Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
protocols::hybridization Namespace Reference

Classes

class  AllResiduesChanged
 (helper) functor class which keeps track of initial phi/psi values. calls of operator ( pose ) compare the initial phi/psi values More...
 
class  BackboneTorsionPerturbation
 
class  BackboneTorsionPerturbationCreator
 
class  BackboneTorsionSampler
 
class  BackboneTorsionSamplerCreator
 
class  CartesianHybridize
 
class  CartesianHybridizeCreator
 
class  CartesianSampler
 
class  CartesianSamplerCreator
 
class  ChunkTrialMover
 
class  DDomainParse
 
class  DomainAssembly
 
class  FoldTreeHybridize
 
class  FoldTreeHybridizeCreator
 
class  hConvergenceCheck
 
class  HybridizeFoldtreeDynamic
 
class  HybridizeProtocol
 
class  HybridizeProtocolCreator
 
class  HybridizeSetup
 
class  HybridizeSetupMover
 
class  HybridizeSetupMoverCreator
 
class  InsertChunkMover
 
class  MRMover
 
class  TemplateHistory
 
class  TMalign
 
class  WeightedFragmentSmoothTrialMover
 
class  WeightedFragmentTrialMover
 

Typedefs

typedef
utility::pointer::owning_ptr
< CartesianHybridize
CartesianHybridizeOP
 
typedef
utility::pointer::owning_ptr
< CartesianHybridize const > 
CartesianHybridizeCOP
 
typedef
utility::pointer::owning_ptr
< CartesianSampler
CartesianSamplerOP
 
typedef
utility::pointer::owning_ptr
< CartesianSampler const > 
CartesianSamplerCOP
 
typedef
utility::pointer::owning_ptr
< ChunkTrialMover
ChunkTrialMoverOP
 
typedef
utility::pointer::owning_ptr
< ChunkTrialMover const > 
ChunkTrialMoverCOP
 
typedef
utility::pointer::owning_ptr
< TemlateAssembly > 
TemlateAssemblyOP
 
typedef
utility::pointer::owning_ptr
< TemlateAssembly const > 
TemlateAssemblyCOP
 
typedef
utility::pointer::owning_ptr
< hConvergenceCheck
hConvergenceCheckOP
 
typedef
utility::pointer::owning_ptr
< FoldTreeHybridize
FoldTreeHybridizeOP
 
typedef
utility::pointer::owning_ptr
< FoldTreeHybridize const > 
FoldTreeHybridizeCOP
 
typedef
utility::pointer::owning_ptr
< HybridizeFoldtreeMover > 
HybridizeFoldtreeMoverOP
 
typedef
utility::pointer::owning_ptr
< HybridizeFoldtreeMover const > 
HybridizeFoldtreeMoverCOP
 
typedef
utility::pointer::owning_ptr
< HybridizeProtocol
HybridizeProtocolOP
 
typedef
utility::pointer::owning_ptr
< HybridizeProtocol const > 
HybridizeProtocolCOP
 
typedef
utility::pointer::owning_ptr
< HybridizeSetup
HybridizeSetupOP
 
typedef
utility::pointer::owning_ptr
< HybridizeSetup const > 
HybridizeSetupCOP
 
typedef
utility::pointer::owning_ptr
< MRMover
MRMoverOP
 
typedef
utility::pointer::owning_ptr
< TemplateHistory
TemplateHistoryOP
 
typedef
utility::pointer::owning_ptr
< TemplateHistory const > 
TemplateHistoryCOP
 
typedef
utility::pointer::owning_ptr
< WeightedFragmentSmoothTrialMover
WeightedFragmentSmoothTrialMoverOP
 
typedef
utility::pointer::owning_ptr
< WeightedFragmentSmoothTrialMover
const > 
WeightedFragmentSmoothTrialMoverCOP
 
typedef
utility::pointer::owning_ptr
< WeightedFragmentTrialMover
WeightedFragmentTrialMoverOP
 
typedef
utility::pointer::owning_ptr
< WeightedFragmentTrialMover
const > 
WeightedFragmentTrialMoverCOP
 

Enumerations

enum  AlignOption { all_chunks, random_chunk }
 

Functions

void add_constraints (core::pose::Pose &pose, Size rsd1, Size rsd2)
 
void optimize (core::pose::Pose &pose, Size rsd1, Size rsd2, core::scoring::ScoreFunctionOP scorefxn, Size ncycles, core::Real max_delta_torsion)
 
void pick_pivots (core::pose::Pose &pose, Size &rsd1, Size &torsion1, Size &rsd2, Size &torsion2, Size variance=5)
 
bool TMalign_poses (core::pose::Pose &aligned_pose, core::pose::Pose const &ref_pose, std::list< Size > const &residue_list, std::list< Size > const &ref_residue_list)
 
void remove_residues (core::pose::Pose &pose, utility::vector1< int > const resnum_list, utility::vector1< int > &remaining_resnum)
 
utility::vector1< Sizefind_uncovered_residues (core::pose::Pose const &pose, utility::vector1< Size > const covered_residues)
 
core::Real gap_distance (Size Seq_gap)
 
core::Size parse_res (core::pose::Pose const &pose, std::string resnum)
 
core::Size get_num_residues_nonvirt (core::pose::Pose const &pose)
 
core::Size get_num_residues_prot (core::pose::Pose const &pose)
 
void setup_centroid_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real > template_weights, std::string cen_cst_file, std::set< core::Size > ignore_res_for_AUTO)
 
void setup_fullatom_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real > template_weights, std::string cen_cst_file, std::string fa_cst_file)
 
void generate_centroid_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real >, std::set< core::Size > ignore_res)
 
void setup_user_coordinate_constraints (core::pose::Pose &pose, utility::vector1< Size > reses)
 
void setup_interface_coordinate_constraints (core::pose::Pose &pose, utility::vector1< bool > ignore_res)
 
void setup_interface_atompair_constraints (core::pose::Pose &pose, utility::vector1< bool > ignore_res)
 
void generate_fullatom_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real > template_weights)
 
void add_strand_pairs_cst (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const strand_pairs)
 
void add_non_protein_cst (core::pose::Pose &pose, core::Real const self_cst_weight, core::Real const het_prot_cst_weight)
 
bool discontinued_upper (core::pose::Pose const &pose, Size const seqpos)
 
bool discontinued_lower (core::pose::Pose const &pose, Size const seqpos)
 
std::list< Sizedownstream_residues_from_jump (core::pose::Pose const &pose, Size const jump_number)
 
void partial_align (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, bool iterate_convergence, utility::vector1< core::Real > distance_thresholds, core::Real min_coverage)
 
void partial_align (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, std::list< Size > const &residue_list, bool iterate_convergence, utility::vector1< core::Real > distance_thresholds, core::Real min_coverage)
 
core::Size atom_map_valid_size (core::pose::Pose const &pose, core::id::AtomID_Map< core::id::AtomID > const &atom_map)
 
core::id::AtomID_Map
< core::id::AtomID
update_atom_map (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real distance_squared_threshold)
 
Size natom_aligned (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real distance_squared_threshold)
 
void get_superposition_transformation (pose::Pose const &mod_pose, pose::Pose const &ref_pose, core::id::AtomID_Map< core::id::AtomID > const &atom_map, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT)
 
void apply_transformation (pose::Pose &mod_pose, std::list< Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT)
 
core::fragment::FragSetOP create_fragment_set (core::pose::Pose const &pose, core::Size len, core::Size nfrag)
 
core::fragment::FragSetOP create_fragment_set_no_ssbias (core::pose::Pose const &pose, core::Size len, core::Size nfrag, char force_ss)
 
core::fragment::FragSetOP create_fragment_set_no_ssbias (core::pose::Pose const &pose, std::set< core::Size > user_pos, core::Size len, core::Size nfrag, char force_ss)
 
protocols::loops::Loops renumber_with_pdb_info (protocols::loops::Loops &template_chunk, core::pose::PoseCOP template_pose)
 
core::Real get_gdtmm (core::pose::Pose &native, core::pose::Pose &pose, core::sequence::SequenceAlignmentOP &aln)
 

Variables

const core::Size DEFAULT_NCYCLES =400
 
static basic::Tracer TR ("protocols.hybridization.CartesianHybridize")
 
static basic::Tracer TR ("protocols.hybridization.CartesianSampler")
 
static
numeric::random::RandomGenerator 
RG (8403155)
 
static basic::Tracer TR ("protocols.electron_density.util")
 
static basic::Tracer TZ ("protocols.hybridization.TemplateHistory")
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
all_chunks 
random_chunk 

Function Documentation

void protocols::hybridization::add_constraints ( core::pose::Pose pose,
Size  rsd1,
Size  rsd2 
)
void protocols::hybridization::add_non_protein_cst ( core::pose::Pose pose,
core::Real const  self_cst_weight,
core::Real const  het_prot_cst_weight 
)
void protocols::hybridization::add_strand_pairs_cst ( core::pose::Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > const  strand_pairs 
)
void protocols::hybridization::apply_transformation ( pose::Pose mod_pose,
std::list< Size > const &  residue_list,
numeric::xyzMatrix< core::Real > const &  R,
numeric::xyzVector< core::Real > const &  preT,
numeric::xyzVector< core::Real > const &  postT 
)
core::Size protocols::hybridization::atom_map_valid_size ( core::pose::Pose const &  pose,
core::id::AtomID_Map< core::id::AtomID > const &  atom_map 
)
core::fragment::FragSetOP protocols::hybridization::create_fragment_set ( core::pose::Pose const &  pose,
core::Size  len,
core::Size  nfrag 
)
core::fragment::FragSetOP protocols::hybridization::create_fragment_set_no_ssbias ( core::pose::Pose const &  pose,
core::Size  len,
core::Size  nfrag,
char  force_ss 
)
core::fragment::FragSetOP protocols::hybridization::create_fragment_set_no_ssbias ( core::pose::Pose const &  pose,
std::set< core::Size user_pos,
core::Size  len,
core::Size  nfrag,
char  force_ss 
)
bool protocols::hybridization::discontinued_lower ( core::pose::Pose const &  pose,
Size const  seqpos 
)
bool protocols::hybridization::discontinued_upper ( core::pose::Pose const &  pose,
Size const  seqpos 
)
std::list< core::Size > protocols::hybridization::downstream_residues_from_jump ( core::pose::Pose const &  pose,
Size const  jump_number 
)
utility::vector1<Size> protocols::hybridization::find_uncovered_residues ( core::pose::Pose const &  pose,
utility::vector1< Size > const  covered_residues 
)
core::Real protocols::hybridization::gap_distance ( Size  Seq_gap)
void protocols::hybridization::generate_centroid_constraints ( core::pose::Pose pose,
utility::vector1< core::pose::PoseCOP templates,
utility::vector1< core::Real ,
std::set< core::Size ignore_res 
)
void protocols::hybridization::generate_fullatom_constraints ( core::pose::Pose pose,
utility::vector1< core::pose::PoseCOP templates,
utility::vector1< core::Real template_weights 
)
core::Real protocols::hybridization::get_gdtmm ( core::pose::Pose native,
core::pose::Pose pose,
core::sequence::SequenceAlignmentOP aln 
)
core::Size protocols::hybridization::get_num_residues_nonvirt ( core::pose::Pose const &  pose)
core::Size protocols::hybridization::get_num_residues_prot ( core::pose::Pose const &  pose)
void protocols::hybridization::get_superposition_transformation ( pose::Pose const &  mod_pose,
pose::Pose const &  ref_pose,
core::id::AtomID_Map< core::id::AtomID > const &  atom_map,
numeric::xyzMatrix< core::Real > &  R,
numeric::xyzVector< core::Real > &  preT,
numeric::xyzVector< core::Real > &  postT 
)
core::Size protocols::hybridization::natom_aligned ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
id::AtomID_Map< id::AtomID > const &  atom_map,
core::Real  distance_squared_threshold 
)
void protocols::hybridization::optimize ( core::pose::Pose pose,
Size  rsd1,
Size  rsd2,
core::scoring::ScoreFunctionOP  scorefxn,
Size  ncycles,
core::Real  max_delta_torsion 
)
core::Size protocols::hybridization::parse_res ( core::pose::Pose const &  pose,
std::string  resnum 
)
void protocols::hybridization::partial_align ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
id::AtomID_Map< id::AtomID > const &  atom_map,
bool  iterate_convergence,
utility::vector1< core::Real distance_thresholds,
core::Real  min_coverage 
)
void protocols::hybridization::partial_align ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
id::AtomID_Map< id::AtomID > const &  atom_map,
std::list< Size > const &  residue_list,
bool  iterate_convergence,
utility::vector1< core::Real distance_thresholds,
core::Real  min_coverage 
)
void protocols::hybridization::pick_pivots ( core::pose::Pose pose,
Size rsd1,
Size torsion1,
Size rsd2,
Size torsion2,
Size  variance = 5 
)
void protocols::hybridization::remove_residues ( core::pose::Pose pose,
utility::vector1< int > const  resnum_list,
utility::vector1< int > &  remaining_resnum 
)
protocols::loops::Loops protocols::hybridization::renumber_with_pdb_info ( protocols::loops::Loops template_chunk,
core::pose::PoseCOP  template_pose 
)
void protocols::hybridization::setup_centroid_constraints ( core::pose::Pose pose,
utility::vector1< core::pose::PoseCOP templates,
utility::vector1< core::Real template_weights,
std::string  cen_cst_file,
std::set< core::Size ignore_res_for_AUTO 
)
void protocols::hybridization::setup_fullatom_constraints ( core::pose::Pose pose,
utility::vector1< core::pose::PoseCOP templates,
utility::vector1< core::Real template_weights,
std::string  cen_cst_file,
std::string  fa_cst_file 
)
void protocols::hybridization::setup_interface_atompair_constraints ( core::pose::Pose pose,
utility::vector1< bool ignore_res 
)
void protocols::hybridization::setup_interface_coordinate_constraints ( core::pose::Pose pose,
utility::vector1< bool ignore_res 
)
void protocols::hybridization::setup_user_coordinate_constraints ( core::pose::Pose pose,
utility::vector1< Size reses 
)
bool protocols::hybridization::TMalign_poses ( core::pose::Pose aligned_pose,
core::pose::Pose const &  ref_pose,
std::list< Size > const &  residue_list,
std::list< Size > const &  ref_residue_list 
)
core::id::AtomID_Map< core::id::AtomID > protocols::hybridization::update_atom_map ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
id::AtomID_Map< id::AtomID > const &  atom_map,
core::Real  distance_squared_threshold 
)

Variable Documentation

const core::Size protocols::hybridization::DEFAULT_NCYCLES =400
numeric::random::RandomGenerator protocols::hybridization::RG(8403155)
static
basic::Tracer protocols::hybridization::TR("protocols.electron_density.util")
static
basic::Tracer protocols::hybridization::TR("protocols.hybridization.CartesianHybridize")
static

Referenced by add_constraints(), protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::hybridization::HybridizeFoldtreeDynamic::add_overlapping_pair_chunks(), protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::hybridization::HybridizeSetup::add_template(), protocols::hybridization::HybridizeProtocol::add_template(), protocols::hybridization::HybridizeSetup::align_by_domain(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::hybridization::WeightedFragmentSmoothTrialMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::hybridization::HybridizeSetupMover::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::FoldTreeHybridize::auto_frag_insertion_weight(), protocols::hybridization::CartesianHybridize::CartesianHybridize(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), create_fragment_set_no_ssbias(), protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts(), downstream_residues_from_jump(), protocols::hybridization::FoldTreeHybridize::filter_templates(), protocols::hybridization::ChunkTrialMover::get_alignment_from_template(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_1mers(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_big_frags(), protocols::hybridization::FoldTreeHybridize::get_residue_weights_for_small_frags(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::hybridization::hConvergenceCheck::operator()(), protocols::hybridization::FoldTreeHybridize::parse_my_tag(), protocols::hybridization::HybridizeSetupMover::parse_my_tag(), pick_pivots(), protocols::hybridization::HybridizeProtocol::read_template_structures(), protocols::hybridization::HybridizeSetup::realign_templates(), protocols::hybridization::DomainAssembly::run(), protocols::hybridization::InsertChunkMover::set_aligned_chunk(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), protocols::hybridization::CartesianHybridize::setup_for_parser(), setup_interface_atompair_constraints(), setup_interface_coordinate_constraints(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), TMalign_poses(), protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

basic::Tracer protocols::hybridization::TR("protocols.hybridization.CartesianSampler")
static
basic::Tracer protocols::hybridization::TZ("protocols.hybridization.TemplateHistory")
static