chemistries

Bindings for protocols::chemistries namespace

class pyrosetta.rosetta.protocols.chemistries.Chemistry

Bases: ChemistryBase

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.chemistries.Chemistry, : pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

Modify the passed ResidueType

if you have a Pose, call the one which takes the Pose context

C++: protocols::chemistries::Chemistry::apply(class core::chemical::MutableResidueType &) –> void

2. apply(self: pyrosetta.rosetta.protocols.chemistries.Chemistry, restype: pyrosetta.rosetta.core.chemical.MutableResidueType, : pyrosetta.rosetta.core.pose.Pose) -> None

Modify the passed ResidueType, context sensitive

By default, not context sensitive - will just redirect to the other function.

C++: protocols::chemistries::Chemistry::apply(class core::chemical::MutableResidueType &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.chemistries.Chemistry, : pyrosetta.rosetta.protocols.chemistries.Chemistry) → pyrosetta.rosetta.protocols.chemistries.Chemistry

C++: protocols::chemistries::Chemistry::operator=(const class protocols::chemistries::Chemistry &) –> class protocols::chemistries::Chemistry &

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.chemistries.Chemistry, : 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::chemistries::Chemistry::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> 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.chemistries.ChemistryCreator

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.chemistries.ChemistryCreator, : pyrosetta.rosetta.protocols.chemistries.ChemistryCreator) → pyrosetta.rosetta.protocols.chemistries.ChemistryCreator

C++: protocols::chemistries::ChemistryCreator::operator=(const class protocols::chemistries::ChemistryCreator &) –> class protocols::chemistries::ChemistryCreator &

create_chemistry(self: pyrosetta.rosetta.protocols.chemistries.ChemistryCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry

C++: protocols::chemistries::ChemistryCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

keyname(self: pyrosetta.rosetta.protocols.chemistries.ChemistryCreator) → str

C++: protocols::chemistries::ChemistryCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.chemistries.ChemistryCreator, : utility::tag::XMLSchemaDefinition) → None

Define the structure of the XML file for the Chemistry that this

ChemistryCreator instantiates using the XML Schema language.

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

class pyrosetta.rosetta.protocols.chemistries.ChemistryFactory

Bases: SingletonBase_protocols_chemistries_ChemistryFactory_t

static chemistry_xml_schema_group_name() → str

C++: protocols::chemistries::ChemistryFactory::chemistry_xml_schema_group_name() –> std::string

define_chemistry_xml_schema(self: pyrosetta.rosetta.protocols.chemistries.ChemistryFactory, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::chemistries::ChemistryFactory::define_chemistry_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.protocols.chemistries.ChemistryFactory, creator: pyrosetta.rosetta.protocols.chemistries.ChemistryCreator) → None

C++: protocols::chemistries::ChemistryFactory::factory_register(class std::shared_ptr<class protocols::chemistries::ChemistryCreator>) –> void

static get_instance() → protocols::chemistries::ChemistryFactory

C++: utility::SingletonBase<protocols::chemistries::ChemistryFactory>::get_instance() –> class protocols::chemistries::ChemistryFactory *

has_type(self: pyrosetta.rosetta.protocols.chemistries.ChemistryFactory, : str) → bool

C++: protocols::chemistries::ChemistryFactory::has_type(const std::string &) const –> bool

new_chemistry(self: pyrosetta.rosetta.protocols.chemistries.ChemistryFactory, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.chemistries.Chemistry

C++: protocols::chemistries::ChemistryFactory::new_chemistry(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

set_throw_on_double_registration(self: pyrosetta.rosetta.protocols.chemistries.ChemistryFactory) → None

C++: protocols::chemistries::ChemistryFactory::set_throw_on_double_registration() –> void

class pyrosetta.rosetta.protocols.chemistries.ChemistryLoader

Bases: DataLoader

A class for loading arbitrary data into the XML chemistries’s basic::datacache::DataMap.

assign(self: pyrosetta.rosetta.protocols.chemistries.ChemistryLoader, : pyrosetta.rosetta.protocols.chemistries.ChemistryLoader) → pyrosetta.rosetta.protocols.chemistries.ChemistryLoader

C++: protocols::chemistries::ChemistryLoader::operator=(const class protocols::chemistries::ChemistryLoader &) –> class protocols::chemistries::ChemistryLoader &

static chemistry_loader_ct_namer(element_name: str) → str

C++: protocols::chemistries::ChemistryLoader::chemistry_loader_ct_namer(const std::string &) –> std::string

load_data(self: pyrosetta.rosetta.protocols.chemistries.ChemistryLoader, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

The ChemistryLoader will create named Chemistrys and load them into the basic::datacache::DataMap

C++: protocols::chemistries::ChemistryLoader::load_data(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

static loader_name() → str

C++: protocols::chemistries::ChemistryLoader::loader_name() –> std::string

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::chemistries::ChemistryLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator

Bases: DataLoaderCreator

assign(self: pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator, : pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator) → pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator

C++: protocols::chemistries::ChemistryLoaderCreator::operator=(const class protocols::chemistries::ChemistryLoaderCreator &) –> class protocols::chemistries::ChemistryLoaderCreator &

create_loader(self: pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator) → pyrosetta.rosetta.protocols.parser.DataLoader

C++: protocols::chemistries::ChemistryLoaderCreator::create_loader() const –> class std::shared_ptr<class protocols::parser::DataLoader>

keyname(self: pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator) → str

C++: protocols::chemistries::ChemistryLoaderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

schema_ct_naming_function(self: pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator) → std::function<std::string (std::string const&)>

C++: protocols::chemistries::ChemistryLoaderCreator::schema_ct_naming_function() const –> class std::function<std::string (const std::string &)>

class pyrosetta.rosetta.protocols.chemistries.PatchChemistry

Bases: Chemistry

add_patch_operation_line(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistry, line: str) → None

C++: protocols::chemistries::PatchChemistry::add_patch_operation_line(const std::string &) –> void

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistry, : pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

C++: protocols::chemistries::PatchChemistry::apply(class core::chemical::MutableResidueType &) –> void

2. apply(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistry, restype: pyrosetta.rosetta.core.chemical.MutableResidueType, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::chemistries::PatchChemistry::apply(class core::chemical::MutableResidueType &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistry, : pyrosetta.rosetta.protocols.chemistries.PatchChemistry) → pyrosetta.rosetta.protocols.chemistries.PatchChemistry

C++: protocols::chemistries::PatchChemistry::operator=(const class protocols::chemistries::PatchChemistry &) –> class protocols::chemistries::PatchChemistry &

static class_name() → str

C++: protocols::chemistries::PatchChemistry::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.chemistries.PatchChemistry) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t

C++: protocols::chemistries::PatchChemistry::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.chemistries.PatchChemistry, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

patch_file(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistry, setting: str) → None

C++: protocols::chemistries::PatchChemistry::patch_file(const std::string &) –> void

patch_name(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistry, setting: str) → None

C++: protocols::chemistries::PatchChemistry::patch_name(const std::string &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::chemistries::PatchChemistry::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.chemistries.PatchChemistryCreator

Bases: ChemistryCreator

assign(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator, : pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator) → pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator

C++: protocols::chemistries::PatchChemistryCreator::operator=(const class protocols::chemistries::PatchChemistryCreator &) –> class protocols::chemistries::PatchChemistryCreator &

create_chemistry(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator) → pyrosetta.rosetta.protocols.chemistries.Chemistry

C++: protocols::chemistries::PatchChemistryCreator::create_chemistry() const –> class std::shared_ptr<class protocols::chemistries::Chemistry>

keyname(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator) → str

C++: protocols::chemistries::PatchChemistryCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator, : utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry

Bases: Chemistry

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry, : pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

C++: protocols::chemistries::WrappedBaseChemistry::apply(class core::chemical::MutableResidueType &) –> void

2. apply(self: pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry, : pyrosetta.rosetta.core.chemical.MutableResidueType, : pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::chemistries::WrappedBaseChemistry::apply(class core::chemical::MutableResidueType &, const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry, : pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry) → pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry

C++: protocols::chemistries::WrappedBaseChemistry::operator=(const class protocols::chemistries::WrappedBaseChemistry &) –> class protocols::chemistries::WrappedBaseChemistry &

get_additional_output(self: pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry) → pyrosetta.rosetta.core.chemical.MutableResidueType

C++: protocols::chemistries::WrappedBaseChemistry::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.chemistries.WrappedBaseChemistry) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t

C++: protocols::chemistries::WrappedBaseChemistry::get_mapping() const –> class core::chemical::AtomRefMapping<void *, void *>

has_additional_output(self: pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry) → bool

C++: protocols::chemistries::WrappedBaseChemistry::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.chemistries.WrappedBaseChemistry, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

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

set_subchemistry(self: pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry, setting: pyrosetta.rosetta.core.chemical.modifications.ChemistryBase) → None

C++: protocols::chemistries::WrappedBaseChemistry::set_subchemistry(class std::shared_ptr<class core::chemical::modifications::ChemistryBase>) –> void

pyrosetta.rosetta.protocols.chemistries.complex_type_name_for_chemistry(chem_type: str) → str

Used to name the xs:complexType for a chemistry that is

created with the “chem_type” tag-name. Does so by prepending “chemistry_” and appending “Type” to the “chem_type”.

C++: protocols::chemistries::complex_type_name_for_chemistry(const std::string &) –> std::string

pyrosetta.rosetta.protocols.chemistries.xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, chem_type: str, chem_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

Define the XML schema definition for a Chemistry which

possibly contains attributes/options, but no sub-tags

C++: protocols::chemistries::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.chemistries.xsd_type_definition_w_attributes_and_repeatable_subelements(xsd: utility::tag::XMLSchemaDefinition, chem_type: str, description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, subelements: utility::tag::XMLSchemaSimpleSubelementList) → None

Define the XML schema definition for a Chemistry that

contains subtags and attributes (aka options).

C++: protocols::chemistries::xsd_type_definition_w_attributes_and_repeatable_subelements(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const class utility::tag::XMLSchemaSimpleSubelementList &) –> void