rdf¶

Bindings for protocols::ligand_docking::rdf namespace

class pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData¶

Bases: pybind11_object

a simple struct for storing information needed to compute an RDF interaction

assign(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData, : pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData) → pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData¶: C++: protocols::ligand_docking::rdf::AtomPairData::operator=(const struct protocols::ligand_docking::rdf::AtomPairData &) –> struct protocols::ligand_docking::rdf::AtomPairData &

property atom_atom_distance¶

property ligand_atom¶

property ligand_atom_charge¶

property ligand_atom_coords¶

property ligand_atom_id¶

property ligand_atom_type¶

property protein_atom¶

property protein_atom_charge¶

property protein_atom_coords¶

property protein_atom_id¶

property protein_atom_type¶

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

Bases: pybind11_object

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, : pyrosetta.rosetta.core.pose.Pose) → None¶

If you have code that needs to be run once per pose (for data caching, etc), put it here.

C++: protocols::ligand_docking::rdf::RDFBase::preamble(class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator¶

Bases: RDFFunctionCreator

Creator to geneate a new RDFBinaryHbondFunction

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

return a pointer to a newly created RDFBinaryHbondFunction

C++: protocols::ligand_docking::rdf::RDFBinaryHbondCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator) → str¶

return the name of the RDFBinaryHbondFunction

C++: protocols::ligand_docking::rdf::RDFBinaryHbondCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction¶

Bases: RDFBase

RDFBinaryHbondFunction returns 1.0 if a pair of atoms are donor and acceptor, 0.0 otherwise.

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

static class_name() → str¶: C++: protocols::ligand_docking::rdf::RDFBinaryHbondFunction::class_name() –> std::string

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags for RDFBinaryHbondFunction tag

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, : pyrosetta.rosetta.core.pose.Pose) → None¶

If you have code that needs to be run once per pose (for data caching, etc), put it here.

C++: protocols::ligand_docking::rdf::RDFBase::preamble(class core::pose::Pose &) –> void

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

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction¶

Bases: RDFBase

RDFBinaryOrbitalFunction returns 1 for various orbital pairs and 0 otherwise

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

static class_name() → str¶: C++: protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::class_name() –> std::string

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags for RDFOrbitalFunction tag

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

update residue neighbors and cache current pose

C++: protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::preamble(class core::pose::Pose &) –> void

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

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator¶

Bases: RDFFunctionCreator

Creator to geneate a new RDFBinaryOrbitalFunction

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

return a pointer to a newly created RDFBinaryOrbitalFunction

C++: protocols::ligand_docking::rdf::RDFBinaryOrbitalFunctionCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator) → str¶

return the name of the RDFBinaryOrbitalFunction

C++: protocols::ligand_docking::rdf::RDFBinaryOrbitalFunctionCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator¶

Bases: RDFFunctionCreator

Creator to geneate a new RDFChargeFunction

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

return a pointer to a newly created RDFElecFunction

C++: protocols::ligand_docking::rdf::RDFChargeCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator) → str¶

return the name of the RDFEtableFunction

C++: protocols::ligand_docking::rdf::RDFChargeCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction¶

Bases: RDFBase

RDFChargeFunction computes fa_elec for a pair of atoms

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

static class_name() → str¶: C++: protocols::ligand_docking::rdf::RDFChargeFunction::class_name() –> std::string

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags for RDFElecFunction tag

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, : pyrosetta.rosetta.core.pose.Pose) → None¶

If you have code that needs to be run once per pose (for data caching, etc), put it here.

C++: protocols::ligand_docking::rdf::RDFBase::preamble(class core::pose::Pose &) –> void

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

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator¶

Bases: RDFFunctionCreator

Creator to geneate a new RDFElecFunction

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

return a pointer to a newly created RDFElecFunction

C++: protocols::ligand_docking::rdf::RDFElecCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator) → str¶

return the name of the RDFEtableFunction

C++: protocols::ligand_docking::rdf::RDFElecCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction¶

Bases: RDFBase

RDFElecFunction computes fa_elec for a pair of atoms

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

static class_name() → str¶: C++: protocols::ligand_docking::rdf::RDFElecFunction::class_name() –> std::string

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags for RDFElecFunction tag

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, : pyrosetta.rosetta.core.pose.Pose) → None¶

If you have code that needs to be run once per pose (for data caching, etc), put it here.

C++: protocols::ligand_docking::rdf::RDFBase::preamble(class core::pose::Pose &) –> void

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

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator¶

Bases: RDFFunctionCreator

Creator to geneate a new RDFEtableFunction

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

return a pointer to a newly created RDFEtableFunction

C++: protocols::ligand_docking::rdf::RDFEtableCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator) → str¶

return the name of the RDFEtableFunction

C++: protocols::ligand_docking::rdf::RDFEtableCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction¶

Bases: RDFBase

RDFEtableFunction computes fa_sol,fa_rep,fa_atr for a pair of atoms

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

static class_name() → str¶: C++: protocols::ligand_docking::rdf::RDFEtableFunction::class_name() –> std::string

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags for RDFEtableFunction tag

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, : pyrosetta.rosetta.core.pose.Pose) → None¶

If you have code that needs to be run once per pose (for data caching, etc), put it here.

C++: protocols::ligand_docking::rdf::RDFBase::preamble(class core::pose::Pose &) –> void

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

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator¶

Bases: pybind11_object

The Creator class is responsible for creating a particular RDF Function class.

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶: C++: protocols::ligand_docking::rdf::RDFFunctionCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator) → str¶: C++: protocols::ligand_docking::rdf::RDFFunctionCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory¶

Bases: SingletonBase_protocols_ligand_docking_rdf_RDFFunctionFactory_t

Create RDFFunctions

define_rdf_function_group(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::ligand_docking::rdf::RDFFunctionFactory::define_rdf_function_group(class utility::tag::XMLSchemaDefinition &) –> void

factory_register(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory, creator: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator) → None¶: C++: protocols::ligand_docking::rdf::RDFFunctionFactory::factory_register(class std::shared_ptr<const class protocols::ligand_docking::rdf::RDFFunctionCreator>) –> void

get_all_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::ligand_docking::rdf::RDFFunctionFactory::get_all_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

static get_instance() → protocols::ligand_docking::rdf::RDFFunctionFactory¶: C++: utility::SingletonBase<protocols::ligand_docking::rdf::RDFFunctionFactory>::get_instance() –> class protocols::ligand_docking::rdf::RDFFunctionFactory *

get_rdf_function(*args, **kwargs)¶

Overloaded function.

get_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory, type_name: str) -> pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase

C++: protocols::ligand_docking::rdf::RDFFunctionFactory::get_rdf_function(const std::string &) –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

get_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase

convienence header for use with RosettaScripts parse_my_tag interface

C++: protocols::ligand_docking::rdf::RDFFunctionFactory::get_rdf_function(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

static rdf_function_ct_namer(: str) → str¶: C++: protocols::ligand_docking::rdf::RDFFunctionFactory::rdf_function_ct_namer(std::string) –> std::string

static rdf_function_group_name() → str¶: C++: protocols::ligand_docking::rdf::RDFFunctionFactory::rdf_function_group_name() –> std::string

static xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, name: str, attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str) → None¶: C++: protocols::ligand_docking::rdf::RDFFunctionFactory::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, std::string, class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, std::string) –> void

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator¶

Bases: RDFFunctionCreator

Creator to geneate a new RDFHbondFunction

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

return a pointer to a newly created RDFHbondFunction

C++: protocols::ligand_docking::rdf::RDFHbondCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator) → str¶

return the name of the RDFHbondFunction

C++: protocols::ligand_docking::rdf::RDFHbondCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction¶

Bases: RDFBase

RDFHbondFunction computes h-bonding energy for a pair of atoms.

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

static class_name() → str¶: C++: protocols::ligand_docking::rdf::RDFHbondFunction::class_name() –> std::string

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags for RDFHbondFunction tag

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setup hbond database for each pose

C++: protocols::ligand_docking::rdf::RDFHbondFunction::preamble(class core::pose::Pose &) –> void

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

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction¶

Bases: RDFBase

RDFOrbitalFunction computes the orbital score energies of a pair of atoms

class FunctionSign¶

Bases: pybind11_object

an enum of the possible states that a signed RDF can have

Members:

LigandPlusProteinMinus

LigandMinusProteinPlus

SameSign

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

property name¶

property value¶

LigandMinusProteinPlus = <FunctionSign.LigandMinusProteinPlus: 1>¶

LigandPlusProteinMinus = <FunctionSign.LigandPlusProteinMinus: 0>¶

SameSign = <FunctionSign.SameSign: 2>¶

add_function_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase, name: str) → None¶

add a function name to the list

C++: protocols::ligand_docking::rdf::RDFBase::add_function_name(const std::string &) –> void

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

static class_name() → str¶: C++: protocols::ligand_docking::rdf::RDFOrbitalFunction::class_name() –> std::string

get_function_names(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase) → pyrosetta.rosetta.utility.vector1_std_string¶

get a list of all the function names which will be present in RDFResultList after operator() is called

C++: protocols::ligand_docking::rdf::RDFBase::get_function_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse tags for RDFOrbitalFunction tag

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

preamble(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

update residue neighbors and cache current pose

C++: protocols::ligand_docking::rdf::RDFOrbitalFunction::preamble(class core::pose::Pose &) –> void

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

class pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator¶

Bases: RDFFunctionCreator

Creator to geneate a new RDFOrbitalFunction

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

create_rdf_function(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator) → pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase¶

return a pointer to a newly created RDFOrbitalFunction

C++: protocols::ligand_docking::rdf::RDFOrbitalFunctionCreator::create_rdf_function() const –> class std::shared_ptr<class protocols::ligand_docking::rdf::RDFBase>

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

type_name(self: pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator) → str¶

return the name of the RDFOrbitalFunction

C++: protocols::ligand_docking::rdf::RDFOrbitalFunctionCreator::type_name() const –> std::string