Classes
class	ChainTerm

class	ExcludedFilter

class	FilterByProxTerm

class	FilterBySASA

class	MasterFilter

class	NeighTeller

class	FilterByIndoleCOO
	Class to filter out constellations that cannot (putatively) be rescued by compounds containing indole and a carboxylic group. More...

class	FilterByTryptamine
	Class to filter out constellations that cannot (putatively) be rescued by tryptamine. More...

class	FilterByAmphetamine
	Class to filter out constellations that cannot (putatively) be rescued by amphetamine. More...

class	FilterByHistamine
	Class to filter out constellations that cannot (putatively) be rescued by histamine. More...

struct	ResMut
	A class to represent the mutation of a residue. More...

class	HBondCommon
	A class to hold data structures and functions shared by filters that consider hydrogen bonding. More...

class	OrientCommon
	A class to hold data structures and functions common to filters that consider how groups of atoms within a constellation are oriented. More...

class	PresenceCommon
	A class to hold data structures and functions shared by filters that check whether the amino acids and atoms they require in the constellation are indeed present. More...

class	ResidueMask

class	SingResCnlCrea

Typedefs
typedef utility::pointer::shared_ptr< ResidueMask >	ResidueMaskOP

Functions
bool	has_aromatic (Pose const &ps, utility::vector1< core::Size > const &cnl)
	: returns true if the given constellation contains at least one aromatic ring; returns false otherwise. More...

void	get_chain_terms (core::pose::Pose const &ps, utility::vector1< ChainTerm > &chains)
	identifies each chain and its N- and C-terminal residues in a pose. More...

void	print_chains (utility::vector1< ChainTerm > const &chains, basic::Tracer &t)
	Prints the N- and C-terminal residues of all chains. More...

xyzVector< Real >	cnl_com (vector1< core::Size > const &cnl, Pose const &ps)
	returns the center of mass of a constellation More...

numeric::xyzVector< core::Real >	cnl_com (utility::vector1< core::Size > const &cnl, core::pose::Pose const &ps)
	returns the center of mass of a constellation More...

bool	has_prox_termini (Pose const &ps, ChainTerm const &chain, core::Size NRES, Real DMAX2)
	Tells whether a chain has proximal N- and C-termini. More...

bool	has_prox_termini (core::pose::Pose const &ps, ChainTerm const &chain, core::Size NRES, core::Real DMAX2)
	tells whether a chain has proximal termini More...

bool	at_interface (Pose const &ps, utility::vector1< core::Size > const &cnl)
	Returns true if a constellation is shared by multiple chains; returns false otherwise. More...

static basic::Tracer	TR ("protocols.constel.NeighTeller")

void	mk_neigh_list (core::Size const tgtnum, utility::vector1< bool > &neighs, Pose &ps)
	Creates the list of residues that are neighbors of a given target residue. More...

void	pair_constel_set_idx2 (core::Size const i, core::Size const j, Pose const &pose_init)
	Outputs all pair-constellations between a given pair of residues. More...

std::string	create_constel_records_from_sfr (Pose const &ps, utility::vector1< core::Size > const &residues_to_print)
	concatenates into a string all the PDB ATOM records of a constellation More...

void	out_pair_constel (ResMut const &mut1, ResMut const &mut2, Pose &ps)
	Outputs to file a constellation obtained from mutating a pair of residues. More...

void	triple_constel_set_idx3 (core::Size const i, core::Size const j, core::Size const k, Pose const &pose_init)
	Outputs all triple-constellations among a given triple of residues. More...

void	out_triple_constel (ResMut const &mut1, ResMut const &mut2, ResMut const &mut3, Pose &ps)
	Outputs to file a constellation obtained from mutating a triple of residues. More...

static basic::Tracer	TR ("src.protocols.constel.SearchOptions")

void	pair_constel_set (int const target_pdb_number, char const target_pdb_chain, Pose &pose_init)
	Searches pair-constellations by target residue. More...

void	pair_constel_set (std::string const &tgtmuts, Pose &pose_init)
	Searches pair-constellations by pair of mutations. More...

void	triple_constel_set (int const target_pdb_number, char const target_pdb_chain, Pose &pose_init)
	Searches for the triple-constellations of a target residue. More...

void	target_constel (std::string &tgtcnl_fil, Pose &ps)
	Searches for a target constellation. More...

Typedef Documentation

◆ ResidueMaskOP

typedef utility::pointer::shared_ptr< ResidueMask > protocols::constel::ResidueMaskOP

Function Documentation

◆ at_interface()

bool protocols::constel::at_interface	(	Pose const &	ps,
		utility::vector1< core::Size > const &	cnl
	)

Returns true if a constellation is shared by multiple chains; returns false otherwise.

Parameters

[in]	ps	pose containing the constellation
[in]	cnl	pose indexes of the residues forming the constellation

References core::chemical::element::N, and core::pose::Pose::pdb_info().

Referenced by core::select::util::calc_interacting_vector(), core::select::util::calc_interface_vector(), and protocols::stepwise::modeler::packer::figure_out_working_interface_res().

◆ cnl_com() [1/2]

numeric::xyzVector<core::Real> protocols::constel::cnl_com	(	utility::vector1< core::Size > const &	cnl,
		core::pose::Pose const &	ps
	)

returns the center of mass of a constellation

◆ cnl_com() [2/2]

xyzVector<Real> protocols::constel::cnl_com	(	vector1< core::Size > const &	cnl,
		Pose const &	ps
	)

returns the center of mass of a constellation

Parameters

[in]	cnl	pose residue indexes of the residues forming the constellation.
[in]	ps	pose to which all residues in the constellation belong.

Remarks: 1. It is assumed that the residues forming the constellation have non-zero occupancy only for the atoms that belong to the constellation. This is guaranteed if the residues forming the constellation were previously passed as arguments to function "SingResCnlCrea::zero_occ_for_deleted_atoms()".

References protocols::membrane::com(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::constel::FilterByProxTerm::is_satisfied().

◆ create_constel_records_from_sfr()

std::string protocols::constel::create_constel_records_from_sfr	(	Pose const &	ps,
		utility::vector1< core::Size > const &	residues_to_print
	)

concatenates into a string all the PDB ATOM records of a constellation

Parameters

[in]	ps	pose containing the constellation
[in]	residues_to_print	pose indexes of the residues forming the constellation

References core::io::pdb::create_pdb_line_from_record(), core::io::pdb::create_records_from_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

Referenced by out_pair_constel(), and out_triple_constel().

◆ get_chain_terms()

void protocols::constel::get_chain_terms	(	core::pose::Pose const &	ps,
		utility::vector1< ChainTerm > &	chains
	)

identifies each chain and its N- and C-terminal residues in a pose.

Parameters

[in]	ps	the pose.
[out]	chains	vector to be filled with ChainTerm items for the chains in the pose.

chains[i] represents the ith chain in the pose built using only the protein residues of pose ps (i=1,...,N, where N is the number of such chains)

References core::pose::Pose::chain_begin(), core::pose::Pose::chain_end(), core::conformation::Residue::is_protein(), core::pose::Pose::num_chains(), core::pose::Pose::pdb_info(), core::io::pose_from_pose(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::constel::FilterByProxTerm::init().

◆ has_aromatic()

bool protocols::constel::has_aromatic	(	Pose const &	ps,
		utility::vector1< core::Size > const &	cnl
	)

: returns true if the given constellation contains at least one aromatic ring; returns false otherwise.

Parameters

[in]	ps	pose containing the constellation
[in]	cnl	pose indexes of the residues forming the constellation

Histidine is considered to be aromatic.

Remarks

It is assumed that:

The residues forming the constellation have non-zero occupancy only for the atoms that belong to the constellation. This is guaranteed if the residues forming the constellation had their indexes previously passed as arguments to function "SingResCnlCrea::zero_occ_for_deleted_atoms()".

References core::conformation::Residue::aa(), core::chemical::aa_his, core::conformation::Residue::atom_index(), core::conformation::Residue::is_aromatic(), core::chemical::element::N, core::pose::Pose::pdb_info(), and core::pose::Pose::residue().

◆ has_prox_termini() [1/2]

bool protocols::constel::has_prox_termini	(	core::pose::Pose const &	ps,
		ChainTerm const &	chain,
		core::Size	NRES,
		core::Real	DMAX2
	)

tells whether a chain has proximal termini

◆ has_prox_termini() [2/2]

bool protocols::constel::has_prox_termini	(	Pose const &	ps,
		ChainTerm const &	chain,
		core::Size	NRES,
		Real	DMAX2
	)

Tells whether a chain has proximal N- and C-termini.

Parameters

[in]	ps	pose to which the chain belongs.
[in]	chain	the chain.
[in]	NRES	number of residues forming either terminus.
[in]	DMAX2	squared maximum distance for proximity.

Returns: true if the chain has proximal termini; false otherwise.

The termini are considered to be proximal if at least one residue on one terminus is within the maximum distance of a residue on the other terminus. Distance is computed on C-alpha atoms.

References protocols::constel::ChainTerm::get_cps(), protocols::constel::ChainTerm::get_nps(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::constel::FilterByProxTerm::init().

◆ mk_neigh_list()

void protocols::constel::mk_neigh_list	(	core::Size const	tgtnum,
		utility::vector1< bool > &	neighs,
		Pose &	ps
	)

Creates the list of residues that are neighbors of a given target residue.

Creates the list of residues that are neighbors of a given residue.

Parameters

[in]	tgtnum	residue number of the target residue in its pose.
[out]	neighs	boolean mask filled in by this function to represent the list of neighbors. neighs[i] will be true if the ith residue in the pose is a neighbor of the target; otherwise neighs[i] will be false.
[in]	ps	pose that the target and its potential neighbors belong to.

References protocols::constel::NeighTeller::isneigh(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by pair_constel_set(), and triple_constel_set().

◆ out_pair_constel()

void protocols::constel::out_pair_constel	(	ResMut const &	mut1,
		ResMut const &	mut2,
		Pose &	ps
	)

Outputs to file a constellation obtained from mutating a pair of residues.

Parameters

[in]	mut1	representation of the mutation of the first residue.
[in]	mut2	representation of the mutation of the second residue.
[in]	ps	Rosetta pose that both residues belong to. In the pose, the occupancy of atoms in either residue is that AFTER the mutation.

Remarks

The file name of the constellation has the following format, SIIIIEC_siiiiec.pdb, where:

S is the first residue's start amino acid type
IIII is a four-digit field indicating the first residue's number in the input PDB file
E is the first residue's end amino acid type
C is the first residue's chain in the input PDB file
s is the second residue's start amino acid type
iiii is a four-digit field indicating the second residue's number in the input PDB file
e is the second residue's end amino acid type
c is the second residue's chain in the input PDB file

This function may set to zero the occupancy of additional atoms of the residues forming the constellation..

References protocols::constel::ResMut::cid, create_constel_records_from_sfr(), protocols::constel::ResMut::eaa, core::conformation::membrane::out, protocols::constel::ResMut::pdbn, protocols::constel::ResMut::psn, protocols::constel::ResMut::saa, protocols::constel::SingResCnlCrea::strip_atoms(), and protocols::constel::SingResCnlCrea::stripped().

Referenced by pair_constel_set(), pair_constel_set_idx2(), and target_constel().

◆ out_triple_constel()

void protocols::constel::out_triple_constel	(	ResMut const &	mut1,
		ResMut const &	mut2,
		ResMut const &	mut3,
		Pose &	ps
	)

Outputs to file a constellation obtained from mutating a triple of residues.

Parameters

[in]	mut1	representation of the mutation of the first residue.
[in]	mut2	representation of the mutation of the second residue.
[in]	mut3	representation of the mutation of the third residue.
[in]	ps	Rosetta pose that all three residues belong to. In the pose, the occupancy of atoms in each residue is that AFTER the mutation.

Remarks

The file name of the constellation has the following format, SIIIIEC_siiiiec_tjjjjfd.pdb, where:

S is the first residue's start amino acid type
IIII is a four-digit field indicating the first residue's number in the input PDB file
E is the first residue's end amino acid type
C is the first residue's chain in the input PDB file
s is the second residue's start amino acid type
iiii is a four-digit field indicating the second residue's number in the input PDB file
e is the second residue's end amino acid type
c is the second residue's chain in the input PDB file
t is the third residue's start amino acid type
jjjj is a four-digit field indicating the third residue's number in the input PDB file
f is the third residue's end amino acid type
d is the third residue's chain in the input PDB file

References protocols::constel::ResMut::cid, create_constel_records_from_sfr(), protocols::constel::ResMut::eaa, core::conformation::membrane::out, protocols::constel::ResMut::pdbn, protocols::constel::ResMut::psn, protocols::constel::ResMut::saa, protocols::constel::SingResCnlCrea::strip_atoms(), and protocols::constel::SingResCnlCrea::stripped().

Referenced by target_constel(), and triple_constel_set_idx3().

◆ pair_constel_set() [1/2]

void protocols::constel::pair_constel_set	(	int const	target_pdb_number,
		char const	target_pdb_chain,
		Pose &	pose_init
	)

Searches pair-constellations by target residue.

Extracts all the constellations formed by a target residue. Each constellation involves a pair of residues: the target residue and one of its neighbors. Different constellations are printed to different files.

Parameters

[in]	target_pdb_number	residue number of the target residue in the input PDB file.
[in]	target_pdb_chain	chain to which the target belongs in the PDB file.
[in]	pose_init	pose to which the target belongs.

References mk_neigh_list(), pair_constel_set_idx2(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

◆ pair_constel_set() [2/2]

void protocols::constel::pair_constel_set	(	std::string const &	tgtmuts,
		Pose &	pose_init
	)

Searches pair-constellations by pair of mutations.

Searches pair-constellations by mutation pair.

Extracts from a pose all the constellations that correspond to a given pair of mutations of amino acid types.

Parameters

[in]	tgtmuts	an AB_CD string identifying the desired pair of mutations, (A->B, C->D), where A, B, C, and D are amino acid types expressed in one-letter code.
[in]	pose_init	pose from which constellations have to be extracted.

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::NeighTeller::isneigh(), core::chemical::oneletter_code_from_aa(), out_pair_constel(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

◆ pair_constel_set_idx2()

void protocols::constel::pair_constel_set_idx2	(	core::Size const	i,
		core::Size const	j,
		Pose const &	pose_init
	)

Outputs all pair-constellations between a given pair of residues.

Parameters

[in]	i	pose index of the 1st residue.
[in]	j	pose index of the 2nd residue.
[in]	pose_init	the pose.

Remarks: Output files have the names and format specified in out_pair_constel()

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::SingResCnlCrea::list_allowable_mutations(), core::chemical::oneletter_code_from_aa(), out_pair_constel(), core::pose::Pose::pdb_info(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

Referenced by pair_constel_set().

◆ print_chains()

void protocols::constel::print_chains	(	utility::vector1< ChainTerm > const &	chains,
		basic::Tracer &	t
	)

Prints the N- and C-terminal residues of all chains.

prints the N- and C-terminal residues of all chains.

Parameters

[in]	chains	vector of ChainTerm items, each representing a different chain.
[out]	t	output tracer

The ith output line represents the ith chain in 'chains', for i=1,...,N, where N is the size of 'chains'.

References protocols::hybridization::t.

◆ target_constel()

void protocols::constel::target_constel	(	std::string &	tgtcnl_fil,
		Pose &	ps
	)

Searches for a target constellation.

Searches a single, target constellation.

Parameters

[in]	tgtcnl_fil	file specifying the target constellation.
[in]	ps	the pose

The format of the input file is as follows:

CID{1} RNU{1} ICO{1} AASTA{1} AAEND{1} ... CID{N} RNU{N} ICO{N} AASTA{N} AAEND{N}

where N is the number of residues forming the constellation and CID{i}, RNU{i}, ICO{i}, AASTA{i}, and AAEND{i} are the chain id, residue number, insertion code, start amino acid type, and end amino acid type of the ith residue contributing to the constellation (i=1,...,N). A blank chain identifier in the PDB file is denoted by ',' (comma); a blank insertion code in the PDB file is denoted by '_' (underscore).

The function exits if any input lines cannot identify any residue.

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::NeighTeller::is_neigh_tree(), core::chemical::element::N, core::chemical::oneletter_code_from_aa(), out_pair_constel(), out_triple_constel(), core::pose::Pose::pdb_info(), core::pose::Pose::size(), TR(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

◆ TR() [1/2]

static basic::Tracer protocols::constel::TR ( "protocols.constel.NeighTeller" )

static

Referenced by protocols::constel::ResidueMask::ResidueMask(), protocols::constel::SingResCnlCrea::strip_atoms(), target_constel(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

◆ TR() [2/2]

static basic::Tracer protocols::constel::TR ( "src.protocols.constel.SearchOptions" )

static

◆ triple_constel_set()

void protocols::constel::triple_constel_set	(	int const	target_pdb_number,
		char const	target_pdb_chain,
		Pose &	pose_init
	)

Searches for the triple-constellations of a target residue.

Searches triple-constellations by target residue.

Each constellation comprises a triple of spatially contiguous residues, among which is the target. Different constellations are printed to different files.

Parameters

[in]	target_pdb_number	residue number of the target residue in the input PDB file.
[in]	target_pdb_chain	chain to which the target belongs in the PDB file.
[in]	pose_init	pose to which the target belongs.

References protocols::constel::NeighTeller::isneigh(), mk_neigh_list(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and triple_constel_set_idx3().

◆ triple_constel_set_idx3()

void protocols::constel::triple_constel_set_idx3	(	core::Size const	i,
		core::Size const	j,
		core::Size const	k,
		Pose const &	pose_init
	)

Outputs all triple-constellations among a given triple of residues.

Parameters

[in]	i	pose index of the 1st residue.
[in]	j	pose index of the 2nd residue.
[in]	k	pose index of the 3rd residue.
[in]	pose_init	the pose.

Remarks: Output files have the names and format specified in out_triple_constel()

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::SingResCnlCrea::list_allowable_mutations(), core::chemical::oneletter_code_from_aa(), out_triple_constel(), core::pose::Pose::pdb_info(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

Referenced by triple_constel_set().

Classes

Typedefs

Functions

Typedef Documentation

◆ ResidueMaskOP

Function Documentation

◆ at_interface()

◆ cnl_com() [1/2]

◆ cnl_com() [2/2]

◆ create_constel_records_from_sfr()

◆ get_chain_terms()

◆ has_aromatic()

◆ has_prox_termini() [1/2]

◆ has_prox_termini() [2/2]

◆ mk_neigh_list()

◆ out_pair_constel()

◆ out_triple_constel()

◆ pair_constel_set() [1/2]

◆ pair_constel_set() [2/2]

◆ pair_constel_set_idx2()

◆ print_chains()

◆ target_constel()

◆ TR() [1/2]

◆ TR() [2/2]

◆ triple_constel_set()

◆ triple_constel_set_idx3()