Logic for selection of abego values. More...

#include <IdealAbegoGenerator.hh>

Inheritance diagram for protocols::denovo_design::components::IdealAbegoGenerator:

Public Types
typedef Segment	Motif

typedef SegmentOP	MotifOP

typedef utility::vector1< MotifOP >	MotifOPs

typedef std::set< core::Size >	LengthSet

typedef std::string	Abego

typedef utility::vector1 < std::string >	Abegos

typedef std::map< std::string, Abegos >	SecstructAbegoMap

Public Member Functions
	IdealAbegoGenerator (std::string const &id_val)

	~IdealAbegoGenerator () override

IdealAbegoGeneratorOP	clone () const

MotifOPs	generate (char abego1, char abego2, LengthSet const &lenset, LengthSet const &cutpoint_set) const
	Given desired lengths, compute a set of idealized loop motifs via Nobu/Rie/YuRu rules. More...

bool	extend_ss (char const secstruct) const
	Returns true if the given SS type should be extended or not. More...

void	set_extend_ss (std::string const &extend_ss)
	if true, secondary structure may be extended to close the loop. Overall size of the insert will not change. Therefore, a 4 residue loop might extend a helix by 2 residues and have a 2-residue ideal loop if extend_ss is true. If extend_ss is false, a 4 residue loop must have four loop residues. More...

void	set_hh_rules_2021 (bool const use_hh_rules)
	if true, the connection rules from https://doi.org/10.1101/2021.03.10.434454 will be used.. If false, all possible abego combinations will be sampled More...

Abegos	retrieve_loop_abegos (char const abego1, char const abego2) const

Private Member Functions
MotifOPs	add_cutpoints (MotifOPs const &orig, LengthSet const &cutpoint_set) const
	takes a list of motifs without cutpoints and generates all permutations with cutpoints from cutpoint_set More...

MotifOPs	extract_ideal_motifs (Abegos const &abegolist, LengthSet const &lenset) const

void	note_fwd_element_extensions (Motif &motif, char const sschar, char const element_abego) const

void	note_rev_element_extensions (Motif &motif, char const sschar, char const element_abego) const

	IdealAbegoGenerator ()

Static Private Member Functions
static Abegos	generate_extended_abegos (Abegos const &no_extension_loops, char const abego_n, char const abego_c)

Private Attributes
std::string	segment_name_

std::string	extend_ss_ = "1"

bool	match_ss_to_abego_ = false

bool	use_hh_rules_2021_ = true

SecstructAbegoMap	extended_abegos_

Static Private Attributes
static Abegos const	ab_no_extension = { "GB", "GBA", "BAA", "GBB", "GBAB", "BAAB" }

static Abegos const	ba_no_extension = { "AB", "GBB", "BAB" }

static Abegos const	bb_no_extension = { "GG", "EA", "AA", "AAG" }

static Abegos const	aa_no_extension

static Abegos const	aa_no_extension_all

static std::map< char, core::Size > const	extension_lengths

Detailed Description

Logic for selection of abego values.

Member Typedef Documentation

typedef std::string protocols::denovo_design::components::IdealAbegoGenerator::Abego

typedef utility::vector1< std::string > protocols::denovo_design::components::IdealAbegoGenerator::Abegos

typedef std::set< core::Size > protocols::denovo_design::components::IdealAbegoGenerator::LengthSet

typedef Segment protocols::denovo_design::components::IdealAbegoGenerator::Motif

typedef SegmentOP protocols::denovo_design::components::IdealAbegoGenerator::MotifOP

typedef utility::vector1< MotifOP > protocols::denovo_design::components::IdealAbegoGenerator::MotifOPs

typedef std::map< std::string, Abegos > protocols::denovo_design::components::IdealAbegoGenerator::SecstructAbegoMap

Constructor & Destructor Documentation

protocols::denovo_design::components::IdealAbegoGenerator::IdealAbegoGenerator ( std::string const & id_val )

References aa_no_extension, aa_no_extension_all, ab_no_extension, ba_no_extension, bb_no_extension, extended_abegos_, and generate_extended_abegos().

protocols::denovo_design::components::IdealAbegoGenerator::~IdealAbegoGenerator ( )

overridedefault

protocols::denovo_design::components::IdealAbegoGenerator::IdealAbegoGenerator ( )

inlineprivate

Member Function Documentation

IdealAbegoGenerator::MotifOPs protocols::denovo_design::components::IdealAbegoGenerator::add_cutpoints	(	MotifOPs const &	orig,
		LengthSet const &	cutpoint_set
	)		const

private

takes a list of motifs without cutpoints and generates all permutations with cutpoints from cutpoint_set

Parameters

[in]	orig	List of motifs without cutpoints
[in]	cutpoint_set	Set of loop-relative indices of cutpoint residues

Returns: MotifOPs of all motifs in orig with all possible cutpoints in cutpoint_set

References core::pack::dunbrack::c.

Referenced by generate().

IdealAbegoGeneratorOP protocols::denovo_design::components::IdealAbegoGenerator::clone ( ) const

bool protocols::denovo_design::components::IdealAbegoGenerator::extend_ss ( char const secstruct ) const

Returns true if the given SS type should be extended or not.

References extend_ss_.

Referenced by retrieve_loop_abegos(), and set_extend_ss().

IdealAbegoGenerator::MotifOPs protocols::denovo_design::components::IdealAbegoGenerator::extract_ideal_motifs	(	Abegos const &	abegolist,
		LengthSet const &	lenset
	)		const

private

References core::scoring::abego, protocols::denovo_design::abego_str(), and segment_name_.

Referenced by generate().

IdealAbegoGenerator::MotifOPs protocols::denovo_design::components::IdealAbegoGenerator::generate	(	char	abego1,
		char	abego2,
		LengthSet const &	lenset,
		LengthSet const &	cutpoint_set
	)		const

Given desired lengths, compute a set of idealized loop motifs via Nobu/Rie/YuRu rules.

Given lengths and abegos to connect, generate a list of motifs.

Parameters

[in]	abego1	Abego of residue immediately before the loop
[in]	abego2	Abego of residue immediately after the loop
[in]	lenset	Set of allowed loop lengths
[in]	cutpoint_set	Set of allowed cutpoint residues. A value of N indicates the Nth residue of the loop is a LOWER_CUTPOINT and the (N+1)th residue is an UPPER_CUTPOINT

Returns: MotifOPs of all ideal loops with given lengths/cutpoints connecting two residues of the given abegos

If extend_ss is true, "extension" of SS elements by adding residues of the same abego type is allowed. For example, connecting A–>A, you might get a 4-residue loop of type A-ABGA-A. If false, only different abegos are allowed, and you might get a 4-residue loop of type A-BGAB-A

Parameters

[in]	abego1	Abego of residue immediately before the loop
[in]	abego2	Abego of residue immediately after the loop
[in]	lenset	Set of allowed loop lengths

Returns: MotifOPs of all ideal loops with given lengths/cutpoints connecting two residues of the given abegos Given desired lengths, compute a set of idealized loop motifs via Nobu/Rie/YuRu rules

Parameters

[in]	abego1	Abego of residue immediately before the loop
[in]	abego2	Abego of residue immediately after the loop
[in]	lenset	Set of allowed loop lengths
[in]	cutpoint_set	Set of allowed cutpoint residues. A value of N indicates the Nth residue of the loop is a LOWER_CUTPOINT and the (N+1)th residue is an UPPER_CUTPOINT

Returns: MotifOPs of all ideal loops with given lengths/cutpoints connecting two residues of the given abegos

If extend_ss is true, "extension" of SS elements by adding residues of the same abego type is allowed. For example, connecting A–>A, you might get a 4-residue loop of type A-ABGA-A. If false, only different abegos are allowed, and you might get a 4-residue loop of type A-BGAB-A

References core::scoring::abego, add_cutpoints(), extract_ideal_motifs(), protocols::denovo_design::components::get_secstruct_from_abego(), match_ss_to_abego_, note_fwd_element_extensions(), note_rev_element_extensions(), retrieve_loop_abegos(), protocols::TR(), and use_hh_rules_2021_.

IdealAbegoGenerator::Abegos protocols::denovo_design::components::IdealAbegoGenerator::generate_extended_abegos	(	Abegos const &	no_extension_loops,
		char const	abego_n,
		char const	abego_c
	)

staticprivate

References extension_lengths.

Referenced by IdealAbegoGenerator().

void protocols::denovo_design::components::IdealAbegoGenerator::note_fwd_element_extensions	(	Motif &	motif,
		char const	sschar,
		char const	element_abego
	)		const

private

References protocols::denovo_design::components::Segment::abego(), protocols::denovo_design::components::Segment::elem_length(), and protocols::denovo_design::components::Segment::set_ss().

Referenced by generate().

void protocols::denovo_design::components::IdealAbegoGenerator::note_rev_element_extensions	(	Motif &	motif,
		char const	sschar,
		char const	element_abego
	)		const

private

References protocols::denovo_design::components::Segment::abego(), protocols::denovo_design::components::Segment::elem_length(), and protocols::denovo_design::components::Segment::set_ss().

Referenced by generate().

IdealAbegoGenerator::Abegos protocols::denovo_design::components::IdealAbegoGenerator::retrieve_loop_abegos	(	char const	abego1,
		char const	abego2
	)		const

References extend_ss(), extended_abegos_, and protocols::TR().

Referenced by generate().

void protocols::denovo_design::components::IdealAbegoGenerator::set_extend_ss ( std::string const & extend_ss )

if true, secondary structure may be extended to close the loop. Overall size of the insert will not change. Therefore, a 4 residue loop might extend a helix by 2 residues and have a 2-residue ideal loop if extend_ss is true. If extend_ss is false, a 4 residue loop must have four loop residues.

References extend_ss(), and extend_ss_.

void protocols::denovo_design::components::IdealAbegoGenerator::set_hh_rules_2021 ( bool const use_hh_rules )

inline

if true, the connection rules from https://doi.org/10.1101/2021.03.10.434454 will be used.. If false, all possible abego combinations will be sampled

References use_hh_rules_2021_.

Member Data Documentation

IdealAbegoGenerator::Abegos const protocols::denovo_design::components::IdealAbegoGenerator::aa_no_extension

staticprivate

Initial value:

= {
"B", "G",
"BB", "GB",
"BAB", "GBB", "BBG",
"BAAB",
}

Referenced by IdealAbegoGenerator().

IdealAbegoGenerator::Abegos const protocols::denovo_design::components::IdealAbegoGenerator::aa_no_extension_all

staticprivate

Initial value:

= {
"B", "G",
"BB", "BG", "GB", "GG",
"BBB", "BBG", "BGB", "BGG", "BAB", "BAG",
"GBB", "GBG", "GGB", "GGG", "GAB", "GAG",
"BBBB", "BBBG", "BBGB", "BBGG", "BBAB", "BBAG",
"BGBB", "BGBG", "BGGB", "BGGG", "BGAB", "BGAG",
"BABB", "BABG", "BAGB", "BAGG", "BAAB", "BAAG",
"GBBB", "GBBG", "GBGB", "GBGG", "GBAB", "GBAG",
"GGBB", "GGBG", "GGGB", "GGGG", "GGAB", "GGAG",
"GABB", "GABG", "GAGB", "GAGG", "GAAB", "GAAG"
}

Referenced by IdealAbegoGenerator().

IdealAbegoGenerator::Abegos const protocols::denovo_design::components::IdealAbegoGenerator::ab_no_extension = { "GB", "GBA", "BAA", "GBB", "GBAB", "BAAB" }

staticprivate

Referenced by IdealAbegoGenerator().

IdealAbegoGenerator::Abegos const protocols::denovo_design::components::IdealAbegoGenerator::ba_no_extension = { "AB", "GBB", "BAB" }

staticprivate

Referenced by IdealAbegoGenerator().

IdealAbegoGenerator::Abegos const protocols::denovo_design::components::IdealAbegoGenerator::bb_no_extension = { "GG", "EA", "AA", "AAG" }

staticprivate

Referenced by IdealAbegoGenerator().

std::string protocols::denovo_design::components::IdealAbegoGenerator::extend_ss_ = "1"

private

Referenced by extend_ss(), and set_extend_ss().

SecstructAbegoMap protocols::denovo_design::components::IdealAbegoGenerator::extended_abegos_

private

Referenced by IdealAbegoGenerator(), and retrieve_loop_abegos().

std::map< char, core::Size > const protocols::denovo_design::components::IdealAbegoGenerator::extension_lengths

staticprivate

Initial value:

= boost::assign::map_list_of

( '-', 0 ) ( 'B', 1 ) ( 'A', 3 )

Referenced by generate_extended_abegos().

bool protocols::denovo_design::components::IdealAbegoGenerator::match_ss_to_abego_ = false

private

Referenced by generate().

std::string protocols::denovo_design::components::IdealAbegoGenerator::segment_name_

private

Referenced by extract_ideal_motifs().

bool protocols::denovo_design::components::IdealAbegoGenerator::use_hh_rules_2021_ = true

private

Referenced by generate(), and set_hh_rules_2021().

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

src/protocols/denovo_design/components/IdealAbegoGenerator.hh
src/protocols/denovo_design/components/IdealAbegoGenerator.cc

Public Types

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation