A class for mapping ResidueType atom references from one to another. It's intended not only for intra ResidueType mapping, but also for mapping corresponding references from one ResidueType to another. More...

#include <AtomRefMapping.hh>

Inheritance diagram for core::chemical::AtomRefMapping< FromRef, ToRef >:

[legend]

Public Types
typedef SubMap::const_iterator	const_iterator

Public Member Functions
	AtomRefMapping ()

	AtomRefMapping (FromRef const &invalid_from, ToRef const &invalid_to)
	Constructor with non-standard invalid values. More...

	AtomRefMapping (bool identity)
	Ctor with explicit identity setting. More...

template<class F = FromRef, class T = ToRef, typename = typename std::enable_if< !std::is_same< F, core::Size >::value && !std::is_same< T, core::Size >::value, int >::type>
	AtomRefMapping (MutableResidueType const &restype)
	Make an explicit identity mapping for the ResType. More...

template<class F = FromRef, class T = ToRef, typename = typename std::enable_if< !std::is_same< F, VD >::value && !std::is_same< T, VD >::value, int >::type>
	AtomRefMapping (ResidueType const &restype)
	Make an explicit identity mapping for the ResType. More...

FromRef const &	invalid_key () const
	What's the invalid value for the keys? More...

ToRef const &	invalid_entry () const
	What's the invalid value for the mapped values? More...

void	identity (bool setting)
	Set the identity flag. More...

bool	identity () const
	Get the identity setting. More...

AtomRefMapping< ToRef, FromRef >	reverse () const
	go from an A->B mapping to a B->A mapping More...

template<class OToRef >
AtomRefMapping< FromRef, OToRef >	downstream_combine (AtomRefMapping< ToRef, OToRef > const &vmap_to_add) const
	Apply a B->C mapping to the current A->B mapping to get an A->C mapping i.e. vmap[j] becomes vmap_to_add[ vmap[j] ]. More...

template<class OFromRef >
AtomRefMapping< OFromRef, ToRef >	upstream_combine (AtomRefMapping< OFromRef, FromRef > const &vmap_to_add) const
	Apply a C->A mapping to the current A->B mapping to get a C->B mapping i.e. vmap[j] becomes vmap[ vmap_to_add[ j ] ]. More...

void	show (std::ostream &output) const

void	clear ()
	Ignore all specializations on this map. More...

void	erase (FromRef const &in)
	Make in act like the default (pay attention to identity_) More...

void	invalidate (FromRef const &in)
	Make the key value an invalid to value (Will work even with identity_ == true) More...

ToRef const	operator[] (FromRef const &in) const

ToRef &	operator[] (FromRef const &in)

FromRef const &	reverse_lookup (ToRef const &out) const
	Gets the key which corresponds to the given mapped value, if any. More...

bool	count (FromRef const &key) const
	Does this map have the given key? More...

bool	empty () const
	Does this mapping contain any explicit (non-identity) mappings? More...

bool	operator== (AtomRefMapping< FromRef, ToRef > const &other) const
	Equality operator. More...

template<class F = FromRef, class T = ToRef, typename = typename std::enable_if< !std::is_same< F, VD >::value && !std::is_same< T, VD >::value, int >::type>
utility::vector1< core::Size >	vectorize (ResidueType const &from_res, ResidueType const &to_res) const
	Make a Size-to-Size vector, indexed by the from, with elements that specify the two entries. More...

const_iterator	begin () const
	An iterator to std::pair(key,value) pairs for explicit entries. More...

const_iterator	end () const
	An iterator to std::pair(key,value) pairs for explicit entries. More...

Private Types
typedef std::map< FromRef, ToRef >	SubMap

Private Attributes
SubMap	mapping_
	The actual mapping. More...

FromRef	invalid_from_
	What value to use for invalid from values. More...

ToRef	invalid_to_
	What value to use for invalid to values. More...

bool	identity_
	Should non-explicitly stated atoms be treated like an identity relation? Only meaningful if the two types are the same. More...

Friends
template<class Foo , class Bar >
class	AtomRefMapping

Detailed Description

template<class FromRef, class ToRef>
class core::chemical::AtomRefMapping< FromRef, ToRef >

A class for mapping ResidueType atom references from one to another. It's intended not only for intra ResidueType mapping, but also for mapping corresponding references from one ResidueType to another.

This is a templated class to cut down on combinitorial complexity.

Member Typedef Documentation

◆ const_iterator

template<class FromRef , class ToRef >

typedef SubMap::const_iterator core::chemical::AtomRefMapping< FromRef, ToRef >::const_iterator

◆ SubMap

template<class FromRef , class ToRef >

typedef std::map< FromRef, ToRef > core::chemical::AtomRefMapping< FromRef, ToRef >::SubMap

private

Constructor & Destructor Documentation

◆ AtomRefMapping() [1/5]

template<class FromRef , class ToRef >

core::chemical::AtomRefMapping< FromRef, ToRef >::AtomRefMapping ( )

inline

◆ AtomRefMapping() [2/5]

template<class FromRef , class ToRef >

core::chemical::AtomRefMapping< FromRef, ToRef >::AtomRefMapping	(	FromRef const &	invalid_from,
		ToRef const &	invalid_to
	)

inline

Constructor with non-standard invalid values.

◆ AtomRefMapping() [3/5]

template<class FromRef , class ToRef >

core::chemical::AtomRefMapping< FromRef, ToRef >::AtomRefMapping ( bool identity )

inline

Ctor with explicit identity setting.

◆ AtomRefMapping() [4/5]

template<class FromRef , class ToRef >

template<class F = FromRef, class T = ToRef, typename = typename std::enable_if< !std::is_same< F, core::Size >::value && !std::is_same< T, core::Size >::value, int >::type>

core::chemical::AtomRefMapping< FromRef, ToRef >::AtomRefMapping ( MutableResidueType const & restype )

inline

Make an explicit identity mapping for the ResType.

Not availible if either ref is a core::Size

References core::chemical::MutableResidueType::atom_iterators(), core::chemical::RefConvert< OutRef >::convert(), and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

◆ AtomRefMapping() [5/5]

template<class FromRef , class ToRef >

template<class F = FromRef, class T = ToRef, typename = typename std::enable_if< !std::is_same< F, VD >::value && !std::is_same< T, VD >::value, int >::type>

core::chemical::AtomRefMapping< FromRef, ToRef >::AtomRefMapping ( ResidueType const & restype )

inline

Make an explicit identity mapping for the ResType.

Not availible if either ref is a VD

References core::chemical::RefConvert< OutRef >::convert(), core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_, and core::chemical::ResidueType::natoms().

Member Function Documentation

◆ begin()

template<class FromRef , class ToRef >

const_iterator core::chemical::AtomRefMapping< FromRef, ToRef >::begin ( ) const

inline

An iterator to std::pair(key,value) pairs for explicit entries.

References core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), and protocols::drug_design::DrugDesignMover::post_process_restype().

◆ clear()

template<class FromRef , class ToRef >

void core::chemical::AtomRefMapping< FromRef, ToRef >::clear ( )

inline

Ignore all specializations on this map.

References core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), protocols::drug_design::ReactionMultiTransform::apply(), protocols::drug_design::SubstituentReplace::apply(), protocols::drug_design::SubstructureReplace::apply(), core::chemical::rdkit::RDMolToRestype::generate_restype(), and core::chemical::rdkit::RestypeToRDMol::Mol().

◆ count()

template<class FromRef , class ToRef >

bool core::chemical::AtomRefMapping< FromRef, ToRef >::count ( FromRef const & key ) const

inline

Does this map have the given key?

References core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by core::chemical::AtomRefMapping< FromRef, ToRef >::downstream_combine(), core::chemical::rdkit::RDMolToRestype::generate_restype(), core::chemical::AtomRefMapping< FromRef, ToRef >::operator==(), core::chemical::AtomRefMapping< FromRef, ToRef >::operator[](), core::chemical::AtomRefMapping< FromRef, ToRef >::reverse(), and core::chemical::AtomRefMapping< FromRef, ToRef >::reverse_lookup().

◆ downstream_combine()

template<class FromRef , class ToRef >

template<class OToRef >

AtomRefMapping<FromRef,OToRef> core::chemical::AtomRefMapping< FromRef, ToRef >::downstream_combine ( AtomRefMapping< ToRef, OToRef > const & vmap_to_add ) const

inline

Apply a B->C mapping to the current A->B mapping to get an A->C mapping i.e. vmap[j] becomes vmap_to_add[ vmap[j] ].

References core::chemical::AtomRefMapping< FromRef, ToRef >::count(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by core::chemical::combine(), protocols::drug_design::DrugDesignMover::emplace_residue_type(), and core::chemical::AtomRefMapping< FromRef, ToRef >::upstream_combine().

◆ empty()

template<class FromRef , class ToRef >

bool core::chemical::AtomRefMapping< FromRef, ToRef >::empty ( ) const

inline

Does this mapping contain any explicit (non-identity) mappings?

References core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), core::chemical::rdkit::find_mapping(), and protocols::drug_design::place_new_restype_rotamer_align().

◆ end()

template<class FromRef , class ToRef >

const_iterator core::chemical::AtomRefMapping< FromRef, ToRef >::end ( ) const

inline

An iterator to std::pair(key,value) pairs for explicit entries.

References core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), and protocols::drug_design::DrugDesignMover::post_process_restype().

◆ erase()

template<class FromRef , class ToRef >

void core::chemical::AtomRefMapping< FromRef, ToRef >::erase ( FromRef const & in )

inline

Make in act like the default (pay attention to identity_)

References core::conformation::membrane::in, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by core::chemical::rdkit::RDMolToRestype::generate_restype().

◆ identity() [1/2]

template<class FromRef , class ToRef >

bool core::chemical::AtomRefMapping< FromRef, ToRef >::identity ( ) const

inline

Get the identity setting.

References core::chemical::AtomRefMapping< FromRef, ToRef >::identity_.

◆ identity() [2/2]

template<class FromRef , class ToRef >

void core::chemical::AtomRefMapping< FromRef, ToRef >::identity ( bool setting )

inline

Set the identity flag.

References core::chemical::AtomRefMapping< FromRef, ToRef >::identity_.

Referenced by protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), protocols::drug_design::SubstituentReplace::apply(), and protocols::drug_design::SubstructureReplace::apply().

◆ invalid_entry()

template<class FromRef , class ToRef >

ToRef const& core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry ( ) const

inline

What's the invalid value for the mapped values?

References core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_.

Referenced by protocols::drug_design::align_residues(), protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::rotamer_gen::RDKitRotamers::generate_conformers(), protocols::ligand_evolution::FragmentLibrary::generate_rotamers(), core::chemical::rdkit::RestypeToRDMol::Mol(), protocols::drug_design::place_new_restype_rotamer_align(), and protocols::drug_design::DrugDesignMover::post_process_restype().

◆ invalid_key()

template<class FromRef , class ToRef >

FromRef const& core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_key ( ) const

inline

What's the invalid value for the keys?

References core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_.

Referenced by protocols::drug_design::DrugDesignMover::post_process_restype().

◆ invalidate()

template<class FromRef , class ToRef >

void core::chemical::AtomRefMapping< FromRef, ToRef >::invalidate ( FromRef const & in )

inline

Make the key value an invalid to value (Will work even with identity_ == true)

References core::conformation::membrane::in, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by core::chemical::modifications::Reprotonate::remove_hydrogens().

◆ operator==()

template<class FromRef , class ToRef >

bool core::chemical::AtomRefMapping< FromRef, ToRef >::operator== ( AtomRefMapping< FromRef, ToRef > const & other ) const

inline

Equality operator.

References core::chemical::AtomRefMapping< FromRef, ToRef >::count(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

◆ operator[]() [1/2]

template<class FromRef , class ToRef >

ToRef& core::chemical::AtomRefMapping< FromRef, ToRef >::operator[] ( FromRef const & in )

inline

References core::chemical::AtomRefMapping< FromRef, ToRef >::count(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity_, core::chemical::RefConvert< OutRef >::identity_pass_through(), core::conformation::membrane::in, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

◆ operator[]() [2/2]

template<class FromRef , class ToRef >

ToRef const core::chemical::AtomRefMapping< FromRef, ToRef >::operator[] ( FromRef const & in ) const

inline

References core::chemical::AtomRefMapping< FromRef, ToRef >::identity_, core::chemical::RefConvert< OutRef >::identity_pass_through(), core::conformation::membrane::in, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

◆ reverse()

template<class FromRef , class ToRef >

AtomRefMapping< ToRef, FromRef > core::chemical::AtomRefMapping< FromRef, ToRef >::reverse ( ) const

inline

go from an A->B mapping to a B->A mapping

References core::chemical::AtomRefMapping< FromRef, ToRef >::count(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by protocols::rotamer_gen::FragmentRotamers::apply(), core::chemical::rdkit::find_mapping(), and protocols::drug_design::ReactionBasedAnalogSampler::find_O3A_mapping().

◆ reverse_lookup()

template<class FromRef , class ToRef >

FromRef const& core::chemical::AtomRefMapping< FromRef, ToRef >::reverse_lookup ( ToRef const & out ) const

inline

Gets the key which corresponds to the given mapped value, if any.

References core::chemical::AtomRefMapping< FromRef, ToRef >::count(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_, core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_, and core::conformation::membrane::out.

Referenced by protocols::drug_design::DrugDesignMover::post_process_restype().

◆ show()

template<class FromRef , class ToRef >

void core::chemical::AtomRefMapping< FromRef, ToRef >::show ( std::ostream & output ) const

inline

References core::chemical::AtomRefMapping< FromRef, ToRef >::identity_, core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_, and core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_.

Referenced by protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), and core::chemical::operator<<().

◆ upstream_combine()

template<class FromRef , class ToRef >

template<class OFromRef >

AtomRefMapping<OFromRef, ToRef> core::chemical::AtomRefMapping< FromRef, ToRef >::upstream_combine ( AtomRefMapping< OFromRef, FromRef > const & vmap_to_add ) const

inline

Apply a C->A mapping to the current A->B mapping to get a C->B mapping i.e. vmap[j] becomes vmap[ vmap_to_add[ j ] ].

References core::chemical::AtomRefMapping< FromRef, ToRef >::downstream_combine().

◆ vectorize()

template<class FromRef , class ToRef >

template<class F = FromRef, class T = ToRef, typename = typename std::enable_if< !std::is_same< F, VD >::value && !std::is_same< T, VD >::value, int >::type>

utility::vector1< core::Size > core::chemical::AtomRefMapping< FromRef, ToRef >::vectorize	(	ResidueType const &	from_res,
		ResidueType const &	to_res
	)		const

inline

Make a Size-to-Size vector, indexed by the from, with elements that specify the two entries.

References core::chemical::RefConvert< OutRef >::convert(), core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_, and core::chemical::ResidueType::natoms().

Friends And Related Function Documentation

◆ AtomRefMapping

template<class FromRef , class ToRef >

template<class Foo , class Bar >

friend class AtomRefMapping

friend

Member Data Documentation

◆ identity_

template<class FromRef , class ToRef >

bool core::chemical::AtomRefMapping< FromRef, ToRef >::identity_

private

Should non-explicitly stated atoms be treated like an identity relation? Only meaningful if the two types are the same.

Referenced by core::chemical::AtomRefMapping< FromRef, ToRef >::downstream_combine(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity(), core::chemical::AtomRefMapping< FromRef, ToRef >::operator==(), core::chemical::AtomRefMapping< FromRef, ToRef >::operator[](), core::chemical::AtomRefMapping< FromRef, ToRef >::reverse(), core::chemical::AtomRefMapping< FromRef, ToRef >::reverse_lookup(), and core::chemical::AtomRefMapping< FromRef, ToRef >::show().

◆ invalid_from_

template<class FromRef , class ToRef >

FromRef core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_from_

private

What value to use for invalid from values.

◆ invalid_to_

template<class FromRef , class ToRef >

ToRef core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_to_

private

What value to use for invalid to values.

Referenced by core::chemical::AtomRefMapping< FromRef, ToRef >::downstream_combine(), core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry(), core::chemical::AtomRefMapping< FromRef, ToRef >::invalidate(), core::chemical::AtomRefMapping< FromRef, ToRef >::operator[](), core::chemical::AtomRefMapping< FromRef, ToRef >::reverse(), and core::chemical::AtomRefMapping< FromRef, ToRef >::reverse_lookup().

◆ mapping_

template<class FromRef , class ToRef >

SubMap core::chemical::AtomRefMapping< FromRef, ToRef >::mapping_

private

The actual mapping.

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

src/core/chemical/AtomRefMapping.hh

Public Types

Public Member Functions

Private Types

Private Attributes

Friends

Detailed Description

template<class FromRef, class ToRef> class core::chemical::AtomRefMapping< FromRef, ToRef >

Member Typedef Documentation

◆ const_iterator

◆ SubMap

Constructor & Destructor Documentation

◆ AtomRefMapping() [1/5]

◆ AtomRefMapping() [2/5]

◆ AtomRefMapping() [3/5]

◆ AtomRefMapping() [4/5]

◆ AtomRefMapping() [5/5]

Member Function Documentation

◆ begin()

◆ clear()

◆ count()

◆ downstream_combine()

◆ empty()

◆ end()

◆ erase()

◆ identity() [1/2]

◆ identity() [2/2]

◆ invalid_entry()

◆ invalid_key()

◆ invalidate()

◆ operator==()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ reverse()

◆ reverse_lookup()

◆ show()

◆ upstream_combine()

◆ vectorize()

Friends And Related Function Documentation

◆ AtomRefMapping

Member Data Documentation

◆ identity_

◆ invalid_from_

◆ invalid_to_

◆ mapping_

template<class FromRef, class ToRef>
class core::chemical::AtomRefMapping< FromRef, ToRef >