analysis

Bindings for protocols::analysis namespace

class pyrosetta.rosetta.protocols.analysis.GlycanInfoMover

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

  1. show(self: pyrosetta.rosetta.protocols.analysis.GlycanInfoMover) -> None

  2. 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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_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_std_allocator_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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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_builtins.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_builtins.pybind11_object

Members:

total

side1

side2

property name
side1 = <InterfaceRegion.side1: 2>
side2 = <InterfaceRegion.side2: 3>
total = <InterfaceRegion.total: 1>
class pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover

Bases: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

  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

  1. 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: pyrosetta.rosetta.protocols.moves.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: pyrosetta.rosetta.protocols.moves.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_std_allocator_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.

  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

  1. 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_builtins.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