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.

_pybind11_conduit_v1_()¶

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

_pybind11_conduit_v1_()¶

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.AtomExistsFilter¶

Bases: Filter

_pybind11_conduit_v1_()¶

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

static class_name() → str¶: C++: protocols::drug_design::AtomExistsFilter::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.drug_design.AtomExistsFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::drug_design::AtomExistsFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.AtomExistsFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::drug_design::AtomExistsFilter::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::drug_design::AtomExistsFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

report_sm(self: pyrosetta.rosetta.protocols.drug_design.AtomExistsFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::drug_design::AtomExistsFilter::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

class pyrosetta.rosetta.protocols.drug_design.AtomExistsFilterCreator¶

Bases: FilterCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.AtomSubstitution¶

Bases: pybind11_object

A class representing a substitution of an atom from an original molecule through a pair of matched templates to a substituted molecule. Intended to be used through MoleculeSubstitution

_pybind11_conduit_v1_()¶

idx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution, sele: pyrosetta.rosetta.protocols.drug_design.MoleculeSelection) → int¶: C++: protocols::drug_design::AtomSubstitution::idx(enum protocols::drug_design::MoleculeSelection) const –> unsigned int

mdx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution) → int¶

The atom index in the original molecule

C++: protocols::drug_design::AtomSubstitution::mdx() const –> unsigned int

ndx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution) → int¶

The atom index in the new (post-replacement) molecule

C++: protocols::drug_design::AtomSubstitution::ndx() const –> unsigned int

rdx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution) → int¶

The atom index in the replacement template

C++: protocols::drug_design::AtomSubstitution::rdx() const –> unsigned int

set_idx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution, sele: pyrosetta.rosetta.protocols.drug_design.MoleculeSelection, setting: int) → None¶: C++: protocols::drug_design::AtomSubstitution::set_idx(enum protocols::drug_design::MoleculeSelection, unsigned int) –> void

set_mdx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution, setting: int) → None¶: C++: protocols::drug_design::AtomSubstitution::set_mdx(unsigned int) –> void

set_ndx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution, setting: int) → None¶: C++: protocols::drug_design::AtomSubstitution::set_ndx(unsigned int) –> void

set_rdx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution, setting: int) → None¶: C++: protocols::drug_design::AtomSubstitution::set_rdx(unsigned int) –> void

set_tdx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution, setting: int) → None¶: C++: protocols::drug_design::AtomSubstitution::set_tdx(unsigned int) –> void

tdx(self: pyrosetta.rosetta.protocols.drug_design.AtomSubstitution) → int¶

The atom index in the template which matches the original molecule

C++: protocols::drug_design::AtomSubstitution::tdx() const –> unsigned int

class pyrosetta.rosetta.protocols.drug_design.ChemicalReaction¶

Bases: pybind11_object

_pybind11_conduit_v1_()¶

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

get_reaction(self: pyrosetta.rosetta.protocols.drug_design.ChemicalReaction) → RDKit::ChemicalReaction¶: C++: protocols::drug_design::ChemicalReaction::get_reaction() const –> const class std::shared_ptr<class RDKit::ChemicalReaction> &

is_reaction_usable(self: pyrosetta.rosetta.protocols.drug_design.ChemicalReaction) → bool¶

is the reaction valid, with usable reaction list (deprecated)

C++: protocols::drug_design::ChemicalReaction::is_reaction_usable() –> bool

load_reagents(self: pyrosetta.rosetta.protocols.drug_design.ChemicalReaction) → None¶: C++: protocols::drug_design::ChemicalReaction::load_reagents() –> void

n_availible_reagents(self: pyrosetta.rosetta.protocols.drug_design.ChemicalReaction, reag_no: int) → int¶: C++: protocols::drug_design::ChemicalReaction::n_availible_reagents(unsigned long) –> unsigned long

nreagents(self: pyrosetta.rosetta.protocols.drug_design.ChemicalReaction) → int¶: C++: protocols::drug_design::ChemicalReaction::nreagents() const –> unsigned long

reaction_name(self: pyrosetta.rosetta.protocols.drug_design.ChemicalReaction) → str¶: C++: protocols::drug_design::ChemicalReaction::reaction_name() const –> const std::string &

reaction_valid(self: pyrosetta.rosetta.protocols.drug_design.ChemicalReaction) → bool¶

Is the reaction valid, or was there an error loading the reaction?: (Doesn’t look at reactants.)

C++: protocols::drug_design::ChemicalReaction::reaction_valid() const –> bool

class pyrosetta.rosetta.protocols.drug_design.ConformationSelectionToRDMol¶

Bases: pybind11_object

_pybind11_conduit_v1_()¶

class pyrosetta.rosetta.protocols.drug_design.DrugDesignMover¶

Bases: Mover

_pybind11_conduit_v1_()¶

add_after_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry) → None¶

Add a chemistry to use

C++: protocols::drug_design::DrugDesignMover::add_after_chemistry(class std::shared_ptr<class protocols::chemistries::Chemistry>) –> void

add_before_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry) → None¶

Add a chemistry to use

C++: protocols::drug_design::DrugDesignMover::add_before_chemistry(class std::shared_ptr<class protocols::chemistries::Chemistry>) –> void

add_chemistry(*args, **kwargs)¶

Overloaded function.

add_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry) -> None
add_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry, weight: float) -> None

Add a chemistry to use

C++: protocols::drug_design::DrugDesignMover::add_chemistry(class std::shared_ptr<class protocols::chemistries::Chemistry>, double) –> void

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

apply DrugDesignMover

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

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

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> str

What chain is the ligand supposed to be?

C++: protocols::drug_design::DrugDesignMover::chain() const –> char

chain(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chain: str) -> None

set the ligand chain to use for design

C++: protocols::drug_design::DrugDesignMover::chain(char) –> void

check_design_position(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, n: int) → bool¶

Is position n a valid designable residue according to the settings

C++: protocols::drug_design::DrugDesignMover::check_design_position(const class core::pose::Pose &, unsigned long) –> bool

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::drug_design::DrugDesignMover::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>

debug_prefix(*args, **kwargs)¶

Overloaded function.

debug_prefix(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> str

What’s the prefix of the filename to which intermediate debug structures are dumped?

C++: protocols::drug_design::DrugDesignMover::debug_prefix() const –> std::string

debug_prefix(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, setting: str) -> None

What’s the prefix of the filename to which intermediate debug structures are dumped?

C++: protocols::drug_design::DrugDesignMover::debug_prefix(const std::string &) –> void

find_design_position(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Determine which residue on this pose should be designed

C++: protocols::drug_design::DrugDesignMover::find_design_position(const class core::pose::Pose &) –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of objectt

C++: protocols::drug_design::DrugDesignMover::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.DrugDesignMover) → str¶: C++: protocols::drug_design::DrugDesignMover::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

maxtrials(*args, **kwargs)¶

Overloaded function.

maxtrials(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> int

Returns maximum number of trials

C++: protocols::drug_design::DrugDesignMover::maxtrials() const –> unsigned long

maxtrials(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, ntrial: int) -> None

set max trials of MC trials

C++: protocols::drug_design::DrugDesignMover::maxtrials(const unsigned long) –> void

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

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

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

parse xml file

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

postfilter(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, setting: pyrosetta.rosetta.protocols.filters.Filter) → None¶

Set the filter to use after redocking

C++: protocols::drug_design::DrugDesignMover::postfilter(const class std::shared_ptr<class protocols::filters::Filter> &) –> void

prefilter(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, setting: pyrosetta.rosetta.protocols.filters.Filter) → None¶

Set the filter to use before redocking

C++: protocols::drug_design::DrugDesignMover::prefilter(const class std::shared_ptr<class protocols::filters::Filter> &) –> 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::DrugDesignMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

redocker(*args, **kwargs)¶

Overloaded function.

redocker(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> pyrosetta.rosetta.protocols.moves.Mover

Return the redocker being used

C++: protocols::drug_design::DrugDesignMover::redocker() const –> class std::shared_ptr<const class protocols::moves::Mover>

redocker(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

set redocking mover

C++: protocols::drug_design::DrugDesignMover::redocker(const class std::shared_ptr<class protocols::moves::Mover> &) –> 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

scorer(*args, **kwargs)¶

Overloaded function.

scorer(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> pyrosetta.rosetta.protocols.filters.Filter

Return the scoring filter

C++: protocols::drug_design::DrugDesignMover::scorer() const –> class std::shared_ptr<const class protocols::filters::Filter>

scorer(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, scorer: pyrosetta.rosetta.protocols.filters.Filter) -> None

Set the scoring filter in use

C++: protocols::drug_design::DrugDesignMover::scorer(const class std::shared_ptr<class protocols::filters::Filter> &) –> 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

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> float

Return the scoring temperature

C++: protocols::drug_design::DrugDesignMover::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, temp: float) -> None

set temperature

C++: protocols::drug_design::DrugDesignMover::temperature(const 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

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.DrugDesignMoverCreator¶

Bases: MoverCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.DrugPolishMover¶

Bases: DrugDesignMover

_pybind11_conduit_v1_()¶

add_after_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry) → None¶

Add a chemistry to use

C++: protocols::drug_design::DrugDesignMover::add_after_chemistry(class std::shared_ptr<class protocols::chemistries::Chemistry>) –> void

add_before_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry) → None¶

Add a chemistry to use

C++: protocols::drug_design::DrugDesignMover::add_before_chemistry(class std::shared_ptr<class protocols::chemistries::Chemistry>) –> void

add_chemistry(*args, **kwargs)¶

Overloaded function.

add_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry) -> None
add_chemistry(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chemistry: pyrosetta.rosetta.protocols.chemistries.Chemistry, weight: float) -> None

Add a chemistry to use

C++: protocols::drug_design::DrugDesignMover::add_chemistry(class std::shared_ptr<class protocols::chemistries::Chemistry>, double) –> void

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

apply DrugPolishMover

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

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

bonus(*args, **kwargs)¶

Overloaded function.

bonus(self: pyrosetta.rosetta.protocols.drug_design.DrugPolishMover) -> float

The bonus given to scoring for applying (another) reaction

C++: protocols::drug_design::DrugPolishMover::bonus() const –> double

bonus(self: pyrosetta.rosetta.protocols.drug_design.DrugPolishMover, setting: float) -> None

The bonus given to scoring for applying (another) reaction

C++: protocols::drug_design::DrugPolishMover::bonus(double) –> void

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> str

What chain is the ligand supposed to be?

C++: protocols::drug_design::DrugDesignMover::chain() const –> char

chain(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, chain: str) -> None

set the ligand chain to use for design

C++: protocols::drug_design::DrugDesignMover::chain(char) –> void

check_design_position(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, n: int) → bool¶

Is position n a valid designable residue according to the settings

C++: protocols::drug_design::DrugDesignMover::check_design_position(const class core::pose::Pose &, unsigned long) –> bool

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.drug_design.DrugPolishMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create copy constructor

C++: protocols::drug_design::DrugPolishMover::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>

debug_prefix(*args, **kwargs)¶

Overloaded function.

debug_prefix(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> str

What’s the prefix of the filename to which intermediate debug structures are dumped?

C++: protocols::drug_design::DrugDesignMover::debug_prefix() const –> std::string

debug_prefix(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, setting: str) -> None

What’s the prefix of the filename to which intermediate debug structures are dumped?

C++: protocols::drug_design::DrugDesignMover::debug_prefix(const std::string &) –> void

find_design_position(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) → int¶

Determine which residue on this pose should be designed

C++: protocols::drug_design::DrugDesignMover::find_design_position(const class core::pose::Pose &) –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.drug_design.DrugPolishMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of objectt

C++: protocols::drug_design::DrugPolishMover::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.DrugPolishMover) → str¶: C++: protocols::drug_design::DrugPolishMover::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

maxtrials(*args, **kwargs)¶

Overloaded function.

maxtrials(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> int

Returns maximum number of trials

C++: protocols::drug_design::DrugDesignMover::maxtrials() const –> unsigned long

maxtrials(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, ntrial: int) -> None

set max trials of MC trials

C++: protocols::drug_design::DrugDesignMover::maxtrials(const unsigned long) –> void

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

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

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

parse xml file

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

postfilter(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, setting: pyrosetta.rosetta.protocols.filters.Filter) → None¶

Set the filter to use after redocking

C++: protocols::drug_design::DrugDesignMover::postfilter(const class std::shared_ptr<class protocols::filters::Filter> &) –> void

prefilter(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, setting: pyrosetta.rosetta.protocols.filters.Filter) → None¶

Set the filter to use before redocking

C++: protocols::drug_design::DrugDesignMover::prefilter(const class std::shared_ptr<class protocols::filters::Filter> &) –> 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::DrugDesignMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

redocker(*args, **kwargs)¶

Overloaded function.

redocker(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> pyrosetta.rosetta.protocols.moves.Mover

Return the redocker being used

C++: protocols::drug_design::DrugDesignMover::redocker() const –> class std::shared_ptr<const class protocols::moves::Mover>

redocker(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

set redocking mover

C++: protocols::drug_design::DrugDesignMover::redocker(const class std::shared_ptr<class protocols::moves::Mover> &) –> 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

scorer(*args, **kwargs)¶

Overloaded function.

scorer(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> pyrosetta.rosetta.protocols.filters.Filter

Return the scoring filter

C++: protocols::drug_design::DrugDesignMover::scorer() const –> class std::shared_ptr<const class protocols::filters::Filter>

scorer(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, scorer: pyrosetta.rosetta.protocols.filters.Filter) -> None

Set the scoring filter in use

C++: protocols::drug_design::DrugDesignMover::scorer(const class std::shared_ptr<class protocols::filters::Filter> &) –> 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

temperature(*args, **kwargs)¶

Overloaded function.

temperature(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover) -> float

Return the scoring temperature

C++: protocols::drug_design::DrugDesignMover::temperature() const –> double

temperature(self: pyrosetta.rosetta.protocols.drug_design.DrugDesignMover, temp: float) -> None

set temperature

C++: protocols::drug_design::DrugDesignMover::temperature(const 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

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.DrugPolishMoverCreator¶

Bases: MoverCreator

_pybind11_conduit_v1_()¶

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

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

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

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

provide_xml_schema(self: pyrosetta.rosetta.protocols.moves.MoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶

Describe the schema for the Mover that this Creator is responsible for

C++: protocols::moves::MoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter¶

Bases: Filter

_pybind11_conduit_v1_()¶

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

static class_name() → str¶: C++: protocols::drug_design::HeteroHeteroBondFilter::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.drug_design.HeteroHeteroBondFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::drug_design::HeteroHeteroBondFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter, pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::drug_design::HeteroHeteroBondFilter::compute(const class core::pose::Pose &) const –> unsigned long

exclude_ates(*args, **kwargs)¶

Overloaded function.

exclude_ates(self: pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter, setting: bool) -> None

C++: protocols::drug_design::HeteroHeteroBondFilter::exclude_ates(bool) –> void

exclude_ates(self: pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter) -> bool

C++: protocols::drug_design::HeteroHeteroBondFilter::exclude_ates() const –> bool

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::drug_design::HeteroHeteroBondFilter::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::drug_design::HeteroHeteroBondFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

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

residue(*args, **kwargs)¶

Overloaded function.

residue(self: pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter, residue: str) -> None

C++: protocols::drug_design::HeteroHeteroBondFilter::residue(const std::string &) –> void

residue(self: pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter) -> str

C++: protocols::drug_design::HeteroHeteroBondFilter::residue() const –> const std::string &

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.drug_design.HeteroHeteroBondFilter, setting: int) -> None

C++: protocols::drug_design::HeteroHeteroBondFilter::threshold(unsigned long) –> void

threshold(self: pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilter) -> int

C++: protocols::drug_design::HeteroHeteroBondFilter::threshold() const –> unsigned long

class pyrosetta.rosetta.protocols.drug_design.HeteroHeteroBondFilterCreator¶

Bases: FilterCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.LigandLocationFilter¶

Bases: Filter

_pybind11_conduit_v1_()¶

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

static class_name() → str¶: C++: protocols::drug_design::LigandLocationFilter::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.drug_design.LigandLocationFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::drug_design::LigandLocationFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute_distance(self: pyrosetta.rosetta.protocols.drug_design.LigandLocationFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::drug_design::LigandLocationFilter::compute_distance(const class core::pose::Pose &) const –> double

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.LigandLocationFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::drug_design::LigandLocationFilter::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::drug_design::LigandLocationFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

report_sm(self: pyrosetta.rosetta.protocols.drug_design.LigandLocationFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::drug_design::LigandLocationFilter::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

class pyrosetta.rosetta.protocols.drug_design.LigandLocationFilterCreator¶

Bases: FilterCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.MoleculeSelection¶

Bases: pybind11_object

Members:

OriginalMol

TemplateMol

ReplaceMol

NewMol

NewMol = <MoleculeSelection.NewMol: 3>¶

OriginalMol = <MoleculeSelection.OriginalMol: 0>¶

ReplaceMol = <MoleculeSelection.ReplaceMol: 2>¶

TemplateMol = <MoleculeSelection.TemplateMol: 1>¶

_pybind11_conduit_v1_()¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution¶

Bases: pybind11_object

A class representing a substitution of a molecule from an original molecule through a pair of matched templates to a substituted molecule.

The MoleculeSubstitution can be made progressively from molecule outwards. It should contain an indexed entry for each item in all four molecules (At least for those molecules which it’s currently aware of.)

_pybind11_conduit_v1_()¶

make_match_vector(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution) → pyrosetta.rosetta.std.vector_std_pair_int_int_t¶

Reconstitute the original pairings.: This is a vector of pairs of (tdx, mdx)

C++: protocols::drug_design::MoleculeSubstitution::make_match_vector() const –> class std::vector<struct std::pair<int, int>, class std::allocator<struct std::pair<int, int> > >

rdx_is_dummy(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, rdx: int) → bool¶: C++: protocols::drug_design::MoleculeSubstitution::rdx_is_dummy(unsigned int) const –> bool

replace_dummies(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution) → pyrosetta.rosetta.utility.vector1_unsigned_int¶

The indexes for dummy atoms on the replacement template

C++: protocols::drug_design::MoleculeSubstitution::replace_dummies() const –> const class utility::vector1<unsigned int, class std::allocator<unsigned int> > &

substitution_for_idx(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, sele: pyrosetta.rosetta.protocols.drug_design.MoleculeSelection, idx: int) → pyrosetta.rosetta.protocols.drug_design.AtomSubstitution¶: C++: protocols::drug_design::MoleculeSubstitution::substitution_for_idx(enum protocols::drug_design::MoleculeSelection, unsigned int) –> class protocols::drug_design::AtomSubstitution &

substitution_for_mdx(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, idx: int) → pyrosetta.rosetta.protocols.drug_design.AtomSubstitution¶: C++: protocols::drug_design::MoleculeSubstitution::substitution_for_mdx(unsigned int) –> class protocols::drug_design::AtomSubstitution &

substitution_for_rdx(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, idx: int) → pyrosetta.rosetta.protocols.drug_design.AtomSubstitution¶: C++: protocols::drug_design::MoleculeSubstitution::substitution_for_rdx(unsigned int) –> class protocols::drug_design::AtomSubstitution &

substitution_for_tdx(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, idx: int) → pyrosetta.rosetta.protocols.drug_design.AtomSubstitution¶: C++: protocols::drug_design::MoleculeSubstitution::substitution_for_tdx(unsigned int) –> class protocols::drug_design::AtomSubstitution &

tdx_is_dummy(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, tdx: int) → bool¶: C++: protocols::drug_design::MoleculeSubstitution::tdx_is_dummy(unsigned int) const –> bool

template_dummies(self: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution) → pyrosetta.rosetta.utility.vector1_unsigned_int¶

The indexes for dummy atoms on the matching template

C++: protocols::drug_design::MoleculeSubstitution::template_dummies() const –> const class utility::vector1<unsigned int, class std::allocator<unsigned int> > &

class pyrosetta.rosetta.protocols.drug_design.NChiFilter¶

Bases: Filter

_pybind11_conduit_v1_()¶

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

static class_name() → str¶: C++: protocols::drug_design::NChiFilter::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.drug_design.NChiFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::drug_design::NChiFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.drug_design.NChiFilter, pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::drug_design::NChiFilter::compute(const class core::pose::Pose &) const –> unsigned long

exclude_proton(*args, **kwargs)¶

Overloaded function.

exclude_proton(self: pyrosetta.rosetta.protocols.drug_design.NChiFilter, setting: bool) -> None

C++: protocols::drug_design::NChiFilter::exclude_proton(bool) –> void

exclude_proton(self: pyrosetta.rosetta.protocols.drug_design.NChiFilter) -> bool

C++: protocols::drug_design::NChiFilter::exclude_proton() const –> bool

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.NChiFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::drug_design::NChiFilter::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::drug_design::NChiFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

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

residue(*args, **kwargs)¶

Overloaded function.

residue(self: pyrosetta.rosetta.protocols.drug_design.NChiFilter, residue: str) -> None

C++: protocols::drug_design::NChiFilter::residue(const std::string &) –> void

residue(self: pyrosetta.rosetta.protocols.drug_design.NChiFilter) -> str

C++: protocols::drug_design::NChiFilter::residue() const –> const std::string &

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.drug_design.NChiFilter, setting: int) -> None

C++: protocols::drug_design::NChiFilter::threshold(unsigned long) –> void

threshold(self: pyrosetta.rosetta.protocols.drug_design.NChiFilter) -> int

C++: protocols::drug_design::NChiFilter::threshold() const –> unsigned long

class pyrosetta.rosetta.protocols.drug_design.NChiFilterCreator¶

Bases: FilterCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.RDKitMetric¶

Bases: RealMetric

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

_pybind11_conduit_v1_()¶

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

_pybind11_conduit_v1_()¶

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.RDKitMetricFilter¶

Bases: Filter

_pybind11_conduit_v1_()¶

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

static class_name() → str¶: C++: protocols::drug_design::RDKitMetricFilter::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.drug_design.RDKitMetricFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::drug_design::RDKitMetricFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

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

fresh_instance(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::drug_design::RDKitMetricFilter::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

lower(*args, **kwargs)¶

Overloaded function.

lower(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter, lower: float) -> None

C++: protocols::drug_design::RDKitMetricFilter::lower(double) –> void

lower(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter) -> float

C++: protocols::drug_design::RDKitMetricFilter::lower() const –> double

metric(*args, **kwargs)¶

Overloaded function.

metric(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter, setting: str) -> None

C++: protocols::drug_design::RDKitMetricFilter::metric(const std::string &) –> void

metric(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter) -> str

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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::drug_design::RDKitMetricFilter::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::drug_design::RDKitMetricFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

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

residue(*args, **kwargs)¶

Overloaded function.

residue(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter, residue: str) -> None

C++: protocols::drug_design::RDKitMetricFilter::residue(const std::string &) –> void

residue(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter) -> str

C++: protocols::drug_design::RDKitMetricFilter::residue() const –> const std::string &

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

upper(*args, **kwargs)¶

Overloaded function.

upper(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter, upper: float) -> None

C++: protocols::drug_design::RDKitMetricFilter::upper(double) –> void

upper(self: pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilter) -> float

C++: protocols::drug_design::RDKitMetricFilter::upper() const –> double

class pyrosetta.rosetta.protocols.drug_design.RDKitMetricFilterCreator¶

Bases: FilterCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover¶

Bases: Mover

_pybind11_conduit_v1_()¶

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

_pybind11_conduit_v1_()¶

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

class pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand¶

Bases: Chemistry

_pybind11_conduit_v1_()¶

apply(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::RandomFragmentLigand::apply(class core::chemical::MutableResidueType &) –> void

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

ccbond(*args, **kwargs)¶

Overloaded function.

ccbond(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand, setting: bool) -> None

C++: protocols::drug_design::RandomFragmentLigand::ccbond(bool) –> void

ccbond(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand) -> bool

C++: protocols::drug_design::RandomFragmentLigand::ccbond() const –> bool

static class_name() → str¶: C++: protocols::drug_design::RandomFragmentLigand::class_name() –> std::string

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.: This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::RandomFragmentLigand::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

keep_atom(*args, **kwargs)¶

Overloaded function.

keep_atom(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand, keep_atom: str) -> None

C++: protocols::drug_design::RandomFragmentLigand::keep_atom(const std::string &) –> void

keep_atom(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand) -> str

C++: protocols::drug_design::RandomFragmentLigand::keep_atom() const –> std::string

keep_bigger(*args, **kwargs)¶

Overloaded function.

keep_bigger(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand, keep_bigger: bool) -> None

C++: protocols::drug_design::RandomFragmentLigand::keep_bigger(bool) –> void

keep_bigger(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigand) -> bool

C++: protocols::drug_design::RandomFragmentLigand::keep_bigger() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

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

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

class pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigandCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

create_chemistry(self: pyrosetta.rosetta.protocols.drug_design.RandomFragmentLigandCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry¶: C++: protocols::drug_design::RandomFragmentLigandCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

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

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

class pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler¶

Bases: Chemistry

class Product¶

Bases: pybind11_object

class HashFunction¶

Bases: pybind11_object

_pybind11_conduit_v1_()¶

_pybind11_conduit_v1_()¶

property fp_¶

property frags_¶

property rdmol_¶

property smiles_¶

class Reagent¶

Bases: pybind11_object

_pybind11_conduit_v1_()¶

property fp_¶

property no_¶

property rdmol_¶

property rxn_¶

_pybind11_conduit_v1_()¶

apply(self: pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::ReactionBasedAnalogSampler::apply(class core::chemical::MutableResidueType &) –> void

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

static class_name() → str¶: C++: protocols::drug_design::ReactionBasedAnalogSampler::class_name() –> std::string

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.: This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::ReactionBasedAnalogSampler::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

load_reactions(*args, **kwargs)¶

Overloaded function.

load_reactions(self: pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler, reaction_dir: str, filename: str) -> None

load reaction files from a designated path (deprecated)

C++: protocols::drug_design::ReactionBasedAnalogSampler::load_reactions(const std::string &, const std::string &) –> void

load_reactions(self: pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler, filename: str) -> None

load reactions from a single file

C++: protocols::drug_design::ReactionBasedAnalogSampler::load_reactions(const std::string &) –> void

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

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

reset_spl_ratio(self: pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSampler) → None¶: C++: protocols::drug_design::ReactionBasedAnalogSampler::reset_spl_ratio() –> void

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

class pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSamplerCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

create_chemistry(self: pyrosetta.rosetta.protocols.drug_design.ReactionBasedAnalogSamplerCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry¶: C++: protocols::drug_design::ReactionBasedAnalogSamplerCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

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

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

class pyrosetta.rosetta.protocols.drug_design.ReactionChemistry¶

Bases: Chemistry

_pybind11_conduit_v1_()¶

add_reaction(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, rxn: RDKit::ChemicalReaction, weight: float) → None¶

Add a reaction to the list of reactions known by this Chemistry.

C++: protocols::drug_design::ReactionChemistry::add_reaction(class std::shared_ptr<class RDKit::ChemicalReaction>, double) –> void

apply(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::ReactionChemistry::apply(class core::chemical::MutableResidueType &) –> void

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

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.: This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::ReactionChemistry::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

reaction_file(*args, **kwargs)¶

Overloaded function.

reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str) -> None
reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str, append: bool) -> None

The file which contains the reactions which to use.

C++: protocols::drug_design::ReactionChemistry::reaction_file(std::string, bool) –> void

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

class pyrosetta.rosetta.protocols.drug_design.ReactionFragment¶

Bases: ReactionChemistry

_pybind11_conduit_v1_()¶

add_reaction(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment, rxn: RDKit::ChemicalReaction, weight: float) → None¶

Add a reaction to the list of reactions to use.: Reaction should be written in the synthetic direction with a single product

C++: protocols::drug_design::ReactionFragment::add_reaction(class std::shared_ptr<class RDKit::ChemicalReaction>, double) –> void

apply(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::ReactionFragment::apply(class core::chemical::MutableResidueType &) –> void

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

static class_name() → str¶: C++: protocols::drug_design::ReactionFragment::class_name() –> std::string

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.: This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::ReactionFragment::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

keep_atom(*args, **kwargs)¶

Overloaded function.

keep_atom(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment, keep_atom: str) -> None

C++: protocols::drug_design::ReactionFragment::keep_atom(const std::string &) –> void

keep_atom(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment) -> str

C++: protocols::drug_design::ReactionFragment::keep_atom() const –> std::string

keep_bigger(*args, **kwargs)¶

Overloaded function.

keep_bigger(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment, setting: bool) -> None

C++: protocols::drug_design::ReactionFragment::keep_bigger(bool) –> void

keep_bigger(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment) -> bool

C++: protocols::drug_design::ReactionFragment::keep_bigger() const –> bool

keep_random(*args, **kwargs)¶

Overloaded function.

keep_random(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment, setting: bool) -> None

C++: protocols::drug_design::ReactionFragment::keep_random(bool) –> void

keep_random(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragment) -> bool

C++: protocols::drug_design::ReactionFragment::keep_random() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

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

reaction_file(*args, **kwargs)¶

Overloaded function.

reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str) -> None
reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str, append: bool) -> None

The file which contains the reactions which to use.

C++: protocols::drug_design::ReactionChemistry::reaction_file(std::string, bool) –> void

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

class pyrosetta.rosetta.protocols.drug_design.ReactionFragmentCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

create_chemistry(self: pyrosetta.rosetta.protocols.drug_design.ReactionFragmentCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry¶: C++: protocols::drug_design::ReactionFragmentCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

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

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

class pyrosetta.rosetta.protocols.drug_design.ReactionGrow¶

Bases: ReactionChemistry

_pybind11_conduit_v1_()¶

add_reaction(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow, rxn: RDKit::ChemicalReaction, weight: float) → None¶

Add a reaction to the list of reactions to use.: Reaction should be written in the synthetic direction with a single product

C++: protocols::drug_design::ReactionGrow::add_reaction(class std::shared_ptr<class RDKit::ChemicalReaction>, double) –> void

apply(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::ReactionGrow::apply(class core::chemical::MutableResidueType &) –> void

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

static class_name() → str¶: C++: protocols::drug_design::ReactionGrow::class_name() –> std::string

fragment_database(*args, **kwargs)¶

Overloaded function.

fragment_database(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow, filename: str) -> None
fragment_database(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow, filename: str, append: bool) -> None

The file which contains the fragments to add to input residue type.

C++: protocols::drug_design::ReactionGrow::fragment_database(std::string, bool) –> void

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.: This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::ReactionGrow::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

prefilter_fragments(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow) → None¶

Reduce the fragment set to those which are compatible with the reactions.

Discarded fragments are discarded permanently. Only call after all reactions are finalized for this Chemistry

C++: protocols::drug_design::ReactionGrow::prefilter_fragments() –> void

prefilter_reactions(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow) → None¶

Filter reaction list for those compatible with the given fragments

Discarded reactions will be discarded permanently. Only call with the finalized fragment list.

C++: protocols::drug_design::ReactionGrow::prefilter_reactions() –> void

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

reaction_file(*args, **kwargs)¶

Overloaded function.

reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str) -> None
reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str, append: bool) -> None

The file which contains the reactions which to use.

C++: protocols::drug_design::ReactionChemistry::reaction_file(std::string, bool) –> void

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

weight_by_property(*args, **kwargs)¶

Overloaded function.

weight_by_property(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow, setting: str) -> None

If not empty, use property weighting based on the given property.

C++: protocols::drug_design::ReactionGrow::weight_by_property(const std::string &) –> void

weight_by_property(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrow) -> str

C++: protocols::drug_design::ReactionGrow::weight_by_property() const –> const std::string &

class pyrosetta.rosetta.protocols.drug_design.ReactionGrowCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

create_chemistry(self: pyrosetta.rosetta.protocols.drug_design.ReactionGrowCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry¶: C++: protocols::drug_design::ReactionGrowCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

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

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

class pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransform¶

Bases: ReactionChemistry

_pybind11_conduit_v1_()¶

add_reaction(self: pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransform, rxn: RDKit::ChemicalReaction, weight: float) → None¶

Add a reaction to the list of reactions to use.: Reaction should be written in the synthetic direction with a single reactant and product

C++: protocols::drug_design::ReactionMultiTransform::add_reaction(class std::shared_ptr<class RDKit::ChemicalReaction>, double) –> void

apply(self: pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransform, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::ReactionMultiTransform::apply(class core::chemical::MutableResidueType &) –> void

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

static class_name() → str¶: C++: protocols::drug_design::ReactionMultiTransform::class_name() –> std::string

get_additional_output(self: pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransform) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.

C++: protocols::drug_design::ReactionMultiTransform::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransform) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::ReactionMultiTransform::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransform) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: protocols::drug_design::ReactionMultiTransform::has_additional_output() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

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

reaction_file(*args, **kwargs)¶

Overloaded function.

reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str) -> None
reaction_file(self: pyrosetta.rosetta.protocols.drug_design.ReactionChemistry, filename: str, append: bool) -> None

The file which contains the reactions which to use.

C++: protocols::drug_design::ReactionChemistry::reaction_file(std::string, bool) –> void

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

class pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransformCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

create_chemistry(self: pyrosetta.rosetta.protocols.drug_design.ReactionMultiTransformCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry¶: C++: protocols::drug_design::ReactionMultiTransformCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

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

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

class pyrosetta.rosetta.protocols.drug_design.SAScoreData¶

Bases: SingletonBase_protocols_drug_design_SAScoreData_t

_pybind11_conduit_v1_()¶

static get_instance() → protocols::drug_design::SAScoreData¶: C++: utility::SingletonBase<protocols::drug_design::SAScoreData>::get_instance() –> class protocols::drug_design::SAScoreData *

class pyrosetta.rosetta.protocols.drug_design.SAScoreFilter¶

Bases: Filter

_pybind11_conduit_v1_()¶

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

calculate_rdkit(self: pyrosetta.rosetta.protocols.drug_design.SAScoreFilter, mol: pyrosetta.rosetta.RDKit.ROMol) → float¶: C++: protocols::drug_design::SAScoreFilter::calculate_rdkit(class RDKit::ROMol &) const –> double

static class_name() → str¶: C++: protocols::drug_design::SAScoreFilter::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.drug_design.SAScoreFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::drug_design::SAScoreFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.drug_design.SAScoreFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::drug_design::SAScoreFilter::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::drug_design::SAScoreFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

report_sm(self: pyrosetta.rosetta.protocols.drug_design.SAScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::drug_design::SAScoreFilter::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.drug_design.SAScoreFilter) -> float

C++: protocols::drug_design::SAScoreFilter::threshold() const –> double

threshold(self: pyrosetta.rosetta.protocols.drug_design.SAScoreFilter, setting: float) -> None

C++: protocols::drug_design::SAScoreFilter::threshold(double) –> void

class pyrosetta.rosetta.protocols.drug_design.SAScoreFilterCreator¶

Bases: FilterCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.drug_design.SubstituentReplace¶

Bases: Chemistry

H_as_dummy(*args, **kwargs)¶

Overloaded function.

H_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, setting: float) -> None

Will hydrogens in the input be converted to dummy stubs?

C++: protocols::drug_design::SubstituentReplace::H_as_dummy(double) –> void

H_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace) -> bool

C++: protocols::drug_design::SubstituentReplace::H_as_dummy() const –> bool

V_as_dummy(*args, **kwargs)¶

Overloaded function.

V_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, setting: float) -> None

Will V atoms (Vanadium, but used commonly in Rosetta for “virtual” designations): in the input be converted to dummy stubs?

C++: protocols::drug_design::SubstituentReplace::V_as_dummy(double) –> void

V_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace) -> bool

C++: protocols::drug_design::SubstituentReplace::V_as_dummy() const –> bool

_pybind11_conduit_v1_()¶

apply(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::SubstituentReplace::apply(class core::chemical::MutableResidueType &) –> void

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

static class_name() → str¶: C++: protocols::drug_design::SubstituentReplace::class_name() –> std::string

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.: This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::SubstituentReplace::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

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

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

substituents_database(*args, **kwargs)¶

Overloaded function.

substituents_database(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, filename: str) -> None
substituents_database(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, filename: str, append: bool) -> None

The file which contains the substituents to add to input residue type.

C++: protocols::drug_design::SubstituentReplace::substituents_database(std::string, bool) –> void

template_database(*args, **kwargs)¶

Overloaded function.

template_database(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, filename: str) -> None
template_database(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, filename: str, append: bool) -> None

The file which contains the templates to search for to add to input residue type.

C++: protocols::drug_design::SubstituentReplace::template_database(std::string, bool) –> void

weight_by_property(*args, **kwargs)¶

Overloaded function.

weight_by_property(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace, setting: str) -> None

If not empty, use property weighting based on the given property.

C++: protocols::drug_design::SubstituentReplace::weight_by_property(const std::string &) –> void

weight_by_property(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplace) -> str

C++: protocols::drug_design::SubstituentReplace::weight_by_property() const –> const std::string &

class pyrosetta.rosetta.protocols.drug_design.SubstituentReplaceCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

create_chemistry(self: pyrosetta.rosetta.protocols.drug_design.SubstituentReplaceCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry¶: C++: protocols::drug_design::SubstituentReplaceCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

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

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

class pyrosetta.rosetta.protocols.drug_design.SubstructureReplace¶

Bases: Chemistry

H_as_dummy(*args, **kwargs)¶

Overloaded function.

H_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace, setting: float) -> None

Will hydrogens in the input be converted to dummy stubs?

C++: protocols::drug_design::SubstructureReplace::H_as_dummy(double) –> void

H_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace) -> bool

C++: protocols::drug_design::SubstructureReplace::H_as_dummy() const –> bool

V_as_dummy(*args, **kwargs)¶

Overloaded function.

V_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace, setting: float) -> None

Will V atoms (Vanadium, but used commonly in Rosetta for “virtual” designations): in the input be converted to dummy stubs?

C++: protocols::drug_design::SubstructureReplace::V_as_dummy(double) –> void

V_as_dummy(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace) -> bool

C++: protocols::drug_design::SubstructureReplace::V_as_dummy() const –> bool

_pybind11_conduit_v1_()¶

apply(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace, : pyrosetta.rosetta.core.chemical.MutableResidueType) → None¶: C++: protocols::drug_design::SubstructureReplace::apply(class core::chemical::MutableResidueType &) –> void

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

static class_name() → str¶: C++: protocols::drug_design::SubstructureReplace::class_name() –> std::string

distance_threshold(*args, **kwargs)¶

Overloaded function.

distance_threshold(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace, setting: float) -> None

The largest distance at which two dummy stubs on the fragments will be considered equivalent.

C++: protocols::drug_design::SubstructureReplace::distance_threshold(double) –> void

distance_threshold(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace) -> float

C++: protocols::drug_design::SubstructureReplace::distance_threshold() const –> double

get_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.MutableResidueType¶

Get additional generated ResidueTypes, if any.: This allows for 1-to-many Chemistries

C++: core::chemical::modifications::ChemistryBase::get_additional_output() –> class std::shared_ptr<class core::chemical::MutableResidueType>

get_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus¶

What was the status of the last call to apply()/get_additional_output()

C++: core::chemical::modifications::ChemistryBase::get_last_status() const –> enum core::chemical::modifications::ChemistryStatus

get_mapping(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶: C++: protocols::drug_design::SubstructureReplace::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → bool¶

Are there alternate ResidueTypes which are availible from the last time we called apply?: (That is, will get_addtional_output() return non-null?)

C++: core::chemical::modifications::ChemistryBase::has_additional_output() const –> bool

name(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → str¶

Return the name of this Chemistry object

C++: core::chemical::modifications::ChemistryBase::name() const –> std::string

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

Initialize any data members of this instance from an input tag: and a DataMap object

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

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

set_last_status(self: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus) → None¶

Set the status of the chemistry object

C++: core::chemical::modifications::ChemistryBase::set_last_status(enum core::chemical::modifications::ChemistryStatus) –> void

substructure_database(*args, **kwargs)¶

Overloaded function.

substructure_database(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace, filename: str) -> None
substructure_database(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace, filename: str, append: bool) -> None

The file which contains the fragments to add to input residue type.

C++: protocols::drug_design::SubstructureReplace::substructure_database(std::string, bool) –> void

weight_by_property(*args, **kwargs)¶

Overloaded function.

weight_by_property(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace, setting: str) -> None

If not empty, use property weighting based on the given property.

C++: protocols::drug_design::SubstructureReplace::weight_by_property(const std::string &) –> void

weight_by_property(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplace) -> str

C++: protocols::drug_design::SubstructureReplace::weight_by_property() const –> const std::string &

class pyrosetta.rosetta.protocols.drug_design.SubstructureReplaceCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

create_chemistry(self: pyrosetta.rosetta.protocols.drug_design.SubstructureReplaceCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry¶: C++: protocols::drug_design::SubstructureReplaceCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

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

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

pyrosetta.rosetta.protocols.drug_design.bond_is_in_ring(rdmol: pyrosetta.rosetta.RDKit.ROMol, atm1: int, atm2: int) → bool¶

Is the bond between the atoms in a ring?

C++: protocols::drug_design::bond_is_in_ring(const class RDKit::ROMol &, unsigned int, unsigned int) –> bool

pyrosetta.rosetta.protocols.drug_design.copy_attached_atoms(*args, **kwargs)¶

Overloaded function.

copy_attached_atoms(molsub: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, source: pyrosetta.rosetta.protocols.drug_design.MoleculeSelection, transform: pyrosetta.rosetta.RDGeom.Transform3D, start: int) -> None
copy_attached_atoms(molsub: pyrosetta.rosetta.protocols.drug_design.MoleculeSubstitution, source: pyrosetta.rosetta.protocols.drug_design.MoleculeSelection, transform: pyrosetta.rosetta.RDGeom.Transform3D, start: int, skip: int) -> None

Copies all atom and bonds attached to start in the source molecule to the new molecule.: If skip is a valid index, it will be supressed in the source molecule, and will not be counted for copying or for attachment purposes The transform is applied to the coordinates of the atom to get the coordinates of the new atom.

C++: protocols::drug_design::copy_attached_atoms(class protocols::drug_design::MoleculeSubstitution &, enum protocols::drug_design::MoleculeSelection, const class RDGeom::Transform3D &, unsigned int, unsigned int) –> void

pyrosetta.rosetta.protocols.drug_design.find_dummies(mol: pyrosetta.rosetta.RDKit.ROMol, dummy_list: pyrosetta.rosetta.utility.vector1_unsigned_int) → None¶

Populate the list with the index of all the dummies in the molecule

Existing contents will be cleared.

C++: protocols::drug_design::find_dummies(const class RDKit::ROMol &, class utility::vector1<unsigned int, class std::allocator<unsigned int> > &) –> void

pyrosetta.rosetta.protocols.drug_design.get_bonded_atom(mol: pyrosetta.rosetta.RDKit.ROMol, idx: int) → int¶

Get the atom number of the atom bonded to idx (it’s the first atom)

C++: protocols::drug_design::get_bonded_atom(const class RDKit::ROMol &, unsigned int) –> unsigned int

pyrosetta.rosetta.protocols.drug_design.get_first_bond(mol: pyrosetta.rosetta.RDKit.ROMol, idx: int) → pyrosetta.rosetta.RDKit.Bond¶

Get the RDKit bond of the first bond to the given atom

C++: protocols::drug_design::get_first_bond(const class RDKit::ROMol &, unsigned int) –> const class RDKit::Bond &

pyrosetta.rosetta.protocols.drug_design.get_first_bondtype(*args, **kwargs)¶

Overloaded function.

get_first_bondtype(mol: pyrosetta.rosetta.RDKit.ROMol, atom: pyrosetta.rosetta.RDKit.Atom) -> RDKit::Bond::BondType

Get the RDKit bond type of the first bond to atom

C++: protocols::drug_design::get_first_bondtype(const class RDKit::ROMol &, const class RDKit::Atom *) –> RDKit::Bond::BondType

get_first_bondtype(mol: pyrosetta.rosetta.RDKit.ROMol, idx: int) -> RDKit::Bond::BondType

Get the RDKit bond type of the first bond to the given atom

C++: protocols::drug_design::get_first_bondtype(const class RDKit::ROMol &, unsigned int) –> RDKit::Bond::BondType

pyrosetta.rosetta.protocols.drug_design.is_dummy(mol: pyrosetta.rosetta.RDKit.ROMol, idx: int) → bool¶

Is the given atom a dummy (atom number 0)?

C++: protocols::drug_design::is_dummy(const class RDKit::ROMol &, unsigned int) –> bool

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