#include <Fingerprint.hh>

Inheritance diagram for protocols::pockets::PlaidFingerprint:

Collaboration 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::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::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

Public Member Functions inherited from protocols::pockets::FingerprintBase
	FingerprintBase ()

virtual	~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

numeric::xyzVector< core::Real >	origin () const

numeric::xyzVector< core::Real >	CoM () const

std::list < spherical_coor_triplet > const &	triplet_fingerprint_data () const

void	CHEAT_CoM (numeric::xyzVector< core::Real > const &inp_CoM)

Private Member Functions
	PlaidFingerprint ()

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, bool const update_derivatives=false)

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

core::conformation::ResidueCOP	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)

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
Protected Attributes inherited from protocols::pockets::FingerprintBase
numeric::xyzVector< core::Real >	origin_

std::list< spherical_coor_triplet >	triplet_fingerprint_data_

numeric::xyzVector< core::Real >	CoM_

Detailed Description

Definition at line 154 of file Fingerprint.hh.

Constructor & Destructor Documentation

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

Definition at line 792 of file Fingerprint.cc.

References core::pose::Pose::apply_transform_Rx_plus_v(), calculate_ligand_CoM(), protocols::pockets::FingerprintBase::CoM(), compute_ligand_resnum(), core::pose::Pose::conformation(), move_ligand_(), pose_, core::conformation::Conformation::residue(), 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

Definition at line 814 of file Fingerprint.cc.

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 move_ligand_().

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

Definition at line 1383 of file Fingerprint.cc.

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 move_ligand_(), and PlaidFingerprint().

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

Definition at line 862 of file Fingerprint.cc.

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

Definition at line 197 of file Fingerprint.hh.

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_resnum ( core::pose::Pose const & pose) const

Definition at line 847 of file Fingerprint.cc.

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

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

inline

Definition at line 195 of file Fingerprint.hh.

References compute_ligand_resnum(), and pose_.

Referenced by apply_rotation_offset_to_pose_(), calculate_ligand_CoM(), compute_ligand_natoms(), compute_ligand_resnum(), dump_oriented_pose_and_fp_to_pdb(), move_ligand_(), PlaidFingerprint(), and rmsd().

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
	)

Definition at line 1288 of file Fingerprint.cc.

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
	)

Definition at line 1303 of file Fingerprint.cc.

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
	)

Definition at line 1296 of file Fingerprint.cc.

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
	)

Definition at line 1311 of file Fingerprint.cc.

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_, 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
	)

Definition at line 1251 of file Fingerprint.cc.

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
	)

Definition at line 1256 of file Fingerprint.cc.

References fp_compare(), 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

Definition at line 1115 of file Fingerprint.cc.

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

Definition at line 1153 of file Fingerprint.cc.

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
	)

Definition at line 1350 of file Fingerprint.cc.

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
	)

Definition at line 1357 of file Fingerprint.cc.

References apply_rotation_offset_to_pose_(), core::pose::Pose::apply_transform_Rx_plus_v(), move_ligand_and_update_rhos_(), protocols::pockets::FingerprintBase::origin(), protocols::pockets::FingerprintBase::origin_, and pose_.

core::conformation::ResidueCOP protocols::pockets::PlaidFingerprint::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
	)

private

Definition at line 875 of file Fingerprint.cc.

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

Referenced by move_ligand_and_update_rhos_(), and PlaidFingerprint().

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,
		bool const	update_derivatives = `false`
	)

inlineprivate

Definition at line 207 of file Fingerprint.hh.

References move_ligand_(), and update_rhos_().

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

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

inline

Definition at line 193 of file Fingerprint.hh.

References pose_.

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

Definition at line 1399 of file Fingerprint.cc.

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
	)

Definition at line 1221 of file Fingerprint.cc.

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
	)

Definition at line 1228 of file Fingerprint.cc.

References fp_compare(), and move_ligand_and_update_rhos_().

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