_Z_TRANS,ZDOCK_LIG_A_ROT,ZDOCK_LIG_B_ROT,ZDOCK_LIG_G_ROT);
newPDB = rotate_ZDOCK_init(pdbL,newPDB);
(*pdbL_addr) = newPDB;
newPDB = NULL;
// TODO : free 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) {
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);
float r11, r21, r31, r12, r22, r32, r13, r23, r33;
if (rev == 0) {
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;
r13 = s_a*s_b;
r23 = -c_a*s_b;
r33 = c_b;
}else { // if we are performing a reverse then need the transpose of the matrix
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;
r31 = s_a*s_b;
r32 = -c_a*s_b;
r33 = c_b;
}
*newX = r11 * oldX + r12 * oldY + r13 * oldZ;
*newY = r21 * oldX + r22 * oldY + r23 * oldZ;
*newZ = r31 * oldX + r32 * oldY + r33 * oldZ;
} /* rotateAtom */
void sphericToxyz(float *x, float *y, float *z, float x0, float y0, float z0, float R, float theta, float phi){
/* Sets the values of x, y and z to the carthesian equivalent of the spherical
......@@ -42,7 +85,7 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
* The xyz system is centered on the center of mass of the pdb parameter.
* We then rotate the pdb by an alpha angle about the axis z, then by a beta
* angle about the axis N and finally by a gamma angle about the axis Z.
* The following image available on wikipedia can help to understand the scheme :
* The following image available on wikipedia may help to understand the scheme :
* https://upload.wikimedia.org/wikipedia/commons/thumb/a/a1/Eulerangles.svg/300px-Eulerangles.svg.png
*/
......@@ -53,20 +96,6 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
float x2i = 0, y2i = 0, z2i = 0;
float x3i = 0, y3i = 0, z3i = 0;
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);
/* Coordinates of the N axis */
float xN = c_a;
float yN = s_a;
float zN = 0;
/* The coordinates of the unit vector for the axis Z can be computed as such : */
float xZ = yN*s_b;
float yZ = -xN*s_b;
float zZ = c_b;
if(newPDB == NULL){
newPDB = allocate_pdb(pdb->nbRes);
......@@ -74,11 +103,14 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
}
memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
if(trans_X >= ZDOCK_GRID_SIZE/2) trans_X -= ZDOCK_GRID_SIZE;
if(trans_Y >= ZDOCK_GRID_SIZE/2) trans_Y -= ZDOCK_GRID_SIZE;
if(trans_Z >= ZDOCK_GRID_SIZE/2) trans_Z -= ZDOCK_GRID_SIZE;
/* New center of the protein */
float newX = pdb->centerX + (trans_X-(ZDOCK_GRID_SIZE/2))*ZDOCK_GRID_UNIT;
float newY = pdb->centerY + (trans_Y-(ZDOCK_GRID_SIZE/2))*ZDOCK_GRID_UNIT;
float newZ = pdb->centerZ + (trans_Z-(ZDOCK_GRID_SIZE/2))*ZDOCK_GRID_UNIT;
float newX = 0;
float newY = 0;
float newZ = 0;
/* This is now the part where we actually compute the rotations, given
......@@ -88,47 +120,61 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
for(i=0;i<pdb->nbRes;i++){
for(j=0;j<pdb->residues[i].nbAtom;j++){
xi = pdb->residues[i].x[j] - pdb->centerX;
yi = pdb->residues[i].y[j] - pdb->centerY;
zi = pdb->residues[i].z[j] - pdb->centerZ;
/* alpha rotation of the residue */
x1i=c_a*xi-s_a*yi;
y1i=c_a*yi+s_a*xi;
z1i=zi;
/* beta rotation of the residue */
x2i = (xN*xN+(1.0-xN*xN)*c_b)*x1i + xN*yN*(1.0-c_b)*y1i + yN*s_b*z1i;
y2i = xN*yN*(1.0-c_b)*x1i + (yN*yN+(1.0-yN*yN)*c_b)*y1i - xN*s_b*z1i;
z2i = -yN*s_b*x1i + xN*s_b*y1i + c_b*z1i;
/* gamma rotation of the residue */
x3i = (xZ*xZ+(1.0-xZ*xZ)*c_g) *x2i + (xZ*yZ*(1.0-c_g)-zZ*s_g)*y2i + (xZ*zZ*(1.0-c_g)+yZ*s_g)*z2i;
y3i = (xZ*yZ*(1.0-c_g)+zZ*s_g)*x2i + (yZ*yZ+(1.0-yZ*yZ)*c_g) *y2i + (yZ*zZ*(1.0-c_g)-xZ*s_g)*z2i;
z3i = (xZ*zZ*(1.0-c_g)-yZ*s_g)*x2i + (yZ*zZ*(1.0-c_g)+xZ*s_g)*y2i + (zZ*zZ+(1.0-zZ*zZ)*c_g) *z2i;
/* Now the residue has been rotated, and we need to translate it
* to its final destination
*/
newPDB->residues[i].x[j] = x3i; // + newX;
newPDB->residues[i].y[j] = y3i; // + newY;
newPDB->residues[i].z[j] = z3i; // + newZ;
xi = pdb->residues[i].x[j];
yi = pdb->residues[i].y[j];
zi = pdb->residues[i].z[j];
// rotate for initial randomization and the pose rotation
if(ZDOCK_PROT_FIXED == 1){ /* The receptor is fixed */
xi += trans_X * ZDOCK_GRID_UNIT;
yi += trans_Y * ZDOCK_GRID_UNIT;
zi += trans_Z * ZDOCK_GRID_UNIT;
rotateAtom(xi, yi, zi, &x1i, &y1i, &z1i, alpha, beta, gamma, ZDOCK_PROT_FIXED);
rotateAtom(x1i, y1i, z1i, &x2i, &y2i, &z2i, ZDOCK_LIG_A_ROT, ZDOCK_LIG_B_ROT, ZDOCK_LIG_G_ROT, ZDOCK_PROT_FIXED);
x2i += ZDOCK_LIG_X_TRANS;
y2i += ZDOCK_LIG_Y_TRANS;
z2i += ZDOCK_LIG_Z_TRANS;
newPDB->residues[i].x[j] = x2i;
newPDB->residues[i].y[j] = y2i;
newPDB->residues[i].z[j] = z2i;
newX += x2i;
newY += y2i;
newZ += z2i;
}else{ /* The ligand is fixed */
rotateAtom(xi, yi, zi, &x1i, &y1i, &z1i, alpha, beta, gamma, ZDOCK_PROT_FIXED);
x2i = x1i - trans_X * ZDOCK_GRID_UNIT + ZDOCK_REC_X_TRANS;
y2i = y1i - trans_Y * ZDOCK_GRID_UNIT + ZDOCK_REC_Y_TRANS;
z2i = z1i - trans_Z * ZDOCK_GRID_UNIT + ZDOCK_REC_Z_TRANS;
rotateAtom(x2i, y2i, z2i, &x3i, &y3i, &z3i, ZDOCK_REC_A_ROT, ZDOCK_REC_B_ROT, ZDOCK_REC_G_ROT, 1);
newPDB->residues[i].x[j] = x3i;
newPDB->residues[i].y[j] = y3i;
newPDB->residues[i].z[j] = z3i;
newX += x3i;
newY += y3i;
newZ += z3i;
}
}
}
newX /= newPDB->nbAtom;
newY /= newPDB->nbAtom;
newZ /= newPDB->nbAtom;
newPDB->centerX = newX;
newPDB->centerY = newY;
newPDB->centerZ = newZ;
printf("NEW : %f %f %f\n",newPDB->centerX,newPDB->centerY,newPDB->centerZ);
printf("trans : %f %f %f\n",trans_X,trans_Y,trans_Z);
return newPDB;
}
struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values* newPDB, float trans_X, float trans_Y, float trans_Z, float alpha, float beta, float gamma){
struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values* newPDB){
/* This function aims at rotating the pdb parameter and gets its new coordinates
* in the newPDB parameter.
* Let the N axis the rotation of the x axis about the z axis by an alpha angle.
......@@ -143,26 +189,6 @@ struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values*
float xi = 0, yi = 0, zi = 0;
float x1i = 0, y1i = 0, z1i = 0;
float x2i = 0, y2i = 0, z2i = 0;
float x3i = 0, y3i = 0, z3i = 0;
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);
/* Coordinates of the N axis */
float xN = c_a;
float yN = s_a;
float zN = 0;
printf("N AXIS : %f %f %f\n",xN,yN,zN);
/* The coordinates of the unit vector for the axis Z can be computed as such :
*/
float xZ = yN*s_b;
float yZ = -xN*s_b;
float zZ = c_b;
printf("Z AXIS : %f %f %f\n",xZ,yZ,zZ);
if(newPDB == NULL){
newPDB = allocate_pdb(pdb->nbRes);
......@@ -176,9 +202,8 @@ struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values*
float newY = 0;
float newZ = 0;
/* This is now the part where we actually compute the rotations, given
* the coordinates for the rotation axis N and Z
/* This is now the part where we actually compute the rotations using
* the given initial informations from ZDOCK
*/
int i = 0, j = 0;
for(i=0;i<pdb->nbRes;i++){
......@@ -188,38 +213,32 @@ struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values*
yi = pdb->residues[i].y[j];
zi = pdb->residues[i].z[j];
/* alpha rotation of the residue */
x1i=c_a*xi-s_a*yi;
y1i=c_a*yi+s_a*xi;
z1i=zi;
/* beta rotation of the residue */
x2i = (xN*xN+(1.0-xN*xN)*c_b)*x1i + xN*yN*(1.0-c_b)*y1i + yN*s_b*z1i;
y2i = xN*yN*(1.0-c_b)*x1i + (yN*yN+(1.0-yN*yN)*c_b)*y1i - xN*s_b*z1i;
z2i = -yN*s_b*x1i + xN*s_b*y1i + c_b*z1i;
/* gamma rotation of the residue */
x3i = (xZ*xZ+(1.0-xZ*xZ)*c_g) *x2i + (xZ*yZ*(1.0-c_g)-zZ*s_g)*y2i + (xZ*zZ*(1.0-c_g)+yZ*s_g)*z2i;
y3i = (xZ*yZ*(1.0-c_g)+zZ*s_g)*x2i + (yZ*yZ+(1.0-yZ*yZ)*c_g) *y2i + (yZ*zZ*(1.0-c_g)-xZ*s_g)*z2i;
z3i = (xZ*zZ*(1.0-c_g)-yZ*s_g)*x2i + (yZ*zZ*(1.0-c_g)+xZ*s_g)*y2i + (zZ*zZ+(1.0-zZ*zZ)*c_g) *z2i;
/* Now the residue has been rotated, and we need to translate it
* to its final destination
*/
newPDB->residues[i].x[j] = x3i - trans_X;
newPDB->residues[i].y[j] = y3i - trans_Y;
newPDB->residues[i].z[j] = z3i - trans_Z;
newX += newPDB->residues[i].x[j];
newY += newPDB->residues[i].y[j];
newZ += newPDB->residues[i].z[j];
if(ZDOCK_PROT_FIXED == 1){ /* means that the receptor is fixed in this case */
rotateAtom(xi, yi, zi, &x1i, &y1i, &z1i, ZDOCK_REC_A_ROT, ZDOCK_REC_B_ROT, ZDOCK_REC_G_ROT, 0);
x1i -= ZDOCK_REC_X_TRANS;
y1i -= ZDOCK_REC_Y_TRANS;
z1i -= ZDOCK_REC_Z_TRANS;
}else{ /* Here the ligand is fixed */
xi -= ZDOCK_LIG_X_TRANS;
yi -= ZDOCK_LIG_Y_TRANS;
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;
newX += x1i;
newY += y1i;
newZ += z1i;
}
}
newX /= newPDB->nbAtom;
newY /= newPDB->nbAtom;
newZ /= newPDB->nbAtom;
newX /= pdb->nbAtom;
newY /= pdb->nbAtom;
newZ /= pdb->nbAtom;
newPDB->centerX = newX;
newPDB->centerY = newY;
newPDB->centerZ = newZ;
......
src/rotation.h
......@@ -13,9 +13,13 @@ struct pdb_values* rotate_global(struct pdb_values* pdb, struct pdb_values* pdbR
struct pdb_values* rotate_HEX(struct pdb_values* pdb, struct pdb_values* newPDB, float trans_X, float trans_Y, float trans_Z, float alpha,float beta,float gamma);
struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values* newPDB, float trans_X, float trans_Y, float trans_Z, float alpha, float beta, float gamma);
struct pdb_values* rotate_ZDOCK_init(struct pdb_values* pdb, struct pdb_values* 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);
void init_ZDOCK(struct pdb_values** pdbR_addr, struct pdb_values** pdbL_addr);
void rotateAtom (float oldX, float oldY, float oldZ,
float *newX, float *newY, float *newZ,
float alpha, float beta, float gamma, int rev);
#endif
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