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// SPDX-License-Identifier: LGPL-3.0-or-later
// Author: Kristian Lytje
#include <em/manager/SmartProteinManager.h>
#include <em/detail/ImageStackBase.h>
#include <em/detail/EMGrid.h>
#include <hist/intensity_calculator/CompositeDistanceHistogram.h>
#include <hist/histogram_manager/PartialHistogramManagerMT.h>
#include <data/Molecule.h>
#include <data/Body.h>
#include <utility/Console.h>
#include <utility/Limit3D.h>
#include <utility/Logging.h>
#include <settings/HistogramSettings.h>
#include <settings/ExvSettings.h>
#include <settings/EMSettings.h>
#include <settings/GridSettings.h>
#include <settings/Flags.h>
#include <vector>
#include <cassert>
using namespace ausaxs;
using namespace ausaxs::em::managers;
using namespace ausaxs::data;
SmartProteinManager::~SmartProteinManager() = default;
std::unique_ptr<hist::ICompositeDistanceHistogram> SmartProteinManager::get_histogram(double cutoff) {
return get_protein(cutoff)->get_histogram();
}
observer_ptr<data::Molecule> SmartProteinManager::get_protein(double cutoff) {
update_protein(cutoff);
auto ax = images->get_header()->get_axes();
// ensure the grid is large enough to contain the entire map
//? is this a waste of time since it is being overwritten for every iteration anyway?
Limit3D limits(ax.x.min, ax.x.max, ax.y.min, ax.y.max, ax.z.min, ax.z.max);
double expand_x = 0.5*limits.x.span()*settings::grid::scaling;
double expand_y = 0.5*limits.y.span()*settings::grid::scaling;
double expand_z = 0.5*limits.z.span()*settings::grid::scaling;
limits.x.min -= expand_x, limits.x.max += expand_x;
limits.y.min -= expand_y, limits.y.max += expand_y;
limits.z.min -= expand_z, limits.z.max += expand_z;
// hydration must be cleared to ensure the grid state will be exactly the same as the one used to generate the hydration
// when the grid is first created, *only* the body atoms are added to the grid, with the hydration being added later
// if we do not clear the hydration now, since it can be bound to individual bodies, the hydration will be added in-between the body atoms,
// potentially leading to a different grid state than the one used to generate the hydration
protein->clear_hydration();
protein->set_grid(std::make_unique<grid::EMGrid>(limits));
for (auto& body : protein->get_bodies()) {
protein->get_grid()->add(body);
}
if (settings::em::hydrate) {protein->generate_new_hydration();}
return protein.get();
}
observer_ptr<const data::Molecule> SmartProteinManager::get_protein() const {
assert(protein != nullptr && "SmartProteinManager::get_protein: Protein has not been initialized yet.");
return protein.get();
}
void SmartProteinManager::set_charge_levels(const std::vector<double>& levels) noexcept {
ProteinManager::set_charge_levels(levels);
protein = nullptr; // the protein must be generated anew to ensure the bodies remains in sync with the new levels
}
std::vector<EMAtom> SmartProteinManager::generate_atoms(double cutoff) const {
// we use a list since we will have to append quite a few other lists to it
std::list<EMAtom> atoms;
const auto& imagestack = images->images();
unsigned int step = settings::em::sample_frequency;
for (unsigned int i = 0; i < imagestack.size(); i += step) {
std::list<EMAtom> im_atoms = imagestack[i].generate_atoms(cutoff);
atoms.splice(atoms.end(), im_atoms); // move im_atoms to end of atoms
}
// convert list to vector
return std::vector<EMAtom>(std::make_move_iterator(std::begin(atoms)), std::make_move_iterator(std::end(atoms)));
}
std::unique_ptr<data::Molecule> SmartProteinManager::generate_new_protein(double cutoff) const {
std::vector<EMAtom> atoms = generate_atoms(cutoff);
std::vector<Body> bodies(charge_levels.size());
std::vector<AtomFF> current_atoms(atoms.size());
if (atoms.empty()) {
console::print_warning("Warning in SmartProteinManager::generate_protein: No voxels found for cutoff \"" + std::to_string(cutoff) + "\".");
return std::make_unique<data::Molecule>(bodies);
}
if (charge_levels.empty()) {
throw except::out_of_bounds("SmartProteinManager::generate_protein: charge_levels is empty.");
}
// sort vector so we can slice it into levels of charge density
std::sort(atoms.begin(), atoms.end(), [] (const EMAtom& atom1, const EMAtom& atom2) {return atom1.charge_density() < atom2.charge_density();});
unsigned int charge_index = 0, atom_index = 0, current_index = 0;
double charge = charge_levels[charge_index]; // initialize charge
while (atoms[atom_index].charge_density() < cutoff) {++atom_index;} // search for first atom with charge larger than the cutoff
while (charge < cutoff) {charge = charge_levels[++charge_index];} // search for first charge level larger than the cutoff
while (atom_index < atoms.size()) {
if (atoms[atom_index].charge_density() < charge) {
current_atoms[current_index++] = atoms[atom_index++].get_atom_ff();
} else {
// create the body for this charge bin
current_atoms.resize(current_index);
bodies[charge_index] = Body(current_atoms);
// prepare the next body
current_index = 0;
current_atoms.resize(atoms.size() - atom_index);
// increment the charge level
if (charge_index+1 == charge_levels.size()) [[unlikely]] {
throw except::unexpected("SmartProteinManager::generate_protein: Reached end of charge levels list.");
}
charge = charge_levels[++charge_index];
}
}
// create the final body of the loop
current_atoms.resize(current_index);
bodies[charge_index] = Body(current_atoms);
return std::make_unique<data::Molecule>(std::move(bodies));
}
void SmartProteinManager::toggle_histogram_manager_init(bool state) {
settings::flags::init_histogram_manager = state;
}
void SmartProteinManager::update_protein(double cutoff) {
if (protein == nullptr || protein->size_atom() == 0) {
// the protein is not initialized, so simply assign it a new one
toggle_histogram_manager_init(false);
logging::log("SmartProteinManager::update_protein: protein is nullptr or empty. Generating new protein.");
protein = generate_new_protein(cutoff);
protein->set_histogram_manager(settings::hist::HistogramManagerChoice::PartialHistogramManagerMT);
previous_cutoff = cutoff;
return;
}
if (cutoff == previous_cutoff) {
logging::log("SmartProteinManager::update_protein: cutoff is the same as previous. Nothing to do.");
return;
}
// sanity check
if (charge_levels.empty()) {
throw except::unexpected("SmartProteinManager::update_protein: charge_levels is empty.");
}
logging::log("SmartProteinManager::update_protein: cutoff = " + std::to_string(cutoff) + ", previous_cutoff = " + std::to_string(previous_cutoff));
// the idea is to generate a new protein with the new cutoff, and then replace the relevant bodies in the old protein with the new ones
// this will trigger the "update" signals for the replaced bodies, which will inform the histogram manager to only recalculate their contributions
std::unique_ptr<data::Molecule> new_protein = generate_new_protein(cutoff);
if (cutoff < previous_cutoff) {
// since cutoff is smaller than previously, we have to change all bins in the range [cutoff, previous_cutoff]
// skip all bins before the relevant range
unsigned int charge_index = 0;
double current_cutoff = charge_levels[0];
while (current_cutoff < cutoff && charge_index < charge_levels.size()) {
current_cutoff = charge_levels[++charge_index];
}
// iterate through the remaining bins, and use a break statement to stop when we leave the relevant range
for (; charge_index < charge_levels.size(); ++charge_index) {
// check if the current bin is inside the range
if (charge_levels[charge_index] < previous_cutoff) {
// if so, we replace it with the new contents
protein->get_body(charge_index) = std::move(new_protein->get_body(charge_index));
} else {
// if we have the same number of atoms as earlier, nothing has changed
if (new_protein->get_body(charge_index).size_atom() == protein->get_body(charge_index).size_atom()) {
break;
}
// otherwise we replace it and stop iterating
protein->get_body(charge_index) = std::move(new_protein->get_body(charge_index));
break;
}
}
} else {
// since cutoff is larger than previously, we have to change all bins in the range [previous_cutoff, cutoff]
// skip all bins before the relevant range
unsigned int charge_index = 0;
double current_cutoff = charge_levels[0];
while (current_cutoff < previous_cutoff && charge_index < charge_levels.size()) {
current_cutoff = charge_levels[++charge_index];
}
// iterate through the remaining bins, and use a break statement to stop when we leave the relevant range
for (; charge_index < charge_levels.size(); ++charge_index) {
// check if the current bin is inside the range
if (charge_levels[charge_index] < cutoff) {
// if so, we replace it with the new contents
protein->get_body(charge_index) = std::move(new_protein->get_body(charge_index));
} else {
// otherwise we replace it and stop iterating
protein->get_body(charge_index) = std::move(new_protein->get_body(charge_index));
break;
}
}
}
previous_cutoff = cutoff;
}
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