protocols::pockets::PlaidFingerprint Class Reference

#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

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_().

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

References core::pose::Pose::apply_transform_Rx_plus_v(), 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 dump_oriented_pose_and_fp_to_pdb(), get_oriented_pose(), and select_conf_and_move_ligand_().

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_().

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(), and core::conformation::Conformation::residue().

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_().

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(), and core::conformation::Conformation::residue().

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().

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_nconformers

(

core::pose::Pose const &

pose

)

const

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

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

inline

References compute_ligand_nconformers(), and pose_.

Referenced by compute_ligand_nconformers().

core::Size protocols::pockets::PlaidFingerprint::compute_ligand_resnum

(

core::pose::Pose const &

pose

)

const

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

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_().

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().

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().

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().

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().

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
	)

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

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().

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().

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
	)

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_().

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().

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
	)

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().

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
	)

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

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

References apply_rotation_offset_to_pose_(), calculate_ligand_CoM(), protocols::pockets::FingerprintBase::CoM(), protocols::pockets::FingerprintBase::CoM_, compute_ligand_resnum(), protocols::pockets::FingerprintBase::multi_origin_list(), protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::num_origins(), protocols::pockets::FingerprintBase::num_origins_, protocols::pockets::FingerprintBase::origin(), protocols::pockets::FingerprintBase::origin_, and pose_.

Referenced by move_ligand_and_update_rhos_(), and PlaidFingerprint().

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

private

References compute_ligand_natoms(), protocols::pockets::convert_cartesian_to_spherical_coor_triplet(), derivs_of_ray_distances_, protocols::pockets::Find_Closest_Intersect_SQ(), protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::num_origins_, protocols::pockets::spherical_coor_triplet::ori, protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, protocols::pockets::spherical_coor_triplet::rho, protocols::pockets::FingerprintBase::triplet_fingerprint_data(), and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

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

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

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_().

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

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