Sails::TorsionAngleRefiner

public inlineTorsionAngleRefiner(std::vector< gemmi::Atom * > & atoms, std::vector< gemmi::Atom > & reference_atoms, Density & density,SuperpositionResult& superposition_result, double length, std::vector< double > & angle_mean, std::vector< double > & angle_range, std::vector< double > & torsion_mean, std::vector< double > & torsion_range)

Refines torsion angles for a set of atoms using reference atoms and density information.

Parameters

• atoms A reference to a vector of Atom pointers.

• reference_atoms A reference to a vector of Atom objects representing the reference atoms.

• density A reference to a Density object.

• superposition_result A reference to a SuperpositionResult object.

• length A double representing the length.

• angle_mean A reference to a vector of doubles representing the mean angles.

• angle_range A reference to a vector of doubles representing the angle ranges.

• torsion_mean A reference to a vector of doubles representing the mean torsions.

• torsion_range A reference to a vector of doubles representing the torsion ranges.

public doublescore_function(std::vector< double > & angles)

Calculates the score function for refining torsion angles based on a set of angles and the density score.

Parameters

• all_angles A reference to a vector of doubles representing the input angles.

Angles are in the order alpha beta gamma psi phi omega

Returns

The calculated score function value.

publicSuperpositionResultrefine()

Refines torsion angles using a Nelder-Mead optimization algorithm.

Returns

A SuperpositionResult object containing the refined residue, transform, and reference residue.

private doublem_length

The length of a linkage bond

private std::vector< double >m_angle_range

Allowed angle range for alpha, beta and gamma linkage angles.

private std::vector< double >m_torsion_range

Allowed angle range for phi, psi and omega linkage torsions.

private std::vector< double >m_angle_mean

Angle mean for alpha, beta and gamma linkage angles.

private std::vector< double >m_torsion_mean

Torsion angle mean range for phi, psi and omega linkage torsions.

private std::vector< gemmi::Atom * >m_all_atoms

List of pointers to all the atoms in the linkage to be refined

private std::vector< gemmi::Atom >m_reference_atoms

List of pointers to reference atoms in the linkage to be refined

private Density *m_density

Density object used for scoring to any derived density method (Xtal or EM)

private gemmi::Residuem_reference_residue

The reference residue used for superpositons

private doublecalculate_penalty_factor() const

Calculates the penalty factor after looking at the scoring method in the m_density object.

Returns

A double representing the penalty factor for the given density method.

private static doublecalculate_penalty(double angle, double angle_mean, double angle_stddev, double penalty_factor)

Calculates the penalty for a given angle based on its deviation from the mean angle using the penalty factor.

Parameters

• angle The angle to calculate the penalty for.

• angle_mean The mean angle.

• angle_stddev The standard deviation of the angle.

• penalty_factor The penalty factor to be applied.

Returns

The penalty value calculated for the given angle.