#include <DarcParticleSwarmMinimizer.hh>

Inheritance diagram for protocols::pockets::DarcParticleSwarmMinimizer:

Public Member Functions
	DarcParticleSwarmMinimizer (NonPlaidFingerprint &nfp_in, PlaidFingerprint &pfp_in, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight, core::optimization::Multivec p_min, core::optimization::Multivec p_max)

	~DarcParticleSwarmMinimizer () override=default

void	score_all_particles (core::optimization::Multifunc &f_fitness, core::optimization::ParticleOPs &particles) override

Public Member Functions inherited from core::optimization::ParticleSwarmMinimizer
	ParticleSwarmMinimizer (Multivec const &p_min, Multivec const &p_max)

	~ParticleSwarmMinimizer () override

ParticleOPs	run (Size num_cycles, Multifunc &f_fitness, Size num_part=50)

ParticleOPs	run (Size num_cycles, Multifunc &f_fitness, Size num_part, Multivec init_values)

void	run (Size num_cycles, Multifunc &f_fitness, ParticleOPs &particles)

void	print_particles (ParticleOPs &particles, std::string header)
	helper function for displaying current particle information; calls the output operator on each particle More...

Private Member Functions
void	fill_atom_arrays_ (core::Size particle_inx, core::conformation::ResidueCOP ligand_rsd, utility::vector1< std::vector< basic::gpu::float4 > > &atoms, utility::vector1< std::vector< basic::gpu::float4 > > &atom_maxmin_phipsi)

core::Real	DarcPSO_fp_compare_ (core::Size particle_inx, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight, utility::vector1< std::vector< basic::gpu::float4 > > &atoms, utility::vector1< std::vector< basic::gpu::float4 > > &atom_maxmin_phipsi)

void	fill_atom_arrays_for_electrostatics_ (core::Size particle_inx, core::pose::Pose ligand_pose_for_elec_calc, std::vector< basic::gpu::float4 > &atoms_coors_and_charge)

core::Real	DarcPSO_elsts_score_ (core::Size particle_inx, core::Size dim_x, core::Size dim_y, core::Size dim_z, core::Real mid_x, core::Real mid_y, core::Real mid_z, core::Real spacing, std::vector< std::vector< std::vector< core::Real > > > espGrid, std::vector< std::vector< std::vector< ElectrostaticpotentialGrid::PtType > > > typGrid, std::vector< basic::gpu::float4 > &atom_coors_charge)

Private Attributes
NonPlaidFingerprint &	nfp_

PlaidFingerprint &	pfp_

core::Real	missing_pt_

core::Real	steric_

core::Real	extra_pt_

core::Size	ligand_natoms_elstscalc_

core::Size	ligand_natoms_shapecalc_

Additional Inherited Members

Constructor & Destructor Documentation

protocols::pockets::DarcParticleSwarmMinimizer::DarcParticleSwarmMinimizer	(	NonPlaidFingerprint &	nfp_in,
		PlaidFingerprint &	pfp_in,
		core::Real const &	missing_point_weight,
		core::Real const &	steric_weight,
		core::Real const &	extra_point_weight,
		core::optimization::Multivec	p_min,
		core::optimization::Multivec	p_max
	)

inline

protocols::pockets::DarcParticleSwarmMinimizer::~DarcParticleSwarmMinimizer ( )

overridedefault

Member Function Documentation

core::Real protocols::pockets::DarcParticleSwarmMinimizer::DarcPSO_elsts_score_	(	core::Size	particle_inx,
		core::Size	dim_x,
		core::Size	dim_y,
		core::Size	dim_z,
		core::Real	mid_x,
		core::Real	mid_y,
		core::Real	mid_z,
		core::Real	spacing,
		std::vector< std::vector< std::vector< core::Real > > >	espGrid,
		std::vector< std::vector< std::vector< ElectrostaticpotentialGrid::PtType > > >	typGrid,
		std::vector< basic::gpu::float4 > &	atom_coors_charge
	)

private

References core::chemical::element::C, protocols::pockets::ElectrostaticpotentialGrid::PROTEIN, protocols::comparative_modeling::features::X, and core::chemical::element::Y.

core::Real protocols::pockets::DarcParticleSwarmMinimizer::DarcPSO_fp_compare_	(	core::Size	particle_inx,
		core::Real const &	missing_point_weight,
		core::Real const &	steric_weight,
		core::Real const &	extra_point_weight,
		utility::vector1< std::vector< basic::gpu::float4 > > &	atoms,
		utility::vector1< std::vector< basic::gpu::float4 > > &	atom_maxmin_phipsi
	)

private

References protocols::pockets::Find_Closest_Intersect_SQ().

void protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_	(	core::Size	particle_inx,
		core::conformation::ResidueCOP	ligand_rsd,
		utility::vector1< std::vector< basic::gpu::float4 > > &	atoms,
		utility::vector1< std::vector< basic::gpu::float4 > > &	atom_maxmin_phipsi
	)

private

References protocols::pockets::convert_cartesian_to_spherical_coor_triplet(), protocols::pockets::spherical_coor_triplet::phi, and protocols::pockets::spherical_coor_triplet::psi.

void protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_	(	core::Size	particle_inx,
		core::pose::Pose	ligand_pose_for_elec_calc,
		std::vector< basic::gpu::float4 > &	atoms_coors_and_charge
	)

private

References core::conformation::Residue::atom(), core::conformation::Residue::atomic_charge(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

void protocols::pockets::DarcParticleSwarmMinimizer::score_all_particles	(	core::optimization::Multifunc &	f_fitness,
		core::optimization::ParticleOPs &	particles
	)

overridevirtual

Reimplemented from core::optimization::ParticleSwarmMinimizer.

References core::chemical::element::N.

Member Data Documentation

core::Real protocols::pockets::DarcParticleSwarmMinimizer::extra_pt_

private

core::Size protocols::pockets::DarcParticleSwarmMinimizer::ligand_natoms_elstscalc_

private

core::Size protocols::pockets::DarcParticleSwarmMinimizer::ligand_natoms_shapecalc_

private

core::Real protocols::pockets::DarcParticleSwarmMinimizer::missing_pt_

private

NonPlaidFingerprint& protocols::pockets::DarcParticleSwarmMinimizer::nfp_

private

PlaidFingerprint& protocols::pockets::DarcParticleSwarmMinimizer::pfp_

private

core::Real protocols::pockets::DarcParticleSwarmMinimizer::steric_

private

The documentation for this class was generated from the following files:

src/protocols/pockets/DarcParticleSwarmMinimizer.hh
src/protocols/pockets/DarcParticleSwarmMinimizer.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation