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protocols::pockets::PlaidFingerprint Class Reference

#include <Fingerprint.hh>

Inheritance diagram for protocols::pockets::PlaidFingerprint:
Inheritance graph
[legend]

Public Member Functions

 PlaidFingerprint (core::pose::Pose const &input_pose, FingerprintBase &fp)
 
core::Real find_optimal_rotation (FingerprintBase &fp, core::Real const &angle_increment, core::Real &optimal_angle1, core::Real &optimal_angle2, core::Real &optimal_angle3, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight)
 
core::Real find_optimal_rotation (FingerprintBase &fp, core::Real const &angle_increment, core::Real &optimal_angle1, core::Real &optimal_angle2, core::Real &optimal_angle3, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight, numeric::xyzVector< core::Real > const &no_CoM_offset)
 
core::Real search_random_poses (FingerprintBase &fp, core::Size const &num_pose_search, core::Real &optimal_angle1, core::Real &optimal_angle2, core::Real &optimal_angle3, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight)
 
core::Real search_random_poses (FingerprintBase &fp, core::Size const &num_pose_search, core::Real &optimal_angle1, core::Real &optimal_angle2, core::Real &optimal_angle3, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight, numeric::xyzVector< core::Real > const &no_CoM_offset)
 
core::Real fp_compare (FingerprintBase &fp, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight) const
 
void fp_compare_deriv (FingerprintBase &fp, core::Real const &missing_point_weight, core::Real const &steric_weight, core::Real const &extra_point_weight, core::Real &dE_dx, core::Real &dE_dy, core::Real &dE_dz, core::Real &dE_dv4, core::Real &dE_dv5, core::Real &dE_dv6) const
 
void dump_oriented_pose_and_fp_to_pdb (std::string const &pose_filename, std::string const &fp_filename, FingerprintBase &fp, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset)
 
void dump_oriented_pose_and_fp_to_pdb (std::string const &pose_filename, std::string const &fp_filename, FingerprintBase &fp, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset, utility::vector1< core::Real > const &original_pocket_angle_transform)
 
void dump_oriented_pose_and_fp_to_pdb (std::string const &pose_filename, std::string const &fp_filename, FingerprintBase &fp, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset, numeric::xyzVector< core::Real > const &CoM_offset)
 
void dump_oriented_pose_and_fp_to_pdb (std::string const &pose_filename, std::string const &fp_filename, FingerprintBase &fp, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset, utility::vector1< core::Real > const &original_pocket_angle_transform, numeric::xyzVector< core::Real > const &CoM_offset)
 
core::pose::Pose get_oriented_pose (FingerprintBase &fp, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset, numeric::xyzVector< core::Real > const &CoM_offset, core::Size const conformer)
 
core::pose::Pose get_oriented_pose (FingerprintBase &fp, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset, utility::vector1< core::Real > const &original_pocket_angle_transform, numeric::xyzVector< core::Real > const &CoM_offset, core::Size const conformer)
 
core::Real rmsd (core::pose::Pose const &original_pose, core::pose::Pose const &oriented_pose)
 
numeric::xyzVector< core::Realcalculate_ligand_CoM (core::pose::Pose const &ligand_pose)
 
core::pose::Posepose ()
 
core::Size compute_ligand_resnum (core::pose::Pose const &pose) const
 
core::Size compute_ligand_resnum () const
 
core::Size compute_ligand_natoms (core::pose::Pose const &pose) const
 
core::Size compute_ligand_natoms () const
 
core::Size compute_ligand_natoms_with_hydrogens (core::pose::Pose const &pose) const
 
core::Size compute_ligand_natoms_with_hydrogens () const
 
core::Size compute_ligand_nconformers (core::pose::Pose const &pose) const
 
core::Size compute_ligand_nconformers () const
 
void move_ligand_and_update_rhos_ (FingerprintBase &fp, numeric::xyzVector< core::Real > const &CoM_offset, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset, core::Size const &conformer, bool const update_derivatives=false)
 
- Public Member Functions inherited from protocols::pockets::FingerprintBase
 FingerprintBase ()
 
void print_to_file (std::string const &output_filename) const
 
void print_to_pdb (std::string const &output_pdbname) const
 
void print_to_pdb (std::string const &output_pdbname, numeric::xyzVector< core::Real > const &translation) const
 
core::Size num_origins () const
 
numeric::xyzVector< core::Realorigin () const
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
multi_origin_list () const
 
numeric::xyzVector< core::RealCoM () const
 
void CHEAT_CoM (numeric::xyzVector< core::Real > const &inp_CoM)
 
std::list
< spherical_coor_triplet >
const & 
triplet_fingerprint_data () const
 
 ~FingerprintBase () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 

Private Member Functions

 PlaidFingerprint ()
 
void update_rhos_ (FingerprintBase &fp, core::conformation::ResidueCOP curr_ligand_rsd, bool const update_derivatives=false)
 
core::conformation::ResidueCOP select_conf_and_move_ligand_ (FingerprintBase &fp, numeric::xyzVector< core::Real > const &CoM_offset, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset, core::Size const &conformer)
 
void apply_rotation_offset_to_pose_ (core::pose::Pose &pose, core::Real const &angle1_offset, core::Real const &angle2_offset, core::Real const &angle3_offset) const
 

Private Attributes

core::pose::Pose pose_
 
std::list< ray_distance_derivsderivs_of_ray_distances_
 

Friends

class FingerprintMultifunc
 
class DarcParticleSwarmMinimizer
 

Additional Inherited Members

- Public Attributes inherited from protocols::pockets::FingerprintBase
numeric::xyzVector< core::RealpocketGrid_mid_
 
numeric::xyzVector< core::RealpocketGrid_dim_
 
core::Real pocketGrid_spacing_
 
- Protected Attributes inherited from protocols::pockets::FingerprintBase
core::Size num_origins_
 
numeric::xyzVector< core::Realorigin_
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
multi_origin_list_
 
numeric::xyzVector< core::RealCoM_
 
std::list< spherical_coor_triplettriplet_fingerprint_data_
 

Constructor & Destructor Documentation

protocols::pockets::PlaidFingerprint::PlaidFingerprint ( core::pose::Pose const &  input_pose,
FingerprintBase fp 
)
protocols::pockets::PlaidFingerprint::PlaidFingerprint ( )
private

Member Function Documentation

void protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_ ( core::pose::Pose pose,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset 
) const
private
numeric::xyzVector< core::Real > protocols::pockets::PlaidFingerprint::calculate_ligand_CoM ( core::pose::Pose const &  ligand_pose)
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms ( core::pose::Pose const &  pose) const
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms ( ) const
inline
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens ( core::pose::Pose const &  pose) const
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens ( ) const
inline
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_nconformers ( core::pose::Pose const &  pose) const
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_nconformers ( ) const
inline
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_resnum ( core::pose::Pose const &  pose) const
core::Size protocols::pockets::PlaidFingerprint::compute_ligand_resnum ( ) const
inline
void protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb ( std::string const &  pose_filename,
std::string const &  fp_filename,
FingerprintBase fp,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset 
)
void protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb ( std::string const &  pose_filename,
std::string const &  fp_filename,
FingerprintBase fp,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset,
utility::vector1< core::Real > const &  original_pocket_angle_transform 
)
void protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb ( std::string const &  pose_filename,
std::string const &  fp_filename,
FingerprintBase fp,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset,
numeric::xyzVector< core::Real > const &  CoM_offset 
)
void protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb ( std::string const &  pose_filename,
std::string const &  fp_filename,
FingerprintBase fp,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset,
utility::vector1< core::Real > const &  original_pocket_angle_transform,
numeric::xyzVector< core::Real > const &  CoM_offset 
)
core::Real protocols::pockets::PlaidFingerprint::find_optimal_rotation ( FingerprintBase fp,
core::Real const &  angle_increment,
core::Real optimal_angle1,
core::Real optimal_angle2,
core::Real optimal_angle3,
core::Real const &  missing_point_weight,
core::Real const &  steric_weight,
core::Real const &  extra_point_weight 
)
core::Real protocols::pockets::PlaidFingerprint::find_optimal_rotation ( FingerprintBase fp,
core::Real const &  angle_increment,
core::Real optimal_angle1,
core::Real optimal_angle2,
core::Real optimal_angle3,
core::Real const &  missing_point_weight,
core::Real const &  steric_weight,
core::Real const &  extra_point_weight,
numeric::xyzVector< core::Real > const &  no_CoM_offset 
)
core::Real protocols::pockets::PlaidFingerprint::fp_compare ( FingerprintBase fp,
core::Real const &  missing_point_weight,
core::Real const &  steric_weight,
core::Real const &  extra_point_weight 
) const
void protocols::pockets::PlaidFingerprint::fp_compare_deriv ( FingerprintBase fp,
core::Real const &  missing_point_weight,
core::Real const &  steric_weight,
core::Real const &  extra_point_weight,
core::Real dE_dx,
core::Real dE_dy,
core::Real dE_dz,
core::Real dE_dv4,
core::Real dE_dv5,
core::Real dE_dv6 
) const
core::pose::Pose protocols::pockets::PlaidFingerprint::get_oriented_pose ( FingerprintBase fp,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset,
numeric::xyzVector< core::Real > const &  CoM_offset,
core::Size const  conformer 
)
core::pose::Pose protocols::pockets::PlaidFingerprint::get_oriented_pose ( FingerprintBase fp,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset,
utility::vector1< core::Real > const &  original_pocket_angle_transform,
numeric::xyzVector< core::Real > const &  CoM_offset,
core::Size const  conformer 
)
void protocols::pockets::PlaidFingerprint::move_ligand_and_update_rhos_ ( FingerprintBase fp,
numeric::xyzVector< core::Real > const &  CoM_offset,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset,
core::Size const &  conformer,
bool const  update_derivatives = false 
)
inline
core::pose::Pose& protocols::pockets::PlaidFingerprint::pose ( )
inline

References pose_.

core::Real protocols::pockets::PlaidFingerprint::rmsd ( core::pose::Pose const &  original_pose,
core::pose::Pose const &  oriented_pose 
)
core::Real protocols::pockets::PlaidFingerprint::search_random_poses ( FingerprintBase fp,
core::Size const &  num_pose_search,
core::Real optimal_angle1,
core::Real optimal_angle2,
core::Real optimal_angle3,
core::Real const &  missing_point_weight,
core::Real const &  steric_weight,
core::Real const &  extra_point_weight 
)
core::Real protocols::pockets::PlaidFingerprint::search_random_poses ( FingerprintBase fp,
core::Size const &  num_pose_search,
core::Real optimal_angle1,
core::Real optimal_angle2,
core::Real optimal_angle3,
core::Real const &  missing_point_weight,
core::Real const &  steric_weight,
core::Real const &  extra_point_weight,
numeric::xyzVector< core::Real > const &  no_CoM_offset 
)
core::conformation::ResidueCOP protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_ ( FingerprintBase fp,
numeric::xyzVector< core::Real > const &  CoM_offset,
core::Real const &  angle1_offset,
core::Real const &  angle2_offset,
core::Real const &  angle3_offset,
core::Size const &  conformer 
)
private
void protocols::pockets::PlaidFingerprint::update_rhos_ ( FingerprintBase fp,
core::conformation::ResidueCOP  curr_ligand_rsd,
bool const  update_derivatives = false 
)
private

Friends And Related Function Documentation

friend class DarcParticleSwarmMinimizer
friend
friend class FingerprintMultifunc
friend

Member Data Documentation

std::list< ray_distance_derivs > protocols::pockets::PlaidFingerprint::derivs_of_ray_distances_
private

Referenced by fp_compare_deriv(), and update_rhos_().

core::pose::Pose protocols::pockets::PlaidFingerprint::pose_
private

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