protocols::cluster::GatherPosesMover Class Reference

#include <cluster.hh>

Inheritance diagram for protocols::cluster::GatherPosesMover:

Collaboration diagram for protocols::cluster::GatherPosesMover:

List of all members.

Public Member Functions
	GatherPosesMover ()
void	set_score_function (core::scoring::ScoreFunctionOP sfxn)
void	set_filter (core::Real filter)
virtual void	apply (core::pose::Pose &pose)
virtual std::string	get_name () const
	Each derived class must specify its name. The class name.
bool	check_tag (const std::string &query_tag)
void	push_back (const core::pose::Pose &pose)
void	clear ()
void	set_cluster_by_protein_backbone (bool const &setting)
void	set_cluster_by_all_atom (bool const &setting)
int	processed () const
std::vector< core::pose::Pose > &	get_pose_list ()
std::vector< std::string > const &	get_tag_list () const
virtual core::Real	get_distance_measure (const core::pose::Pose &pose1, const core::pose::Pose &pose2) const
Protected Attributes
std::vector< core::pose::Pose >	poselist

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Constructor & Destructor Documentation

protocols::cluster::GatherPosesMover::GatherPosesMover

(

)

References protocols::cluster::read_template_scores(), and protocols::cluster::tr().

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Member Function Documentation

void protocols::cluster::GatherPosesMover::apply

(

core::pose::Pose &

pose

)

[virtual]

Implements protocols::moves::Mover.

Reimplemented in protocols::cluster::AssignToClustersMover.

References core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::Energies::clear(), core::pose::Pose::energies(), protocols::jobdist::extract_tag_from_pose(), core::pose::get_all_score_line_strings(), get_distance_measure(), protocols::moves::Mover::get_native_pose(), core::pose::getPoseExtraScores(), poselist, core::pose::setPoseExtraScores(), and protocols::cluster::tr().

bool protocols::cluster::GatherPosesMover::check_tag

(

const std::string &

query_tag

)

void protocols::cluster::GatherPosesMover::clear

(

)

[inline]

References poselist.

Referenced by protocols::cluster::ClusterBase::create_constraints().

Real protocols::cluster::GatherPosesMover::get_distance_measure	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)		const [virtual]

Reimplemented in protocols::cluster::ClusterPhilStyle_Loop.

References core::scoring::all_atom_rmsd(), core::scoring::CA_gdtmm(), core::scoring::CA_rmsd(), core::scoring::CA_rmsd_symmetric(), core::scoring::invert_exclude_residues(), core::scoring::is_protein_backbone(), core::conformation::Residue::is_RNA(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::scoring::residue_sc_rmsd_no_super(), core::scoring::rmsd_with_super(), core::pose::Pose::total_residue(), and protocols::cluster::tr().

Referenced by protocols::cluster::ClusterBase::add_structure(), apply(), and protocols::cluster::ClusterBase::calculate_distance_matrix().

std::string protocols::cluster::GatherPosesMover::get_name

(

)

const [virtual]

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Reimplemented in protocols::cluster::EnsembleConstraints, protocols::cluster::EnsembleConstraints_Simple, protocols::cluster::ClusterBase, protocols::cluster::ClusterPhilStyle, protocols::cluster::ClusterPhilStyle_Loop, and protocols::cluster::AssignToClustersMover.

std::vector< core::pose::Pose >& protocols::cluster::GatherPosesMover::get_pose_list

(

)

[inline]

References poselist.

std::vector< std::string > const& protocols::cluster::GatherPosesMover::get_tag_list

(

)

const [inline]

int protocols::cluster::GatherPosesMover::processed

(

)

const [inline]

Reimplemented in protocols::cluster::AssignToClustersMover.

void protocols::cluster::GatherPosesMover::push_back

(

const core::pose::Pose &

pose

)

[inline]

References poselist.

Referenced by protocols::cluster::ClusterBase::create_constraints(), protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group(), and protocols::cluster::ClusterBase::sort_each_group_by_energy().

void protocols::cluster::GatherPosesMover::set_cluster_by_all_atom

(

bool const &

setting

)

[inline]

void protocols::cluster::GatherPosesMover::set_cluster_by_protein_backbone

(

bool const &

setting

)

[inline]

void protocols::cluster::GatherPosesMover::set_filter

(

core::Real

filter

)

void protocols::cluster::GatherPosesMover::set_score_function

(

core::scoring::ScoreFunctionOP

sfxn

)

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Member Data Documentation

std::vector< core::pose::Pose > protocols::cluster::GatherPosesMover::poselist [protected]

Referenced by protocols::cluster::ClusterBase::add_structure(), protocols::cluster::AssignToClustersMover::apply(), apply(), protocols::cluster::ClusterBase::calculate_distance_matrix(), protocols::cluster::ClusterBase::clean_pose_store(), clear(), protocols::cluster::ClusterBase::create_constraints(), protocols::cluster::EnsembleConstraints_Simple::createConstraints(), protocols::cluster::ClusterPhilStyle::do_clustering(), get_pose_list(), protocols::cluster::ClusterBase::limit_groups(), protocols::cluster::ClusterBase::print_cluster_assignment(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), protocols::cluster::ClusterBase::print_summary(), push_back(), protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group(), protocols::cluster::ClusterBase::return_lowest_poses_in_clusters(), protocols::cluster::ClusterBase::return_top_poses_in_clusters(), protocols::cluster::ClusterBase::sort_each_group_by_energy(), and protocols::cluster::ClusterBase::sort_groups_by_energy().

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

• src/protocols/cluster/cluster.hh
• src/protocols/cluster/cluster.cc