protocols::recon_design Namespace Reference

Classes
class	FindConsensusSequence
	Takes in multiple poses from the VectorPoseJobDistributor and finds the consensus sequence that optimizes energy of all input poses. Used in conjuction with MSDMover at the end of a protocol to make sure that you end up with one multistate solution. Only accessible through recon application. More...
class	FindConsensusSequenceCreator
class	FitnessFilter
	Returns the sum of energy of input poses. Only accessible through recon application. More...
class	FitnessFilterCreator
class	MSDMover
	Multistate design mover used for RECON multistate design Takes in multiple poses, applies residue linking constraints based on sequence of all input poses and runs a design submover that has been specified in the tag Only accessible through recon application. More...
class	MSDMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< FindConsensusSequence >	FindConsensusSequenceOP
typedef utility::pointer::shared_ptr< FindConsensusSequence const >	FindConsensusSequenceCOP
typedef utility::pointer::shared_ptr< FitnessFilter >	FitnessFilterOP
typedef utility::pointer::shared_ptr< FitnessFilter const >	FitnessFilterCOP
typedef utility::pointer::shared_ptr< MSDMover >	MSDMoverOP
typedef utility::pointer::shared_ptr< MSDMover const >	MSDMoverCOP

Functions
static basic::Tracer	TR ("protocols.recon_design.FindConsensusSequence")
static basic::Tracer	TR ("protocols.recon_design.FitnessFilter")
static basic::Tracer	TR ("protocols.recon_design.MSDMover")
utility::vector1< core::Size >	get_designable_residues (core::pose::Pose &pose, std::string resfile)
	Based on a pose and a resfile, get the indices of all designable residues. More...
utility::vector1< std::string >	get_designable_sequence (core::pose::Pose &pose, utility::vector1< core::Size > designable_residues)
	Based on a pose and the indices of all designable residues, get a string of all designable AAs concatenated. More...
utility::vector1< std::string >	get_candidate_AAs (utility::vector1< utility::vector1< std::string > > const &other_pose_sequences, core::Size position_no)
	Based on a list of sequences from poses, get all the AAs present at the position given by position_no. More...
core::Size	find_pose_in_vector (core::pose::Pose const &pose, utility::vector1< core::pose::PoseOP > &poses)
	Given a list of poses, find the index of a particular pose. More...

Typedef Documentation

FindConsensusSequenceCOP

typedef utility::pointer::shared_ptr< FindConsensusSequence const > protocols::recon_design::FindConsensusSequenceCOP

FindConsensusSequenceOP

typedef utility::pointer::shared_ptr< FindConsensusSequence > protocols::recon_design::FindConsensusSequenceOP

FitnessFilterCOP

typedef utility::pointer::shared_ptr< FitnessFilter const > protocols::recon_design::FitnessFilterCOP

FitnessFilterOP

typedef utility::pointer::shared_ptr< FitnessFilter > protocols::recon_design::FitnessFilterOP

MSDMoverCOP

typedef utility::pointer::shared_ptr< MSDMover const > protocols::recon_design::MSDMoverCOP

MSDMoverOP

typedef utility::pointer::shared_ptr< MSDMover > protocols::recon_design::MSDMoverOP

Function Documentation

find_pose_in_vector()

core::Size protocols::recon_design::find_pose_in_vector	(	core::pose::Pose const &	pose,
		utility::vector1< core::pose::PoseOP > &	poses
	)

Given a list of poses, find the index of a particular pose.

References core::pose::getPoseExtraScore().

Referenced by protocols::recon_design::FindConsensusSequence::apply(), and protocols::recon_design::MSDMover::setup_mover().

get_candidate_AAs()

utility::vector1< std::string > protocols::recon_design::get_candidate_AAs	(	utility::vector1< utility::vector1< std::string > > const &	other_pose_sequences,
		core::Size	position_no
	)

Based on a list of sequences from poses, get all the AAs present at the position given by position_no.

Based on a list of sequences from poses, get all the AAs present at the position given by position_no

Referenced by protocols::recon_design::FindConsensusSequence::apply(), protocols::recon_design::MSDMover::apply_linked_constraints(), and protocols::recon_design::FindConsensusSequence::apply_mpi().

get_designable_residues()

utility::vector1< core::Size > protocols::recon_design::get_designable_residues	(	core::pose::Pose &	pose,
		std::string	resfile
	)

Based on a pose and a resfile, get the indices of all designable residues.

References core::pack::task::parse_resfile().

Referenced by protocols::recon_design::FindConsensusSequence::apply_mpi(), protocols::recon_design::MSDMover::apply_mpi(), protocols::recon_design::FindConsensusSequence::parse_resfiles(), and protocols::recon_design::MSDMover::parse_resfiles().

get_designable_sequence()

utility::vector1< std::string > protocols::recon_design::get_designable_sequence	(	core::pose::Pose &	pose,
		utility::vector1< core::Size >	designable_residues
	)

Based on a pose and the indices of all designable residues, get a string of all designable AAs concatenated.

Based on a pose and the indices of all designable residues, get a string of all designable AAs concatenated

References core::chemical::ResidueTypeBase::base_name(), and core::pose::Pose::residue_type().

Referenced by protocols::recon_design::FindConsensusSequence::apply(), protocols::recon_design::MSDMover::apply(), protocols::recon_design::FindConsensusSequence::apply_mpi(), and protocols::recon_design::MSDMover::apply_mpi().

TR() [1/3]

static basic::Tracer protocols::recon_design::TR ( "protocols.recon_design.FindConsensusSequence"  )

static

Referenced by protocols::recon_design::MSDMover::apply(), protocols::recon_design::MSDMover::apply_linked_constraints(), protocols::recon_design::FindConsensusSequence::apply_mpi(), protocols::recon_design::MSDMover::apply_mpi(), protocols::recon_design::FindConsensusSequence::pick_consensus_AA(), protocols::recon_design::FindConsensusSequence::pick_consensus_AA_mpi(), protocols::recon_design::MSDMover::run_post_design_mover(), and protocols::recon_design::FindConsensusSequence::test_AA().

TR() [2/3]

static basic::Tracer protocols::recon_design::TR ( "protocols.recon_design.FitnessFilter"  )

static

TR() [3/3]

static basic::Tracer protocols::recon_design::TR ( "protocols.recon_design.MSDMover"  )

static