indexed_structure_store¶

Bindings for protocols::indexed_structure_store namespace

class pyrosetta.rosetta.protocols.indexed_structure_store.BackboneStub¶

Bases: pybind11_object

property index_match¶

property rmsd_match¶

property ss_index_match¶

class pyrosetta.rosetta.protocols.indexed_structure_store.BackboneStubVectorRMSDComparator¶: Bases: pybind11_object

class pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend¶

Bases: FragmentStoreProvider

append_to_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend, fragment_store: protocols::indexed_structure_store::FragmentStore, store_name: str, group_field: str, group_type: str) → None¶: C++: protocols::indexed_structure_store::BinaryFragmentStoreBackend::append_to_fragment_store(class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>, std::string, std::string, std::string) –> void

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend, : pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend) → pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend¶: C++: protocols::indexed_structure_store::BinaryFragmentStoreBackend::operator=(const class protocols::indexed_structure_store::BinaryFragmentStoreBackend &) –> class protocols::indexed_structure_store::BinaryFragmentStoreBackend &

get_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend, store_name: str) → protocols::indexed_structure_store::FragmentStore¶: C++: protocols::indexed_structure_store::BinaryFragmentStoreBackend::get_fragment_store(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>

set_target_filename(self: pyrosetta.rosetta.protocols.indexed_structure_store.BinaryFragmentStoreBackend, target_filename: str) → None¶: C++: protocols::indexed_structure_store::BinaryFragmentStoreBackend::set_target_filename(std::string) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend¶

Bases: StructureStoreProvider

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend, : pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend) → pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend¶: C++: protocols::indexed_structure_store::DirStructureStoreBackend::operator=(const class protocols::indexed_structure_store::DirStructureStoreBackend &) –> class protocols::indexed_structure_store::DirStructureStoreBackend &

can_load(self: pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend, store_path: str) → bool¶: C++: protocols::indexed_structure_store::DirStructureStoreBackend::can_load(std::string) –> bool

can_write(self: pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend, store_path: str) → bool¶: C++: protocols::indexed_structure_store::DirStructureStoreBackend::can_write(std::string) –> bool

load_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend, store_path: str) → protocols::indexed_structure_store::StructureStore¶: C++: protocols::indexed_structure_store::DirStructureStoreBackend::load_store(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::StructureStore>

write_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend, store_path: str, store: protocols::indexed_structure_store::StructureStore) → None¶: C++: protocols::indexed_structure_store::DirStructureStoreBackend::write_store(std::string, class protocols::indexed_structure_store::StructureStore &) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookup¶

Bases: pybind11_object

property config¶

property query_stats¶

class pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig, : pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig) → pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig¶: C++: protocols::indexed_structure_store::DirectSegmentLookupConfig::operator=(const struct protocols::indexed_structure_store::DirectSegmentLookupConfig &) –> struct protocols::indexed_structure_store::DirectSegmentLookupConfig &

property max_insertion_length¶

property rmsd_tolerance¶

property segment_cluster_tolerance¶

class pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupResult¶

Bases: pybind11_object

property query_results¶

property result_residues¶

class pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup, : pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup¶: C++: protocols::indexed_structure_store::FragmentLookup::operator=(const class protocols::indexed_structure_store::FragmentLookup &) –> class protocols::indexed_structure_store::FragmentLookup &

fragment_specification(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification¶: C++: protocols::indexed_structure_store::FragmentLookup::fragment_specification() –> const struct protocols::indexed_structure_store::FragmentSpecification &

lookup_closest_fragment(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup, input: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult¶: C++: protocols::indexed_structure_store::FragmentLookup::lookup_closest_fragment(class numeric::xyzVector<double> *) –> class protocols::indexed_structure_store::FragmentLookupResult

lookup_fragment(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup, input: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult¶: C++: protocols::indexed_structure_store::FragmentLookup::lookup_fragment(class numeric::xyzVector<double> *) –> class protocols::indexed_structure_store::FragmentLookupResult

store(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore¶: C++: protocols::indexed_structure_store::FragmentLookup::store() –> class std::shared_ptr<const class protocols::indexed_structure_store::FragmentStore>

class pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult¶

Bases: pybind11_object

property found_match¶

property match_index¶

property match_rmsd¶

property match_rmsd_threshold¶

property match_score¶

class pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification, : pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification¶: C++: protocols::indexed_structure_store::FragmentSpecification::operator=(const struct protocols::indexed_structure_store::FragmentSpecification &) –> struct protocols::indexed_structure_store::FragmentSpecification &

coordinates_per_fragment(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification) → int¶: C++: protocols::indexed_structure_store::FragmentSpecification::coordinates_per_fragment() const –> unsigned long

property fragment_atoms¶

property fragment_length¶

class pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore¶

Bases: pybind11_object

add_threshold_distance_allFrag(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore, distance: float) → None¶: C++: protocols::indexed_structure_store::FragmentStore::add_threshold_distance_allFrag(double) –> void

delete_homologs(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore) → None¶: C++: protocols::indexed_structure_store::FragmentStore::delete_homologs() –> void

property fragment_coordinates¶

property fragment_specification¶

property fragment_threshold_distances¶

generate_residue_subset_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore, residues: pyrosetta.rosetta.std.vector_unsigned_long) → None¶: C++: protocols::indexed_structure_store::FragmentStore::generate_residue_subset_fragment_store(class std::vector<unsigned long, class std::allocator<unsigned long> >) –> void

get_fragmentLookup(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore) → protocols::indexed_structure_store::FragmentLookup¶: C++: protocols::indexed_structure_store::FragmentStore::get_fragmentLookup() –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentLookup>

get_fragment_coordinates(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore, position: int) → pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t¶: C++: protocols::indexed_structure_store::FragmentStore::get_fragment_coordinates(unsigned long) –> class std::vector<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_homologs(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore) → pyrosetta.rosetta.std.set_std_string_t¶: C++: protocols::indexed_structure_store::FragmentStore::get_homologs() –> class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >

get_self_ptr(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore¶

self pointer

C++: protocols::indexed_structure_store::FragmentStore::get_self_ptr() –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>

property hash_id¶

property int64_groups¶

property num_fragments_¶

property realVector_groups¶

property real_groups¶

property residue_subset_fragment_store¶

resize(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore, num_fragments: int) → None¶: C++: protocols::indexed_structure_store::FragmentStore::resize(unsigned long) –> void

property string_groups¶

class pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager¶

Bases: SingletonBase_protocols_indexed_structure_store_FragmentStoreManager_t

SSHashedFragmentStore(*args, **kwargs)¶

Overloaded function.

SSHashedFragmentStore(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager) -> protocols::indexed_structure_store::SSHashedFragmentStore
SSHashedFragmentStore(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, store_path: str) -> protocols::indexed_structure_store::SSHashedFragmentStore
SSHashedFragmentStore(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, store_path: str, store_format: str) -> protocols::indexed_structure_store::SSHashedFragmentStore
SSHashedFragmentStore(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, store_path: str, store_format: str, store_compression: str) -> protocols::indexed_structure_store::SSHashedFragmentStore

C++: protocols::indexed_structure_store::FragmentStoreManager::SSHashedFragmentStore(std::string, std::string, std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::SSHashedFragmentStore>

find_previously_loaded_fragmentStore(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, fragment_store_path: str) → pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t¶: C++: protocols::indexed_structure_store::FragmentStoreManager::find_previously_loaded_fragmentStore(const std::string &) –> class std::map<unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore> > > >

static get_instance() → protocols::indexed_structure_store::FragmentStoreManager¶: C++: utility::SingletonBase<protocols::indexed_structure_store::FragmentStoreManager>::get_instance() –> class protocols::indexed_structure_store::FragmentStoreManager *

load_and_hash_fragmentStore(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, fragment_store_path: str, fragment_store_compression: str, fragment_size: int) → pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t¶: C++: protocols::indexed_structure_store::FragmentStoreManager::load_and_hash_fragmentStore(const std::string &, const std::string &, const unsigned long &) –> class std::map<unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore> > > >

load_fragment_lookup(*args, **kwargs)¶

Overloaded function.

load_fragment_lookup(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, lookup_name: str) -> pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup

C++: protocols::indexed_structure_store::FragmentStoreManager::load_fragment_lookup(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentLookup>

load_fragment_lookup(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, lookup_name: str, store_path: str) -> pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup

C++: protocols::indexed_structure_store::FragmentStoreManager::load_fragment_lookup(std::string, std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentLookup>

load_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, lookup_name: str, store_path: str, fields_to_load: pyrosetta.rosetta.utility.vector1_std_string, fields_to_load_types: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore¶: C++: protocols::indexed_structure_store::FragmentStoreManager::load_fragment_store(std::string, std::string, class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<std::string, class std::allocator<std::string > >) –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>

load_grouped_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, group_field: str, lookup_name: str, store_path: str, fields_to_load: pyrosetta.rosetta.utility.vector1_std_string, fields_to_load_types: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t¶: C++: protocols::indexed_structure_store::FragmentStoreManager::load_grouped_fragment_store(std::string, std::string, std::string, class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<std::string, class std::allocator<std::string > >) –> class std::map<unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore> > > >

register_store_provider(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, priority: int, name: str, backend: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider) → None¶: C++: protocols::indexed_structure_store::FragmentStoreManager::register_store_provider(long, std::string, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStoreProvider>) –> void

resolve_store_path(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager, store_path: str) → str¶: C++: protocols::indexed_structure_store::FragmentStoreManager::resolve_store_path(std::string) –> std::string

class pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider¶

Bases: pybind11_object

append_to_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider, fragment_store: protocols::indexed_structure_store::FragmentStore, store_name: str, group_field: str, group_type: str) → None¶: C++: protocols::indexed_structure_store::FragmentStoreProvider::append_to_fragment_store(class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>, std::string, std::string, std::string) –> void

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider, : pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider) → pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider¶: C++: protocols::indexed_structure_store::FragmentStoreProvider::operator=(const class protocols::indexed_structure_store::FragmentStoreProvider &) –> class protocols::indexed_structure_store::FragmentStoreProvider &

get_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider, store_name: str) → protocols::indexed_structure_store::FragmentStore¶: C++: protocols::indexed_structure_store::FragmentStoreProvider::get_fragment_store(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>

set_target_filename(self: pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreProvider, target_filename: str) → None¶: C++: protocols::indexed_structure_store::FragmentStoreProvider::set_target_filename(std::string) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend¶

Bases: StructureStoreProvider

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend, : pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend) → pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend¶: C++: protocols::indexed_structure_store::JSONStructureStoreBackend::operator=(const class protocols::indexed_structure_store::JSONStructureStoreBackend &) –> class protocols::indexed_structure_store::JSONStructureStoreBackend &

can_load(self: pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend, store_path: str) → bool¶: C++: protocols::indexed_structure_store::JSONStructureStoreBackend::can_load(std::string) –> bool

can_write(self: pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend, store_path: str) → bool¶: C++: protocols::indexed_structure_store::JSONStructureStoreBackend::can_write(std::string) –> bool

load_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend, store_path: str) → protocols::indexed_structure_store::StructureStore¶: C++: protocols::indexed_structure_store::JSONStructureStoreBackend::load_store(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::StructureStore>

write_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend, store_path: str, store: protocols::indexed_structure_store::StructureStore) → None¶: C++: protocols::indexed_structure_store::JSONStructureStoreBackend::write_store(std::string, class protocols::indexed_structure_store::StructureStore &) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store.OverlapDeleteMode¶

Bases: pybind11_object

Members:

DELETE_UPSTREAM

DELETE_DOWNSTREAM

DELETE_DOWNSTREAM = <OverlapDeleteMode.DELETE_DOWNSTREAM: 1>¶

DELETE_UPSTREAM = <OverlapDeleteMode.DELETE_UPSTREAM: 0>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry, : pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry) → pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry¶: C++: protocols::indexed_structure_store::ResidueBackboneEntry::operator=(const struct protocols::indexed_structure_store::ResidueBackboneEntry &) –> struct protocols::indexed_structure_store::ResidueBackboneEntry &

property omega¶

property phi¶

property psi¶

class pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry¶

Bases: pybind11_object

property bb¶

property cen¶

property chain_ending¶

static comp_id(a: pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry, b: pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry) → bool¶: C++: protocols::indexed_structure_store::ResidueEntry::comp_id(struct protocols::indexed_structure_store::ResidueEntry, struct protocols::indexed_structure_store::ResidueEntry) –> bool

property orient¶

property residue_id¶

property sc¶

property ss¶

property structure_id¶

class pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry¶

Bases: pybind11_object

property C¶

property CA¶

property N¶

property O¶

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry, : pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry) → pyrosetta.rosetta.protocols.indexed_structure_store.ResidueOrientEntry¶: C++: protocols::indexed_structure_store::ResidueOrientEntry::operator=(const struct protocols::indexed_structure_store::ResidueOrientEntry &) –> struct protocols::indexed_structure_store::ResidueOrientEntry &

class pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry¶

Bases: pybind11_object

property aa¶

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry, : pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry) → pyrosetta.rosetta.protocols.indexed_structure_store.ResidueSidechainEntry¶: C++: protocols::indexed_structure_store::ResidueSidechainEntry::operator=(const struct protocols::indexed_structure_store::ResidueSidechainEntry &) –> struct protocols::indexed_structure_store::ResidueSidechainEntry &

property chi1¶

property chi2¶

property chi3¶

property chi4¶

class pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore¶

Bases: pybind11_object

get_fragment_coordinates(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, db_index: int, match_index: int) → pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_coordinates(unsigned long, unsigned long) –> class std::vector<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

get_fragment_length(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore) → int¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_length() –> unsigned long

get_fragment_store(*args, **kwargs)¶

Overloaded function.

get_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, db_index: int) -> pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore

C++: protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_store(unsigned long) –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>

get_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore) -> pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore

C++: protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_store() –> class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>

get_hashed_fragment_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore) → pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::get_hashed_fragment_store() –> class std::map<unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::shared_ptr<class protocols::indexed_structure_store::FragmentStore> > > >

get_valid_resid(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → int¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::get_valid_resid(const class core::pose::Pose &, int) –> unsigned long

load_prehashed_fragmentStore(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, fragment_store_path: str) → None¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::load_prehashed_fragmentStore(const std::string &) –> void

lookback(*args, **kwargs)¶

Overloaded function.

lookback(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) -> float

C++: protocols::indexed_structure_store::SSHashedFragmentStore::lookback(const class core::pose::Pose &, unsigned long) –> double

lookback(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, frag_ss: str, find_closest: bool) -> float

C++: protocols::indexed_structure_store::SSHashedFragmentStore::lookback(const class core::pose::Pose &, unsigned long, std::string, bool) –> double

lookback_account_for_dssp_inaccuracy(*args, **kwargs)¶

Overloaded function.

lookback_account_for_dssp_inaccuracy(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, find_closest: bool, rms_threshold: float) -> float

C++: protocols::indexed_structure_store::SSHashedFragmentStore::lookback_account_for_dssp_inaccuracy(const class core::pose::Pose &, unsigned long, bool, double) –> double

lookback_account_for_dssp_inaccuracy(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, frags_ss: str, find_closest: bool, rms_threshold: float) -> float

C++: protocols::indexed_structure_store::SSHashedFragmentStore::lookback_account_for_dssp_inaccuracy(const class core::pose::Pose &, unsigned long, std::string, bool, double) –> double

lookback_account_for_dssp_inaccuracy(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, frag_ss: str, match_rmsd: float, match_index: int, match_ss_index: int) -> float

C++: protocols::indexed_structure_store::SSHashedFragmentStore::lookback_account_for_dssp_inaccuracy(const class core::pose::Pose &, unsigned long, std::string, double &, unsigned long &, unsigned long &) –> double

lookback_stub(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, coordinates: pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t, resTypeBeforeLoop: str, resTypeAfterLoop: str, loop_length: int, top_match_rmsd: float, stubVector: pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub, stubRmsdThreshold: float) → None¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::lookback_stub(class std::vector<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, char, char, unsigned long, double &, class utility::vector1<struct protocols::indexed_structure_store::BackboneStub, class std::allocator<struct protocols::indexed_structure_store::BackboneStub> > &, double) –> void

max_rmsd_in_region(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, pose: pyrosetta.rosetta.core.pose.Pose, resids: pyrosetta.rosetta.utility.vector1_unsigned_long) → float¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::max_rmsd_in_region(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> double

potential_valid_ss_strings(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, frag_ss: str) → pyrosetta.rosetta.std.set_std_string_t¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::potential_valid_ss_strings(std::string) –> class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >

set_threshold_distance(self: pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore, threshold_distance: float) → None¶: C++: protocols::indexed_structure_store::SSHashedFragmentStore::set_threshold_distance(double) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfile¶

Bases: pybind11_object

property config¶

property query_stats¶

segment_profile(self: pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfile, structure_store: protocols::indexed_structure_store::StructureStore, structure_db: protocols::indexed_structure_store::search::StructureDatabase, context: pyrosetta.rosetta.core.pose.Pose, segment_start: int, segment_end: int) → pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileResult¶: C++: protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(class protocols::indexed_structure_store::StructureStore &, class protocols::indexed_structure_store::search::StructureDatabase &, class core::pose::Pose &, unsigned long, unsigned long) –> struct protocols::indexed_structure_store::SegmentSequenceProfileResult

class pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig, : pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig) → pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig¶: C++: protocols::indexed_structure_store::SegmentSequenceProfileConfig::operator=(const struct protocols::indexed_structure_store::SegmentSequenceProfileConfig &) –> struct protocols::indexed_structure_store::SegmentSequenceProfileConfig &

property pseudocount¶

property rmsd_tolerance¶

class pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileResult¶

Bases: pybind11_object

property counts¶

property frequencies¶

property log_odds¶

property query_results¶

class pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend¶

Bases: StructureStoreProvider

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend, : pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend) → pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend¶: C++: protocols::indexed_structure_store::SilentStructureStoreBackend::operator=(const class protocols::indexed_structure_store::SilentStructureStoreBackend &) –> class protocols::indexed_structure_store::SilentStructureStoreBackend &

can_load(self: pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend, store_path: str) → bool¶: C++: protocols::indexed_structure_store::SilentStructureStoreBackend::can_load(std::string) –> bool

can_write(self: pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend, store_path: str) → bool¶: C++: protocols::indexed_structure_store::SilentStructureStoreBackend::can_write(std::string) –> bool

load_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend, store_path: str) → protocols::indexed_structure_store::StructureStore¶: C++: protocols::indexed_structure_store::SilentStructureStoreBackend::load_store(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::StructureStore>

write_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend, store_path: str, store: protocols::indexed_structure_store::StructureStore) → None¶: C++: protocols::indexed_structure_store::SilentStructureStoreBackend::write_store(std::string, class protocols::indexed_structure_store::StructureStore &) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store.StructureEntry¶

Bases: pybind11_object

static comp_id(a: pyrosetta.rosetta.protocols.indexed_structure_store.StructureEntry, b: pyrosetta.rosetta.protocols.indexed_structure_store.StructureEntry) → bool¶: C++: protocols::indexed_structure_store::StructureEntry::comp_id(struct protocols::indexed_structure_store::StructureEntry, struct protocols::indexed_structure_store::StructureEntry) –> bool

property id¶

class pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager¶

Bases: SingletonBase_protocols_indexed_structure_store_StructureStoreManager_t

delete_structure_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager, store_path: str) → None¶: C++: protocols::indexed_structure_store::StructureStoreManager::delete_structure_store(std::string) –> void

static get_instance() → protocols::indexed_structure_store::StructureStoreManager¶: C++: utility::SingletonBase<protocols::indexed_structure_store::StructureStoreManager>::get_instance() –> class protocols::indexed_structure_store::StructureStoreManager *

load_structure_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager, store_path: str) → protocols::indexed_structure_store::StructureStore¶: C++: protocols::indexed_structure_store::StructureStoreManager::load_structure_store(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::StructureStore>

register_store_provider(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager, priority: int, name: str, backend: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider) → None¶: C++: protocols::indexed_structure_store::StructureStoreManager::register_store_provider(long, std::string, class std::shared_ptr<class protocols::indexed_structure_store::StructureStoreProvider>) –> void

write_structure_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager, store_path: str, store: protocols::indexed_structure_store::StructureStore) → None¶: C++: protocols::indexed_structure_store::StructureStoreManager::write_structure_store(std::string, class protocols::indexed_structure_store::StructureStore &) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider, : pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider) → pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider¶: C++: protocols::indexed_structure_store::StructureStoreProvider::operator=(const class protocols::indexed_structure_store::StructureStoreProvider &) –> class protocols::indexed_structure_store::StructureStoreProvider &

can_load(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider, store_path: str) → bool¶: C++: protocols::indexed_structure_store::StructureStoreProvider::can_load(std::string) –> bool

can_write(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider, store_path: str) → bool¶: C++: protocols::indexed_structure_store::StructureStoreProvider::can_write(std::string) –> bool

load_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider, store_path: str) → protocols::indexed_structure_store::StructureStore¶: C++: protocols::indexed_structure_store::StructureStoreProvider::load_store(std::string) –> class std::shared_ptr<class protocols::indexed_structure_store::StructureStore>

write_store(self: pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider, store_path: str, store: protocols::indexed_structure_store::StructureStore) → None¶: C++: protocols::indexed_structure_store::StructureStoreProvider::write_store(std::string, class protocols::indexed_structure_store::StructureStore &) –> void

class pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Real¶

Bases: map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t

items(self: pyrosetta.rosetta.std.map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t) → pyrosetta.rosetta.std.ItemsView[map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t]¶

keys(self: pyrosetta.rosetta.std.map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t) → pyrosetta.rosetta.std.KeysView[map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t]¶

values(self: pyrosetta.rosetta.std.map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t) → pyrosetta.rosetta.std.ValuesView[map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t]¶

class pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Size¶

Bases: map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t

items(self: pyrosetta.rosetta.std.map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t) → pyrosetta.rosetta.std.ItemsView[map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t]¶

keys(self: pyrosetta.rosetta.std.map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t) → pyrosetta.rosetta.std.KeysView[map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t]¶

values(self: pyrosetta.rosetta.std.map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t) → pyrosetta.rosetta.std.ValuesView[map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t]¶

class pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_vector_Real¶

Bases: map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t

items(self: pyrosetta.rosetta.std.map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t) → pyrosetta.rosetta.std.ItemsView[map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t]¶

keys(self: pyrosetta.rosetta.std.map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t) → pyrosetta.rosetta.std.KeysView[map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t]¶

values(self: pyrosetta.rosetta.std.map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t) → pyrosetta.rosetta.std.ValuesView[map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t]¶

pyrosetta.rosetta.protocols.indexed_structure_store.append_pose_by_bond(upstream_pose: pyrosetta.rosetta.core.pose.Pose, downstream_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::indexed_structure_store::append_pose_by_bond(class core::pose::Pose &, class core::pose::Pose &) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.indexed_structure_store.append_pose_with_overlap(upstream_pose: pyrosetta.rosetta.core.pose.Pose, downstream_pose: pyrosetta.rosetta.core.pose.Pose, overlap: int, delete_overlap: pyrosetta.rosetta.protocols.indexed_structure_store.OverlapDeleteMode) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::indexed_structure_store::append_pose_with_overlap(class core::pose::Pose &, class core::pose::Pose &, unsigned long, enum protocols::indexed_structure_store::OverlapDeleteMode) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.indexed_structure_store.apply_residue_entries_to_pose(residue_entries: ndarray::Array[pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry, ndim=1, contiguous=0], pose: pyrosetta.rosetta.core.pose.Pose, start_residue: int = 1, apply_bb: bool = True, apply_sidechain: bool = True, apply_orient: bool = True) → None¶: Apply components residue entry array to pose conformation.

pyrosetta.rosetta.protocols.indexed_structure_store.extract_residue_entries(pose: pyrosetta.rosetta.core.pose.Pose, ignore_non_protein: bool = False) → ndarray::Array[pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry, ndim=1, contiguous=0]¶: Extract residue entry array from pose.

pyrosetta.rosetta.protocols.indexed_structure_store.extract_residue_entry(res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry¶: Extract residue entry from residue.

pyrosetta.rosetta.protocols.indexed_structure_store.initial_pose_for_residues(residue_entries: ndarray::Array[pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry, ndim=1, contiguous=0], residue_type: str = 'fa_standard', auto_termini: bool = True) → pyrosetta.rosetta.core.pose.Pose¶: Create initial pose from residue array sequence.

pyrosetta.rosetta.protocols.indexed_structure_store.pose_from_store(store: protocols::indexed_structure_store::StructureStore, structure_id: int) → pyrosetta.rosetta.core.pose.Pose¶: Get pose for given structure in store.

pyrosetta.rosetta.protocols.indexed_structure_store.residue_entries_to_pose(residue_entries: ndarray::Array[pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry, ndim=1, contiguous=0], residue_type: str = 'fa_standard', auto_termini: bool = True) → pyrosetta.rosetta.core.pose.Pose¶: Create pose from residue entry array.