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INTBuilder
Commit fdc0b3c8 by Chloe Dequeker
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first commit for HEX

parent b20bc0f0
Showing with 258 additions and 51 deletions
src/INTBuilder.c
......@@ -284,10 +284,12 @@ int main(int argc, char** argv){
pdbR = readPDB(receptor);
pdbL = readPDB(ligand);
/* 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);
if(MAXDo || HCMD2){
/* 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);
}
if(complexPDB){ /* If we are building for a given complex, no rotation */
/* Write the number of the conformation and get the interface */
......@@ -298,14 +300,25 @@ int main(int argc, char** argv){
}
}else if(target_conf > 0){ /* If we are building a specific conformation */
dalpha = dock_res->alpha[target_conf] - alpha;
dbeta = dock_res->beta[target_conf] - beta;
dgamma = dock_res->gamma[target_conf] - gamma;
newPDB = rotate_sophie(pdbL,pdbR,NULL,dock_res->distCenters[target_conf],
dock_res->theta[target_conf],dock_res->phi[target_conf],
dalpha,dbeta,dgamma,dock_res,target_conf);
if(MAXDo || HCMD2){
dalpha = dock_res->alpha[target_conf] - alpha;
dbeta = dock_res->beta[target_conf] - beta;
dgamma = dock_res->gamma[target_conf] - gamma;
newPDB = rotate_sophie(pdbL,pdbR,NULL,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){
newPDB = rotate_HEX(pdbL,pdbR,NULL,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,NULL,dock_res->distCenters[target_conf],
dock_res->theta[target_conf],dock_res->phi[target_conf],
alpha,beta,gamma);
}
/* Write the number of the conformation and get the interface */
if(!doNotOutputINT){
......@@ -325,21 +338,32 @@ int main(int argc, char** argv){
continue;
}
/* compute the rotation angles dalpha, dbeta and dgamma
* from the angles alpha and beta of the CA 1 and the
* angle gamma computed after rotation of alpha and beta
* for the CA 5
*/
dalpha = dock_res->alpha[i] - alpha;
dbeta = dock_res->beta[i] - beta;
dgamma = dock_res->gamma[i] - gamma;
/* This is the rotated PDB
* pdbL doesn't change throughout the program
*/
newPDB = rotate_sophie(pdbL, pdbR, newPDB, dock_res->distCenters[i],
dock_res->theta[i], dock_res->phi[i],
dalpha, dbeta, dgamma, dock_res, i);
if(MAXDo || HCMD2){
/* compute the rotation angles dalpha, dbeta and dgamma
* from the angles alpha and beta of the CA 1 and the
* angle gamma computed after rotation of alpha and beta
* for the CA 5
*/
dalpha = dock_res->alpha[i] - alpha;
dbeta = dock_res->beta[i] - beta;
dgamma = dock_res->gamma[i] - gamma;
/* This is the rotated PDB
* pdbL doesn't change throughout the program
*/
newPDB = rotate_sophie(pdbL, pdbR, newPDB, dock_res->distCenters[i],
dock_res->theta[i], dock_res->phi[i],
dalpha, dbeta, dgamma, dock_res, i);
}else if(HEX){
newPDB = rotate_HEX(pdbL,pdbR,NULL,dock_res->trans_X[i],
dock_res->trans_Y[i],dock_res->trans_Z[i],
dock_res->alpha[i],dock_res->beta[i],
dock_res->gamma[i]);
}else{
newPDB = rotate_global(pdbL,pdbR,NULL,dock_res->distCenters[i],
dock_res->theta[i],dock_res->phi[i],
alpha,beta,gamma);
}
/* Write the number of the conformation and get the interface */
if(!doNotOutputINT){
......
src/allocate.c
......@@ -47,27 +47,15 @@ struct docking_results* allocate_dockingResults(int nbConf){
dock_res->beta = NULL;
dock_res->gamma = NULL;
dock_res->t_conf = NULL;
dock_res->trans_X = NULL;
dock_res->trans_Y = NULL;
dock_res->trans_Z = NULL;
dock_res->listEner = malloc((2*nbConf)*sizeof(float));
if(dock_res->listEner == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->distCenters = malloc((2*nbConf)*sizeof(float));
if(dock_res->distCenters == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->theta = malloc((2*nbConf)*sizeof(float));
if(dock_res->theta == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->phi = malloc((2*nbConf)*sizeof(float));
if(dock_res->phi == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->alpha = malloc((2*nbConf)*sizeof(float));
if(dock_res->alpha == NULL){
perror("malloc");
......@@ -90,15 +78,74 @@ struct docking_results* allocate_dockingResults(int nbConf){
exit(EXIT_FAILURE);
}
/* Only HEX uses translation values */
if(HEX){
dock_res->trans_X = malloc((2*nbConf)*sizeof(int));
if(dock_res->trans_X == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->trans_Y = malloc((2*nbConf)*sizeof(int));
if(dock_res->trans_Y == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->trans_Z = malloc((2*nbConf)*sizeof(int));
if(dock_res->trans_Z == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
}else{
dock_res->distCenters = malloc((2*nbConf)*sizeof(float));
if(dock_res->distCenters == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->theta = malloc((2*nbConf)*sizeof(float));
if(dock_res->theta == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->phi = malloc((2*nbConf)*sizeof(float));
if(dock_res->phi == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
}
dock_res->distCenters = malloc((2*nbConf)*sizeof(float));
if(dock_res->distCenters == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->theta = malloc((2*nbConf)*sizeof(float));
if(dock_res->theta == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
dock_res->phi = malloc((2*nbConf)*sizeof(float));
if(dock_res->phi == NULL){
perror("malloc");
exit(EXIT_FAILURE);
}
for(i=0;i<nbConf;i++){
dock_res->listEner[i] = 0;
dock_res->distCenters[i] = 0;
dock_res->theta[i] = 0;
dock_res->phi[i] = 0;
dock_res->alpha[i] = 0;
dock_res->beta[i] = 0;
dock_res->gamma[i] = 0;
dock_res->t_conf[i] = 0;
if(HEX){
dock_res->trans_X = 0;
dock_res->trans_Y = 0;
dock_res->trans_Z = 0;
}else{
dock_res->distCenters[i] = 0;
dock_res->theta[i] = 0;
dock_res->phi[i] = 0;
}
}
......
src/fileIO.c
......@@ -9,21 +9,34 @@ struct docking_results* getDataForComplex(){
char* buf = NULL;
FILE* condFile_stream = NULL;
int numberOfConf = 0, rc = 0;
int idConf = 0, buf4 = 0;
int idConf = 0, buf4 = 0, i = 0;
float buf3 = 0;
size_t len = 2000;
struct docking_results* dock_res = NULL;
condFile_stream = fopen(dockingFile,"r");
if(HEX){
for(i=0;i<NB_HEADER_LINE_HEX;i++){
getline(&buf,&len,condFile_stream);
}
}
/* Get the number of conformations */
rc = fscanf(condFile_stream,"%f",&buf3);
rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
if(HEX){
rc = fscanf(condFile_stream,"%f %f",&buf3,&buf3);
}else{
rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
}
if(buf3 > numberOfConf)
numberOfConf = (int) buf3;
while(!feof(condFile_stream)){
rc = fscanf(condFile_stream,"%f",&buf3);
if(HEX){
rc = fscanf(condFile_stream,"%f %f",&buf3,&buf3);
}else{
rc = fscanf(condFile_stream,"%f",&buf3);
}
rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
if(buf3 > numberOfConf)
numberOfConf = (int) buf3;
......@@ -32,8 +45,12 @@ struct docking_results* getDataForComplex(){
rewind(condFile_stream);
/* This is with the first MAXDo format */
if(!HCMD2){
if(MAXDo){
rc = getline(&buf,&len,condFile_stream); /* Get rid of the first line */
}else if(HEX){
for(i=0;i<NB_HEADER_LINE_HEX;i++){
getline(&buf,&len,condFile_stream);
}
}
/* Now that we know how many conformations we are dealing with
......@@ -46,6 +63,8 @@ struct docking_results* getDataForComplex(){
if(MAXDo){ /* First MAXDo format */
rc = fscanf(condFile_stream,"%d %d",&idConf,&buf4);
}else if(HEX){
rc = fscanf(condFile_stream,"%d %d",&buf4,&idConf);
}else{
/* Else, that means that we have a format where
* values for distance between center follows directly
......@@ -64,7 +83,12 @@ struct docking_results* getDataForComplex(){
/* printf("curConf : %d\n",idConf); */
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]);
if(HEX){
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]);
}
// TODO : Is this necessary for HEX ?
rc = getline(&buf,&len,condFile_stream); /* Get rid of the rest of the line */
/* theta and phi angles are written in Radian already
......
src/param.c
......@@ -123,6 +123,8 @@ struct argLine* parseLineOfArgument(int argc, char** argv){
HCMD2 = 1;
}else if(strcmp(argv[i],"-MAXDo") == 0){
MAXDo = 1;
}else if(strcmp(argv[i],"-HEX") == 0){
HEX = 1;
}else if(strcmp(argv[i],"--atom-res") == 0){
atom_res = 1;
}else if(strcmp(argv[i],"-noOutput") == 0){
......
src/rotation.c
......@@ -15,6 +15,110 @@ void sphericToxyz(float *x, float *y, float *z, float x0, float y0, float z0, fl
*z = z0 + R * cos(theta);
}
struct pdb_values* rotate_HEX(struct pdb_values* pdb, struct pdb_values* pdbR, 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;
/* 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;
if(newPDB == NULL){
newPDB = allocate_pdb(pdb->nbRes);
newPDB->nbAtom = pdb->nbAtom;
}
memcpy(newPDB->residues,pdb->residues,pdb->nbRes*sizeof(struct residue));
float newX = pdbR->centerX + trans_X;
float newY = pdbR->centerY + trans_Y;
float newZ = pdbR->centerZ + trans_Z;
/* 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] - 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;
/* We also translate the coordinates of the first and fifth CA, even
* though they are not used afterwards. This is for the sake of
* having the right values at the right places
*/
newPDB->xCA1 = (newPDB->xCA1 - pdb->centerX) + newX;
newPDB->yCA1 = (newPDB->yCA1 - pdb->centerY) + newY;
newPDB->zCA1 = (newPDB->zCA1 - pdb->centerZ) + newZ;
newPDB->xCA5 = (newPDB->xCA5 - pdb->centerX) + newX;
newPDB->yCA5 = (newPDB->yCA5 - pdb->centerY) + newY;
newPDB->zCA5 = (newPDB->zCA5 - pdb->centerZ) + newZ;
newPDB->centerX = newX;
newPDB->centerY = newY;
newPDB->centerZ = newZ;
}
}
return newPDB;
}
struct pdb_values* rotate_global(struct pdb_values* pdb, struct pdb_values* pdbR, struct pdb_values* newPDB, float R, float theta, float phi, float alpha,float beta,float gamma){
/* This function aims at rotating the pdb parameter and gets its new coordinates
* in the newPDB parameter.
......
src/rotation.h
......@@ -11,4 +11,5 @@ void sphericToxyz(float *x, float *y, float *z, float x0, float y0, float z0, fl
struct pdb_values* rotate_global(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 pdb_values* rotate_HEX(struct pdb_values* pdb, struct pdb_values* pdbR, struct pdb_values* newPDB, float trans_X, float trans_Y, float trans_Z, float alpha,float beta,float gamma);
#endif
src/struct.h
......@@ -17,6 +17,7 @@
* two residues are in contact */
#define DIST_FOR_CLASH 2 /* Distance in Angstrom under which we consider
* the contact is a clash */
#define NB_HEADER_LINE_HEX 5 /* Number of header lines at the top of a hex 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"
......@@ -26,6 +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 HEX; /* 1 if this is HEX format */
int complexPDB; /* 1 if we are computing the interface of a given complex */
int doNotOutputINT; /* 1 if we don't want to output the interface */
int atom_res; /* 1 if we want a resolution at atom's level */
......@@ -81,6 +83,9 @@ struct docking_results {
float* alpha; /* alpha angle */
float* beta; /* beta angle */
float* gamma; /* Gamma angle */
float* trans_X;
float* trans_Y;
float* trans_Z;
int* t_conf; /* 1 for a conformation position if it exists, 0 otherwise */
int nbConf; /* Number of conformations */
};
......
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