archive

Bindings for protocols::jd2::archive namespace

class pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase

Bases: pybind11_object

This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.

assign(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase

C++: protocols::jd2::archive::AbstractArchiveBase::operator=(const class protocols::jd2::archive::AbstractArchiveBase &) –> class protocols::jd2::archive::AbstractArchiveBase &

finished(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → bool

is archive converged ?

C++: protocols::jd2::archive::AbstractArchiveBase::finished() const –> bool

generate_batch(*args, **kwargs)

Overloaded function.

1. generate_batch(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) -> None

create a new batch with manager().start_new_batch() and manager().finalize_batch();

C++: protocols::jd2::archive::AbstractArchiveBase::generate_batch() –> void

2. generate_batch(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch, : int) -> int

create a batch for the current stage, return ct != 0 if more batches should be created at current stage. (e.g., harvest_batches)

C++: protocols::jd2::archive::AbstractArchiveBase::generate_batch(class protocols::jd2::archive::Batch &, unsigned long) –> unsigned long

idle(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → None

do some computations on archive that can be done while we are waiting

C++: protocols::jd2::archive::AbstractArchiveBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

C++: protocols::jd2::archive::AbstractArchiveBase::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

initialize(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → None

C++: protocols::jd2::archive::AbstractArchiveBase::initialize() –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

read_structures(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, returned_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) → None

read ‘returned_decoys’ from ‘batch’ into archive.

C++: protocols::jd2::archive::AbstractArchiveBase::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → bool

restore archive

C++: protocols::jd2::archive::AbstractArchiveBase::restore_from_file() –> bool

save_status(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : pyrosetta.rosetta.std.ostream) → None

C++: protocols::jd2::archive::AbstractArchiveBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) -> None

2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, suffix: str) -> None

save archive to file .. you can put ‘suffix’ at end of dirname to save other snapshots than the ‘current’

C++: protocols::jd2::archive::AbstractArchiveBase::save_to_file(std::string) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) → None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) → None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

still_interested(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) → bool

old-batches might be outdated and should not be computed anymore

return true for this query if this is the case for old_batch

C++: protocols::jd2::archive::AbstractArchiveBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

class pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase

Bases: AbstractArchiveBase

accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_structure(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) → bool

add structure to Archive.. return false if structure is rejected.

C++: protocols::jd2::archive::ArchiveBase::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase

C++: protocols::jd2::archive::ArchiveBase::operator=(const class protocols::jd2::archive::ArchiveBase &) –> class protocols::jd2::archive::ArchiveBase &

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

finished(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::finished() const –> bool

generate_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::generate_batch() –> void

idle(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

called when nothing is happening

C++: protocols::jd2::archive::ArchiveBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

read externally provided structures from decoy_file into archive

C++: protocols::jd2::archive::ArchiveBase::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

initialize(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) → None

SilentFileData contains the new structures belonging to this batch.

C++: protocols::jd2::archive::ArchiveBase::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

static register_options() → None

C++: protocols::jd2::archive::ArchiveBase::register_options() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.istream) → None

C++: protocols::jd2::archive::ArchiveBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.ostream) → None

save and restore status of archive to file-system

C++: protocols::jd2::archive::ArchiveBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) -> None

2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, suffix: str) -> None

save and restore archive to file-system

C++: protocols::jd2::archive::ArchiveBase::save_to_file(std::string) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) → None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) → None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) → None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) → bool

old-batches might be outdated and should not be computed anymore

return true for this query if this is the case for old_batch

C++: protocols::jd2::archive::AbstractArchiveBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

class pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager

Bases: BaseArchiveManager

ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys

he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY .

assign(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, : pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager

C++: protocols::jd2::archive::BaseArchiveManager::operator=(const class protocols::jd2::archive::BaseArchiveManager &) –> class protocols::jd2::archive::BaseArchiveManager &

batches(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch

C++: protocols::jd2::archive::BaseArchiveManager::batches() const –> const class utility::vector1<class protocols::jd2::archive::Batch, class std::allocator<class protocols::jd2::archive::Batch> > &

cancel_batches_previous_to(*args, **kwargs)

Overloaded function.

1. cancel_batches_previous_to(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id: int) -> None

2. cancel_batches_previous_to(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id: int, allow_reading_of_decoys: bool) -> None

C++: protocols::jd2::archive::BaseArchiveManager::cancel_batches_previous_to(unsigned long, bool) –> void

finalize_batch(*args, **kwargs)

Overloaded function.

1. finalize_batch(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, : pyrosetta.rosetta.protocols.jd2.archive.Batch) -> None

2. finalize_batch(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, : pyrosetta.rosetta.protocols.jd2.archive.Batch, reread: bool) -> None

C++: protocols::jd2::archive::BaseArchiveManager::finalize_batch(class protocols::jd2::archive::Batch &, bool) –> void

go(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager, : pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveManager::go(class std::shared_ptr<class protocols::jd2::archive::ArchiveBase>) –> void

last_batch_id(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → int

C++: protocols::jd2::archive::BaseArchiveManager::last_batch_id() const –> unsigned long

static register_options() → None

C++: protocols::jd2::archive::ArchiveManager::register_options() –> void

restore_archive(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager) → bool

C++: protocols::jd2::archive::ArchiveManager::restore_archive() –> bool

save_archive(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager) → None

C++: protocols::jd2::archive::ArchiveManager::save_archive() –> void

start_new_batch(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → pyrosetta.rosetta.protocols.jd2.archive.Batch

C++: protocols::jd2::archive::BaseArchiveManager::start_new_batch() –> class protocols::jd2::archive::Batch &

unfinished_batches(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager) → int

C++: protocols::jd2::archive::ArchiveManager::unfinished_batches() const –> unsigned long

class pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager

Bases: pybind11_object

ArchiveManager is responsible for communication with JobDistributor and organization of Batches and returning decoys

he owns an Archive (AbstractArchiveBase) that will be handed the decoys and is asked to generate_batch() if the QUEUE_EMPTY .

assign(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, : pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager

C++: protocols::jd2::archive::BaseArchiveManager::operator=(const class protocols::jd2::archive::BaseArchiveManager &) –> class protocols::jd2::archive::BaseArchiveManager &

batches(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch

C++: protocols::jd2::archive::BaseArchiveManager::batches() const –> const class utility::vector1<class protocols::jd2::archive::Batch, class std::allocator<class protocols::jd2::archive::Batch> > &

cancel_batches_previous_to(*args, **kwargs)

Overloaded function.

1. cancel_batches_previous_to(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id: int) -> None

2. cancel_batches_previous_to(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, batch_id: int, allow_reading_of_decoys: bool) -> None

C++: protocols::jd2::archive::BaseArchiveManager::cancel_batches_previous_to(unsigned long, bool) –> void

finalize_batch(*args, **kwargs)

Overloaded function.

1. finalize_batch(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, : pyrosetta.rosetta.protocols.jd2.archive.Batch) -> None

2. finalize_batch(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager, : pyrosetta.rosetta.protocols.jd2.archive.Batch, reread: bool) -> None

C++: protocols::jd2::archive::BaseArchiveManager::finalize_batch(class protocols::jd2::archive::Batch &, bool) –> void

last_batch_id(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → int

C++: protocols::jd2::archive::BaseArchiveManager::last_batch_id() const –> unsigned long

restore_archive(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → bool

C++: protocols::jd2::archive::BaseArchiveManager::restore_archive() –> bool

save_archive(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → None

C++: protocols::jd2::archive::BaseArchiveManager::save_archive() –> void

start_new_batch(self: pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager) → pyrosetta.rosetta.protocols.jd2.archive.Batch

C++: protocols::jd2::archive::BaseArchiveManager::start_new_batch() –> class protocols::jd2::archive::Batch &

class pyrosetta.rosetta.protocols.jd2.archive.Batch

Bases: pybind11_object

a Batch represents a directory “batch_000xxx” that contains flags, broker-setup input-files and output-files

the Batch-class helps to get the correct file- and directory names,

and has some knowledge about its status: finished, unfinished … decoys already processed by Archive

all_broker_files(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::all_broker_files() const –> std::string

allow_reading_cancelled_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → bool

batch has finished

C++: protocols::jd2::archive::Batch::allow_reading_cancelled_decoys() const –> bool

alternative_decoys_out(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::alternative_decoys_out() const –> std::string

assign(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, : pyrosetta.rosetta.protocols.jd2.archive.Batch) → pyrosetta.rosetta.protocols.jd2.archive.Batch

C++: protocols::jd2::archive::Batch::operator=(const class protocols::jd2::archive::Batch &) –> class protocols::jd2::archive::Batch &

batch(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

some useful file- and directory names

C++: protocols::jd2::archive::Batch::batch() const –> std::string

broker_file(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::broker_file() const –> std::string

decoys_returned(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → int

how many structures have been processed by archive already

C++: protocols::jd2::archive::Batch::decoys_returned() const –> unsigned long

dir(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::dir() const –> std::string

extra_broker_files(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::extra_broker_files() const –> std::string

flag_file(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::flag_file() const –> std::string

has_finished(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → bool

batch has finished

C++: protocols::jd2::archive::Batch::has_finished() const –> bool

has_silent_in(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → bool

has input decoys

C++: protocols::jd2::archive::Batch::has_silent_in() const –> bool

id(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → int

batch id

C++: protocols::jd2::archive::Batch::id() const –> unsigned long

intermediate_structs(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → bool

writes out intermediate decoys

C++: protocols::jd2::archive::Batch::intermediate_structs() const –> bool

is_cancelled(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → bool

batch has finished

C++: protocols::jd2::archive::Batch::is_cancelled() const –> bool

mark_as_cancelled(*args, **kwargs)

Overloaded function.

1. mark_as_cancelled(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) -> None

2. mark_as_cancelled(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, allow_reading_of_decoys: bool) -> None

C++: protocols::jd2::archive::Batch::mark_as_cancelled(bool) –> void

mark_as_finished(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → None

C++: protocols::jd2::archive::Batch::mark_as_finished() –> void

mark_as_invalid(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → None

C++: protocols::jd2::archive::Batch::mark_as_invalid() –> void

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → int

nstruct …

C++: protocols::jd2::archive::Batch::nstruct() –> unsigned long &

read_info_file(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → None

C++: protocols::jd2::archive::Batch::read_info_file() –> void

score_file(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::score_file() const –> std::string

set_decoys_returned(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, setting: int) → None

C++: protocols::jd2::archive::Batch::set_decoys_returned(unsigned long) –> void

set_has_silent_in(*args, **kwargs)

Overloaded function.

1. set_has_silent_in(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) -> None

2. set_has_silent_in(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, setting: bool) -> None

Setters

C++: protocols::jd2::archive::Batch::set_has_silent_in(bool) –> void

set_id(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, id: int) → None

C++: protocols::jd2::archive::Batch::set_id(unsigned long) –> void

set_intermediate_structs(*args, **kwargs)

Overloaded function.

1. set_intermediate_structs(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) -> None

2. set_intermediate_structs(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, setting: bool) -> None

C++: protocols::jd2::archive::Batch::set_intermediate_structs(bool) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, : pyrosetta.rosetta.std.ostream) -> None

2. show(self: pyrosetta.rosetta.protocols.jd2.archive.Batch, : pyrosetta.rosetta.std.ostream, single_line: bool) -> None

C++: protocols::jd2::archive::Batch::show(std::ostream &, bool) const –> void

silent_in(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::silent_in() const –> std::string

silent_out(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → str

C++: protocols::jd2::archive::Batch::silent_out() const –> std::string

user_options(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → pyrosetta.rosetta.utility.options.OptionCollection

C++: protocols::jd2::archive::Batch::user_options() –> class utility::options::OptionCollection &

valid(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → bool

C++: protocols::jd2::archive::Batch::valid() const –> bool

write_info_file(self: pyrosetta.rosetta.protocols.jd2.archive.Batch) → None

read and write BATCH_INFO ( decoys_returned/ finished etc.. )

C++: protocols::jd2::archive::Batch::write_info_file() const –> void

class pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive

Bases: Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive, : pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive) → pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive

C++: protocols::jd2::archive::EXCN_Archive::operator=(const class protocols::jd2::archive::EXCN_Archive &) –> class protocols::jd2::archive::EXCN_Archive &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) → None

Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) → None

Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) → int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

2. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) → None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) → str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) → str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) → str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive

Bases: ArchiveBase

This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.

accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) → bool

add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) );

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, batch: protocols::jd2::archive::Batch) → bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::EvaluatedArchive::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive

C++: protocols::jd2::archive::EvaluatedArchive::operator=(const class protocols::jd2::archive::EvaluatedArchive &) –> class protocols::jd2::archive::EvaluatedArchive &

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::finished() const –> bool

generate_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::generate_batch() –> void

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

called when nothing is happening

C++: protocols::jd2::archive::ArchiveBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

overloaded to make input decoys appear the same as decoys coming from batches

C++: protocols::jd2::archive::EvaluatedArchive::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

initialize(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) → None

only overloaded this to add some verbosity each time we read structures

C++: protocols::jd2::archive::EvaluatedArchive::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

static register_options() → None

Archive specific options

C++: protocols::jd2::archive::EvaluatedArchive::register_options() –> void

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

recompute all score-values of all decoys and re-order the archive by (new) select_score

C++: protocols::jd2::archive::EvaluatedArchive::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → bool

overloaded that we can sort the pool after reading

C++: protocols::jd2::archive::EvaluatedArchive::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.istream) → None

C++: protocols::jd2::archive::ArchiveBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.ostream) → None

save and restore status of archive to file-system

C++: protocols::jd2::archive::ArchiveBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) -> None

2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, suffix: str) -> None

overloaded to save / restore the variance_archive_

C++: protocols::jd2::archive::EvaluatedArchive::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, col: str) → float

C++: protocols::jd2::archive::EvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) → float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) → None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) → None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) → None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) → None

set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

set common evaluators: eg. ConstraintEvaluator if -cst_file is present

C++: protocols::jd2::archive::EvaluatedArchive::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) → bool

old-batches might be outdated and should not be computed anymore

return true for this query if this is the case for old_batch

C++: protocols::jd2::archive::AbstractArchiveBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

class pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor

Bases: MPIFileBufJobDistributor

JobDistributor for the iterative ArchiveManager/Archive Framework

This job distributor is meant for running iterative jobs with the ArchiveManager/Archive Framework.

could vary greatly. In this configuration the three first nodes are dedicated processes (JobDistributor, FileBuffer, and ArchiveManger ) and the remaining CPUs form slave or worker nodes. This JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.

class CompletionMessage

Bases: pybind11_object

CompletionMessage(s) are send to the ArchiveManager whenever more than nr_notify decoys have been finished / or when the full batch is finished.

property bad

property batch_id

property final

property good

property msg_tag

property njobs

add_batch(*args, **kwargs)

Overloaded function.

1. add_batch(self: pyrosetta.rosetta.protocols.jd2.JobDistributor, : str) -> None

2. add_batch(self: pyrosetta.rosetta.protocols.jd2.JobDistributor, : str, id: int) -> None

add a new batch ( name will be interpreted as flag_file )

C++: protocols::jd2::JobDistributor::add_batch(const std::string &, unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.jd2.JobDistributor, : pyrosetta.rosetta.protocols.jd2.JobDistributor) → pyrosetta.rosetta.protocols.jd2.JobDistributor

C++: protocols::jd2::JobDistributor::operator=(const class protocols::jd2::JobDistributor &) –> class protocols::jd2::JobDistributor &

current_batch_id(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → int

what is the current batch number ? — refers to position in batches_

C++: protocols::jd2::JobDistributor::current_batch_id() const –> unsigned long

current_job(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → protocols::jd2::Job

Movers may ask their controlling job distributor for information about the current job.

They may also write information to this job for later output, though this use is now discouraged as the addition of the MultiplePoseMover now means that a single job may include several separate trajectories.

C++: protocols::jd2::JobDistributor::current_job() const –> class std::shared_ptr<class protocols::jd2::Job>

current_job_id(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → int

integer access - which job are we on?

C++: protocols::jd2::JobDistributor::current_job_id() const –> unsigned long

current_output_name(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → str

Movers may ask their controlling job distributor for the output name as defined by the Job and JobOutputter.

C++: protocols::jd2::JobDistributor::current_output_name() const –> std::string

get_current_batch(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → str

what is the current batch ? — name refers to the flag-file used for this batch

C++: protocols::jd2::JobDistributor::get_current_batch() const –> std::string

static get_instance() → pyrosetta.rosetta.protocols.jd2.JobDistributor

C++: protocols::jd2::JobDistributor::get_instance() –> class protocols::jd2::JobDistributor *

get_new_job_id(self: pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor) → int

dummy for master/slave version

C++: protocols::jd2::MPIFileBufJobDistributor::get_new_job_id() –> unsigned long

go(self: pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor, mover: pyrosetta.rosetta.protocols.moves.Mover) → None

overloaded to also start the ArchiveManager process

C++: protocols::jd2::archive::MPIArchiveJobDistributor::go(class std::shared_ptr<class protocols::moves::Mover>) –> void

static has_been_instantiated() → bool

Has the job distributor been instantiated?

Returns true for yes and false for no.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::jd2::JobDistributor::has_been_instantiated() –> bool

increment_client_rank(self: pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor) → int

C++: protocols::jd2::MPIFileBufJobDistributor::increment_client_rank() –> unsigned long

is_archive_rank(self: pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor) → bool

C++: protocols::jd2::archive::MPIArchiveJobDistributor::is_archive_rank() const –> bool

job_failed(self: pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor, pose: pyrosetta.rosetta.core.pose.Pose, will_retry: bool) → None

C++: protocols::jd2::MPIFileBufJobDistributor::job_failed(class core::pose::Pose &, bool) –> void

job_inputter(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → pyrosetta.rosetta.protocols.jd2.JobInputter

JobInputter access

C++: protocols::jd2::JobDistributor::job_inputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>

job_inputter_input_source(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum

The input source for the current JobInputter.

C++: protocols::jd2::JobDistributor::job_inputter_input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum

job_outputter(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → pyrosetta.rosetta.protocols.jd2.JobOutputter

Movers (or derived classes) may ask for the JobOutputter

C++: protocols::jd2::JobDistributor::job_outputter() const –> class std::shared_ptr<class protocols::jd2::JobOutputter>

job_succeeded(self: pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor, pose: pyrosetta.rosetta.core.pose.Pose, runtime: float, tag: str) → None

dummy for master/slave version

C++: protocols::jd2::MPIFileBufJobDistributor::job_succeeded(class core::pose::Pose &, double, const std::string &) –> void

mark_current_job_id_for_repetition(self: pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor) → None

dummy for master/slave version

C++: protocols::jd2::MPIFileBufJobDistributor::mark_current_job_id_for_repetition() –> void

min_client_rank(self: pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor) → int

return rank of first worker process (there might be more dedicated processes, e.g., ArchiveManager…)

C++: protocols::jd2::MPIFileBufJobDistributor::min_client_rank() const –> unsigned long

mpi_finalize(self: pyrosetta.rosetta.protocols.jd2.JobDistributor, finalize: bool) → None

should the go() function call MPI_finalize()? It probably should, this is true by default.

C++: protocols::jd2::JobDistributor::mpi_finalize(bool) –> void

remove_bad_inputs_from_job_list(self: pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor) → None

dummy for master/slave version

C++: protocols::jd2::MPIFileBufJobDistributor::remove_bad_inputs_from_job_list() –> void

restart(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → None

C++: protocols::jd2::JobDistributor::restart() –> void

set_archive(self: pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor, : pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::MPIArchiveJobDistributor::set_archive(class std::shared_ptr<class protocols::jd2::archive::ArchiveBase>) –> void

set_job_inputter(self: pyrosetta.rosetta.protocols.jd2.JobDistributor, new_job_inputter: pyrosetta.rosetta.protocols.jd2.JobInputter) → None

Set the JobInputter and reset the Job list – this is not something you want to do

after go() has been called, but before it has returned.

C++: protocols::jd2::JobDistributor::set_job_inputter(class std::shared_ptr<class protocols::jd2::JobInputter>) –> void

set_job_outputter(self: pyrosetta.rosetta.protocols.jd2.JobDistributor, new_job_outputter: pyrosetta.rosetta.protocols.jd2.JobOutputter) → None

Movers (or derived classes) may ask for the JobOutputter

C++: protocols::jd2::JobDistributor::set_job_outputter(const class std::shared_ptr<class protocols::jd2::JobOutputter> &) –> void

total_nr_jobs(self: pyrosetta.rosetta.protocols.jd2.JobDistributor) → int

C++: protocols::jd2::JobDistributor::total_nr_jobs() const –> unsigned long

class pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive

Bases: EvaluatedArchive

This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.

accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) → bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, batch: protocols::jd2::archive::Batch) → bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::EvaluatedArchive::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, : pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) → pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::operator=(const class protocols::jd2::archive::NormalizedEvaluatedArchive &) –> class protocols::jd2::archive::NormalizedEvaluatedArchive &

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

determine_score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) → bool

determine variation of scores (those that are non-zeros in select_weights_ )

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations() const –> bool

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::finished() const –> bool

generate_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::generate_batch() –> void

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

called when nothing is happening

C++: protocols::jd2::archive::ArchiveBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

overloaded to make input decoys appear the same as decoys coming from batches

C++: protocols::jd2::archive::EvaluatedArchive::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

init_from_options(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) → None

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::init_from_options() –> void

initialize(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) → None

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) → None

only overloaded this to add some verbosity each time we read structures

C++: protocols::jd2::archive::EvaluatedArchive::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

static register_options() → None

Archive specific options

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::register_options() –> void

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) → None

recompute all score-values of all decoys and re-order the archive by (new) select_score

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) → bool

overloaded that we can sort the pool after reading

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.istream) → None

C++: protocols::jd2::archive::ArchiveBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.ostream) → None

save and restore status of archive to file-system

C++: protocols::jd2::archive::ArchiveBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> None

2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, suffix: str) -> None

overloaded to save / restore the variance_archive_

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col: str) → float

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) → float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) → None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) → None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) → None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) → None

set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

set common evaluators: eg. ConstraintEvaluator if -cst_file is present

C++: protocols::jd2::archive::EvaluatedArchive::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) → bool

old-batches might be outdated and should not be computed anymore

return true for this query if this is the case for old_batch

C++: protocols::jd2::archive::AbstractArchiveBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

class pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive

Bases: EvaluatedArchive

accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive, : pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : pyrosetta.rosetta.protocols.jd2.archive.Batch) → bool

C++: protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, batch: protocols::jd2::archive::Batch) → bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::EvaluatedArchive::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive, : pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive) → pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive

C++: protocols::jd2::archive::VarianceStatisticsArchive::operator=(const class protocols::jd2::archive::VarianceStatisticsArchive &) –> class protocols::jd2::archive::VarianceStatisticsArchive &

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::finished() const –> bool

generate_batch(self: pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive) → None

C++: protocols::jd2::archive::VarianceStatisticsArchive::generate_batch() –> void

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

called when nothing is happening

C++: protocols::jd2::archive::ArchiveBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive, : pyrosetta.rosetta.core.io.silent.SilentFileData) → None

overloaded to make input decoys appear the same as decoys coming from batches

C++: protocols::jd2::archive::VarianceStatisticsArchive::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

initialize(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) → str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) → None

only overloaded this to add some verbosity each time we read structures

C++: protocols::jd2::archive::EvaluatedArchive::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

static register_options() → None

Archive specific options

C++: protocols::jd2::archive::EvaluatedArchive::register_options() –> void

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) → None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

recompute all score-values of all decoys and re-order the archive by (new) select_score

C++: protocols::jd2::archive::EvaluatedArchive::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → bool

overloaded that we can sort the pool after reading

C++: protocols::jd2::archive::EvaluatedArchive::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.istream) → None

C++: protocols::jd2::archive::ArchiveBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t) → None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, : pyrosetta.rosetta.std.ostream) → None

save and restore status of archive to file-system

C++: protocols::jd2::archive::ArchiveBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) -> None

2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, suffix: str) -> None

overloaded to save / restore the variance_archive_

C++: protocols::jd2::archive::EvaluatedArchive::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, col: str) → float

C++: protocols::jd2::archive::EvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) → float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_insertion_prob(self: pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive, setting: float) → None

C++: protocols::jd2::archive::VarianceStatisticsArchive::set_insertion_prob(double) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) → None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) → None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) → None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) → None

set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) → None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

set common evaluators: eg. ConstraintEvaluator if -cst_file is present

C++: protocols::jd2::archive::EvaluatedArchive::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) → bool

old-batches might be outdated and should not be computed anymore

return true for this query if this is the case for old_batch

C++: protocols::jd2::archive::AbstractArchiveBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) → int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) → pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

pyrosetta.rosetta.protocols.jd2.archive.report_batch_inconsistency(new_batch: protocols::jd2::archive::Batch, tag: str) → None

C++: protocols::jd2::archive::report_batch_inconsistency(class protocols::jd2::archive::Batch &, const std::string &) –> void