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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::pockets::DarcParticleSwarmMinimizer Class Reference

#include <DarcParticleSwarmMinimizer.hh>

Inheritance diagram for protocols::pockets::DarcParticleSwarmMinimizer:
Inheritance graph
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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

NonPlaidFingerprintnfp_
 
PlaidFingerprintpfp_
 
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
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
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
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
void protocols::pockets::DarcParticleSwarmMinimizer::score_all_particles ( core::optimization::Multifunc f_fitness,
core::optimization::ParticleOPs particles 
)
overridevirtual

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: