Protein load_protein(const boost::filesystem::path & protein_path,
const boost::optional<boost::filesystem::path> & secondary_structure_path) {
LOGI << "loading protein file";
ProteinFileFactory pf;
std::shared_ptr<ProteinFile> protein_file(pf.create(protein_path));
SecondaryStructureFileFactory ssf;
if (secondary_structure_path) {
LOGI << "loading secondary structure file";
std::shared_ptr<SecondaryStructureFile> secondary_structure_file(
ssf.create(*secondary_structure_path));
return Protein(protein_file, secondary_structure_file);
} else {
return Protein(protein_file);
}
}
int main (int argc, char *argv[]) {
if (argc < PDB_INDEX+1)
{
cout <<"Usage:"<<argv[0]<<" monomer.ruf.pstrm\n";
exit(1);
}//end of if
coord_struct asa;
int i,j;
char p_n[20];
vector<char> chain;
vector<aa> w_c, w_c2;
vector<aa_asa> std_asa;
vector<naa2>w_c4;
vector<naa>w_c3;
vector<residue>a_w_c;
vector<protein_rou> proteins_rou;
char *c_a;
c_a=new char[1];
vector<protein> whole_protein;
vector<aa> wc_c_aa2,wc_t_aa2;
vector<naa> wc_c_aa3,wc_t_aa3;
ifstream protein_file("monomer_u.txt",ios::in);
char *file_name;
file_name=new char[10];
while(protein_file>>file_name)
{
read_asa_file(w_c,asa,file_name);
cal_tot_asa_of_res(w_c4,w_c);
// cout<<setiosflags(ios::left)<<setw(15)<<file_name<<setiosflags(ios::left)<<setw(10)<<w_c.size()<<endl;
// w_c.clear();
//geo_cen_of_res(wc_c_aa3,wc_c_aa2,a_w_c,w_c);
//res_alpha_atom(wc_c_aa3,wc_c_aa2,a_w_c,w_c);
//cout<<whole_protein.size()<<endl;
geo_cen_of_side_chain2(wc_c_aa3,wc_c_aa2,w_c);
ter_atom_of_side_chain2(wc_t_aa3,wc_t_aa2,w_c);
for(i=0;i<wc_c_aa3.size();i++)
{
wc_c_aa3[i].angle_t=1000;
}
for(i=0;i<wc_c_aa3.size();i++)
{
for(j=0;j<wc_t_aa3.size();j++)
{
if(wc_c_aa3[i].res_num==wc_t_aa3[j].res_num&&wc_c_aa3[i].chain_type==wc_t_aa3[j].chain_type&&
(strncmp(wc_c_aa3[i].res_id,wc_t_aa3[j].res_id,3)==0))
{
wc_c_aa3[i].angle_t=wc_t_aa3[j].angle;
}//end of if
}//end of for
}// end of for
for(i=0;i<wc_c_aa3.size();i++)
{
for(j=0;j<w_c4.size();j++)
{
if(wc_c_aa3[i].res_num==w_c4[j].res_num&&wc_c_aa3[i].chain_type==w_c4[j].chain_type&&
(strncmp(wc_c_aa3[i].res_id,w_c4[j].res_id,3)==0))
{
wc_c_aa3[i].asa=w_c4[j].tot_atom_asa;
}//end of if
}//end of for
}// end of for
/*
cout<<setiosflags(ios::left)<<setw(8)<<"res_num"
<<setiosflags(ios::left)<<setw(8)<<"res_id"
<<setiosflags(ios::left)<<setw(8)<<"ch_type"
<<setiosflags(ios::left)<<setw(8)<<"an_c_c"
<<setiosflags(ios::left)<<setw(8)<<"an_c_t"
<<setiosflags(ios::left)<<setw(8)<<"asa"<<endl;
for(i=0;i<wc_c_aa3.size();i++)
{
cout<<setiosflags(ios::left)<<setw(8)<<wc_c_aa3[i].res_num
<<setiosflags(ios::left)<<setw(8)<<wc_c_aa3[i].res_id
<<setiosflags(ios::left)<<setw(8)<<wc_c_aa3[i].chain_type
<<setiosflags(ios::fixed)
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<wc_c_aa3[i].angle
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<wc_c_aa3[i].angle_t
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<wc_c_aa3[i].asa<<endl;
}//end of for
*/
residue one_residue;
one_residue.res_id=new char[5];
protein one_protein;
one_protein.protein_name=new char[10];
strcpy(one_protein.protein_name,strtok(file_name,"."));
for(i=0;i<wc_c_aa3.size();i++)
{
one_residue.res_id=wc_c_aa3[i].res_id;
one_residue.res_num=wc_c_aa3[i].res_num;
one_residue.chain_type=wc_c_aa3[i].chain_type;
one_residue.angle=wc_c_aa3[i].angle;
one_residue.asa=wc_c_aa3[i].asa;
one_protein.residue_str.push_back(one_residue);
}
whole_protein.push_back(one_protein);
one_protein.residue_str.clear();
wc_c_aa2.clear();
wc_t_aa2.clear();
wc_c_aa3.clear();
wc_t_aa3.clear();
w_c4.clear();
w_c.clear();
}//end of while
//these two functions are in read_dimer.cpp file
read_pdb_file(proteins_rou,argv[PDB_INDEX]);
calculate_roughness_of_residue(proteins_rou);
ofstream output("results3_asa.txt",ios::out);
int m,n,tt;
for(i=0;i<whole_protein.size();i++)
{
for(m=0;m<whole_protein[i].residue_str.size();m++)
{whole_protein[i].residue_str[m].roughness=-100;}
}
for(j=0;j<proteins_rou.size();j++)
{
for(n=0;n<proteins_rou[j].w_c_rou.size();n++)
{
proteins_rou[j].w_c_rou[n].asa=0;
}
}
tt=0;
for(i=0;i<whole_protein.size();i++)
{
for(j=0;j<proteins_rou.size();j++)
{
if(strcmp(whole_protein[i].protein_name,strtok(proteins_rou[j].protein_rou_id,"."))==0)
{
for(m=0;m<whole_protein[i].residue_str.size();m++)
{
for(n=0;n<proteins_rou[j].w_c_rou.size();n++)
{
if(whole_protein[i].residue_str[m].res_num==proteins_rou[j].w_c_rou[n].res_num&&
*whole_protein[i].residue_str[m].res_id==*proteins_rou[j].w_c_rou[n].res_id&&
whole_protein[i].residue_str[m].chain_type==*proteins_rou[j].w_c_rou[n].chain_type&&
whole_protein[i].residue_str[m].asa>5&&
proteins_rou[j].w_c_rou[n].roughness>0
)
{
output<<setiosflags(ios::left)<<setw(10)<<whole_protein[i].protein_name
<<setiosflags(ios::left)<<setw(6)<<whole_protein[i].residue_str[m].res_num
<<setiosflags(ios::left)<<setw(4)<<whole_protein[i].residue_str[m].res_id
<<setiosflags(ios::left)<<setw(3)<<whole_protein[i].residue_str[m].chain_type
<<setiosflags(ios::left)<<setw(10)<<proteins_rou[j].protein_rou_id
<<setiosflags(ios::left)<<setw(6)<<proteins_rou[j].w_c_rou[n].res_num
<<setiosflags(ios::left)<<setw(4)<<proteins_rou[j].w_c_rou[n].res_id
<<setiosflags(ios::left)<<setw(3)<<proteins_rou[j].w_c_rou[n].chain_type
<<setiosflags(ios::fixed)
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<whole_protein[i].residue_str[m].angle
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<whole_protein[i].residue_str[m].asa
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<proteins_rou[j].w_c_rou[n].roughness<<endl;
whole_protein[i].residue_str[m].roughness=proteins_rou[j].w_c_rou[n].roughness;
proteins_rou[j].w_c_rou[n].asa=whole_protein[i].residue_str[m].asa;
tt=tt+1;
}//end if
}//end for
}//end of for
}//end of if
}//end of for
}//end of for
ofstream output1("results3_asa1.txt",ios::out);
for(i=0;i<whole_protein.size();i++)
{
for(m=0;m<whole_protein[i].residue_str.size();m++)
{
if(whole_protein[i].residue_str[m].roughness>0)
{
output1<<setiosflags(ios::left)<<setw(10)<<whole_protein[i].protein_name
<<setiosflags(ios::left)<<setw(6)<<whole_protein[i].residue_str[m].res_num
<<setiosflags(ios::left)<<setw(4)<<whole_protein[i].residue_str[m].res_id
<<setiosflags(ios::left)<<setw(3)<<whole_protein[i].residue_str[m].chain_type
<<setiosflags(ios::fixed)
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<whole_protein[i].residue_str[m].angle
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<whole_protein[i].residue_str[m].asa
<<whole_protein[i].residue_str[m].roughness<<endl;
}
}
}
ofstream output2("results3_asa2.txt",ios::out);
for(j=0;j<proteins_rou.size();j++)
{
for(n=0;n<proteins_rou[j].w_c_rou.size();n++)
{
if(proteins_rou[j].w_c_rou[n].asa>5)
{
output2<<setiosflags(ios::left)<<setw(10)<<proteins_rou[j].protein_rou_id
<<setiosflags(ios::left)<<setw(6)<<proteins_rou[j].w_c_rou[n].res_num
<<setiosflags(ios::left)<<setw(4)<<proteins_rou[j].w_c_rou[n].res_id
<<setiosflags(ios::left)<<setw(3)<<proteins_rou[j].w_c_rou[n].chain_type
<<setiosflags(ios::fixed)
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<proteins_rou[j].w_c_rou[n].roughness
<<setiosflags(ios::left)<<setprecision(2)<<setw(8)<<proteins_rou[j].w_c_rou[n].asa<<endl;
}
}
}
sum_and_output(whole_protein);
sum_and_output3(whole_protein);
sum_and_output5(whole_protein);
cout<<"total surface residue(asa>5 and roughness>0) is:"<<tt<<endl;
protein_file.close();
return(0);
}//end of main
