core::id::SequenceMapping Class Reference

#include <SequenceMapping.hh>

Inheritance diagram for core::id::SequenceMapping:

Public Member Functions
	SequenceMapping ()
	ctor More...
	SequenceMapping (Size const s1, Size const s2)
	ctor More...
	SequenceMapping (utility::vector1< Size > const &mapping)
	ctor More...
	SequenceMapping (conformation::signals::LengthEvent const &event)
	convenience constructor from LengthEvent More...
	~SequenceMapping () override
	dtor More...
	SequenceMapping (SequenceMapping const &src)
	copy constructor More...
SequenceMapping &	operator= (SequenceMapping const &src)
Size	get_corresponding_residue_in_current (Size original_resnum) const
	A->B; Get the corresponding (new) resnum (B) from the old (A). More...
Size	operator[] (Size const pos1) const
	A->B; Get a list of the old residues contained in this class (all A residues). More...
Size &	operator[] (Size const pos1)
void	resize (Size const s1, Size const s2, bool clear_values=true)
	resize More...
void	reverse ()
	go from an A->B mapping to a B->A mapping More...
void	downstream_combine (core::id::SequenceMapping const &smap_to_add)
	Apply a B->C mapping to the current A->B mapping to get an A->C mapping i.e. smap[j] becomes smap_to_add[ smap[j] ]. More...
void	upstream_combine (core::id::SequenceMapping const &smap_to_add)
	Apply a C->A mapping to the current A->B mapping to get a C->B mapping i.e. smap[j] becomes smap[ smap_to_add[ j ] ]. More...
Size	size1 () const
	size of target sequence More...
Size	size2 () const
	size of aligned sequence ??? More...
void	set_offset (int setting)
bool	all_aligned () const
bool	is_identity () const
bool	is_identity_ignore_gaps () const
void	size2 (Size const s2)
void	push_back (Size const al)
void	delete_source_residue (Size const pos1)
void	show () const
void	show (std::ostream &output) const
void	insert_source_residue (Size const pos1)
void	insert_aligned_residue (Size const pos1, Size const pos2)
void	insert_aligned_residue_safe (Size const pos1, Size const pos2)
	same as insert_aligned_residue, but a couple of extra checks on size1 and size2. More...
void	insert_target_residue (Size const pos)
void	delete_target_residue (Size const pos)
void	clear ()
virtual bool	operator== (SequenceMapping const &rhs) const
	Equality operator. More...
virtual bool	same_type_as_me (SequenceMapping const &other) const
	virtual function for ensuring both sequence mappings are the same type; essential for a valid equality operator. More...
utility::vector1< core::Size > const &	mapping () const
void	mapping (utility::vector1< core::Size > const &mapping)
std::string	to_string () const

Static Public Member Functions
static SequenceMapping	identity (Size const size)
	Construct an identity mapping, which means that for all positions, i in seq1 maps to i in seq2. More...

Private Attributes
Size	size2_
utility::vector1< Size >	mapping_

Constructor & Destructor Documentation

SequenceMapping() [1/5]

core::id::SequenceMapping::SequenceMapping ( )

inline

ctor

SequenceMapping() [2/5]

core::id::SequenceMapping::SequenceMapping ( Size const  s1, Size const  s2  )

inline

ctor

SequenceMapping() [3/5]

core::id::SequenceMapping::SequenceMapping

(

utility::vector1< Size > const &

mapping

)

ctor

SequenceMapping() [4/5]

core::id::SequenceMapping::SequenceMapping

(

conformation::signals::LengthEvent const &

event

)

convenience constructor from LengthEvent

References core::conformation::signals::LengthEvent::conformation_size, core::conformation::signals::LengthEvent::INVALIDATE, core::conformation::signals::LengthEvent::length_change, mapping_, core::conformation::signals::LengthEvent::RESIDUE_APPEND, core::conformation::signals::LengthEvent::RESIDUE_DELETE, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, and core::conformation::signals::LengthEvent::tag.

~SequenceMapping()

core::id::SequenceMapping::~SequenceMapping ( )

overridedefault

dtor

SequenceMapping() [5/5]

core::id::SequenceMapping::SequenceMapping

(

SequenceMapping const &

src

)

copy constructor

Member Function Documentation

all_aligned()

bool core::id::SequenceMapping::all_aligned

(

)

const

References mapping_, and size1().

Referenced by protocols::loops::apply_sequence_mapping().

clear()

void core::id::SequenceMapping::clear

(

)

References mapping_, and size2_.

Referenced by core::sequence::read_alignment_file().

delete_source_residue()

void core::id::SequenceMapping::delete_source_residue

(

Size const

pos1

)

References mapping_.

Referenced by protocols::loops::apply_sequence_mapping().

delete_target_residue()

void core::id::SequenceMapping::delete_target_residue

(

Size const

pos

)

References mapping_, size1(), and size2_.

Referenced by core::kinematics::FoldTree::delete_jump_seqpos(), and core::kinematics::FoldTree::delete_seqpos_simple().

downstream_combine()

void core::id::SequenceMapping::downstream_combine

(

core::id::SequenceMapping const &

smap_to_add

)

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

References mapping_, size2(), and size2_.

Referenced by core::id::combine_sequence_mappings().

get_corresponding_residue_in_current()

Size core::id::SequenceMapping::get_corresponding_residue_in_current

(

Size

original_resnum

)

const

A->B; Get the corresponding (new) resnum (B) from the old (A).

Get the corresponding (new) resnum from the old.

References mapping_.

Referenced by protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints(), core::conformation::carbohydrates::GlycanTreeSet::on_length_change(), and core::conformation::carbohydrates::GlycanTree::update_on_length_change().

identity()

static SequenceMapping core::id::SequenceMapping::identity ( Size const  size )

inlinestatic

Construct an identity mapping, which means that for all positions, i in seq1 maps to i in seq2.

References is_identity(), and size1().

Referenced by protocols::comparative_modeling::RecoverSideChainsMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::constraint_generator::AtomPairConstraintGenerator::create_sequence_mapping(), protocols::constraint_generator::generate_seqmap_from_poses(), is_identity(), and is_identity_ignore_gaps().

insert_aligned_residue()

void core::id::SequenceMapping::insert_aligned_residue	(	Size const	pos1,
		Size const	pos2
	)

References mapping_.

Referenced by protocols::loops::apply_sequence_mapping(), and protocols::jumping::ResiduePairJumpSetup::generate_jump_frags().

insert_aligned_residue_safe()

void core::id::SequenceMapping::insert_aligned_residue_safe	(	Size const	pos1,
		Size const	pos2
	)

same as insert_aligned_residue, but a couple of extra checks on size1 and size2.

References mapping_, protocols::mean_field::max(), size1(), and size2().

Referenced by protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::simple_moves::RepeatPropagationMover::setup_repeat_seqmap(), and core::sequence::simple_mapping_from_file().

insert_source_residue()

void core::id::SequenceMapping::insert_source_residue

(

Size const

pos1

)

References mapping_.

Referenced by protocols::loops::extend_sequence_mapping().

insert_target_residue()

void core::id::SequenceMapping::insert_target_residue

(

Size const

pos

)

References mapping_, size1(), and size2_.

Referenced by protocols::loops::extend_sequence_mapping().

is_identity()

bool core::id::SequenceMapping::is_identity

(

)

const

References identity(), mapping_, and size1().

Referenced by protocols::loops::apply_sequence_mapping(), protocols::fold_from_loops::utils::Nub::fix_fragments(), and identity().

is_identity_ignore_gaps()

bool core::id::SequenceMapping::is_identity_ignore_gaps

(

)

const

References identity(), mapping_, and size1().

mapping() [1/2]

utility::vector1< core::Size > const& core::id::SequenceMapping::mapping ( ) const

inline

References mapping_.

Referenced by mapping(), core::sequence::DerivedSequenceMapping::operator=(), operator=(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::remap_residues(), and upstream_combine().

mapping() [2/2]

void core::id::SequenceMapping::mapping ( utility::vector1< core::Size > const &  mapping )

inline

References mapping(), and mapping_.

operator=()

SequenceMapping & core::id::SequenceMapping::operator=

(

SequenceMapping const &

src

)

References mapping(), mapping_, size2(), and size2_.

operator==()

bool core::id::SequenceMapping::operator== ( SequenceMapping const &  rhs ) const

virtual

Equality operator.

References mapping_, same_type_as_me(), and size2_.

operator[]() [1/2]

Size & core::id::SequenceMapping::operator[]

(

Size const

pos1

)

References mapping_.

operator[]() [2/2]

Size core::id::SequenceMapping::operator[]

(

Size const

pos1

)

const

A->B; Get a list of the old residues contained in this class (all A residues).

References mapping_.

push_back()

void core::id::SequenceMapping::push_back

(

Size const

al

)

References mapping_.

Referenced by protocols::relax::coordinate_constrain_selection(), protocols::loops::extend_sequence_mapping(), protocols::star::Extender::Extender(), protocols::comparative_modeling::loops_from_transitive_alignments(), core::sequence::read_alignment_file(), and core::pack::task::PackerTask_::remap_residue_level_tasks().

resize()

void core::id::SequenceMapping::resize	(	Size const	s1,
		Size const	s2,
		bool	clear_values = true
	)

resize

Parameters

[in]	s1	new size of the target sequence
[in]	s2	new size of the aligned sequence
[in]	clear_values	optional parameter, defaults to true. By default, reset mapping to empty. Cases where passing clear_values as false is desired should be rare.

References mapping_, and size2_.

Referenced by protocols::rbsegment_relax::setup_pose_from_rbsegs().

reverse()

void core::id::SequenceMapping::reverse

(

)

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

References mapping_, size1(), and size2_.

Referenced by protocols::constraint_generator::CoordinateConstraintGenerator::align_reference_pose(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), core::sequence::mapping_to_alignment(), core::pack::task::PackerTask_::remap_residue_level_tasks(), protocols::abinitio::Template::Template(), protocols::loops::trim_back_sequence_mapping(), and protocols::hybridization::HybridizeProtocol::validate_template().

same_type_as_me()

bool core::id::SequenceMapping::same_type_as_me ( SequenceMapping const &  other ) const

virtual

virtual function for ensuring both sequence mappings are the same type; essential for a valid equality operator.

Referenced by operator==().

set_offset()

void core::id::SequenceMapping::set_offset

(

int

setting

)

References mapping_, and size1().

Referenced by protocols::abinitio::Template::Template().

show() [1/2]

void core::id::SequenceMapping::show

(

)

const

References core::id::TR().

Referenced by protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::comparative_modeling::get_qt_mapping_general(), protocols::comparative_modeling::loops_from_alignment(), protocols::comparative_modeling::loops_from_transitive_alignments(), and core::id::operator<<().

show() [2/2]

void core::id::SequenceMapping::show

(

std::ostream &

output

)

const

References mapping_, and size1().

size1()

Size core::id::SequenceMapping::size1

(

)

const

size of target sequence

access

References mapping_.

Referenced by all_aligned(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::comparative_modeling::Align_RmsdEvaluator::apply(), protocols::loops::apply_sequence_mapping(), delete_target_residue(), protocols::loops::extend_sequence_mapping(), protocols::loop_grower::FragmentExtension::get_unaligned(), identity(), insert_aligned_residue_safe(), insert_target_residue(), is_identity(), is_identity_ignore_gaps(), core::sequence::mapping_to_alignment(), protocols::abinitio::Template::pick_large_frags(), core::sequence::read_alignment_file(), reverse(), set_offset(), show(), protocols::abinitio::Template::Template(), to_string(), core::sequence::transitive_map(), and protocols::loops::trim_back_sequence_mapping().

size2() [1/2]

Size core::id::SequenceMapping::size2

(

)

const

size of aligned sequence ???

References size2_.

Referenced by protocols::loops::apply_sequence_mapping(), downstream_combine(), protocols::loops::extend_sequence_mapping(), insert_aligned_residue_safe(), core::sequence::DerivedSequenceMapping::operator=(), operator=(), core::sequence::read_alignment_file(), core::sequence::transitive_map(), and protocols::loops::trim_back_sequence_mapping().

size2() [2/2]

void core::id::SequenceMapping::size2

(

Size const

s2

)

References size2_.

to_string()

std::string core::id::SequenceMapping::to_string

(

)

const

References mapping_, and size1().

Referenced by protocols::fold_from_loops::utils::map_by_residue_subsets().

upstream_combine()

void core::id::SequenceMapping::upstream_combine

(

core::id::SequenceMapping const &

smap_to_add

)

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

References mapping(), and mapping_.

Member Data Documentation

mapping_

utility::vector1< Size > core::id::SequenceMapping::mapping_

private

Referenced by all_aligned(), clear(), delete_source_residue(), delete_target_residue(), downstream_combine(), get_corresponding_residue_in_current(), insert_aligned_residue(), insert_aligned_residue_safe(), insert_source_residue(), insert_target_residue(), is_identity(), is_identity_ignore_gaps(), mapping(), operator=(), operator==(), operator[](), push_back(), resize(), reverse(), SequenceMapping(), set_offset(), show(), size1(), to_string(), and upstream_combine().

size2_

Size core::id::SequenceMapping::size2_

private

Referenced by clear(), delete_target_residue(), downstream_combine(), insert_target_residue(), operator=(), operator==(), resize(), reverse(), and size2().

---

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

• src/core/id/SequenceMapping.hh
• src/core/id/SequenceMapping.cc