wum¶

Bindings for protocols::wum namespace

class pyrosetta.rosetta.protocols.wum.WUM_MPI_TAGS¶

Bases: pybind11_builtins.pybind11_object

Members:

WUM_MPI_REQUEST_WU

WUM_MPI_SEND_WU

WUM_MPI_DATA_BLOCK

WUM_MPI_SPINDOWN

WUM_MPI_end

class pyrosetta.rosetta.protocols.wum.WorkUnitBase¶

Bases: pybind11_builtins.pybind11_object

The base class for all work units

add_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, mpi_rank: int) → None¶

Adds to the blacklist

C++: protocols::wum::WorkUnitBase::add_blacklist(int) –> void

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

clear_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Erases the blacklist

C++: protocols::wum::WorkUnitBase::clear_blacklist() –> void

clear_serial_data(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Remove all data, make sure that the memory is also cleared, hence the cals to reserve

C++: protocols::wum::WorkUnitBase::clear_serial_data() –> void

clone(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → pyrosetta.rosetta.protocols.wum.WorkUnitBase¶: C++: protocols::wum::WorkUnitBase::clone() const –> class std::shared_ptr<class protocols::wum::WorkUnitBase>

extra_data_1(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Accessor to the extra_data_1 and 3 field of the header

C++: protocols::wum::WorkUnitBase::extra_data_1() –> unsigned long

extra_data_2(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::extra_data_2() –> unsigned long

extra_data_3(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::extra_data_3() –> unsigned long

get_options(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → str¶

Optain the options string from the header

C++: protocols::wum::WorkUnitBase::get_options() const –> std::string

get_run_time(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Returns the differrence between unix start and stop times

C++: protocols::wum::WorkUnitBase::get_run_time() –> unsigned long

get_wu_type(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → str¶

Accessor to header structure, return the WorkUnit Type

C++: protocols::wum::WorkUnitBase::get_wu_type() const –> std::string

id(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Accessor to the ID of the WorkUnit

C++: protocols::wum::WorkUnitBase::id() –> unsigned long

in_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, mpi_rank: int) → bool¶

Finds in blacklist, true if is, false if it isn’t

C++: protocols::wum::WorkUnitBase::in_blacklist(int) –> bool

last_received_from(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::last_received_from() –> unsigned long

mem_footprint(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Return the memory usage of this WorkUnit

C++: protocols::wum::WorkUnitBase::mem_footprint() const –> unsigned long

print(*args, **kwargs)¶

Overloaded function.

print(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, out: pyrosetta.rosetta.std.ostream) -> None
print(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, out: pyrosetta.rosetta.std.ostream, verbose: bool) -> None

Print header information to the stream, single line by default or verbose if verbose is set to true

C++: protocols::wum::WorkUnitBase::print(class std::basic_ostream<char> &, bool) const –> void

run(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Run the workunit - overloaded by children of this class

C++: protocols::wum::WorkUnitBase::run() –> void

set_extra_data_1(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_1(const unsigned long) –> void

set_extra_data_2(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_2(const unsigned long) –> void

set_extra_data_3(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_3(const unsigned long) –> void

set_options(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, text: str) → None¶

Accesor to the “options” text field

C++: protocols::wum::WorkUnitBase::set_options(const class std::basic_string<char> &) –> void

set_wu_type(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, text: str) → None¶

Accessor to header structure, sets the WorkUnit Type

C++: protocols::wum::WorkUnitBase::set_wu_type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.wum.WorkUnitList¶

Bases: pybind11_builtins.pybind11_object

WOrkUnitList is a store for WorkUnitCOPs. THe purpose of this class is to store all the possible WorkUnits that a protocol might need. When needed these are cloned and then used. THis class acts like a library of WorkUnit blueprints.

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

get_work_unit(*args, **kwargs)¶

Overloaded function.

get_work_unit(self: pyrosetta.rosetta.protocols.wum.WorkUnitList, name: str) -> pyrosetta.rosetta.protocols.wum.WorkUnitBase

Return a COP to a workunit with a given name. If multiple WUs were registered with the same name, the first is returned.

C++: protocols::wum::WorkUnitList::get_work_unit(const class std::basic_string<char> &) const –> const class std::shared_ptr<const class protocols::wum::WorkUnitBase>

get_work_unit(self: pyrosetta.rosetta.protocols.wum.WorkUnitList, wu: pyrosetta.rosetta.protocols.wum.WorkUnitBase) -> pyrosetta.rosetta.protocols.wum.WorkUnitBase

Return an OP to a workunit with the same name as the one given as a parameter.

C++: protocols::wum::WorkUnitList::get_work_unit(const class protocols::wum::WorkUnitBase &) const –> const class std::shared_ptr<const class protocols::wum::WorkUnitBase>

get_work_unit_clone(*args, **kwargs)¶

Overloaded function.

get_work_unit_clone(self: pyrosetta.rosetta.protocols.wum.WorkUnitList, name: str) -> pyrosetta.rosetta.protocols.wum.WorkUnitBase

Return an OP to a workunit with a given name but clone it.

C++: protocols::wum::WorkUnitList::get_work_unit_clone(const class std::basic_string<char> &) const –> const class std::shared_ptr<class protocols::wum::WorkUnitBase>

get_work_unit_clone(self: pyrosetta.rosetta.protocols.wum.WorkUnitList, wu: pyrosetta.rosetta.protocols.wum.WorkUnitBase) -> pyrosetta.rosetta.protocols.wum.WorkUnitBase

Return an OP to a workunit with the same name as the one given as a parameter, but as a clone

C++: protocols::wum::WorkUnitList::get_work_unit_clone(const class protocols::wum::WorkUnitBase &) const –> const class std::shared_ptr<class protocols::wum::WorkUnitBase>

merge(self: pyrosetta.rosetta.protocols.wum.WorkUnitList, source: pyrosetta.rosetta.protocols.wum.WorkUnitList) → None¶: C++: protocols::wum::WorkUnitList::merge(const class protocols::wum::WorkUnitList &) –> void

register_work_unit(self: pyrosetta.rosetta.protocols.wum.WorkUnitList, name: str, the_work_unit: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Add a WorkUnit to the list, each workunit must be named with a string that is used later to retrieve it !

C++: protocols::wum::WorkUnitList::register_work_unit(const class std::basic_string<char> &, class std::shared_ptr<class protocols::wum::WorkUnitBase>) –> void

class pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper¶

Bases: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore

This WorkUnit type can encapsulate any MoverOP. When registering this WOrkunit provide it with a MoverOP and then, when executed on the slaves, this workunit will run the mover On every single input structure and return the results.

add_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, mpi_rank: int) → None¶

Adds to the blacklist

C++: protocols::wum::WorkUnitBase::add_blacklist(int) –> void

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

clear_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Erases the blacklist

C++: protocols::wum::WorkUnitBase::clear_blacklist() –> void

clear_serial_data(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Remove all data, make sure that the memory is also cleared, hence the cals to reserve

C++: protocols::wum::WorkUnitBase::clear_serial_data() –> void

clone(self: pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper) → pyrosetta.rosetta.protocols.wum.WorkUnitBase¶: C++: protocols::wum::WorkUnit_MoverWrapper::clone() const –> class std::shared_ptr<class protocols::wum::WorkUnitBase>

decoys(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → pyrosetta.rosetta.protocols.wum.SilentStructStore¶

Accessor for decoy store

C++: protocols::wum::WorkUnit_SilentStructStore::decoys() –> class protocols::wum::SilentStructStore &

deserialize(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → None¶

Make ready for working

C++: protocols::wum::WorkUnit_SilentStructStore::deserialize() –> void

extra_data_1(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Accessor to the extra_data_1 and 3 field of the header

C++: protocols::wum::WorkUnitBase::extra_data_1() –> unsigned long

extra_data_2(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::extra_data_2() –> unsigned long

extra_data_3(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::extra_data_3() –> unsigned long

get_options(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → str¶

Optain the options string from the header

C++: protocols::wum::WorkUnitBase::get_options() const –> std::string

get_run_time(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Returns the differrence between unix start and stop times

C++: protocols::wum::WorkUnitBase::get_run_time() –> unsigned long

get_wu_type(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → str¶

Accessor to header structure, return the WorkUnit Type

C++: protocols::wum::WorkUnitBase::get_wu_type() const –> std::string

id(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Accessor to the ID of the WorkUnit

C++: protocols::wum::WorkUnitBase::id() –> unsigned long

in_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, mpi_rank: int) → bool¶

Finds in blacklist, true if is, false if it isn’t

C++: protocols::wum::WorkUnitBase::in_blacklist(int) –> bool

last_received_from(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::last_received_from() –> unsigned long

mem_footprint(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Return the memory usage of this WorkUnit

C++: protocols::wum::WorkUnitBase::mem_footprint() const –> unsigned long

print(*args, **kwargs)¶

Overloaded function.

print(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, out: pyrosetta.rosetta.std.ostream) -> None
print(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, out: pyrosetta.rosetta.std.ostream, verbose: bool) -> None

Print header information to the stream, single line by default or verbose if verbose is set to true

C++: protocols::wum::WorkUnitBase::print(class std::basic_ostream<char> &, bool) const –> void

run(self: pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper) → None¶: C++: protocols::wum::WorkUnit_MoverWrapper::run() –> void

serialize(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → None¶

write decoys into serial data store overwritinge whatever was there before. It basically syncs the silent struct store with the derial data

C++: protocols::wum::WorkUnit_SilentStructStore::serialize() –> void

set_extra_data_1(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_1(const unsigned long) –> void

set_extra_data_2(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_2(const unsigned long) –> void

set_extra_data_3(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_3(const unsigned long) –> void

set_options(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, text: str) → None¶

Accesor to the “options” text field

C++: protocols::wum::WorkUnitBase::set_options(const class std::basic_string<char> &) –> void

set_wu_type(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, text: str) → None¶

Accessor to header structure, sets the WorkUnit Type

C++: protocols::wum::WorkUnitBase::set_wu_type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore¶

Bases: pyrosetta.rosetta.protocols.wum.WorkUnitBase

This WorkUnit type has structures in it. Most Workunits should derive from this one rather THe the Base class.

add_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, mpi_rank: int) → None¶

Adds to the blacklist

C++: protocols::wum::WorkUnitBase::add_blacklist(int) –> void

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

clear_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Erases the blacklist

C++: protocols::wum::WorkUnitBase::clear_blacklist() –> void

clear_serial_data(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → None¶

Remove all data, make sure that the memory is also cleared, hence the cals to reserve

C++: protocols::wum::WorkUnitBase::clear_serial_data() –> void

clone(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → pyrosetta.rosetta.protocols.wum.WorkUnitBase¶: C++: protocols::wum::WorkUnit_SilentStructStore::clone() const –> class std::shared_ptr<class protocols::wum::WorkUnitBase>

decoys(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → pyrosetta.rosetta.protocols.wum.SilentStructStore¶

Accessor for decoy store

C++: protocols::wum::WorkUnit_SilentStructStore::decoys() –> class protocols::wum::SilentStructStore &

deserialize(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → None¶

Make ready for working

C++: protocols::wum::WorkUnit_SilentStructStore::deserialize() –> void

extra_data_1(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Accessor to the extra_data_1 and 3 field of the header

C++: protocols::wum::WorkUnitBase::extra_data_1() –> unsigned long

extra_data_2(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::extra_data_2() –> unsigned long

extra_data_3(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::extra_data_3() –> unsigned long

get_options(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → str¶

Optain the options string from the header

C++: protocols::wum::WorkUnitBase::get_options() const –> std::string

get_run_time(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Returns the differrence between unix start and stop times

C++: protocols::wum::WorkUnitBase::get_run_time() –> unsigned long

get_wu_type(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → str¶

Accessor to header structure, return the WorkUnit Type

C++: protocols::wum::WorkUnitBase::get_wu_type() const –> std::string

id(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Accessor to the ID of the WorkUnit

C++: protocols::wum::WorkUnitBase::id() –> unsigned long

in_blacklist(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, mpi_rank: int) → bool¶

Finds in blacklist, true if is, false if it isn’t

C++: protocols::wum::WorkUnitBase::in_blacklist(int) –> bool

last_received_from(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶: C++: protocols::wum::WorkUnitBase::last_received_from() –> unsigned long

mem_footprint(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase) → int¶

Return the memory usage of this WorkUnit

C++: protocols::wum::WorkUnitBase::mem_footprint() const –> unsigned long

print(*args, **kwargs)¶

Overloaded function.

print(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, out: pyrosetta.rosetta.std.ostream) -> None
print(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, out: pyrosetta.rosetta.std.ostream, verbose: bool) -> None

Print header information to the stream, single line by default or verbose if verbose is set to true

C++: protocols::wum::WorkUnitBase::print(class std::basic_ostream<char> &, bool) const –> void

run(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → None¶

This Work unit doesnt do anything - its just keeps the structures

C++: protocols::wum::WorkUnit_SilentStructStore::run() –> void

serialize(self: pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore) → None¶

write decoys into serial data store overwritinge whatever was there before. It basically syncs the silent struct store with the derial data

C++: protocols::wum::WorkUnit_SilentStructStore::serialize() –> void

set_extra_data_1(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_1(const unsigned long) –> void

set_extra_data_2(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_2(const unsigned long) –> void

set_extra_data_3(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, value: int) → None¶: C++: protocols::wum::WorkUnitBase::set_extra_data_3(const unsigned long) –> void

set_options(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, text: str) → None¶

Accesor to the “options” text field

C++: protocols::wum::WorkUnitBase::set_options(const class std::basic_string<char> &) –> void

set_wu_type(self: pyrosetta.rosetta.protocols.wum.WorkUnitBase, text: str) → None¶

Accessor to header structure, sets the WorkUnit Type

C++: protocols::wum::WorkUnitBase::set_wu_type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.wum.find_SilentStructOPs¶

Bases: pybind11_builtins.pybind11_object

this little class is a predicate for finding silent structures in say a vector of silent structures

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

pyrosetta.rosetta.protocols.wum.generate_unique_structure_id() → str¶: C++: protocols::wum::generate_unique_structure_id() –> std::string

pyrosetta.rosetta.protocols.wum.get_time() → float¶

Get a time in seconds. If MPI is enabled you’ll get an accuracy of microsecs

C++: protocols::wum::get_time() –> double

pyrosetta.rosetta.protocols.wum.mpi_npes() → int¶

Helper function - returns total number of nodes

C++: protocols::wum::mpi_npes() –> int

pyrosetta.rosetta.protocols.wum.mpi_rank() → int¶

Helper function - returns rank of the current node.

C++: protocols::wum::mpi_rank() –> int