#include <PCSLigandTransformMover.hh>

Inheritance diagram for protocols::nmr::pcs::PCSLigandTransformMover:

[legend]

Classes
class	LMMinPCSDataRef
	Utility class of PCSLigandTransformMover which holds references to PCSData used in lmmin (Levenberg Marquardt minimization) function. More...

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

typedef core::scoring::nmr::Matrix	Matrix

typedef core::scoring::nmr::pcs::PCSData	PCSData

typedef core::scoring::nmr::pcs::PCSDataOP	PCSDataOP

typedef core::scoring::nmr::pcs::PCSDataCOP	PCSDataCOP

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::conformation::Residue	Residue

typedef numeric::geometry::BoundingBox< core::Vector >	BoundingBox

typedef core::scoring::nmr::Vec5	Vec5

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Public Member Functions
	PCSLigandTransformMover ()
	Default constructor. More...

	PCSLigandTransformMover (PCSDataCOP data, ScoreFunctionCOP sfxn)

	PCSLigandTransformMover (PCSLigandTransformMover const &other)
	Copy constructor. More...

PCSLigandTransformMover &	operator= (PCSLigandTransformMover const &rhs)
	Assignment operator. More...

	~PCSLigandTransformMover () override
	Destructor. More...

std::string	get_name () const override
	Get the name of this mover. More...

void	apply (Pose &pose) override
	Perform grid search of ligand position by minimizing the PCS score. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
	Parse tags of XML script. More...

PCSData const &	get_pcs_data () const

ScoreFunctionCOP	get_scorefunction ()

BoundingBox const &	get_gridsearch_range () const

Real	get_trans_step () const

Real	get_rot_step () const

Real	get_resolution_damping () const

bool	optimized_transform () const

char	get_chain () const

void	set_scorefunction (ScoreFunctionOP sfxn)

void	set_gridsearch_range (BoundingBox const &box)

void	set_gridsearch_range (Vector const &lower, Vector const &upper)

void	set_trans_step (Real step)

void	set_rot_step (Real step)

void	set_resolution_damping (Real damping)

void	do_optimized_transform ()

void	undo_optimized_transform ()

void	set_chain (char const c)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Create XML schema definition for PREMover. More...

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
void	reset_grid_and_bounding_box (Pose const &pose, core::Size const &ligand_resid)
	Build grid around protein and fill it with non-ligand atoms Update the bounding box of the xyz grid search to span the range: [ min_xyz atom_grid - nbr_radius, max_xyz atom_grid + nbr_radius ]. More...

Vector	define_ligand_frame_origin (Residue const &ligand)
	The local frame of the ligand is located in the ligand's center of mass and has unit basis. More...

bool	next_ligand_position (Vector &xyz)
	Traverse ligand center to next xyz point (in Angstrom) More...

bool	next_ligand_orientation (Vector &abc)
	Change ligand orientation to new alpha, beta, gamma angles (in degree) More...

Vector	local_rotation (Matrix const &R, Vector const &ori, Vector const &v)
	Perform rotation of vector v by matrix R in local frame centered at point ori and with unit basis. More...

std::map< core::Size, Vector >	build_ligand_atom_xyz_table (Residue const &ligand)
	Build map of atom index and xyz coordinates for ligand residue. More...

void	find_best_ligand_pose_with_grid_search (core::Size const &resid, Residue const &ligand, Vector &position, Vector &orientation)
	Find the best position and orientation for this residue according to the PCS data using a grid search. More...

void	optimize_ligand_pose_with_nls (Residue const &ligand, Vector &position, Vector &orientation)
	Optimize the ligand position and orientation by NLS. More...

void	move_ligand_close_to_surface (Pose &pose, core::Size const &ligand_resid)
	Move ligand residue closer to protein surface. To this end, the ligand is simply moved along the jump with the protein in 0.1 Ang steps until an increase in the fa_rep score is monitored. More...

Real	damped_resolution (Real rmax, Real rmin)
	Calculate the damped resolution in the range [rmax, rmin] using the damping parameter. More...

Private Attributes
PCSDataCOP	pcs_data_
	experimental PCS data for all lanthanides and tagging sites More...

std::string	pcs_data_file_
	The file from which to read the PCS data at apply time. More...

ScoreFunctionCOP	sfxn_
	a scorefunction to monitor if ligand touches the protein More...

AtomGrid	grid_
	voxelgrid that spans around the protein and which is used for clash check More...

BoundingBox	gs_box_
	Bounding box of the ligand xyz position grid search. More...

Real	trans_step_
	translational stepsize (in Ang.) of grid search More...

Real	rot_step_
	rotational stepsize (in degree) of grid search More...

Real	rsol_damping_
	smoothening parameter that can be used to damp the resolution of the atom clash check with the voxel grid. Takes values between 0.0 and 1.0 More...

bool	optimize_transform_
	do further optimization of position and orientation as by grid search More...

char	chain_
	ligand chain More...

Friends
void	pcs_lmmin (Real const par, int, void const data, Real fvec, int )
	pcs error function used in the lmmin function More...

Additional Inherited Members
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Member Typedef Documentation

◆ BoundingBox

typedef numeric::geometry::BoundingBox< core::Vector > protocols::nmr::pcs::PCSLigandTransformMover::BoundingBox

◆ Matrix

typedef core::scoring::nmr::Matrix protocols::nmr::pcs::PCSLigandTransformMover::Matrix

◆ PCSData

typedef core::scoring::nmr::pcs::PCSData protocols::nmr::pcs::PCSLigandTransformMover::PCSData

◆ PCSDataCOP

typedef core::scoring::nmr::pcs::PCSDataCOP protocols::nmr::pcs::PCSLigandTransformMover::PCSDataCOP

◆ PCSDataOP

typedef core::scoring::nmr::pcs::PCSDataOP protocols::nmr::pcs::PCSLigandTransformMover::PCSDataOP

◆ Pose

typedef core::pose::Pose protocols::nmr::pcs::PCSLigandTransformMover::Pose

◆ Real

typedef core::Real protocols::nmr::pcs::PCSLigandTransformMover::Real

◆ Residue

typedef core::conformation::Residue protocols::nmr::pcs::PCSLigandTransformMover::Residue

◆ ScoreFunctionCOP

typedef core::scoring::ScoreFunctionCOP protocols::nmr::pcs::PCSLigandTransformMover::ScoreFunctionCOP

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::nmr::pcs::PCSLigandTransformMover::ScoreFunctionOP

◆ Size

typedef core::Size protocols::nmr::pcs::PCSLigandTransformMover::Size

◆ Vec5

typedef core::scoring::nmr::Vec5 protocols::nmr::pcs::PCSLigandTransformMover::Vec5

◆ Vector

typedef core::Vector protocols::nmr::pcs::PCSLigandTransformMover::Vector

Constructor & Destructor Documentation

◆ PCSLigandTransformMover() [1/3]

protocols::nmr::pcs::PCSLigandTransformMover::PCSLigandTransformMover ( )

Default constructor.

Referenced by clone().

◆ PCSLigandTransformMover() [2/3]

protocols::nmr::pcs::PCSLigandTransformMover::PCSLigandTransformMover	(	PCSDataCOP	data,
		ScoreFunctionCOP	sfxn
	)

◆ PCSLigandTransformMover() [3/3]

protocols::nmr::pcs::PCSLigandTransformMover::PCSLigandTransformMover ( PCSLigandTransformMover const & other )

default

Copy constructor.

◆ ~PCSLigandTransformMover()

protocols::nmr::pcs::PCSLigandTransformMover::~PCSLigandTransformMover ( )

override

Destructor.

Member Function Documentation

◆ apply()

void protocols::nmr::pcs::PCSLigandTransformMover::apply ( Pose & pose )

overridevirtual

Perform grid search of ligand position by minimizing the PCS score.

Implements protocols::moves::Mover.

References chain_, define_ligand_frame_origin(), find_best_ligand_pose_with_grid_search(), core::pose::get_resnums_for_chain(), local_rotation(), move_ligand_close_to_surface(), core::conformation::Residue::natoms(), optimize_ligand_pose_with_nls(), optimize_transform_, pcs_data_, pcs_data_file_, reset_grid_and_bounding_box(), core::pose::Pose::residue(), rot_step_, core::pose::Pose::set_xyz(), protocols::nmr::pcs::TR(), trans_step_, and core::conformation::Residue::xyz().

◆ build_ligand_atom_xyz_table()

std::map< core::Size, core::Vector > protocols::nmr::pcs::PCSLigandTransformMover::build_ligand_atom_xyz_table ( Residue const & ligand )

private

Build map of atom index and xyz coordinates for ligand residue.

References protocols::sewing::data_storage::ligand.

Referenced by optimize_ligand_pose_with_nls().

◆ clone()

protocols::moves::MoverOP protocols::nmr::pcs::PCSLigandTransformMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

Reimplemented from protocols::moves::Mover.

References PCSLigandTransformMover().

◆ damped_resolution()

core::Real protocols::nmr::pcs::PCSLigandTransformMover::damped_resolution	(	Real	rmax,
		Real	rmin
	)

private

Calculate the damped resolution in the range [rmax, rmin] using the damping parameter.

References rsol_damping_.

Referenced by find_best_ligand_pose_with_grid_search(), and reset_grid_and_bounding_box().

◆ define_ligand_frame_origin()

core::Vector protocols::nmr::pcs::PCSLigandTransformMover::define_ligand_frame_origin ( Residue const & ligand )

private

The local frame of the ligand is located in the ligand's center of mass and has unit basis.

References core::pose::center_of_mass(), and protocols::sewing::data_storage::ligand.

Referenced by apply(), and find_best_ligand_pose_with_grid_search().

◆ do_optimized_transform()

void protocols::nmr::pcs::PCSLigandTransformMover::do_optimized_transform ( )

inline

References optimize_transform_.

◆ find_best_ligand_pose_with_grid_search()

void protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search	(	core::Size const &	resid,
		Residue const &	ligand,
		Vector &	position,
		Vector &	orientation
	)

private

Find the best position and orientation for this residue according to the PCS data using a grid search.

References damped_resolution(), define_ligand_frame_origin(), grid_, gs_box_, protocols::sewing::data_storage::ligand, local_rotation(), protocols::mean_field::max(), next_ligand_orientation(), next_ligand_position(), pcs_data_, core::scoring::nmr::pcs_func(), core::scoring::nmr::rotation_matrix_from_euler_angles(), protocols::nmr::pcs::AtomGridPoint::set_coordinates(), and protocols::nmr::pcs::TR().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::nmr::pcs::PCSLigandTransformMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

Reimplemented from protocols::moves::Mover.

◆ get_chain()

char protocols::nmr::pcs::PCSLigandTransformMover::get_chain ( ) const

inline

References chain_.

◆ get_gridsearch_range()

BoundingBox const& protocols::nmr::pcs::PCSLigandTransformMover::get_gridsearch_range ( ) const

inline

References gs_box_.

◆ get_name()

std::string protocols::nmr::pcs::PCSLigandTransformMover::get_name ( ) const

overridevirtual

Get the name of this mover.

Implements protocols::moves::Mover.

References mover_name().

◆ get_pcs_data()

PCSData const& protocols::nmr::pcs::PCSLigandTransformMover::get_pcs_data ( ) const

inline

References pcs_data_.

◆ get_resolution_damping()

Real protocols::nmr::pcs::PCSLigandTransformMover::get_resolution_damping ( ) const

inline

References rsol_damping_.

◆ get_rot_step()

Real protocols::nmr::pcs::PCSLigandTransformMover::get_rot_step ( ) const

inline

References rot_step_.

◆ get_scorefunction()

ScoreFunctionCOP protocols::nmr::pcs::PCSLigandTransformMover::get_scorefunction ( )

inline

References sfxn_.

◆ get_trans_step()

Real protocols::nmr::pcs::PCSLigandTransformMover::get_trans_step ( ) const

inline

References trans_step_.

◆ local_rotation()

core::Vector protocols::nmr::pcs::PCSLigandTransformMover::local_rotation	(	Matrix const &	R,
		Vector const &	ori,
		Vector const &	v
	)

private

Perform rotation of vector v by matrix R in local frame centered at point ori and with unit basis.

Referenced by apply(), and find_best_ligand_pose_with_grid_search().

◆ move_ligand_close_to_surface()

void protocols::nmr::pcs::PCSLigandTransformMover::move_ligand_close_to_surface	(	Pose &	pose,
		core::Size const &	ligand_resid
	)

private

Move ligand residue closer to protein surface. To this end, the ligand is simply moved along the jump with the protein in 0.1 Ang steps until an increase in the fa_rep score is monitored.

References protocols::rigid::RigidBodyTransMover::apply(), core::pose::Pose::energies(), core::scoring::fa_rep, core::pose::Pose::fold_tree(), core::kinematics::get_foldtree_which_partitions(), core::kinematics::jump_which_partitions(), protocols::rigid::RigidBodyTransMover::step_size(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), protocols::nmr::pcs::TR(), and protocols::rigid::RigidBodyTransMover::trans_axis().

Referenced by apply().

◆ mover_name()

std::string protocols::nmr::pcs::PCSLigandTransformMover::mover_name ( )

static

Referenced by get_name(), protocols::nmr::pcs::PCSLigandTransformMoverCreator::keyname(), and provide_xml_schema().

◆ next_ligand_orientation()

bool protocols::nmr::pcs::PCSLigandTransformMover::next_ligand_orientation ( Vector & abc )

private

Change ligand orientation to new alpha, beta, gamma angles (in degree)

References rot_step_.

Referenced by find_best_ligand_pose_with_grid_search().

◆ next_ligand_position()

bool protocols::nmr::pcs::PCSLigandTransformMover::next_ligand_position ( Vector & xyz )

private

Traverse ligand center to next xyz point (in Angstrom)

References gs_box_, trans_step_, and protocols::kinmatch::xyz().

Referenced by find_best_ligand_pose_with_grid_search().

◆ operator=()

PCSLigandTransformMover & protocols::nmr::pcs::PCSLigandTransformMover::operator= ( PCSLigandTransformMover const & rhs )

default

Assignment operator.

◆ optimize_ligand_pose_with_nls()

void protocols::nmr::pcs::PCSLigandTransformMover::optimize_ligand_pose_with_nls	(	Residue const &	ligand,
		Vector &	position,
		Vector &	orientation
	)

private

Optimize the ligand position and orientation by NLS.

References build_ligand_atom_xyz_table(), protocols::sewing::data_storage::ligand, pcs_data_, pcs_lmmin, protocols::nmr::pcs::TR(), and trans_step_.

Referenced by apply().

◆ optimized_transform()

bool protocols::nmr::pcs::PCSLigandTransformMover::optimized_transform ( ) const

inline

References optimize_transform_.

◆ parse_my_tag()

void protocols::nmr::pcs::PCSLigandTransformMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

Parse tags of XML script.

Reimplemented from protocols::moves::Mover.

References chain_, protocols::abinitio::filename(), core::scoring::parse_score_function(), pcs_data_file_, sfxn_, and protocols::nmr::pcs::TR().

◆ provide_xml_schema()

void protocols::nmr::pcs::PCSLigandTransformMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Create XML schema definition for PREMover.

Create XML schema definition for PCSLigandTransformMover.

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::nmr::pcs::PCSLigandTransformMoverCreator::provide_xml_schema().

◆ reset_grid_and_bounding_box()

void protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box	(	Pose const &	pose,
		core::Size const &	ligand_resid
	)

private

Build grid around protein and fill it with non-ligand atoms Update the bounding box of the xyz grid search to span the range: [ min_xyz atom_grid - nbr_radius, max_xyz atom_grid + nbr_radius ].

References core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), damped_resolution(), grid_, gs_box_, core::conformation::Residue::is_virtual_residue(), core::chemical::ResidueType::nbr_radius(), core::pose::Pose::residue(), core::pose::Pose::total_atoms(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ set_chain()

void protocols::nmr::pcs::PCSLigandTransformMover::set_chain ( char const c )

inline

References chain_.

◆ set_gridsearch_range() [1/2]

void protocols::nmr::pcs::PCSLigandTransformMover::set_gridsearch_range ( BoundingBox const & box )

inline

References gs_box_.

◆ set_gridsearch_range() [2/2]

void protocols::nmr::pcs::PCSLigandTransformMover::set_gridsearch_range	(	Vector const &	lower,
		Vector const &	upper
	)

inline

References gs_box_.

◆ set_resolution_damping()

void protocols::nmr::pcs::PCSLigandTransformMover::set_resolution_damping ( Real damping )

inline

References rsol_damping_.

◆ set_rot_step()

void protocols::nmr::pcs::PCSLigandTransformMover::set_rot_step ( Real step )

inline

References rot_step_.

◆ set_scorefunction()

void protocols::nmr::pcs::PCSLigandTransformMover::set_scorefunction ( ScoreFunctionOP sfxn )

inline

References sfxn_.

◆ set_trans_step()

void protocols::nmr::pcs::PCSLigandTransformMover::set_trans_step ( Real step )

inline

References trans_step_.

◆ undo_optimized_transform()

void protocols::nmr::pcs::PCSLigandTransformMover::undo_optimized_transform ( )

inline

References optimize_transform_.

Friends And Related Function Documentation

◆ pcs_lmmin

void pcs_lmmin	(	Real const *	par,
		int	,
		void const *	data,
		Real *	fvec,
		int *
	)

friend

pcs error function used in the lmmin function

par is an array of the positional parameters to be fitted [x, y, z, alpha, beta, gamma]
data is a pointer to the LMMinPCSDataRef container reference
fvc is an array holding the residuals of the fit calculation

Referenced by optimize_ligand_pose_with_nls().

Member Data Documentation

◆ chain_

char protocols::nmr::pcs::PCSLigandTransformMover::chain_

private

ligand chain

Referenced by apply(), get_chain(), parse_my_tag(), and set_chain().

◆ grid_

AtomGrid protocols::nmr::pcs::PCSLigandTransformMover::grid_

private

voxelgrid that spans around the protein and which is used for clash check

Referenced by find_best_ligand_pose_with_grid_search(), and reset_grid_and_bounding_box().

◆ gs_box_

BoundingBox protocols::nmr::pcs::PCSLigandTransformMover::gs_box_

private

Bounding box of the ligand xyz position grid search.

Referenced by find_best_ligand_pose_with_grid_search(), get_gridsearch_range(), next_ligand_position(), reset_grid_and_bounding_box(), and set_gridsearch_range().

◆ optimize_transform_

bool protocols::nmr::pcs::PCSLigandTransformMover::optimize_transform_

private

do further optimization of position and orientation as by grid search

Referenced by apply(), do_optimized_transform(), optimized_transform(), and undo_optimized_transform().

◆ pcs_data_

PCSDataCOP protocols::nmr::pcs::PCSLigandTransformMover::pcs_data_

private

experimental PCS data for all lanthanides and tagging sites

Referenced by apply(), find_best_ligand_pose_with_grid_search(), get_pcs_data(), and optimize_ligand_pose_with_nls().

◆ pcs_data_file_

std::string protocols::nmr::pcs::PCSLigandTransformMover::pcs_data_file_

private

The file from which to read the PCS data at apply time.

Referenced by apply(), and parse_my_tag().

◆ rot_step_

Real protocols::nmr::pcs::PCSLigandTransformMover::rot_step_

private

rotational stepsize (in degree) of grid search

Referenced by apply(), get_rot_step(), next_ligand_orientation(), and set_rot_step().

◆ rsol_damping_

Real protocols::nmr::pcs::PCSLigandTransformMover::rsol_damping_

private

smoothening parameter that can be used to damp the resolution of the atom clash check with the voxel grid. Takes values between 0.0 and 1.0

Referenced by damped_resolution(), get_resolution_damping(), and set_resolution_damping().

◆ sfxn_

ScoreFunctionCOP protocols::nmr::pcs::PCSLigandTransformMover::sfxn_

private

a scorefunction to monitor if ligand touches the protein

Referenced by get_scorefunction(), parse_my_tag(), and set_scorefunction().

◆ trans_step_

Real protocols::nmr::pcs::PCSLigandTransformMover::trans_step_

private

translational stepsize (in Ang.) of grid search

Referenced by apply(), get_trans_step(), next_ligand_position(), optimize_ligand_pose_with_nls(), and set_trans_step().

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

src/protocols/nmr/pcs/PCSLigandTransformMover.hh
src/protocols/nmr/pcs/PCSLigandTransformMover.cc

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Member Typedef Documentation

◆ BoundingBox

◆ Matrix

◆ PCSData

◆ PCSDataCOP

◆ PCSDataOP

◆ Pose

◆ Real

◆ Residue

◆ ScoreFunctionCOP

◆ ScoreFunctionOP

◆ Size

◆ Vec5

◆ Vector

Constructor & Destructor Documentation

◆ PCSLigandTransformMover() [1/3]

◆ PCSLigandTransformMover() [2/3]

◆ PCSLigandTransformMover() [3/3]

◆ ~PCSLigandTransformMover()

Member Function Documentation

◆ apply()

◆ build_ligand_atom_xyz_table()

◆ clone()

◆ damped_resolution()

◆ define_ligand_frame_origin()

◆ do_optimized_transform()

◆ find_best_ligand_pose_with_grid_search()

◆ fresh_instance()

◆ get_chain()

◆ get_gridsearch_range()

◆ get_name()

◆ get_pcs_data()

◆ get_resolution_damping()

◆ get_rot_step()

◆ get_scorefunction()

◆ get_trans_step()

◆ local_rotation()

◆ move_ligand_close_to_surface()

◆ mover_name()

◆ next_ligand_orientation()

◆ next_ligand_position()

◆ operator=()

◆ optimize_ligand_pose_with_nls()

◆ optimized_transform()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ reset_grid_and_bounding_box()

◆ set_chain()

◆ set_gridsearch_range() [1/2]

◆ set_gridsearch_range() [2/2]

◆ set_resolution_damping()

◆ set_rot_step()

◆ set_scorefunction()

◆ set_trans_step()

◆ undo_optimized_transform()

Friends And Related Function Documentation

◆ pcs_lmmin

Member Data Documentation

◆ chain_

◆ grid_

◆ gs_box_

◆ optimize_transform_

◆ pcs_data_

◆ pcs_data_file_

◆ rot_step_

◆ rsol_damping_

◆ sfxn_

◆ trans_step_