drug_design¶

bcl

Bindings for protocols::drug_design namespace

class pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover¶

Bases: Mover

Apply a given Chemistry modifier to the ResidueType at a given position, then replace the ResidueType at that position.

add_chemistry(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, setting: pyrosetta.rosetta.protocols.chemistries.Chemistry) → None¶: C++: protocols::drug_design::ApplyChemistryMover::add_chemistry(class std::shared_ptr<class protocols::chemistries::Chemistry>) –> void

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

Apply the mover

C++: protocols::drug_design::ApplyChemistryMover::apply(class core::pose::Pose &) –> void

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

chemistries(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_chemistries_Chemistry_t¶

returns by value and not by reference so you get a COP and can’t modify the chemistries

C++: protocols::drug_design::ApplyChemistryMover::chemistries() const –> class utility::vector1<class std::shared_ptr<const class protocols::chemistries::Chemistry>, class std::allocator<class std::shared_ptr<const class protocols::chemistries::Chemistry> > >

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.drug_design.ApplyChemistryMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::drug_design::ApplyChemistryMover::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.drug_design.ApplyChemistryMover) → pyrosetta.rosetta.protocols.moves.Mover¶

required in the context of the parser/scripting scheme

C++: protocols::drug_design::ApplyChemistryMover::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.drug_design.ApplyChemistryMover) → str¶: C++: protocols::drug_design::ApplyChemistryMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

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

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

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

static mover_name() → str¶: C++: protocols::drug_design::ApplyChemistryMover::mover_name() –> std::string

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

new_name(*args, **kwargs)¶

Overloaded function.

new_name(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover) -> str

C++: protocols::drug_design::ApplyChemistryMover::new_name() const –> const std::string &

new_name(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, setting: str) -> None

C++: protocols::drug_design::ApplyChemistryMover::new_name(const std::string &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse XML tag (to use this Mover in Rosetta Scripts)

C++: protocols::drug_design::ApplyChemistryMover::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::drug_design::ApplyChemistryMover::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

residue_id(*args, **kwargs)¶

Overloaded function.

residue_id(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover) -> int

C++: protocols::drug_design::ApplyChemistryMover::residue_id() const –> unsigned long

residue_id(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, setting: int) -> None

Set the residues to act on – Pose number: The set value will take precedence over previously set residue specifications (and will clear the residue selector & residue string settings)

C++: protocols::drug_design::ApplyChemistryMover::residue_id(unsigned long) –> void

residue_selector(*args, **kwargs)¶

Overloaded function.

residue_selector(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Mover Methods ///

C++: protocols::drug_design::ApplyChemistryMover::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

residue_selector(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

Set the residues to act on – Residue selector: The set value will take precedence over previously set residue specifications

C++: protocols::drug_design::ApplyChemistryMover::residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

residues(*args, **kwargs)¶

Overloaded function.

residues(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover) -> str

C++: protocols::drug_design::ApplyChemistryMover::residues() const –> const std::string &

residues(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, setting: str) -> None

Set the residues to act on – comma-separated list of (string) residues: The set value will take precedence over previously set residue specifications (and will clear the residue selector)

C++: protocols::drug_design::ApplyChemistryMover::residues(const std::string &) –> 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.drug_design.ApplyChemistryMover) -> None
show(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::drug_design::ApplyChemistryMover::show(std::ostream &) const –> void

tag(*args, **kwargs)¶

Overloaded function.

tag(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover) -> str

C++: protocols::drug_design::ApplyChemistryMover::tag() const –> const std::string &

tag(self: pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover, setting: str) -> None

C++: protocols::drug_design::ApplyChemistryMover::tag(const std::string &) –> 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.drug_design.ApplyChemistryMoverCreator¶

Bases: MoverCreator

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.ConformationSelectionToRDMol¶: Bases: pybind11_object

class pyrosetta.rosetta.protocols.drug_design.RDKitMetric¶

Bases: RealMetric

A SimpleMetric which measures properties calcualted by RDKit on a ligand.

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the pose as a score.

labeled as out_label.

Score is added to the SimpleMetricData cache: Data is output into the final score file, but can be accessed if needed through the cache.

C++: core::simple_metrics::RealMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

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

cached_calculate(*args, **kwargs)¶

Overloaded function.

cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> float
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> float
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> float
cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool) -> float

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,
for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

C++: core::simple_metrics::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Calculate the metric.

C++: protocols::drug_design::RDKitMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶: C++: protocols::drug_design::RDKitMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator¶: C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

get_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶

Output data name will be prefix+custom_type+type+suffix

C++: core::simple_metrics::SimpleMetric::get_custom_type() const –> std::string

get_final_sm_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

C++: core::simple_metrics::SimpleMetric::get_final_sm_type() const –> std::string

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.RealMetric) → pyrosetta.rosetta.utility.vector1_std_string¶

Get the metric name(s) that this Metric will calculate

C++: core::simple_metrics::RealMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

metric(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric) → str¶

Name of the metric

C++: protocols::drug_design::RDKitMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric) → str¶

Name of the class

C++: protocols::drug_design::RDKitMetric::name() const –> std::string

static name_static() → str¶

Name of the class for creator.

C++: protocols::drug_design::RDKitMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) → None¶

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

called by parse_my_tag – should not be used directly

C++: protocols::drug_design::RDKitMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : 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 simple metrics wishing to provide citation information.

C++: core::simple_metrics::SimpleMetric::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

rdkit_metric(*args, **kwargs)¶

Overloaded function.

rdkit_metric(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric, setting: str) -> None

C++: protocols::drug_design::RDKitMetric::rdkit_metric(const std::string &) –> void

rdkit_metric(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric) -> str

C++: protocols::drug_design::RDKitMetric::rdkit_metric() const –> const std::string &

residue_selector(*args, **kwargs)¶

Overloaded function.

residue_selector(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric, residue: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::drug_design::RDKitMetric::residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

residue_selector(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetric) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::drug_design::RDKitMetric::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) → None¶: C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

simple_metric_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) → str¶: C++: core::simple_metrics::SimpleMetric::simple_metric_type() const –> std::string

class pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator¶

Bases: SimpleMetricCreator

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

create_simple_metric(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator) → pyrosetta.rosetta.core.simple_metrics.SimpleMetric¶

Instantiate a particular SimpleMetric

C++: protocols::drug_design::RDKitMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator) → str¶

Return a string that will be used to instantiate the particular SimpleMetric

C++: protocols::drug_design::RDKitMetricCreator::keyname() const –> std::string

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

class pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover¶

Bases: Mover

add_scores_for_chain(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover, pose: pyrosetta.rosetta.core.pose.Pose, chain: str) → None¶: C++: protocols::drug_design::RDKitMetricsMover::add_scores_for_chain(class core::pose::Pose &, const std::string &) const –> void

add_scores_for_residue(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → None¶: C++: protocols::drug_design::RDKitMetricsMover::add_scores_for_residue(class core::pose::Pose &, unsigned long) const –> void

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

apply RDKitMetricsMover

C++: protocols::drug_design::RDKitMetricsMover::apply(class core::pose::Pose &) –> void

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

chains(*args, **kwargs)¶

Overloaded function.

chains(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover, setting: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::drug_design::RDKitMetricsMover::chains(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

chains(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::drug_design::RDKitMetricsMover::chains() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

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.drug_design.RDKitMetricsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::drug_design::RDKitMetricsMover::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.drug_design.RDKitMetricsMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of objectt

C++: protocols::drug_design::RDKitMetricsMover::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.drug_design.RDKitMetricsMover) → str¶: C++: protocols::drug_design::RDKitMetricsMover::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_tag(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → str¶: C++: protocols::drug_design::RDKitMetricsMover::get_tag(class core::pose::Pose &, unsigned long) const –> std::string

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

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

static mover_name() → str¶: C++: protocols::drug_design::RDKitMetricsMover::mover_name() –> std::string

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse xml file

C++: protocols::drug_design::RDKitMetricsMover::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::drug_design::RDKitMetricsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

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

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

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

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

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

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

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

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

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

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

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

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

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

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

set_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.drug_design.RDKitMetricsMoverCreator¶

Bases: MoverCreator

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

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

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

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

pyrosetta.rosetta.protocols.drug_design.place_new_restype_no_align(pose: pyrosetta.rosetta.core.pose.Pose, position: int, new_restype: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Replaces the residue at the given position in the pose with the new residue type.: Does no alignment - assumes that the internal coordinates of the new restype are properly set.

C++: protocols::drug_design::place_new_restype_no_align(class core::pose::Pose &, unsigned long, const class core::chemical::ResidueType &) –> void