pack_daemon

Bindings for protocols::pack_daemon namespace

class pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker

Bases: QuickRepacker

assign(self: pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker, : pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker) → pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker

C++: protocols::pack_daemon::BasicSimAnnealerRepacker::operator=(const class protocols::pack_daemon::BasicSimAnnealerRepacker &) –> class protocols::pack_daemon::BasicSimAnnealerRepacker &

repack(self: pyrosetta.rosetta.protocols.pack_daemon.BasicSimAnnealerRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::BasicSimAnnealerRepacker::repack(const class utility::vector0<int, class std::allocator<int> > &) –> struct std::pair<class utility::vector1<int, class std::allocator<int> >, double>

class pyrosetta.rosetta.protocols.pack_daemon.DaemonSet

Bases: pybind11_object

activate_daemon_mode(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → None

receive and respond to remote repacking requests from node 0 until

a spin-down signal is broadcast. This function does not return until all MPI requests have completed.

C++: protocols::pack_daemon::DaemonSet::activate_daemon_mode() –> void

add_npd_property_calculator_for_state(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, daemon_index: int, npd_property: str, npd_index: int) → None

C++: protocols::pack_daemon::DaemonSet::add_npd_property_calculator_for_state(unsigned long, const std::string &, unsigned long) –> void

add_npdpro_calculator_creator(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, : protocols::pack_daemon::NPDPropCalculatorCreator) → None

C++: protocols::pack_daemon::DaemonSet::add_npdpro_calculator_creator(class std::shared_ptr<class protocols::pack_daemon::NPDPropCalculatorCreator>) –> void

add_pack_daemon(*args, **kwargs)

Overloaded function.

1. add_pack_daemon(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, daemon_index: int, pdb_name: str, correspondence_file_name: str, secondary_resfile: str) -> None

Each daemon is associated with an index representing its position in

some master list somewhere. The DaemonSet is responsible for keeping this index.

C++: protocols::pack_daemon::DaemonSet::add_pack_daemon(unsigned long, const std::string &, const std::string &, const std::string &) –> void

2. add_pack_daemon(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, daemon_index: int, pose_file_name: str, pose: pyrosetta.rosetta.core.pose.Pose, correspondence_file_filename: str, correspondence_file: pyrosetta.rosetta.std.istream, secondary_refile_file_filename: str, secondary_resfile: pyrosetta.rosetta.std.istream) -> None

C++: protocols::pack_daemon::DaemonSet::add_pack_daemon(unsigned long, const std::string &, const class core::pose::Pose &, const std::string &, std::istream &, const std::string &, std::istream &) –> void

assign(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, : pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → pyrosetta.rosetta.protocols.pack_daemon.DaemonSet

C++: protocols::pack_daemon::DaemonSet::operator=(const class protocols::pack_daemon::DaemonSet &) –> class protocols::pack_daemon::DaemonSet &

compute_energy_for_assignment(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → Tuple[pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t, pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t]

Compute the state energies and, for those states requiring non-pairwise-decomposable-properties,

the non-pairwise decomposable properties as well. Return them as a pair of lists.

C++: protocols::pack_daemon::DaemonSet::compute_energy_for_assignment(const class protocols::genetic_algorithm::Entity &) –> struct std::pair<class std::list<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > >, class std::list<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > >

daemons(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_std_shared_ptr_const_protocols_pack_daemon_PackDaemon_t

C++: protocols::pack_daemon::DaemonSet::daemons() const –> class utility::vector1<struct std::pair<unsigned long, class std::shared_ptr<const class protocols::pack_daemon::PackDaemon> >, class std::allocator<struct std::pair<unsigned long, class std::shared_ptr<const class protocols::pack_daemon::PackDaemon> > > >

entity_resfile(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → pyrosetta.rosetta.core.pack.task.ResfileContents

C++: protocols::pack_daemon::DaemonSet::entity_resfile() const –> class std::shared_ptr<const class core::pack::task::ResfileContents>

entity_task(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::pack_daemon::DaemonSet::entity_task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

mark_entity_as_unimportant(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → None

C++: protocols::pack_daemon::DaemonSet::mark_entity_as_unimportant(const class protocols::genetic_algorithm::Entity &) –> void

mark_last_entity_as_important(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → None

C++: protocols::pack_daemon::DaemonSet::mark_last_entity_as_important() –> void

n_npd_properties(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → int

C++: protocols::pack_daemon::DaemonSet::n_npd_properties() const –> unsigned long

ndaemons(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → int

C++: protocols::pack_daemon::DaemonSet::ndaemons() const –> unsigned long

set_dlig_nmeg_limit(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, setting: int) → None

restrict the amount of memory spent on storing Rotamer Pair Energies in the

DoubleLazyInteractionGraph;

C++: protocols::pack_daemon::DaemonSet::set_dlig_nmeg_limit(unsigned long) –> void

set_entity_resfile(*args, **kwargs)

Overloaded function.

1. set_entity_resfile(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, resfile: str) -> None

C++: protocols::pack_daemon::DaemonSet::set_entity_resfile(const std::string &) –> void

2. set_entity_resfile(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, resfile: pyrosetta.rosetta.std.istream, resfile_name: str) -> None

C++: protocols::pack_daemon::DaemonSet::set_entity_resfile(std::istream &, const std::string &) –> void

set_include_background_energies(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, setting: bool) → None

C++: protocols::pack_daemon::DaemonSet::set_include_background_energies(bool) –> void

set_score_function(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::pack_daemon::DaemonSet::set_score_function(const class core::scoring::ScoreFunction &) –> void

set_task_factory(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet, factory: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::pack_daemon::DaemonSet::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

setup_daemons(self: pyrosetta.rosetta.protocols.pack_daemon.DaemonSet) → None

call daemon->setup() on all daemons, which will trigger the

precomputation of all rotamer pair energies.

C++: protocols::pack_daemon::DaemonSet::setup_daemons() –> void

class pyrosetta.rosetta.protocols.pack_daemon.DaemonSetMessage

Bases: pybind11_object

Members:

error_message

success_message

add_daemon

evaluate_entity

keep_rotamer_assignment_for_last_entity

discard_old_entity

geneate_pose_from_old_state

spin_down

n_daemon_set_messages

add_daemon = <DaemonSetMessage.add_daemon: 2>

discard_old_entity = <DaemonSetMessage.discard_old_entity: 5>

error_message = <DaemonSetMessage.error_message: 0>

evaluate_entity = <DaemonSetMessage.evaluate_entity: 3>

geneate_pose_from_old_state = <DaemonSetMessage.geneate_pose_from_old_state: 6>

keep_rotamer_assignment_for_last_entity = <DaemonSetMessage.keep_rotamer_assignment_for_last_entity: 4>

n_daemon_set_messages = <DaemonSetMessage.n_daemon_set_messages: 8>

property name

spin_down = <DaemonSetMessage.spin_down: 7>

success_message = <DaemonSetMessage.success_message: 1>

property value

class pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker

Bases: RotamerSubsetRepacker

assign(self: pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker, : pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker) → pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker

C++: protocols::pack_daemon::DenseIGRepacker::operator=(const class protocols::pack_daemon::DenseIGRepacker &) –> class protocols::pack_daemon::DenseIGRepacker &

create_dense_pdig_from_rot_to_pack(self: pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int, rot_subsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets) → pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph

C++: protocols::pack_daemon::DenseIGRepacker::create_dense_pdig_from_rot_to_pack(const class utility::vector0<int, class std::allocator<int> > &, class std::shared_ptr<class core::pack::rotamer_set::RotamerSubsets>) –> class std::shared_ptr<class core::pack::interaction_graph::DensePDInteractionGraph>

create_rotamer_subsets_from_rot_to_pack(self: pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets

C++: protocols::pack_daemon::RotamerSubsetRepacker::create_rotamer_subsets_from_rot_to_pack(const class utility::vector0<int, class std::allocator<int> > &) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSubsets>

repack(self: pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::DenseIGRepacker::repack(const class utility::vector0<int, class std::allocator<int> > &) –> struct std::pair<class utility::vector1<int, class std::allocator<int> >, double>

set_MCA(self: pyrosetta.rosetta.protocols.pack_daemon.DenseIGRepacker) → None

C++: protocols::pack_daemon::DenseIGRepacker::set_MCA() –> void

class pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker

Bases: RotamerSubsetRepacker

assign(self: pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker, : pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker) → pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker

C++: protocols::pack_daemon::DoubleDenseIGRepacker::operator=(const class protocols::pack_daemon::DoubleDenseIGRepacker &) –> class protocols::pack_daemon::DoubleDenseIGRepacker &

create_dense_pdig_from_rot_to_pack(self: pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int, rot_subsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets) → pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph

C++: protocols::pack_daemon::DoubleDenseIGRepacker::create_dense_pdig_from_rot_to_pack(const class utility::vector0<int, class std::allocator<int> > &, class std::shared_ptr<class core::pack::rotamer_set::RotamerSubsets>) –> class std::shared_ptr<class core::pack::interaction_graph::DoubleDensePDInteractionGraph>

create_rotamer_subsets_from_rot_to_pack(self: pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets

C++: protocols::pack_daemon::RotamerSubsetRepacker::create_rotamer_subsets_from_rot_to_pack(const class utility::vector0<int, class std::allocator<int> > &) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSubsets>

repack(self: pyrosetta.rosetta.protocols.pack_daemon.DoubleDenseIGRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::DoubleDenseIGRepacker::repack(const class utility::vector0<int, class std::allocator<int> > &) –> struct std::pair<class utility::vector1<int, class std::allocator<int> >, double>

class pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction

Bases: MultistateAggregateFunction

add_file_contents(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, fname: str, contents: str) → None

Pair a file name with a string – instead of opening a file

when asked to read this file, the DAF will use the contents of the file as provided. Useful for testing purposes.

C++: protocols::pack_daemon::DynamicAggregateFunction::add_file_contents(const std::string &, const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, : pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction) → pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction

C++: protocols::pack_daemon::DynamicAggregateFunction::operator=(const class protocols::pack_daemon::DynamicAggregateFunction &) –> class protocols::pack_daemon::DynamicAggregateFunction &

evaluate(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, : pyrosetta.rosetta.utility.vector1_double, npd_properties: pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → float

C++: protocols::pack_daemon::DynamicAggregateFunction::evaluate(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class protocols::genetic_algorithm::Entity &) –> double

file_inputs_for_job(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, job_index: int) → pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames

C++: protocols::pack_daemon::DynamicAggregateFunction::file_inputs_for_job(int) const –> const class protocols::pack_daemon::StructureFileNames &

function_expression(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, function: pyrosetta.rosetta.numeric.expression_parser.FunctionToken, args: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::DynamicAggregateFunction::function_expression(class std::shared_ptr<const class numeric::expression_parser::FunctionToken>, const class utility::vector1<class std::shared_ptr<const class numeric::expression_parser::Expression>, class std::allocator<class std::shared_ptr<const class numeric::expression_parser::Expression> > > &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

num_npd_properties(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction) → int

C++: protocols::pack_daemon::DynamicAggregateFunction::num_npd_properties() const –> unsigned long

num_npd_properties_for_state(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, state_id: int) → int

C++: protocols::pack_daemon::DynamicAggregateFunction::num_npd_properties_for_state(unsigned long) const –> unsigned long

num_states(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction) → int

C++: protocols::pack_daemon::DynamicAggregateFunction::num_states() const –> unsigned long

read_all_variables_from_input_file(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, input: pyrosetta.rosetta.std.istream) → None

Initialize from an input stream without trying to communicate with

remote nodes

C++: protocols::pack_daemon::DynamicAggregateFunction::read_all_variables_from_input_file(std::istream &) –> void

select_relevant_states(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, en: pyrosetta.rosetta.utility.vector1_double, npd: pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::pack_daemon::DynamicAggregateFunction::select_relevant_states(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class protocols::genetic_algorithm::Entity &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_num_entity_elements(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, setting: int) → None

C++: protocols::pack_daemon::DynamicAggregateFunction::set_num_entity_elements(unsigned long) –> void

set_score_function(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::pack_daemon::DynamicAggregateFunction::set_score_function(const class core::scoring::ScoreFunction &) –> void

state_name(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, state_index: int) → str

C++: protocols::pack_daemon::DynamicAggregateFunction::state_name(unsigned long) const –> std::string

variable_expression(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::DynamicAggregateFunction::variable_expression(const class numeric::expression_parser::ArithmeticASTValue &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

class pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver

Bases: DynamicAggregateFunction

add_file_contents(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, fname: str, contents: str) → None

Pair a file name with a string – instead of opening a file

when asked to read this file, the DAF will use the contents of the file as provided. Useful for testing purposes.

C++: protocols::pack_daemon::DynamicAggregateFunction::add_file_contents(const std::string &, const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver, : pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver) → pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver

C++: protocols::pack_daemon::DynamicAggregateFunctionDriver::operator=(const class protocols::pack_daemon::DynamicAggregateFunctionDriver &) –> class protocols::pack_daemon::DynamicAggregateFunctionDriver &

evaluate(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, : pyrosetta.rosetta.utility.vector1_double, npd_properties: pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → float

C++: protocols::pack_daemon::DynamicAggregateFunction::evaluate(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class protocols::genetic_algorithm::Entity &) –> double

file_inputs_for_job(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, job_index: int) → pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames

C++: protocols::pack_daemon::DynamicAggregateFunction::file_inputs_for_job(int) const –> const class protocols::pack_daemon::StructureFileNames &

function_expression(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, function: pyrosetta.rosetta.numeric.expression_parser.FunctionToken, args: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::DynamicAggregateFunction::function_expression(class std::shared_ptr<const class numeric::expression_parser::FunctionToken>, const class utility::vector1<class std::shared_ptr<const class numeric::expression_parser::Expression>, class std::allocator<class std::shared_ptr<const class numeric::expression_parser::Expression> > > &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

initialize_from_input_file(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver, daemon_set: protocols::pack_daemon::DaemonSet, input: pyrosetta.rosetta.std.istream) → None

C++: protocols::pack_daemon::DynamicAggregateFunctionDriver::initialize_from_input_file(class std::shared_ptr<class protocols::pack_daemon::DaemonSet>, std::istream &) –> void

num_npd_properties(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction) → int

C++: protocols::pack_daemon::DynamicAggregateFunction::num_npd_properties() const –> unsigned long

num_npd_properties_for_state(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, state_id: int) → int

C++: protocols::pack_daemon::DynamicAggregateFunction::num_npd_properties_for_state(unsigned long) const –> unsigned long

num_states(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction) → int

C++: protocols::pack_daemon::DynamicAggregateFunction::num_states() const –> unsigned long

read_all_variables_from_input_file(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, input: pyrosetta.rosetta.std.istream) → None

Initialize from an input stream without trying to communicate with

remote nodes

C++: protocols::pack_daemon::DynamicAggregateFunction::read_all_variables_from_input_file(std::istream &) –> void

select_relevant_states(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, en: pyrosetta.rosetta.utility.vector1_double, npd: pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::pack_daemon::DynamicAggregateFunction::select_relevant_states(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class protocols::genetic_algorithm::Entity &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_num_entity_elements(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, setting: int) → None

C++: protocols::pack_daemon::DynamicAggregateFunction::set_num_entity_elements(unsigned long) –> void

set_score_function(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::pack_daemon::DynamicAggregateFunction::set_score_function(const class core::scoring::ScoreFunction &) –> void

state_name(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, state_index: int) → str

C++: protocols::pack_daemon::DynamicAggregateFunction::state_name(unsigned long) const –> std::string

variable_expression(self: pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::DynamicAggregateFunction::variable_expression(const class numeric::expression_parser::ArithmeticASTValue &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

class pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence

Bases: pybind11_object

add_resid_to_entity_list(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, EntityID: int, ResID: int) → None

C++: protocols::pack_daemon::EntityCorrespondence::add_resid_to_entity_list(unsigned long, unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, : pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence) → pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence

C++: protocols::pack_daemon::EntityCorrespondence::operator=(const class protocols::pack_daemon::EntityCorrespondence &) –> class protocols::pack_daemon::EntityCorrespondence &

entity_for_residue(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, resid: int) → int

C++: protocols::pack_daemon::EntityCorrespondence::entity_for_residue(unsigned long) const –> unsigned long

initialize_from_correspondence_file(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, : pyrosetta.rosetta.std.istream) → None

C++: protocols::pack_daemon::EntityCorrespondence::initialize_from_correspondence_file(std::istream &) –> void

n_residues_for_entity(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, entity_id: int) → int

C++: protocols::pack_daemon::EntityCorrespondence::n_residues_for_entity(unsigned long) const –> unsigned long

num_entities(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence) → int

C++: protocols::pack_daemon::EntityCorrespondence::num_entities() const –> unsigned long

num_residues(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence) → int

C++: protocols::pack_daemon::EntityCorrespondence::num_residues() const –> unsigned long

set_num_entities(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, num_entities: int) → None

C++: protocols::pack_daemon::EntityCorrespondence::set_num_entities(unsigned long) –> void

set_pose(self: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pack_daemon::EntityCorrespondence::set_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.EntityFunc

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFunc, : pyrosetta.rosetta.protocols.pack_daemon.EntityFunc) → pyrosetta.rosetta.protocols.pack_daemon.EntityFunc

C++: protocols::pack_daemon::EntityFunc::operator=(const class protocols::pack_daemon::EntityFunc &) –> class protocols::pack_daemon::EntityFunc &

evaluate(*args, **kwargs)

Overloaded function.

1. evaluate(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFunc, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) -> float

2. evaluate(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFunc, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity, verbose: bool) -> float

C++: protocols::pack_daemon::EntityFunc::evaluate(const class protocols::genetic_algorithm::Entity &, bool) –> double

function_expression(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFunc, function: pyrosetta.rosetta.numeric.expression_parser.FunctionToken, args: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::EntityFunc::function_expression(class std::shared_ptr<const class numeric::expression_parser::FunctionToken>, const class utility::vector1<class std::shared_ptr<const class numeric::expression_parser::Expression>, class std::allocator<class std::shared_ptr<const class numeric::expression_parser::Expression> > > &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

initialize_from_input_file(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFunc, input: pyrosetta.rosetta.std.istream) → None

C++: protocols::pack_daemon::EntityFunc::initialize_from_input_file(std::istream &) –> void

set_num_entity_elements(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFunc, num_ee: int) → None

C++: protocols::pack_daemon::EntityFunc::set_num_entity_elements(unsigned long) –> void

variable_expression(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFunc, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::EntityFunc::variable_expression(const class numeric::expression_parser::ArithmeticASTValue &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

class pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator

Bases: ExpressionCreator

assign(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator) → pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator

C++: numeric::expression_parser::ExpressionCreator::operator=(const class numeric::expression_parser::ExpressionCreator &) –> class numeric::expression_parser::ExpressionCreator &

create_expression_tree(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) → numeric::expression_parser::Expression

C++: numeric::expression_parser::ExpressionCreator::create_expression_tree(const class numeric::expression_parser::ArithmeticASTExpression &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

handle_function_expression(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator, function: pyrosetta.rosetta.numeric.expression_parser.FunctionToken, args: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::EntityFuncExpressionCreator::handle_function_expression(class std::shared_ptr<const class numeric::expression_parser::FunctionToken>, const class utility::vector1<class std::shared_ptr<const class numeric::expression_parser::Expression>, class std::allocator<class std::shared_ptr<const class numeric::expression_parser::Expression> > > &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

handle_variable_expression(self: pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::EntityFuncExpressionCreator::handle_variable_expression(const class numeric::expression_parser::ArithmeticASTValue &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

visit(*args, **kwargs)

Overloaded function.

1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTExpression &) –> void

2. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTAndClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTAndClause &) –> void

3. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTOrClause &) –> void

4. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTFunction &) –> void

5. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTTerm &) –> void

6. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTFactor &) –> void

7. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTValue &) –> void

8. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestTerm &) –> void

9. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestAndClause &) –> void

10. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestOrClause &) –> void

11. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestExpression &) –> void

12. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTNode &) –> void

class pyrosetta.rosetta.protocols.pack_daemon.ExpExpression

Bases: UnaryExpression

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: numeric::expression_parser::UnaryExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.ExpExpression, : pyrosetta.rosetta.protocols.pack_daemon.ExpExpression) → pyrosetta.rosetta.protocols.pack_daemon.ExpExpression

C++: protocols::pack_daemon::ExpExpression::operator=(const class protocols::pack_daemon::ExpExpression &) –> class protocols::pack_daemon::ExpExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.ExpExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::ExpExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker

Bases: RotamerSubsetRepacker

assign(self: pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker, : pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker) → pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker

C++: protocols::pack_daemon::FASTER_IG_Repacker::operator=(const class protocols::pack_daemon::FASTER_IG_Repacker &) –> class protocols::pack_daemon::FASTER_IG_Repacker &

create_faster_ig_from_rot_to_pack(self: pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int, rot_subsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets) → pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph

C++: protocols::pack_daemon::FASTER_IG_Repacker::create_faster_ig_from_rot_to_pack(const class utility::vector0<int, class std::allocator<int> > &, class std::shared_ptr<class core::pack::rotamer_set::RotamerSubsets>) –> class std::shared_ptr<class core::pack::interaction_graph::FASTERInteractionGraph>

create_rotamer_subsets_from_rot_to_pack(self: pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets

C++: protocols::pack_daemon::RotamerSubsetRepacker::create_rotamer_subsets_from_rot_to_pack(const class utility::vector0<int, class std::allocator<int> > &) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSubsets>

repack(self: pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::FASTER_IG_Repacker::repack(const class utility::vector0<int, class std::allocator<int> > &) –> struct std::pair<class utility::vector1<int, class std::allocator<int> >, double>

set_ciBR_only(self: pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker, setting: bool) → None

C++: protocols::pack_daemon::FASTER_IG_Repacker::set_ciBR_only(bool) –> void

set_num_sa(self: pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker, setting: int) → None

C++: protocols::pack_daemon::FASTER_IG_Repacker::set_num_sa(int) –> void

set_sa_scale(self: pyrosetta.rosetta.protocols.pack_daemon.FASTER_IG_Repacker, setting: float) → None

C++: protocols::pack_daemon::FASTER_IG_Repacker::set_sa_scale(double) –> void

class pyrosetta.rosetta.protocols.pack_daemon.InSetExpression

Bases: UnaryExpression

Returns “true” if the expression ex evaluates to one of a set of indicated values.

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: numeric::expression_parser::UnaryExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression, : pyrosetta.rosetta.protocols.pack_daemon.InSetExpression) → pyrosetta.rosetta.protocols.pack_daemon.InSetExpression

C++: protocols::pack_daemon::InSetExpression::operator=(const class protocols::pack_daemon::InSetExpression &) –> class protocols::pack_daemon::InSetExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::InSetExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

value_set(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression, values: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::pack_daemon::InSetExpression::value_set(const class utility::vector1<double, class std::allocator<double> > &) –> void

class pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression

Bases: VectorExpression

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::IterativeVectorExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

active_variables_vector(self: pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression) → pyrosetta.rosetta.utility.vector1_std_list_std_string_t

C++: protocols::pack_daemon::IterativeVectorExpression::active_variables_vector() const –> class utility::vector1<class std::list<std::string, class std::allocator<std::string > >, class std::allocator<class std::list<std::string, class std::allocator<std::string > > > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression, : pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression) → pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression

C++: protocols::pack_daemon::IterativeVectorExpression::operator=(const class protocols::pack_daemon::IterativeVectorExpression &) –> class protocols::pack_daemon::IterativeVectorExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

DO NOT CALL THIS FUNCTION. Vector expressions cannot

be differentiated.

C++: protocols::pack_daemon::VectorExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

initialize(self: pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression, vector_varnames: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t, expresion_ast: pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression, expression_creator: protocols::pack_daemon::VectorExpressionCreator) → None

C++: protocols::pack_daemon::IterativeVectorExpression::initialize(const class std::map<std::string, class std::shared_ptr<const class protocols::pack_daemon::VectorExpression>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::pack_daemon::VectorExpression> > > > &, const class numeric::expression_parser::ArithmeticASTExpression &, class protocols::pack_daemon::VectorExpressionCreator &) –> void

local_variable(self: pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.VariableExpression

C++: protocols::pack_daemon::IterativeVectorExpression::local_variable(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::VariableExpression>

name(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → str

C++: protocols::pack_daemon::VectorExpression::name() const –> const std::string &

size(self: pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression) → int

C++: protocols::pack_daemon::IterativeVectorExpression::size() const –> unsigned long

vector_values(self: pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pack_daemon::IterativeVectorExpression::vector_values() const –> class utility::vector1<double, class std::allocator<double> >

class pyrosetta.rosetta.protocols.pack_daemon.LnExpression

Bases: UnaryExpression

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: numeric::expression_parser::UnaryExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.LnExpression, : pyrosetta.rosetta.protocols.pack_daemon.LnExpression) → pyrosetta.rosetta.protocols.pack_daemon.LnExpression

C++: protocols::pack_daemon::LnExpression::operator=(const class protocols::pack_daemon::LnExpression &) –> class protocols::pack_daemon::LnExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.LnExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::LnExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction

Bases: MultistateFitnessFunction

aggregate_function(*args, **kwargs)

Overloaded function.

1. aggregate_function(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, func: pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction) -> None

C++: protocols::pack_daemon::MultistateFitnessFunction::aggregate_function(class std::shared_ptr<class protocols::pack_daemon::MultistateAggregateFunction>) –> void

2. aggregate_function(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) -> pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction

C++: protocols::pack_daemon::MultistateFitnessFunction::aggregate_function() const –> class std::shared_ptr<const class protocols::pack_daemon::MultistateAggregateFunction>

assign(self: pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction, : pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction) → pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction

C++: protocols::pack_daemon::MPIMultistateFitnessFunction::operator=(const class protocols::pack_daemon::MPIMultistateFitnessFunction &) –> class protocols::pack_daemon::MPIMultistateFitnessFunction &

clear_history(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) → None

C++: protocols::pack_daemon::MultistateFitnessFunction::clear_history() –> void

daemon_set(*args, **kwargs)

Overloaded function.

1. daemon_set(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, ds: protocols::pack_daemon::DaemonSet) -> None

C++: protocols::pack_daemon::MultistateFitnessFunction::daemon_set(class std::shared_ptr<class protocols::pack_daemon::DaemonSet>) –> void

2. daemon_set(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) -> protocols::pack_daemon::DaemonSet

C++: protocols::pack_daemon::MultistateFitnessFunction::daemon_set() const –> class std::shared_ptr<const class protocols::pack_daemon::DaemonSet>

evaluate(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → float

C++: protocols::pack_daemon::MultistateFitnessFunction::evaluate(class protocols::genetic_algorithm::Entity &) –> double

npd_properties(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pack_daemon::MultistateFitnessFunction::npd_properties() const –> const class utility::vector1<double, class std::allocator<double> > &

send_spin_down_signal(self: pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction) → None

Spin down the other nodes. No entity evaluation may follow

the spin down call

C++: protocols::pack_daemon::MPIMultistateFitnessFunction::send_spin_down_signal() –> void

set_history_size(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, history_size: int) → None

C++: protocols::pack_daemon::MultistateFitnessFunction::set_history_size(unsigned long) –> void

set_num_npd_properties(self: pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction, n_npd_properties: int) → None

Inform this MPIMultistateFitnessFunction how many non-pairwise decomposable

properties will be computed for all states

C++: protocols::pack_daemon::MPIMultistateFitnessFunction::set_num_npd_properties(unsigned long) –> void

set_num_pack_daemons(self: pyrosetta.rosetta.protocols.pack_daemon.MPIMultistateFitnessFunction, n_daemons: int) → None

Inform this MPIMultistateFitnessFunction how many PackDaemons

are running on all nodes (counting this one) which it may be unaware of.

C++: protocols::pack_daemon::MPIMultistateFitnessFunction::set_num_pack_daemons(unsigned long) –> void

state_energies(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pack_daemon::MultistateFitnessFunction::state_energies() const –> const class utility::vector1<double, class std::allocator<double> > &

class pyrosetta.rosetta.protocols.pack_daemon.Mean

Bases: VectorFunction

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.Mean) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::Mean::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.Mean, : pyrosetta.rosetta.protocols.pack_daemon.Mean) → pyrosetta.rosetta.protocols.pack_daemon.Mean

C++: protocols::pack_daemon::Mean::operator=(const class protocols::pack_daemon::Mean &) –> class protocols::pack_daemon::Mean &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.Mean, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::Mean::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction, : pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction) → pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction

C++: protocols::pack_daemon::MultistateAggregateFunction::operator=(const class protocols::pack_daemon::MultistateAggregateFunction &) –> class protocols::pack_daemon::MultistateAggregateFunction &

evaluate(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → float

C++: protocols::pack_daemon::MultistateAggregateFunction::evaluate(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class protocols::genetic_algorithm::Entity &) –> double

select_relevant_states(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::pack_daemon::MultistateAggregateFunction::select_relevant_states(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class protocols::genetic_algorithm::Entity &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction

Bases: FitnessFunction

aggregate_function(*args, **kwargs)

Overloaded function.

1. aggregate_function(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, func: pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction) -> None

C++: protocols::pack_daemon::MultistateFitnessFunction::aggregate_function(class std::shared_ptr<class protocols::pack_daemon::MultistateAggregateFunction>) –> void

2. aggregate_function(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) -> pyrosetta.rosetta.protocols.pack_daemon.MultistateAggregateFunction

C++: protocols::pack_daemon::MultistateFitnessFunction::aggregate_function() const –> class std::shared_ptr<const class protocols::pack_daemon::MultistateAggregateFunction>

assign(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, : pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) → pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction

C++: protocols::pack_daemon::MultistateFitnessFunction::operator=(const class protocols::pack_daemon::MultistateFitnessFunction &) –> class protocols::pack_daemon::MultistateFitnessFunction &

clear_history(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) → None

C++: protocols::pack_daemon::MultistateFitnessFunction::clear_history() –> void

daemon_set(*args, **kwargs)

Overloaded function.

1. daemon_set(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, ds: protocols::pack_daemon::DaemonSet) -> None

C++: protocols::pack_daemon::MultistateFitnessFunction::daemon_set(class std::shared_ptr<class protocols::pack_daemon::DaemonSet>) –> void

2. daemon_set(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) -> protocols::pack_daemon::DaemonSet

C++: protocols::pack_daemon::MultistateFitnessFunction::daemon_set() const –> class std::shared_ptr<const class protocols::pack_daemon::DaemonSet>

evaluate(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, entity: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → float

C++: protocols::pack_daemon::MultistateFitnessFunction::evaluate(class protocols::genetic_algorithm::Entity &) –> double

npd_properties(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pack_daemon::MultistateFitnessFunction::npd_properties() const –> const class utility::vector1<double, class std::allocator<double> > &

set_history_size(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction, history_size: int) → None

C++: protocols::pack_daemon::MultistateFitnessFunction::set_history_size(unsigned long) –> void

state_energies(self: pyrosetta.rosetta.protocols.pack_daemon.MultistateFitnessFunction) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pack_daemon::MultistateFitnessFunction::state_energies() const –> const class utility::vector1<double, class std::allocator<double> > &

class pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator, : pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator) → pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator

C++: protocols::pack_daemon::NPDPropCalculator::operator=(const class protocols::pack_daemon::NPDPropCalculator &) –> class protocols::pack_daemon::NPDPropCalculator &

calculate(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator, p: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::pack_daemon::NPDPropCalculator::calculate(const class core::pose::Pose &) –> double

setup(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::pack_daemon::NPDPropCalculator::setup(const class core::pose::Pose &, const class core::pack::task::PackerTask &) –> void

class pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator, : pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator) → pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator

C++: protocols::pack_daemon::NPDPropCalculatorCreator::operator=(const class protocols::pack_daemon::NPDPropCalculatorCreator &) –> class protocols::pack_daemon::NPDPropCalculatorCreator &

calculator_name(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator) → str

C++: protocols::pack_daemon::NPDPropCalculatorCreator::calculator_name() const –> std::string

new_calculator(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculatorCreator) → pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator

C++: protocols::pack_daemon::NPDPropCalculatorCreator::new_calculator() const –> class std::shared_ptr<class protocols::pack_daemon::NPDPropCalculator>

class pyrosetta.rosetta.protocols.pack_daemon.PackDaemon

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → pyrosetta.rosetta.protocols.pack_daemon.PackDaemon

C++: protocols::pack_daemon::PackDaemon::operator=(const class protocols::pack_daemon::PackDaemon &) –> class protocols::pack_daemon::PackDaemon &

assign_last_rotamers_to_pose(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::pack_daemon::PackDaemon::assign_last_rotamers_to_pose(class core::pose::Pose &) const –> void

best_assignment(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::PackDaemon::best_assignment() const –> const struct std::pair<class utility::vector1<int, class std::allocator<int> >, double> &

compute_energy_for_assignment(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → float

Repack the structure with the Entity

This function proceeds in two steps: it creates a list of rotamer indices to be used during the repacking, and then it uses that list to repack the rotamers. The first step is taken care of by the select_rotamer_subset method.

C++: protocols::pack_daemon::PackDaemon::compute_energy_for_assignment(const class protocols::genetic_algorithm::Entity &) –> double

correspondence(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence

C++: protocols::pack_daemon::PackDaemon::correspondence() const –> class std::shared_ptr<const class protocols::pack_daemon::EntityCorrespondence>

ig(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph

C++: protocols::pack_daemon::PackDaemon::ig() const –> class std::shared_ptr<const class core::pack::interaction_graph::FixedBBInteractionGraph>

last_assignment(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::PackDaemon::last_assignment() const –> const struct std::pair<class utility::vector1<int, class std::allocator<int> >, double> &

mark_entity_as_unimportant(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → None

C++: protocols::pack_daemon::PackDaemon::mark_entity_as_unimportant(const class protocols::genetic_algorithm::Entity &) –> void

mark_last_entity_as_important(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → None

C++: protocols::pack_daemon::PackDaemon::mark_last_entity_as_important() –> void

pose(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pack_daemon::PackDaemon::pose() const –> class std::shared_ptr<const class core::pose::Pose>

print_entity_history(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → None

C++: protocols::pack_daemon::PackDaemon::print_entity_history() const –> void

recreate_pose_for_entity(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::pack_daemon::PackDaemon::recreate_pose_for_entity(const class protocols::genetic_algorithm::Entity &) const –> class std::shared_ptr<class core::pose::Pose>

rot_sets(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: protocols::pack_daemon::PackDaemon::rot_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::pack_daemon::PackDaemon::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

select_rotamer_subset(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → pyrosetta.rosetta.utility.vector0_int

C++: protocols::pack_daemon::PackDaemon::select_rotamer_subset(const class protocols::genetic_algorithm::Entity &) const –> class utility::vector0<int, class std::allocator<int> >

set_dlig_nmeg_limit(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, setting: int) → None

restrict the amount of memory spent on storing Rotamer Pair Energies in the

DoubleLazyInteractionGraph;

C++: protocols::pack_daemon::PackDaemon::set_dlig_nmeg_limit(unsigned long) –> void

set_entity_correspondence(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence) → None

C++: protocols::pack_daemon::PackDaemon::set_entity_correspondence(const class protocols::pack_daemon::EntityCorrespondence &) –> void

set_include_background_energies(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, setting: bool) → None

C++: protocols::pack_daemon::PackDaemon::set_include_background_energies(bool) –> void

set_pose_and_task(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::pack_daemon::PackDaemon::set_pose_and_task(const class core::pose::Pose &, const class core::pack::task::PackerTask &) –> void

set_score_function(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::pack_daemon::PackDaemon::set_score_function(const class core::scoring::ScoreFunction &) –> void

setup(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → None

C++: protocols::pack_daemon::PackDaemon::setup() –> void

task(self: pyrosetta.rosetta.protocols.pack_daemon.PackDaemon) → pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::pack_daemon::PackDaemon::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

class pyrosetta.rosetta.protocols.pack_daemon.PowExpression

Bases: BinaryExpression

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: numeric::expression_parser::BinaryExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.PowExpression, : pyrosetta.rosetta.protocols.pack_daemon.PowExpression) → pyrosetta.rosetta.protocols.pack_daemon.PowExpression

C++: protocols::pack_daemon::PowExpression::operator=(const class protocols::pack_daemon::PowExpression &) –> class protocols::pack_daemon::PowExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.PowExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::PowExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e1(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e1() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e2(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e2() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_first_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e1: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_first_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_second_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e2: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_second_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker, : pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker) → pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker

C++: protocols::pack_daemon::QuickRepacker::operator=(const class protocols::pack_daemon::QuickRepacker &) –> class protocols::pack_daemon::QuickRepacker &

repack(self: pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::QuickRepacker::repack(const class utility::vector0<int, class std::allocator<int> > &) –> struct std::pair<class utility::vector1<int, class std::allocator<int> >, double>

class pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker

Bases: QuickRepacker

assign(self: pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker, : pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker) → pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker

C++: protocols::pack_daemon::RotamerSubsetRepacker::operator=(const class protocols::pack_daemon::RotamerSubsetRepacker &) –> class protocols::pack_daemon::RotamerSubsetRepacker &

create_rotamer_subsets_from_rot_to_pack(self: pyrosetta.rosetta.protocols.pack_daemon.RotamerSubsetRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets

C++: protocols::pack_daemon::RotamerSubsetRepacker::create_rotamer_subsets_from_rot_to_pack(const class utility::vector0<int, class std::allocator<int> > &) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSubsets>

repack(self: pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::QuickRepacker::repack(const class utility::vector0<int, class std::allocator<int> > &) –> struct std::pair<class utility::vector1<int, class std::allocator<int> >, double>

class pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames, : pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames) → pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames

C++: protocols::pack_daemon::StructureFileNames::operator=(const class protocols::pack_daemon::StructureFileNames &) –> class protocols::pack_daemon::StructureFileNames &

property correspondence_file_name_

property pdb_name_

property resfile_name_

class pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression

Bases: VariableExpression

Stores the result of the surragate expression as if this expression were a variable, but defers to the root expression for questions of deriviatives and which variables are active (this is not a real variable).

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::SurrogateVariableExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, : pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression) → pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression

C++: protocols::pack_daemon::SurrogateVariableExpression::operator=(const class protocols::pack_daemon::SurrogateVariableExpression &) –> class protocols::pack_daemon::SurrogateVariableExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::SurrogateVariableExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

name(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression) → str

C++: numeric::expression_parser::VariableExpression::name() const –> std::string

root_expression(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, setting: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: protocols::pack_daemon::SurrogateVariableExpression::root_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_value(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression, value: float) → None

C++: numeric::expression_parser::VariableExpression::set_value(double) –> void

class pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet, : pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet) → pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet

C++: protocols::pack_daemon::TopEntitySet::operator=(const class protocols::pack_daemon::TopEntitySet &) –> class protocols::pack_daemon::TopEntitySet &

clear(self: pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet) → None

C++: protocols::pack_daemon::TopEntitySet::clear() –> void

desired_entity_history_size(*args, **kwargs)

Overloaded function.

1. desired_entity_history_size(self: pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet, setting: int) -> None

C++: protocols::pack_daemon::TopEntitySet::desired_entity_history_size(unsigned long) –> void

2. desired_entity_history_size(self: pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet) -> int

C++: protocols::pack_daemon::TopEntitySet::desired_entity_history_size() const –> unsigned long

index_of_entity(self: pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet, ent: pyrosetta.rosetta.protocols.genetic_algorithm.Entity) → int

C++: protocols::pack_daemon::TopEntitySet::index_of_entity(const class protocols::genetic_algorithm::Entity &) const –> unsigned long

pop(self: pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet) → Tuple[pyrosetta.rosetta.protocols.genetic_algorithm.Entity, Tuple[pyrosetta.rosetta.utility.vector1_double, pyrosetta.rosetta.utility.vector1_double]]

remove the worst entity from the set and return it

C++: protocols::pack_daemon::TopEntitySet::pop() –> struct std::pair<class std::shared_ptr<class protocols::genetic_algorithm::Entity>, struct std::pair<class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> > > >

size(self: pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet) → int

C++: protocols::pack_daemon::TopEntitySet::size() const –> unsigned long

class pyrosetta.rosetta.protocols.pack_daemon.VMax

Bases: VectorFunction

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.VMax) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::VMax::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VMax, : pyrosetta.rosetta.protocols.pack_daemon.VMax) → pyrosetta.rosetta.protocols.pack_daemon.VMax

C++: protocols::pack_daemon::VMax::operator=(const class protocols::pack_daemon::VMax &) –> class protocols::pack_daemon::VMax &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VMax, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VMax::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VMaxBy

Bases: VectorFunction2

Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the largest value in expression 1

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::VMaxBy::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy, : pyrosetta.rosetta.protocols.pack_daemon.VMaxBy) → pyrosetta.rosetta.protocols.pack_daemon.VMaxBy

C++: protocols::pack_daemon::VMaxBy::operator=(const class protocols::pack_daemon::VMaxBy &) –> class protocols::pack_daemon::VMaxBy &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VMaxBy::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e1(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e1() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e2(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e2() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_first_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e1: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_first_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_second_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e2: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_second_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VMin

Bases: VectorFunction

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.VMin) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::VMin::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VMin, : pyrosetta.rosetta.protocols.pack_daemon.VMin) → pyrosetta.rosetta.protocols.pack_daemon.VMin

C++: protocols::pack_daemon::VMin::operator=(const class protocols::pack_daemon::VMin &) –> class protocols::pack_daemon::VMin &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VMin, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VMin::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VMinBy

Bases: VectorFunction2

Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the smallest value in expression 1

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::VMinBy::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy, : pyrosetta.rosetta.protocols.pack_daemon.VMinBy) → pyrosetta.rosetta.protocols.pack_daemon.VMinBy

C++: protocols::pack_daemon::VMinBy::operator=(const class protocols::pack_daemon::VMinBy &) –> class protocols::pack_daemon::VMinBy &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VMinBy::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e1(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e1() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e2(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e2() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_first_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e1: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_first_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_second_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e2: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_second_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression

Bases: VectorExpression

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: protocols::pack_daemon::VariableVectorExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

active_variables_vector(self: pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression) → pyrosetta.rosetta.utility.vector1_std_list_std_string_t

C++: protocols::pack_daemon::VariableVectorExpression::active_variables_vector() const –> class utility::vector1<class std::list<std::string, class std::allocator<std::string > >, class std::allocator<class std::list<std::string, class std::allocator<std::string > > > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression, : pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression) → pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression

C++: protocols::pack_daemon::VariableVectorExpression::operator=(const class protocols::pack_daemon::VariableVectorExpression &) –> class protocols::pack_daemon::VariableVectorExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

DO NOT CALL THIS FUNCTION. Vector expressions cannot

be differentiated.

C++: protocols::pack_daemon::VectorExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

name(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → str

C++: protocols::pack_daemon::VectorExpression::name() const –> const std::string &

size(self: pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression) → int

Returns the number of variable expressions this VectorExpression points at

C++: protocols::pack_daemon::VariableVectorExpression::size() const –> unsigned long

vector_values(self: pyrosetta.rosetta.protocols.pack_daemon.VariableVectorExpression) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pack_daemon::VariableVectorExpression::vector_values() const –> class utility::vector1<double, class std::allocator<double> >

class pyrosetta.rosetta.protocols.pack_daemon.VectorExpression

Bases: Expression

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.Expression) → pyrosetta.rosetta.std.list_std_string_t

C++: numeric::expression_parser::Expression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

active_variables_vector(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → pyrosetta.rosetta.utility.vector1_std_list_std_string_t

C++: protocols::pack_daemon::VectorExpression::active_variables_vector() const –> class utility::vector1<class std::list<std::string, class std::allocator<std::string > >, class std::allocator<class std::list<std::string, class std::allocator<std::string > > > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression, : pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → pyrosetta.rosetta.protocols.pack_daemon.VectorExpression

C++: protocols::pack_daemon::VectorExpression::operator=(const class protocols::pack_daemon::VectorExpression &) –> class protocols::pack_daemon::VectorExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

DO NOT CALL THIS FUNCTION. Vector expressions cannot

be differentiated.

C++: protocols::pack_daemon::VectorExpression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

name(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → str

C++: protocols::pack_daemon::VectorExpression::name() const –> const std::string &

size(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → int

Returns the number of vector values that this Expression returns without

computing those values.

C++: protocols::pack_daemon::VectorExpression::size() const –> unsigned long

vector_values(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::pack_daemon::VectorExpression::vector_values() const –> class utility::vector1<double, class std::allocator<double> >

class pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator

Bases: ExpressionCreator

assign(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator) → pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator

C++: numeric::expression_parser::ExpressionCreator::operator=(const class numeric::expression_parser::ExpressionCreator &) –> class numeric::expression_parser::ExpressionCreator &

create_expression_tree(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) → numeric::expression_parser::Expression

C++: numeric::expression_parser::ExpressionCreator::create_expression_tree(const class numeric::expression_parser::ArithmeticASTExpression &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

handle_function_expression(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator, function: pyrosetta.rosetta.numeric.expression_parser.FunctionToken, args: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_numeric_expression_parser_Expression_t) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VectorExpressionCreator::handle_function_expression(class std::shared_ptr<const class numeric::expression_parser::FunctionToken>, const class utility::vector1<class std::shared_ptr<const class numeric::expression_parser::Expression>, class std::allocator<class std::shared_ptr<const class numeric::expression_parser::Expression> > > &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

handle_variable_expression(self: pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VectorExpressionCreator::handle_variable_expression(const class numeric::expression_parser::ArithmeticASTValue &) –> class std::shared_ptr<const class numeric::expression_parser::Expression>

visit(*args, **kwargs)

Overloaded function.

1. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTExpression &) –> void

2. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTAndClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTAndClause &) –> void

3. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTOrClause &) –> void

4. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTFunction &) –> void

5. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTTerm &) –> void

6. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTFactor &) –> void

7. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTValue &) –> void

8. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestTerm &) –> void

9. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestAndClause &) –> void

10. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestOrClause &) –> void

11. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTRestExpression &) –> void

12. visit(self: pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode) -> None

C++: numeric::expression_parser::ExpressionCreator::visit(const class numeric::expression_parser::ArithmeticASTNode &) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VectorFunction

Bases: UnaryExpression

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: numeric::expression_parser::UnaryExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VectorFunction, : pyrosetta.rosetta.protocols.pack_daemon.VectorFunction) → pyrosetta.rosetta.protocols.pack_daemon.VectorFunction

C++: protocols::pack_daemon::VectorFunction::operator=(const class protocols::pack_daemon::VectorFunction &) –> class protocols::pack_daemon::VectorFunction &

differentiate(self: pyrosetta.rosetta.numeric.expression_parser.Expression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

Returns the expression for the partial derivative of this expression

by the variable named varname. If the partial derivative is always zero with respect to varname, returns null.

C++: numeric::expression_parser::Expression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2

Bases: BinaryExpression

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.std.list_std_string_t

C++: numeric::expression_parser::BinaryExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2, : pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2) → pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2

C++: protocols::pack_daemon::VectorFunction2::operator=(const class protocols::pack_daemon::VectorFunction2 &) –> class protocols::pack_daemon::VectorFunction2 &

differentiate(self: pyrosetta.rosetta.numeric.expression_parser.Expression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

Returns the expression for the partial derivative of this expression

by the variable named varname. If the partial derivative is always zero with respect to varname, returns null.

C++: numeric::expression_parser::Expression::differentiate(const std::string &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e1(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e1() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e2(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e2() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_first_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e1: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_first_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_second_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e2: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_second_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

pyrosetta.rosetta.protocols.pack_daemon.create_entity_resfile_contents(resfile: pyrosetta.rosetta.std.istream, resfile_name: str, entity_resfile_contents: pyrosetta.rosetta.core.pack.task.ResfileContents, entity_task: pyrosetta.rosetta.core.pack.task.PackerTask, num_entities: int) → None

C++: protocols::pack_daemon::create_entity_resfile_contents(std::istream &, const std::string &, class std::shared_ptr<class core::pack::task::ResfileContents> &, class std::shared_ptr<class core::pack::task::PackerTask> &, unsigned long &) –> void

pyrosetta.rosetta.protocols.pack_daemon.initialize_ga_randomizer_from_entity_task(rand: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, entity_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::pack_daemon::initialize_ga_randomizer_from_entity_task(class std::shared_ptr<class protocols::genetic_algorithm::PositionSpecificRandomizer>, class std::shared_ptr<class core::pack::task::PackerTask>) –> void

pyrosetta.rosetta.protocols.pack_daemon.initialize_task_from_entity_resfile_and_secondary_resfile(pose: pyrosetta.rosetta.core.pose.Pose, ec: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, entity_resfile_contents: pyrosetta.rosetta.core.pack.task.ResfileContents, secondary_resfile_contents: pyrosetta.rosetta.core.pack.task.ResfileContents, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::pack_daemon::initialize_task_from_entity_resfile_and_secondary_resfile(const class core::pose::Pose &, class std::shared_ptr<const class protocols::pack_daemon::EntityCorrespondence>, const class core::pack::task::ResfileContents &, const class core::pack::task::ResfileContents &, class std::shared_ptr<class core::pack::task::PackerTask>) –> void