comparative_modeling¶
Bindings for protocols::comparative_modeling namespace
- class pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator¶
Bases:
EvaluatorCreator
creator for the AlignRmsdTargetEvaluatorCreator class
- add_evaluators(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, eval: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) None ¶
C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(class protocols::evaluation::MetaPoseEvaluator &) const –> void
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, : pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator ¶
C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::operator=(const class protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator &) –> class protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator &
- register_options(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) None ¶
C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::register_options() –> void
- type_name(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) str ¶
C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::type_name() const –> std::string
- class pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator¶
Bases:
AlignEvaluator
- applicable(*args, **kwargs)¶
Overloaded function.
applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool
C++: protocols::evaluation::SingleValuePoseEvaluator<double>::applicable(const class core::pose::Pose &) const –> bool
applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool
C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, ss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None
C++: protocols::comparative_modeling::Align_RmsdEvaluator::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void
apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, : pyrosetta.rosetta.core.pose.Pose) -> float
C++: protocols::comparative_modeling::Align_RmsdEvaluator::apply(class core::pose::Pose &) const –> double
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, : pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator ¶
C++: protocols::comparative_modeling::Align_RmsdEvaluator::operator=(const class protocols::comparative_modeling::Align_RmsdEvaluator &) –> class protocols::comparative_modeling::Align_RmsdEvaluator &
- calc_gdt(*args, **kwargs)¶
Overloaded function.
calc_gdt(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting: bool) -> None
C++: protocols::comparative_modeling::Align_RmsdEvaluator::calc_gdt(const bool) –> void
calc_gdt(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool
C++: protocols::comparative_modeling::Align_RmsdEvaluator::calc_gdt() const –> bool
- gdt_by_TM(*args, **kwargs)¶
Overloaded function.
gdt_by_TM(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting: bool) -> None
C++: protocols::comparative_modeling::Align_RmsdEvaluator::gdt_by_TM(const bool) –> void
gdt_by_TM(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool
C++: protocols::comparative_modeling::Align_RmsdEvaluator::gdt_by_TM() const –> bool
- get_alignment(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.sequence.SequenceAlignment ¶
C++: protocols::evaluation::AlignEvaluator::get_alignment(const class core::pose::Pose &) const –> class std::shared_ptr<class core::sequence::SequenceAlignment>
- name(*args, **kwargs)¶
Overloaded function.
name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str
C++: protocols::evaluation::SingleValuePoseEvaluator<double>::name(unsigned long) const –> std::string
name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str
C++: protocols::evaluation::PoseEvaluator::name(unsigned long) const –> std::string
- native_pose(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::evaluation::AlignEvaluator::native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- report_aln_components(*args, **kwargs)¶
Overloaded function.
report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, setting: bool) -> None
C++: protocols::evaluation::AlignEvaluator::report_aln_components(const bool) –> void
report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) -> bool
C++: protocols::evaluation::AlignEvaluator::report_aln_components() const –> bool
- report_gdt_components(*args, **kwargs)¶
Overloaded function.
report_gdt_components(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting: bool) -> None
C++: protocols::comparative_modeling::Align_RmsdEvaluator::report_gdt_components(const bool) –> void
report_gdt_components(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool
C++: protocols::comparative_modeling::Align_RmsdEvaluator::report_gdt_components() const –> bool
- size(*args, **kwargs)¶
Overloaded function.
size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int
C++: protocols::evaluation::SingleValuePoseEvaluator<double>::size() const –> unsigned long
size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int
C++: protocols::evaluation::PoseEvaluator::size() const –> unsigned long
- tag(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) str ¶
C++: protocols::evaluation::AlignEvaluator::tag() const –> std::string
- class pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator¶
Bases:
AlignEvaluator
- applicable(*args, **kwargs)¶
Overloaded function.
applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool
C++: protocols::evaluation::SingleValuePoseEvaluator<double>::applicable(const class core::pose::Pose &) const –> bool
applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool
C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, ss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None
C++: protocols::comparative_modeling::Align_RotamerEvaluator::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void
apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, : pyrosetta.rosetta.core.pose.Pose) -> float
C++: protocols::comparative_modeling::Align_RotamerEvaluator::apply(class core::pose::Pose &) const –> double
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, : pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator ¶
C++: protocols::comparative_modeling::Align_RotamerEvaluator::operator=(const class protocols::comparative_modeling::Align_RotamerEvaluator &) –> class protocols::comparative_modeling::Align_RotamerEvaluator &
- chi_dev(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) float ¶
C++: protocols::comparative_modeling::Align_RotamerEvaluator::chi_dev() const –> double
- get_alignment(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.sequence.SequenceAlignment ¶
C++: protocols::evaluation::AlignEvaluator::get_alignment(const class core::pose::Pose &) const –> class std::shared_ptr<class core::sequence::SequenceAlignment>
- name(*args, **kwargs)¶
Overloaded function.
name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str
C++: protocols::evaluation::SingleValuePoseEvaluator<double>::name(unsigned long) const –> std::string
name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str
C++: protocols::evaluation::PoseEvaluator::name(unsigned long) const –> std::string
- native_pose(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::evaluation::AlignEvaluator::native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- report_aln_components(*args, **kwargs)¶
Overloaded function.
report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, setting: bool) -> None
C++: protocols::evaluation::AlignEvaluator::report_aln_components(const bool) –> void
report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) -> bool
C++: protocols::evaluation::AlignEvaluator::report_aln_components() const –> bool
- size(*args, **kwargs)¶
Overloaded function.
size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int
C++: protocols::evaluation::SingleValuePoseEvaluator<double>::size() const –> unsigned long
size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int
C++: protocols::evaluation::PoseEvaluator::size() const –> unsigned long
- tag(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) str ¶
C++: protocols::evaluation::AlignEvaluator::tag() const –> std::string
- class pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster¶
Bases:
pybind11_object
- add_aln(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, aln_in: pyrosetta.rosetta.core.sequence.SequenceAlignment) None ¶
C++: protocols::comparative_modeling::AlignmentCluster::add_aln(class core::sequence::SequenceAlignment &) –> void
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, : pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster ¶
C++: protocols::comparative_modeling::AlignmentCluster::operator=(const class protocols::comparative_modeling::AlignmentCluster &) –> class protocols::comparative_modeling::AlignmentCluster &
- get_aln(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, index: int) pyrosetta.rosetta.core.sequence.SequenceAlignment ¶
C++: protocols::comparative_modeling::AlignmentCluster::get_aln(unsigned long) –> class core::sequence::SequenceAlignment
- get_clusterCenter(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) pyrosetta.rosetta.core.sequence.SequenceAlignment ¶
C++: protocols::comparative_modeling::AlignmentCluster::get_clusterCenter() –> class core::sequence::SequenceAlignment
- merge(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, cluster_in: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) None ¶
C++: protocols::comparative_modeling::AlignmentCluster::merge(class std::shared_ptr<class protocols::comparative_modeling::AlignmentCluster>) –> void
- output(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, alignment_out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::comparative_modeling::AlignmentCluster::output(std::ostream &) –> void
- overlap(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, cluster_in: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) float ¶
C++: protocols::comparative_modeling::AlignmentCluster::overlap(class std::shared_ptr<class protocols::comparative_modeling::AlignmentCluster>) –> double
- size(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) float ¶
C++: protocols::comparative_modeling::AlignmentCluster::size() –> double
- class pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering, : pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering) pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering ¶
C++: protocols::comparative_modeling::AlignmentClustering::operator=(const class protocols::comparative_modeling::AlignmentClustering &) –> class protocols::comparative_modeling::AlignmentClustering &
- class pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet¶
Bases:
pybind11_object
- alignments(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment ¶
- Gets the next alignment from the stream. Might be the same
alignment every time, or might be a different alignment after each call to this function.
C++: protocols::comparative_modeling::AlignmentSet::alignments() const –> class utility::vector1<class core::sequence::SequenceAlignment, class std::allocator<class core::sequence::SequenceAlignment> >
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet, : pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet ¶
C++: protocols::comparative_modeling::AlignmentSet::operator=(const class protocols::comparative_modeling::AlignmentSet &) –> class protocols::comparative_modeling::AlignmentSet &
- insert(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment) None ¶
C++: protocols::comparative_modeling::AlignmentSet::insert(class core::sequence::SequenceAlignment) –> void
- size(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) int ¶
C++: protocols::comparative_modeling::AlignmentSet::size() const –> unsigned long
- class pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover¶
Bases:
Mover
- alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) pyrosetta.rosetta.core.sequence.SequenceAlignment ¶
Returns the SequenceAlignment object used in threading.
C++: protocols::comparative_modeling::ExtraThreadingMover::alignment() –> class core::sequence::SequenceAlignment
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
C++: protocols::comparative_modeling::ExtraThreadingMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover ¶
C++: protocols::comparative_modeling::ExtraThreadingMover::operator=(const class protocols::comparative_modeling::ExtraThreadingMover &) –> class protocols::comparative_modeling::ExtraThreadingMover &
- 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.comparative_modeling.ExtraThreadingMover) str ¶
C++: protocols::comparative_modeling::ExtraThreadingMover::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_qt_mapping(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.SequenceMapping ¶
Returns the SequenceMapping between query and template.
C++: protocols::comparative_modeling::ExtraThreadingMover::get_qt_mapping(const class core::pose::Pose &) const –> class core::id::SequenceMapping
- 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
- query_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) int ¶
- Returns the index of the query sequence in SequenceAlignment
object.
C++: protocols::comparative_modeling::ExtraThreadingMover::query_index() const –> unsigned long
- 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
- template_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) int ¶
- Returns the index of the template sequence in SequenceAlignment
object.
C++: protocols::comparative_modeling::ExtraThreadingMover::template_index() const –> unsigned long
- 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.comparative_modeling.GenericJobInputter¶
Bases:
JobInputter
This is the simplest implementation of JobInputter
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, : pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter ¶
C++: protocols::comparative_modeling::GenericJobInputter::operator=(const class protocols::comparative_modeling::GenericJobInputter &) –> class protocols::comparative_modeling::GenericJobInputter &
- fill_jobs(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, jobs: protocols::jd2::JobsContainer) None ¶
this function determines what jobs exist
C++: protocols::comparative_modeling::GenericJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void
- get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.protocols.jd2.JobInputter ¶
Get self owning pointers.
C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t ¶
Get self weak pointers.
C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>
- input_source(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum ¶
- Return the type of input source that the GenericJobInputter is currently
using.
Always POSE.
C++: protocols::comparative_modeling::GenericJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum
- static job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) str ¶
- call this with input_source() to get the input source of a
particular job inputter
C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string
- pose_from_job(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) None ¶
- this function is responsible for filling the pose reference with
the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.
C++: protocols::comparative_modeling::GenericJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void
- update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) None ¶
This function is only called by certain JobInputters to update the jobs list after it has already been created.
An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.
C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void
- updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) bool ¶
Does this type of JobInputter update the jobs list?
False by default. Override this function in derived classes to make it true.
C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool
- class pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator¶
Bases:
JobInputterCreator
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator, : pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator ¶
C++: protocols::comparative_modeling::GenericJobInputterCreator::operator=(const class protocols::comparative_modeling::GenericJobInputterCreator &) –> class protocols::comparative_modeling::GenericJobInputterCreator &
- create_JobInputter(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) pyrosetta.rosetta.protocols.jd2.JobInputter ¶
C++: protocols::comparative_modeling::GenericJobInputterCreator::create_JobInputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>
- keyname(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) str ¶
C++: protocols::comparative_modeling::GenericJobInputterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet¶
Bases:
ConstraintSet
- add_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst: pyrosetta.rosetta.core.scoring.constraints.Constraint) None ¶
C++: core::scoring::constraints::ConstraintSet::add_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>) –> void
- add_constraints(*args, **kwargs)¶
Overloaded function.
add_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> None
C++: core::scoring::constraints::ConstraintSet::add_constraints(class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >) –> void
add_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None
add another constraint set to this constraint set
C++: core::scoring::constraints::ConstraintSet::add_constraints(const class std::shared_ptr<const class core::scoring::constraints::ConstraintSet>) –> void
- add_dof_constraint(*args, **kwargs)¶
Overloaded function.
add_dof_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, id: pyrosetta.rosetta.core.id.DOF_ID, func: pyrosetta.rosetta.core.scoring.func.Func) -> None
add_dof_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, id: pyrosetta.rosetta.core.id.DOF_ID, func: pyrosetta.rosetta.core.scoring.func.Func, t: pyrosetta.rosetta.core.scoring.ScoreType) -> None
- Note – still hacky. Will not be included in packing, just scoring
and minimization
C++: core::scoring::constraints::ConstraintSet::add_dof_constraint(const class core::id::DOF_ID &, class std::shared_ptr<class core::scoring::func::Func>, const enum core::scoring::ScoreType &) –> void
- assign(*args, **kwargs)¶
Overloaded function.
assign(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rhs: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::operator=(const class core::scoring::constraints::ConstraintSet &) –> class core::scoring::constraints::ConstraintSet &
assign(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, : pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::operator=(const class protocols::comparative_modeling::IgnoreSubsetConstraintSet &) –> class protocols::comparative_modeling::IgnoreSubsetConstraintSet &
- attach_to_conformation(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, conformation: pyrosetta.rosetta.std.weak_ptr_const_core_conformation_Conformation_t) None ¶
C++: core::scoring::constraints::ConstraintSet::attach_to_conformation(class std::weak_ptr<const class core::conformation::Conformation>) –> void
- clear(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None ¶
C++: core::scoring::constraints::ConstraintSet::clear() –> void
- clear_sequence_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None ¶
Discard any and all sequence constraints in the sequence_constraints_ list.
C++: core::scoring::constraints::ConstraintSet::clear_sequence_constraints() –> void
- clone(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) pyrosetta.rosetta.core.scoring.constraints.ConstraintSet ¶
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::clone() const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>
- deprecated_eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
- Switching over to a pairwise decomposable eval-atom-deriv system for
RTMin means deprecating the old “evaluate an atom’s derivative wrt the entire structure” This function is preserved (for now) for use by the RNA_TorsionEnergy
C++: core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void
- detach_from_conformation(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None ¶
C++: core::scoring::constraints::ConstraintSet::detach_from_conformation() –> void
- detached_clone(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) pyrosetta.rosetta.core.scoring.constraints.ConstraintSet ¶
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::detached_clone() const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>
- detached_copy(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, src: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None ¶
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::detached_copy(const class core::scoring::constraints::ConstraintSet &) –> void
- eval_intrares_energy(*args, **kwargs)¶
Overloaded function.
eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None
C++: core::scoring::constraints::ConstraintSet::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void
eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None
C++: core::scoring::constraints::ConstraintSet::eval_intrares_energy(const class core::conformation::Residue &, class core::scoring::EMapVector &) const –> void
- eval_multibody_atom_derivative(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
- evaluate the derivatives for an atom that contains 3- or higher-body
constraints. Such derivatives cannot be evalauated in an extra-posal context (e.g. such as in RTMin).
C++: core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void
- eval_non_residue_pair_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None ¶
- Does NOT zero the emap values, just adds the additional contribution to the
existing emap energies (so can be called inside finalize_total_energies)
C++: core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void
- get_all_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t ¶
- Returns all constraints in the set as a flat list, regardless of
type.
C++: core::scoring::constraints::ConstraintSet::get_all_constraints() const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >
- has_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool ¶
C++: core::scoring::constraints::ConstraintSet::has_constraints() const –> bool
- has_dof_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool ¶
C++: core::scoring::constraints::ConstraintSet::has_dof_constraints() const –> bool
- has_intra_residue_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool ¶
C++: core::scoring::constraints::ConstraintSet::has_intra_residue_constraints() const –> bool
- has_non_residue_pair_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool ¶
C++: core::scoring::constraints::ConstraintSet::has_non_residue_pair_constraints() const –> bool
- has_residue_pair_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool ¶
C++: core::scoring::constraints::ConstraintSet::has_residue_pair_constraints() const –> bool
- ignore(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos: int) bool ¶
- Returns true if we’re supposed to ignore this sequence position,
false otherwise.
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore(const int) const –> bool
- ignore_list(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) pyrosetta.rosetta.std.set_int_t ¶
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore_list() const –> class std::set<int, struct std::less<int>, class std::allocator<int> >
- ignore_residue(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos: int) None ¶
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore_residue(const int) –> void
- is_empty(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) bool ¶
C++: core::scoring::constraints::ConstraintSet::is_empty() const –> bool
- n_sequence_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) int ¶
Get the number of sequence constraints.
C++: core::scoring::constraints::ConstraintSet::n_sequence_constraints() const –> unsigned long
- on_connection_change(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, event: pyrosetta.rosetta.core.conformation.signals.ConnectionEvent) None ¶
C++: core::scoring::constraints::ConstraintSet::on_connection_change(const struct core::conformation::signals::ConnectionEvent &) –> void
- on_length_change(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, event: pyrosetta.rosetta.core.conformation.signals.LengthEvent) None ¶
C++: core::scoring::constraints::ConstraintSet::on_length_change(const struct core::conformation::signals::LengthEvent &) –> void
- remap_residue_positions(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, smap: pyrosetta.rosetta.core.id.SequenceMapping) None ¶
- remaps the constraints in this particular constraint set according
to brief the passed in sequence mapping — redundant with remapped_clone!!!
C++: core::scoring::constraints::ConstraintSet::remap_residue_positions(const class core::id::SequenceMapping &) –> void
- remapped_clone(*args, **kwargs)¶
Overloaded function.
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet
remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet
- Copies the data from this ConstraintSet into a new object and
returns its OP; atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. nullptr = identity mapping to the new object. This will really clone all constraints since they have to change their atom-numbers and residue-numbers
C++: core::scoring::constraints::ConstraintSet::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>
- remove_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, object_comparison: bool) bool ¶
- Returns true if the constraint was successfully found and removed.
if object comparison is set to true, the constraint to be removed is found through the Constraint::== operator and not through pointer comparison
C++: core::scoring::constraints::ConstraintSet::remove_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>, bool) –> bool
- remove_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, object_comparison: bool) bool ¶
C++: core::scoring::constraints::ConstraintSet::remove_constraints(class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >, bool) –> bool
- residue_pair_constraint_exists(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos1: int, pos2: int) bool ¶
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_constraint_exists(const int, const int) const –> bool
- residue_pair_constraints_exists(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pos: int) bool ¶
C++: core::scoring::constraints::ConstraintSet::residue_pair_constraints_exists(const unsigned long) const –> bool
- residue_pair_energy(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None ¶
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void
- revision_id(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) int ¶
C++: core::scoring::constraints::ConstraintSet::revision_id() const –> unsigned long
- same_type_as_me(*args, **kwargs)¶
Overloaded function.
same_type_as_me(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> bool
same_type_as_me(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, recurse: bool) -> bool
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::same_type_as_me(const class core::scoring::constraints::ConstraintSet &, bool) const –> bool
- sequence_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, index: int) pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint ¶
Get the owning pointer to the Nth sequence constraint.
C++: core::scoring::constraints::ConstraintSet::sequence_constraint(const unsigned long) const –> class std::shared_ptr<const class core::scoring::aa_composition_energy::SequenceConstraint>
- setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: core::scoring::constraints::ConstraintSet::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void
- setup_for_minimizing_for_residue(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) None ¶
- Allow the parent class implementation to add the residue constraints
for this residue to the res_data_cache if this residue is not being ignored.
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class core::scoring::ResSingleMinimizationData &) const –> void
- setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, respair_data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) None ¶
- Allow the parent class implenetation to add the residue-pair constraints
for this residue pair to the respair_data_cache if neither residues are being ignored.
C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, class core::scoring::ResPairMinimizationData &) const –> void
- setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: core::scoring::constraints::ConstraintSet::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void
- show(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::scoring::constraints::ConstraintSet::show(std::ostream &) const –> void
- show_definition(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None ¶
C++: core::scoring::constraints::ConstraintSet::show_definition(std::ostream &, const class core::pose::Pose &) const –> void
- show_numbers(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::scoring::constraints::ConstraintSet::show_numbers(std::ostream &) const –> void
- show_violations(*args, **kwargs)¶
Overloaded function.
show_violations(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int, threshold: float) -> int
C++: core::scoring::constraints::ConstraintSet::show_violations(std::ostream &, class core::pose::Pose &, unsigned long, double) const –> unsigned long
- steal_def_clone(*args, **kwargs)¶
Overloaded function.
steal_def_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet
steal_def_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet
- like remapped_clone, but constraints also steal_def from src-pose
use, e.g., to get a new set of CoordinateConstraints for given xyz coordinates in src-pose
C++: core::scoring::constraints::ConstraintSet::steal_def_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>
- class pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::comparative_modeling::LoopRelaxThreadingMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover ¶
C++: protocols::comparative_modeling::LoopRelaxThreadingMover::operator=(const class protocols::comparative_modeling::LoopRelaxThreadingMover &) –> class protocols::comparative_modeling::LoopRelaxThreadingMover &
- 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.comparative_modeling.LoopRelaxThreadingMover) str ¶
C++: protocols::comparative_modeling::LoopRelaxThreadingMover::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
- setup(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) None ¶
C++: protocols::comparative_modeling::LoopRelaxThreadingMover::setup() –> 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.comparative_modeling.MultiThreadingMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
C++: protocols::comparative_modeling::MultiThreadingMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover ¶
C++: protocols::comparative_modeling::MultiThreadingMover::operator=(const class protocols::comparative_modeling::MultiThreadingMover &) –> class protocols::comparative_modeling::MultiThreadingMover &
- build_loops(*args, **kwargs)¶
Overloaded function.
build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, setting: bool) -> None
C++: protocols::comparative_modeling::MultiThreadingMover::build_loops(bool) –> void
build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool
C++: protocols::comparative_modeling::MultiThreadingMover::build_loops() const –> bool
- 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>
- frag_libs(*args, **kwargs)¶
Overloaded function.
frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
C++: protocols::comparative_modeling::MultiThreadingMover::frag_libs() const –> class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >
frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, new_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> None
C++: protocols::comparative_modeling::MultiThreadingMover::frag_libs(class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >) –> void
- 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.comparative_modeling.MultiThreadingMover) str ¶
C++: protocols::comparative_modeling::MultiThreadingMover::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
- min_loop_size(*args, **kwargs)¶
Overloaded function.
min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, new_size: int) -> None
C++: protocols::comparative_modeling::MultiThreadingMover::min_loop_size(const unsigned long) –> void
min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> int
C++: protocols::comparative_modeling::MultiThreadingMover::min_loop_size() const –> unsigned long
- 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
- randomize_loop_coords(*args, **kwargs)¶
Overloaded function.
randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, setting: bool) -> None
C++: protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords(bool) –> void
randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool
C++: protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords() –> bool
- 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
- repack_query(*args, **kwargs)¶
Overloaded function.
repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, setting: bool) -> None
C++: protocols::comparative_modeling::MultiThreadingMover::repack_query(bool) –> void
repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool
C++: protocols::comparative_modeling::MultiThreadingMover::repack_query() 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.comparative_modeling.PartialThreadingMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
C++: protocols::comparative_modeling::PartialThreadingMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover) pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover ¶
C++: protocols::comparative_modeling::PartialThreadingMover::operator=(const class protocols::comparative_modeling::PartialThreadingMover &) –> class protocols::comparative_modeling::PartialThreadingMover &
- 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.comparative_modeling.PartialThreadingMover) str ¶
C++: protocols::comparative_modeling::PartialThreadingMover::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.comparative_modeling.RecoverSideChainsMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::comparative_modeling::RecoverSideChainsMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &
- 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.comparative_modeling.RecoverSideChainsMover) str ¶
C++: protocols::comparative_modeling::RecoverSideChainsMover::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.comparative_modeling.StealLigandMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::comparative_modeling::StealLigandMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &
- 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.comparative_modeling.StealLigandMover) str ¶
C++: protocols::comparative_modeling::StealLigandMover::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.comparative_modeling.StealSideChainsMover¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
maps from pose to source_
C++: protocols::comparative_modeling::StealSideChainsMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &
- 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.comparative_modeling.StealSideChainsMover) str ¶
C++: protocols::comparative_modeling::StealSideChainsMover::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.comparative_modeling.ThreadingJob¶
Bases:
InnerJob
The InnerThreadingJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is. InnerThreadingJobs are relatively heavy; there is no need to duplicate a series of InnerThreadingJobs for each index into nstruct. The companion ThreadingJob class handles the nstruct index and has a pointer to an InnerThreadingJob (which is shared across many ThreadingJobs). InnerThreadingJob also holds a PoseOP to maintain the unmodified input pose for that job.
- alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) pyrosetta.rosetta.core.sequence.SequenceAlignment ¶
the alignment for this Job
C++: protocols::comparative_modeling::ThreadingJob::alignment() const –> const class core::sequence::SequenceAlignment &
- alignment_id(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) str ¶
convenience : alignment id
C++: protocols::comparative_modeling::ThreadingJob::alignment_id() const –> std::string
- bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob) bool ¶
C++: protocols::jd2::InnerJob::bad() const –> bool
- clone(self: pyrosetta.rosetta.protocols.jd2.InnerJob) pyrosetta.rosetta.protocols.jd2.InnerJob ¶
Return an owning pointer to a copy of this object.
C++: protocols::jd2::InnerJob::clone() const –> class std::shared_ptr<class protocols::jd2::InnerJob>
- static current_job() pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob ¶
- Convenience function to get the current ThreadingJob from JD2
Will return a nullptr if we can’t get a ThreadingJob from JD2
C++: protocols::comparative_modeling::ThreadingJob::current_job() –> const class protocols::comparative_modeling::ThreadingJob *
- extra_residues_to_steal(*args, **kwargs)¶
Overloaded function.
extra_residues_to_steal(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) -> pyrosetta.rosetta.utility.vector1_unsigned_long
returns list of extra residues to steal
C++: protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &
extra_residues_to_steal(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
C++: protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void
- get_pose(self: pyrosetta.rosetta.protocols.jd2.InnerJob) pyrosetta.rosetta.core.pose.Pose ¶
- return a COP to the input pose
DO NOT USE OUTSIDE OF JD2 NAMESPACE
C++: protocols::jd2::InnerJob::get_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- input_tag(self: pyrosetta.rosetta.protocols.jd2.InnerJob) str ¶
return the input tag (a string of space separated PDB filenames)
C++: protocols::jd2::InnerJob::input_tag() const –> const std::string &
- loops(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, nres: int) pyrosetta.rosetta.protocols.loops.Loops ¶
returns the “standard” loop definition (as conservative as possible)
C++: protocols::comparative_modeling::ThreadingJob::loops(unsigned long) const –> class protocols::loops::Loops
- nstruct_max(self: pyrosetta.rosetta.protocols.jd2.InnerJob) int ¶
C++: protocols::jd2::InnerJob::nstruct_max() const –> unsigned long
- optional_output_name(*args, **kwargs)¶
Overloaded function.
optional_output_name(self: pyrosetta.rosetta.protocols.jd2.InnerJob) -> str
returns a job name controlled by the mover. Must be turned with the optional_output_name out flag. This flag is typically used in conjuction with a mover
C++: protocols::jd2::InnerJob::optional_output_name() const –> const std::string &
optional_output_name(self: pyrosetta.rosetta.protocols.jd2.InnerJob, output_name: str) -> None
sets a job name controlled by the mover
C++: protocols::jd2::InnerJob::optional_output_name(std::string) –> void
- same(self: pyrosetta.rosetta.protocols.jd2.InnerJob, other: pyrosetta.rosetta.protocols.jd2.InnerJob) bool ¶
- returns true if this is the same as other;
does not call other.same()
C++: protocols::jd2::InnerJob::same(const class protocols::jd2::InnerJob &) const –> bool
- set_bad(*args, **kwargs)¶
Overloaded function.
set_bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob) -> None
set_bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob, value: bool) -> None
C++: protocols::jd2::InnerJob::set_bad(bool) –> void
- show(self: pyrosetta.rosetta.protocols.jd2.InnerJob, out: pyrosetta.rosetta.std.ostream) None ¶
C++: protocols::jd2::InnerJob::show(std::ostream &) const –> void
- class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter¶
Bases:
JobInputter
This is the simplest implementation of JobInputter
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, : pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter ¶
C++: protocols::comparative_modeling::ThreadingJobInputter::operator=(const class protocols::comparative_modeling::ThreadingJobInputter &) –> class protocols::comparative_modeling::ThreadingJobInputter &
- fill_jobs(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, jobs: protocols::jd2::JobsContainer) None ¶
this function determines what jobs exist
C++: protocols::comparative_modeling::ThreadingJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void
- get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.protocols.jd2.JobInputter ¶
Get self owning pointers.
C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t ¶
Get self weak pointers.
C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>
- input_source(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum ¶
- Return the type of input source that the ThreadingJobInputter is
currently using for template structures.
C++: protocols::comparative_modeling::ThreadingJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum
- static job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) str ¶
- call this with input_source() to get the input source of a
particular job inputter
C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string
- pose_from_job(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) None ¶
- this function is responsible for filling the pose reference with
the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.
C++: protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void
- update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) None ¶
This function is only called by certain JobInputters to update the jobs list after it has already been created.
An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.
C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void
- updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) bool ¶
Does this type of JobInputter update the jobs list?
False by default. Override this function in derived classes to make it true.
C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool
- class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator¶
Bases:
JobInputterCreator
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator, : pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator ¶
C++: protocols::comparative_modeling::ThreadingJobInputterCreator::operator=(const class protocols::comparative_modeling::ThreadingJobInputterCreator &) –> class protocols::comparative_modeling::ThreadingJobInputterCreator &
- create_JobInputter(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) pyrosetta.rosetta.protocols.jd2.JobInputter ¶
C++: protocols::comparative_modeling::ThreadingJobInputterCreator::create_JobInputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>
- keyname(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) str ¶
C++: protocols::comparative_modeling::ThreadingJobInputterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover¶
Bases:
Mover
- alignment(*args, **kwargs)¶
Overloaded function.
alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> pyrosetta.rosetta.core.sequence.SequenceAlignment
Returns the SequenceAlignment object used in threading.
C++: protocols::comparative_modeling::ThreadingMover::alignment() –> class core::sequence::SequenceAlignment
alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_align: pyrosetta.rosetta.core.sequence.SequenceAlignment) -> None
Sets the SequenceAlignment associated with this object.
C++: protocols::comparative_modeling::ThreadingMover::alignment(class core::sequence::SequenceAlignment) –> void
- apply(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Threads the given Pose onto the template_pose with the
SequenceAlignment provided.
C++: protocols::comparative_modeling::ThreadingMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover ¶
C++: protocols::comparative_modeling::ThreadingMover::operator=(const class protocols::comparative_modeling::ThreadingMover &) –> class protocols::comparative_modeling::ThreadingMover &
- build_loops(*args, **kwargs)¶
Overloaded function.
build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, setting: bool) -> None
C++: protocols::comparative_modeling::ThreadingMover::build_loops(bool) –> void
build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
C++: protocols::comparative_modeling::ThreadingMover::build_loops() const –> bool
- 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.comparative_modeling.ThreadingMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::comparative_modeling::ThreadingMover::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>
- frag_libs(*args, **kwargs)¶
Overloaded function.
frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t
C++: protocols::comparative_modeling::ThreadingMover::frag_libs() const –> class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >
frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> None
C++: protocols::comparative_modeling::ThreadingMover::frag_libs(class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::comparative_modeling::ThreadingMover::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.comparative_modeling.ThreadingMover) str ¶
C++: protocols::comparative_modeling::ThreadingMover::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_qt_mapping(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.SequenceMapping ¶
Returns the SequenceMapping between query and template.
C++: protocols::comparative_modeling::ThreadingMover::get_qt_mapping(const class core::pose::Pose &) const –> class core::id::SequenceMapping
- 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
- min_loop_size(*args, **kwargs)¶
Overloaded function.
min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_size: int) -> None
C++: protocols::comparative_modeling::ThreadingMover::min_loop_size(const unsigned long) –> void
min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> int
C++: protocols::comparative_modeling::ThreadingMover::min_loop_size() const –> unsigned long
- 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
- query_index(*args, **kwargs)¶
Overloaded function.
query_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> int
- Returns the index of the query sequence in SequenceAlignment
object.
C++: protocols::comparative_modeling::ThreadingMover::query_index() const –> unsigned long
query_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_index: int) -> None
Sets the index of the query sequence in SequenceAlignment object.
C++: protocols::comparative_modeling::ThreadingMover::query_index(unsigned long) –> void
- randomize_loop_coords(*args, **kwargs)¶
Overloaded function.
randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, setting: bool) -> None
C++: protocols::comparative_modeling::ThreadingMover::randomize_loop_coords(bool) –> void
randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
C++: protocols::comparative_modeling::ThreadingMover::randomize_loop_coords() –> bool
- 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
- repack_query(*args, **kwargs)¶
Overloaded function.
repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, setting: bool) -> None
C++: protocols::comparative_modeling::ThreadingMover::repack_query(bool) –> void
repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> bool
C++: protocols::comparative_modeling::ThreadingMover::repack_query() 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
- template_index(*args, **kwargs)¶
Overloaded function.
template_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> int
- Returns the index of the template sequence in SequenceAlignment
object.
C++: protocols::comparative_modeling::ThreadingMover::template_index() const –> unsigned long
template_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_index: int) -> None
- Sets the index of the template sequence in SequenceAlignment
object.
C++: protocols::comparative_modeling::ThreadingMover::template_index(unsigned long) –> void
- template_pose(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, template_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::comparative_modeling::ThreadingMover::template_pose(class core::pose::Pose) –> 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 &
- pyrosetta.rosetta.protocols.comparative_modeling.alignments_from_cmd_line() pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet ¶
C++: protocols::comparative_modeling::alignments_from_cmd_line() –> class protocols::comparative_modeling::AlignmentSet
- pyrosetta.rosetta.protocols.comparative_modeling.bounded_loops_from_alignment(num_residues: int, min_size: int, alignment: pyrosetta.rosetta.core.sequence.SequenceAlignment, unaligned_regions: pyrosetta.rosetta.protocols.loops.Loops) None ¶
- Identifies consecutive stretches of unaligned residues by scanning
the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>.
C++: protocols::comparative_modeling::bounded_loops_from_alignment(const unsigned long, const unsigned long, const class core::sequence::SequenceAlignment &, class std::shared_ptr<class protocols::loops::Loops> &) –> void
- pyrosetta.rosetta.protocols.comparative_modeling.cm_main() None ¶
Initiates LoopRelaxThreadingMover using the job distributor (jd2)
C++: protocols::comparative_modeling::cm_main() –> void
- pyrosetta.rosetta.protocols.comparative_modeling.gather_coords(*args, **kwargs)¶
Overloaded function.
gather_coords(model: pyrosetta.rosetta.core.pose.Pose, native: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, natoms: int, p1a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, p2a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t) -> None
gather_coords(model: pyrosetta.rosetta.core.pose.Pose, native: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, natoms: int, p1a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, p2a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, atom_name: str) -> None
C++: protocols::comparative_modeling::gather_coords(const class core::pose::Pose &, const class core::pose::Pose &, const class core::sequence::SequenceAlignment &, int &, class ObjexxFCL::FArray2D<double> &, class ObjexxFCL::FArray2D<double> &, const std::string &) –> void
- pyrosetta.rosetta.protocols.comparative_modeling.get_qt_mapping_general(query_pose: pyrosetta.rosetta.core.pose.Pose, align: pyrosetta.rosetta.core.sequence.SequenceAlignment, template_pose: pyrosetta.rosetta.core.pose.Pose, query_index: int, template_index: int) pyrosetta.rosetta.core.id.SequenceMapping ¶
C++: protocols::comparative_modeling::get_qt_mapping_general(const class core::pose::Pose &, const class core::sequence::SequenceAlignment &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> class core::id::SequenceMapping
- pyrosetta.rosetta.protocols.comparative_modeling.initialize_ss(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::comparative_modeling::initialize_ss(class core::pose::Pose &) –> void
- pyrosetta.rosetta.protocols.comparative_modeling.loops_are_closed(pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::comparative_modeling::loops_are_closed(class core::pose::Pose &) –> bool
- pyrosetta.rosetta.protocols.comparative_modeling.loops_from_alignment(nres: int, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, min_loop_size: int) pyrosetta.rosetta.protocols.loops.Loops ¶
C++: protocols::comparative_modeling::loops_from_alignment(unsigned long, const class core::sequence::SequenceAlignment &, const unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>
- pyrosetta.rosetta.protocols.comparative_modeling.loops_from_transitive_alignments(nres1: int, aln1: pyrosetta.rosetta.core.sequence.SequenceAlignment, nres2: int, aln2: pyrosetta.rosetta.core.sequence.SequenceAlignment, min_loop_size: int) pyrosetta.rosetta.protocols.loops.Loops ¶
C++: protocols::comparative_modeling::loops_from_transitive_alignments(unsigned long, const class core::sequence::SequenceAlignment &, unsigned long, const class core::sequence::SequenceAlignment &, const unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>
- pyrosetta.rosetta.protocols.comparative_modeling.poses_from_cmd_line(fn_list: pyrosetta.rosetta.utility.vector1_std_string) pyrosetta.rosetta.std.map_std_string_core_pose_Pose ¶
C++: protocols::comparative_modeling::poses_from_cmd_line(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class std::map<std::string, class core::pose::Pose, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::pose::Pose> > >
- pyrosetta.rosetta.protocols.comparative_modeling.randomize_selected_atoms(query_pose: pyrosetta.rosetta.core.pose.Pose, selected: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) None ¶
C++: protocols::comparative_modeling::randomize_selected_atoms(class core::pose::Pose &, const class core::id::AtomID_Map<bool> &) –> void
- pyrosetta.rosetta.protocols.comparative_modeling.rebuild_loops_until_closed(query_pose: pyrosetta.rosetta.core.pose.Pose, min_loop_size: int, max_times: int, loop_mover_name: str) None ¶
C++: protocols::comparative_modeling::rebuild_loops_until_closed(class core::pose::Pose &, const unsigned long, const unsigned long, const std::string &) –> void
- pyrosetta.rosetta.protocols.comparative_modeling.steal_ligands(dest_pose: pyrosetta.rosetta.core.pose.Pose, source_pose_in: pyrosetta.rosetta.core.pose.Pose, anchor_atom_dest: pyrosetta.rosetta.core.id.NamedAtomID, anchor_atom_source: pyrosetta.rosetta.core.id.NamedAtomID, ligand_indices: pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) None ¶
- Function for stealing ligands from a given Pose
and adding them to source_pose.
- : The parameters are:
dest_pose Pose to which ligands are added.
source_pose_in Pose from which ligands and orientations are taken.
anchor_atom_dest anchor atom providing reference in dest_pose for ligand orientation.
anchor_atom_source anchor atom providing reference in source_pose for ligand orientation.
ligand_indices list of AtomID entries for ligand, one per ligand. Ligand orientation is determined by orientation between anchor_atom_source and each ligand AtomID.
C++: protocols::comparative_modeling::steal_ligands(class core::pose::Pose &, const class core::pose::Pose &, const class core::id::NamedAtomID &, const class core::id::NamedAtomID &, const class utility::vector1<class core::id::NamedAtomID, class std::allocator<class core::id::NamedAtomID> > &) –> void
- pyrosetta.rosetta.protocols.comparative_modeling.templates_from_cmd_line() pyrosetta.rosetta.utility.vector1_core_pose_Pose ¶
C++: protocols::comparative_modeling::templates_from_cmd_line() –> class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> >