#include <SubstituentReplace.hh>

Inheritance diagram for protocols::drug_design::SubstituentReplace:

[legend]

Public Member Functions
	SubstituentReplace ()

void	apply (core::chemical::MutableResidueType &) override
	Modify the passed ResidueType. More...

void	template_database (std::string filename, bool append=false)
	The file which contains the templates to search for to add to input residue type. More...

void	substituents_database (std::string filename, bool append=false)
	The file which contains the substituents to add to input residue type. More...

void	H_as_dummy (core::Real setting)
	Will hydrogens in the input be converted to dummy stubs? More...

bool	H_as_dummy () const

void	V_as_dummy (core::Real setting)
	Will V atoms (Vanadium, but used commonly in Rosetta for "virtual" designations) in the input be converted to dummy stubs? More...

bool	V_as_dummy () const

void	weight_by_property (std::string const &setting)
	If not empty, use property weighting based on the given property. More...

std::string const &	weight_by_property () const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datacache) override
	Initialize any data members of this instance from an input tag and a DataMap object. More...

core::chemical::VDVDMapping	get_mapping () const override
	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. More...

Public Member Functions inherited from protocols::chemistries::Chemistry
	Chemistry (std::string const &name)

virtual void	apply (core::chemical::MutableResidueType &restype, core::pose::Pose const &)
	Modify the passed ResidueType, context sensitive. More...

Public Member Functions inherited from core::chemical::modifications::ChemistryBase
	ChemistryBase (std::string const &name)

std::string	name () const
	Return the name of this Chemistry object. More...

virtual bool	has_additional_output () const
	Are there alternate ResidueTypes which are availible from the last time we called apply? (That is, will get_addtional_output() return non-null?) More...

virtual core::chemical::MutableResidueTypeOP	get_additional_output ()
	Get additional generated ResidueTypes, if any. This allows for 1-to-many Chemistries. More...

ChemistryStatus	get_last_status () const
	What was the status of the last call to apply()/get_additional_output() More...

void	set_last_status (ChemistryStatus setting)
	Set the status of the chemistry object. More...

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
MoleculeSubstitutionOP	pick_replacement (MoleculeSubstitutionOP template_molsub, unsigned int &tdx_out) const

Private Attributes
utility::vector1< ::RDKit::ROMolOP >	templates_
	The templates to possibly use. More...

utility::vector1< ::RDKit::ROMolOP >	substituents_
	The fragments to apply. More...

bool	H_as_dummy_
	Do we consider Hydrogens to be dummy atoms? More...

bool	V_as_dummy_
	Do we consider V atoms to be dummy atoms? More...

std::string	property_name_
	If not empty, pick fragments based on the weighting by the given property. More...

core::chemical::VDVDMapping	mapping_

Constructor & Destructor Documentation

◆ SubstituentReplace()

protocols::drug_design::SubstituentReplace::SubstituentReplace ( )

Member Function Documentation

◆ apply()

void protocols::drug_design::SubstituentReplace::apply ( core::chemical::MutableResidueType & )

overridevirtual

Modify the passed ResidueType.

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

Implements protocols::chemistries::Chemistry.

◆ class_name()

std::string protocols::drug_design::SubstituentReplace::class_name ( )

static

Referenced by protocols::drug_design::SubstituentReplaceCreator::keyname(), and provide_xml_schema().

◆ get_mapping()

core::chemical::VDVDMapping protocols::drug_design::SubstituentReplace::get_mapping ( ) const

overridevirtual

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.

Get the vertex mapping that was used for the last apply() The base class implementation defaults to an identity mapping.

Reimplemented from core::chemical::modifications::ChemistryBase.

References mapping_.

◆ H_as_dummy() [1/2]

bool protocols::drug_design::SubstituentReplace::H_as_dummy ( ) const

inline

References H_as_dummy_.

Referenced by parse_my_tag().

◆ H_as_dummy() [2/2]

void protocols::drug_design::SubstituentReplace::H_as_dummy ( core::Real setting )

inline

Will hydrogens in the input be converted to dummy stubs?

References H_as_dummy_.

◆ parse_my_tag()

void protocols::drug_design::SubstituentReplace::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datacache
	)

overridevirtual

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

Implements protocols::chemistries::Chemistry.

References H_as_dummy(), substituents_, substituents_database(), template_database(), templates_, protocols::drug_design::TR(), V_as_dummy(), and weight_by_property().

◆ pick_replacement()

MoleculeSubstitutionOP protocols::drug_design::SubstituentReplace::pick_replacement	(	MoleculeSubstitutionOP	template_molsub,
		unsigned int &	tdx_out
	)		const

private

References protocols::drug_design::bond_is_in_ring(), protocols::drug_design::convert_matchvect_to_map(), protocols::drug_design::get_bonded_atom(), protocols::drug_design::AtomSubstitution::invalid_index, property_name_, substituents_, and protocols::drug_design::TR().

Referenced by apply().

◆ provide_xml_schema()

void protocols::drug_design::SubstituentReplace::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::chemistries::xsd_type_definition_w_attributes().

Referenced by protocols::drug_design::SubstituentReplaceCreator::provide_xml_schema().

◆ substituents_database()

void protocols::drug_design::SubstituentReplace::substituents_database	(	std::string	filename,
		bool	append = `false`
	)

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

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

References protocols::abinitio::filename(), core::chemical::rdkit::load_sdf(), substituents_, and protocols::drug_design::TR().

Referenced by parse_my_tag().

◆ template_database()

void protocols::drug_design::SubstituentReplace::template_database	(	std::string	filename,
		bool	append = `false`
	)

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

References protocols::abinitio::filename(), protocols::drug_design::find_dummies(), core::chemical::rdkit::get_name(), H_as_dummy_, core::chemical::rdkit::load_sdf(), templates_, protocols::drug_design::TR(), and V_as_dummy_.

Referenced by parse_my_tag().

◆ V_as_dummy() [1/2]

bool protocols::drug_design::SubstituentReplace::V_as_dummy ( ) const

inline

References V_as_dummy_.

Referenced by parse_my_tag().

◆ V_as_dummy() [2/2]

void protocols::drug_design::SubstituentReplace::V_as_dummy ( core::Real setting )

inline

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

References V_as_dummy_.

◆ weight_by_property() [1/2]

std::string const& protocols::drug_design::SubstituentReplace::weight_by_property ( ) const

inline

References property_name_.

Referenced by parse_my_tag().

◆ weight_by_property() [2/2]

void protocols::drug_design::SubstituentReplace::weight_by_property ( std::string const & setting )

inline

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

References property_name_.

Member Data Documentation

◆ H_as_dummy_

bool protocols::drug_design::SubstituentReplace::H_as_dummy_

private

Do we consider Hydrogens to be dummy atoms?

Referenced by H_as_dummy(), and template_database().

◆ mapping_

core::chemical::VDVDMapping protocols::drug_design::SubstituentReplace::mapping_

private

Referenced by apply(), and get_mapping().

◆ property_name_

std::string protocols::drug_design::SubstituentReplace::property_name_

private

If not empty, pick fragments based on the weighting by the given property.

Referenced by pick_replacement(), and weight_by_property().

◆ substituents_

utility::vector1< ::RDKit::ROMolOP > protocols::drug_design::SubstituentReplace::substituents_

private

The fragments to apply.

Referenced by apply(), parse_my_tag(), pick_replacement(), and substituents_database().

◆ templates_

utility::vector1< ::RDKit::ROMolOP > protocols::drug_design::SubstituentReplace::templates_

private

The templates to possibly use.

Referenced by apply(), parse_my_tag(), and template_database().

◆ V_as_dummy_

bool protocols::drug_design::SubstituentReplace::V_as_dummy_

private

Do we consider V atoms to be dummy atoms?

Referenced by template_database(), and V_as_dummy().

The documentation for this class was generated from the following files:

src/protocols/drug_design/SubstituentReplace.hh
src/protocols/drug_design/SubstituentReplace.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ SubstituentReplace()

Member Function Documentation

◆ apply()

◆ class_name()

◆ get_mapping()

◆ H_as_dummy() [1/2]

◆ H_as_dummy() [2/2]

◆ parse_my_tag()

◆ pick_replacement()

◆ provide_xml_schema()

◆ substituents_database()

◆ template_database()

◆ V_as_dummy() [1/2]

◆ V_as_dummy() [2/2]

◆ weight_by_property() [1/2]

◆ weight_by_property() [2/2]

Member Data Documentation

◆ H_as_dummy_

◆ mapping_

◆ property_name_

◆ substituents_

◆ templates_

◆ V_as_dummy_