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INTBuilder
Commit 7ae24af0 by Chloe Dequeker
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ZDOCK : advancements

parent 1c912015
Showing with 191 additions and 47 deletions
src/INTBuilder.c
......@@ -325,6 +325,21 @@ int main(int argc, char** argv){
dock_res->trans_Y[target_conf],dock_res->trans_Z[target_conf],
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],
dock_res->gamma[target_conf]);
}else{
newPDB = rotate_global(pdbL,pdbR,newPDB,dock_res->distCenters[target_conf],
dock_res->theta[target_conf],dock_res->phi[target_conf],
......@@ -371,7 +386,10 @@ 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],
......
src/allocate.c
......@@ -85,7 +85,7 @@ struct docking_results* allocate_dockingResults(int nbConf){
}
/* Only HEX uses translation values */
if(HEX){
if(HEX || ZDOCK){
dock_res->trans_X = malloc((2*nbConf)*sizeof(int));
if(dock_res->trans_X == NULL){
perror("malloc");
......@@ -128,7 +128,7 @@ struct docking_results* allocate_dockingResults(int nbConf){
dock_res->beta[i] = 0;
dock_res->gamma[i] = 0;
dock_res->t_conf[i] = 0;
if(HEX){
if(HEX || ZDOCK){
dock_res->trans_X[i] = 0;
dock_res->trans_Y[i] = 0;
dock_res->trans_Z[i] = 0;
......
src/fileIO.c
......@@ -7,6 +7,7 @@
struct docking_results* getDataForComplex(){
char* buf = NULL;
char buf2[100] = "";
FILE* condFile_stream = NULL;
int numberOfConf = 0, rc = 0;
int idConf = 0, buf4 = 0, i = 0;
......@@ -18,16 +19,16 @@ struct docking_results* getDataForComplex(){
if(HEX){
for(i=0;i<NB_HEADER_LINE_HEX;i++){
getline(&buf,&len,condFile_stream);
rc = getline(&buf,&len,condFile_stream);
}
}
if(ZDOCK){
getline(&buf,&len,condFile_stream);
fscanf(condFile_stream,"%f %f %f",&ZDOCK_REC_A_ROT,&ZDOCK_REC_B_ROT,&ZDOCK_REC_G_ROT);
fscanf(condFile_stream,"%f %f %f",&ZDOCK_LIG_A_ROT,&ZDOCK_LIG_B_ROT,&ZDOCK_LIG_G_ROT);
fscanf(condFile_stream,"%s %f %f %f",buf,&ZDOCK_REC_X_TRANS,&ZDOCK_REC_Y_TRANS,&ZDOCK_REC_Z_TRANS);
fscanf(condFile_stream,"%s %f %f %f",buf,&ZDOCK_LIG_X_TRANS,&ZDOCK_LIG_Y_TRANS,&ZDOCK_LIG_Z_TRANS);
rc = fscanf(condFile_stream,"%d %f %d",&ZDOCK_GRID_SIZE,&ZDOCK_GRID_UNIT,&ZDOCK_PROT_FIXED);
rc = fscanf(condFile_stream,"%f %f %f",&ZDOCK_REC_A_ROT,&ZDOCK_REC_B_ROT,&ZDOCK_REC_G_ROT);
rc = fscanf(condFile_stream,"%f %f %f",&ZDOCK_LIG_A_ROT,&ZDOCK_LIG_B_ROT,&ZDOCK_LIG_G_ROT);
rc = fscanf(condFile_stream,"%s %f %f %f",buf2,&ZDOCK_REC_X_TRANS,&ZDOCK_REC_Y_TRANS,&ZDOCK_REC_Z_TRANS);
rc = fscanf(condFile_stream,"%s %f %f %f",buf2,&ZDOCK_LIG_X_TRANS,&ZDOCK_LIG_Y_TRANS,&ZDOCK_LIG_Z_TRANS);
}
/* Get the number of conformations */
......@@ -36,8 +37,11 @@ struct docking_results* getDataForComplex(){
}else{
rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
}
if(buf3 > numberOfConf)
if(ZDOCK){
numberOfConf++;
}else if(buf3 > numberOfConf){
numberOfConf = (int) buf3;
}
while(!feof(condFile_stream)){
if(HEX){
......@@ -46,18 +50,27 @@ struct docking_results* getDataForComplex(){
rc = fscanf(condFile_stream,"%f",&buf3);
}
rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
if(buf3 > numberOfConf)
if(ZDOCK){
if(feof(condFile_stream)){
break;
}
numberOfConf++;
}else if(buf3 > numberOfConf)
numberOfConf = (int) buf3;
}
//numberOfConf++;
if(ZDOCK)
numberOfConf--;
rewind(condFile_stream);
/* This is with the first MAXDo format */
if(MAXDo){
rc = getline(&buf,&len,condFile_stream); /* Get rid of the first line */
}else if(ZDOCK){
for(i=0;i<NB_HEADER_LINE_ZDOCK;i++)
rc = getline(&buf,&len,condFile_stream);
}else if(HEX){
for(i=0;i<NB_HEADER_LINE_HEX;i++){
getline(&buf,&len,condFile_stream);
rc = getline(&buf,&len,condFile_stream);
}
}
......@@ -73,7 +86,9 @@ struct docking_results* getDataForComplex(){
rc = fscanf(condFile_stream,"%d %d",&idConf,&buf4);
}else if(HEX){
rc = fscanf(condFile_stream,"%d %d %f %f",&buf4,&idConf,&buf3,&buf3);
}else{
}else if(ZDOCK){
idConf++;
}else {
/* Else, that means that we have a format where
* values for distance between center follows directly
* the ID of the conformation.
......@@ -89,14 +104,16 @@ struct docking_results* getDataForComplex(){
break;
}
if(HEX){
rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->trans_X[idConf],&dock_res->trans_Y[idConf],&dock_res->trans_Z[idConf],&dock_res->alpha[idConf],&dock_res->beta[idConf],&dock_res->gamma[idConf]);
}else if(ZDOCK){
rc = fscanf(condFile_stream,"%f %f %f %f %f %f",&dock_res->alpha[idConf],&dock_res->beta[idConf],&dock_res->gamma[idConf],&dock_res->trans_X[idConf],&dock_res->trans_Y[idConf],&dock_res->trans_Z[idConf]);
}else{
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 */
/* theta and phi angles are written in Radian already
* However that is not the case for alpha, beta and gamma angles
*/
......@@ -112,6 +129,11 @@ struct docking_results* getDataForComplex(){
dock_res->beta[idConf] = dock_res->beta[idConf] * COEF_DEGREE_TO_RADIAN;
dock_res->gamma[idConf] = dock_res->gamma[idConf] * COEF_DEGREE_TO_RADIAN;
}
/* This happens when we arrive on the last line */
if(feof(condFile_stream)){
break;
}
}
dock_res->nbConf = numberOfConf;
......
src/param.c
......@@ -8,10 +8,10 @@
void print_usage() {
printf("Usage: \n"
printf("Usage:\n"
"Mandatory\n"
"=========\n\n"
"<-dockingFile> MAXDo file that needs to be analysed\n"
"<-dockingFile> docking file that needs to be analysed\n"
"OR\n"
"<-complex> This option means that we look at two PDBs instead of looking\n"
" at the dockingFile. Both PBDs for '-rec' and '-lig' must be in\n"
......@@ -41,6 +41,8 @@ void print_usage() {
"<-MAXDo>...........Means that the docking file is in the original MAXDo format\n"
"OR\n"
"<-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"
);
}
......@@ -70,12 +72,14 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
target_conf = -1;
DIST_FOR_CONTACT = -1;
ZDOCK_GRID_UNIT = 0;
ZDOCK_LIG_X_ROT = 0;
ZDOCK_LIG_Y_ROT = 0;
ZDOCK_LIG_Z_ROT = 0;
ZDOCK_REC_X_ROT = 0;
ZDOCK_REC_Y_ROT = 0;
ZDOCK_REC_Z_ROT = 0;
ZDOCK_GRID_SIZE = 0;
ZDOCK_PROT_FIXED = 0;
ZDOCK_LIG_A_ROT = 0;
ZDOCK_LIG_B_ROT = 0;
ZDOCK_LIG_G_ROT = 0;
ZDOCK_REC_A_ROT = 0;
ZDOCK_REC_B_ROT = 0;
ZDOCK_REC_G_ROT = 0;
ZDOCK_LIG_X_TRANS= 0;
ZDOCK_LIG_Y_TRANS= 0;
ZDOCK_LIG_Z_TRANS= 0;
......
src/rotation.c
......@@ -10,13 +10,13 @@ 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(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 = newPDB;
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;
// TODO : free pdbR
newPDB = rotate_ZDOCK(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);
pdbL = newPDB;
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);
(*pdbL_addr) = newPDB;
newPDB = NULL;
// TODO : free pdbL
}
......@@ -46,6 +46,8 @@ 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;
......@@ -61,14 +63,10 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
float yN = s_a;
float zN = 0;
/* The coordinates of the unit vector for the axis Z can be computed as such :
* xZ : c_b
* yZ : c_a * s_b
* zZ : s_a * s_b
*/
float xZ = c_b;
float yZ = c_a * s_b;
float zZ = s_a * s_b;
/* 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);
......@@ -78,9 +76,9 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
/* New center of the protein */
float newX = pdb->centerX + trans_X;
float newY = pdb->centerY + trans_Y;
float newZ = pdb->centerZ + trans_Z;
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;
/* This is now the part where we actually compute the rotations, given
......@@ -114,13 +112,114 @@ struct pdb_values* rotate_ZDOCK(struct pdb_values* pdb, struct pdb_values* newPD
/* 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;
newPDB->residues[i].x[j] = x3i; // + newX;
newPDB->residues[i].y[j] = y3i; // + newY;
newPDB->residues[i].z[j] = z3i; // + newZ;
}
}
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){
/* 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.
* Let the Z axis the rotation of the z axis about the N axis by a beta angle.
*
* 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 :
* https://upload.wikimedia.org/wikipedia/commons/thumb/a/a1/Eulerangles.svg/300px-Eulerangles.svg.png
*/
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);
newPDB->nbAtom = pdb->nbAtom;
}
memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
/* New center of the protein */
float newX = 0;
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
*/
int i = 0, j = 0;
for(i=0;i<pdb->nbRes;i++){
for(j=0;j<pdb->residues[i].nbAtom;j++){
xi = pdb->residues[i].x[j];
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];
}
}
newX /= newPDB->nbAtom;
newY /= newPDB->nbAtom;
newZ /= newPDB->nbAtom;
newPDB->centerX = newX;
newPDB->centerY = newY;
newPDB->centerZ = newZ;
......@@ -215,13 +314,10 @@ struct pdb_values* rotate_global(struct pdb_values* pdb, struct pdb_values* pdbR
float zN = 0;
/* The coordinates of the unit vector for the axis Z can be computed as such :
* xZ : c_b
* yZ : c_a * s_b
* zZ : s_a * s_b
*/
float xZ = c_b;
float yZ = c_a * s_b;
float zZ = s_a * s_b;
float xZ = yN*s_b;
float yZ = -xN*s_b;
float zZ = c_b;
if(newPDB == NULL){
newPDB = allocate_pdb(pdb->nbRes);
......
src/rotation.h
......@@ -13,6 +13,8 @@ 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(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);
......
src/struct.h
......@@ -16,7 +16,7 @@
#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 */
/* 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"
......@@ -46,6 +46,8 @@ 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;
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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