END_TEST
START_TEST(test_ieng)
{
zero_grads(test_ag);
check_grads(test_ag, delta, ieng);
}
END_TEST
START_TEST(test_aeng)
{
zero_grads(test_ag);
//check_grads(test_ag, delta, aeng);
}
void check_grads(struct atomgrp *ag, double d, void (*efun)(struct atomgrp *, double*))
{
int n=ag->natoms, i;
double en, en1, t;
double *fs=malloc(3*n*sizeof(double));
//en0
en=0;
(*efun)(ag, &en);
for(i=0; i<n; i++)
{
//x
en1=0;
t=ag->atoms[i].X;
ag->atoms[i].X=d+t;
(*efun)(ag, &en1);
ag->atoms[i].X=t;
fs[3*i]=(en-en1)/d;
//y
en1=0;
t=ag->atoms[i].Y;
ag->atoms[i].Y=d+t;
(*efun)(ag, &en1);
ag->atoms[i].Y=t;
fs[3*i+1]=(en-en1)/d;
//z
en1=0;
t=ag->atoms[i].Z;
ag->atoms[i].Z=d+t;
(*efun)(ag, &en1);
ag->atoms[i].Z=t;
fs[3*i+2]=(en-en1)/d;
}
en=0;
zero_grads(ag);
(*efun)(ag, &en);
char msg[256];
for(i=0; i<n; i++)
{
sprintf(msg,
"\n(atom: %d) calc: (%lf, %lf, %lf): numerical: (%lf, %lf, %lf)\n",
i,
ag->atoms[i].GX, ag->atoms[i].GY, ag->atoms[i].GZ,
fs[3*i],fs[3*i+1],fs[3*i+2]);
ck_assert_msg(fabs(ag->atoms[i].GX - fs[3*i]) < tolerance, msg);
ck_assert_msg(fabs(ag->atoms[i].GY - fs[3*i+1]) < tolerance, msg);
ck_assert_msg(fabs(ag->atoms[i].GZ - fs[3*i+2]) < tolerance, msg);
}
free(fs);
}
void check_epeng_grads(struct atomgrp *ag, struct grid* pot, double d,
void (*efun)(double, struct atomgrp *, double*, struct grid*))
{
int n=ag->natoms, i;
double en, en1, t;
double *fs=(double*)_mol_malloc(3*n*sizeof(double));
//en0
en=0;
// (*efun)(ag, &en);
(*efun)(1.0,ag, &en, pot);
for(i=0; i<n; i++)
{
//x
en1=0;
t=ag->atoms[i].X;
ag->atoms[i].X=d+t;
// (*efun)(ag, &en1);
(*efun)(1.0,ag, &en1, pot);
ag->atoms[i].X=t;
fs[3*i]=(en-en1)/d;
//y
en1=0;
t=ag->atoms[i].Y;
ag->atoms[i].Y=d+t;
// (*efun)(ag, &en1);
(*efun)(1.0,ag, &en1, pot);
ag->atoms[i].Y=t;
fs[3*i+1]=(en-en1)/d;
//z
en1=0;
t=ag->atoms[i].Z;
ag->atoms[i].Z=d+t;
// (*efun)(ag, &en1);
(*efun)(1.0,ag, &en1, pot);
ag->atoms[i].Z=t;
fs[3*i+2]=(en-en1)/d;
}
en=0;
zero_grads(ag);
// (*efun)(ag, &en);
(*efun)(1.0,ag, &en, pot);
for(i=0; i<n; i++)
{
printf("%d calculated: %lf %lf %lf\n",
i,ag->atoms[i].GX,ag->atoms[i].GY,ag->atoms[i].GZ);
printf("%d numerical : %lf %lf %lf\n",
i,fs[3*i],fs[3*i+1],fs[3*i+2]);
}
free(fs);
}
int main(int argc, char* argv[]){
// Input Files //
/* Intro Message */
printf("\n");
printf("A Program to Repack Protein Side-chains for Protein Docking Refinement Procedures\n");
printf("Copyright (c) 2014, Structural Bioinformatics Laboratory, Boston University\n");
printf("Author: Mohammad Moghadasi ([email protected]) \n");
if(argc!=10){
printf("Usage:\n ./main \n Complex_IN.pdb Complex_IN.psf Complex_IN.mol2 Complex_IN_Ligand.pdb\n Libmol-param-file charmm-param-file.prm charmm-rtf-file.rtf rotamer-library-binary-file.txt\n Complex_OUT.pdb\n \n");
exit(EXIT_FAILURE);
}
char* ifile = argv[1]; //pdb file of both receptor and ligand
char* psffile = argv[2]; //charmm type psf file
char* mol2file = argv[3]; //mol2 file
char* pdbfilelig = argv[4]; //pdb file of ligand
char* atom_prm_file = argv[5]; //libmol parameter file
prmfile = argv[6]; //charmm type parameter file
rtffile = argv[7]; //charmm type connectivity file
char* rotamer_library_file = argv[8]; //rotamer raw library file
char* ofile = argv[9]; //output file
// Filling the atom_group struct //
struct prm *atomprm = read_prm(atom_prm_file,_MOL_VERSION_);
struct atomgrp* ag = read_file_atomgrp(ifile, atomprm, -1);
read_ff_charmm(psffile, prmfile, rtffile, ag);
if(!read_hybridization_states_from_mol2(mol2file,ag)){
exit (EXIT_FAILURE);
}
fix_acceptor_bases(ag,atomprm);
struct List lig_list;
read_fix(pdbfilelig,&lig_list.n,&lig_list.K);
fixed_init(ag);
fixed_update_unfreeze_all(ag);
zero_grads(ag);
fill_ingrp(ag);
struct agsetup* ags;
ags = malloc(sizeof(struct agsetup));
init_nblst(ag,ags);
update_nblst(ag,ags);
// Mark interface residues //
int num_of_res_interface;
int res_list_interface[ag->nres];
mark_interface_residues(ag,ags,lig_list, lig_rec_dist ,&num_of_res_interface,res_list_interface);
// Initialize side chain rotamer library //
//nrotCoef = 3;
nrotCoef = 1;
MAX_ROT = 245;
MAX_RES = ag->nres;//needed for full_pack
cutoff = 3;
// Reslist //
struct ifres_list* reslist;
ifres_list_malloc( &reslist );
reslist->num_of_ifres = num_of_res_interface;
for(int r = 0; r < reslist->num_of_ifres ; r++)
reslist->ifres_num[r] = res_list_interface[r];
// Library //
char *rotamer_lib;
load_file_to_memory(rotamer_library_file, &rotamer_lib);
struct rot_info *rotinf;
init_rotinf(ag, num_of_res_interface, res_list_interface, rotamer_lib, &rotinf);
struct ifres_list* reslist_minor;
ifres_list_malloc( &reslist_minor ) ;
// MAIN FUNCITION //
//
clock_t start, finish;
start = clock();
full_pack(ag,lig_list,rotinf,num_of_res_interface, reslist_minor);
finish = clock();
if(0) printf("Processing Time = %f\n",((double)(finish-start)/CLOCKS_PER_SEC));
// Writing the atom_group into a PDB //
write_pdb_traj_nopar(ag,ifile,ofile);
// Free memory //
Free_ifres_list( &reslist_minor );
free(rotamer_lib);
return 0;
}
void check_speng_grads(int nstart, int nend,
struct atomgrp *ag, double d, double stens,
double* hx0, double* hy0, double* hz0,
int nx, int ny, int nz,
double dcx, double dcy, double dcz,
double cx, double cy, double cz, double w,
void (*efun)(double, double, struct atomgrp *, double*,
double*, double*, double*,
int,int,int,
double,double,double,
double,double,double,double))
{
int n=ag->natoms, i;
double en, en1, t;
double *fs=(double*)_mol_malloc(3*n*sizeof(double));
//en0
en=0;
// (*efun)(ag, &en);
// (*efun)(1.0,ag, &en, pot);
(*efun)( 1.0, stens, ag, &en,
hx0,hy0,hz0,
nx,ny,nz,
dcx, dcy, dcz,
cx,cy,cz,w);
for(i=nstart; i<=nend; i++)
{
printf("i= %d\n",i);
//x
en1=0;
t=ag->atoms[i].X;
ag->atoms[i].X=d+t;
// (*efun)(ag, &en1);
// (*efun)(1.0,ag, &en1, pot);
(*efun)( 1.0, stens, ag, &en1,
hx0,hy0,hz0,
nx,ny,nz,
dcx, dcy, dcz,
cx,cy,cz,w);
ag->atoms[i].X=t;
fs[3*i]=(en-en1)/d;
//y
en1=0;
t=ag->atoms[i].Y;
ag->atoms[i].Y=d+t;
// (*efun)(ag, &en1);
// (*efun)(1.0,ag, &en1, pot);
(*efun)( 1.0, stens, ag, &en1,
hx0,hy0,hz0,
nx,ny,nz,
dcx, dcy, dcz,
cx,cy,cz,w);
ag->atoms[i].Y=t;
fs[3*i+1]=(en-en1)/d;
//z
en1=0;
t=ag->atoms[i].Z;
ag->atoms[i].Z=d+t;
// (*efun)(ag, &en1);
// (*efun)(1.0,ag, &en1, pot);
(*efun)( 1.0, stens, ag, &en1,
hx0,hy0,hz0,
nx,ny,nz,
dcx, dcy, dcz,
cx,cy,cz,w);
ag->atoms[i].Z=t;
fs[3*i+2]=(en-en1)/d;
}
en=0;
zero_grads(ag);
// (*efun)(ag, &en);
// (*efun)(1.0,ag, &en, pot);
(*efun)( 1.0, stens, ag, &en,
hx0,hy0,hz0,
nx,ny,nz,
dcx, dcy, dcz,
cx,cy,cz,w);
for(i=nstart; i<=nend; i++)
{
printf("%d calculated: %lf %lf %lf\n",
i,ag->atoms[i].GX,ag->atoms[i].GY,ag->atoms[i].GZ);
printf("%d numerical : %lf %lf %lf\n",
i,fs[3*i],fs[3*i+1],fs[3*i+2]);
}
free(fs);
}
