John W. Campbell
This section of the Java Development Library is with classes which are
specifically written for use in programs associated with Protein
Crystallography.
List of sections:
Data Storage Classes
Diffraction Data Module (DDM)
Space Group Symmetry
Diffraction Image Classes
Image Reader Classes
Crystallographic Calculations
Reflection Lists
Orientation Refinement
JdlPXImage User Defined Options
These classes are for storing some basics sets of crystallographic
parameters, in particular those required for the prediction of
diffraction patterns.
List of subsections in this section:
Cell Parameters
Reciprocal Cell Parameters
Unique Cell Parameters
Unique ReciprocalCell Parameters
X-ray Source
Detector Basics
Positioned Detector
Positioned Crystal
Detector Limits
The JdlCell class stores a real cell and has methods
to determine the corresponding reciprocal cell if required.
Document Link: Cell - JdlCell
The JdlReciprocalCell class stores a reciprocal cell and has methods
to determine the corresponding real cell if required.
Document Link: Reciprocal Cell - JdlReciprocalCell
The JdlUniqueCell class stores a real cell as the unique cell
parameters appropriate to its crystal system and has methods
to return that data or re-generate a full set of cell parameters.
Document Link: Unique Cell - JdlUniqueCell
The JdlUniqueReciprocalCell class stores a reciprocal cell as the unique
reciprocal cell parameters appropriate to its crystal system and has methods
to return that data or re-generate a full set of reciprocal cell parameters.
Document Link: Unique Reciprocal Cell - JdlUniqueReciprocalCell
The JdlXraySource class stores parameters related to the X-ray source.
Document Link: X-ray Source Parameters - JdlXraySource
The JdlDetectorBasics class stores the basic set of parameters
defining a detector system for collecting protein crystallographic
data with a flat detector.
Document Link: Detector Object - JdlDetectorBasics
The JdlPositionedDetector class stores details of a set (positioned)
detector. This includes references to a JdlXraySource and
a JdlDetectorBasics object and has additional parameters (e.g.
the crystal to detector distance and detector rotation angles) to
define the current position of the detector setup.
Document Link: Positioned Detector Object - JdlPositionedDetector
The JdlPositionedCrystal class stores details of a set crystal with
one or two additional parameters directly relevant to the prediction
of diffraction images.
Document Link: Positioned Crystal Object - JdlPositionedCrystal
The JdlDetectorLimits class stores some limits which may be used to
select parts of a detector image for processing. Note that the maximum
radius 'rmax' is not stored here but is stored in a JdlPositionedDetector
object.
Document Link: Detector Limits - JdlDetectorLimits
The Diffraction Data Module (DDM) defines a set of parameters
for use in the initial stages of processing or predicting sets of
protein crystallographic X-ray diffraction images.
List of subsections in this section:
DDM Class
The JdlDiffractionDataModule class implements the Diffraction Data
Module, defining the DDM keyworded parameters, and having a range
of methods including those to set and get parameter values, to
read and parse DDM files and to write DDM data files.
Document Link: Diffraction Data Module Class - JdlDiffractionDataModule
These classes handle the space group symmetry.
List of subsections in this section:
Symmetry
Symmetry Operators
The JdlSymmetry class stores and processes space group symmetry.
Document Link: Space Group Symmetry - JdlSymmetry
The JdlSymops class contains a built in list of symmetry operators
for most of the space groups used in Protein Crystallography. It
is based on the data from a CCP4 symops.lib file and an updated
version of the object can be prepared from such a file using
the MakeJdlSymops program.
Document Link: Symmetry Operators - JdlSymops
This class provides a means for reading and storing X-ray diffraction
images. It supports a range of currently used image file formats which
could be extended as needed in the future.
List of subsections in this section:
Diffraction Image
Image Data Class
Collect Images
Axis Order
The JdlDiffractionImage class reads in, stores and manipulates the data
of an X-ray diffraction image.
Document Link: Diffraction Image - JdlDiffractionImage
The JdlImageData class provides an object to hold details of an image
to be passed between image handling objects such as the JdlPXImage
display object. Such an object may be returned from a JdlDiffractionImage
object in the JdlPX section of the package if this was used. The object
may also, optionally, hold a background image associated with the stored image.
Document Link: Image Data - JdlImageData
The JdlImageCollector class collects together a set of images, either
adding (and averaging) them or overlaying them by taking the maximum
of the values at each pixel.
Document Link: Image Collector - JdlImageCollector
The JdlAxisOrder class sets up image axis order data based on an axis
order string (e.g. +xd-yd). The methods available return an order code
based on the MOSFLM program coordinate axes convention as used in
other JDL classes.
Document Link: Axis Order - JdlAxisOrder
These classes provide an Interface used by the JdlDiffractionImage
and JdlImageData classes to read image files and varios classes implementing
this interface to read a selection of X-ray diffraction image file types.
List of subsections in this section:
Image Reader Interface
Basic Image Reader
ADSC Image Reader
MAR Image Reader
WI Image Reader
Picture Image Reader
An interface for classes which can read in an image from a file and store
the data and related parameters as defined in a JdlImageData object.
Document Link: Image Reader Interface - JdlImageReader
Image reader to read a variety of image file formats which can be defined
by a small selection of parameters.
Document Link: Basic Image Reader - JdlBasicImageReader
Image reader to read ADSC images in their original format or in imgCIF/CBF
format.
Document Link: ADSC Image Reader - JdlADSCImageReader
Image reader to read MAR format image files (raw or compressed).
Document Link: Mar Image Reader - JdlMarImageReader
Image reader to read image files as written by the 'Write Image' (WI)
option of the PXImage program.
Document Link: WI Image Reader - JdlWIReader
Image reader to read picture files supported by Java e.g. JPEG/PNG/GIF
files. These can then be displayed with the PXImage program though
that is not its primary purpose.
Document Link: Picture Image Reader - JdlPictureImageReader
This section contains classes with methods to carry out some basic
crystallographic calculations.
List of subsections in this section:
Crystal Calculations Class
Resolution
Distortion Corrections
Re-assign Rotation Reflection Flags
Re-assign Laue Spot Flags
Predict Laue Harmonic Deconvolution
Test Lambda Curve
IPDISP Options
The JdlCrystalCalculations class provides some static methods to
perform selected crystallographic calculations. These include methods
for converting between detector and reciprocal lattice coordinates,
setting up crystallographic matrices and predicting reflections for
Rotation and Laue images and Unique data sets. In the latter cases,
the output format for the reflection/spot/unique lists is not
fixed by the methods but is carried
out by a class implementing an appropriate output handler method; this
allows for their use in a wider context than within the use of the
JDL classes where specific classes for handling reflection/spot
lists are used (see also the Reflection Lists section).
Document Link: Crystallographic Calculations - JdlCrystalCalculations
The JdlResolution class calculates, from the cell constants,
coefficients which are then used to determine the resolution of
individual reflections as required.
Document Link: Resolution Calculation - JdlResolution
The JdlDistortionCorrections class stores the parameters required for
making distortion corrections to image spot positions for X-ray
diffraction images and provides methods to apply/remove these corrections.
Document Link: Image Distortion Corrections - JdlDistortionCorrections
The JdlReflectionReflag class is used by a JdlView JdlPXSimulations
object to reassign some reflection flags when using the interactive
Rotation plots option.
Document Link: Re-flag Reflection - JdlReflectionReflag
The JdlLaueSpotReflag class is used by a JdlView JdlPXSimulations
object to reassign some spot flags when using the interactive
Laue plots option.
Document Link: Re-flag Laue Spot - JdlLaueSpotReflag
The JdlLaueDeconvPredictor class predicts the potential deconvolution
of Laue reflections from multiple spots recorded at different wavelengths.
Document Link: Laue Deconvolution Predictor - JdlLaueDeconvPredictor
The JdlTestLambdaCurve class provides a test wavelength normalisation
curve for use in test predictions of Laue harmonics deconvolution.
Document Link: Lambda Curve - JdlTestLambdaCurve
The JdlIPDispOptions class provides some user options for a JdlPXImage
object based on options which were available in the CCP4 image display program
IPDISP (Phil Evans). Options are available to measure the image centre,
display resolution circles, calculate the resolution of a spot, calculate
a cell spacing and fit a circle to a set of selected points.
Document Link: IPDISP Calculations - JdlIPDispOptions
This section contains classes to store and manipulate lists of predicted
Rotation, Laue or Unique reflections. Interface classes for the output
of predicted reflections to be used in conjunction with the prediction
methods in the JdlCrystalCalculations class (see above).
List of subsections in this section:
Predicted Reflection List
Predicted Reflection
Reflection Output Handler
Predicted Laue Spots List
Generated Laue Spot
Predicted Laue Spot
Laue Spot Output Handler
Unique Reflections List
Unique Reflection
Unique Reflection Output Handler
Search Image Spots List
Search Image Spot
The JdlPredictedReflectionsList class stores a list of predicted reflections
for a Rotation image and manipulate reflections in that list. It
has a method to predict the list using a method from the
JdlCrystalCalculations class. A method is also available to determine
the spatially overlapped spots.
Document Link: Predicted Reflections List - JdlPredictedReflectionsList
The JdlPredictedReflection class stores details of a predicted
reflection (indices, detector position other parameters) as stored in
the predicted relections list described above. Most
of the item values are accessible via public fields.
Document Link: Predicted Reflection - JdlPredictedReflection
The JdlRotReflOutputHandler class provides an interface for outputting
predicted reflection details (Rotation method) for the reflection
prediction methods in the JdlCrystalCalculations class.
Document Link: Output Rotation Reflections - JdlRotReflOutputHandler
The JdlPredictedLaueSpotsList class stores a list of predicted spots
for a Laue image and manipulate spotss in that list. It
has a method to predict the list using a method from the
JdlCrystalCalculations class. A method is also available to determine
the spatially overlapped spots.
Document Link: Predicted Laue Spots List - JdlPredictedLaueSpotsList
The JdlGeneratedLaueSpot class stores details of a predicted Laue spot as
it is generated. It is used by the Laue prediction methods in the
JdlCrystalCalculations class and is passed to the the spot
output method of a class implementing the JdlLaueSpotOutputHandler
interface.
Document Link: Generated Laue Spot - JdlGeneratedLaueSpot
The JdlPredictedLaueSpot class stores details of a predicted
Laue spot (indices, multiplicity, wavelength, detector position
other parameters) as stored in the predicted Laue spots list described above.
Most of the item values are accessible via public fields.
Document Link: Predicted Laue Spot - JdlPredictedLaueSpot
The JdlLaueSpotOutputHandler class provides an interface for outputting
predicted spot details (Laue method) for the spot
prediction methods in the JdlCrystalCalculations class.
Document Link: Output Laue Spots - JdlLaueSpotsOutputHandler
The JdlUniqueReflectionsList class stores a list of unique reflections
with measurement counts. The class has methods for adding/deleting
reflections and sorting the reflection list. It has a method
for generating the unique reflections (using a method in the
JdlCrystalCalculations class) given the appropriate, cell,
symmetry, wavelength and resolution parameters. In general, reflections are
handled as JdlUniqueReflection objects.
Document Link: Unique Reflections List - JdlUniqueReflectionsList
The JdlUniqueReflection class stores details of a unique reflection
with a series of items to hold counts of measurements associated with
that reflection so that unique data coverage may be analysed.
Document Link: Unique Reflection - JdlUniqueReflection
The JdlUnqReflOutputHandler class provides an interface for outputting
unique reflection details for the unique reflection
prediction method in the JdlCrystalCalculations class.
Document Link: Output Unique Reflections - JdlUnqReflOutputHandler
The JdlSearchImageSpotsList class stores a list of spot positions found
from a search of an X-ray diffraction image.
Document Link: Search Spots List - JdlSearchImageSpotsList
The JdlSearchImageSpot class stores details of a spot position found
from a search of an X-ray diffraction image.
Document Link: Spot from Image Search - JdlSearchImageSpot
This section contains classes used in refining a crystal orientation and
related parameters using data from an observed diffraction pattern (rotation
method).
List of subsections in this section:
Refine Orientation
Refined Parameters
Observed Reflection
The JdlRefineOrientation class is used to refine a crystal setting and
related parameters using a set of observed reflection positions (rotation
method of data collection).
Document Link: Refine orientation - JdlRefineOrientation
The JdlRefinedOrientationParameters class stores details of the refined
parameters as returned by the JdlRefineOrientation class methods.
Document Link: Refined Orientation Parameters - JdlRefinedOrientationParameters
The JdlObservedReflection class stores details of an observed reflection
position with assigned indices and a flag indicating whether or not
it is to be used in a refinement.
Document Link: Observed Reflection - JdlObservedReflection
This section contains classes for additional 'user defined' options which
may be passed to the JdlPXImage class (from JdlView) to enhance its
functionality. The classes passed to JdlPXImage must implement the
JdlPXImageUserOptions interface. Supporting classes specific to these
classes are also included in this section.
List of subsections in this section:
Find Spots
Read/Write DDM Data
Find Crystal Setting
Setting Determination
Setting Solution
The JdlFindSpotsOptions class provides 'user defined' options for JdlPXImage
for searching for spots on the image and, if required, marking the found
spot positions on the image.
Document Link: Find Spots Options - JdlFindSpotsOptions
The JdlImgDDM class provides 'user defined' options for JdlPXImage
for reading, editing and writing a Diffraction Data Module (DDM) parameters
file relating to the image. Such data are also accessible to other
JdlPXImageUserOptions implementing classes.
Document Link: Image DDM Options - JdlImgDDM
The JdlFindSettingOptions class provides 'user defined' options for JdlPXImage
for determining a crystal orientation for a known cell using Fourier
transform based methods. The class includes options for image background
calculation and searching for spots on the image.
Document Link: Find Setting Options - JdlFindSettingOptions
The JdlSetting3DFT class is used in support of the Find Crystal Setting
'user defined' options for JdlPXImage as implemented in the
JdlFindSettingOptions class. It uses 3-D Fourier transform calculations
based on a set of observed spot positions found from an image search
and peak searches at the appropriate cell vector distances.
Document Link: Crystal Setting Finder - JdlSetting3DFT
The JdlSettingSolution class is used to store details of a crystal
setting determined using the JdlSetting3DFT class methods.
Document Link: Setting Solution - JdlSettingSolution
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