protocols::generalized_kinematic_closure Namespace Reference

Namespaces
	filter
	perturber
	selector

Classes
class	GeneralizedKIC
class	GeneralizedKICCreator

Typedefs
typedef utility::pointer::shared_ptr< GeneralizedKIC >	GeneralizedKICOP
typedef utility::pointer::shared_ptr< GeneralizedKIC const >	GeneralizedKICCOP
typedef utility::vector1< GeneralizedKICOP >	GeneralizedKICOPs
typedef utility::vector1< GeneralizedKICCOP >	GeneralizedKICCOPs

Functions
static basic::Tracer	TR ("protocols.generalized_kinematic_closure.GeneralizedKIC")
std::string	gen_kic_subelement_mangler (std::string const &element_name)
std::string	gen_kic_sample_cis_subelement_mangler (std::string const &element_name)
std::string	gen_kic_add_pert_subelement_mangler (std::string const &element_name)
std::string	gen_kic_add_filter_subelement_mangler (std::string const &element_name)
static basic::Tracer	TR ("protocols.generalized_kinematic_closure.util")
bool	is_in_list (core::Size const val, utility::vector1< core::Size > const &list)
	Function to determine whether a value is in a list. More...
bool	original_pose_residue_is_in_residue_map (core::Size const residue_index, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	function to determine whether a residue index from the original pose is in the residue_map list. More...
void	set_loop_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &t_ang, utility::vector1< core::Real > const &b_ang, utility::vector1< core::Real > const &b_len)
	Set the loop pose conformation based on a set of results from kinematic closure. More...
void	set_loop_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &t_ang)
	Set the loop pose conformation based on a set of results from kinematic closure. More...
void	copy_loop_pose_to_original (core::pose::Pose &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map)
	Copy the atom positions of the residues in the loop pose to the original pose. More...
void	correct_polymer_dependent_atoms_in_pose_segment (core::pose::Pose &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	Update the polymer bond-dependent atom positions for every residue in the residue map. More...
void	general_set_phi (core::pose::Pose &pose, core::Size const residue_index, core::Real const &phi_value)
	Sets phi for an L-alpha amino acid, even if the nitrogen has a nonstandard connection. More...
void	general_set_psi (core::pose::Pose &pose, core::Size const residue_index, core::Real const &psi_value)
	Sets psi for an L-alpha amino acid, even if the carbonyl carbon has a nonstandard connection. More...
core::Size	get_original_pose_rsd (core::Size const perturbedloop_rsd, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the perturbed loop, return the corresponding residue index in the original pose. More...

Typedef Documentation

GeneralizedKICCOP

typedef utility::pointer::shared_ptr< GeneralizedKIC const > protocols::generalized_kinematic_closure::GeneralizedKICCOP

GeneralizedKICCOPs

typedef utility::vector1<GeneralizedKICCOP> protocols::generalized_kinematic_closure::GeneralizedKICCOPs

GeneralizedKICOP

typedef utility::pointer::shared_ptr< GeneralizedKIC > protocols::generalized_kinematic_closure::GeneralizedKICOP

GeneralizedKICOPs

typedef utility::vector1<GeneralizedKICOP> protocols::generalized_kinematic_closure::GeneralizedKICOPs

Function Documentation

copy_loop_pose_to_original()

void protocols::generalized_kinematic_closure::copy_loop_pose_to_original	(	core::pose::Pose &	original_pose,
		core::pose::Pose const &	loop_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map
	)

Copy the atom positions of the residues in the loop pose to the original pose.

References core::conformation::Residue::atom_name(), core::conformation::Residue::has(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), TR(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Residue::xyz().

Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC(), and protocols::generalized_kinematic_closure::GeneralizedKIC::set_final_solution().

correct_polymer_dependent_atoms_in_pose_segment()

void protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment	(	core::pose::Pose &	original_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map
	)

Update the polymer bond-dependent atom positions for every residue in the residue map.

References core::pose::Pose::conformation(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), and core::conformation::Conformation::residue().

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC(), and protocols::generalized_kinematic_closure::GeneralizedKIC::set_final_solution().

gen_kic_add_filter_subelement_mangler()

std::string protocols::generalized_kinematic_closure::gen_kic_add_filter_subelement_mangler

(

std::string const &

element_name

)

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::provide_xml_schema().

gen_kic_add_pert_subelement_mangler()

std::string protocols::generalized_kinematic_closure::gen_kic_add_pert_subelement_mangler

(

std::string const &

element_name

)

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::provide_xml_schema().

gen_kic_sample_cis_subelement_mangler()

std::string protocols::generalized_kinematic_closure::gen_kic_sample_cis_subelement_mangler

(

std::string const &

element_name

)

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::provide_xml_schema().

gen_kic_subelement_mangler()

std::string protocols::generalized_kinematic_closure::gen_kic_subelement_mangler

(

std::string const &

element_name

)

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::provide_xml_schema().

general_set_phi()

void protocols::generalized_kinematic_closure::general_set_phi	(	core::pose::Pose &	pose,
		core::Size const	residue_index,
		core::Real const &	phi_value
	)

Sets phi for an L-alpha amino acid, even if the nitrogen has a nonstandard connection.

References core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connection_incomplete(), core::chemical::ResidueType::is_alpha_aa(), core::conformation::Residue::is_lower_terminus(), core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Conformation::set_torsion_angle(), TR(), core::conformation::Residue::type(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama().

general_set_psi()

void protocols::generalized_kinematic_closure::general_set_psi	(	core::pose::Pose &	pose,
		core::Size const	residue_index,
		core::Real const &	psi_value
	)

Sets psi for an L-alpha amino acid, even if the carbonyl carbon has a nonstandard connection.

References core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connection_incomplete(), core::chemical::ResidueType::is_alpha_aa(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Conformation::set_torsion_angle(), TR(), core::conformation::Residue::type(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama().

get_original_pose_rsd()

core::Size protocols::generalized_kinematic_closure::get_original_pose_rsd	(	core::Size const	perturbedloop_rsd,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map
	)

Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the perturbed loop, return the corresponding residue index in the original pose.

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), and protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots().

is_in_list()

bool protocols::generalized_kinematic_closure::is_in_list	(	core::Size const	val,
		utility::vector1< core::Size > const &	list
	)

Function to determine whether a value is in a list.

References protocols::hybridization::val.

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs().

original_pose_residue_is_in_residue_map()

bool protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map	(	core::Size const	residue_index,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map
	)

function to determine whether a residue index from the original pose is in the residue_map list.

Returns true if the residue index in the original pose has been mapped to a residue in the loop, false otherwise.

Parameters

[in]	residue_index	- The index of a residue in the original pose.
[in]	residue_map	- A vector of pairs of indices. Each pair is (index in loop, index in original pose).

Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), and protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check().

set_loop_pose() [1/2]

void protocols::generalized_kinematic_closure::set_loop_pose	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	t_ang
	)

Set the loop pose conformation based on a set of results from kinematic closure.

This version ONLY sets mainchain torsions, and does no rebuilding of mainchain O or H atoms.

Parameters

[in,out]	pose	– A pose consisting of the loop to be closed only.
[in]	atomlist	– A list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.
[in]	torsions	– The torsion angles values to set.

References core::pose::Pose::conformation(), core::conformation::Conformation::set_torsion_angle(), and core::pose::Pose::update_residue_neighbors().

set_loop_pose() [2/2]

void protocols::generalized_kinematic_closure::set_loop_pose	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	t_ang,
		utility::vector1< core::Real > const &	b_ang,
		utility::vector1< core::Real > const &	b_len
	)

Set the loop pose conformation based on a set of results from kinematic closure.

Parameters

[in,out]	pose	– A pose consisting of the loop to be closed only.
[in]	atomlist	– A list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.
[in]	t_ang	– The torsion angles values to set.
[in]	b_ang	– The bond angle values to set.
[in]	b_len	– The bond length values to set.
[in,out]	pose	– A pose consisting of the loop to be closed only.
[in]	atomlist	– A list of AtomIDs and corresponding xyz coordinates (though we don't use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.
[in]	torsions	– The torsion angles values to set.
[in]	bondangles	– The bond angle values to set.
[in]	bondlengths	– The bond length values to set.

References core::pose::Pose::conformation(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::set_torsion_angle(), TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_rmsd_selector(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC(), and protocols::generalized_kinematic_closure::GeneralizedKIC::set_final_solution().

TR() [1/2]

static basic::Tracer protocols::generalized_kinematic_closure::TR ( "protocols.generalized_kinematic_closure.GeneralizedKIC"  )

static

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::add_loop_residue(), protocols::generalized_kinematic_closure::GeneralizedKIC::add_tail_residue(), protocols::generalized_kinematic_closure::GeneralizedKIC::apply(), protocols::generalized_kinematic_closure::GeneralizedKIC::apply_perturbations(), copy_loop_pose_to_original(), protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC(), protocols::generalized_kinematic_closure::GeneralizedKIC::filter_solutions(), general_set_phi(), general_set_psi(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::set_closure_attempts(), protocols::generalized_kinematic_closure::GeneralizedKIC::set_final_solution(), set_loop_pose(), and protocols::generalized_kinematic_closure::GeneralizedKIC::set_ntries_before_giving_up().

TR() [2/2]

static basic::Tracer protocols::generalized_kinematic_closure::TR ( "protocols.generalized_kinematic_closure.util"  )

static