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protocols::indexed_structure_store Namespace Reference

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Classes

struct  _map_string_vector_Real
 
struct  _map_string_vector_Size
 
struct  _map_string_vector_vector_Real
 
class  BinaryFragmentStoreBackend
 
struct  DirectSegmentLookup
 
struct  DirectSegmentLookupConfig
 
struct  DirectSegmentLookupResult
 
class  DirStructureStoreBackend
 
class  FragmentLookup
 
class  FragmentLookupResult
 
struct  FragmentSpecification
 
class  FragmentStore
 
class  FragmentStoreManager
 
class  FragmentStoreProvider
 
class  JSONStructureStoreBackend
 
class  PoseUtilityPlaceholder
 
struct  ResidueBackboneEntry
 
struct  ResidueEntry
 
struct  ResidueOrientEntry
 
struct  ResidueSidechainEntry
 
struct  SegmentSequenceProfile
 
struct  SegmentSequenceProfileConfig
 
struct  SegmentSequenceProfileResult
 
class  SilentStructureStoreBackend
 
class  SSHashedFragmentStore
 
struct  StructureEntry
 
struct  StructureRecord
 
class  StructureStore
 
class  StructureStoreManager
 
class  StructureStoreProvider
 

Typedefs

typedef
utility::pointer::shared_ptr
< FragmentLookup
FragmentLookupOP
 
typedef
utility::pointer::shared_ptr
< FragmentLookup const > 
FragmentLookupCOP
 
typedef
utility::pointer::weak_ptr
< FragmentLookup
FragmentLookupAP
 
typedef
utility::pointer::weak_ptr
< FragmentLookup const > 
FragmentLookupCAP
 
typedef
utility::pointer::shared_ptr
< FragmentStore
FragmentStoreOP
 
typedef
utility::pointer::shared_ptr
< FragmentStore const > 
FragmentStoreCOP
 
typedef
utility::pointer::shared_ptr
< FragmentStoreProvider
FragmentStoreProviderOP
 
typedef
utility::pointer::shared_ptr
< FragmentStoreProvider const > 
FragmentStoreProviderCOP
 
typedef
utility::pointer::shared_ptr
< StructureStore
StructureStoreOP
 
typedef
utility::pointer::shared_ptr
< StructureStore const > 
StructureStoreCOP
 
typedef
utility::pointer::weak_ptr
< StructureStore
StructureStoreAP
 
typedef
utility::pointer::shared_ptr
< StructureStoreProvider
StructureStoreProviderOP
 
typedef
utility::pointer::shared_ptr
< StructureStoreProvider const > 
StructureStoreProviderCOP
 

Enumerations

enum  OverlapDeleteMode { DELETE_UPSTREAM, DELETE_DOWNSTREAM }
 

Functions

static basic::Tracer TR ("core.indexed_structure_store.BinaryFragmentStoreBackend")
 
void to_json (nlohmann::json &j, const ResidueBackboneEntry &i)
 
void from_json (const nlohmann::json &j, ResidueBackboneEntry &i)
 
void to_json (nlohmann::json &j, const ResidueSidechainEntry &i)
 
void from_json (const nlohmann::json &j, ResidueSidechainEntry &i)
 
void to_json (nlohmann::json &j, const ResidueOrientEntry &i)
 
void from_json (const nlohmann::json &j, ResidueOrientEntry &i)
 
void to_json (nlohmann::json &j, const ResidueEntry &i)
 
void from_json (const nlohmann::json &j, ResidueEntry &i)
 
void to_json (nlohmann::json &j, const StructureEntry &i)
 
void from_json (const nlohmann::json &j, StructureEntry &i)
 
ndarray::Array< ResidueEntry, 1, 1 > _pose_res (core::pose::Pose &pose, core::Size start_res, core::Size end_res)
 
void to_json (nlohmann::json &j, const DirectSegmentLookupConfig &c)
 
void from_json (const nlohmann::json &j, DirectSegmentLookupConfig &c)
 
static basic::Tracer TR ("core.indexed_structure_store.DirStructureStoreBackend")
 
std::ostream & operator<< (std::ostream &os, const FragmentSpecification &s)
 
static basic::Tracer TR ("core.indexed_structure_store.FragmentStoreManager")
 
static basic::Tracer TR ("core.indexed_structure_store.JSONStructureStoreBackend")
 
void to_json (json &j, const StructureRecord &i)
 
void from_json (const json &j, StructureRecord &i)
 
ndarray::ArrayRef< float, 4, 1 > orient_array (ndarray::Array< ResidueEntry, 2 > res)
 
ndarray::ArrayRef< float, 3, 1 > orient_array (ndarray::Array< ResidueEntry, 1 > res)
 
ndarray::ArrayRef< float, 2, 1 > orient_array (ResidueEntry &src)
 
ResidueEntry extract_residue_entry (core::conformation::Residue const &res)
 
ndarray::Array< ResidueEntry, 1 > extract_residue_entries (core::pose::Pose const &pose, bool ignore_non_protein)
 
void apply_residue_entries_to_pose (ndarray::Array< ResidueEntry, 1 > residue_entries, core::pose::Pose &pose, core::Size start_residue, bool apply_bb, bool apply_sidechain, bool apply_orient)
 
core::pose::PoseOP residue_entries_to_pose (ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 > residue_entries, std::string residue_type, bool auto_termini)
 
template<typename Range >
std::string to_str (Range range)
 
template<typename Range , typename Op >
std::vector< size_t > index_if (Range const &r, Op &pred)
 
core::pose::PoseOP initial_pose_for_residues (ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 > residue_entries, std::string residue_type, bool auto_termini)
 
core::pose::PoseOP residue_entries_to_pose (ndarray::Array< ResidueEntry, 1 > residue_entries, std::string residue_type="fa_standard", bool auto_termini=true)
 
template<typename ResidueRange >
core::pose::PoseOP residue_entries_to_pose (ResidueRange residue_entries, std::string residue_type="fa_standard", bool auto_termini=true)
 
core::pose::PoseOP initial_pose_for_residues (ndarray::Array< ResidueEntry, 1 > residue_entries, std::string residue_type="fa_standard", bool auto_termini=true)
 
core::pose::PoseOP pose_from_store (StructureStore &store, uint32_t structure_id)
 
template<typename Module >
void bind_pose_utility (Module &m)
 
void to_json (nlohmann::json &j, const SegmentSequenceProfileConfig &c)
 
void from_json (const nlohmann::json &j, SegmentSequenceProfileConfig &c)
 
static basic::Tracer TR ("core.indexed_structure_store.SilentStructureStoreBackend")
 
template<typename Module >
void bind_StructureStore (Module &m)
 
static basic::Tracer TR ("core.indexed_structure_store.StructureStoreManager")
 
core::pose::PoseOP append_pose_by_bond (core::pose::Pose &upstream_pose, core::pose::Pose &downstream_pose)
 
core::pose::PoseOP append_pose_with_overlap (core::pose::Pose &upstream_pose, core::pose::Pose &downstream_pose, core::Size overlap, OverlapDeleteMode delete_overlap)
 

Typedef Documentation

typedef utility::pointer::weak_ptr<FragmentLookup const> protocols::indexed_structure_store::FragmentLookupCAP
typedef utility::pointer::shared_ptr<FragmentLookup const> protocols::indexed_structure_store::FragmentLookupCOP
typedef utility::pointer::shared_ptr<FragmentStore const> protocols::indexed_structure_store::FragmentStoreCOP
typedef utility::pointer::shared_ptr<StructureStore const> protocols::indexed_structure_store::StructureStoreCOP

Enumeration Type Documentation

Enumerator
DELETE_UPSTREAM 
DELETE_DOWNSTREAM 

Function Documentation

ndarray::Array<ResidueEntry, 1, 1> protocols::indexed_structure_store::_pose_res ( core::pose::Pose pose,
core::Size  start_res,
core::Size  end_res 
)
core::pose::PoseOP protocols::indexed_structure_store::append_pose_by_bond ( core::pose::Pose upstream_pose,
core::pose::Pose downstream_pose 
)
core::pose::PoseOP protocols::indexed_structure_store::append_pose_with_overlap ( core::pose::Pose upstream_pose,
core::pose::Pose downstream_pose,
core::Size  overlap,
OverlapDeleteMode  delete_overlap 
)
void protocols::indexed_structure_store::apply_residue_entries_to_pose ( ndarray::Array< ResidueEntry, 1 >  residue_entries,
core::pose::Pose pose,
core::Size  start_residue,
bool  apply_bb,
bool  apply_sidechain,
bool  apply_orient 
)
template<typename Module >
void protocols::indexed_structure_store::bind_pose_utility ( Module &  m)
template<typename Module >
void protocols::indexed_structure_store::bind_StructureStore ( Module &  m)
ndarray::Array< ResidueEntry, 1 > protocols::indexed_structure_store::extract_residue_entries ( core::pose::Pose const &  pose,
bool  ignore_non_protein 
)
ResidueEntry protocols::indexed_structure_store::extract_residue_entry ( core::conformation::Residue const &  res)
void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j,
SegmentSequenceProfileConfig &  c 
)
inline
void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j,
DirectSegmentLookupConfig &  c 
)
inline
void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j,
ResidueBackboneEntry &  i 
)
inline
void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j,
ResidueSidechainEntry &  i 
)
inline
void protocols::indexed_structure_store::from_json ( const json &  j,
StructureRecord &  i 
)
inline
void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j,
ResidueOrientEntry &  i 
)
inline
void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j,
ResidueEntry &  i 
)
inline
void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j,
StructureEntry &  i 
)
inline
template<typename Range , typename Op >
std::vector<size_t> protocols::indexed_structure_store::index_if ( Range const &  r,
Op &  pred 
)

References core::scoring::pair.

core::pose::PoseOP protocols::indexed_structure_store::initial_pose_for_residues ( ndarray::Array< ResidueEntry, 1 >  residue_entries,
std::string  residue_type = "fa_standard",
bool  auto_termini = true 
)
core::pose::PoseOP protocols::indexed_structure_store::initial_pose_for_residues ( ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 >  residue_entries,
std::string  residue_type,
bool  auto_termini 
)
std::ostream& protocols::indexed_structure_store::operator<< ( std::ostream &  os,
const FragmentSpecification &  s 
)
ndarray::ArrayRef<float, 4, 1> protocols::indexed_structure_store::orient_array ( ndarray::Array< ResidueEntry, 2 >  res)
inline
ndarray::ArrayRef<float, 3, 1> protocols::indexed_structure_store::orient_array ( ndarray::Array< ResidueEntry, 1 >  res)
inline
ndarray::ArrayRef<float, 2, 1> protocols::indexed_structure_store::orient_array ( ResidueEntry &  src)
inline
core::pose::PoseOP protocols::indexed_structure_store::pose_from_store ( StructureStore &  store,
uint32_t  structure_id 
)
core::pose::PoseOP protocols::indexed_structure_store::residue_entries_to_pose ( ndarray::Array< ResidueEntry, 1 >  residue_entries,
std::string  residue_type = "fa_standard",
bool  auto_termini = true 
)
template<typename ResidueRange >
core::pose::PoseOP protocols::indexed_structure_store::residue_entries_to_pose ( ResidueRange  residue_entries,
std::string  residue_type = "fa_standard",
bool  auto_termini = true 
)
core::pose::PoseOP protocols::indexed_structure_store::residue_entries_to_pose ( ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 >  residue_entries,
std::string  residue_type,
bool  auto_termini 
)
void protocols::indexed_structure_store::to_json ( nlohmann::json &  j,
const DirectSegmentLookupConfig &  c 
)
inline
void protocols::indexed_structure_store::to_json ( nlohmann::json &  j,
const SegmentSequenceProfileConfig &  c 
)
inline
void protocols::indexed_structure_store::to_json ( nlohmann::json &  j,
const ResidueBackboneEntry &  i 
)
inline
void protocols::indexed_structure_store::to_json ( nlohmann::json &  j,
const ResidueSidechainEntry &  i 
)
inline
void protocols::indexed_structure_store::to_json ( json &  j,
const StructureRecord &  i 
)
inline
void protocols::indexed_structure_store::to_json ( nlohmann::json &  j,
const ResidueOrientEntry &  i 
)
inline
void protocols::indexed_structure_store::to_json ( nlohmann::json &  j,
const ResidueEntry &  i 
)
inline
void protocols::indexed_structure_store::to_json ( nlohmann::json &  j,
const StructureEntry &  i 
)
inline
template<typename Range >
std::string protocols::indexed_structure_store::to_str ( Range  range)

References core::sequence::end.

static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.BinaryFragmentStoreBackend"  )
static
static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.FragmentStoreManager"  )
static
static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.DirStructureStoreBackend"  )
static
static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.SilentStructureStoreBackend"  )
static
static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.JSONStructureStoreBackend"  )
static
static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.StructureStoreManager"  )
static