#include <Fingerprint.hh>

Inheritance diagram for protocols::pockets::PlaidFingerprint:

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::Real >	calculate_ligand_CoM (core::pose::Pose const &ligand_pose)

core::pose::Pose &	pose ()

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::Real >	origin () const

utility::vector1< numeric::xyzVector< core::Real > >	multi_origin_list () const

numeric::xyzVector< core::Real >	CoM () 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_derivs >	derivs_of_ray_distances_

Friends
class	FingerprintMultifunc

class	DarcParticleSwarmMinimizer

Additional Inherited Members
Public Attributes inherited from protocols::pockets::FingerprintBase
numeric::xyzVector< core::Real >	pocketGrid_mid_

numeric::xyzVector< core::Real >	pocketGrid_dim_

core::Real	pocketGrid_spacing_

Protected Attributes inherited from protocols::pockets::FingerprintBase
core::Size	num_origins_

numeric::xyzVector< core::Real >	origin_

utility::vector1< numeric::xyzVector< core::Real > >	multi_origin_list_

numeric::xyzVector< core::Real >	CoM_

std::list< spherical_coor_triplet >	triplet_fingerprint_data_

Constructor & Destructor Documentation

◆ PlaidFingerprint() [1/2]

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

References core::pose::Pose::apply_transform_Rx_plus_v(), calculate_ligand_CoM(), protocols::pockets::FingerprintBase::CoM(), compute_ligand_resnum(), core::pose::Pose::conformation(), pose_, core::conformation::Conformation::residue(), select_conf_and_move_ligand_(), and update_rhos_().

◆ PlaidFingerprint() [2/2]

protocols::pockets::PlaidFingerprint::PlaidFingerprint ( )

private

Member Function Documentation

◆ apply_rotation_offset_to_pose_()

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

References core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::atom(), compute_ligand_natoms(), compute_ligand_resnum(), core::pose::Pose::conformation(), pose(), core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

Referenced by dump_oriented_pose_and_fp_to_pdb(), get_oriented_pose(), and select_conf_and_move_ligand_().

◆ calculate_ligand_CoM()

numeric::xyzVector< core::Real > protocols::pockets::PlaidFingerprint::calculate_ligand_CoM ( core::pose::Pose const & ligand_pose )

References core::conformation::Residue::atom(), compute_ligand_natoms(), compute_ligand_resnum(), core::pose::Pose::conformation(), core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

Referenced by get_oriented_pose(), PlaidFingerprint(), and select_conf_and_move_ligand_().

◆ compute_ligand_natoms() [1/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms ( ) const

inline

References compute_ligand_natoms(), and pose_.

Referenced by apply_rotation_offset_to_pose_(), calculate_ligand_CoM(), compute_ligand_natoms(), and update_rhos_().

◆ compute_ligand_natoms() [2/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms ( core::pose::Pose const & pose ) const

References compute_ligand_resnum(), core::pose::Pose::conformation(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), pose(), and core::conformation::Conformation::residue().

◆ compute_ligand_natoms_with_hydrogens() [1/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens ( ) const

inline

References compute_ligand_natoms_with_hydrogens(), and pose_.

Referenced by compute_ligand_natoms_with_hydrogens().

◆ compute_ligand_natoms_with_hydrogens() [2/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens ( core::pose::Pose const & pose ) const

References compute_ligand_resnum(), core::pose::Pose::conformation(), core::conformation::Residue::natoms(), pose(), and core::conformation::Conformation::residue().

◆ compute_ligand_nconformers() [1/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_nconformers ( ) const

inline

References compute_ligand_nconformers(), and pose_.

Referenced by compute_ligand_nconformers().

◆ compute_ligand_nconformers() [2/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_nconformers ( core::pose::Pose const & pose ) const

References pose(), and core::pose::Pose::size().

◆ compute_ligand_resnum() [1/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_resnum ( ) const

inline

References compute_ligand_resnum(), and pose_.

Referenced by apply_rotation_offset_to_pose_(), calculate_ligand_CoM(), compute_ligand_natoms(), compute_ligand_natoms_with_hydrogens(), compute_ligand_resnum(), dump_oriented_pose_and_fp_to_pdb(), get_oriented_pose(), PlaidFingerprint(), rmsd(), and select_conf_and_move_ligand_().

◆ compute_ligand_resnum() [2/2]

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_resnum ( core::pose::Pose const & pose ) const

References core::conformation::Residue::is_protein(), pose(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ dump_oriented_pose_and_fp_to_pdb() [1/4]

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
	)

Referenced by dump_oriented_pose_and_fp_to_pdb().

◆ dump_oriented_pose_and_fp_to_pdb() [2/4]

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
	)

References dump_oriented_pose_and_fp_to_pdb().

◆ dump_oriented_pose_and_fp_to_pdb() [3/4]

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
	)

References dump_oriented_pose_and_fp_to_pdb().

◆ dump_oriented_pose_and_fp_to_pdb() [4/4]

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
	)

References apply_rotation_offset_to_pose_(), core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::atom(), protocols::pockets::FingerprintBase::CoM_, compute_ligand_resnum(), core::pose::Pose::conformation(), move_ligand_and_update_rhos_(), core::conformation::Residue::natoms(), protocols::pockets::FingerprintBase::origin(), protocols::pockets::FingerprintBase::origin_, core::conformation::membrane::out, pose_, protocols::pockets::FingerprintBase::print_to_pdb(), core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

◆ find_optimal_rotation() [1/2]

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
	)

◆ find_optimal_rotation() [2/2]

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
	)

References fp_compare(), protocols::mean_field::max(), and move_ligand_and_update_rhos_().

◆ fp_compare()

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

References core::scoring::electron_density::square(), protocols::pockets::FingerprintBase::triplet_fingerprint_data(), and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

Referenced by find_optimal_rotation(), protocols::pockets::FingerprintMultifunc::operator()(), and search_random_poses().

◆ fp_compare_deriv()

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

References derivs_of_ray_distances_, protocols::pockets::FingerprintBase::triplet_fingerprint_data(), and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

Referenced by protocols::pockets::FingerprintMultifunc::dfunc().

◆ get_oriented_pose() [1/2]

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
	)

◆ get_oriented_pose() [2/2]

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
	)

References apply_rotation_offset_to_pose_(), core::pose::Pose::apply_transform_Rx_plus_v(), calculate_ligand_CoM(), protocols::pockets::FingerprintBase::CoM(), protocols::pockets::FingerprintBase::CoM_, compute_ligand_resnum(), protocols::pockets::FingerprintBase::origin(), protocols::pockets::FingerprintBase::origin_, pose_, and update_rhos_().

◆ move_ligand_and_update_rhos_()

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

References select_conf_and_move_ligand_(), and update_rhos_().

Referenced by protocols::pockets::FingerprintMultifunc::dfunc(), dump_oriented_pose_and_fp_to_pdb(), find_optimal_rotation(), protocols::pockets::FingerprintMultifunc::operator()(), and search_random_poses().

◆ pose()

core::pose::Pose& protocols::pockets::PlaidFingerprint::pose ( )

inline

References pose_.

Referenced by apply_rotation_offset_to_pose_(), compute_ligand_natoms(), compute_ligand_natoms_with_hydrogens(), compute_ligand_nconformers(), and compute_ligand_resnum().

◆ rmsd()

core::Real protocols::pockets::PlaidFingerprint::rmsd	(	core::pose::Pose const &	original_pose,
		core::pose::Pose const &	oriented_pose
	)

References core::conformation::Residue::atom(), compute_ligand_resnum(), core::pose::Pose::conformation(), core::conformation::Residue::nheavyatoms(), core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

◆ search_random_poses() [1/2]

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
	)

◆ search_random_poses() [2/2]

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
	)

References fp_compare(), protocols::mean_field::max(), and move_ligand_and_update_rhos_().

◆ select_conf_and_move_ligand_()

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

Referenced by move_ligand_and_update_rhos_(), and PlaidFingerprint().

◆ update_rhos_()

void protocols::pockets::PlaidFingerprint::update_rhos_	(	FingerprintBase &	fp,
		core::conformation::ResidueCOP	curr_ligand_rsd,
		bool const	update_derivatives = `false`
	)

private

Referenced by get_oriented_pose(), move_ligand_and_update_rhos_(), and PlaidFingerprint().

Friends And Related Function Documentation

◆ DarcParticleSwarmMinimizer

friend class DarcParticleSwarmMinimizer

friend

◆ FingerprintMultifunc

friend class FingerprintMultifunc

friend

Member Data Documentation

◆ derivs_of_ray_distances_

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

private

Referenced by fp_compare_deriv(), and update_rhos_().

◆ pose_

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

private

Referenced by compute_ligand_natoms(), compute_ligand_natoms_with_hydrogens(), compute_ligand_nconformers(), compute_ligand_resnum(), dump_oriented_pose_and_fp_to_pdb(), get_oriented_pose(), PlaidFingerprint(), pose(), and select_conf_and_move_ligand_().

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

src/protocols/pockets/Fingerprint.hh
src/protocols/pockets/Fingerprint.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ PlaidFingerprint() [1/2]

◆ PlaidFingerprint() [2/2]

Member Function Documentation

◆ apply_rotation_offset_to_pose_()

◆ calculate_ligand_CoM()

◆ compute_ligand_natoms() [1/2]

◆ compute_ligand_natoms() [2/2]

◆ compute_ligand_natoms_with_hydrogens() [1/2]

◆ compute_ligand_natoms_with_hydrogens() [2/2]

◆ compute_ligand_nconformers() [1/2]

◆ compute_ligand_nconformers() [2/2]

◆ compute_ligand_resnum() [1/2]

◆ compute_ligand_resnum() [2/2]

◆ dump_oriented_pose_and_fp_to_pdb() [1/4]

◆ dump_oriented_pose_and_fp_to_pdb() [2/4]

◆ dump_oriented_pose_and_fp_to_pdb() [3/4]

◆ dump_oriented_pose_and_fp_to_pdb() [4/4]

◆ find_optimal_rotation() [1/2]

◆ find_optimal_rotation() [2/2]

◆ fp_compare()

◆ fp_compare_deriv()

◆ get_oriented_pose() [1/2]

◆ get_oriented_pose() [2/2]

◆ move_ligand_and_update_rhos_()

◆ pose()

◆ rmsd()

◆ search_random_poses() [1/2]

◆ search_random_poses() [2/2]

◆ select_conf_and_move_ligand_()

◆ update_rhos_()

Friends And Related Function Documentation

◆ DarcParticleSwarmMinimizer

◆ FingerprintMultifunc

Member Data Documentation

◆ derivs_of_ray_distances_

◆ pose_