constraint_generator

Bindings for protocols::constraint_generator namespace

class pyrosetta.rosetta.protocols.constraint_generator.AddConstraints

Bases: Mover

Adds constraints generated by ConstraintGenerators to a pose

add_generator(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints, cst_generator: protocols::constraint_generator::ConstraintGenerator) → None

C++: protocols::constraint_generator::AddConstraints::add_generator(class std::shared_ptr<const class protocols::constraint_generator::ConstraintGenerator>) –> void

apply(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::constraint_generator::AddConstraints::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints, : pyrosetta.rosetta.protocols.constraint_generator.AddConstraints) → pyrosetta.rosetta.protocols.constraint_generator.AddConstraints

C++: protocols::constraint_generator::AddConstraints::operator=(const class protocols::constraint_generator::AddConstraints &) –> class protocols::constraint_generator::AddConstraints &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::constraint_generator::AddConstraints::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::constraint_generator::AddConstraints::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints) → str

C++: protocols::constraint_generator::AddConstraints::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str

C++: protocols::constraint_generator::AddConstraints::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::constraint_generator::AddConstraints::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraints, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows this mover to provide citations for itself and for any modules that it invokes.

This override cites Tom Linsky, who created the constraint generator framework.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::AddConstraints::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::AddConstraints::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator, : pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator) → pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator

C++: protocols::constraint_generator::AddConstraintsCreator::operator=(const class protocols::constraint_generator::AddConstraintsCreator &) –> class protocols::constraint_generator::AddConstraintsCreator &

create_mover(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::constraint_generator::AddConstraintsCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator) → str

C++: protocols::constraint_generator::AddConstraintsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::AddConstraintsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator

Bases: ConstraintGenerator

Generates atom pair constraints for a set of residues from the current or reference pose

class MappedAtom

Bases: pybind11_object

property pose_atom

property ref_atom

apply(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::AtomPairConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator

C++: protocols::constraint_generator::AtomPairConstraintGenerator::operator=(const class protocols::constraint_generator::AtomPairConstraintGenerator &) –> class protocols::constraint_generator::AtomPairConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::AtomPairConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::AtomPairConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Tom Linsky, who created the constraint generator framework.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::AtomPairConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_ca_only(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, ca_only: bool) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_ca_only(const bool) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

set_max_distance(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, max_dist: float) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_max_distance(const double) –> void

set_min_seq_sep(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, min_seq_sep: int) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_min_seq_sep(const unsigned long) –> void

set_reference_pose(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, ref_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_reference_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_residue_selector(const class core::select::residue_selector::ResidueSelector &) –> void

set_sd(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, sd: float) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_sd(const double) –> void

set_secondary_residue_selector(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_secondary_residue_selector(const class core::select::residue_selector::ResidueSelector &) –> void

set_unweighted_function(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, unweighted: bool) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_unweighted_function(const bool) –> void

set_use_harmonic_function(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, use_harmonic: bool) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_use_harmonic_function(const bool) –> void

set_weight(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator, weight: float) → None

C++: protocols::constraint_generator::AtomPairConstraintGenerator::set_weight(const double) –> void

class pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator

C++: protocols::constraint_generator::AtomPairConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::AtomPairConstraintGeneratorCreator &) –> class protocols::constraint_generator::AtomPairConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::AtomPairConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::AtomPairConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::AtomPairConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

Bases: pybind11_object

pure virtual base class

apply(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

generates constraints and adds them to the pose

C++: protocols::constraint_generator::ConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::ConstraintGenerator::operator=(const class protocols::constraint_generator::ConstraintGenerator &) –> class protocols::constraint_generator::ConstraintGenerator &

class_name(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::class_name() const –> const std::string &

clone(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::ConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

This base class version does nothing. It should be overridden by derived classes.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::ConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

class pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator

C++: protocols::constraint_generator::ConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::ConstraintGeneratorCreator &) –> class protocols::constraint_generator::ConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

Instantiate a particular ConstraintGenerator

C++: protocols::constraint_generator::ConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator) → str

Return a string that will be used to instantiate the particular ConstraintGenerator

C++: protocols::constraint_generator::ConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator, : utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::ConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory

Bases: SingletonBase_protocols_constraint_generator_ConstraintGeneratorFactory_t

static complex_type_name_for_constraint_generator(constraint_name: str) → str

C++: protocols::constraint_generator::ConstraintGeneratorFactory::complex_type_name_for_constraint_generator(const std::string &) –> std::string

static constraint_generator_xml_schema_group_name() → str

C++: protocols::constraint_generator::ConstraintGeneratorFactory::constraint_generator_xml_schema_group_name() –> std::string

define_constraint_generator_xml_schema_group(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::ConstraintGeneratorFactory::define_constraint_generator_xml_schema_group(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory, creator: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator) → None

C++: protocols::constraint_generator::ConstraintGeneratorFactory::factory_register(class std::shared_ptr<class protocols::constraint_generator::ConstraintGeneratorCreator>) –> void

get_citation_humanreadable(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory, cst_generator_name: str) → str

Get a human-readable listing of the citations for a given cst generator, by generator name.

Returns an empty string if there are no citations.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::ConstraintGeneratorFactory::get_citation_humanreadable(const std::string &) const –> std::string

static get_instance() → protocols::constraint_generator::ConstraintGeneratorFactory

C++: utility::SingletonBase<protocols::constraint_generator::ConstraintGeneratorFactory>::get_instance() –> class protocols::constraint_generator::ConstraintGeneratorFactory *

has_type(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory, constraint_generator_name: str) → bool

C++: protocols::constraint_generator::ConstraintGeneratorFactory::has_type(const std::string &) const –> bool

new_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory, constraint_generator_name: str, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::ConstraintGeneratorFactory::new_constraint_generator(const std::string &, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory, cst_generator_name: str, xsd: utility::tag::XMLSchemaDefinition) → None

Get the XML schema for a given constraint generator.

Throws an error if the constraint generator is unknown to Rosetta.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::constraint_generator::ConstraintGeneratorFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void

static xsd_constraint_generator_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, constraint_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::constraint_generator::ConstraintGeneratorFactory::xsd_constraint_generator_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

class pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager

Bases: SingletonBase_protocols_constraint_generator_ConstraintsManager_t

Manages lists of constraints generated by ConstraintGenerators

static get_instance() → protocols::constraint_generator::ConstraintsManager

C++: utility::SingletonBase<protocols::constraint_generator::ConstraintsManager>::get_instance() –> class protocols::constraint_generator::ConstraintsManager *

has_stored_constraints(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager, pose: pyrosetta.rosetta.core.pose.Pose, name: str) → bool

Checks to see whether constraints exist in datacache under the given name

Pose where constraints are cached

Name under which constraints may be stored

C++: protocols::constraint_generator::ConstraintsManager::has_stored_constraints(const class core::pose::Pose &, const std::string &) const –> bool

remove_constraints(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager, pose: pyrosetta.rosetta.core.pose.Pose, name: str) → None

Clears constraints stored under the given name

If constraints are not found under the given name, or there is no

cached data, this will do nothing.

Pose where constraints are cached

Name under which constraints are cached

C++: protocols::constraint_generator::ConstraintsManager::remove_constraints(class core::pose::Pose &, const std::string &) const –> void

retrieve_constraints(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager, pose: pyrosetta.rosetta.core.pose.Pose, name: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

Retrieves constraints from the pose datacache with the given name.

Pose where constraints are cached

Name under which constraints are stored

Const reference to list of stored constraints

C++: protocols::constraint_generator::ConstraintsManager::retrieve_constraints(const class core::pose::Pose &, const std::string &) const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &

store_constraints(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager, pose: pyrosetta.rosetta.core.pose.Pose, name: str, csts: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) → None

Stores the given constraints in the pose datacache, under the name given.

Pose where constraints will be cached

Name under which constraints will be stored

Constraints to cache

C++: protocols::constraint_generator::ConstraintsManager::store_constraints(class core::pose::Pose &, const std::string &, const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap

Bases: CacheableData

Cacheable data map to cache constraint pointers in the pose.

assign(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap, : pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap

C++: protocols::constraint_generator::ConstraintsMap::operator=(const class protocols::constraint_generator::ConstraintsMap &) –> class protocols::constraint_generator::ConstraintsMap &

clone(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::constraint_generator::ConstraintsMap::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

valid_names_string(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap) → str

prints out comma-separated list of constraint set names

C++: protocols::constraint_generator::ConstraintsMap::valid_names_string() const –> std::string

class pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator

Bases: ConstraintGenerator

Generates coodinate constraints

apply(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::CoordinateConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator

C++: protocols::constraint_generator::CoordinateConstraintGenerator::operator=(const class protocols::constraint_generator::CoordinateConstraintGenerator &) –> class protocols::constraint_generator::CoordinateConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::CoordinateConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::CoordinateConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Tom Linsky, who created the constraint generator framework.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::CoordinateConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_ambiguous_hnq(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, ambiguous_hnq: bool) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_ambiguous_hnq(const bool) –> void

set_bounded(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, bounded: bool) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_bounded(const bool) –> void

set_bounded_width(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, bounded_width: float) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_bounded_width(const double) –> void

set_ca_only(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, ca_only: bool) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_ca_only(const bool) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

set_reference_pose(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, refpose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_reference_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sd(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, sd: float) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_sd(const double) –> void

set_sidechain(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator, sidechain: bool) → None

C++: protocols::constraint_generator::CoordinateConstraintGenerator::set_sidechain(const bool) –> void

class pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator

C++: protocols::constraint_generator::CoordinateConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::CoordinateConstraintGeneratorCreator &) –> class protocols::constraint_generator::CoordinateConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::CoordinateConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::CoordinateConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::CoordinateConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator

Bases: ConstraintGenerator

A cst generator that creates Dihedral constraints for specified residues using a residue selector.

Uses CircularHarmonic constraints, since CircularGaussian func does not exist. By default, works on Protein and carbohydrate BB dihedrals. You must set either the set of atom names or phi/psi/omega. Will only work on ONE type of dihedral angle.

apply(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::DihedralConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator

C++: protocols::constraint_generator::DihedralConstraintGenerator::operator=(const class protocols::constraint_generator::DihedralConstraintGenerator &) –> class protocols::constraint_generator::DihedralConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::DihedralConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::DihedralConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

get_dihedral_angle(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator) → float

C++: protocols::constraint_generator::DihedralConstraintGenerator::get_dihedral_angle() const –> double

get_use_custom_dihedral_angle(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator) → bool

C++: protocols::constraint_generator::DihedralConstraintGenerator::get_use_custom_dihedral_angle() const –> bool

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Jared Adolf-Bryfogle.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::DihedralConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::DihedralConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_custom_dihedral(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID) → None

MANUALLY set the dihedrals we will work with.

IGNORES Residue selector, but allows setting dihedrals for ANY torsion.

C++: protocols::constraint_generator::DihedralConstraintGenerator::set_custom_dihedral(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) –> void

set_dihedral_angle(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, dihedral_angle: float) → None

Set the desired dihedral angle in degrees. This is not compatible if you use_custom_dihedral_angle

set_custom_dihedral. If you do call this function in addition to setting a custom dihedral, no constraints will be applied and an error will be returned.

C++: protocols::constraint_generator::DihedralConstraintGenerator::set_dihedral_angle(double) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::DihedralConstraintGenerator::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sd_degree(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, sd_degree: float) → None

Set the standard deviation for the dihedral constraint. Default is 16.0.

This which was found by taking the mean SD of all dihedral angles of either PHI or PSI for each North CDR Cluster. This is a fairly tight constraint and allows a bit of movement while not changing overall struture much.

Set this in Degrees.

C++: protocols::constraint_generator::DihedralConstraintGenerator::set_sd_degree(double) –> void

set_torsion_type(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, torsion: pyrosetta.rosetta.core.id.MainchainTorsionType) → None

Set the torsion type we will be working with.

C++: protocols::constraint_generator::DihedralConstraintGenerator::set_torsion_type(enum core::id::MainchainTorsionType) –> void

set_use_custom_dihedral_angle(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator, use_custom_dihedral_angle: bool) → None

C++: protocols::constraint_generator::DihedralConstraintGenerator::set_use_custom_dihedral_angle(bool) –> void

class pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator

C++: protocols::constraint_generator::DihedralConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::DihedralConstraintGeneratorCreator &) –> class protocols::constraint_generator::DihedralConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::DihedralConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::DihedralConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::DihedralConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator

Bases: ConstraintGenerator

Generates AtomPair constraints to enforce a given distance between two residue subsets

apply(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::DistanceConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator

C++: protocols::constraint_generator::DistanceConstraintGenerator::operator=(const class protocols::constraint_generator::DistanceConstraintGenerator &) –> class protocols::constraint_generator::DistanceConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::DistanceConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::DistanceConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Tom Linsky, who created the constraint generator framework.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::DistanceConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::DistanceConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_function(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator, func_def_str: str) → None

C++: protocols::constraint_generator::DistanceConstraintGenerator::set_function(const std::string &) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

class pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator

C++: protocols::constraint_generator::DistanceConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::DistanceConstraintGeneratorCreator &) –> class protocols::constraint_generator::DistanceConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::DistanceConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::DistanceConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::DistanceConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed

Bases: Exception

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

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

assign(self: pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed, : pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed) → pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed

C++: protocols::constraint_generator::EXCN_RemoveCstsFailed::operator=(const class protocols::constraint_generator::EXCN_RemoveCstsFailed &) –> class protocols::constraint_generator::EXCN_RemoveCstsFailed &

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

Invoke a crash log for throwing this exception.

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

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

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

Present this exception to the user.

Will invoke crash log reporting, if applicable

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

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

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

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

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

msg(*args, **kwargs)

Overloaded function.

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

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

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

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

Will set the raw message.

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

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

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

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

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

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

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator

Bases: ConstraintGenerator

This constraint generator generates constraints for favoring formation of hydrogen bonds

apply(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::operator=(const class protocols::constraint_generator::HydrogenBondConstraintGenerator &) –> class protocols::constraint_generator::HydrogenBondConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_tag(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Tom Linsky, who created the constraint generator framework.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_angle1_func(*args, **kwargs)

Overloaded function.

1. set_angle1_func(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, func_def: str) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle1_func(const std::string &) –> void

2. set_angle1_func(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, angle_func: pyrosetta.rosetta.core.scoring.func.Func) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle1_func(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_angle2_func(*args, **kwargs)

Overloaded function.

1. set_angle2_func(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, func_def: str) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle2_func(const std::string &) –> void

2. set_angle2_func(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, angle_func: pyrosetta.rosetta.core.scoring.func.Func) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle2_func(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_angle_sd(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, sd: float) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle_sd(const double) –> void

set_atom_pair_func(*args, **kwargs)

Overloaded function.

1. set_atom_pair_func(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, func_def: str) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atom_pair_func(const std::string &) –> void

2. set_atom_pair_func(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, atompairfunc: pyrosetta.rosetta.core.scoring.func.Func) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atom_pair_func(class std::shared_ptr<class core::scoring::func::Func>) –> void

set_atom_pair_sd(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, sd: float) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atom_pair_sd(const double) –> void

set_atoms1(*args, **kwargs)

Overloaded function.

1. set_atoms1(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, atoms_str: str) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms1(const std::string &) –> void

2. set_atoms1(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, atoms: pyrosetta.rosetta.std.set_std_string_t) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms1(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

set_atoms2(*args, **kwargs)

Overloaded function.

1. set_atoms2(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, atoms_str: str) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms2(const std::string &) –> void

2. set_atoms2(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, atoms: pyrosetta.rosetta.std.set_std_string_t) -> None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms2(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

set_bounded(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, bounded: bool) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_bounded(const bool) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

set_residue_selector1(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_residue_selector1(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_residue_selector2(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGenerator::set_residue_selector2(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator

C++: protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator &) –> class protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondInfo

Bases: SingletonBase_protocols_constraint_generator_HydrogenBondInfo_t

Database to lookup atoms for hydrogen bonding

static get_instance() → protocols::constraint_generator::HydrogenBondInfo

C++: utility::SingletonBase<protocols::constraint_generator::HydrogenBondInfo>::get_instance() –> class protocols::constraint_generator::HydrogenBondInfo *

class pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom

Bases: pybind11_object

angle(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom) → float

C++: protocols::constraint_generator::HydrogenBondingAtom::angle() const –> double

assign(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom, : pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom) → pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom

C++: protocols::constraint_generator::HydrogenBondingAtom::operator=(const class protocols::constraint_generator::HydrogenBondingAtom &) –> class protocols::constraint_generator::HydrogenBondingAtom &

atom2(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom) → str

C++: protocols::constraint_generator::HydrogenBondingAtom::atom2() const –> const std::string &

atom3(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom) → str

C++: protocols::constraint_generator::HydrogenBondingAtom::atom3() const –> const std::string &

dihedrals(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom) → pyrosetta.rosetta.std.list_double_t

C++: protocols::constraint_generator::HydrogenBondingAtom::dihedrals() const –> const class std::list<double, class std::allocator<double> > &

distance(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom) → float

C++: protocols::constraint_generator::HydrogenBondingAtom::distance() const –> double

hb_atom(self: pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondingAtom) → str

C++: protocols::constraint_generator::HydrogenBondingAtom::hb_atom() const –> const std::string &

class pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator

Bases: ConstraintGenerator

Generates constraints for membrane spans to stay in the membrane

apply(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::MembraneSpanConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator

C++: protocols::constraint_generator::MembraneSpanConstraintGenerator::operator=(const class protocols::constraint_generator::MembraneSpanConstraintGenerator &) –> class protocols::constraint_generator::MembraneSpanConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::MembraneSpanConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::MembraneSpanConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Jonathan Weinstein.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::MembraneSpanConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::MembraneSpanConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

class pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator

C++: protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator &) –> class protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator

Bases: ConstraintGenerator

This constraint generator takes residue selectors for a residue containing metal ion(s) and for residue(s) for which to set up contacts. It allows users to specify which base atoms will be used to define angles/dihedrals to constrain; ideal values for angles/dihedrals/distances; and an option to constrain to native values.

apply(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::operator=(const class protocols::constraint_generator::MetalContactsConstraintGenerator &) –> class protocols::constraint_generator::MetalContactsConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

get_base_atom_name(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → str

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_base_atom_name() const –> std::string

get_base_base_atom_name(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → str

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_base_base_atom_name() const –> std::string

get_constrain_to_closest(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → bool

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_constrain_to_closest() const –> bool

get_contact_resnum_string(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → str

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_contact_resnum_string() const –> std::string

get_contact_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_contact_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

get_dist_cutoff_multiplier(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → float

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_dist_cutoff_multiplier() const –> double

get_ideal_angle_about_contact(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_angle_about_contact() const –> class utility::vector1<double, class std::allocator<double> >

get_ideal_angle_about_metal(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_angle_about_metal() const –> class utility::vector1<double, class std::allocator<double> >

get_ideal_dihedral_3(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_dihedral_3() const –> class utility::vector1<double, class std::allocator<double> >

get_ideal_dihedral_about_contact(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_dihedral_about_contact() const –> class utility::vector1<double, class std::allocator<double> >

get_ideal_dihedral_about_metal(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_dihedral_about_metal() const –> class utility::vector1<double, class std::allocator<double> >

get_ideal_distance(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → float

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_distance() const –> double

get_ligand_atom_name(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → str

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ligand_atom_name() const –> std::string

get_ligand_resnum_string(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → str

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ligand_resnum_string() const –> std::string

get_ligand_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_ligand_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

get_score_against_internal_contacts(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → bool

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_score_against_internal_contacts() const –> bool

get_use_contact_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → bool

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_use_contact_selector() const –> bool

get_use_ligand_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator) → bool

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::get_use_ligand_selector() const –> bool

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Sharon Guffy.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_base_atom_name(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : str) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_base_atom_name(std::string) –> void

set_base_base_atom_name(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : str) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_base_base_atom_name(std::string) –> void

set_constrain_to_closest(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : bool) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_constrain_to_closest(bool) –> void

set_contact_resnum_string(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : str) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_contact_resnum_string(std::string) –> void

set_contact_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_contact_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_dist_cutoff_multiplier(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : float) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_dist_cutoff_multiplier(double) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

set_ideal_angle_about_contact(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_angle_about_contact(class utility::vector1<double, class std::allocator<double> >) –> void

set_ideal_angle_about_metal(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_angle_about_metal(class utility::vector1<double, class std::allocator<double> >) –> void

set_ideal_dihedral_3(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_dihedral_3(class utility::vector1<double, class std::allocator<double> >) –> void

set_ideal_dihedral_about_contact(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_dihedral_about_contact(class utility::vector1<double, class std::allocator<double> >) –> void

set_ideal_dihedral_about_metal(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_dihedral_about_metal(class utility::vector1<double, class std::allocator<double> >) –> void

set_ideal_distance(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : float) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_distance(double) –> void

set_ligand_atom_name(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : str) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ligand_atom_name(std::string) –> void

set_ligand_resnum_string(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : str) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ligand_resnum_string(std::string) –> void

set_ligand_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_ligand_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_score_against_internal_contacts(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : bool) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_score_against_internal_contacts(bool) –> void

set_use_contact_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : bool) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_use_contact_selector(bool) –> void

set_use_ligand_selector(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator, : bool) → None

C++: protocols::constraint_generator::MetalContactsConstraintGenerator::set_use_ligand_selector(bool) –> void

class pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator

C++: protocols::constraint_generator::MetalContactsConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::MetalContactsConstraintGeneratorCreator &) –> class protocols::constraint_generator::MetalContactsConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::MetalContactsConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::MetalContactsConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::MetalContactsConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints

Bases: Mover

Removes constraints generated by a ConstraintGenerator

add_generator(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints, generator: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → None

C++: protocols::constraint_generator::RemoveConstraints::add_generator(class std::shared_ptr<const class protocols::constraint_generator::ConstraintGenerator>) –> void

apply(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::constraint_generator::RemoveConstraints::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints, : pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints) → pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints

C++: protocols::constraint_generator::RemoveConstraints::operator=(const class protocols::constraint_generator::RemoveConstraints &) –> class protocols::constraint_generator::RemoveConstraints &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::constraint_generator::RemoveConstraints::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::constraint_generator::RemoveConstraints::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints) → str

C++: protocols::constraint_generator::RemoveConstraints::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str

C++: protocols::constraint_generator::RemoveConstraints::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::constraint_generator::RemoveConstraints::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Tom Linsky, who created the constraint generator framework.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::RemoveConstraints::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::RemoveConstraints::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator, : pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator) → pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator

C++: protocols::constraint_generator::RemoveConstraintsCreator::operator=(const class protocols::constraint_generator::RemoveConstraintsCreator &) –> class protocols::constraint_generator::RemoveConstraintsCreator &

create_mover(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::constraint_generator::RemoveConstraintsCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator) → str

C++: protocols::constraint_generator::RemoveConstraintsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::RemoveConstraintsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator

Bases: ConstraintGenerator

Generates atom pair constraints for a set of residues in the current pose

apply(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::operator=(const class protocols::constraint_generator::ResidueTypeConstraintGenerator &) –> class protocols::constraint_generator::ResidueTypeConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

get_favor_native_bonus(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator) → float

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::get_favor_native_bonus() const –> double

get_reference_pose(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::get_reference_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_residue_selector(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::get_residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

get_rsd_type_name3(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator) → str

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::get_rsd_type_name3() const –> std::string

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Sharon Guffy.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_favor_native_bonus(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator, bonus: float) → None

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::set_favor_native_bonus(double) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

set_reference_pose(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::set_reference_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_rsd_type_name3(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator, name3: str) → None

C++: protocols::constraint_generator::ResidueTypeConstraintGenerator::set_rsd_type_name3(std::string) –> void

class pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator

C++: protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator &) –> class protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator

Bases: ConstraintGenerator

Generates distance constraints between the upper and lower termini

apply(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::constraint_generator::TerminiConstraintGenerator::apply(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

assign(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator, : pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator

C++: protocols::constraint_generator::TerminiConstraintGenerator::operator=(const class protocols::constraint_generator::TerminiConstraintGenerator &) –> class protocols::constraint_generator::TerminiConstraintGenerator &

static class_name() → str

C++: protocols::constraint_generator::TerminiConstraintGenerator::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::TerminiConstraintGenerator::clone() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator) → str

C++: protocols::constraint_generator::ConstraintGenerator::id() const –> const std::string &

max_distance(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator) → float

C++: protocols::constraint_generator::TerminiConstraintGenerator::max_distance() const –> double

min_distance(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator) → float

C++: protocols::constraint_generator::TerminiConstraintGenerator::min_distance() const –> double

parse_my_tag(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

parses XML tag – calls protected parse_tag() function

C++: protocols::constraint_generator::ConstraintGenerator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList.

This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Cites Tom Linsky, who created the constraint generator framework.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::constraint_generator::TerminiConstraintGenerator::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::TerminiConstraintGenerator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_id(self: pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator, id: str) → None

C++: protocols::constraint_generator::ConstraintGenerator::set_id(const std::string &) –> void

set_max_distance(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator, dist: float) → None

C++: protocols::constraint_generator::TerminiConstraintGenerator::set_max_distance(const double) –> void

set_min_distance(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator, dist: float) → None

C++: protocols::constraint_generator::TerminiConstraintGenerator::set_min_distance(const double) –> void

set_sd(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator, sd: float) → None

C++: protocols::constraint_generator::TerminiConstraintGenerator::set_sd(const double) –> void

set_weight(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator, weight: float) → None

C++: protocols::constraint_generator::TerminiConstraintGenerator::set_weight(const double) –> void

weight(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator) → float

C++: protocols::constraint_generator::TerminiConstraintGenerator::weight() const –> double

class pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator

Bases: ConstraintGeneratorCreator

assign(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator, : pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator

C++: protocols::constraint_generator::TerminiConstraintGeneratorCreator::operator=(const class protocols::constraint_generator::TerminiConstraintGeneratorCreator &) –> class protocols::constraint_generator::TerminiConstraintGeneratorCreator &

create_constraint_generator(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator) → pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator

C++: protocols::constraint_generator::TerminiConstraintGeneratorCreator::create_constraint_generator() const –> class std::shared_ptr<class protocols::constraint_generator::ConstraintGenerator>

keyname(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator) → str

C++: protocols::constraint_generator::TerminiConstraintGeneratorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::constraint_generator::TerminiConstraintGeneratorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.constraint_generator.attributes_for_parse_constraint_generators(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

Appends the attributes read by parse_constraint_generators

C++: protocols::constraint_generator::attributes_for_parse_constraint_generators(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.constraint_generator.compute_nres_in_asymmetric_unit(pose: pyrosetta.rosetta.core.pose.Pose) → int

find number of residues – if pose is symetric,

returns nubmer of symmetry-independent residues

C++: protocols::constraint_generator::compute_nres_in_asymmetric_unit(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.constraint_generator.create_func(func_def: str) → pyrosetta.rosetta.core.scoring.func.Func

creates a function from a text definition

C++: protocols::constraint_generator::create_func(const std::string &) –> class std::shared_ptr<class core::scoring::func::Func>

pyrosetta.rosetta.protocols.constraint_generator.generate_seqmap_from_poses(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.id.SequenceMapping

creates a sequencemapping from pose1 to pose2

C++: protocols::constraint_generator::generate_seqmap_from_poses(const class core::pose::Pose &, const class core::pose::Pose &) –> class core::id::SequenceMapping

pyrosetta.rosetta.protocols.constraint_generator.get_native_pose() → pyrosetta.rosetta.core.pose.Pose

gets native pose from command line option, if one is specified

C++: protocols::constraint_generator::get_native_pose() –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.constraint_generator.parse_constraint_generators(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_constraint_generator_ConstraintGenerator_t

parses constraint generators from a tag

returns vector of ConstraintGeneratorCOPs

C++: protocols::constraint_generator::parse_constraint_generators(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> class utility::vector1<class std::shared_ptr<const class protocols::constraint_generator::ConstraintGenerator>, class std::allocator<class std::shared_ptr<const class protocols::constraint_generator::ConstraintGenerator> > >

pyrosetta.rosetta.protocols.constraint_generator.parse_custom_torsion(atom_names: str, resnums: str, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

Turn two strings, comma-separated with atom names and resnums into a custom dihedral vector.

C++: protocols::constraint_generator::parse_custom_torsion(const std::string &, const std::string &, const class core::pose::Pose &) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.protocols.constraint_generator.parse_torsion_type(torsion_name: str) → pyrosetta.rosetta.core.id.MainchainTorsionType

Get the MainchainTorsionType from a string (phi/psi/omega/omega2/omega3).

C++: protocols::constraint_generator::parse_torsion_type(const std::string &) –> enum core::id::MainchainTorsionType

pyrosetta.rosetta.protocols.constraint_generator.scalar_weighted(func: pyrosetta.rosetta.core.scoring.func.Func, weight: float) → pyrosetta.rosetta.core.scoring.func.Func

helper function to wrap a function with a scalar weighted function

C++: protocols::constraint_generator::scalar_weighted(class std::shared_ptr<class core::scoring::func::Func>, const double) –> class std::shared_ptr<class core::scoring::func::Func>