Skip to content

Commit

Permalink
Merge pull request #262 from envidian/leak_fix
Browse files Browse the repository at this point in the history 
Fix leak in Vina::m_scoring_function reported by valgrind
  • Loading branch information
@joanimato
joanimato authored Jan 9, 2025
2 parents 986e7b6 + 2214bbb commit d8a0d53
Show file tree
Hide file tree
Showing 3 changed files with 40 additions and 20 deletions.
25 changes: 23 additions & 2 deletions src/lib/scoring_function.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,10 @@ enum scoring_function_choice {SF_VINA, SF_AD42, SF_VINARDO};

class ScoringFunction {
public:
ScoringFunction() { }
ScoringFunction() {
m_num_potentials = 0;
m_num_conf_independents = 0;
}
ScoringFunction(const scoring_function_choice sf_choice, const flv& weights){
switch (sf_choice)
{
Expand Down Expand Up @@ -94,7 +97,25 @@ class ScoringFunction {
m_num_conf_independents = m_conf_independents.size();
m_weights = weights;
};
~ScoringFunction() { }
void Destroy()
{
for (auto p : m_potentials)
{
delete p;
}
m_potentials.clear();
m_num_potentials = 0;
for (auto p : m_conf_independents)
{
delete p;
}
m_conf_independents.clear();
m_num_conf_independents = 0;
}
~ScoringFunction() {
Destroy();
}

fl eval(atom& a, atom& b, fl r) const{ // intentionally not checking for cutoff
fl acc = 0;
VINA_FOR (i, m_num_potentials)
Expand Down
32 changes: 15 additions & 17 deletions src/lib/vina.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ void Vina::set_receptor(const std::string& rigid_name, const std::string& flex_n
}

// CONDITIONS 4, 5, 6, 7 (rigid_name and flex_name are empty strings per default)
m_receptor = parse_receptor_pdbqt(rigid_name, flex_name, m_scoring_function.get_atom_typing());
m_receptor = parse_receptor_pdbqt(rigid_name, flex_name, m_scoring_function->get_atom_typing());

m_model = m_receptor;
m_receptor_initialized = true;
Expand All @@ -97,7 +97,7 @@ void Vina::set_ligand_from_string(const std::string& ligand_string) {
exit(EXIT_FAILURE);
}

atom_type::t atom_typing = m_scoring_function.get_atom_typing();
atom_type::t atom_typing = m_scoring_function->get_atom_typing();

if (!m_receptor_initialized) {
// This situation will happen if we don't need a receptor and we are using affinity maps
Expand All @@ -113,7 +113,7 @@ void Vina::set_ligand_from_string(const std::string& ligand_string) {
m_model.append(parse_ligand_pdbqt_from_string(ligand_string, atom_typing));

// Because we precalculate ligand atoms interactions
precalculate_byatom precalculated_byatom(m_scoring_function, m_model);
precalculate_byatom precalculated_byatom(*m_scoring_function, m_model);

// Check that all atom types are in the grid (if initialized)
if (m_map_initialized) {
Expand Down Expand Up @@ -142,7 +142,7 @@ void Vina::set_ligand_from_string(const std::vector<std::string>& ligand_string)
exit(EXIT_FAILURE);
}

atom_type::t atom_typing = m_scoring_function.get_atom_typing();
atom_type::t atom_typing = m_scoring_function->get_atom_typing();

if (!m_receptor_initialized) {
// This situation will happen if we don't need a receptor and we are using affinity maps
Expand All @@ -158,7 +158,7 @@ void Vina::set_ligand_from_string(const std::vector<std::string>& ligand_string)
m_model.append(parse_ligand_pdbqt_from_string(ligand_string[i], atom_typing));

// Because we precalculate ligand atoms interactions
precalculate_byatom precalculated_byatom(m_scoring_function, m_model);
precalculate_byatom precalculated_byatom(*m_scoring_function, m_model);

// Check that all atom types are in the grid (if initialized)
if (m_map_initialized) {
Expand Down Expand Up @@ -280,9 +280,8 @@ void Vina::set_ad4_weights(double weight_ad4_vdw , double weight_ad4_hb,
}

void Vina::set_forcefield() {
ScoringFunction scoring_function(m_sf_choice, m_weights);
// Store in Vina object
m_scoring_function = scoring_function;
// Store in Vina object
m_scoring_function = std::make_shared<ScoringFunction>(m_sf_choice, m_weights);
}

std::vector<double> Vina::grid_dimensions_from_ligand(double buffer_size) {
Expand Down Expand Up @@ -335,7 +334,7 @@ void Vina::compute_vina_maps(double center_x, double center_y, double center_z,
vec center(center_x, center_y, center_z);
const fl slope = 1e6; // FIXME: too large? used to be 100
szv atom_types;
atom_type::t atom_typing = m_scoring_function.get_atom_typing();
atom_type::t atom_typing = m_scoring_function->get_atom_typing();

/* Atom types initialization
If a ligand was defined before, we only use those present in the ligand
Expand All @@ -344,7 +343,7 @@ void Vina::compute_vina_maps(double center_x, double center_y, double center_z,
if (m_ligand_initialized)
atom_types = m_model.get_movable_atom_types(atom_typing);
else
atom_types = m_scoring_function.get_atom_types();
atom_types = m_scoring_function->get_atom_types();

// Grid dimensions
VINA_FOR_IN(i, gd) {
Expand All @@ -361,7 +360,7 @@ void Vina::compute_vina_maps(double center_x, double center_y, double center_z,
}

// Initialize the scoring function
precalculate precalculated_sf(m_scoring_function);
precalculate precalculated_sf(*m_scoring_function);
// Store it now in Vina object because of non_cache
m_precalculated_sf = precalculated_sf;

Expand Down Expand Up @@ -407,7 +406,7 @@ void Vina::load_maps(std::string maps) {

// Check that all the affinity map are present for ligands/flex residues (if initialized already)
if (m_ligand_initialized) {
atom_type::t atom_typing = m_scoring_function.get_atom_typing();
atom_type::t atom_typing = m_scoring_function->get_atom_typing();
szv atom_types = m_model.get_movable_atom_types(atom_typing);

if (m_sf_choice == SF_VINA || m_sf_choice == SF_VINARDO) {
Expand All @@ -430,12 +429,12 @@ void Vina::write_maps(const std::string& map_prefix, const std::string& gpf_file
}

szv atom_types;
atom_type::t atom_typing = m_scoring_function.get_atom_typing();
atom_type::t atom_typing = m_scoring_function->get_atom_typing();

if (m_ligand_initialized)
atom_types = m_model.get_movable_atom_types(atom_typing);
else
atom_types = m_scoring_function.get_atom_types();
atom_types = m_scoring_function->get_atom_types();

if (m_sf_choice == SF_VINA || m_sf_choice == SF_VINARDO) {
doing("Writing Vina maps", m_verbosity, 0);
Expand Down Expand Up @@ -721,7 +720,7 @@ std::vector<double> Vina::score(double intramolecular_energy) {
lig_intra = m_model.evali(m_precalculated_byatom, authentic_v); // [2] ligand_i -- ligand_i
intra = flex_grids + intra_pairs + lig_intra;
// Total
total = m_scoring_function.conf_independent(m_model, inter + intra - intramolecular_energy); // we pass intermolecular energy from the best pose
total = m_scoring_function->conf_independent(m_model, inter + intra - intramolecular_energy); // we pass intermolecular energy from the best pose
// Torsion, we want to know how much torsion penalty was added to the total energy
conf_independent = total - (inter + intra - intramolecular_energy);
} else {
Expand All @@ -735,7 +734,7 @@ std::vector<double> Vina::score(double intramolecular_energy) {
lig_intra = m_model.evali(m_precalculated_byatom, authentic_v); // [2] ligand_i -- ligand_i
intra = flex_grids + intra_pairs + lig_intra;
// Torsion
conf_independent = m_scoring_function.conf_independent(m_model, 0); // [3] we can pass e=0 because we do not modify the energy like in vina
conf_independent = m_scoring_function->conf_independent(m_model, 0); // [3] we can pass e=0 because we do not modify the energy like in vina
// Total
total = inter + conf_independent; // (+ intra - intra)
}
Expand Down Expand Up @@ -1033,7 +1032,6 @@ Vina::~Vina() {
// scoring function
scoring_function_choice m_sf_choice;
flv m_weights;
ScoringFunction m_scoring_function;
precalculate_byatom m_precalculated_byatom;
precalculate m_precalculated_sf;
// maps
Expand Down
3 changes: 2 additions & 1 deletion src/lib/vina.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
#include "utils.h"
#include "scoring_function.h"
#include "precalculate.h"
#include <memory>


class vina_runtime_error : public std::exception {
Expand Down Expand Up @@ -160,7 +161,7 @@ class Vina {
// scoring function
scoring_function_choice m_sf_choice;
flv m_weights;
ScoringFunction m_scoring_function;
std::shared_ptr<ScoringFunction> m_scoring_function;
precalculate_byatom m_precalculated_byatom;
precalculate m_precalculated_sf;
// maps
Expand Down

0 comments on commit d8a0d53

Please sign in to comment.