void Model::output_statistics_pro_DNA_contact_pairs(std::ostream& o)
{
int i, j, k;
Atom atmp1, atmp2, atmp3, atmp4;
Residue rtmp1, rtmp2;
ChainType ct_tmp;
int pg_size, dg_size;
double cg_dist = 0;
double aa_dist_min = 0;
std::string groove_info;
std::vector<Atom> tmp_cg_pro_group;
std::vector<Atom> tmp_cg_dna_group;
std::vector<Residue> tmp_residue_pro_group;
std::vector<Residue> tmp_residue_dna_group;
int tmp_resid_serial = 0;
int tmp_chain_serial = -1;
for (i = 0; i < n_chain_; ++i) {
ct_tmp = v_chains_[i].get_chain_type();
if (ct_tmp == none || ct_tmp == water || ct_tmp == other)
continue;
++tmp_chain_serial;
int m_chain_size = v_chains_[i].get_size();
if (ct_tmp == protein) {
for (j = 0; j < m_chain_size; ++j) {
rtmp1 = v_chains_[i].get_residue(j);
atmp1 = rtmp1.get_cg_C_alpha();
++tmp_resid_serial;
atmp1.set_residue_serial(tmp_resid_serial);
atmp1.set_chain_ID(tmp_chain_serial + 97);
tmp_cg_pro_group.push_back(atmp1);
tmp_residue_pro_group.push_back(rtmp1);
}
} else if (ct_tmp == DNA) {
Residue rtmp_P, rtmp_S, rtmp_B, rtmp_P_1;
for (j = 0; j < m_chain_size; ++j) {
// Add CG Phosphate;
rtmp1 = v_chains_[i].get_residue(j);
if (j != 0) {
atmp1 = rtmp1.get_cg_P();
++tmp_resid_serial;
atmp1.set_residue_serial(tmp_resid_serial);
atmp1.set_chain_ID(tmp_chain_serial + 97);
tmp_cg_dna_group.push_back(atmp1);
}
// Add CG Sugar;
atmp1 = rtmp1.get_cg_S();
++tmp_resid_serial;
atmp1.set_residue_serial(tmp_resid_serial);
atmp1.set_chain_ID(tmp_chain_serial + 97);
tmp_cg_dna_group.push_back(atmp1);
// Add CG Base;
atmp1 = rtmp1.get_cg_B();
++tmp_resid_serial;
atmp1.set_residue_serial(tmp_resid_serial);
atmp1.set_chain_ID(tmp_chain_serial + 97);
tmp_cg_dna_group.push_back(atmp1);
rtmp_P = rtmp_P_1;
rtmp_P_1.reset();
rtmp_P.set_residue_serial(rtmp1.get_residue_serial());
rtmp_P_1.set_residue_serial(rtmp1.get_residue_serial());
rtmp_S.set_residue_serial(rtmp1.get_residue_serial());
rtmp_B.set_residue_serial(rtmp1.get_residue_serial());
rtmp_P.set_chain_ID(rtmp1.get_chain_ID());
rtmp_P_1.set_chain_ID(rtmp1.get_chain_ID());
rtmp_S.set_chain_ID(rtmp1.get_chain_ID());
rtmp_B.set_chain_ID(rtmp1.get_chain_ID());
for (k = 0; k < rtmp1.get_size(); ++k) {
atmp1 = rtmp1.get_atom(k);
std::string aname = atmp1.get_atom_name();
if (aname == "O3' ") {
rtmp_P_1.add_atom(atmp1);
} else if (aname == "P " || aname == "OP1 " || aname == "OP2 " ||
aname == "O5' " || aname == "O1P " || aname == "O2P ") {
rtmp_P.add_atom(atmp1);
} else {
std::string::size_type np;
np = aname.find("'");
if (np == std::string::npos) {
rtmp_B.add_atom(atmp1);
} else {
rtmp_S.add_atom(atmp1);
}
}
}
if (j != 0)
tmp_residue_dna_group.push_back(rtmp_P);
tmp_residue_dna_group.push_back(rtmp_S);
tmp_residue_dna_group.push_back(rtmp_B);
rtmp_P.reset();
rtmp_S.reset();
rtmp_B.reset();
}
} else if (ct_tmp == RNA || ct_tmp == na) {
for (j = 0; j < m_chain_size; ++j) {
if (j != 0) {
tmp_resid_serial += 3;
} else {
tmp_resid_serial += 2;
}
}
} else if (ct_tmp == ion) {
++tmp_resid_serial;
}
}
// Check vector sizes...
if (tmp_cg_pro_group.size() != tmp_residue_pro_group.size()) {
std::cout << " ~ PINANG::model_statistics.cpp ~ \n";
std::cout << "ERROR in getting protein atom group and residue group. \n";
exit(EXIT_SUCCESS);
} else {
pg_size = int(tmp_cg_pro_group.size());
}
if (tmp_cg_dna_group.size() != tmp_residue_dna_group.size()) {
std::cout << " ~ PINANG::model_statistics.cpp ~ \n";
std::cout << "ERROR in getting DNA atom group and residue group. \n";
exit(EXIT_SUCCESS);
} else {
dg_size = int(tmp_cg_dna_group.size());
}
for (i = 0; i < pg_size; ++i) {
atmp1 = tmp_cg_pro_group[i];
rtmp1 = tmp_residue_pro_group[i];
for (j = 0; j < dg_size; ++j) {
atmp2 = tmp_cg_dna_group[j];
rtmp2 = tmp_residue_dna_group[j];
aa_dist_min = residue_min_distance(rtmp1, rtmp2, atmp3, atmp4);
if (aa_dist_min < g_pro_DNA_aa_cutoff && aa_dist_min > 0) {
cg_dist = atom_distance(atmp1, atmp2);
groove_info = get_DNA_atom_position_info(atmp4.get_residue_name(), atmp4.get_atom_name());
o << " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ \n";
o << "distance ~ aa > " << std::setiosflags(std::ios_base::fixed) << std::setprecision(6)
<< std::setw(9) << aa_dist_min << " : [ " << atmp3.get_chain_ID() << " "
<< atmp3.get_residue_name() << " " << std::setw(4) << atmp3.get_residue_serial() << " : "
<< atmp3.get_atom_name() << "] -- [ " << atmp4.get_chain_ID() << " "
<< atmp4.get_residue_name() << " " << std::setw(4) << atmp4.get_residue_serial() << " : "
<< atmp4.get_atom_name() << "] " << groove_info << "\n";
o << "distance ~ cg | " << std::setiosflags(std::ios_base::fixed) << std::setprecision(6)
<< std::setw(9) << cg_dist << " : [ " << atmp1.get_chain_ID() << " "
<< atmp1.get_residue_name() << " " << std::setw(4) << atmp1.get_residue_serial() << " : "
<< atmp1.get_atom_name() << "] -- [ " << atmp2.get_chain_ID() << " "
<< atmp2.get_residue_name() << " " << std::setw(4) << atmp2.get_residue_serial() << " : "
<< atmp2.get_atom_name() << "] " << groove_info << "\n";
if (atmp2.get_atom_name() == "DB ") {
o << "REMARK : " << atmp1.get_residue_name() << " - " << atmp2.get_residue_name() << " \n";
o << tmp_residue_dna_group[j - 1];
o << "TER \n";
o << rtmp2;
o << "TER \n";
o << rtmp1;
o << "TER \n";
o << tmp_cg_dna_group[j - 1];
o << "TER \n";
o << atmp2;
o << "TER \n";
o << atmp1;
o << "TER \n";
o << "ENDMDL \n";
}
}
}
}
}
/** atom SASA modification from one contact */
__inline__ static int mod_atom_sasa(Str *pdb, Topol *topol, Type *type, \
MolSasa *molSasa, ConstantSasa *constant_sasa, double connectivityParameter, \
int i, int j, float rSolvent)
{
double atomRadius_i, atomRadius_j;
double atomParameter_i, atomParameter_j;
double ci1, cj1, cc2, ci3, cj3, bij, bji;
float atomDistance = 0.;
float cutoffRadius = 0.;
/*___________________________________________________________________________*/
/* safety check */
if (i == j) {
fprintf(stderr, "Problematic conformation at atoms %d %d\n",
pdb->atom[i].atomNumber, pdb->atom[i+1].atomNumber);
/*Warning("Atom distances too short? Probably incorrect POPS results!");*/
Error("Serious conformational problems in input structure.\nCheck the atom numbers listed above for steric clashes.");
}
/*___________________________________________________________________________*/
/* initialise */
/* atom specific radius */
atomRadius_i = constant_sasa->atomDataSasa[type->residueType[i]][type->atomType[i]].radius;
atomRadius_j = constant_sasa->atomDataSasa[type->residueType[j]][type->atomType[j]].radius;
/* atom specific parameter */
atomParameter_i = constant_sasa->atomDataSasa[type->residueType[i]][type->atomType[i]].parameter;
atomParameter_j = constant_sasa->atomDataSasa[type->residueType[j]][type->atomType[j]].parameter;
/*___________________________________________________________________________*/
/* skip overlap area computation if the two atoms i,j do not overlap */
if ((cutoffRadius = cutoff_radius(type, constant_sasa, i, j, rSolvent)) < \
(atomDistance = atom_distance(pdb, i, j)))
return(1);
/* shortest atomic bond length is .74 A in hydrogen */
if (atomDistance < .74) {
fprintf(stderr, "Atom distance %d %d = %f Angstrom\n",
pdb->atom[i].atomNumber, pdb->atom[j].atomNumber, atomDistance);
Warning("Atom distance too short! Probably incorrect POPS results!");
}
/*___________________________________________________________________________*/
/* compute c[ij]1 */
ci1 = compute_c1(atomRadius_i, rSolvent);
cj1 = compute_c1(atomRadius_j, rSolvent);
/* compute cc2 */
cc2 = cutoffRadius - atomDistance;
/* compute c[ij]3 */
ci3 = compute_c3(atomRadius_j, atomRadius_i, atomDistance);
cj3 = compute_c3(atomRadius_i, atomRadius_j, atomDistance);
/* compute b[ij,ji] */
bij = ci1 * cc2 * ci3;
bji = cj1 * cc2 * cj3;
/* compute c[ij]; jk: moved to atom_sasa formula */
/*ci = pCon * bij;
cj = pCon * bji;*/
/* count overlaps */
++ molSasa->atomSasa[i].nOverlap;
/* count overlaps */
++ molSasa->atomSasa[i].nOverlap;
++ molSasa->atomSasa[j].nOverlap;
/* compute atom SASA for atoms i and j */
molSasa->atomSasa[i].sasa = atom_sasa(molSasa, i, connectivityParameter, bij, atomParameter_i);
molSasa->atomSasa[j].sasa = atom_sasa(molSasa, j, connectivityParameter, bji, atomParameter_j);
/* record parameters: increment neighbour index */
++ topol->neighbourPar[i][0];
++ topol->neighbourPar[j][0];
/* record parameter product 'p_ij * b_ij' */
topol->neighbourPar[i][(int)topol->neighbourPar[i][0]] = connectivityParameter * bij;
topol->neighbourPar[j][(int)topol->neighbourPar[j][0]] = connectivityParameter * bji;
return(0);
}
