rotamer_gen¶

Bindings for protocols::rotamer_gen namespace

class pyrosetta.rosetta.protocols.rotamer_gen.FragmentRotamers¶

Bases: Chemistry

_pybind11_conduit_v1_()¶

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

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

static class_name() → str¶: C++: protocols::rotamer_gen::FragmentRotamers::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.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶

Get the vertex mapping that was used for the last apply() or get_additional_output(): This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping.

C++: core::chemical::modifications::ChemistryBase::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.rotamer_gen.FragmentRotamers, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::rotamer_gen::FragmentRotamers::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::rotamer_gen::FragmentRotamers::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.rotamer_gen.FragmentRotamersCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

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

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

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

class pyrosetta.rosetta.protocols.rotamer_gen.RDKitRotamers¶

Bases: Chemistry

_pybind11_conduit_v1_()¶

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

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

static class_name() → str¶: C++: protocols::rotamer_gen::RDKitRotamers::class_name() –> std::string

static generate_conformers(*args, **kwargs)¶

Overloaded function.

generate_conformers(rsdtype: pyrosetta.rosetta.core.chemical.MutableResidueType, nconf: int) -> pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t
generate_conformers(rsdtype: pyrosetta.rosetta.core.chemical.MutableResidueType, nconf: int, minimize: bool) -> pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t

C++: protocols::rotamer_gen::RDKitRotamers::generate_conformers(const class core::chemical::MutableResidueType &, unsigned long, bool) –> class utility::vector1<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<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.core.chemical.modifications.ChemistryBase) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶

Get the vertex mapping that was used for the last apply() or get_additional_output(): This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping.

C++: core::chemical::modifications::ChemistryBase::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.rotamer_gen.RDKitRotamers, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::rotamer_gen::RDKitRotamers::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::rotamer_gen::RDKitRotamers::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.rotamer_gen.RDKitRotamersCreator¶

Bases: ChemistryCreator

_pybind11_conduit_v1_()¶

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

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

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

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