protocols::drug_design::RandomFragmentLigand Class Reference

#include <RandomFragmentLigand.hh>

Inheritance diagram for protocols::drug_design::RandomFragmentLigand:

Public Member Functions
	RandomFragmentLigand ()
void	keep_bigger (bool keep_bigger)
void	keep_atom (std::string const &keep_atom)
void	ccbond (bool setting)
bool	keep_bigger () const
std::string	keep_atom () const
bool	ccbond () const
void	apply (core::chemical::MutableResidueType &) override
	Modify the passed ResidueType. More...
void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) 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 Attributes
bool	keep_bigger_
	Keep the fragment which is bigger. More...
std::string	keep_atom_
	Keep the fragment which contains the given atom. More...
bool	ccbond_
	Only break C-C bonds. More...
core::chemical::VDVDMapping	mapping_

Constructor & Destructor Documentation

RandomFragmentLigand()

protocols::drug_design::RandomFragmentLigand::RandomFragmentLigand

(

)

Member Function Documentation

apply()

void protocols::drug_design::RandomFragmentLigand::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.

References core::chemical::MutableResidueType::add_atom(), core::chemical::MutableResidueType::add_bond(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::MutableResidueType::assign_internal_coordinates(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::autodetermine_chi_bonds(), core::chemical::BondNotInRing, core::chemical::element::C, ccbond_, protocols::simple_filters::coords(), core::chemical::MutableResidueType::delete_atom(), core::chemical::MutableResidueType::delete_bond(), core::chemical::modifications::determine_coordinates(), core::chemical::ElementSet::element(), core::chemical::ResidueTypeBase::element_set(), core::chemical::Atom::element_type(), core::chemical::modifications::FAIL_DO_NOT_RETRY, core::chemical::find_bonds_in_rings(), core::chemical::find_nbr_dist(), core::chemical::ResidueTypeBase::gasteiger_atom_typeset(), core::chemical::MutableResidueType::graph(), core::chemical::element::H, core::chemical::MutableResidueType::has(), core::chemical::Atom::ideal_xyz(), keep_atom(), keep_atom_, keep_bigger_, mapping_, core::chemical::modifications::ChemistryBase::name(), core::chemical::ResidueTypeBase::name(), core::chemical::element::name_from_elements(), core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::nbr_atom(), core::chemical::MutableResidueType::nbr_radius(), core::chemical::MutableResidueType::nbr_vertex(), core::chemical::MutableResidueType::null_vertex, core::scoring::rg, core::chemical::rosetta_recharge_fullatom(), core::chemical::rosetta_retype_fullatom(), core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset(), core::chemical::modifications::ChemistryBase::set_last_status(), core::chemical::MutableResidueType::show_all_atom_names(), protocols::analysis::side1, protocols::analysis::side2, core::chemical::SingleBond, core::chemical::modifications::SUCCESS, core::id::to_string(), and protocols::drug_design::TR().

ccbond() [1/2]

bool protocols::drug_design::RandomFragmentLigand::ccbond ( ) const

inline

References ccbond_.

Referenced by parse_my_tag().

ccbond() [2/2]

void protocols::drug_design::RandomFragmentLigand::ccbond ( bool  setting )

inline

References ccbond_.

class_name()

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

static

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

get_mapping()

core::chemical::VDVDMapping protocols::drug_design::RandomFragmentLigand::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_.

keep_atom() [1/2]

std::string protocols::drug_design::RandomFragmentLigand::keep_atom ( ) const

inline

References keep_atom_.

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

keep_atom() [2/2]

void protocols::drug_design::RandomFragmentLigand::keep_atom

(

std::string const &

keep_atom

)

References keep_atom(), keep_atom_, and core::chemical::orbitals::strip_whitespace().

keep_bigger() [1/2]

bool protocols::drug_design::RandomFragmentLigand::keep_bigger ( ) const

inline

References keep_bigger_.

Referenced by parse_my_tag().

keep_bigger() [2/2]

void protocols::drug_design::RandomFragmentLigand::keep_bigger ( bool  keep_bigger )

inline

References keep_bigger(), and keep_bigger_.

Referenced by keep_bigger().

parse_my_tag()

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

overridevirtual

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

Implements protocols::chemistries::Chemistry.

References ccbond(), keep_atom(), keep_atom_, keep_bigger(), and keep_bigger_.

provide_xml_schema()

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

static

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

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

Member Data Documentation

ccbond_

bool protocols::drug_design::RandomFragmentLigand::ccbond_

private

Only break C-C bonds.

Referenced by apply(), and ccbond().

keep_atom_

std::string protocols::drug_design::RandomFragmentLigand::keep_atom_

private

Keep the fragment which contains the given atom.

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

keep_bigger_

bool protocols::drug_design::RandomFragmentLigand::keep_bigger_

private

Keep the fragment which is bigger.

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

mapping_

core::chemical::VDVDMapping protocols::drug_design::RandomFragmentLigand::mapping_

private

Referenced by apply(), and get_mapping().

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

• src/protocols/drug_design/RandomFragmentLigand.hh
• src/protocols/drug_design/RandomFragmentLigand.cc