evolution¶

AlignmentCleanerTools

Bindings for protocols::evolution namespace

class pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost¶

Bases: Filter

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts.

apply(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::evolution::AASynthesisFitnessCost::apply(const class core::pose::Pose &) const –> bool

static class_name() → str¶: C++: protocols::evolution::AASynthesisFitnessCost::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AASynthesisFitnessCost::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::evolution::AASynthesisFitnessCost::compute(const class core::pose::Pose &) const –> double

fitnessCostPerATP(*args, **kwargs)¶

Overloaded function.

fitnessCostPerATP(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost) -> float

C++: protocols::evolution::AASynthesisFitnessCost::fitnessCostPerATP() const –> double

fitnessCostPerATP(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost, c: float) -> None

C++: protocols::evolution::AASynthesisFitnessCost::fitnessCostPerATP(const double &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AASynthesisFitnessCost::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

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

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost) → str¶: C++: protocols::evolution::AASynthesisFitnessCost::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::evolution::AASynthesisFitnessCost::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::evolution::AASynthesisFitnessCost::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::evolution::AASynthesisFitnessCost::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::evolution::AASynthesisFitnessCost::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost) -> int

C++: protocols::evolution::AASynthesisFitnessCost::threshold() const –> unsigned long

threshold(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost, t: int) -> None

C++: protocols::evolution::AASynthesisFitnessCost::threshold(const unsigned long &) –> void

class pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCostFilterCreator¶

Bases: FilterCreator

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

create_filter(self: pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCostFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AASynthesisFitnessCostFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

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

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

class pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder¶

Bases: Filter

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts.

alignment_file(*args, **kwargs)¶

Overloaded function.

alignment_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) -> str

C++: protocols::evolution::AlignmentAAFinder::alignment_file() const –> std::string

alignment_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, a: str) -> None

C++: protocols::evolution::AlignmentAAFinder::alignment_file(const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, p: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::evolution::AlignmentAAFinder::apply(const class core::pose::Pose &) const –> bool

available_AAs_file(*args, **kwargs)¶

Overloaded function.

available_AAs_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) -> str

C++: protocols::evolution::AlignmentAAFinder::available_AAs_file() const –> std::string

available_AAs_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, a: str) -> None

C++: protocols::evolution::AlignmentAAFinder::available_AAs_file(const std::string &) –> void

static class_name() → str¶: C++: protocols::evolution::AlignmentAAFinder::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AlignmentAAFinder::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

exclude_AA_threshold(*args, **kwargs)¶

Overloaded function.

exclude_AA_threshold(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) -> float

C++: protocols::evolution::AlignmentAAFinder::exclude_AA_threshold() const –> double

exclude_AA_threshold(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, t: float) -> None

C++: protocols::evolution::AlignmentAAFinder::exclude_AA_threshold(const double &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AlignmentAAFinder::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

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

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

indel_motif_radius(*args, **kwargs)¶

Overloaded function.

indel_motif_radius(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) -> int

C++: protocols::evolution::AlignmentAAFinder::indel_motif_radius() const –> unsigned long

indel_motif_radius(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, r: int) -> None

C++: protocols::evolution::AlignmentAAFinder::indel_motif_radius(const unsigned long &) –> void

loop_seqid_threshold(*args, **kwargs)¶

Overloaded function.

loop_seqid_threshold(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) -> float

C++: protocols::evolution::AlignmentAAFinder::loop_seqid_threshold() const –> double

loop_seqid_threshold(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, t: float) -> None

C++: protocols::evolution::AlignmentAAFinder::loop_seqid_threshold(const double &) –> void

name(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) → str¶: C++: protocols::evolution::AlignmentAAFinder::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::evolution::AlignmentAAFinder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::evolution::AlignmentAAFinder::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

relax_mover(*args, **kwargs)¶

Overloaded function.

relax_mover(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) -> pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::evolution::AlignmentAAFinder::relax_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

relax_mover(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::evolution::AlignmentAAFinder::relax_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

report(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::evolution::AlignmentAAFinder::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::evolution::AlignmentAAFinder::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::evolution::AlignmentAAFinder::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::evolution::AlignmentAAFinder::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.evolution.AlignmentAAFinderFilterCreator¶

Bases: FilterCreator

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

create_filter(self: pyrosetta.rosetta.protocols.evolution.AlignmentAAFinderFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AlignmentAAFinderFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

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

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

class pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter¶

Bases: Filter

test whether a pose contains a comment that evaluates to a predefined value. This is useful in controlling execution flow in RosettaScripts.

alignment_file(*args, **kwargs)¶

Overloaded function.

alignment_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> str

C++: protocols::evolution::AlignmentGapInserter::alignment_file() const –> std::string

alignment_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, a: str) -> None

C++: protocols::evolution::AlignmentGapInserter::alignment_file(const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, p: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::evolution::AlignmentGapInserter::apply(const class core::pose::Pose &) const –> bool

available_AAs_file(*args, **kwargs)¶

Overloaded function.

available_AAs_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> str

C++: protocols::evolution::AlignmentGapInserter::available_AAs_file() const –> std::string

available_AAs_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, a: str) -> None

C++: protocols::evolution::AlignmentGapInserter::available_AAs_file(const std::string &) –> void

static class_name() → str¶: C++: protocols::evolution::AlignmentGapInserter::class_name() –> std::string

cleaned_alignment_file(*args, **kwargs)¶

Overloaded function.

cleaned_alignment_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> str

C++: protocols::evolution::AlignmentGapInserter::cleaned_alignment_file() const –> std::string

cleaned_alignment_file(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, a: str) -> None

C++: protocols::evolution::AlignmentGapInserter::cleaned_alignment_file(const std::string &) –> void

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AlignmentGapInserter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

find_char_location_in_string(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, string: str, findIt: str) → pyrosetta.rosetta.utility.vector0_unsigned_long¶: C++: protocols::evolution::AlignmentGapInserter::find_char_location_in_string(const std::string &, const char) const –> class utility::vector0<unsigned long, class std::allocator<unsigned long> >

fresh_instance(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AlignmentGapInserter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

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

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

indel_motif_radius(*args, **kwargs)¶

Overloaded function.

indel_motif_radius(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> int

C++: protocols::evolution::AlignmentGapInserter::indel_motif_radius() const –> unsigned long

indel_motif_radius(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, r: int) -> None

C++: protocols::evolution::AlignmentGapInserter::indel_motif_radius(const unsigned long &) –> void

loop_seqid_thresholds(*args, **kwargs)¶

Overloaded function.

loop_seqid_thresholds(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds() const –> class utility::vector1<double, class std::allocator<double> >

loop_seqid_thresholds(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, v: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::evolution::AlignmentGapInserter::loop_seqid_thresholds(const class utility::vector1<double, class std::allocator<double> > &) –> void

max_score_diffs(*args, **kwargs)¶

Overloaded function.

max_score_diffs(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::evolution::AlignmentGapInserter::max_score_diffs() const –> class utility::vector1<double, class std::allocator<double> >

max_score_diffs(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, v: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::evolution::AlignmentGapInserter::max_score_diffs(const class utility::vector1<double, class std::allocator<double> > &) –> void

name(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) → str¶: C++: protocols::evolution::AlignmentGapInserter::name() const –> std::string

nbr_e_threshold(*args, **kwargs)¶

Overloaded function.

nbr_e_threshold(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> float

C++: protocols::evolution::AlignmentGapInserter::nbr_e_threshold() const –> double

nbr_e_threshold(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, t: float) -> None

C++: protocols::evolution::AlignmentGapInserter::nbr_e_threshold(const double &) –> void

only_clean_seq_num(*args, **kwargs)¶

Overloaded function.

only_clean_seq_num(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> int

C++: protocols::evolution::AlignmentGapInserter::only_clean_seq_num() const –> unsigned long

only_clean_seq_num(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, t: int) -> None

C++: protocols::evolution::AlignmentGapInserter::only_clean_seq_num(const unsigned long &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::evolution::AlignmentGapInserter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::evolution::AlignmentGapInserter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::evolution::AlignmentGapInserter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::evolution::AlignmentGapInserter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::evolution::AlignmentGapInserter::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::evolution::AlignmentGapInserter::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.evolution.AlignmentGapInserterFilterCreator¶

Bases: FilterCreator

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

create_filter(self: pyrosetta.rosetta.protocols.evolution.AlignmentGapInserterFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::evolution::AlignmentGapInserterFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

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

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

class pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover¶

Bases: GenericMonteCarloMover

accept(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, provisional_scores: pyrosetta.rosetta.utility.vector1_double, mca_status: pyrosetta.rosetta.protocols.moves.MCA) → None¶

Does what the mover needs to do when a pose is accepted, given a pose and scores

C++: protocols::monte_carlo::GenericMonteCarloMover::accept(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &, const enum protocols::moves::MCA) –> void

accept_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::accept_counter() const –> unsigned long

adaptation_period(*args, **kwargs)¶

Overloaded function.

adaptation_period(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, a: int) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptation_period(const unsigned long) –> void

adaptation_period(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> int

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptation_period() const –> unsigned long

adaptive(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive() const –> const class utility::vector1<bool, class std::allocator<bool> > &

adaptive_movers(*args, **kwargs)¶

Overloaded function.

adaptive_movers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, a: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers(const bool) –> void

adaptive_movers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers() const –> bool

add_filter(*args, **kwargs)¶

Overloaded function.

add_filter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str) -> None
add_filter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str, rank_by: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::add_filter(class std::shared_ptr<class protocols::filters::Filter>, const bool, const double, const std::string &, bool) –> void

add_trigger(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, trigger: std::function<bool (unsigned long, unsigned long, core::pose::Pose const&, std::shared_ptr<core::scoring::ScoreFunction>)>) → int¶

Adds a new trigger, returning its id.

Example: #include <functional>

bool no_op(core::Size stage,
core::Size num_stages, core::Size cycle, core::Size num_cycles, const core::pose::Pose&, core::scoring::ScoreFunctionOP) {}

Trigger callback = std::bind(&no_op, STAGE, NUM_STAGES, _1, _2, _3, _4); core::Size trigger_id = add_trigger(callback);

The current stage and number of stages must be bound at creation time. This information provides the triggers with context about the current progress of the simulation as a whole.

If the trigger returns true, rescoring occurs.

C++: protocols::monte_carlo::GenericMonteCarloMover::add_trigger(const class std::function<bool (unsigned long, unsigned long, const class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>)> &) –> unsigned long

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

apply EvolutionaryDynamicsMover (Mover)

C++: protocols::evolution::EvolutionaryDynamicsMover::apply(class core::pose::Pose &) –> void

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

boltz_rank(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::boltz_rank() const –> bool

boltzmann(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, pose: pyrosetta.rosetta.core.pose.Pose, random_nums: pyrosetta.rosetta.utility.vector1_double) → bool¶

core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria

C++: protocols::evolution::EvolutionaryDynamicsMover::boltzmann(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) –> bool

branch_length(*args, **kwargs)¶

Overloaded function.

branch_length(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, m: float) -> None

C++: protocols::evolution::EvolutionaryDynamicsMover::branch_length(const double) –> void

branch_length(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover) -> float

C++: protocols::evolution::EvolutionaryDynamicsMover::branch_length() const –> double

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.evolution.EvolutionaryDynamicsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::evolution::EvolutionaryDynamicsMover::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>

current_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → float¶

return the lowest score

C++: protocols::monte_carlo::GenericMonteCarloMover::current_score() const –> double

static define_composition_schema(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

disable_fitness_evaluation(*args, **kwargs)¶

Overloaded function.

disable_fitness_evaluation(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, d: bool) -> None

C++: protocols::evolution::EvolutionaryDynamicsMover::disable_fitness_evaluation(const bool) –> void

disable_fitness_evaluation(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover) -> bool

C++: protocols::evolution::EvolutionaryDynamicsMover::disable_fitness_evaluation() const –> bool

drift(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::drift() const –> bool

filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t¶: C++: protocols::monte_carlo::GenericMonteCarloMover::filters() const –> const class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > > &

fresh_instance(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of objectt

C++: protocols::evolution::EvolutionaryDynamicsMover::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.evolution.EvolutionaryDynamicsMover) → str¶: C++: protocols::evolution::EvolutionaryDynamicsMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → None¶

initialize object used in constructor

C++: protocols::monte_carlo::GenericMonteCarloMover::initialize() –> void

keep_filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::keep_filters() const –> bool

last_accepted_pose(*args, **kwargs)¶

Overloaded function.

last_accepted_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the last accepted pose

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose() const –> class std::shared_ptr<class core::pose::Pose>

last_accepted_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose(class std::shared_ptr<class core::pose::Pose>) –> void

last_accepted_score(*args, **kwargs)¶

Overloaded function.

last_accepted_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> float

return the last accepted score

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score() const –> double

last_accepted_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, score: float) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score(const double) –> void

last_accepted_scores(*args, **kwargs)¶

Overloaded function.

last_accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

last_accepted_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

last_tested_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::monte_carlo::GenericMonteCarloMover::last_tested_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

load_trial_number_from_checkpoint(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::load_trial_number_from_checkpoint(class core::pose::Pose &) –> unsigned long

lowest_score(*args, **kwargs)¶

Overloaded function.

lowest_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> float

return the lowest score

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score() const –> double

lowest_score(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, score: float) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score(const double) –> void

lowest_score_pose(*args, **kwargs)¶

Overloaded function.

lowest_score_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the lowest score pose

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose() const –> class std::shared_ptr<class core::pose::Pose>

lowest_score_pose(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose(class std::shared_ptr<class core::pose::Pose>) –> void

lowest_scores(*args, **kwargs)¶

Overloaded function.

lowest_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

lowest_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::lowest_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

max_accepted_trials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns maximum number of accepted trials

C++: protocols::monte_carlo::GenericMonteCarloMover::max_accepted_trials() const –> unsigned long

maxtrials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns maximum number of trials

C++: protocols::monte_carlo::GenericMonteCarloMover::maxtrials() const –> unsigned long

mc_accpeted(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.protocols.moves.MCA¶

return mc_accepted

C++: protocols::monte_carlo::GenericMonteCarloMover::mc_accpeted() const –> enum protocols::moves::MCA

mover(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::monte_carlo::GenericMonteCarloMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

static mover_name() → str¶: C++: protocols::evolution::EvolutionaryDynamicsMover::mover_name() –> std::string

mover_stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → basic::datacache::DataMapObj<bool>¶: C++: protocols::monte_carlo::GenericMonteCarloMover::mover_stopping_condition() const –> class std::shared_ptr<class basic::datacache::DataMapObj<bool> >

mutation_rate(*args, **kwargs)¶

Overloaded function.

mutation_rate(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, m: float) -> None

C++: protocols::evolution::EvolutionaryDynamicsMover::mutation_rate(const double) –> void

mutation_rate(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover) -> float

C++: protocols::evolution::EvolutionaryDynamicsMover::mutation_rate() const –> double

n_nucleotide_mut_trials_corrected(*args, **kwargs)¶

Overloaded function.

n_nucleotide_mut_trials_corrected(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, n: float) -> None

C++: protocols::evolution::EvolutionaryDynamicsMover::n_nucleotide_mut_trials_corrected(const double) –> void

n_nucleotide_mut_trials_corrected(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover) -> float

C++: protocols::evolution::EvolutionaryDynamicsMover::n_nucleotide_mut_trials_corrected() const –> double

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

num_designable(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → int¶: C++: protocols::monte_carlo::GenericMonteCarloMover::num_designable(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask> &) –> unsigned long

num_rejections(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::monte_carlo::GenericMonteCarloMover::num_rejections() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

num_triggers(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns the number of triggers

C++: protocols::monte_carlo::GenericMonteCarloMover::num_triggers() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::monte_carlo::GenericMonteCarloMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &) –> void

population_size(*args, **kwargs)¶

Overloaded function.

population_size(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, s: float) -> None

C++: protocols::evolution::EvolutionaryDynamicsMover::population_size(const double) –> void

population_size(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover) -> float

C++: protocols::evolution::EvolutionaryDynamicsMover::population_size() const –> double

preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::preapply() const –> bool

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

Provide the citation.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::evolution::EvolutionaryDynamicsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

recover_low(*args, **kwargs)¶

Overloaded function.

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

return the simulation state to the lowest energy structure we’ve seen

C++: protocols::monte_carlo::GenericMonteCarloMover::recover_low(class core::pose::Pose &) –> void

recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::recover_low() const –> 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

remove_trigger(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, trigger_id: int) → None¶

Removes the trigger with the specified id

C++: protocols::monte_carlo::GenericMonteCarloMover::remove_trigger(unsigned long) –> void

reset(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

reset MC iterations, with pose used for the last & best structures

C++: protocols::monte_carlo::GenericMonteCarloMover::reset(class core::pose::Pose &) –> void

reset_baselines(*args, **kwargs)¶

Overloaded function.

reset_baselines(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, r: bool) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::reset_baselines(const bool) –> void

reset_baselines(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> bool

C++: protocols::monte_carlo::GenericMonteCarloMover::reset_baselines() 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

sample_types(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::monte_carlo::GenericMonteCarloMover::sample_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

save_trial_number_to_checkpoint(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, i: int) → None¶: C++: protocols::monte_carlo::GenericMonteCarloMover::save_trial_number_to_checkpoint(const unsigned long) const –> void

saved_accept_file_name(*args, **kwargs)¶

Overloaded function.

saved_accept_file_name(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> str

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name() const –> std::string

saved_accept_file_name(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : str) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name(const std::string) –> void

saved_trial_number_file(*args, **kwargs)¶

Overloaded function.

saved_trial_number_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> str

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file() const –> std::string

saved_trial_number_file(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, : str) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file(const std::string) –> void

score_function(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶

Return the score function in use

C++: protocols::monte_carlo::GenericMonteCarloMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::monte_carlo::GenericMonteCarloMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_boltz_rank(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, boltz_rank: bool) → None¶

if boltz_rank=true, rank structures by the temperature-weighted

sum of scores, rather than a single filter

The score used here is the effective combined energy function that the Monte Carlo sampler is sampling over.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_boltz_rank(const bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_drift(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, drift: bool) → None¶

if drift=false, the pose is set back to the initial pose at each MC trial: Of course, this is not MC sampling.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_drift(const bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_keep_filters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, k: bool) → None¶: C++: protocols::monte_carlo::GenericMonteCarloMover::set_keep_filters(const bool) –> void

set_max_accepted_trials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, n_max_accepted_trial: int) → None¶

set max accepted trials of MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_max_accepted_trials(const unsigned long) –> void

set_maxtrials(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, ntrial: int) → None¶

set max trials of MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_maxtrials(const unsigned long) –> void

set_mover(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, mover: pyrosetta.rosetta.protocols.moves.Mover) → None¶

set mover

C++: protocols::monte_carlo::GenericMonteCarloMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> 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_preapply(*args, **kwargs)¶

Overloaded function.

set_preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> None
set_preapply(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, preapply: bool) -> None

if preapply=true, auto-accept the first application of the submover,: ignoring boltzman criteria.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_preapply(const bool) –> void

set_recover_low(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, recover_low: bool) → None¶

if recover_low=true, after apply() the structure: is the lowest energy structure, rather than the last accepted structure.

C++: protocols::monte_carlo::GenericMonteCarloMover::set_recover_low(const bool) –> void

set_sampletype(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, type: str) → None¶

set sample type, max or min: when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score

C++: protocols::monte_carlo::GenericMonteCarloMover::set_sampletype(const std::string &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Pose is evaluated by ScoreFunctionOP during MC trials

C++: protocols::monte_carlo::GenericMonteCarloMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_stop_sampling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, stop_sampling: bool) → None¶

if set to true, the MC mover will stop sampling

C++: protocols::monte_carlo::GenericMonteCarloMover::set_stop_sampling(const bool) –> void

set_task_scaling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, scaling: int) → None¶

set task multiplier to calculate trials from task

C++: protocols::monte_carlo::GenericMonteCarloMover::set_task_scaling(const unsigned long) –> void

set_temperature(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, temp: float) → None¶

set temperature

C++: protocols::monte_carlo::GenericMonteCarloMover::set_temperature(const double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

show_counters(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None¶

show counters of ntrial and acceptance ratio

C++: protocols::monte_carlo::GenericMonteCarloMover::show_counters(std::ostream &) const –> void

show_scores(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None¶

show scores of last_accepted_score and “best_score” ( = flip_sign_ * lowest_score )

C++: protocols::monte_carlo::GenericMonteCarloMover::show_scores(std::ostream &) const –> void

stop_sampling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → bool¶: C++: protocols::monte_carlo::GenericMonteCarloMover::stop_sampling() const –> bool

stopping_condition(*args, **kwargs)¶

Overloaded function.

stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::stopping_condition(class std::shared_ptr<class protocols::filters::Filter>) –> void

stopping_condition(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::monte_carlo::GenericMonteCarloMover::stopping_condition() const –> class std::shared_ptr<class protocols::filters::Filter>

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

task_factory(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::monte_carlo::GenericMonteCarloMover::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

task_scaling(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) → int¶

Returns the task scaling value

C++: protocols::monte_carlo::GenericMonteCarloMover::task_scaling() const –> unsigned long

temperatures(*args, **kwargs)¶

Overloaded function.

temperatures(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::monte_carlo::GenericMonteCarloMover::temperatures() const –> class utility::vector1<double, class std::allocator<double> >

temperatures(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, temps: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::temperatures(const class utility::vector1<double, class std::allocator<double> > &) –> 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

total_trials(*args, **kwargs)¶

Overloaded function.

total_trials(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover, m: float) -> None

C++: protocols::evolution::EvolutionaryDynamicsMover::total_trials(const double) –> void

total_trials(self: pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover) -> float

C++: protocols::evolution::EvolutionaryDynamicsMover::total_trials() const –> double

trial_counter(*args, **kwargs)¶

Overloaded function.

trial_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover) -> int

C++: protocols::monte_carlo::GenericMonteCarloMover::trial_counter() const –> unsigned long

trial_counter(self: pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover, i: int) -> None

C++: protocols::monte_carlo::GenericMonteCarloMover::trial_counter(const unsigned long) –> 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.evolution.EvolutionaryDynamicsMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.evolution.NucleotideMutation¶

Bases: Mover

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines.

add_nt_seq_to_pose(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::evolution::NucleotideMutation::add_nt_seq_to_pose(class core::pose::Pose &) –> void

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

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

bbnbrs(*args, **kwargs)¶

Overloaded function.

bbnbrs(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) -> int

C++: protocols::evolution::NucleotideMutation::bbnbrs() const –> unsigned long

bbnbrs(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, n: int) -> None

C++: protocols::evolution::NucleotideMutation::bbnbrs(const unsigned long) –> void

cache_task(*args, **kwargs)¶

Overloaded function.

cache_task(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) -> bool

C++: protocols::evolution::NucleotideMutation::cache_task() const –> bool

cache_task(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, cache: bool) -> None

C++: protocols::evolution::NucleotideMutation::cache_task(bool) –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::evolution::NucleotideMutation::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

compute_folding_energies(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, is_flexible: pyrosetta.rosetta.utility.vector1_bool, is_mutpos: pyrosetta.rosetta.utility.vector1_bool, bbnbrs: int, flexbb: bool) → None¶: C++: protocols::evolution::NucleotideMutation::compute_folding_energies(class std::shared_ptr<class core::scoring::ScoreFunction>, class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long, bool) –> void

continue_if_silent(*args, **kwargs)¶

Overloaded function.

continue_if_silent(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) -> bool

C++: protocols::evolution::NucleotideMutation::continue_if_silent() const –> bool

continue_if_silent(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, c: bool) -> None

C++: protocols::evolution::NucleotideMutation::continue_if_silent(const bool) –> void

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>

find_neighbors(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, is_mutated: pyrosetta.rosetta.utility.vector1_bool, pose: pyrosetta.rosetta.core.pose.Pose, is_flexible: pyrosetta.rosetta.utility.vector1_bool, heavyatom_distance_threshold: float) → None¶: C++: protocols::evolution::NucleotideMutation::find_neighbors(const class utility::vector1<bool, class std::allocator<bool> > &, const class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> > &, const double) –> void

flexbb(*args, **kwargs)¶

Overloaded function.

flexbb(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) -> bool

C++: protocols::evolution::NucleotideMutation::flexbb() const –> bool

flexbb(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, f: bool) -> None

C++: protocols::evolution::NucleotideMutation::flexbb(const bool) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::evolution::NucleotideMutation::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.evolution.NucleotideMutation) → str¶: C++: protocols::evolution::NucleotideMutation::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 > > &

init_sequence(*args, **kwargs)¶

Overloaded function.

init_sequence(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) -> str

C++: protocols::evolution::NucleotideMutation::init_sequence() const –> std::string

init_sequence(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, s: str) -> None

C++: protocols::evolution::NucleotideMutation::init_sequence(const std::string &) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::evolution::NucleotideMutation::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::evolution::NucleotideMutation::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::evolution::NucleotideMutation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::evolution::NucleotideMutation::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::evolution::NucleotideMutation::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::evolution::NucleotideMutation::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

task_factory(self: pyrosetta.rosetta.protocols.evolution.NucleotideMutation, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::evolution::NucleotideMutation::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.evolution.NucleotideMutationCreator¶

Bases: MoverCreator

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

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

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

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