anchored_design¶
Bindings for protocols::anchored_design namespace
- class pyrosetta.rosetta.protocols.anchored_design.Anchor¶
Bases:
pybind11_object
Anchor class provides for the “anchor” part of a scaffold in anchored interface design
Anchor class implements the code to read in an anchor file, stores the definition of the anchor, and provides access methods for setting move maps. It reads in PDB-keyed information, but converts it to pose resid information and internally stores only the latter.
- assign(self: pyrosetta.rosetta.protocols.anchored_design.Anchor, rhs: pyrosetta.rosetta.protocols.anchored_design.Anchor) pyrosetta.rosetta.protocols.anchored_design.Anchor ¶
assignment operator
C++: protocols::anchored_design::Anchor::operator=(const class protocols::anchored_design::Anchor &) –> class protocols::anchored_design::Anchor &
- end(self: pyrosetta.rosetta.protocols.anchored_design.Anchor) int ¶
returns end of anchor (as pose resid)
C++: protocols::anchored_design::Anchor::end() const –> unsigned long
- get_filename(self: pyrosetta.rosetta.protocols.anchored_design.Anchor) str ¶
getter for filename for anchorfile
C++: protocols::anchored_design::Anchor::get_filename() const –> const std::string &
- read_anchorfile(*args, **kwargs)¶
Overloaded function.
read_anchorfile(self: pyrosetta.rosetta.protocols.anchored_design.Anchor, pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None
method to read an anchor file. Pose is necessary to reference against
C++: protocols::anchored_design::Anchor::read_anchorfile(const class core::pose::Pose &, const std::string &) –> void
read_anchorfile(self: pyrosetta.rosetta.protocols.anchored_design.Anchor, pose: pyrosetta.rosetta.core.pose.Pose) -> None
method to read an anchor file. Pose is necessary to reference against. Checks internal data for filename.
C++: protocols::anchored_design::Anchor::read_anchorfile(const class core::pose::Pose &) –> void
- read_options(self: pyrosetta.rosetta.protocols.anchored_design.Anchor) None ¶
read option system into internal data
C++: protocols::anchored_design::Anchor::read_options() –> void
- set_filename(self: pyrosetta.rosetta.protocols.anchored_design.Anchor, filename: str) None ¶
setter for filename for anchorfile
C++: protocols::anchored_design::Anchor::set_filename(const std::string &) –> void
- start(self: pyrosetta.rosetta.protocols.anchored_design.Anchor) int ¶
returns start of anchor (as pose resid)
C++: protocols::anchored_design::Anchor::start() const –> unsigned long
- class pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData¶
Bases:
pybind11_object
This data class wraps all the data needed for the AnchoredDesign movers.
This data class keeps the anchor, mobile loops, and movemaps associated with the loops all together.
It generates its own movemaps.
- anchor_end(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) int ¶
access for anchor end
C++: protocols::anchored_design::AnchorMoversData::anchor_end() const –> unsigned long
- anchor_noise_constraints_setup(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
set up constraints for anchor_noise_constraints_mode
C++: protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(class core::pose::Pose &) –> void
- anchor_start(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) int ¶
//////////////////////////anchor functions//////////////////////////////////////////////
access for anchor start
C++: protocols::anchored_design::AnchorMoversData::anchor_start() const –> unsigned long
- anchored_loop(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.protocols.loops.Loop ¶
//////////////loops and movemap functions//////////////////////////////////////////////
access anchored loop
C++: protocols::anchored_design::AnchorMoversData::anchored_loop() const –> const class protocols::loops::Loop &
- assign(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, rhs: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData ¶
assignment operator
C++: protocols::anchored_design::AnchorMoversData::operator=(const class protocols::anchored_design::AnchorMoversData &) –> class protocols::anchored_design::AnchorMoversData &
- autogenerate_constseq_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, seq: str) pyrosetta.rosetta.core.fragment.FragSet ¶
brew its own sequence-specific frags
C++: protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags(const std::string &) –> class std::shared_ptr<const class core::fragment::FragSet>
- autogenerate_design_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.fragment.FragSet ¶
brew its own design frags (LLLLL secondary structure)
C++: protocols::anchored_design::AnchorMoversData::autogenerate_design_frags() –> class std::shared_ptr<const class core::fragment::FragSet>
- autogenerate_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
figure out what type of fragments to use, and use them; pose needed to make packertask to detect if design is occuring
C++: protocols::anchored_design::AnchorMoversData::autogenerate_frags(const class core::pose::Pose &) –> void
- clone(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData ¶
C++: protocols::anchored_design::AnchorMoversData::clone() const –> class std::shared_ptr<class protocols::anchored_design::AnchorMoversData>
- get_VDW_weight(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) float ¶
VDW weight in centroid scorefunction
C++: protocols::anchored_design::AnchorMoversData::get_VDW_weight() const –> double
- get_akash_dyepos(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) int ¶
dye position used in dye modeling publication
C++: protocols::anchored_design::AnchorMoversData::get_akash_dyepos() const –> unsigned long
- get_allow_anchor_repack(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) bool ¶
allow anchor to repack
C++: protocols::anchored_design::AnchorMoversData::get_allow_anchor_repack() const –> bool
- get_anchor_noise_constraints_mode(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) bool ¶
special anchor_noise_constraints_mode
C++: protocols::anchored_design::AnchorMoversData::get_anchor_noise_constraints_mode() const –> bool
- get_anchor_via_constraints(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) bool ¶
used to test anchoring via constraints
C++: protocols::anchored_design::AnchorMoversData::get_anchor_via_constraints() const –> bool
- get_centroid_scorefunction(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
access centroid scorefunction
C++: protocols::anchored_design::AnchorMoversData::get_centroid_scorefunction() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- get_centroid_scorefunction_min(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
access centroid scorefunction for minimization
C++: protocols::anchored_design::AnchorMoversData::get_centroid_scorefunction_min() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- get_chainbreak_weight(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) float ¶
chainbreak weight in fullatom scorefunction
C++: protocols::anchored_design::AnchorMoversData::get_chainbreak_weight() const –> double
- get_frag3(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) str ¶
copy of cmdline option frag3
C++: protocols::anchored_design::AnchorMoversData::get_frag3() const –> const std::string &
- get_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.fragment.FragSet ¶
/////////////////////scfxn, packertask, fragments accessors//////////////////////////////
access fragments object
C++: protocols::anchored_design::AnchorMoversData::get_frags() const –> class std::shared_ptr<const class core::fragment::FragSet>
- get_fullatom_scorefunction(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
access fullatom scorefunction
C++: protocols::anchored_design::AnchorMoversData::get_fullatom_scorefunction() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- get_late_factory(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
access packertask factory
C++: protocols::anchored_design::AnchorMoversData::get_late_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- get_loop_file(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) str ¶
copy of cmdline option loop_file
C++: protocols::anchored_design::AnchorMoversData::get_loop_file() const –> const std::string &
- get_no_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) bool ¶
do not use fragments?
C++: protocols::anchored_design::AnchorMoversData::get_no_frags() const –> bool
- get_resfile_1(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) str ¶
resfile for design
C++: protocols::anchored_design::AnchorMoversData::get_resfile_1() const –> const std::string &
- get_resfile_2(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) str ¶
later-stage resfile if desired
C++: protocols::anchored_design::AnchorMoversData::get_resfile_2() const –> const std::string &
- get_super_secret_fixed_interface_mode(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) bool ¶
special super_secret_fixed_interface_mode
C++: protocols::anchored_design::AnchorMoversData::get_super_secret_fixed_interface_mode() const –> bool
- get_task(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.pack.task.PackerTask ¶
return packertask from factory
C++: protocols::anchored_design::AnchorMoversData::get_task(const class core::pose::Pose &) const –> class std::shared_ptr<class core::pack::task::PackerTask>
- get_task_factory(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.pack.task.TaskFactory ¶
access packertask factory
C++: protocols::anchored_design::AnchorMoversData::get_task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>
- get_unbound_mode(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) bool ¶
used for unbound mode
C++: protocols::anchored_design::AnchorMoversData::get_unbound_mode() const –> bool
- interface_calc(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) str ¶
get string name for interface_calc_
C++: protocols::anchored_design::AnchorMoversData::interface_calc() const –> const std::string &
- loop(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, i: int) pyrosetta.rosetta.protocols.loops.Loop ¶
accessor for a loop
C++: protocols::anchored_design::AnchorMoversData::loop(unsigned long) const –> const class protocols::loops::Loop &
- loops(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.protocols.loops.Loops ¶
accessor for loops object
C++: protocols::anchored_design::AnchorMoversData::loops() const –> const class protocols::loops::Loops &
- movemap_cen(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, i: int) pyrosetta.rosetta.core.kinematics.MoveMap ¶
accessor for omega-variable movemap (most movers); centroid phase (no anchor movement)
C++: protocols::anchored_design::AnchorMoversData::movemap_cen(unsigned long) const –> class std::shared_ptr<class core::kinematics::MoveMap>
- movemap_cen_all(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.kinematics.MoveMap ¶
access for movemap that covers all loops; centroid
C++: protocols::anchored_design::AnchorMoversData::movemap_cen_all() const –> class std::shared_ptr<class core::kinematics::MoveMap>
- movemap_cen_omegafixed(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, i: int) pyrosetta.rosetta.core.kinematics.MoveMap ¶
accessor for omega-fixed movemap (appropriate for CCD movers); centroid phase
C++: protocols::anchored_design::AnchorMoversData::movemap_cen_omegafixed(unsigned long) const –> class std::shared_ptr<class core::kinematics::MoveMap>
- movemap_fa(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, i: int) pyrosetta.rosetta.core.kinematics.MoveMap ¶
accessor for omega-variable movemap (most movers); fullatom phase (may allow anchor movement w/constraints)
C++: protocols::anchored_design::AnchorMoversData::movemap_fa(unsigned long) const –> class std::shared_ptr<class core::kinematics::MoveMap>
- movemap_fa_all(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) pyrosetta.rosetta.core.kinematics.MoveMap ¶
access for movemap that covers all loops; fullatom
C++: protocols::anchored_design::AnchorMoversData::movemap_fa_all() const –> class std::shared_ptr<class core::kinematics::MoveMap>
- movemap_fa_omegafixed(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, i: int) pyrosetta.rosetta.core.kinematics.MoveMap ¶
accessor for omega-fixed movemap (appropriate for CCD movers); fullatom phase (may allow anchor movement w/constraints)
C++: protocols::anchored_design::AnchorMoversData::movemap_fa_omegafixed(unsigned long) const –> class std::shared_ptr<class core::kinematics::MoveMap>
- neighborhood_calc(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) str ¶
get string name for neighborhood_calc_
C++: protocols::anchored_design::AnchorMoversData::neighborhood_calc() const –> const std::string &
- num_loops(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) int ¶
number of loops/mms
C++: protocols::anchored_design::AnchorMoversData::num_loops() const –> unsigned long
- pick_new_cutpoints(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, reset_always: bool) None ¶
randomly reset loop cutpoints. Useful only when starting structure is well-closed. Best for MPI-style runs
C++: protocols::anchored_design::AnchorMoversData::pick_new_cutpoints(bool) –> void
- read_options(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData) None ¶
read options from the option system
C++: protocols::anchored_design::AnchorMoversData::read_options() –> void
- set_VDW_weight(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, VDW_weight: float) None ¶
VDW weight in centroid scorefunction
C++: protocols::anchored_design::AnchorMoversData::set_VDW_weight(double) –> void
- set_akash_dyepos(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, akash_dyepos: int) None ¶
/////////////option system replacement/////////////////////////////
dye position used in dye modeling publication
C++: protocols::anchored_design::AnchorMoversData::set_akash_dyepos(const unsigned long) –> void
- set_allow_anchor_repack(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, allow_anchor_repack: bool) None ¶
allow anchor to repack
C++: protocols::anchored_design::AnchorMoversData::set_allow_anchor_repack(bool) –> void
- set_anchor_noise_constraints_mode(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, anchor_noise_constraints_mode: bool) None ¶
special anchor_noise_constraints_mode
C++: protocols::anchored_design::AnchorMoversData::set_anchor_noise_constraints_mode(bool) –> void
- set_anchor_via_constraints(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, anchor_via_constraints: bool) None ¶
used to test anchoring via constraints
C++: protocols::anchored_design::AnchorMoversData::set_anchor_via_constraints(bool) –> void
- set_centroid_scorefunction(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, : pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
set centroid scorefunction
C++: protocols::anchored_design::AnchorMoversData::set_centroid_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_chainbreak_weight(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, chainbreak_weight: float) None ¶
chainbreak weight in fullatom scorefunction
C++: protocols::anchored_design::AnchorMoversData::set_chainbreak_weight(double) –> void
- set_frag3(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, frag3: str) None ¶
copy of cmdline option frag3
C++: protocols::anchored_design::AnchorMoversData::set_frag3(const std::string &) –> void
- set_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, : pyrosetta.rosetta.core.fragment.FragSet) None ¶
////////////////set functions/////////////////////////////////////////////////////////
set fragments object
C++: protocols::anchored_design::AnchorMoversData::set_frags(class std::shared_ptr<class core::fragment::FragSet>) –> void
- set_fullatom_scorefunction(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, : pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
set fullatom scorefunction
C++: protocols::anchored_design::AnchorMoversData::set_fullatom_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
- set_loops_and_anchor(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, anchor: pyrosetta.rosetta.protocols.anchored_design.Anchor, loops: pyrosetta.rosetta.protocols.loops.Loops) None ¶
set up kinematics’ loops and anchors
C++: protocols::anchored_design::AnchorMoversData::set_loops_and_anchor(class std::shared_ptr<const class protocols::anchored_design::Anchor>, class protocols::loops::Loops) –> void
- set_no_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, no_frags: bool) None ¶
do not use fragments?
C++: protocols::anchored_design::AnchorMoversData::set_no_frags(bool) –> void
- set_resfile_1(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, resfile_1: str) None ¶
resfile for design
C++: protocols::anchored_design::AnchorMoversData::set_resfile_1(const std::string &) –> void
- set_resfile_2(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, resfile_2: str) None ¶
later-stage resfile if desired
C++: protocols::anchored_design::AnchorMoversData::set_resfile_2(const std::string &) –> void
- set_super_secret_fixed_interface_mode(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, super_secret_fixed_interface_mode: bool) None ¶
special super_secret_fixed_interface_mode
C++: protocols::anchored_design::AnchorMoversData::set_super_secret_fixed_interface_mode(bool) –> void
- set_task_factory(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, : pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
set packertask factory
C++: protocols::anchored_design::AnchorMoversData::set_task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
- set_unbound_mode(self: pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData, unbound_mode: bool) None ¶
used for unbound mode
C++: protocols::anchored_design::AnchorMoversData::set_unbound_mode(bool) –> void
- class pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::anchored_design::AnchoredDesignMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, rhs: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover ¶
assignment operator
C++: protocols::anchored_design::AnchoredDesignMover::operator=(const class protocols::anchored_design::AnchoredDesignMover &) –> class protocols::anchored_design::AnchoredDesignMover &
- calculate_rmsd(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, start_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
calculate RMSD if desired; protected internally
C++: protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(const class core::pose::Pose &, class std::shared_ptr<const class core::pose::Pose>) –> void
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::anchored_design::AnchoredDesignMover::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>
- delete_interface_native_sidechains(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
This function repacks the interface with use_input_sc forcibly off for benchmarking purposes.
C++: protocols::anchored_design::AnchoredDesignMover::delete_interface_native_sidechains(class core::pose::Pose &) const –> void
- filter(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
runs varous filtering checks on the finished pose; sets MoverStatus for failure as needed
C++: protocols::anchored_design::AnchoredDesignMover::filter(class core::pose::Pose &) –> void
- forget_initial_loops(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
implements the “extended” field of the loop file specification - sets extended phi/psi as needed
C++: protocols::anchored_design::AnchoredDesignMover::forget_initial_loops(class core::pose::Pose &) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::anchored_design::AnchoredDesignMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_RMSD_only_this(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) str ¶
run only RMSD calculations against this input, don’t do actual AnchoredDesign
C++: protocols::anchored_design::AnchoredDesignMover::get_RMSD_only_this() const –> const std::string &
- 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_autoinitialize(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
whether to automatically initialize from the options system; defaults to true
C++: protocols::anchored_design::AnchoredDesignMover::get_autoinitialize() const –> bool
- 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_delete_interface_native_sidechains(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
C++: protocols::anchored_design::AnchoredDesignMover::get_delete_interface_native_sidechains() const –> bool
- get_filter_SASA(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) float ¶
filter based on complex SASA
C++: protocols::anchored_design::AnchoredDesignMover::get_filter_SASA() const –> double
- get_filter_omega(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
filter based on omega angles in the loops - filter out cis omegas
C++: protocols::anchored_design::AnchoredDesignMover::get_filter_omega() const –> bool
- get_filter_score(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) float ¶
filter based on total complex score
C++: protocols::anchored_design::AnchoredDesignMover::get_filter_score() const –> 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_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.anchored_design.AnchoredDesignMover) str ¶
C++: protocols::anchored_design::AnchoredDesignMover::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_randomize_input_sequence(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
randomize_input_sequence to complement loop extension in forgetting the input
C++: protocols::anchored_design::AnchoredDesignMover::get_randomize_input_sequence() const –> bool
- get_refine_only(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
skip the perturbation step - useful when you already have a good structure
C++: protocols::anchored_design::AnchoredDesignMover::get_refine_only() const –> bool
- get_rmsd(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
run RMSD calculations
C++: protocols::anchored_design::AnchoredDesignMover::get_rmsd() const –> bool
- 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_show_extended(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
show_extended demonstrates that the code really forgets the input structure
C++: protocols::anchored_design::AnchoredDesignMover::get_show_extended() const –> bool
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- get_vary_cutpoints(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
pick a different cutpoint than the input; useful when you want to sample cutpoints
C++: protocols::anchored_design::AnchoredDesignMover::get_vary_cutpoints() const –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static 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
- perturb_anchor(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
handles perturbing the initial anchor placement
C++: protocols::anchored_design::AnchoredDesignMover::perturb_anchor(class core::pose::Pose &) const –> 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
- randomize_input_sequence(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
randomize the input loop sequence. Useful if you have reason to believe the starting loop sequence is biasing to a particular unwanted structure in centroid mode. Acts only on designable positions.
C++: protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(class core::pose::Pose &) const –> void
- read_options(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) None ¶
read in options from the options system
C++: protocols::anchored_design::AnchoredDesignMover::read_options() –> 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.anchored_design.AnchoredDesignMover) bool ¶
C++: protocols::anchored_design::AnchoredDesignMover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover) bool ¶
C++: protocols::anchored_design::AnchoredDesignMover::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_RMSD_only_this(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, RMSD_only_this: str) None ¶
run only RMSD calculations against this input, don’t do actual AnchoredDesign
C++: protocols::anchored_design::AnchoredDesignMover::set_RMSD_only_this(const std::string &) –> void
- set_autoinitialize(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, autoinitialize: bool) None ¶
whether to automatically initialize from the options system; defaults to true
C++: protocols::anchored_design::AnchoredDesignMover::set_autoinitialize(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_delete_interface_native_sidechains(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, delete_interface_native_sidechains: bool) None ¶
delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode
C++: protocols::anchored_design::AnchoredDesignMover::set_delete_interface_native_sidechains(const bool) –> void
- set_filter_SASA(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, filter_SASA: float) None ¶
filter based on complex SASA
C++: protocols::anchored_design::AnchoredDesignMover::set_filter_SASA(const double) –> void
- set_filter_omega(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, filter_omega: bool) None ¶
filter based on omega angles in the loops - filter out cis omegas
C++: protocols::anchored_design::AnchoredDesignMover::set_filter_omega(const bool) –> void
- set_filter_score(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, filter_score: float) None ¶
filter based on total complex score
C++: protocols::anchored_design::AnchoredDesignMover::set_filter_score(const double) –> void
- set_fold_tree_and_cutpoints(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
creates the anchored design fold tree and applies it to the pose
C++: protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(class core::pose::Pose &) –> 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_randomize_input_sequence(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, randomize_input_sequence: bool) None ¶
randomize_input_sequence to complement loop extension in forgetting the input
C++: protocols::anchored_design::AnchoredDesignMover::set_randomize_input_sequence(const bool) –> void
- set_refine_only(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, refine_only: bool) None ¶
skip the perturbation step - useful when you already have a good structure
C++: protocols::anchored_design::AnchoredDesignMover::set_refine_only(const bool) –> void
- set_rmsd(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, rmsd: bool) None ¶
run RMSD calculations
C++: protocols::anchored_design::AnchoredDesignMover::set_rmsd(const bool) –> void
- set_show_extended(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, show_extended: bool) None ¶
show_extended demonstrates that the code really forsets the input structure
C++: protocols::anchored_design::AnchoredDesignMover::set_show_extended(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_vary_cutpoints(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover, vary_cutpoints: bool) None ¶
pick a different cutpoint than the input; useful when you want to sample cutpoints
C++: protocols::anchored_design::AnchoredDesignMover::set_vary_cutpoints(const bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::anchored_design::AnchoredPerturbMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, : pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover ¶
C++: protocols::anchored_design::AnchoredPerturbMover::operator=(const class protocols::anchored_design::AnchoredPerturbMover &) –> class protocols::anchored_design::AnchoredPerturbMover &
- 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_debug(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) bool ¶
debugging mode activates a bunch of extra output
C++: protocols::anchored_design::AnchoredPerturbMover::get_debug() const –> bool
- 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_min_type(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) str ¶
what minimizer type to use?
C++: protocols::anchored_design::AnchoredPerturbMover::get_min_type() const –> const std::string &
- get_name(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) str ¶
C++: protocols::anchored_design::AnchoredPerturbMover::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_no_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) bool ¶
do not use fragments?
C++: protocols::anchored_design::AnchoredPerturbMover::get_no_frags() const –> bool
- get_nonpivot_torsion_sampling(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) bool ¶
use nonpivot torsion sampling for KIC?
C++: protocols::anchored_design::AnchoredPerturbMover::get_nonpivot_torsion_sampling() const –> bool
- get_perturb_CCD_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) bool ¶
do not perform CCD style closure (use KIC only)
C++: protocols::anchored_design::AnchoredPerturbMover::get_perturb_CCD_off() const –> bool
- get_perturb_KIC_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) bool ¶
do not perform KIC style closure (use CCD only)
C++: protocols::anchored_design::AnchoredPerturbMover::get_perturb_KIC_off() const –> bool
- get_perturb_cycles(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) int ¶
number of MC cycles
C++: protocols::anchored_design::AnchoredPerturbMover::get_perturb_cycles() const –> unsigned long
- get_perturb_show(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) bool ¶
show perturb result structure?
C++: protocols::anchored_design::AnchoredPerturbMover::get_perturb_show() const –> bool
- get_perturb_temp(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) float ¶
MC temperature
C++: protocols::anchored_design::AnchoredPerturbMover::get_perturb_temp() const –> double
- 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
- read_options(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover) None ¶
read in options from the options system
C++: protocols::anchored_design::AnchoredPerturbMover::read_options() –> 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_debug(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, debug: bool) None ¶
debugging mode activates a bunch of extra output
C++: protocols::anchored_design::AnchoredPerturbMover::set_debug(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_min_type(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, min_type: str) None ¶
what minimizer type to use?
C++: protocols::anchored_design::AnchoredPerturbMover::set_min_type(const std::string &) –> 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_no_frags(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, no_frags: bool) None ¶
do not use fragments?
C++: protocols::anchored_design::AnchoredPerturbMover::set_no_frags(const bool) –> void
- set_nonpivot_torsion_sampling(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, nonpivot_torsion_sampling: bool) None ¶
use nonpivot torsion sampling for KIC?
C++: protocols::anchored_design::AnchoredPerturbMover::set_nonpivot_torsion_sampling(const bool) –> void
- set_perturb_CCD_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_CCD_off: bool) None ¶
do not perform CCD style closure (use KIC only)
C++: protocols::anchored_design::AnchoredPerturbMover::set_perturb_CCD_off(const bool) –> void
- set_perturb_KIC_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_KIC_off: bool) None ¶
do not perform KIC style closure (use CCD only)
C++: protocols::anchored_design::AnchoredPerturbMover::set_perturb_KIC_off(const bool) –> void
- set_perturb_cycles(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_cycles: int) None ¶
number of MC cycles
C++: protocols::anchored_design::AnchoredPerturbMover::set_perturb_cycles(const unsigned long) –> void
- set_perturb_show(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_show: bool) None ¶
show perturb result structure?
C++: protocols::anchored_design::AnchoredPerturbMover::set_perturb_show(const bool) –> void
- set_perturb_temp(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover, perturb_temp: float) None ¶
MC temperature
C++: protocols::anchored_design::AnchoredPerturbMover::set_perturb_temp(const double) –> 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.anchored_design.AnchoredRefineMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::anchored_design::AnchoredRefineMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, : pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover ¶
C++: protocols::anchored_design::AnchoredRefineMover::operator=(const class protocols::anchored_design::AnchoredRefineMover &) –> class protocols::anchored_design::AnchoredRefineMover &
- 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_debug(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) bool ¶
debugging mode activates a bunch of extra output
C++: protocols::anchored_design::AnchoredRefineMover::get_debug() const –> bool
- 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_min_type(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) str ¶
what minimizer type to use?
C++: protocols::anchored_design::AnchoredRefineMover::get_min_type() const –> const std::string &
- get_name(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) str ¶
C++: protocols::anchored_design::AnchoredRefineMover::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_nonpivot_torsion_sampling(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) bool ¶
use nonpivot torsion sampling for KIC?
C++: protocols::anchored_design::AnchoredRefineMover::get_nonpivot_torsion_sampling() const –> bool
- get_refine_CCD_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) bool ¶
do not perform CCD style closure (use KIC only)
C++: protocols::anchored_design::AnchoredRefineMover::get_refine_CCD_off() const –> bool
- get_refine_KIC_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) bool ¶
do not perform KIC style closure (use CCD only)
C++: protocols::anchored_design::AnchoredRefineMover::get_refine_KIC_off() const –> bool
- get_refine_cycles(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) int ¶
number of MC cycles
C++: protocols::anchored_design::AnchoredRefineMover::get_refine_cycles() const –> unsigned long
- get_refine_repack_cycles(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) int ¶
how many cycles between repack/design opportunities?
C++: protocols::anchored_design::AnchoredRefineMover::get_refine_repack_cycles() const –> unsigned long
- get_refine_temp(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) float ¶
MC temperature
C++: protocols::anchored_design::AnchoredRefineMover::get_refine_temp() const –> double
- 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
- get_vicinity_degree(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) float ¶
KIC vicinity sampling degrees
C++: protocols::anchored_design::AnchoredRefineMover::get_vicinity_degree() const –> double
- get_vicinity_sampling(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) bool ¶
KIC use vicinity sampling?
C++: protocols::anchored_design::AnchoredRefineMover::get_vicinity_sampling() const –> bool
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static 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
- read_options(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover) None ¶
read in options from the options system
C++: protocols::anchored_design::AnchoredRefineMover::read_options() –> 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_debug(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, debug: bool) None ¶
debugging mode activates a bunch of extra output
C++: protocols::anchored_design::AnchoredRefineMover::set_debug(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_min_type(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, min_type: str) None ¶
what minimizer type to use?
C++: protocols::anchored_design::AnchoredRefineMover::set_min_type(const std::string &) –> 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_nonpivot_torsion_sampling(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, nonpivot_torsion_sampling: bool) None ¶
use nonpivot torsion sampling for KIC?
C++: protocols::anchored_design::AnchoredRefineMover::set_nonpivot_torsion_sampling(const bool) –> void
- set_refine_CCD_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, refine_CCD_off: bool) None ¶
do not perform CCD style closure (use KIC only)
C++: protocols::anchored_design::AnchoredRefineMover::set_refine_CCD_off(const bool) –> void
- set_refine_KIC_off(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, refine_KIC_off: bool) None ¶
do not perform KIC style closure (use CCD only)
C++: protocols::anchored_design::AnchoredRefineMover::set_refine_KIC_off(const bool) –> void
- set_refine_cycles(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, refine_cycles: int) None ¶
number of MC cycles
C++: protocols::anchored_design::AnchoredRefineMover::set_refine_cycles(const unsigned long) –> void
- set_refine_repack_cycles(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, refine_repack_cycles: int) None ¶
how many cycles between repack/design opportunities?
C++: protocols::anchored_design::AnchoredRefineMover::set_refine_repack_cycles(const unsigned long) –> void
- set_refine_temp(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, refine_temp: float) None ¶
MC temperature
C++: protocols::anchored_design::AnchoredRefineMover::set_refine_temp(const double) –> 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_vicinity_degree(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, vicinity_degree: int) None ¶
KIC vicinity sampling degrees
C++: protocols::anchored_design::AnchoredRefineMover::set_vicinity_degree(const unsigned long) –> void
- set_vicinity_sampling(self: pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover, vicinity_sampling: bool) None ¶
KIC use vicinity sampling?
C++: protocols::anchored_design::AnchoredRefineMover::set_vicinity_sampling(const bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &