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protocols::comparative_modeling Namespace Reference

Namespaces

 features
 

Classes

class  Align_RmsdEvaluator
 
class  Align_RotamerEvaluator
 
class  AlignmentCluster
 
class  AlignmentClustering
 
class  AlignmentSet
 
class  AlignRmsdTargetEvaluatorCreator
 creator for the AlignRmsdTargetEvaluatorCreator class More...
 
class  ExtraThreadingMover
 
class  GenericJobInputter
 
class  GenericJobInputterCreator
 
class  IgnoreSubsetConstraintSet
 
class  LoopRelaxMover
 
class  LoopRelaxMoverCreator
 
class  LoopRelaxThreadingMover
 
class  MultiThreadingMover
 
class  PartialThreadingMover
 
class  RecoverSideChainsMover
 
class  StealLigandMover
 
class  StealSideChainsMover
 
class  ThreadingJob
 
class  ThreadingJobInputter
 
class  ThreadingJobInputterCreator
 
class  ThreadingMover
 

Typedefs

typedef
utility::pointer::shared_ptr
< Align_RmsdEvaluator
Align_RmsdEvaluatorOP
 
typedef
utility::pointer::shared_ptr
< Align_RmsdEvaluator const > 
Align_RmsdEvaluatorCOP
 
typedef
utility::pointer::shared_ptr
< Align_RotamerEvaluator
Align_RotamerEvaluatorOP
 
typedef
utility::pointer::shared_ptr
< Align_RotamerEvaluator const > 
Align_RotamerEvaluatorCOP
 
typedef
utility::pointer::shared_ptr
< AlignmentCluster
AlignmentClusterOP
 
typedef
utility::pointer::shared_ptr
< AlignmentCluster const > 
AlignmentClusterCOP
 
typedef
utility::pointer::shared_ptr
< AlignmentClustering
AlignmentClusteringOP
 
typedef
utility::pointer::shared_ptr
< AlignmentClustering const > 
AlignmentClusteringCOP
 
typedef
utility::pointer::shared_ptr
< AlignmentSet
AlignmentSetOP
 
typedef
utility::pointer::shared_ptr
< AlignmentSet const > 
AlignmentSetCOP
 
typedef
utility::pointer::shared_ptr
< IgnoreSubsetConstraintSet
IgnoreSubsetConstraintSetOP
 
typedef
utility::pointer::shared_ptr
< IgnoreSubsetConstraintSet
const > 
IgnoreSubsetConstraintSetCOP
 
typedef
utility::pointer::shared_ptr
< LoopRelaxMover
LoopRelaxMoverOP
 
typedef
utility::pointer::shared_ptr
< LoopRelaxMover const > 
LoopRelaxMoverCOP
 
typedef
utility::pointer::shared_ptr
< LoopRelaxThreadingMover
LoopRelaxThreadingMoverOP
 
typedef
utility::pointer::shared_ptr
< LoopRelaxThreadingMover
const > 
LoopRelaxThreadingMoverCOP
 
typedef
utility::pointer::shared_ptr
< RecoverSideChainsMover
RecoverSideChainsMoverOP
 
typedef
utility::pointer::shared_ptr
< RecoverSideChainsMover const > 
RecoverSideChainsMoverCOP
 
typedef
utility::pointer::shared_ptr
< StealLigandMover
StealLigandMoverOP
 
typedef
utility::pointer::shared_ptr
< StealLigandMover const > 
StealLigandMoverCOP
 
typedef
utility::pointer::shared_ptr
< StealSideChainsMover
StealSideChainsMoverOP
 
typedef
utility::pointer::shared_ptr
< StealSideChainsMover const > 
StealSideChainsMoverCOP
 
typedef
utility::pointer::shared_ptr
< ThreadingJob
ThreadingJobOP
 
typedef
utility::pointer::shared_ptr
< ThreadingJob const > 
ThreadingJobCOP
 
typedef
utility::pointer::shared_ptr
< ThreadingJobInputter
ThreadingJobInputterOP
 
typedef
utility::pointer::shared_ptr
< ThreadingJobInputter const > 
ThreadingJobInputterCOP
 

Functions

utility::vector1
< core::pack::dunbrack::RotVector
rots_from_pose (core::pose::Pose const &pose)
 
utility::vector1
< utility::vector1< core::Real > > 
chis_from_pose (core::pose::Pose const &pose)
 
void cm_main ()
 Initiates LoopRelaxThreadingMover using the job distributor (jd2) More...
 
void gather_coords (core::pose::Pose const &model, core::pose::Pose const &native, core::sequence::SequenceAlignment const &aln, int &natoms, ObjexxFCL::FArray2D< core::Real > &p1a, ObjexxFCL::FArray2D< core::Real > &p2a, std::string const &atom_name="CA")
 
static basic::Tracer tr ("protocols.comparative_modeling.extra_threading")
 
static basic::Tracer TR ("protocols.looprelax")
 
static basic::Tracer tr ("protocols.threading")
 
static basic::Tracer tr ("protocols.comparative_modeling.threading")
 
static basic::Tracer tr ("protocols.comparative_modeling.ThreadingJob")
 
static basic::Tracer tr ("protocols.comparative_modeling.ThreadingJobInputter")
 
std::map< std::string,
utility::vector1< core::Size > > 
read_extra_residues (utility::vector1< std::string > const &fns)
 
static basic::Tracer tr ("protocols.comparative_modeling.threading")
 
static basic::Tracer tr ("protocols.comparative_modeling.util")
 
core::id::SequenceMapping get_qt_mapping_general (core::pose::Pose const &query_pose, core::sequence::SequenceAlignment const &align, core::pose::Pose const &template_pose, core::Size const query_index, core::Size const template_index)
 
void bounded_loops_from_alignment (const core::Size num_residues, const core::Size min_size, const core::sequence::SequenceAlignment &alignment, protocols::loops::LoopsOP &unaligned_regions)
 Identifies consecutive stretches of unaligned residues by scanning the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>. More...
 
protocols::loops::LoopsOP loops_from_alignment (core::Size nres, core::sequence::SequenceAlignment const &aln, core::Size const min_loop_size)
 
protocols::loops::LoopsOP loops_from_transitive_alignments (core::Size nres1, core::sequence::SequenceAlignment const &aln1, core::Size nres2, core::sequence::SequenceAlignment const &aln2, core::Size const min_loop_size)
 
protocols::loops::LoopsOP pick_loops_unaligned (core::Size nres, utility::vector1< core::Size > const &unaligned_residues, core::Size min_loop_size)
 
protocols::loops::LoopsOP pick_loops_chainbreak (core::pose::Pose &query_pose, core::Size min_loop_size)
 
void rebuild_loops_until_closed (core::pose::Pose &query_pose, core::Size const min_loop_size, core::Size const max_rebuild, std::string const &loop_mover_name)
 
void steal_ligands (core::pose::Pose &dest_pose, core::pose::Pose const &source_pose_in, core::id::NamedAtomID const &anchor_atom_dest, core::id::NamedAtomID const &anchor_atom_source, utility::vector1< core::id::NamedAtomID > const &ligand_indices)
 Function for stealing ligands from a given Pose and adding them to source_pose. More...
 
void initialize_ss (core::pose::Pose &pose)
 
utility::vector1
< core::pose::Pose
templates_from_cmd_line ()
 
bool loops_are_closed (core::pose::Pose &pose)
 
std::map< std::string,
core::pose::Pose
poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
 
AlignmentSet alignments_from_cmd_line ()
 
void randomize_selected_atoms (core::pose::Pose &query_pose, core::id::AtomID_Mask const &selected)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AlignmentCluster const > protocols::comparative_modeling::AlignmentClusterCOP
typedef utility::pointer::shared_ptr< AlignmentSet const > protocols::comparative_modeling::AlignmentSetCOP
typedef utility::pointer::shared_ptr< AlignmentSet > protocols::comparative_modeling::AlignmentSetOP
typedef utility::pointer::shared_ptr< LoopRelaxMover const > protocols::comparative_modeling::LoopRelaxMoverCOP
typedef utility::pointer::shared_ptr< LoopRelaxMover > protocols::comparative_modeling::LoopRelaxMoverOP
typedef utility::pointer::shared_ptr< StealLigandMover const > protocols::comparative_modeling::StealLigandMoverCOP
typedef utility::pointer::shared_ptr< ThreadingJob const > protocols::comparative_modeling::ThreadingJobCOP
typedef utility::pointer::shared_ptr< ThreadingJob > protocols::comparative_modeling::ThreadingJobOP

Function Documentation

AlignmentSet protocols::comparative_modeling::alignments_from_cmd_line ( )
void protocols::comparative_modeling::bounded_loops_from_alignment ( const core::Size  num_residues,
const core::Size  min_size,
const core::sequence::SequenceAlignment alignment,
protocols::loops::LoopsOP unaligned_regions 
)

Identifies consecutive stretches of unaligned residues by scanning the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>.

The premise underlying this tortuous method is simple– identify aligned/unaligned regions in a sequence alignment with the constraint that each region has a certain minimum length.

The current implementation achieves this goal in a roundabout manner by making use of existing, less specialized utility functions.

References NO_LOOP_SIZE_CST, pick_loops_unaligned(), and core::sequence::SequenceAlignment::sequence_mapping().

Referenced by protocols::nonlocal::find_regions_with_minimum_size().

utility::vector1< utility::vector1< core::Real > > protocols::comparative_modeling::chis_from_pose ( core::pose::Pose const &  pose)
void protocols::comparative_modeling::cm_main ( )
void protocols::comparative_modeling::gather_coords ( core::pose::Pose const &  model,
core::pose::Pose const &  native,
core::sequence::SequenceAlignment const &  aln,
int &  natoms,
ObjexxFCL::FArray2D< core::Real > &  p1a,
ObjexxFCL::FArray2D< core::Real > &  p2a,
std::string const &  atom_name = "CA" 
)
core::id::SequenceMapping protocols::comparative_modeling::get_qt_mapping_general ( core::pose::Pose const &  query_pose,
core::sequence::SequenceAlignment const &  align,
core::pose::Pose const &  template_pose,
core::Size const  query_index,
core::Size const  template_index 
)
void protocols::comparative_modeling::initialize_ss ( core::pose::Pose pose)
bool protocols::comparative_modeling::loops_are_closed ( core::pose::Pose pose)
protocols::loops::LoopsOP protocols::comparative_modeling::loops_from_alignment ( core::Size  nres,
core::sequence::SequenceAlignment const &  aln,
core::Size const  min_loop_size 
)
protocols::loops::LoopsOP protocols::comparative_modeling::loops_from_transitive_alignments ( core::Size  nres1,
core::sequence::SequenceAlignment const &  aln1,
core::Size  nres2,
core::sequence::SequenceAlignment const &  aln2,
core::Size const  min_loop_size 
)
protocols::loops::LoopsOP protocols::comparative_modeling::pick_loops_chainbreak ( core::pose::Pose query_pose,
core::Size  min_loop_size 
)
protocols::loops::LoopsOP protocols::comparative_modeling::pick_loops_unaligned ( core::Size  nres,
utility::vector1< core::Size > const &  unaligned_residues,
core::Size  min_loop_size 
)
std::map< std::string, core::pose::Pose > protocols::comparative_modeling::poses_from_cmd_line ( utility::vector1< std::string > const &  fn_list)
void protocols::comparative_modeling::randomize_selected_atoms ( core::pose::Pose query_pose,
core::id::AtomID_Mask const &  selected 
)
std::map< std::string, utility::vector1< core::Size > > protocols::comparative_modeling::read_extra_residues ( utility::vector1< std::string > const &  fns)
void protocols::comparative_modeling::rebuild_loops_until_closed ( core::pose::Pose query_pose,
core::Size const  min_loop_size,
core::Size const  max_rebuild,
std::string const &  loop_mover_name 
)
utility::vector1< core::pack::dunbrack::RotVector > protocols::comparative_modeling::rots_from_pose ( core::pose::Pose const &  pose)
void protocols::comparative_modeling::steal_ligands ( core::pose::Pose dest_pose,
core::pose::Pose const &  source_pose_in,
core::id::NamedAtomID const &  anchor_atom_dest,
core::id::NamedAtomID const &  anchor_atom_source,
utility::vector1< core::id::NamedAtomID > const &  ligand_indices 
)

Function for stealing ligands from a given Pose and adding them to source_pose.

: The parameters are:

  • dest_pose Pose to which ligands are added.
  • source_pose_in Pose from which ligands and orientations are taken.
  • anchor_atom_dest anchor atom providing reference in dest_pose for ligand orientation.
  • anchor_atom_source anchor atom providing reference in source_pose for ligand orientation.
  • ligand_indices list of AtomID entries for ligand, one per ligand. Ligand orientation is determined by orientation between anchor_atom_source and each ligand AtomID.

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::append_residue_by_jump(), core::id::NamedAtomID::atom(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::residue(), core::id::NamedAtomID::rsd(), core::pose::Pose::set_jump(), core::pose::Pose::size(), tr(), and core::id::NamedAtomID::valid().

Referenced by protocols::comparative_modeling::StealLigandMover::apply().

utility::vector1< core::pose::Pose > protocols::comparative_modeling::templates_from_cmd_line ( )
static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.ThreadingJob"  )
static
static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.ThreadingJobInputter"  )
static
static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.threading"  )
static
static basic::Tracer protocols::comparative_modeling::tr ( "protocols.threading"  )
static
static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.extra_threading"  )
static
static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.threading"  )
static
static basic::Tracer protocols::comparative_modeling::tr ( "protocols.comparative_modeling.util"  )
static
static basic::Tracer protocols::comparative_modeling::TR ( "protocols.looprelax"  )
static