protocols::constel::HBondCommon Class Reference

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

#include <Primitives.hh>

Static Public Member Functions
static void	init ()
	Initializes the data structures of this class. More...
static bool	is_rmoi_hbonded (core::pose::Pose const &ps, utility::vector1< core::Size > const &cnl, core::Size const im, bool const is_donor, utility::vector1< std::string > const &hb_atoms)
	Tells whether a residue's moiety forms hydrogen bonds. More...

Static Public Attributes
static core::scoring::hbonds::HBondDatabaseCOP	hb_database
	common database for the computation of hydrogen bonds More...

Detailed Description

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

Member Function Documentation

void protocols::constel::HBondCommon::init ( void  )

static

Initializes the data structures of this class.

References core::scoring::hbonds::HBondDatabase::get_database(), and hb_database.

bool protocols::constel::HBondCommon::is_rmoi_hbonded ( core::pose::Pose const &  ps, utility::vector1< core::Size > const &  cnl, core::Size const  im, bool const  is_donor, utility::vector1< std::string > const &  hb_atoms  )

static

Tells whether a residue's moiety forms hydrogen bonds.

Given a residue's moiety in a constellation, returns true if it forms at least a hydrogen bond; returns false otherwise.

Parameters

[in]	ps	pose to which the constellation belongs.
[in]	cnl	indexes in the pose of the residues that contribute atoms to the constellation.
[in]	im	index in cnl of the residue providing the moiety in question.
[in]	is_donor	boolean flag indicating whether the moiety has to be considered a donor (true) or an acceptor (false) of hydrogen bonds.
[in]	hb_atoms	names of the moiety's atoms whose hydrogen bonds are relevant.

Remarks

Assumption: the atom names in 'hb_atoms' are consistent with the value of 'is_donor'. Note: this function neglects hydrogen bonds formed by the moiety and any atom in the side chain of a residue that contributes to the constellation. Such a neglection is overrestrictive with respect to those atoms in the side chain that are not part of the constellation.

References core::scoring::hbonds::HBondSet::atom_hbonds(), core::scoring::hbonds::HBondSet::clear(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), hb_database, core::scoring::hbonds::identify_hbonds_1way(), core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), and core::scoring::Energies::tenA_neighbor_graph().

Referenced by protocols::constel::FilterByIndoleCOO::is_satisfied(), protocols::constel::FilterByTryptamine::is_satisfied(), protocols::constel::FilterByAmphetamine::is_satisfied(), and protocols::constel::FilterByHistamine::is_satisfied().

Member Data Documentation

core::scoring::hbonds::HBondDatabaseCOP protocols::constel::HBondCommon::hb_database

static

common database for the computation of hydrogen bonds

common database for computation of hydrogen bonds

Referenced by init(), and is_rmoi_hbonded().

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

• src/protocols/constel/Primitives.hh
• src/protocols/constel/Primitives.cc