flexpep_docking¶
Bindings for protocols::flexpep_docking namespace
- class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio¶
Bases:
Mover- apply(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio, pose: pyrosetta.rosetta.core.pose.Pose) None¶
C++: protocols::flexpep_docking::FlexPepDockingAbInitio::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio¶
C++: protocols::flexpep_docking::FlexPepDockingAbInitio::operator=(const class protocols::flexpep_docking::FlexPepDockingAbInitio &) –> class protocols::flexpep_docking::FlexPepDockingAbInitio &
- 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.flexpep_docking.FlexPepDockingAbInitio) str¶
C++: protocols::flexpep_docking::FlexPepDockingAbInitio::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.flexpep_docking.FlexPepDockingFlags¶
Bases:
pybind11_object- assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::operator=(const class protocols::flexpep_docking::FlexPepDockingFlags &) –> class protocols::flexpep_docking::FlexPepDockingFlags &
- property backrub_opt¶
- property boost_fa_atr¶
- clone(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::clone() const –> class std::shared_ptr<class protocols::flexpep_docking::FlexPepDockingFlags>
- property design_peptide¶
- property dumpPDB_abinitio¶
- property dumpPDB_hires¶
- property dumpPDB_lowres¶
- property extend¶
- property frag3_weight¶
- property frag5_weight¶
- property frag9_weight¶
- property hb_filter¶
- property hotspot_filter¶
- is_ligand_present(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::is_ligand_present(const class core::pose::Pose &) const –> bool
- property lowres_abinitio¶
- property lowres_preoptimize¶
- property mcm_cycles¶
- property min_only¶
- property min_receptor_bb¶
- property no_prepack1¶
- property no_prepack2¶
- property pSer2Asp_centroid¶
- property pSer2Glu_centroid¶
- property params_file¶
- property pep_fold_only¶
- property pep_refine¶
- property peptide_anchors¶
- peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) str¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_chain() const –> char
- property peptide_cuts¶
- peptide_first_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res() const –> unsigned long
- peptide_last_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res() const –> unsigned long
- property peptide_loop_model¶
- peptide_nres(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres() const –> unsigned long
- property place_peptide¶
- property ppk_only¶
- property ramp_fa_rep¶
- property ramp_rama¶
- property randomRBstart¶
- property random_phi_psi_pert¶
- property random_phi_psi_pert_size¶
- property rbMCM¶
- property rb_rot_size¶
- property rb_trans_size¶
- property recal_foldtree¶
- property receptor_anchor_pos¶
- receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) str¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_chain() const –> std::string
- receptor_first_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res() const –> unsigned long
- receptor_last_res(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_last_res() const –> unsigned long
- receptor_nres(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) int¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::receptor_nres() const –> unsigned long
- ref_start_struct(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) str¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::ref_start_struct() const –> std::string
- property rep_ramp_cycles¶
- property sample_pc¶
- property score_filter¶
- property score_only¶
- setDefaultAnchors(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) None¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(class core::pose::Pose &) –> void
- set_peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, ch: str) None¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::set_peptide_chain(char) –> void
- set_receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, ch: str) None¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::set_receptor_chain(std::string) –> void
- set_user_defined_peptide(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, state: bool) None¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_peptide(bool) –> void
- set_user_defined_receptor(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, state: bool) None¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::set_user_defined_receptor(bool) –> void
- property slideintocontact¶
- property smove_angle_range¶
- property torsionsMCM¶
- updateChains(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, pose: pyrosetta.rosetta.core.pose.Pose) None¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::updateChains(const class core::pose::Pose &) –> void
- updateChainsAndAnchors_fromParamsFile(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags, params_file: str) None¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::updateChainsAndAnchors_fromParamsFile(const std::string &) –> void
- user_defined_peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::user_defined_peptide_chain() const –> bool
- user_defined_receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::user_defined_receptor_chain() const –> bool
- valid_anchors(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_anchors() const –> bool
- valid_chain_info(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_chain_info() const –> bool
- valid_peptide_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_peptide_chain() const –> bool
- valid_receptor_chain(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_receptor_chain() const –> bool
- valid_ref_start_struct(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) bool¶
C++: protocols::flexpep_docking::FlexPepDockingFlags::valid_ref_start_struct() const –> bool
- class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes¶
Bases:
Mover- apply(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None¶
C++: protocols::flexpep_docking::FlexPepDockingLowRes::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes¶
C++: protocols::flexpep_docking::FlexPepDockingLowRes::operator=(const class protocols::flexpep_docking::FlexPepDockingLowRes &) –> class protocols::flexpep_docking::FlexPepDockingLowRes &
- 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.flexpep_docking.FlexPepDockingLowRes) str¶
C++: protocols::flexpep_docking::FlexPepDockingLowRes::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.flexpep_docking.FlexPepDockingPoseMetrics¶
Bases:
pybind11_object- assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics¶
C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::operator=(const class protocols::flexpep_docking::FlexPepDockingPoseMetrics &) –> class protocols::flexpep_docking::FlexPepDockingPoseMetrics &
- calc_frac_native_contacts(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, native: pyrosetta.rosetta.core.pose.Pose, final: pyrosetta.rosetta.core.pose.Pose, threashold: float) float¶
C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_native_contacts(const class core::pose::Pose &, const class core::pose::Pose &, double) const –> double
- calc_interface_metrics(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, pose: pyrosetta.rosetta.core.pose.Pose, rb_jump: int, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.std.map_std_string_double¶
C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics(class core::pose::Pose &, unsigned long, class std::shared_ptr<class core::scoring::ScoreFunction>) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >
- calc_pep_scores(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, pose: pyrosetta.rosetta.core.pose.Pose, pepScore: float, pepScore_noref: float) None¶
C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores(const class core::pose::Pose &, double &, double &) const –> void
- calc_phipsi_RMSD(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, res_subset: pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t) float¶
C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(const class core::pose::Pose &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<bool> &) const –> double
- isInContact(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, threashold: float) bool¶
C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact(const class core::conformation::Residue &, const class core::conformation::Residue &, double) const –> bool
- set_flags(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics, flags: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags) None¶
C++: protocols::flexpep_docking::FlexPepDockingPoseMetrics::set_flags(class std::shared_ptr<const class protocols::flexpep_docking::FlexPepDockingFlags>) –> void
- class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol¶
Bases:
Mover- apply(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None¶
C++: protocols::flexpep_docking::FlexPepDockingProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol¶
C++: protocols::flexpep_docking::FlexPepDockingProtocol::operator=(const class protocols::flexpep_docking::FlexPepDockingProtocol &) –> class protocols::flexpep_docking::FlexPepDockingProtocol &
- 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.flexpep_docking.FlexPepDockingProtocol) pyrosetta.rosetta.protocols.moves.Mover¶
C++: protocols::flexpep_docking::FlexPepDockingProtocol::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.flexpep_docking.FlexPepDockingProtocol) str¶
C++: protocols::flexpep_docking::FlexPepDockingProtocol::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::flexpep_docking::FlexPepDockingProtocol::mover_name() –> std::string
- static name() str¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None¶
C++: protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None¶
Provide the citation.
C++: protocols::flexpep_docking::FlexPepDockingProtocol::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None¶
C++: protocols::flexpep_docking::FlexPepDockingProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_default(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol) None¶
setup that is called from constructor
C++: protocols::flexpep_docking::FlexPepDockingProtocol::set_default() –> 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 &
- view(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol, view_in: bool) None¶
setter
C++: protocols::flexpep_docking::FlexPepDockingProtocol::view(bool) –> void
- class pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator¶
Bases:
MoverCreator- assign(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator, : pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator) pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator¶
C++: protocols::flexpep_docking::FlexPepDockingProtocolCreator::operator=(const class protocols::flexpep_docking::FlexPepDockingProtocolCreator &) –> class protocols::flexpep_docking::FlexPepDockingProtocolCreator &
- create_mover(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover¶
C++: protocols::flexpep_docking::FlexPepDockingProtocolCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator) str¶
C++: protocols::flexpep_docking::FlexPepDockingProtocolCreator::keyname() const –> std::string