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

private std::vector< double >m_angle_range

private std::vector< double >m_torsion_range

private std::vector< double >m_angle_mean

private std::vector< double >m_torsion_mean

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

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

privateDensity*m_density

private gemmi::Residuem_reference_residue

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.