void get_residue_solvent_accessibility(const IMP::Particles& atom_particles,
const IMP::Particles& residue_particles,
const std::vector<int>& atom_2_residue_map,
std::vector<float>& residue_solvent_accessibility) {
IMP::saxs::FormFactorTable* ft = IMP::saxs::default_form_factor_table();
IMP::saxs::FormFactorType ff_type = IMP::saxs::HEAVY_ATOMS;
for(unsigned int i=0; i<atom_particles.size(); i++) {
float radius = ft->get_radius(atom_particles[i], ff_type);
IMP::core::XYZR::setup_particle(atom_particles[i], 2.0*radius);
}
IMP::Floats surface_area;
IMP::saxs::SolventAccessibleSurface s;
surface_area = s.get_solvent_accessibility(IMP::core::XYZRs(atom_particles));
// sum up individual atom areas into residue area
residue_solvent_accessibility.clear();
residue_solvent_accessibility.insert(residue_solvent_accessibility.begin(),
residue_particles.size(), 0.0);
for(unsigned int i=0; i<atom_particles.size(); i++) {
// convert from 0-1 range to actual area in A^2
float radius = IMP::core::XYZR(atom_particles[i]).get_radius();
float area = surface_area[i] * 4*IMP::algebra::PI*radius*radius;
residue_solvent_accessibility[atom_2_residue_map[i]] += area;
}
// compute solvent accessability percentage
std::map<IMP::atom::ResidueType, float> residue_type_area_map_;
residue_type_area_map_[IMP::atom::ALA] = 113.0;
residue_type_area_map_[IMP::atom::ARG] = 241.0;
residue_type_area_map_[IMP::atom::ASP] = 151.0;
residue_type_area_map_[IMP::atom::ASN] = 158.0;
residue_type_area_map_[IMP::atom::CYS] = 140.0;
residue_type_area_map_[IMP::atom::GLN] = 189.0;
residue_type_area_map_[IMP::atom::GLU] = 183.0;
residue_type_area_map_[IMP::atom::GLY] = 85.0;
residue_type_area_map_[IMP::atom::HIS] = 194.0;
residue_type_area_map_[IMP::atom::ILE] = 182.0;
residue_type_area_map_[IMP::atom::LEU] = 180.0;
residue_type_area_map_[IMP::atom::LYS] = 211.0;
residue_type_area_map_[IMP::atom::MET] = 204.0;
residue_type_area_map_[IMP::atom::PHE] = 218.0;
residue_type_area_map_[IMP::atom::PRO] = 143.0;
residue_type_area_map_[IMP::atom::SER] = 122.0;
residue_type_area_map_[IMP::atom::THR] = 146.0;
residue_type_area_map_[IMP::atom::TYR] = 229.0;
residue_type_area_map_[IMP::atom::TRP] = 259.0;
residue_type_area_map_[IMP::atom::VAL] = 160.0;
residue_type_area_map_[IMP::atom::UNK] = 113.0;
for(unsigned int i=0; i<residue_particles.size(); i++) {
IMP::atom::ResidueType residue_type =
IMP::atom::Residue(residue_particles[i]).get_residue_type();
float residue_area = residue_type_area_map_.find(residue_type)->second;
std::cerr << residue_type.get_string() << " "
<< residue_solvent_accessibility[i]
<< " " << residue_area << std::endl;
residue_solvent_accessibility[i] /= residue_area;
}
}
void get_residue_solvent_accessibility(const IMP::Particles& residue_particles,
IMP::Floats& residue_solvent_accessibility) {
IMP::saxs::FormFactorTable* ft = IMP::saxs::default_form_factor_table();
IMP::saxs::FormFactorType ff_type = IMP::saxs::CA_ATOMS;
for(unsigned int p_index=0; p_index<residue_particles.size(); p_index++) {
float radius = ft->get_radius(residue_particles[p_index], ff_type);
IMP::core::XYZR::setup_particle(residue_particles[p_index], radius);
}
IMP::saxs::SolventAccessibleSurface s;
residue_solvent_accessibility =
s.get_solvent_accessibility(IMP::core::XYZRs(residue_particles));
}
float EMFit::compute_volume(const IMP::Particles& particles) {
IMP::saxs::FormFactorTable* ft = IMP::saxs::get_default_form_factor_table();
float volume = 0.0;
float c = (4.0 / 3.0) * IMP::algebra::PI;
for (unsigned int pindex = 0; pindex < particles.size(); pindex++) {
float radius = ft->get_radius(particles[pindex]);
// volume = 4/3 * pi * r^3
volume += c * radius * radius * radius;
// add radius to particle. it is needed later for sampled density map
IMP::core::XYZR::setup_particle(particles[pindex], radius);
}
return volume;
}