metal_interface¶

Bindings for protocols::metal_interface namespace

class pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints¶

Bases: pybind11_object

Add metalsite geometry constraints to pose

add_constraints(self: pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::metal_interface::AddZincSiteConstraints::add_constraints(class core::pose::Pose &) –> void

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

evaluate_constraints(self: pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(const class core::pose::Pose &) –> void

output_constraints_file(self: pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::metal_interface::AddZincSiteConstraints::output_constraints_file(const class core::pose::Pose &) –> void

view_constraints_in_pymol(self: pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::metal_interface::AddZincSiteConstraints::view_constraints_in_pymol(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.metal_interface.MatchGrafter¶

Bases: pybind11_object

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

build_combined_pose_with_zinc_overlay(self: pyrosetta.rosetta.protocols.metal_interface.MatchGrafter, partner1: pyrosetta.rosetta.core.pose.Pose, partner2: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(class core::pose::Pose &, class core::pose::Pose &) –> class core::pose::Pose

ensure_proper_his_tautomers(self: pyrosetta.rosetta.protocols.metal_interface.MatchGrafter, combined: pyrosetta.rosetta.core.pose.Pose, metalsite_seqpos: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

graft(self: pyrosetta.rosetta.protocols.metal_interface.MatchGrafter, match: pyrosetta.rosetta.core.pose.Pose, partner_ungrafted: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::metal_interface::MatchGrafter::graft(class core::pose::Pose &, class core::pose::Pose &) –> class core::pose::Pose

class pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue¶

Bases: pybind11_object

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

get_ligand_atom_id(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue) → pyrosetta.rosetta.core.id.AtomID¶: C++: protocols::metal_interface::MetalSiteResidue::get_ligand_atom_id() –> class core::id::AtomID

get_ligand_atom_name(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue) → str¶: C++: protocols::metal_interface::MetalSiteResidue::get_ligand_atom_name() –> std::string

get_ligand_atom_xyz(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::metal_interface::MetalSiteResidue::get_ligand_atom_xyz() –> class numeric::xyzVector<double>

get_pre_ligand_atom_id(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue) → pyrosetta.rosetta.core.id.AtomID¶: C++: protocols::metal_interface::MetalSiteResidue::get_pre_ligand_atom_id() –> class core::id::AtomID

get_pre_pre_ligand_atom_id(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue) → pyrosetta.rosetta.core.id.AtomID¶: C++: protocols::metal_interface::MetalSiteResidue::get_pre_pre_ligand_atom_id() –> class core::id::AtomID

get_resname(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue) → str¶: C++: protocols::metal_interface::MetalSiteResidue::get_resname() –> std::string

get_seqpos(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue) → int¶: C++: protocols::metal_interface::MetalSiteResidue::get_seqpos() –> unsigned long

set_ligand_atom_id(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue, ligand_atom_id: pyrosetta.rosetta.core.id.AtomID) → None¶: C++: protocols::metal_interface::MetalSiteResidue::set_ligand_atom_id(class core::id::AtomID) –> void

set_ligand_atom_name(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue, ligand_atom_name: str) → None¶: C++: protocols::metal_interface::MetalSiteResidue::set_ligand_atom_name(std::string) –> void

set_ligand_atom_xyz(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue, ligand_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::metal_interface::MetalSiteResidue::set_ligand_atom_xyz(class numeric::xyzVector<double>) –> void

set_pre_ligand_atom_id(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue, pre_ligand_atom_id: pyrosetta.rosetta.core.id.AtomID) → None¶: C++: protocols::metal_interface::MetalSiteResidue::set_pre_ligand_atom_id(class core::id::AtomID) –> void

set_pre_pre_ligand_atom_id(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue, pre_pre_ligand_atom_id: pyrosetta.rosetta.core.id.AtomID) → None¶: C++: protocols::metal_interface::MetalSiteResidue::set_pre_pre_ligand_atom_id(class core::id::AtomID) –> void

set_resname(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue, resname: str) → None¶: C++: protocols::metal_interface::MetalSiteResidue::set_resname(std::string) –> void

set_seqpos(self: pyrosetta.rosetta.protocols.metal_interface.MetalSiteResidue, seqpos: int) → None¶: C++: protocols::metal_interface::MetalSiteResidue::set_seqpos(unsigned long) –> void

class pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover¶

Bases: Mover

A mover that removes the connections to metals that were added by the SetupMetalsMover or by the -auto_setup_metals flag.

This mover:

Removes the bonds between metals and metal-binding residues.
Reverts metal-liganding residues back to their pre-bonded types.
Reverts metals back to their pre-bonded types.

Vikram K. Mulligan (vmulligan.org)

apply(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the mover.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::apply(class core::pose::Pose &) –> void

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

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.metal_interface.RemoveMetalConnectionsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::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.metal_interface.RemoveMetalConnectionsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::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.metal_interface.RemoveMetalConnectionsMover) → str¶

Returns “RemoveMetalConnectionsMover”.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::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¶

Returns “RemoveMetalConnectionsMover”. Useful in situations in which: an instance is not available.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover, 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::metal_interface::RemoveMetalConnectionsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList.

This mover is unpublished. It returns Vikram K. Mulligan as its author.

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

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

Provide a user- or machine-readable description of this mover’s XML interface.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::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

residue_selector(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Gets the residue selector for selecting residues from which metal bonds

will be removed.

If a polymer residue AND a metal that it binds are selected, the corresponding metal bonds and variants are removed.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

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_residue_selector(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Sets the residue selector for selecting residues from which metal bonds

will be removed.

If a polymer residue AND a metal that it binds are selected, the corresponding metal bonds and variants are removed.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::set_residue_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> 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.

show(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover) -> None
show(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover, output: pyrosetta.rosetta.std.ostream) -> None

Summarize this mover’s configuration.

C++: protocols::metal_interface::RemoveMetalConnectionsMover::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.

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

Set the ‘type’ string

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

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.metal_interface.RemoveMetalConnectionsMoverCreator¶

Bases: MoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::metal_interface::RemoveMetalConnectionsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator) → str¶: C++: protocols::metal_interface::RemoveMetalConnectionsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::metal_interface::RemoveMetalConnectionsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover¶

Bases: Mover

ZincHeterodimerMover is a mover for the ZincHeterodimerDesign protocol

apply(self: pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::metal_interface::ZincHeterodimerMover::apply(class core::pose::Pose &) –> void

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

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.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::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.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::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.metal_interface.ZincHeterodimerMover) → str¶: C++: protocols::metal_interface::ZincHeterodimerMover::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 name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> 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.

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

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

Set the ‘type’ string

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

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.metal_interface.ZincSiteFinder¶

Bases: pybind11_object

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

check_for_parse_error(self: pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder) → bool¶: C++: protocols::metal_interface::ZincSiteFinder::check_for_parse_error() –> bool

find_zinc_site(self: pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_metal_interface_MetalSiteResidue_t¶: C++: protocols::metal_interface::ZincSiteFinder::find_zinc_site(const class core::pose::Pose &) –> class utility::vector1<class std::shared_ptr<class protocols::metal_interface::MetalSiteResidue>, class std::allocator<class std::shared_ptr<class protocols::metal_interface::MetalSiteResidue> > >

set_expecting_n_ligands(self: pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder, n: int) → None¶: C++: protocols::metal_interface::ZincSiteFinder::set_expecting_n_ligands(unsigned long) –> void

pyrosetta.rosetta.protocols.metal_interface.find_closest_atom(res: pyrosetta.rosetta.core.conformation.Residue, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → str¶: C++: protocols::metal_interface::find_closest_atom(const class core::conformation::Residue &, const class numeric::xyzVector<double> &) –> std::string