generalized_kinematic_closure

• filter
• perturber
• selector

Bindings for protocols::generalized_kinematic_closure namespace

class pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC

Bases: Mover

add_atomset_to_perturber_atomset_list(*args, **kwargs)

Overloaded function.

1. add_atomset_to_perturber_atomset_list(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, atomset: pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) -> None

Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list(const unsigned long, const class utility::vector1<class core::id::NamedAtomID, class std::allocator<class core::id::NamedAtomID> > &) –> void

2. add_atomset_to_perturber_atomset_list(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, atomset: pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) -> None

Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes. This operates on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list(const class utility::vector1<class core::id::NamedAtomID, class std::allocator<class core::id::NamedAtomID> > &) –> void

add_filter(*args, **kwargs)

Overloaded function.

1. add_filter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) -> None

Add a new filter to the list of filters.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter() –> void

2. add_filter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filtertype: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type) -> None

Add a new filter to the list of filters, setting the filter type.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter(const enum protocols::generalized_kinematic_closure::filter::filter_type &) –> void

3. add_filter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filtertypename: str) -> None

Add a new filter to the list of filters, setting the filter type by name.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter(const std::string &) –> void

add_filter_parameter(*args, **kwargs)

Overloaded function.

1. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, param_name: str, value: float) -> None

Add a real-valued parameter to a filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const unsigned long, const std::string &, const double &) –> void

2. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, param_name: str, value: int) -> None

Add an integer-valued parameter to a filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const unsigned long, const std::string &, const unsigned long) –> void

3. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, param_name: str, value: bool) -> None

Add a Boolean-valued parameter to a filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const unsigned long, const std::string &, const bool) –> void

4. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, param_name: str, value: str) -> None

Add a string-valued parameter to a filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const unsigned long, const std::string &, const std::string &) –> void

5. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, param_name: str, value: float) -> None

Add a real-valued parameter to the last filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const std::string &, const double &) –> void

6. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, param_name: str, value: int) -> None

Add an integer-valued parameter to the last filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const std::string &, const unsigned long) –> void

7. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, param_name: str, value: bool) -> None

Add a Boolean-valued parameter to the last filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const std::string &, const bool) –> void

8. add_filter_parameter(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, param_name: str, value: str) -> None

Add a string-valued parameter to the last filter’s parameter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter(const std::string &, const std::string &) –> void

add_loop_residue(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, residue_index: int) → None

Add a residue (by index in the pose) to the list of residues making up the loop to be closed.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_loop_residue(const unsigned long) –> void

add_perturber(*args, **kwargs)

Overloaded function.

1. add_perturber(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) -> None

Add a new perturber to the list of perturbers.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber() –> void

2. add_perturber(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, effect: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> None

Add a new perturber to the list of perturbers, setting the effect.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber(const enum protocols::generalized_kinematic_closure::perturber::perturber_effect &) –> void

3. add_perturber(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, effectname: str) -> None

Add a new perturber to the list of perturbers, setting the effect by effect name string.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber(const std::string &) –> void

add_residue_to_perturber_residue_list(*args, **kwargs)

Overloaded function.

1. add_residue_to_perturber_residue_list(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, residue_index: int) -> None

Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE,

not the loop in isolation.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_residue_to_perturber_residue_list(const unsigned long, const unsigned long) –> void

2. add_residue_to_perturber_residue_list(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, residue_index: int) -> None

Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE,

not the loop in isolation. This version acts on the last perturber added.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_residue_to_perturber_residue_list(const unsigned long) –> void

add_tail_residue(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, residue_index: int) → None

Add a residue (by index in the pose) to the list of residues making up the tails attached to

the loop to be closed.

“Tails” are residues that are not part of the loop to be closed, but which are attached to

the loop and which “come along for the ride” as the loop moves.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_tail_residue(const unsigned long) –> void

add_value_to_perturber_value_list(*args, **kwargs)

Overloaded function.

1. add_value_to_perturber_value_list(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, val: float) -> None

Add a value to the list of values that a perturber takes.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list(const unsigned long, const double &) –> void

2. add_value_to_perturber_value_list(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, val: float) -> None

Add a value to the list of values that a perturber takes. This operates on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list(const double &) –> void

apply(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, pose: pyrosetta.rosetta.core.pose.Pose) → None

Actually apply the mover to the pose.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, : pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::operator=(const class protocols::generalized_kinematic_closure::GeneralizedKIC &) –> class protocols::generalized_kinematic_closure::GeneralizedKIC &

attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → bool

Gets whether we are attaching a BOINC “ghost” pose observer.

Only does anything in the BOINC graphics build.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::attach_boinc_ghost_observer() const –> bool

check_loop_residues_sensible(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, pose: pyrosetta.rosetta.core.pose.Pose) → None

Check that loop residues haven’t been specified multiple times.

Also checks that the loop residues are all within the pose.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::check_loop_residues_sensible(const class core::pose::Pose &) –> void

check_tail_residues_sensible(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, pose: pyrosetta.rosetta.core.pose.Pose) → None

Check that tail residues haven’t been specified multiple times,

and that the tail residues don’t overlap with loop residues.

Also checks that the tail residues are all within the pose.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::check_tail_residues_sensible(const class core::pose::Pose &) –> void

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

clear_loop_residues(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → None

Clears the list of loop residues

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::clear_loop_residues() –> void

clear_perturber_residue_list(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_idx: int) → None

Clears the list of perturber residues for perturber perturber_idx

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::clear_perturber_residue_list(const unsigned long) –> void

clear_perturber_residue_lists(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → None

Clears the list of perturber residues

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::clear_perturber_residue_lists() –> void

clear_stored_solutions(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → None

Clear the stored solution poses.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::clear_stored_solutions() –> void

clone(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → pyrosetta.rosetta.protocols.moves.Mover

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

close_bond(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, rsd1: int, at1: str, rsd2: int, at2: str, rsd1_before: int, at1_before: str, rsd2_after: int, at2_after: str, bondlength: float, bondangle1: float, bondangle2: float, torsion: float, randomize_this_torsion: bool, randomize_flanking_torsions: bool) → None

Tells GeneralizedKIC to close a bond, setting bond length, bond angle, and bond torsion values. This

actually just adds appropriate set_dihedral, set_bondangle, and set_bondlength perturbers to the perturber list. Note that subsequent perturbers OR the closure itself can overwrite the bond length, bond angle, or torsion angles set here.

– The index of the first atom’s residue (indexed based on residue indices in the original pose).

– The name of the first atom defining the bond to be closed.

– The index of the second atom’s residue (indexed based on residue indices in the original pose).

– The name of the second atom defining the bond to be closed.

– The length of the bond between the two atoms.

– The bond angle defined by (atom preceding at1 in the chain to be closed), (atm1), (atm2).

– The bond angle defined by (atm1), (atm2), (atom following at2 in the chain to be closed).

– The torsion angle defined by (atom preceding at1 in the chain to be closed), (atm1), (atm2), (atom following at2 in the chain to be closed).

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::close_bond(const unsigned long, const std::string &, const unsigned long, const std::string &, const unsigned long, const std::string &, const unsigned long, const std::string &, const double &, const double &, const double &, const double &, const bool, const bool) –> void

correct_polymer_dependent_atoms(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → bool

Gets whether this mover corrects positions of polymer-dependent atoms.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::correct_polymer_dependent_atoms() const –> bool

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>

dont_fail_if_no_solution_found(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → bool

Gets whether the mover sets its status to failure of no solution is found.

True means it does NOT fail if no solution is found. False is the default (fail if no solution found).

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::dont_fail_if_no_solution_found() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::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_build_ideal_geometry(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → bool

Get whether or not this mover builds ideal geometry for the loop, or uses the existing geometry,

imperfect bond lengths/angles and all.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::get_build_ideal_geometry() –> bool

get_closure_attempts(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → int

Returns the number of closure attempts.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::get_closure_attempts() const –> unsigned long

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.generalized_kinematic_closure.GeneralizedKIC) → str

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::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_ntries_before_giving_up(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → int

Gets number of tries before giving up.

The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::get_ntries_before_giving_up() const –> unsigned long

get_selector_type(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type

Get the selector (the algorithm controlling how a solution will be chosen

from among the solutions passing filters).

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::get_selector_type() const –> enum protocols::generalized_kinematic_closure::selector::selector_type

get_selector_type_name(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → str

Get the name of the selector (the algorithm controlling how a solution will be chosen

from among the solutions passing filters).

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::get_selector_type_name() const –> std::string

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

last_run_successful(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → bool

Returns whether or not the last call to apply() sucessfully closed the loop. Defaults to false if

apply() hasn’t yet been called.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::last_run_successful() –> bool

load_filter_bin_params(*args, **kwargs)

Overloaded function.

1. load_filter_bin_params(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, bin_params_file: str) -> None

Initialize a filter’s BinTransitionCalculator object, and load a bin_params file.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::load_filter_bin_params(const unsigned long, const std::string &) –> void

2. load_filter_bin_params(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, bin_params_file: str) -> None

Initialize a filter’s BinTransitionCalculator object, and load a bin_params file.

This acts on the last filter in the filter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::load_filter_bin_params(const std::string &) –> void

load_perturber_bin_params(*args, **kwargs)

Overloaded function.

1. load_perturber_bin_params(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, bin_params_file: str) -> None

Initialize a perturber’s BinTransitionCalculator object, and load a bin_params file.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::load_perturber_bin_params(const unsigned long, const std::string &) –> void

2. load_perturber_bin_params(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, bin_params_file: str) -> None

Initialize a perturber’s BinTransitionCalculator object, and load a bin_params file.

This acts on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::load_perturber_bin_params(const std::string &) –> void

low_memory_mode(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → bool

Gets whether we’re using low-memory mode.

If false (the default) then a vector of result poses is stored. This can use a lot of memory, though. If true, then only loop DOFs are stored. This loses the results of applying any preselection movers, though.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::low_memory_mode() const –> bool

min_solution_count(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC) → int

Gets the number of solutions that must be found before stopping prematurely (i.e.

before n_closure_attempts_ is reached).

If nonzero, attempts are made until the specified number of solutions are found OR n_closure_attempts_ is reached (or we give up because ntries_before_giving_up_ is reached without finding any solutions). If zero, n_closure_attempts_ attempts are made, and then a solution is chosen from among the successful solutions (or we give up because ntries_before_giving_up_ is reached without finding any solutions.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::min_solution_count() const –> unsigned long

static mover_name() → str

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::mover_name() –> std::string

static name() → str

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

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::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_attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, setting: bool) → None

Sets whether we are attaching a BOINC “ghost” pose observer.

Only does anything in the BOINC graphics build.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_attach_boinc_ghost_observer(const bool) –> void

set_build_ideal_geometry(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, buildideal: bool) → None

Set whether or not this mover builds ideal geometry for the loop, or uses the existing geometry,

imperfect bond lengths/angles and all.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_build_ideal_geometry(const bool) –> void

set_closure_attempts(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, attempts: int) → None

Set the number of closure attempts.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_closure_attempts(const unsigned long) –> void

set_correct_polymer_dependent_atoms(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, setting: bool) → None

Sets whether this mover corrects positions of polymer-dependent atoms.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_correct_polymer_dependent_atoms(const bool) –> 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_dont_fail_if_no_solution_found(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, setting: bool) → None

Sets whether the mover sets its status to failure of no solution is found.

True means it does NOT fail if no solution is found. False is the default (fail if no solution found).

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_dont_fail_if_no_solution_found(const bool) –> void

set_filter_attach_boinc_ghost_observer(*args, **kwargs)

Overloaded function.

1. set_filter_attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, setting: bool) -> None

Set whether the filter’s generated poses should be used for BOINC graphics.

Does nothing outside of the BOINC build.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_attach_boinc_ghost_observer(const unsigned long, const bool) –> void

2. set_filter_attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, setting: bool) -> None

Set whether the filter’s generated poses should be used for BOINC graphics.

Does nothing outside of the BOINC build. This version acts on the last filter in the filter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_attach_boinc_ghost_observer(const bool) –> void

set_filter_bin(*args, **kwargs)

Overloaded function.

1. set_filter_bin(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, name_in: str) -> None

Set the bin name that a backbone_bin filter is looking for.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_bin(const unsigned long, const std::string &) –> void

2. set_filter_bin(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, name_in: str) -> None

Set the bin name that a backbone_bin filter is looking for.

This version acts on the last filter in the filter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_bin(const std::string &) –> void

set_filter_rama_cutoff_energy(*args, **kwargs)

Overloaded function.

1. set_filter_rama_cutoff_energy(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, cutoff_energy: float) -> None

Set the rama term cutoff energy for the alpha_aa_rama_check filter.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_rama_cutoff_energy(const unsigned long, const double &) –> void

2. set_filter_rama_cutoff_energy(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, cutoff_energy: float) -> None

Set the rama term cutoff energy for the alpha_aa_rama_check filter.

This version acts on the last filter in the filter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_rama_cutoff_energy(const double &) –> void

set_filter_resnum(*args, **kwargs)

Overloaded function.

1. set_filter_resnum(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, filter_index: int, value: int) -> None

Set the residue number that a backbone_bin filter is acting on.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_resnum(const unsigned long, const unsigned long) –> void

2. set_filter_resnum(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, value: int) -> None

Set the residue number that a backbone_bin filter is acting on.

This version acts on the last filter in the filter list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_filter_resnum(const unsigned long) –> 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_low_memory_mode(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, setting: bool) → None

Sets whether we’re using low-memory mode.

If false (the default) then a vector of result poses is stored. This can use a lot of memory, though. If true, then only loop DOFs are stored. This loses the results of applying any preselection movers, though.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_low_memory_mode(const bool) –> void

set_min_solution_count(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, count_in: int) → None

Sets the number of solutions that must be found before stopping prematurely (i.e.

before n_closure_attempts_ is reached).

If nonzero, attempts are made until the specified number of solutions are found OR n_closure_attempts_ is reached (or we give up because ntries_before_giving_up_ is reached without finding any solutions). If zero, n_closure_attempts_ attempts are made, and then a solution is chosen from among the successful solutions (or we give up because ntries_before_giving_up_ is reached without finding any solutions.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_min_solution_count(const unsigned long) –> 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_ntries_before_giving_up(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, ntries: int) → None

Sets number of tries before giving up.

If this is set to 0, then no such check is made. The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_ntries_before_giving_up(const unsigned long) –> void

set_perturber_attach_boinc_ghost_observer(*args, **kwargs)

Overloaded function.

1. set_perturber_attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, setting: bool) -> None

Set whether the perturber’s generated poses should be used for BOINC graphics.

Does nothing outside of the BOINC build.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_attach_boinc_ghost_observer(const unsigned long, const bool) –> void

2. set_perturber_attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, setting: bool) -> None

Set whether the perturber’s generated poses should be used for BOINC graphics.

Does nothing outside of the BOINC build. This version acts on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_attach_boinc_ghost_observer(const bool) –> void

set_perturber_bin(*args, **kwargs)

Overloaded function.

1. set_perturber_bin(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, bin: str) -> None

Set the bin for the set_backbone_bin perturber.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_bin(const unsigned long, const std::string &) –> void

2. set_perturber_bin(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, bin: str) -> None

Set the bin for the set_backbone_bin perturber.

This acts on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_bin(const std::string &) –> void

set_perturber_custom_rama_table(*args, **kwargs)

Overloaded function.

1. set_perturber_custom_rama_table(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, table_name: str) -> None

Set the custom Ramachandran table for the randomize_alpha_backbone_by_rama perturber.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_custom_rama_table(const unsigned long, const std::string &) –> void

2. set_perturber_custom_rama_table(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, table_type: pyrosetta.rosetta.core.scoring.Rama_Table_Type) -> None

Set the custom Ramachandran table for the randomize_alpha_backbone_by_rama perturber.

This version works by Rama_Table_Type.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_custom_rama_table(const unsigned long, const enum core::scoring::Rama_Table_Type) –> void

3. set_perturber_custom_rama_table(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, table_name: str) -> None

Set the curstom Ramachandran table for the randomize_alpha_backbone_by_rama perturber.

This acts on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_custom_rama_table(const std::string &) –> void

4. set_perturber_custom_rama_table(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, table_type: pyrosetta.rosetta.core.scoring.Rama_Table_Type) -> None

Set the curstom Ramachandran table for the randomize_alpha_backbone_by_rama perturber.

This acts on the last perturber in the perturber list, and works by Rama_Table_Type.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_custom_rama_table(const enum core::scoring::Rama_Table_Type) –> void

set_perturber_effect(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, effect: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) → None

Set a perturber’s effect.

– The index in the list of perturbers already added.

—The perturber effect type, based on the perturber::perturber_effect enum (e.g. set_dihedral, randomize_backbone, etc.).

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_effect(const unsigned long, const enum protocols::generalized_kinematic_closure::perturber::perturber_effect &) –> void

set_perturber_iterations(*args, **kwargs)

Overloaded function.

1. set_perturber_iterations(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, val: int) -> None

Set the number of iterations for a perturber.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_iterations(const unsigned long, const unsigned long) –> void

2. set_perturber_iterations(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, val: int) -> None

Set the number of iterations for a perturber.

This acts on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_iterations(const unsigned long) –> void

set_perturber_must_switch_bins(*args, **kwargs)

Overloaded function.

1. set_perturber_must_switch_bins(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, perturber_index: int, val: bool) -> None

Set whether the perturb_backbone_by_bins perturber requires residues to change their torsion

bins every move, or whether they can stay within the same bin.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_must_switch_bins(const unsigned long, const bool) –> void

2. set_perturber_must_switch_bins(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, val: bool) -> None

Set whether the perturb_backbone_by_bins perturber requires residues to change their torsion

bins every move, or whether they can stay within the same bin.

This acts on the last perturber in the perturber list.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_must_switch_bins(const bool) –> void

set_pivot_atoms(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, rsd1: int, at1: str, rsd2: int, at2: str, rsd3: int, at3: str) → None

Function to set the pivot atoms for kinematic closure:

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_pivot_atoms(const unsigned long, const std::string &, const unsigned long, const std::string &, const unsigned long, const std::string &) –> void

set_preselection_mover(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, mover: pyrosetta.rosetta.protocols.moves.Mover) → None

Sets the mover that will be applied to all solutions that pass filters prior to applying the selector.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_preselection_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

set_selector_kbt(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, kbt: float) → None

Set the selector’s Boltzmann temperature value.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_kbt(const double &) –> void

set_selector_scorefunction(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set the selector’s scorefunction.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_selector_type(*args, **kwargs)

Overloaded function.

1. set_selector_type(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, stype: pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type) -> None

Set the selector (the algorithm controlling how a solution will be chosen

from among the solutions passing filters).

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_type(const enum protocols::generalized_kinematic_closure::selector::selector_type &) –> void

2. set_selector_type(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC, stypename: str) -> None

Set the selector (the algorithm controlling how a solution will be chosen

from among the solutions passing filters). This sets the selector by name.

C++: protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_type(const std::string &) –> 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.generalized_kinematic_closure.GeneralizedKICCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator, : pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator) → pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator

C++: protocols::generalized_kinematic_closure::GeneralizedKICCreator::operator=(const class protocols::generalized_kinematic_closure::GeneralizedKICCreator &) –> class protocols::generalized_kinematic_closure::GeneralizedKICCreator &

create_mover(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator) → str

C++: protocols::generalized_kinematic_closure::GeneralizedKICCreator::keyname() const –> std::string

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

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

pyrosetta.rosetta.protocols.generalized_kinematic_closure.copy_loop_pose_to_original(original_pose: pyrosetta.rosetta.core.pose.Pose, loop_pose: pyrosetta.rosetta.core.pose.Pose, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, tail_residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

Copy the atom positions of the residues in the loop pose to the original pose.

C++: protocols::generalized_kinematic_closure::copy_loop_pose_to_original(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

pyrosetta.rosetta.protocols.generalized_kinematic_closure.correct_polymer_dependent_atoms_in_pose_segment(original_pose: pyrosetta.rosetta.core.pose.Pose, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

Update the polymer bond-dependent atom positions for every residue in the

residue map.

C++: protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

pyrosetta.rosetta.protocols.generalized_kinematic_closure.general_set_phi(pose: pyrosetta.rosetta.core.pose.Pose, residue_index: int, phi_value: float) → None

Sets phi for an L-alpha amino acid, even if the nitrogen has a nonstandard connection.

C++: protocols::generalized_kinematic_closure::general_set_phi(class core::pose::Pose &, const unsigned long, const double &) –> void

pyrosetta.rosetta.protocols.generalized_kinematic_closure.general_set_psi(pose: pyrosetta.rosetta.core.pose.Pose, residue_index: int, psi_value: float) → None

Sets psi for an L-alpha amino acid, even if the carbonyl carbon has a nonstandard connection.

C++: protocols::generalized_kinematic_closure::general_set_psi(class core::pose::Pose &, const unsigned long, const double &) –> void

pyrosetta.rosetta.protocols.generalized_kinematic_closure.get_original_pose_rsd(perturbedloop_rsd: int, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → int

Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >,

and a residue index in the perturbed loop, return the corresponding residue index in the original pose.

C++: protocols::generalized_kinematic_closure::get_original_pose_rsd(const unsigned long, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> unsigned long

pyrosetta.rosetta.protocols.generalized_kinematic_closure.is_in_list(val: int, list: pyrosetta.rosetta.utility.vector1_unsigned_long) → bool

Function to determine whether a value is in a list.

C++: protocols::generalized_kinematic_closure::is_in_list(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool

pyrosetta.rosetta.protocols.generalized_kinematic_closure.original_pose_residue_is_in_residue_map(residue_index: int, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → bool

function to determine whether a residue index from the original pose is in the residue_map list.

C++: protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(const unsigned long, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> bool

pyrosetta.rosetta.protocols.generalized_kinematic_closure.set_loop_pose(*args, **kwargs)

Overloaded function.

1. set_loop_pose(pose: pyrosetta.rosetta.core.pose.Pose, atomlist: pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t, t_ang: pyrosetta.rosetta.utility.vector1_double, b_ang: pyrosetta.rosetta.utility.vector1_double, b_len: pyrosetta.rosetta.utility.vector1_double) -> None

Set the loop pose conformation based on a set of results from kinematic closure.

– A pose consisting of the loop to be closed only.

—A list of AtomIDs and corresponding xyz coordinates (though we don’t use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.

– The torsion angles values to set.

—The bond angle values to set.

– The bond length values to set.

C++: protocols::generalized_kinematic_closure::set_loop_pose(class core::pose::Pose &, const class utility::vector1<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> > > > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

2. set_loop_pose(pose: pyrosetta.rosetta.core.pose.Pose, atomlist: pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t, t_ang: pyrosetta.rosetta.utility.vector1_double) -> None

Set the loop pose conformation based on a set of results from kinematic closure.

This version ONLY sets mainchain torsions, and does no rebuilding of mainchain O or H atoms.

—A pose consisting of the loop to be closed only.

– A list of AtomIDs and corresponding xyz coordinates (though we don’t use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.

—The torsion angles values to set.

C++: protocols::generalized_kinematic_closure::set_loop_pose(class core::pose::Pose &, const class utility::vector1<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> > > > &, const class utility::vector1<double, class std::allocator<double> > &) –> void