analysis¶

Bindings for protocols::analysis namespace

class pyrosetta.rosetta.protocols.analysis.GlycanInfoMover¶

Bases: Mover

Simple class for outputting glycan information. Currently, it simply prints the information.

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

Apply the mover

C++: protocols::analysis::GlycanInfoMover::apply(class core::pose::Pose &) –> void

apply_const(self: pyrosetta.rosetta.protocols.analysis.GlycanInfoMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::analysis::GlycanInfoMover::apply_const(const class core::pose::Pose &) –> void

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

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

required in the context of the parser/scripting scheme

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

required in the context of the parser/scripting scheme

C++: protocols::analysis::GlycanInfoMover::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_attachment_point_string(self: pyrosetta.rosetta.protocols.analysis.GlycanInfoMover, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) → str¶

Get a string of where the attachment is occuring (1/4 etc.)

C++: protocols::analysis::GlycanInfoMover::get_attachment_point_string(const class core::pose::Pose &, unsigned long) –> std::string

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.analysis.GlycanInfoMover) → str¶: C++: protocols::analysis::GlycanInfoMover::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::analysis::GlycanInfoMover::mover_name() –> std::string

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

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

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

Provide the citation.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::analysis::GlycanInfoMover::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.analysis.GlycanInfoMover) → bool¶: C++: protocols::analysis::GlycanInfoMover::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.analysis.GlycanInfoMover) -> None
show(self: pyrosetta.rosetta.protocols.analysis.GlycanInfoMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::analysis::GlycanInfoMover::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.analysis.GlycanInfoMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover¶

Bases: Mover

Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method.

add_score_info_to_pose(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Add all the scoring data normally output via job to the pose instead. Can’t add this to method due to const apply.: Use after you have used the apply for the class.

C++: protocols::analysis::InterfaceAnalyzerMover::add_score_info_to_pose(class core::pose::Pose &) –> void

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

apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects).: It will add data to the pose for output into a scorefile.

C++: protocols::analysis::InterfaceAnalyzerMover::apply(class core::pose::Pose &) –> void

apply_const(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Apply method for const pose. Used by InterfaceFeatures reporter

C++: protocols::analysis::InterfaceAnalyzerMover::apply_const(const class core::pose::Pose &) –> void

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

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.analysis.InterfaceAnalyzerMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::analysis::InterfaceAnalyzerMover::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.analysis.InterfaceAnalyzerMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::analysis::InterfaceAnalyzerMover::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_all_data(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → pyrosetta.rosetta.protocols.analysis.InterfaceData¶

Get all interface data.

C++: protocols::analysis::InterfaceAnalyzerMover::get_all_data() –> struct protocols::analysis::InterfaceData

get_all_per_residue_data(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData¶

Get all per residue interface data.

C++: protocols::analysis::InterfaceAnalyzerMover::get_all_per_residue_data() –> struct protocols::analysis::PerResidueInterfaceData

get_centroid_dG(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_centroid_dG() –> double

get_chain_groups(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_set_unsigned_long_t¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_chain_groups() –> class utility::vector1<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > > >

get_complex_energy(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_complex_energy() –> double

get_complexed_sasa(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_complexed_sasa() –> double

get_crossterm_interface_energy(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_crossterm_interface_energy() –> double

get_crossterm_interface_energy_ratio(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_crossterm_interface_energy_ratio() –> double

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_fixed_chains(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → pyrosetta.rosetta.std.set_int_t¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_fixed_chains() –> class std::set<int, struct std::less<int>, class std::allocator<int> >

get_gly_interface_energy(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶

Return the interface energy of an all glycine interface (like bb-bb energies)

C++: protocols::analysis::InterfaceAnalyzerMover::get_gly_interface_energy() –> double

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_interface_dG(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_interface_dG() const –> double

get_interface_delta_hbond_unsat(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → int¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_hbond_unsat() –> unsigned long

get_interface_delta_sasa(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_sasa() –> double

get_interface_packstat(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_interface_packstat() –> double

get_interface_set(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → pyrosetta.rosetta.std.set_unsigned_long_t¶

Get the residues at the interface in question

C++: protocols::analysis::InterfaceAnalyzerMover::get_interface_set() –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

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_multichain_constructor(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → bool¶

Return boolean if a multichain (fixedchain) constructor was used

C++: protocols::analysis::InterfaceAnalyzerMover::get_multichain_constructor() –> bool

get_name(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → str¶: C++: protocols::analysis::InterfaceAnalyzerMover::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_num_interface_residues(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → int¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_num_interface_residues() –> unsigned long

get_pack_input(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → bool¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_pack_input() –> bool

get_per_residue_energy(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶

return the average per residue interface energy

C++: protocols::analysis::InterfaceAnalyzerMover::get_per_residue_energy() –> double

get_pymol_sel_hbond_unsat(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → str¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_hbond_unsat() –> std::string

get_pymol_sel_interface(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → str¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_interface() –> std::string

get_pymol_sel_packing(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → str¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_pymol_sel_packing() –> std::string

get_scorefile_reporting_prefix(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → str¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_scorefile_reporting_prefix() 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_separated_interface_energy(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_separated_interface_energy() –> double

get_separated_interface_energy_ratio(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_separated_interface_energy_ratio() –> double

get_side1_nres(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → int¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_side1_nres() –> unsigned long

get_side1_score(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_side1_score() –> double

get_side2_nres(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → int¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_side2_nres() –> unsigned long

get_side2_score(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_side2_score() –> double

get_total_Hbond_E(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → float¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_total_Hbond_E() –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

get_use_centroid_dG(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → bool¶: C++: protocols::analysis::InterfaceAnalyzerMover::get_use_centroid_dG() const –> bool

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 > > &

init_on_new_input(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Explicitly initialize settings on apply - not at the constructor, since this can hold state, and some protocols use apply multiple times.

C++: protocols::analysis::InterfaceAnalyzerMover::init_on_new_input(const class core::pose::Pose &) –> void

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::analysis::InterfaceAnalyzerMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

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

C++: protocols::analysis::InterfaceAnalyzerMover::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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::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.analysis.InterfaceAnalyzerMover) → bool¶: C++: protocols::analysis::InterfaceAnalyzerMover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → bool¶: C++: protocols::analysis::InterfaceAnalyzerMover::reinitialize_for_new_input() const –> bool

report_data(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → None¶

Print data to tracer or scorefile if tracer is not set (default).

C++: protocols::analysis::InterfaceAnalyzerMover::report_data() –> void

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_calc_dSASA(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, calc_dSASA: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_calc_dSASA(bool) –> void

set_calc_hbond_sasaE(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, calc_hbond_sasaE: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_calc_hbond_sasaE(const bool) –> void

set_compute_interface_delta_hbond_unsat(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, IDHU: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_delta_hbond_unsat(const bool) –> void

set_compute_interface_energy(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, iface_en: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_energy(const bool) –> void

set_compute_interface_sc(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, compute_interface_sc: bool) → None¶

Compute the Lawrence and Coleman Shape Complementarity score?

C++: protocols::analysis::InterfaceAnalyzerMover::set_compute_interface_sc(const bool) –> void

set_compute_packstat(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, compute_packstat: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_compute_packstat(const bool) –> void

set_compute_separated_sasa(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, compute_separated_sasa: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_compute_separated_sasa(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_defaults(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_defaults() –> void

set_detect_disulfide_in_separated_pose(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, detect_disulfide_in_separated_pose: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_detect_disulfide_in_separated_pose(const bool) –> 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_interface(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, interface: str) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_interface(const std::string &) –> void

set_interface_jump(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, interface_jump: int) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_interface_jump(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_pack_input(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, pack_input: bool) → None¶

Repack the interface of the complex before separation.

C++: protocols::analysis::InterfaceAnalyzerMover::set_pack_input(const bool) –> void

set_pack_rounds(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, pack_rounds: int) → None¶

If pack separated or together is set, this controls how many rounds of packing we do.: Default is 1, but that certainly may not be enough…

C++: protocols::analysis::InterfaceAnalyzerMover::set_pack_rounds(unsigned long) –> void

set_pack_separated(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, pack_separated: bool) → None¶

Repack the interface of the complex after separation.

C++: protocols::analysis::InterfaceAnalyzerMover::set_pack_separated(const bool) –> void

set_scorefile_reporting_prefix(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, prefix: str) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_scorefile_reporting_prefix(const std::string &) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_scorefunction(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_skip_reporting(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, skip_reporting: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_skip_reporting(const bool) –> 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

set_use_centroid_dG(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, use_centroid: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_use_centroid_dG(const bool) –> void

set_use_jobname(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, use_jobname: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_use_jobname(const bool) –> void

set_use_resfile(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, use_resfile: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_use_resfile(const bool) –> void

set_use_tracer(self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, tracer: bool) → None¶: C++: protocols::analysis::InterfaceAnalyzerMover::set_use_tracer(const bool) –> 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.analysis.InterfaceAnalyzerMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.analysis.InterfaceData¶

Bases: pybind11_object

All interface data. Unless otherwise specified, they refer specifically to the interface

All vectors correspond to InterfaceRegion enums

property aromatic_dG_fraction¶

property aromatic_dSASA_fraction¶

property aromatic_nres¶

assign(self: pyrosetta.rosetta.protocols.analysis.InterfaceData, : pyrosetta.rosetta.protocols.analysis.InterfaceData) → pyrosetta.rosetta.protocols.analysis.InterfaceData¶: C++: protocols::analysis::InterfaceData::operator=(const struct protocols::analysis::InterfaceData &) –> struct protocols::analysis::InterfaceData &

property centroid_dG¶

property complex_total_energy¶

property complexed_SASA¶

property complexed_interface_score¶

property crossterm_interface_energy¶

property crossterm_interface_energy_dSASA_ratio¶

property dG¶

property dG_dSASA_ratio¶

property dSASA¶

property dSASA_sc¶

property delta_unsat_hbonds¶

property dhSASA¶

property dhSASA_rel_by_charge¶

property dhSASA_sc¶

property gly_dG¶

property hbond_E_fraction¶

property interface_hbonds¶

property interface_nres¶

property interface_residues¶

property interface_to_surface_fraction¶

property packstat¶

property pymol_sel_hbond_unsat¶

property pymol_sel_interface¶

property pymol_sel_packing¶

property sc_value¶

property separated_SASA¶

property separated_interface_score¶

property separated_total_energy¶

property ss_helix_nres¶

property ss_loop_nres¶

property ss_sheet_nres¶

property total_hb_E¶

class pyrosetta.rosetta.protocols.analysis.InterfaceRegion¶

Bases: pybind11_object

Members:

total

side1

side2

property name¶

side1 = <InterfaceRegion.side1: 2>¶

side2 = <InterfaceRegion.side2: 3>¶

total = <InterfaceRegion.total: 1>¶

property value¶

class pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None¶

apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object.

C++: protocols::analysis::LoopAnalyzerMover::apply(class core::pose::Pose &) –> void

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

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.analysis.LoopAnalyzerMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::analysis::LoopAnalyzerMover::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.analysis.LoopAnalyzerMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::analysis::LoopAnalyzerMover::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_chainbreak_scores(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → pyrosetta.rosetta.utility.vector1_double¶

Return the vector of chainbreak scores

C++: protocols::analysis::LoopAnalyzerMover::get_chainbreak_scores() –> class utility::vector1<double, class std::allocator<double> >

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_loops(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → pyrosetta.rosetta.protocols.loops.Loops¶

get loops object, because public setters/getters are a rule

C++: protocols::analysis::LoopAnalyzerMover::get_loops() const –> class std::shared_ptr<const class protocols::loops::Loops>

get_max_chainbreak(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → float¶: C++: protocols::analysis::LoopAnalyzerMover::get_max_chainbreak() const –> double

get_max_omega(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → float¶: C++: protocols::analysis::LoopAnalyzerMover::get_max_omega() const –> double

get_max_pbond(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → float¶: C++: protocols::analysis::LoopAnalyzerMover::get_max_pbond() const –> double

get_max_rama(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → float¶: C++: protocols::analysis::LoopAnalyzerMover::get_max_rama() const –> double

get_name(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → str¶: C++: protocols::analysis::LoopAnalyzerMover::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_total_score(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → float¶

Return the total score found from the last apply call

C++: protocols::analysis::LoopAnalyzerMover::get_total_score() const –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶: C++: protocols::moves::Mover::get_type() const –> std::string

get_use_tracer(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover) → bool¶

get tracer bool, because public setters/getters are a rule

C++: protocols::analysis::LoopAnalyzerMover::get_use_tracer() const –> bool

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::analysis::LoopAnalyzerMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover, 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::analysis::LoopAnalyzerMover::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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::analysis::LoopAnalyzerMover::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.analysis.LoopAnalyzerMover) → bool¶: C++: protocols::analysis::LoopAnalyzerMover::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_loops(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover, loops: pyrosetta.rosetta.protocols.loops.Loops) → None¶

////////////////getters, setters/////////////

set loops object, because public setters/getters are a rule

C++: protocols::analysis::LoopAnalyzerMover::set_loops(class std::shared_ptr<const class protocols::loops::Loops>) –> 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

set_use_tracer(self: pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover, tracer: bool) → None¶

set tracer bool, because public setters/getters are a rule

C++: protocols::analysis::LoopAnalyzerMover::set_use_tracer(bool) –> 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.analysis.LoopAnalyzerMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.analysis.PackStatMover¶

Bases: Mover

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

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

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.analysis.PackStatMover) → str¶: C++: protocols::analysis::PackStatMover::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.analysis.PerResidueInterfaceData¶

Bases: pybind11_object

All per residue interface data and residue averages.: Interface Residues only

Vector1 correspond to residues in the pose. avg vector1 sets correspond to InterfaceRegion enums: total, side1, side

property SASA¶

assign(self: pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData, : pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData) → pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData¶: C++: protocols::analysis::PerResidueInterfaceData::operator=(const struct protocols::analysis::PerResidueInterfaceData &) –> struct protocols::analysis::PerResidueInterfaceData &

property complexed_energy¶

property complexed_sasa¶

property dG¶

property dSASA¶

property dSASA_fraction¶

property dSASA_sc¶

property dhSASA¶

property dhSASA_rel_by_charge¶

property dhSASA_sc¶

property interface_residues¶

property regional_avg_per_residue_SASA_int¶

property regional_avg_per_residue_SASA_sep¶

property regional_avg_per_residue_dG¶

property regional_avg_per_residue_dSASA¶

property regional_avg_per_residue_energy_int¶

property regional_avg_per_residue_energy_sep¶

property separated_energy¶

property separated_sasa¶