// Main function
void main(void) {
reset_peripheral(); initClock(); initTimer(); initDisplay(); initPin();
initGPIO(); initADC(); initConsole(); int i = 0;
//init_password();
send_data();
initCircBuf (&speed_buffer, BUF_SIZE); init_set_speed_data(&speed_set_data);
int screen = 0; int screen_prev = 0; float speed = 0; float buffed_speed = 0;
int fake_speed = 0; float acc = 0; float max_acc = 0; //float fuel_eco = 0;
float distance = 0;
bool fix = 0; uint8_t satillite = 0; float quality = 0; clock time;
int aim_pos = 0; unsigned long adc = 0; //int error_stepper = 0;
IntMasterEnable();
while(1){
//reading data
read_data = split_data(UART_char_data_old, read_data); // decode data
speed = read_speed(); //read data into variables
adc = run_adc()/7;
//calculations
aim_pos = speed_feedback(buffed_speed, encoder_1/40, speed_set_data.speed);
if (speed_set_data.enable == 1){
step_motor_control(encoder_1/40, aim_pos);
}
//sending fake data
fake_speed = (int)adc;//= random_at_most(100/1.852);
send_info(fake_speed);//knots
//storing data
store_speed(speed);
buffed_speed = analysis_speed();
acc = read_acceleration(buffed_speed);
max_acc = max_acc_func(acc, max_acc);
time = read_time();
satillite = read_satillite();
fix = read_fix();
quality = read_quality();
debounce_button(); // debounce buttons
screen = read_button_screen(screen, fix);
distance = read_distance();
select_read(); //need a mosfet for turning power off
// select adds a an on and off switch yo
if (screen == 1){
if(screen_prev != 1 && screen == 1){
speed_set_data.speed = buffed_speed;
}
speed_set_data.speed = set_speed(speed_set_data.speed); // set the speed to cruise at
}
if (screen == 2){ //0 to 100
acceleration_test(speed);
}
// refresh chainging
if (fix == 1 && speed_set_data.old == speed_set_data.speed && refresh_rate < 4){
UARTSend((unsigned char *)PMTK_SET_NMEA_UPDATE_5HZ, 18, 0);
refresh_rate += 1;
}
if (i >= 50){
display(screen, buffed_speed, acc, max_acc, speed_set_data.speed, satillite,
encoder_1/40, time, distance, quality, UART_char_data_old, aim_pos, adc, acc_times);
i = 0;
}
screen_prev = screen;
i++;
}
}
static void read_vector(vms_vector *v,CFILE *file)
{
v->x = read_fix(file);
v->y = read_fix(file);
v->z = read_fix(file);
}
int load_mine_data_compiled(CFILE *LoadFile)
{
int i,segnum,sidenum;
ubyte version;
short temp_short;
ushort temp_ushort;
ubyte bit_mask;
// For compiled levels, textures map to themselves, prevent tmap_override always being gray,
// bug which Matt and John refused to acknowledge, so here is Mike, fixing it.
#ifdef EDITOR
for (i=0; i<MAX_TEXTURES; i++)
tmap_xlate_table[i] = i;
#endif
// memset( Segments, 0, sizeof(segment)*MAX_SEGMENTS );
fuelcen_reset();
//=============================== Reading part ==============================
// cfread( &version, sizeof(ubyte), 1, LoadFile ); // 1 byte = compiled version
version = read_byte(LoadFile);
Assert( version==COMPILED_MINE_VERSION );
// cfread( &temp_ushort, sizeof(ushort), 1, LoadFile ); // 2 bytes = Num_vertices
// Num_vertices = temp_ushort;
Num_vertices = read_short(LoadFile);
Assert( Num_vertices <= MAX_VERTICES );
// cfread( &temp_ushort, sizeof(ushort), 1, LoadFile ); // 2 bytes = Num_segments
// Num_segments = INTEL_SHORT(temp_ushort);
Num_segments = read_short(LoadFile);
Assert( Num_segments <= MAX_SEGMENTS );
// cfread( Vertices, sizeof(vms_vector), Num_vertices, LoadFile );
for (i = 0; i < Num_vertices; i++)
read_vector( &(Vertices[i]), LoadFile);
for (segnum=0; segnum<Num_segments; segnum++ ) {
#ifdef EDITOR
Segments[segnum].segnum = segnum;
Segments[segnum].group = 0;
#endif
cfread( &bit_mask, sizeof(ubyte), 1, LoadFile );
#if defined(SHAREWARE) && !defined(MACINTOSH)
// -- read_special(segnum,bit_mask,LoadFile);
read_verts(segnum,LoadFile);
read_children(segnum,bit_mask,LoadFile);
#else
read_children(segnum,bit_mask,LoadFile);
read_verts(segnum,LoadFile);
// --read_special(segnum,bit_mask,LoadFile);
#endif
Segments[segnum].objects = -1;
// Read fix Segments[segnum].static_light (shift down 5 bits, write as short)
// cfread( &temp_ushort, sizeof(temp_ushort), 1, LoadFile );
// temp_ushort = read_short(LoadFile);
// Segment2s[segnum].static_light = ((fix)temp_ushort) << 4;
//cfread( &Segments[segnum].static_light, sizeof(fix), 1, LoadFile );
// Read the walls as a 6 byte array
for (sidenum=0; sidenum<MAX_SIDES_PER_SEGMENT; sidenum++ ) {
Segments[segnum].sides[sidenum].pad = 0;
}
cfread( &bit_mask, sizeof(ubyte), 1, LoadFile );
for (sidenum=0; sidenum<MAX_SIDES_PER_SEGMENT; sidenum++) {
ubyte byte_wallnum;
if (bit_mask & (1 << sidenum)) {
cfread( &byte_wallnum, sizeof(ubyte), 1, LoadFile );
if ( byte_wallnum == 255 )
Segments[segnum].sides[sidenum].wall_num = -1;
else
Segments[segnum].sides[sidenum].wall_num = byte_wallnum;
} else
Segments[segnum].sides[sidenum].wall_num = -1;
}
for (sidenum=0; sidenum<MAX_SIDES_PER_SEGMENT; sidenum++ ) {
if ( (Segments[segnum].children[sidenum]==-1) || (Segments[segnum].sides[sidenum].wall_num!=-1) ) {
// Read short Segments[segnum].sides[sidenum].tmap_num;
// cfread( &temp_ushort, sizeof(ushort), 1, LoadFile );
temp_ushort = read_short(LoadFile);
Segments[segnum].sides[sidenum].tmap_num = temp_ushort & 0x7fff;
if (!(temp_ushort & 0x8000))
Segments[segnum].sides[sidenum].tmap_num2 = 0;
else {
// Read short Segments[segnum].sides[sidenum].tmap_num2;
// cfread( &Segments[segnum].sides[sidenum].tmap_num2, sizeof(short), 1, LoadFile );
Segments[segnum].sides[sidenum].tmap_num2 = read_short(LoadFile);
}
// Read uvl Segments[segnum].sides[sidenum].uvls[4] (u,v>>5, write as short, l>>1 write as short)
for (i=0; i<4; i++ ) {
// cfread( &temp_short, sizeof(short), 1, LoadFile );
temp_short = read_short(LoadFile);
Segments[segnum].sides[sidenum].uvls[i].u = ((fix)temp_short) << 5;
// cfread( &temp_short, sizeof(short), 1, LoadFile );
temp_short = read_short(LoadFile);
Segments[segnum].sides[sidenum].uvls[i].v = ((fix)temp_short) << 5;
// cfread( &temp_ushort, sizeof(temp_ushort), 1, LoadFile );
temp_ushort = read_short(LoadFile);
Segments[segnum].sides[sidenum].uvls[i].l = ((fix)temp_ushort) << 1;
//cfread( &Segments[segnum].sides[sidenum].uvls[i].l, sizeof(fix), 1, LoadFile );
}
} else {
Segments[segnum].sides[sidenum].tmap_num = 0;
Segments[segnum].sides[sidenum].tmap_num2 = 0;
for (i=0; i<4; i++ ) {
Segments[segnum].sides[sidenum].uvls[i].u = 0;
Segments[segnum].sides[sidenum].uvls[i].v = 0;
Segments[segnum].sides[sidenum].uvls[i].l = 0;
}
}
}
}
#if 0
{
FILE *fp;
fp = fopen("segments.out", "wt");
for (i = 0; i <= Highest_segment_index; i++) {
side sides[MAX_SIDES_PER_SEGMENT]; // 6 sides
short children[MAX_SIDES_PER_SEGMENT]; // indices of 6 children segments, front, left, top, right, bottom, back
short verts[MAX_VERTICES_PER_SEGMENT]; // vertex ids of 4 front and 4 back vertices
int objects; // pointer to objects in this segment
for (j = 0; j < MAX_SIDES_PER_SEGMENT; j++) {
byte type; // replaces num_faces and tri_edge, 1 = quad, 2 = 0:2 triangulation, 3 = 1:3 triangulation
ubyte pad; //keep us longword alligned
short wall_num;
short tmap_num;
short tmap_num2;
uvl uvls[4];
vms_vector normals[2]; // 2 normals, if quadrilateral, both the same.
fprintf(fp, "%d\n", Segments[i].sides[j].type;
fprintf(fp, "%d\n", Segments[i].sides[j].pad;
fprintf(fp, "%d\n", Segments[i].sides[j].wall_num;
fprintf(fp, "%d\n", Segments[i].tmap_num
}
fclose(fp);
}
#endif
Highest_vertex_index = Num_vertices-1;
Highest_segment_index = Num_segments-1;
validate_segment_all(); // Fill in side type and normals.
// MIKE!!!!! You should know better than this when the mac is involved!!!!!!
for (i=0; i<Num_segments; i++) {
// NO NO!!!! cfread( &Segment2s[i], sizeof(segment2), 1, LoadFile );
Segment2s[i].special = read_byte(LoadFile);
Segment2s[i].matcen_num = read_byte(LoadFile);
Segment2s[i].value = read_byte(LoadFile);
Segment2s[i].s2_flags = read_byte(LoadFile);
Segment2s[i].static_light = read_fix(LoadFile);
fuelcen_activate( &Segments[i], Segment2s[i].special );
}
reset_objects(1); //one object, the player
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;
}
