void setup(void)
{
test_ag = read_pdb_nopar("1rei_nmin.pdb");
read_ff_charmm("1rei_nmin.psf", "parm.prm", "pdbamino.rtf", test_ag);
fixed_init(test_ag);
fixed_update(test_ag, 0, NULL); // Make nothing fixed
}
int main(int argc, char **argv)
{
FIXED *fixed;
RECORD *record;
DBUG_ENTER("main");
DBUG_PROCESS(argv[0]);
DBUG_PUSH("d:t");
if(!(fixed = fixed_init(0)))
{
fprintf(stderr, "Couldn't allocate FIXED\n");
exit(1);
}
fixed_options(fixed)->gap = 1;
fixed_file_def(fixed, usps_state, 36);
fixed_dump(fixed);
fixed_open(fixed, argv[1], 'r');
while(record = fixed_read_next(fixed))
{
record_dump(record);
record_free(record);
}
fixed_close(fixed);
fixed_free(fixed);
DBUG_RETURN(0);
}
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;
}
