datacache¶

Bindings for core::pose::datacache namespace

class pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

Bases: pybind11_builtins.pybind11_object

Base class for Pose/Conformation observers that are stored in: a Pose’s DataCache.
Classes derived from CacheableObserver whose instances are: stored inside a Pose’s ObserverCache will be cloned and re-attached to the new Pose instance upon Pose copy construction/assignment. CacheableObservers should not need to attach themselves independently unless necessary – attach/detach should be done through the ObserverCache’s interface. For example, the ObserverCache can attach the observer upon calling ObserverCache::set().
When deriving from this class remember that Links or pointers to: subjects stored in classes are not to be copied when copy constructor/assignment is called.

assign(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, rval: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

copy assignment

Subject being observed (represented by Link/pointer) is not copied!

C++: core::pose::datacache::CacheableObserver::operator=(const class core::pose::datacache::CacheableObserver &) –> class core::pose::datacache::CacheableObserver &

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

attach to Pose/Conformation: Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

clone this object

Subject (represented by Link/pointer) is not copied!

C++: core::pose::datacache::CacheableObserver::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

create(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

create a new instance of this object

C++: core::pose::datacache::CacheableObserver::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → None¶

detach from Pose/Conformation

Derived classes do not overload this method – see

detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

is_attached(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → bool¶

is this observer attached to a Pose/Conformation?

C++: core::pose::datacache::CacheableObserver::is_attached() const –> bool

class pyrosetta.rosetta.core.pose.datacache.CacheableObserverType¶

Bases: pybind11_builtins.pybind11_object

enum indexing the data types stored in a Pose’s internal DataCache

Members:

LENGTH_EVENT_COLLECTOR

SPECIAL_SEGMENTS_OBSERVER

ENZDES_OBSERVER

STRUCTUREDATA_OBSERVER

PYMOL_OBSERVER

GLYCAN_TREE_OBSERVER

num_cacheable_data_types

class pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Holds a smart pointer (no longer a raw pointer) to a Pose so that it can be tucked inside another Pose.

assign(self: pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr, : pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr) → pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr¶: C++: core::pose::datacache::CacheablePoseRawPtr::operator=(const class core::pose::datacache::CacheablePoseRawPtr &) –> class core::pose::datacache::CacheablePoseRawPtr &

clone(self: pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::pose::datacache::CacheablePoseRawPtr::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

pose(self: pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::pose::datacache::CacheablePoseRawPtr::pose() –> class std::shared_ptr<class core::pose::Pose>

class pyrosetta.rosetta.core.pose.datacache.LengthEventCollector¶

Bases: pyrosetta.rosetta.core.pose.datacache.CacheableObserver

a cacheable observer that keeps track of what length events occured

assign(self: pyrosetta.rosetta.core.pose.datacache.LengthEventCollector, rval: pyrosetta.rosetta.core.pose.datacache.LengthEventCollector) → pyrosetta.rosetta.core.pose.datacache.LengthEventCollector¶

copy assignment

Subject being observed (represented by Link/pointer) is not copied!

C++: core::pose::datacache::LengthEventCollector::operator=(const class core::pose::datacache::LengthEventCollector &) –> class core::pose::datacache::LengthEventCollector &

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

attach to Pose/Conformation: Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clear_events(self: pyrosetta.rosetta.core.pose.datacache.LengthEventCollector) → None¶: C++: core::pose::datacache::LengthEventCollector::clear_events() –> void

clone(self: pyrosetta.rosetta.core.pose.datacache.LengthEventCollector) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

clone this object

Subject (represented by Link/pointer) is not copied!

C++: core::pose::datacache::LengthEventCollector::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

create(self: pyrosetta.rosetta.core.pose.datacache.LengthEventCollector) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

create a new instance of this object

C++: core::pose::datacache::LengthEventCollector::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → None¶

detach from Pose/Conformation

Derived classes do not overload this method – see

detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

events(self: pyrosetta.rosetta.core.pose.datacache.LengthEventCollector) → pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent¶: C++: core::pose::datacache::LengthEventCollector::events() const –> const class utility::vector1<struct core::conformation::signals::LengthEvent, class std::allocator<struct core::conformation::signals::LengthEvent> > &

is_attached(self: pyrosetta.rosetta.core.pose.datacache.LengthEventCollector) → bool¶

is this observer attached to a Pose/Conformation?

C++: core::pose::datacache::LengthEventCollector::is_attached() const –> bool

class pyrosetta.rosetta.core.pose.datacache.ObserverCache¶

Bases: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t

A DataCache storing Pose/Conformation observers derived from core::pose::datacache::CacheableObserver.

assign(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache, rval: pyrosetta.rosetta.core.pose.datacache.ObserverCache) → pyrosetta.rosetta.core.pose.datacache.ObserverCache¶

copy assignment

C++: core::pose::datacache::ObserverCache::operator=(const class core::pose::datacache::ObserverCache &) –> class core::pose::datacache::ObserverCache &

attach(*args, **kwargs)¶

Overloaded function.

attach(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache) -> None

attach all stored observers to the Pose

C++: core::pose::datacache::ObserverCache::attach() –> void

attach(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache, slot: int) -> None

attach an observer in a particular slot to the Pose

Attach the observer in this slot.

C++: core::pose::datacache::ObserverCache::attach(unsigned long) –> void

clear(*args, **kwargs)¶

Overloaded function.

clear(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache) -> None

clear all the observers

C++: core::pose::datacache::ObserverCache::clear() –> void

clear(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache, slot: int) -> None

clear the observer in a selected slot

C++: core::pose::datacache::ObserverCache::clear(unsigned long) –> void

detach(*args, **kwargs)¶

Overloaded function.

detach(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache) -> None

detach all observers from the Pose

C++: core::pose::datacache::ObserverCache::detach() –> void

detach(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache, slot: int) -> None

detach an observer in a particular slot to the Pose

Detach the observer in this slot.

C++: core::pose::datacache::ObserverCache::detach(unsigned long) –> void

get(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t, slot: int) → core::pose::datacache::CacheableObserver¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::get(unsigned long) –> class core::pose::datacache::CacheableObserver &

get_const_ptr(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t, slot: int) → core::pose::datacache::CacheableObserver¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::get_const_ptr(unsigned long) const –> class std::shared_ptr<const class core::pose::datacache::CacheableObserver>

get_ptr(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t, slot: int) → core::pose::datacache::CacheableObserver¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::get_ptr(unsigned long) –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

get_raw_const_ptr(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t, slot: int) → core::pose::datacache::CacheableObserver¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::get_raw_const_ptr(unsigned long) const –> const class core::pose::datacache::CacheableObserver *

get_raw_ptr(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t, slot: int) → core::pose::datacache::CacheableObserver¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::get_raw_ptr(unsigned long) –> class core::pose::datacache::CacheableObserver *

has(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t, slot: int) → bool¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::has(unsigned long) const –> bool

is_attached(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache, slot: int) → bool¶

is the observer in the slot attached to the Pose?

true if attached, false if not attached or no observer

exists in the slot

C++: core::pose::datacache::ObserverCache::is_attached(unsigned long) const –> bool

resize(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t, n_slots: int) → None¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::resize(unsigned long) –> void

set(*args, **kwargs)¶

Overloaded function.

set(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache, slot: int, observer: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) -> None

store a copy of the observer in the given slot and attach it to

the Pose

slot to use.

The Observer to clone() and store.

this function exists to ensure the base class version is: overridden

C++: core::pose::datacache::ObserverCache::set(unsigned long, class std::shared_ptr<class core::pose::datacache::CacheableObserver>) –> void

set(self: pyrosetta.rosetta.core.pose.datacache.ObserverCache, slot: int, observer: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, auto_attach: bool) -> None

store a copy of the observer in the given slot

slot to use.

The Observer to clone() and store.

Attach the observer to the Pose?

C++: core::pose::datacache::ObserverCache::set(unsigned long, class std::shared_ptr<class core::pose::datacache::CacheableObserver>, bool) –> void

size(self: pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t) → int¶: C++: basic::datacache::DataCache<core::pose::datacache::CacheableObserver>::size() const –> unsigned long

class pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

data about each residue. Once stored in a pose, data can be retrieved in the following manner:

#include <core/pose/util.hh> bool is_conserved = core::pose::is_position_conserved_residue(pose, residue)

assign(self: pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore, : pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore) → pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore¶: C++: core::pose::datacache::PositionConservedResiduesStore::operator=(const class core::pose::datacache::PositionConservedResiduesStore &) –> class core::pose::datacache::PositionConservedResiduesStore &

clone(self: pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore) → pyrosetta.rosetta.basic.datacache.CacheableData¶

Creates a copy of this instance

C++: core::pose::datacache::PositionConservedResiduesStore::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

is_conserved(self: pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore, residue: int) → bool¶

Returns true if <residue> is positionally conserved, false otherwise

C++: core::pose::datacache::PositionConservedResiduesStore::is_conserved(unsigned long) const –> bool

set_conserved(self: pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore, residue: int, conserved: bool) → None¶

Updates the positional conservation of <residue>

C++: core::pose::datacache::PositionConservedResiduesStore::set_conserved(unsigned long, bool) –> void

class pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver¶

Bases: pyrosetta.rosetta.core.pose.datacache.CacheableObserver

observer that tracks the fate of a one or more segments (i.e. pose residues) of interest. note: the convention should be that a segment.second marks the end of the segment but is not part of it, i.e. the last position of a segment is segment.second - 1 reason: some peculiar stuff regarding the meaning of length events

add_segment(self: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver, begin: int, end: int) → None¶: C++: core::pose::datacache::SpecialSegmentsObserver::add_segment(unsigned long, unsigned long) –> void

assign(self: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver, rval: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver) → pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver¶: C++: core::pose::datacache::SpecialSegmentsObserver::operator=(const class core::pose::datacache::SpecialSegmentsObserver &) –> class core::pose::datacache::SpecialSegmentsObserver &

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

attach to Pose/Conformation: Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clear(self: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver) → None¶: C++: core::pose::datacache::SpecialSegmentsObserver::clear() –> void

clone(self: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

clone this object

Subject (represented by Link/pointer) is not copied!

C++: core::pose::datacache::SpecialSegmentsObserver::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

create(self: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver¶

create a new instance of this object

C++: core::pose::datacache::SpecialSegmentsObserver::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → None¶

detach from Pose/Conformation

Derived classes do not overload this method – see

detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

is_attached(self: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver) → bool¶

is this observer attached to a Pose/Conformation?

C++: core::pose::datacache::SpecialSegmentsObserver::is_attached() const –> bool

segments(self: pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶: C++: core::pose::datacache::SpecialSegmentsObserver::segments() const –> const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &

set_farray_from_sso(array: ObjexxFCL::FArray1D<bool>, pose: pyrosetta.rosetta.core.pose.Pose, value: bool) → None¶

utility function that sets all elements found in the: SpecialSegmentsObserver in the pose to value

C++: core::pose::datacache::SpecialSegmentsObserver::set_farray_from_sso(class ObjexxFCL::FArray1D<bool> &, const class core::pose::Pose &, const bool) –> void