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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::Sizeget_designable_residues (core::pose::Pose &pose, std::string resfile)
 Based on a pose and a resfile, get the indices of all designable residues. More...
 
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< std::string > 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

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

Function Documentation

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().

utility::vector1< std::string > protocols::recon_design::get_candidate_AAs ( utility::vector1< std::string >  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

References core::chemical::aa_from_oneletter_code(), and core::chemical::name_from_aa().

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

utility::vector1< core::Size > protocols::recon_design::get_designable_residues ( core::pose::Pose pose,
std::string  resfile 
)
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::conformation::Residue::name1(), and core::pose::Pose::residue().

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().

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