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protocols::denovo_design::connection::ConnectionArchitect Class Reference

Architect for covalently joining two segments of a pose. More...

#include <ConnectionArchitect.hh>

Inheritance diagram for protocols::denovo_design::connection::ConnectionArchitect:
Inheritance graph
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Public Types

typedef std::pair< std::string,
std::string > 		SegmentPair
 
typedef utility::vector1
< SegmentPair > 		SegmentPairs
 
typedef std::set< core::Size > LengthSet
 
typedef architects::Lengths Lengths
 

Public Member Functions

 ConnectionArchitect (std::string const &id_value)
 
 ~ConnectionArchitect () override
 
std::string type () const override
 simply returns the name of this type of architect More...
 
virtual ConnectionArchitectOP clone () const
 
void apply (components::StructureData &sd) const
 does the work of modifying the StructureData More...
 
void apply (components::StructureData &sd, core::Real &random) const
 applies with a specific random number More...
 
MotifOPs compute_connection_candidates (components::StructureData const &sd) const
 computes a list of possible motifs More...
 
SegmentNames const & segment1_ids () const
 returns list of allowed segment 1 ids More...
 
void set_segment1_ids (std::string const &segment1_str)
 sets list of segment1 ids from string More...
 
void set_segment1_ids (SegmentNames const &segments)
 sets list of segment1 ids from list More...
 
SegmentNames const & segment2_ids () const
 returns list of allowed segment2 ids More...
 
void set_segment2_ids (std::string const &segment2_str)
 sets list of segment2 ids from string More...
 
void set_segment2_ids (SegmentNames const &segments)
 sets list of segment1 ids from list More...
 
core::Size user_chain1 () const
 gets user-specified chain number for the lower chain to be connected. 0 if not specified More...
 
void set_user_chain1 (core::Size const chain)
 sets user-specified chain number for the lower chain to be connected. 0 if unspecified More...
 
core::Size user_chain2 () const
 gets user-specified chain number for the upper chain to be connected. 0 if not specified More...
 
void set_user_chain2 (core::Size const chain)
 sets user-specified chain number for the upper chain to be connected. 0 if unspecified More...
 
void set_motifs (std::string const &motif_str, std::string const &cutpoints_str)
 sets motifs using a motif string and a string of cutpoints More...
 
void set_motifs (MotifCOPs const &motifs)
 sets motifs via a vector More...
 
void set_ideal_abego (bool const use_ideal_abego, std::string const &extend_ss)
 sets whether to use "ideal abego" loops according to Koga papers More...
 
void set_use_hh_abego_rules (bool const use_rules)
 sets whether or not to use the newer HH rules (https://doi.org/10.1101/2021.03.10.434454) More...
 
void set_bridge (bool const bridge)
 sets whether to always try to bridge. If true, a random cutpoint will be selected in the connection if the chains to be connected have different movable groups More...
 
- Public Member Functions inherited from protocols::denovo_design::architects::StructureArchitect
 StructureArchitect (std::string const &id)
 
 ~StructureArchitect () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 
std::string const & id () const
 
void set_id (std::string const &new_id)
 

Static Public Member Functions

static std::string class_name ()
 
static void attributes_for_parse_my_tag (utility::tag::AttributeList &attlist)
 
- Static Public Member Functions inherited from protocols::denovo_design::architects::StructureArchitect
static void attributes_for_parse_my_tag (utility::tag::AttributeList &attlist)
 

Static Public Attributes

static std::string const DATA_MAP_NAME = "ConnectionArchitects"
 

Protected Member Functions

void parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 companion function: attributes_for_parse_my_tag More...
 

Private Member Functions

MotifOPs compute_connection_candidates (components::StructureData const &sd, AreConnectablePredicate const &connectable) const
 Get list of segment pairs allowed to be connected. More...
 
SegmentPairs segment_pairs (components::StructureData const &sd) const
 
SegmentPairs combine_segment_names (SegmentNames const &seg1s, SegmentNames const &seg2s) const
 
MotifOP choose_motif (MotifOPs const &motifs, core::Real &random) const
 
void connect (components::StructureData &sd, Motif &motif) const
 creates StructureData from given Motif More...
 
LengthSet lengths () const
 
LengthSet cutpoints () const
 returns a set of valid loop index cutpoints More...
 
MotifOPs motifs_for_pair (SegmentPair const &pair, components::StructureData const &sd, LengthSet const &length_set, LengthSet const &cutpoint_set) const
 
MotifCOPs parse_motif_string (std::string const &motifs) const
 
SegmentNames available_upper_termini (components::StructureData const &sd) const
 
SegmentNames available_lower_termini (components::StructureData const &sd) const
 finds usable/available upper termini (i.e. those for comp1) More...
 

Private Attributes

bool bridge_
 
components::IdealAbegoGeneratorOP ideal_abego_
 
MotifCOPs motifs_
 
SegmentNames segment1_ids_
 
SegmentNames segment2_ids_
 
core::Size chain1_
 
core::Size chain2_
 

Detailed Description

Architect for covalently joining two segments of a pose.

Member Typedef Documentation

typedef architects::Lengths protocols::denovo_design::connection::ConnectionArchitect::Lengths
typedef std::set< core::Size > protocols::denovo_design::connection::ConnectionArchitect::LengthSet
typedef std::pair< std::string, std::string > protocols::denovo_design::connection::ConnectionArchitect::SegmentPair
typedef utility::vector1< SegmentPair > protocols::denovo_design::connection::ConnectionArchitect::SegmentPairs

Constructor & Destructor Documentation

protocols::denovo_design::connection::ConnectionArchitect::ConnectionArchitect ( std::string const &  id_value)
protocols::denovo_design::connection::ConnectionArchitect::~ConnectionArchitect ( )
overridedefault

Member Function Documentation

void protocols::denovo_design::connection::ConnectionArchitect::apply ( components::StructureData &  sd) const

does the work of modifying the StructureData

References protocols::rigid::random, and core::scoring::rg.

void protocols::denovo_design::connection::ConnectionArchitect::apply ( components::StructureData &  sd,
core::Real &  random 
) const

applies with a specific random number

References choose_motif(), compute_connection_candidates(), connect(), protocols::denovo_design::architects::StructureArchitect::id(), segment1_ids_, and segment2_ids_.

void protocols::denovo_design::connection::ConnectionArchitect::attributes_for_parse_my_tag ( utility::tag::AttributeList &  attlist)
static

References protocols::denovo_design::architects::StructureArchitect::attributes_for_parse_my_tag().

Referenced by protocols::denovo_design::architects::CompoundArchitect::provide_xml_schema(), and protocols::denovo_design::movers::BridgeChainsMover::setup_attlist_for_derived_classes().

SegmentNames protocols::denovo_design::connection::ConnectionArchitect::available_lower_termini ( components::StructureData const &  sd) const
private

finds usable/available upper termini (i.e. those for comp1)

References protocols::denovo_design::components::StructureData::available_lower_termini(), protocols::denovo_design::components::StructureData::has_free_lower_terminus(), segment2_ids_, and protocols::TR().

Referenced by segment_pairs().

SegmentNames protocols::denovo_design::connection::ConnectionArchitect::available_upper_termini ( components::StructureData const &  sd) const
private

References protocols::denovo_design::components::StructureData::available_upper_termini(), protocols::denovo_design::components::StructureData::has_free_upper_terminus(), segment1_ids_, and protocols::TR().

Referenced by segment_pairs().

MotifOP protocols::denovo_design::connection::ConnectionArchitect::choose_motif ( MotifOPs const &  motifs,
core::Real &  random 
) const
private

References protocols::denovo_design::extract_int().

Referenced by apply().

static std::string protocols::denovo_design::connection::ConnectionArchitect::class_name ( )
inlinestatic

Referenced by type().

ConnectionArchitectOP protocols::denovo_design::connection::ConnectionArchitect::clone ( ) const
virtual

Referenced by protocols::denovo_design::architects::CompoundArchitect::add_connection().

ConnectionArchitect::SegmentPairs protocols::denovo_design::connection::ConnectionArchitect::combine_segment_names ( SegmentNames const &  seg1s,
SegmentNames const &  seg2s 
) const
private

Referenced by segment_pairs().

MotifOPs protocols::denovo_design::connection::ConnectionArchitect::compute_connection_candidates ( components::StructureData const &  sd) const

computes a list of possible motifs

Referenced by apply().

MotifOPs protocols::denovo_design::connection::ConnectionArchitect::compute_connection_candidates ( components::StructureData const &  sd,
AreConnectablePredicate const &  connectable 
) const
private

Get list of segment pairs allowed to be connected.

References cutpoints(), lengths(), motifs_for_pair(), segment_pairs(), and protocols::TR().

void protocols::denovo_design::connection::ConnectionArchitect::connect ( components::StructureData &  sd,
Motif &  motif 
) const
private

creates StructureData from given Motif

creates StructureData from given ConnectionInfo object

References protocols::denovo_design::components::StructureData::add_segment(), protocols::denovo_design::components::StructureData::choose_new_movable_group(), protocols::denovo_design::components::StructureData::connect_segments(), protocols::denovo_design::components::StructureData::delete_leading_residues(), protocols::denovo_design::components::StructureData::delete_trailing_residues(), protocols::denovo_design::components::Segment::elem_length(), protocols::denovo_design::components::Segment::lower_segment(), protocols::denovo_design::components::StructureData::move_segment(), protocols::denovo_design::components::StructureData::set_data_str(), protocols::denovo_design::components::Segment::set_lower_segment(), protocols::denovo_design::components::StructureData::set_movable_group(), protocols::denovo_design::components::Segment::set_upper_segment(), protocols::TR(), and protocols::denovo_design::components::Segment::upper_segment().

Referenced by apply().

ConnectionArchitect::LengthSet protocols::denovo_design::connection::ConnectionArchitect::cutpoints ( ) const
private

returns a set of valid loop index cutpoints

References motifs_.

Referenced by compute_connection_candidates(), and set_motifs().

ConnectionArchitect::LengthSet protocols::denovo_design::connection::ConnectionArchitect::lengths ( ) const
private

References motifs_.

Referenced by compute_connection_candidates().

MotifOPs protocols::denovo_design::connection::ConnectionArchitect::motifs_for_pair ( SegmentPair const &  pair,
components::StructureData const &  sd,
LengthSet const &  length_set,
LengthSet const &  cutpoint_set 
) const
private

References protocols::denovo_design::components::StructureData::abego(), ideal_abego_, motifs_, protocols::denovo_design::components::StructureData::segment(), protocols::denovo_design::components::Segment::start(), and protocols::denovo_design::components::Segment::stop().

Referenced by compute_connection_candidates().

MotifCOPs protocols::denovo_design::connection::ConnectionArchitect::parse_motif_string ( std::string const &  motifs) const
private

Referenced by set_motifs().

void protocols::denovo_design::connection::ConnectionArchitect::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overrideprotectedvirtual

companion function: attributes_for_parse_my_tag

Implements protocols::denovo_design::architects::StructureArchitect.

References set_ideal_abego(), set_motifs(), set_segment1_ids(), set_segment2_ids(), set_use_hh_abego_rules(), set_user_chain1(), set_user_chain2(), user_chain1(), and user_chain2().

SegmentNames const & protocols::denovo_design::connection::ConnectionArchitect::segment1_ids ( ) const

returns list of allowed segment 1 ids

References segment1_ids_.

SegmentNames const & protocols::denovo_design::connection::ConnectionArchitect::segment2_ids ( ) const

returns list of allowed segment2 ids

References segment2_ids_.

ConnectionArchitect::SegmentPairs protocols::denovo_design::connection::ConnectionArchitect::segment_pairs ( components::StructureData const &  sd) const
private

References available_lower_termini(), available_upper_termini(), core::pack::dunbrack::c, chain1_, chain2_, combine_segment_names(), protocols::denovo_design::architects::StructureArchitect::id(), segment1_ids_, segment2_ids_, protocols::denovo_design::components::StructureData::segments_begin(), and protocols::denovo_design::components::StructureData::segments_end().

Referenced by compute_connection_candidates().

void protocols::denovo_design::connection::ConnectionArchitect::set_bridge ( bool const  bridge)

sets whether to always try to bridge. If true, a random cutpoint will be selected in the connection if the chains to be connected have different movable groups

References bridge_.

Referenced by set_motifs().

void protocols::denovo_design::connection::ConnectionArchitect::set_ideal_abego ( bool const  use_ideal_abego,
std::string const &  extend_ss 
)

sets whether to use "ideal abego" loops according to Koga papers

References ideal_abego_.

Referenced by parse_tag().

void protocols::denovo_design::connection::ConnectionArchitect::set_motifs ( std::string const &  motif_str,
std::string const &  cutpoints_str 
)

sets motifs using a motif string and a string of cutpoints

References bridge_, cutpoints(), motifs_, parse_motif_string(), set_bridge(), and protocols::TR().

Referenced by parse_tag().

void protocols::denovo_design::connection::ConnectionArchitect::set_motifs ( MotifCOPs const &  motifs)

sets motifs via a vector

References motifs_.

void protocols::denovo_design::connection::ConnectionArchitect::set_segment1_ids ( std::string const &  segment1_str)

sets list of segment1 ids from string

References protocols::denovo_design::connection::parse_segment_names().

Referenced by protocols::denovo_design::movers::ExtendChainMover::apply(), and parse_tag().

void protocols::denovo_design::connection::ConnectionArchitect::set_segment1_ids ( SegmentNames const &  segments)

sets list of segment1 ids from list

References segment1_ids_.

void protocols::denovo_design::connection::ConnectionArchitect::set_segment2_ids ( std::string const &  segment2_str)

sets list of segment2 ids from string

References protocols::denovo_design::connection::parse_segment_names().

Referenced by protocols::denovo_design::movers::ExtendChainMover::apply(), and parse_tag().

void protocols::denovo_design::connection::ConnectionArchitect::set_segment2_ids ( SegmentNames const &  segments)

sets list of segment1 ids from list

References segment2_ids_.

void protocols::denovo_design::connection::ConnectionArchitect::set_use_hh_abego_rules ( bool const  use_rules)

sets whether or not to use the newer HH rules (https://doi.org/10.1101/2021.03.10.434454)

References ideal_abego_.

Referenced by parse_tag().

void protocols::denovo_design::connection::ConnectionArchitect::set_user_chain1 ( core::Size const  chain)

sets user-specified chain number for the lower chain to be connected. 0 if unspecified

References chain1_.

Referenced by parse_tag().

void protocols::denovo_design::connection::ConnectionArchitect::set_user_chain2 ( core::Size const  chain)

sets user-specified chain number for the upper chain to be connected. 0 if unspecified

References chain2_.

Referenced by parse_tag().

std::string protocols::denovo_design::connection::ConnectionArchitect::type ( ) const
overridevirtual

simply returns the name of this type of architect

Implements protocols::denovo_design::architects::StructureArchitect.

References class_name().

core::Size protocols::denovo_design::connection::ConnectionArchitect::user_chain1 ( ) const

gets user-specified chain number for the lower chain to be connected. 0 if not specified

References chain1_.

Referenced by parse_tag().

core::Size protocols::denovo_design::connection::ConnectionArchitect::user_chain2 ( ) const

gets user-specified chain number for the upper chain to be connected. 0 if not specified

References chain2_.

Referenced by parse_tag().

Member Data Documentation

bool protocols::denovo_design::connection::ConnectionArchitect::bridge_
private

Referenced by set_bridge(), and set_motifs().

core::Size protocols::denovo_design::connection::ConnectionArchitect::chain1_
private

Referenced by segment_pairs(), set_user_chain1(), and user_chain1().

core::Size protocols::denovo_design::connection::ConnectionArchitect::chain2_
private

Referenced by segment_pairs(), set_user_chain2(), and user_chain2().

std::string const protocols::denovo_design::connection::ConnectionArchitect::DATA_MAP_NAME = "ConnectionArchitects"
static

Referenced by protocols::denovo_design::connection::retrieve_connection_architect(), and protocols::denovo_design::connection::store_connection_architect().

components::IdealAbegoGeneratorOP protocols::denovo_design::connection::ConnectionArchitect::ideal_abego_
private

Referenced by motifs_for_pair(), set_ideal_abego(), and set_use_hh_abego_rules().

MotifCOPs protocols::denovo_design::connection::ConnectionArchitect::motifs_
private

Referenced by cutpoints(), lengths(), motifs_for_pair(), and set_motifs().

SegmentNames protocols::denovo_design::connection::ConnectionArchitect::segment1_ids_
private

Referenced by apply(), available_upper_termini(), segment1_ids(), segment_pairs(), and set_segment1_ids().

SegmentNames protocols::denovo_design::connection::ConnectionArchitect::segment2_ids_
private

Referenced by apply(), available_lower_termini(), segment2_ids(), segment_pairs(), and set_segment2_ids().

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