// ============================================================
// Function : calculateE()
// ------------------------------------------------------------
//
// ============================================================
double amberTorsion::calculateE(int k)
{
energy = 0.0;
double *xyz = pAmber->getCoords();
int nTorsions = 0;
int *torsions = 0;
double *torsionParams = 0;
if (k == 0) {
nTorsions = pAmber->getNumTorsions();
torsions = pAmber->getTorsions();
torsionParams = pAmber->getTorsionParams();
}
else {
nTorsions = pAmber->getNumImpropers();
torsions = pAmber->getImpropers();
torsionParams = pAmber->getImproperParams();
}
/*
torsionParams[j] = pTorsionParam->Vn / pTorsionParam->npth;
torsionParams[j+1] = pTorsionParam->Nt;
torsionParams[j+2] = pTorsionParam->gamma;
*/
double tor = 0.0;
int j = 0;
for (int i = 0; i <= nTorsions*4-4; i+=4) {
tor = torsion(xyz[torsions[i ]*3], xyz[torsions[i ]*3+1], xyz[torsions[i ]*3+2],
xyz[torsions[i+1]*3], xyz[torsions[i+1]*3+1], xyz[torsions[i+1]*3+2],
xyz[torsions[i+2]*3], xyz[torsions[i+2]*3+1], xyz[torsions[i+2]*3+2],
xyz[torsions[i+3]*3], xyz[torsions[i+3]*3+1], xyz[torsions[i+3]*3+2]);
energy += ( torsionParams[j] * (1 + cos(torsionParams[j+1] * tor - torsionParams[j+2]) ));
j+=3;
}
return energy;
}
void protein_from_pdb(char * file_name, LinusProtein *p)
{
Atom3d * atoms; // array of Atoms
char atm[5];
char aname[6];
char rname[4]; //replaced res_name
int anum; //replaced serial
int rnum; //replaced res_seq
int num_atoms=0; // number of lines in .pdb file //replaced count
int num_res = 0;
double x;
double y;
double z;
double occupancy;
double tempFactor;
char buff[BUFSIZ];
char *aname_seen; // atom names seen array
//int res_start_end[2]; // array containing start/end info for residue in .pdb //replaced numres
int start, end, res_size;
int i, j; // loop variables
int current_res = -1;
int na = 0; // atom indices
int nr = -1; // residue indices
int *fai; // na array // replaced f
int *rnum_arr; // replaced respdbnum
strcpy(p->name, "PROT"); // name protein PROT
strcpy(p->filename, file_name); // protein filename is first command line argument
//printf("Name %s, Filename %s\n", p->name, p->filename);
FILE *file = fopen(p->filename, "r");
// Get file line count to allocate matrices
p->num_chi_atoms=0;
while (fgets(buff, sizeof buff, file) != NULL)
{
if (sscanf(buff, "%s %d %s %s %d %lf %lf %lf %lf %lf \n",
atm, &anum, aname, rname, &rnum, &x, &y, &z,
&occupancy, &tempFactor) == 10)
{
//printf("%s\n",rname);
if(rnum != current_res)
{
num_res++;
num_atoms+=get_res_size(rname);
//printf("Res %s res size %d\n", rname, get_res_size(rname));
p->num_chi_atoms += get_chi_res_size(rname);
current_res = rnum;
}
}
}
//printf("Num of chi atoms %d\n", p->num_chi_atoms);
//printf("Num of atoms is %d & Num_residues is %d\n", num_atoms,num_res);
// Dynamic allocations based on # lines in .pdb file & residue information
p->res_names = (char **)malloc(num_res * sizeof(char *));
p->mesostates = (char **)malloc(num_res * sizeof(char *));
for (i = 0; i < num_res; i++)
{
p->res_names[i] = (char *)malloc(sizeof(char)*4);
p->mesostates[i] = (char *)malloc(sizeof(char)*3);
strcpy(p->mesostates[i],"--");
}
p->atoms = malloc(num_atoms * sizeof(Atom3d));
//printf("Start phi psi ome chi allocation\n");
p->phi_atoms = malloc(num_res * sizeof(int));
p->psi_atoms = malloc(num_res * sizeof(int));
p->omega_atoms = malloc(num_res * sizeof(int));
//printf("Finished phi psi \nStart chi allocation\n");
p->chi_atoms = malloc(p->num_chi_atoms * sizeof(int));
//printf("Success allocating phi psi ome chi\n");
p->res_num = malloc(num_atoms * sizeof(int));
p->res_fai = malloc((num_res+1) * sizeof(int));
p->res_helix_wt = malloc((num_res) * sizeof(double));
p->res_strand_wt = malloc((num_res) * sizeof(double));
p->res_turn1_wt = malloc((num_res) * sizeof(double));
p->res_turn2_wt = malloc((num_res) * sizeof(double));
p->res_coil_wt = malloc((num_res) * sizeof(double));
p->res_PII_wt = malloc((num_res) * sizeof(double));
p->orig_fp_distance = malloc((num_res) * sizeof(double));
p->orig_sp_angle = malloc((num_res) * sizeof(double));
p->orig_tp_torsion = malloc((num_res) * sizeof(double));
p->res_f_mean = malloc((num_res) * sizeof(double));
p->res_f_sd = malloc((num_res) * sizeof(double));
p->res_y_mean = malloc((num_res) * sizeof(double));
p->res_y_sd = malloc((num_res) * sizeof(double));
p->res_acprat = malloc((num_res) * sizeof(double));
p->pmeso_wt = (double **) malloc((num_res-1) * sizeof(double *));
for(i=0; i<num_res-1; i++)
{
p->pmeso_wt[i] = (double *) malloc(144 * sizeof(double));
}
//printf("Finished allocating memory\n");
// Fill up LinusProtein
i = 0;
rewind(file);
while (fgets(buff, sizeof buff, file) != NULL)
{
if (sscanf(buff, "%s %d%*c%4[ 0-9A-Z]%*c%s %d %lf %lf %lf %lf %lf \n",
atm, &anum, aname, rname, &rnum, &x, &y, &z,
&occupancy, &tempFactor) == 10)
{
if (!strcmp(atm, "ATOM"))
{
//printf("-%s-%d-%s-%s-%d-%lf-%lf-%lf-%lf-%lf-\n", atm,anum,aname,rname,rnum,x,y, z,occupancy,tempFactor);
//na = na + 1;
if (rnum != current_res) // handles atoms up to max(rnum)-1
{
nr = nr + 1;
j = nr;
p->res_fai[j] = na;
na += get_res_size(rname);
strcpy(p->res_names[j], rname);
p->res_num[j] = rnum;
current_res = rnum;
// New use of start/end
//start = na;
//end = get_res_size(rname); // this may be case specific
}
if (!strcmp(aname, "OXT"))
{
na = na - 1;
continue;
}
i++;
} // end atm if-loop
} // end sscanf if-loop
} // end while loop
//fclose(file);
//printf("Checking 2\n");
p->num_atoms = num_atoms;;
p->num_res = num_res;
p->res_fai[num_res] = num_atoms;
int atm_ctr=0;
int s=0;
for (i=0; i<num_res; i++)
{
int start, end;
get_res_range(p->res_names[i],&start,&end);
for(j=start; j<end; j++)
{
strcpy(p->atoms[atm_ctr].name,atm_name_arr[j]);
p->atoms[atm_ctr].resnum = i;
//printf("%d %s %s %d\n",atm_ctr,p->atoms[atm_ctr].name,p->res_names[i],i);
atm_ctr++;
}
}
j=-1;
rewind(file);
while (fgets(buff, sizeof buff, file) != NULL)
{
if (sscanf(buff, "%s %d%*c%4[ 0-9A-Z]%*c%s %d %lf %lf %lf %lf %lf \n",
atm, &anum, aname, rname, &rnum, &x, &y, &z,
&occupancy, &tempFactor) == 10)
{
if (!strcmp(atm, "ATOM"))
{
//printf("-%s-%d-%s-%s-%d-%lf-%lf-%lf-%lf-%lf-\n", atm,anum,aname,rname,rnum,x,y, z,occupancy,tempFactor);
if (rnum != current_res) // handles atoms up to max(rnum)-1
{
j = j + 1;
current_res = rnum;
}
int idx = get_linusRes_index(rname,aname); // get index for linusRes arrays
if(idx == -1)
{
//printf("Error unknown atom name!");
exit(1);
}
//strcpy(p->atoms[i].name,aname);
int atm_ind = get_atom_ind_with_name(p->atoms,p->res_fai[j],p->res_fai[j+1],aname);
//printf("%d %s pdb %s atoms %s fai %d fai+1 %d atm_ind %d\n",j,p->res_names[j],aname,p->atoms[atm_ind].name,p->res_fai[j],p->res_fai[j+1],atm_ind);
p->atoms[atm_ind].radius = vdw_radius_arr[idx];
p->atoms[atm_ind].bsep0 = bsep0_arr[idx];
p->atoms[atm_ind].bsep1 = bsep1_arr[idx];
strcpy(p->atoms[atm_ind].first_name,first_name_arr[idx]);
p->atoms[atm_ind].fp = first_offset_arr[idx];
strcpy(p->atoms[atm_ind].second_name,second_name_arr[idx]);
p->atoms[atm_ind].sp = second_offset_arr[idx];
strcpy(p->atoms[atm_ind].third_name, third_name_arr[idx]);
p->atoms[atm_ind].tp = third_offset_arr[idx];
p->atoms[atm_ind].sasa = 0.0;
p->atoms[atm_ind].sasarad = 0.0;
//printf("First %s Second %s Third %s\n", first_name_arr[idx], second_name_arr[idx],third_name_arr[idx]);
//printf("Res %s Resnum %d Atom %s Atomnum %d First %s Second %s Third %s\n",rname,rnum, aname, i,p->atoms[i].first_name, p->atoms[i].second_name, p->atoms[i].third_name);
p->atoms[atm_ind].x = x;
p->atoms[atm_ind].y = y;
p->atoms[atm_ind].z = z;
//printf("X %lf Y %lf Z %lf\n",p->atoms[atm_ind].x,p->atoms[atm_ind].y,p->atoms[atm_ind].z);
} // end atm if-loop
} // end sscanf if-loop
} // end while loop
fclose(file);
// Finish filling atoms array info
//From LinusMol init
int r;
for(r=0; r<num_res; r++)
{
p->res_helix_wt[r] = 0.1;
p->res_strand_wt[r] = 0.4;
p->res_turn1_wt[r] = 0.05;
p->res_turn2_wt[r] = 0.05;
p->res_coil_wt[r] = 0.20;
p->res_PII_wt[r] = 0.10;
p->res_f_mean[r] = 0.0;
p->res_f_sd[r] = 99.0;
p->res_y_mean[r] = 0.0;
p->res_y_sd[r] = 99.0;
p->res_acprat[r] = 0.0;
}
for(r=0; r<144; r++)
{
p->pmeso_grid[r] = 0.0;
}
p->pmeso_grid[35] = 1.0; //set Ck as probability 1.0
int q;
for(r=0; r<num_res-2; r++) // subtract 2 because ACE and NME don't have pmeso_weights
{
for(q=0; q<144; q++)
{
p->pmeso_wt[r][q] = p->pmeso_grid[q];
}
}
/*
int g;
for (g=0;g<num_res;g++)
{
printf("Testing residues %s\n",p->res_names[g]);
}
*/
// Create and initilaize Z matrix
int n;
for (n=0; n < num_atoms; n++)
{
// printf("Atom name %s Fp %d %s Resnum %d resnum %d\n",p->atoms[n].name, p->atoms[n].fp,p->atoms[n].first_name, p->atoms[n].resnum, num_res);
//printf("Atom name %s %d\n",p->atoms[n].name, p->atoms[n].resnum);
int fp = p->atoms[n].fp + p->atoms[n].resnum;
if(fp >= 0 && fp < num_res)
{
int m = get_atom_ind_with_name(p->atoms, p->res_fai[fp],p->res_fai[fp+1],p->atoms[n].first_name);
p->atoms[n].fp_distance = distance(&p->atoms[n],&p->atoms[m]);
p->atoms[n].fp_ind = m;
//printf(" 1 parent %d %s %lf\n",p->atoms[n].fp_ind,p->atoms[p->atoms[n].fp_ind].name,p->atoms[n].fp_distance);
}
else
{
p->atoms[n].fp_ind = -1;
p->atoms[n].fp_distance = 0.0;
}
//printf("1 second_parent %s\n",p->atoms[n].second_parent->name);
//printf("1 third_parent %s\n",p->atoms[n].third_parent->name);
int sp = p->atoms[n].sp + p->atoms[n].resnum;
if(sp >= 0 && sp < num_res)
{
//atoms[n].sp_ind = get_atom_ind_with_name(p->atoms, p->res_fai[sp],p->res_fai[sp+1],p->atoms[n].second_name);
int m = get_atom_ind_with_name(p->atoms, p->res_fai[sp],p->res_fai[sp+1],p->atoms[n].second_name);
p->atoms[n].sp_angle = angle(&p->atoms[n],&p->atoms[p->atoms[n].fp_ind],&p->atoms[m]);
p->atoms[n].sp_ind = m;
//printf(" 2 parent %s %lf\n",p->atoms[m].name,p->atoms[n].sp_angle);
}
else
{
p->atoms[n].sp_ind = -1;
p->atoms[n].sp_angle = 0.0;
}
int tp = p->atoms[n].tp + p->atoms[n].resnum;
if(tp >= 0 && tp < num_res)
{
p->atoms[n].tp_ind = get_atom_ind_with_name(p->atoms, p->res_fai[tp],p->res_fai[tp+1],p->atoms[n].third_name);
p->atoms[n].tp_torsion = torsion(&p->atoms[n],&p->atoms[p->atoms[n].fp_ind],&p->atoms[p->atoms[n].sp_ind],&p->atoms[p->atoms[n].tp_ind]);
//printf(" 3 parent %s %lf\n",p->atoms[p->atoms[n].tp_ind].name,p->atoms[n].tp_torsion);
}
else
{
p->atoms[n].tp_ind = -1;
p->atoms[n].tp_torsion = 0.0;
}
}
/*
for(i=0;i<p->num_atoms;i++)
{
printf(" Atom %s fp %s sp %s tp %s\n",p->atoms[i].name, p->atoms[p->atoms[i].fp_ind].name,
p->atoms[p->atoms[i].sp_ind].name,p->atoms[p->atoms[i].tp_ind].name);
}
*/
commit_coords_range(p->atoms, 0,num_atoms);
// Fill up Phiatoms, Psiatoms, Omeatoms & Chiatoms
int k;
int chi_num=0;
for(k=0; k<num_res; k++)
{
p->phi_atoms[k] = get_atom_ind_with_name(p->atoms, p->res_fai[k],p->res_fai[k+1]," C ");
p->psi_atoms[k] = get_atom_ind_with_name(p->atoms, p->res_fai[k],p->res_fai[k+1]," O ");
p->omega_atoms[k] = get_atom_ind_with_name(p->atoms, p->res_fai[k],p->res_fai[k+1]," CA ");
//printf("Phi atom name %s res %d %lf %lf %lf tor %lf\n",p->atoms[p->phi_atoms[k]].name, p->atoms[p->phi_atoms[k]].resnum,p->atoms[p->phi_atoms[k]].x,p->atoms[p->phi_atoms[k]].y,p->atoms[p->phi_atoms[k]].z,p->atoms[p->phi_atoms[k]].tp_torsion);
// printf("psi atom name %s res %d %lf %lf %lf tor %lf\n",p->atoms[p->psi_atoms[k]].name, p->atoms[p->psi_atoms[k]].resnum,p->atoms[p->psi_atoms[k]].x,p->atoms[p->psi_atoms[k]].y,p->atoms[p->psi_atoms[k]].z,p->atoms[p->psi_atoms[k]].tp_torsion);
//printf("omega atom name %s res %d %lf %lf %lf tor %lf\n",p->atoms[p->omega_atoms[k]].name, p->atoms[p->omega_atoms[k]].resnum,p->atoms[p->omega_atoms[k]].x,p->atoms[p->omega_atoms[k]].y,p->atoms[p->omega_atoms[k]].z,p->atoms[p->omega_atoms[k]].tp_torsion);
// Fill up chi atoms
int chi_idx = get_chi_res_index(p->res_names[k]);
//printf("Chi idx %d\n",chi_idx);
// printf("Residue %s %d\n",p->res_names[k],k);
//printf("Residue %s %d\n",p->res_names[k],k);
if(chi_idx != -1)
{
int u;
int num_chi = chi_size[chi_idx]/2;
//printf("Num chi %d\n", num_chi);
for(u=0; u<num_chi; u++)
{
//get_atom_with_name(p->chi_atoms[chi_num],p->atoms,p->res_fai[k],p->res_fai[k+1],chi_atoms[chi_idx][u]);
int m = get_atom_ind_with_name(p->atoms,p->res_fai[k],p->res_fai[k+1],chi_atoms[chi_idx][u]);
//printf("Chi atoms for res %s : %s\n", p->res_names[k],p->atoms[p->chi_atoms[chi_num]].name);
if(m > -1)
{
p->chi_atoms[chi_num] = m;
chi_num++;
}
}
}
}
p->num_chi_atoms = chi_num;
/*
free(atm);
free(aname);
free(rname);
free(p->atoms);
free(p->res_names);
free(p->res_fai);
for (i = 0; i < num_res; i++)
{
free(p->res_names[i]);
}
free(p->res_num);
*/
}
