Class for assigning backbone suites to an RNA. More...

#include <RnaSuite.hpp>

Public Member Functions
	RnaSuite (const AtomicGroup &group, const string suite_defintion, const double suiteness_cutoff_)

	RnaSuite (const AtomicGroup &group, const string suite_definition)

void	assignSuitenameSuites ()
	Method to assign residues to backbone suites from Richardson et al.

void	calculateBackboneDihedrals ()
	Method to calculate backbone dihedrals for each RNA residue.

void	defineSuites (const string &suite_definition)
	Method to define suites used for assignment.

void	extractRnaBackboneAtoms (const AtomicGroup &group)
	Method to extract RNA backbone atoms from an AtomicGroup.

vector< string >	getSuiteDDGs () const
	Method to return the current indices into delta delta gamma clusters.

vector< vector< double > >	getSuiteDihedrals () const
	Method to return the current backbone dihedrals.

vector< string >	getSuiteNames () const
	Method to return the current assigned suite names.

vector< int >	getSuiteResids () const
	Method to return the suite residue indices.

vector< string >	getSuiteResnames () const
	Method to return the suite residue names.

double	getSuitenessCutoff () const
	Method to return the cutoff for the suiteness score of non-outliers.

vector< double >	getSuitenessScores () const
	Method to return the current suiteness scores.

void	printBackboneAtoms () const
	Method to print groups of backbone atoms for each dihedral.

void	printBackboneDihedrals () const
	Method to print backbone dihedrals for each residue.

void	printReferenceSuites () const
	Method to print reference suite names and mean dihedrals.

void	printSuites () const
	Method to print suite names, suiteness scores, and dihedrals.

void	setSuitenessCutoff (const double suiteness_cutoff_)
	Method to set the cutoff for the suiteness score of non-outliers.

Detailed Description

Class for assigning backbone suites to an RNA.

This class acts on an AtomicGroup and assigns backbone suites to any RNA residues present. It also calculates the "suiteness" score that describes how well the residue fits into its assigned suite. The constructor requires that the user specifies a path to a file defining reference suites. The suites from Richardson et al. (2008) RNA 14, 465-481 are included in $LOOS/share/suitename_definitions.dat

Member Function Documentation

◆ assignSuitenameSuites()

void loos::RnaSuite::assignSuitenameSuites ( )

Method to assign residues to backbone suites from Richardson et al.

This method assigns residues to one of the reference suites defined in the constructor. The suite of a residue is defined from delta of the previous residue to delta of the current residue.

◆ calculateBackboneDihedrals()

void loos::RnaSuite::calculateBackboneDihedrals ( )

Method to calculate backbone dihedrals for each RNA residue.

This method calculates the six RNA backbone dihedrals (i.e. alpha, beta, gamma, delta, epsilon, and zeta) for each residue.

◆ defineSuites()

void loos::RnaSuite::defineSuites ( const string & suite_definition )

Method to define suites used for assignment.

This method defines reference suites. The argument must be a path to a file containing records consisting of fields with a width of eight characters. An example file for the suites defined in Richardson et al. (2008) RNA 14, 465-481 is included in $LOOS/share/suitename_definitions.dat. Records can be:

suite name ddg delta(i-1) epsilon zeta alpha beta gamma delta(i) Define a reference suite with name given in field 2, ddg_index given in field 3, and dihedrals of the cluster center given in fields 4 through 10.

width delta(i-1) epsilon zeta alpha beta gamma delta Define default widths for scaled hyperellipsoid distances.

domsat sat_name dom_name dihedral_index sat_width dom_width Define dominant-satellite pair with name of satellite suite in field 2, name of dominant suite in field 3, index of dihedral dimension with altered width in field 4, width of that dimension for satellite suite in field 5, and width of that dimension for dominant suite in field 6. Additional dimensions and width can be specified in fields 7 through 9, fields 10 through 12, etc.

dihedral min max Define allowed ranges for a dihedral. "dihedral" can be one of "delta", "epsilon", "zeta", "alpha", "beta", or "gamma". The minimum value is given in field 2 and maximum value in field 3.

◆ extractRnaBackboneAtoms()

void loos::RnaSuite::extractRnaBackboneAtoms ( const AtomicGroup & group )

Method to extract RNA backbone atoms from an AtomicGroup.

This method selects RNA backbone atoms (i.e. P, O5', C5', C4', C3', and O3') and splits them into AtomicGroups by residue id.

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