4.10.6 - Setting Solution - JdlSettingSolution

John W. Campbell

4.10.6.1 Introduction

Class, fields, constructor and methods:

4.10.6.2 Class Details

Package:

Jdl.JdlPX;

Class name:

JdlSettingSolution

Class definition:

public class JdlSettingSolution

Extends:

Object

Implements:

Cloneable

Actions:

none

4.10.6.3 Accessible Fields

public int nvect

Number of vectors used from 3DFT search (For a good solution should be 3 but may be 2 as an orientation can be determined from just a pair of cell vectors).

public boolean[] found_vec

Flags indicating which vectors were used from the 3DFT search.

public JdlVec[] peak_vectors

Array of peak positions for the three cell vectors.

public int[] peak_heights

Array of peak heights for the three cell vectors. For a vector not found in the original search the peak height calculated may be less than the used peak threshold value (or even negative).

public JdlCell cell_from_peaks

Cell vectors from peak positions if nvect=3 (otherwise may be null or have zero values)

public int num_checked_vec

Number of cell related vectors for which peak heights were checked; i.e. number of main cell vectors (100, 010, 001) and related cell vectors (011, 101, 110, and 111) (+ a centering vector if appropriate).

public boolean[] checked_vec_found

Array of 'peak found' flags for the 'num_checked_vec' checked cell related vectors; true = found (above threshold), false = not found (not above threshold)

public int[] checked_vec_heights

Array of peak heights for the ncheck checked cell related vectors.

public double[] phi_initial

Missetting angles (phi_x, phi_y, phi_z) from initial solution.

public boolean vecref

Missetting angles refined against peak vectors flag = true yes, = false no.

public double vecref_fmin_before

Missetting angles refinement - fmin before refinement (-1.0 if not set)

public double vecref_fmin_after

Missetting angles refinement - fmin after refinement (-1.0 if not set)

public double[] phi_vecref

Missetting angles (phi_x, phi_y, phi_z) refined against vector peak positions (initially set to phi_initial values).

4.10.6.4 Constructor

4.10.6.4.1 Introduction

Constructor:

4.10.6.4.2 Constructor

Constructor Definition:

public JdlSettingSolution(int nvect, boolean[] found, JdlVec[] peak_vec, int[] peak_height, JdlCell cell, int nchk, boolean[] chk_found, int[] chk_height, Jdl3x3 umatr, double[] phis)

Parameters List:

nvect

Number of vectors used from 3DFT search (2 or 3)

found

Array of 3 flags indicating which two or three vectors were found from the 3D search (true=found, false = not found)

peak_vec

The three cell vector peak positions.

peak_height

The three cell vector peak heights.

cell

A JdlCell object containing the six cell vectors found from the peak positions in Angstroms and degrees - must be given if nvect=3 but may be zero valued or null otherwise.

nchk

Number of cell related vectors for which peak heights were checked.

chk_found

Array of checked vectors found flags.

chk_height

Array of checked vector heights.

umatr

The 'U' matrix.

phis

Array with the initial missetting angles calculated for the solution.

4.10.6.5 Refinement Method

4.10.6.5.1 Introduction

Method:

4.10.6.5.2 Initial Refinement - refineMissettingAgainstVectors

Method Definition:

public void refineMissettingAgainstVectors(JdlCell cell, double alam)

Parameters List:

cell

The real cell.

alam

The wavelength in Angstroms.

4.10.6.6 Listing Methods

4.10.6.6.1 Introduction

Methods:

4.10.6.6.2 List Contents - listContents

Method Definition:

public void listContents(int level)

Parameters List:

level

Listing level (1-3)

4.10.6.6.3 List Contents - listContents

Method Definition:

public void listContents(String str, int level)

Parameters List:

str

A string to identify the solution

level

Listing level (1-3)