Hacking KiNG - Kinemage Home Page
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1. functions receive the KPoint picked by the mouse or nu11 if none the coordinates of the click and the original MouseEvent The drag functions don t get coordinates directly but instead get the number of pixels the mouse has moved in x and y since the previous call to drag The variable mouseDragMode Is set to MODE_HORIZONTAL Or MODE VERTICAL if the drag started as primarily horizontal or vertical which simplifies implementing behaviors like Navigate s zoom Vs clip The variables isNearTop and isNearBottom allow for switching on behaviors like the pinwheel rotation that occurs when you drag near the top of the graphics area I anticipated that many tools would want to display a non modal dialog box when they were active like the Draw New tool does Thus if a tool returns a non null component from getToolPanel it will automatically be placed in a dialog that pops up when start is called via the show method and disappears when stop is called via the hide method The initDialog method was added later as a place to do things like add a menu bar to the dialog because the dialog variable is still nu11 during the constructor The whole thing is far more trouble and confusion than it s worth but I m too lazy to take it out now and force other tools to implement this behavior for themselves If you don t want to deal with it just let getToolPanel continue to return null and create your own dia2. sections that are currently being manipulated by the modeling tools The molten sections with their gaps filled in with coordinates from the frozen conformation constitute a complete molten conformation for the whole structure even though many parts of it are not actively being remodeled Each of these states can be retrieved as either a ModelState object or a temporary PDB file Tools or plugins that wish to interact with the model manager must implement the Remodeler interface and then call ModelManager2 registerTool to register themselves For convenience new tools may extend the abstract ModelingTool class which automates the process of finding a reference to the model mananger Whenever a tool wants to change the model conformation it calls ModelManager2 requestStateRefresh Each registered Remodeler is then queried in turn fed a starting ModelState and prompted to either return it unchanged or to create a new ModelState descended from the input modify it and return that Remodelers must not modify the input state directly but because of the hierarchical layered design of ModelStates the cost of making a change is only linear in the size of the change not linear in the size of the entire model In this way each Remodeler composites its own contributions onto the transformation from frozen state to molten state Thus one tool might move the backbone another might rotate a sidechain riding on that backbone and
3. driftwood isosurface EdgePlotter and is used by MarchingCubes to create the mesh or translucent triangle surface directly in memory from Vector or TrianglePoints EDMapPlugin was included in the main king package because it s not optional the Kinglet applet may try to create EDMapWindows directly in response to certain lt PARAM gt tags All that s left is a run down of the rest of the GUI code Keep in mind that all of the GUI makes heavy use of driftwood gui ReflectiveAction for event handling Without it I would have to write hundreds of small anonymous inner classes That way gives you more compile time type safety and is the Java standard but it becomes very costly to store that many classes in the JAR file and in memory even though they re small My way is much more efficient and I think much easier to read at the expense of some compile time safety checks KinTree implements the hierarchy editor using a JTree remember that all the classes descended from AGE implement TreeNode It s large because of all the tree manipulation functions Cut Copy and Paste are particularly lengthy None of it s terribly complicated though Some of those functions use the GroupEditor and PointEditor classes which are also used by the Edit Properties tool to modify groups subgroups lists and points The editors use instances of ColorPicker to graphically set the color of lists and points All of the m
4. friends but modified so that the user can pick one isolated polygon in the density like a phosphate peak in RNA and the tool will group all those vectors together and highlight them I m sure the mechanics of rearranging the vectorlist connectivity are very interesting here It also searches the electron density map for the highest density node with that polygon s bounding box and marks it as a suggested atom location king tool model This package contains a set of highly interdependent tools and plugins for modifying protein structure as represented in a Protein Data Bank PDB coordinate file The system is centered around the ModelManager2 plugin which other tools can access via the ToolBox s getPluginList method ModelManager2 requires both a kinemage and a PDB file unlike Mage the kinemage must already be loaded in KiNG as usual and the user is prompted to load a PDB into the model manager as soon as any tool makes a request that requires structural information It makes correlations between the graphics display and the invisible structural data typically by comparing Cartesian coordinates but sometimes based on kinemage point ID and atom or residue names The manager uses the driftwood moldb2 system to load store manipulate and save structural data ModelManager2 thinks about structure in terms of a static frozen conformation that represents the molecule as it currently stands and zero or more dynamic molten
5. http math nist gov javanumerics jama and has been stable since 9 11 2000 version 1 0 1 Should a new version be released the code can be dropped into the tree as is I ve made no modifications to it Driftwood got its name because it s one of the few words that contains my initials in order IWD and because its an apt metaphor for these little bits of floating code driftwood data This package defines my own implementation of a hash table plus doubly linked list Java provides this in the form of java util LinkedHashMap but only as of version 1 4 Also the standard implemention lacks any means of walking the linked list from an arbitrary starting point which is basically what makes this data structure useful in my opinion The algorithms are adapted from Introduction to Algorithms by Cormen Leiserson Rivest and Stein UberMap is the hash table implementation and uberSet is a lightweight implementation backed by an UberMap instance This is the same relationship java util HashMap and java util HashSet have driftwood gui This package contains a multitude of utility classes for constructing graphical user interfaces GUIs usually using the Swing toolkit that is part of Java Many of them are fairly simple and won t be mentioned here but several are worth elaborating on ReflectiveAction is used extensively throughout KiNG In the standard Java event model most GUI widgets generate an ActionEvent when som
6. structure in driftwood moldb2 but by now this awkward system is fairly well enshrined in the KiNG code There are at least two functionalities that are implemented directly as part of AcE that really should not have been part of these classes the checkboxes for turning groups on and off and the TreeNode interface The problem with the buttons was that the button had to be renamed whenever the group subgroup list was renamed The better solution would have been to recreate all the buttons every time a renaming occurred so that the button itself didn t have to be part of the ace class As a result we are limited to one and only one checkbox controlling any particular AGE which totally rules out multiple views of the same kinemage for better or worse Implementing TreeNode directly in AGE means that groups subgroups lists can be used directly in the JTree component of the hierarchy editor and it simplifies implementing the cut copy paste operations The downside is that it makes AGE unnecessarily complicated and may limit us to only one JTree at a time I don t know A better solution would have been to create MutableTreeNode wrappers around the AGEs Rounding out the container classes are MasterGroup and AnimationGroup which are and were originally respectively AGEs too MasterGroup implements a master button and pointmasters but doesn t actually keep track of its children anymore Masters are implemented by
7. ToolBox is a central part of KiNG s model for user interaction because it manages all the plugins that appear in the Tools menu At any given time there is one and only one active tool a specific kind of plugin which receives all the mouse and keyboard events from the ToolBox which in turn has received them from KinCanvas In fact this is the distinction between tools and plugins tools receive user input from the graphics area clicking dragging etc and ordinary plugins do not Thus there can be only one tool type plugin active at a time but any number of other plugins may be in use ToolBoxMw is a subclass that adds support for mouse wheel events which were added in Java 1 4 KinCanvas uses reflection to first try creating a ToolBoxmm and if that fails it creates an ordinary ToolBox instead That way Java 1 4 users get mouse wheel support but KiNG still runs with Java 1 3 The ToolBox loads the plugins and tools via reflection so that KING won t crash if they can t be loaded This is important both because some tools reside in other JAR files that could be missing and because some tools require Java 1 4 and will not work with earlier versions of Java The loading procedure uses a service provider model like the javax imageio package Thus in every JAR the file META INF services king Plugin contains the fully qualified class names of all plugins that should be loaded from that JAR one per line Every JAR file on the curr
8. for 3 D geometric calculations i e for calculations on points in R There are two interfaces Tuple3 and MutableTuple3 and one concrete implementation Triple of points in 3 D Triple represents either points or vectors depending on context and provides functions for dot product cross product etc Transform uses a 4x4 matrix to define rotations translations etc Transforms can be pre or post multiplied together Finally three utility classes Builder encodes some basic geometrical constructions like Dave s construct4 in Mage SuperPoser implements an algorithm for least squares superpositioning of two sets of points LsqPlane uses the singular value decomposition from JAMA to find the least squares plane through a cloud of points driftwood util This package contains miscellaneous utility classes for string manipulation and I O Strings provides several common parsing and formatting operations Props is an enhanced version of java util Preferences with automated parsing of numeric strings and fail fast behavior by default outputStreamTee SoftOutputStream and SoftLog together provide memory sensitive caching of messages written to standard output and standard error StreamTank collects output like an OutputStream then lets you read it back out as an InputStream ProcessTank leverages that to collect output from some external process Packages chiropraxis The classes in the chiropraxis group encapsulate a lot of higher level m
9. have actually been included in the base tool class but instead the tools just call e g rotate or zoom iN ToolServices when they get a mouse event However measures and markers do have to be separate from the tool implementations because as a user you don t want the markers measures state to be tied to which tool is active If that were true your markers would jump around just because you switched from Edit Properties to Move Point or a Mage like construct4 tool wouldn t be able to see the measurements you just made with the Navigate tool Thus markers and measures reside in ToolServices Since they don t have to deal with input from the graphics area plugins are easier to write than tools so Pll cover the Plugin class first Plugin is an abstract base class that all plugins and tools extend either directly or indirectly Most plugins should extend Plugin directly It defines several useful variables for accessing other parts of the drawing event system references to the ToolBox its ToolServices instance the KinCanvas that owns them and of course to KingMain There are only two methods a Plugin must implement The first is get ToolsMenuItem which returns a single JMenulItem to appear in KiNG s Tools menu If you need multiple menu items for your plugin put them in a JMenu and return that instead The second is getHelpMenultem which returns a JMenuItem for KiING s Help menu that provides help on using this plugin E
10. is sometimes useful when you re trying to do multi threaded things such as file loading king tool The king tool package and its subpackages contain a fair collection of different tools and plugins for doing various things some related to our research some not This is the part of KiNG undergoing the most active development so this section is almost certainly out of date already The operation of all these tools and plugins is well described in the user manual so this overview will seek to highlight features of their implementation that may be of interest to other developers After all the existing tools are the best reference on how to write new ones See above for a general description of how to create new tools and plugins The king tool model package for tools that work with PDB structure files is more complex than most of the others so it will be treated separately in the next section MovePointTool and EditPropertiesTool are two of the basic kinemage editing tools MovePoint tool uses KingView translateRotated to convert a movement in the scaled rotated graphics space back to a change of coordinates in the kinemage model space It also overrides mousePressed to find the picked point at the start of a drag which is something most drag operations don t need Edit Properties is a minimally different from BasicTool it just uses king GroupEditor and king PointEditor to alter the kinemage Dock30n3Tool is a m
11. that s water under the bridge now Two abstract classes AHE and AGE provide much of the shared functionality for the data structure classes AHE Abstract Hierarchy Element is the parent of all the KPoints and of AGE and its descendants see below It provides the concepts of having a name point ID or list subgroup group name of belonging to a parent e g the parent of a list is a subgroup and belonging to a kinemage and of being on i e its checkbox is checked and being visible i e all its parents are also on AHE also provides the basic hooks for being rotated and drawn to the screen because it implements TransformSignalSubscriber This mechanism will be discussed further in the section on KiNG s rendering engine AGE Abstract Grouping Element extends AHE to provide the shared functionality for everything that contains child nodes Kinemages KGroups KSubgroups and KLists This is the level where masters lens dominant and similar properties are implemented All of these grouping or container classes are part of a doubly linked tree rooted in the kinemage itself i e every node knows both its parent and its children Unfortunately this isn t really coordinated very well so to for example add a new subgroup to an existing group add has to be called on the group and setowner has to be called on the subgroup I ve done a better job coordinating maintenance of the same sort of tree
12. Hacking KiNG This document is intended to provide a field guide to the code for KiNG and its associated libraries Driftwood and Chiropraxis For more information please see the relevant Javadocs and ultimately the code itself In particular most of the references for the various published algorithms are somewhere in the Javadocs Some parts of the code are better commented than others but it s mostly pretty comprehensible If not you can often use the incomprehensible parts without having to understand how they work The first part of this discussion will provide an overview of all the code starting with driftwood building chiropraxis on top of that and finally building king on top of them both The second part will cover the organizational principles behind the layout of code and resources compiling and building maintaining documentation and distributing finished applications KiNG is always changing This document was written in the early spring of 2004 roughly version 1 22 and within a few months several major changes have already occurred So take this document with a grain of salt the final authority is the Javadocs and the code In brief here are some of the major changes The drawing system has been reworked to use a Painter that basically replaces a java awt Graphics object This allows us to do other types of non Java rendering such as OpenGL via the JOGL library The plugin system has been totally overhauled to fol
13. KiNG The PrefsEditor class provides a GUI for modifying some of these configurable properties at runtime As mentioned above the major subsystems are instantiated in KingMain Main called after the constructor They include KinStable MainWindow and ContentPane KinfileI0 KinCanvas UIMenus UIText and KinTree These subsystem heads all have references back to the KingMain object that created them allowing them to retrieve references to each other as needed At the same time KingMain sets the font magnification useful for those who can t see well and for giving presentations captures standard output and error for logging purposes and installs drag and drop handlers The drag and drop handlers FileDropHandler for the graphics window MacDropTarget for the Finder and the Dock are created using the Java Reflection API so that the attempt will fail gracefully on machines that don t support it VMs before 1 4 and non Macs respectively This is a technique I use in several other places most notably with the tool plugin architecture Only after all of this infrastructure is in place are files from the command line or lt PARAM gt tags actually loaded KinStable is a container for all the currently open kinemages think horses stable not solid as a rock stable It provides mechanisms to add open append and remove close kinemage and owns the GUI kinemage chooser box To actually open or save a kinemage clients call methods
14. a third might idealize the covalent geometry of that sidechain To make a permanent change to the frozen model a Remodeler calls requestStateChange That one tool is then asked to calculate a modified conformation for the frozen state via the same process used to compute the molten state above The tool is then unregistered so that it won t apply the same modification again to the molten state and the molten state recomputed as above The tool must re register itself to begin a new round of remodeling of course tools can abort a modeling operation by unregistering themselves directly So far all the remodeling has changed only the coordinates of atoms If a tool needs to add remove or replace atoms or residues e g mutate a sidechain it needs to change both the Model and the ModelState To do this one calls replaceModelAndState This requires that nothing in the model be currently molten because if the Model is changed while other tools are reshaping it the atoms they thought they were moving could disappear out from under them All of the changes to the Mode1 and the frozen ModelState are tracked by ModelManager2 s undo system and are fully reversible provided that the client cloned the original Mode1 and modified the clone instead of modifying the original The changes to the molten Mode1State are of course transient by nature so there s really nothing to undo for them In addition to the frozen and molten models and the u
15. and user controls zoom clip animate efc When it receives a notifyChange message from KingMain that the kinemage structure has changed it refreshes the list of checkboxes with help from the current Kinemage object MainWindow used to perform all of these functions but they were factored out into ContentPane So that the GUI could be placed into either a free floating JFrame like MainWindow or into a web page embedded Japplet like Kinglet MainWindow now is an empty shell that does very little except set its title Obviously the graphics space dominates the GUI and it is embodied in the Kincanvas class It doesn t really do much in and of itself but it coordinates a lot of things The one thing that is wholly contained within Kincanvas is the zoom and clipping slider controls and the math that makes them exponential rather than linear Otherwise Kincanvas delegates It contains a king core Engine that it uses to do the primary drawing both for painting the screen and for printing It also contains a ToolBox instance which is the top of the tool plugin hierarchy KinCanvas calls the ToolBox to do extra painting like point ID and distance readouts The whole drawing hierarchy is implemented using the SignalTransform system described above for king core KinCanvas also receives all the mouse and keyboard events for the graphics area but passes them to the ToolBox which in turn passes them to the current active tool
16. ary relationships among a lot of sequences spit out by Dezymer for scaffolds that had been reshaped with Backrub in different ways chiropraxis rotarama This package contains all the code for rotamer and Ramachandran evaluations There s not much code but the lookup tables take up many megabytes so I wanted to make this stuff easy to separate out that would be a lot of dead weight to carry in a project that didn t use these functions NDFloatTable is a generic implementation of an N dimensional array of floating point numbers This is the sort of thing you need for doing a four dimensional histogram of arginine rotamers for instance Each dimension can wrap so that 0 is the same as 360 etc It also has functions for doing density traces in N dimensions using either Gaussian or cosine smoothing functions This means you can write a point at some arbitrary location and it will be spread around to the nearby bins you can read the density at an arbitrary point and it will be estimated via linear interpolation from the nearest neighbors The code for this is highly recursive and quite hairy You ve been warned NDFloatTables can be saved to disk in a binary format and loaded into memory again this is how the Ramachandran and rotamer data is stored The silk smoothing package contains a more sophisticated version of this code that can read amp write a text based format too it also supports double precision float
17. d pass of the rendering process During the first pass in response to a TransformSignal all of the points are rotated and scaled and registered with the Engine to be drawn via the addPaintable function Balls and spheres are also recorded in a hashtable via the addShortener function so that lines whose endpoints match with the center of the ball can be shortened to make the balls look more realistically three dimensional As the rotated points are registered to be drawn the ones that fall inside the visible slab clipping planes are sorted into one of 1000 bins based on their z coordinate This allows me to draw them in roughly back to front order I call the bins a z buffer which I think is not quite the correct name for it All the points are drawn regardless of whether they ll be covered up later there are no provisions for hidden surface removal In a figure consisting mostly of dots and vectors I doubt it s worth the effort The z buffer is wiped clean before every new rendering operation but between renderings the information is cached and used for picking Thus the picking algorithm can traverse the z buffer front to back looking for points that approximately match the mouse click position Engine also contains a plethora of public variables that control various aspects of the rendering process depth cueing mode background color etc they mostly match the options in KiNG s Display menu These values can be adjusted to
18. ed it s an acronym for Kinemage Next Generation The word kinemage is itself a contraction of kinetic image king core This package comprises the minimal subset of classes to parse kinemage format files store and manipulate them in memory and write them back out For just creating kinemages from scratch it s usually easier to write the file yourself directly However this package could conceivably be used by another kinemage editing or display program to handle the input and output A note I sometimes use the term group to refer specifically to a kinemage group and sometimes I use it generically to mean group subgroup or list The intended meaning should be fairly clear from the context The data structure is the object oriented hierarchical tree that you would expect it mirrors the structure of kinemage files Thus a Kinemage object is at the top it contains KGroups they contain KSubgroups they contain KLists and they contain various subclasses of KPoint Note that all the kinds of lists are identical internally it s the kind of points in them that determines what kind of list you have This means that technically you can have all different kinds of points in the same list if you wanted to although there s no support for writing this out to a file I m not sure I would do it this way again if I were to start over I might have multiple kinds of lists and only one kind of point instead but
19. ed from the more complex BasicToo1 class but the good news is that BasicTool has no abstract methods that must be overridden it s completely functional out of the box In fact it s actually the implementation of the default Navigate tool that provides Mage like navigation through the kinemage Tools have the same menu item requirements as plugins and the help system is identical Thus it s usually sufficient to override toString and either getHelpAnchor Or getHelpURL with that information BasicTool will create appropriate items in the Tools and Help menu for you As mentioned above only one Tool can be active at a time Thus tools receive start and stop messages when they are de activated A tool will receive a reset when the active kinemage changes Tools can implement MouseListener and MouseMotionListener methods directly but it s usually more convenient to allow BasicTool to parse those into clicks drags and mouse wheel events Each type of mouse event belongs to one of four classes which are determined by which mouse button is used for multi button mice and or by which keyboard modifiers were held down The classes are normal left mouse button Shift right mouse button Ctrl middle mouse button and Shift Ctrl left and right mouse buttons together for drag but not click Three events and four states lead to twelve listener functions see the BasicTool code for their default implementations The click
20. ence You can ignore these or rewrite them for your own use The build process does make use of version information in resource packagename version props In fact it updates the build number every time a build occurs This makes it easier to track the exact version and build date for a distributed JAR file I take dependency management seriously because I m serious about wanting other to reuse my code I know from the experience of trying to borrow other people s libraries that unless I can cut out just the small subset of functionality I m interested in I m not going to use the library who wants to drag around hundreds of kilobytes of dead weight Thus as I outlined below driftwood has no dependencies chiropraxis depends only on driftwood and for some functions other third party libraries and king is allowed to depend on both driftwood and chiropraxis I also try to minimize or eliminate dependencies among the subpackages whenever possible A great free tool for querying and visualizing these dependencies is Dependency Finder http depfind sourceforge net I use it frequently for dissecting and refactoring my own code as well as for trying to understand other people s code Distribution and installers For those familiar with running Java programs the JAR files or distribution bundles created by Ant are all that s needed However for KiNG users I wanted a more novice friendly distribution method I found the
21. ent classpath can contain such a file so plugins can be compiled into their own JAR files and be detected by KiNG at runtime rather than at compile time In order for KiNG to detect plugin JARs they must either be in the special plugins folder or on the Java classpath The plugins folder is found in the same place as king jar and will be searched for JAR files containing plugins when the ToolBox is loaded The plugins folder is the preferred method and the easiest but JARs may instead be placed directly on the classpath by using the cp switch for java or by referencing them in the manifest of the king jar file but this is strongly discouraged ToolBox also contains the code to build the Tools menu and the tool related items in the Help menu The name of the submenu that each plugin should appear in is determined by an item in the king prefs file king king_prefs in the JAR or king prefs in the user s home directory named fully qualified PluginClassName menuName The special values lt main menu gt and lt not shown gt either place the plugin directly into the Tools menu or suppress its menu item altogether respectively The user can customize these settings so the ones provided in the JAR just serve as a default ToolBox also contains a ToolServices instance which has the code for picking measuring markers crosshair and Mage measures and the common mouse actions rotate translate clip and zoom Many of these could
22. enus are defined and either handled directly or delegated elsewhere in UIMenus which is another monster file It also holds the timer for auto animation and owns instances of PointFinder for the Edit Find dialog and ViewEditor for editing views PointFinder uses gnu regexp regular expressions to drive the search because Java didn t come with regular expression packages of its own until version 1 4 Note that UIMenus has mechanisms for rebuilding the Views and Animations menus which need updating when kinemages are un loaded If I weren t so lazy I would split this into one file per major menu to increase maintainability which is actually what I did already with the Display menu UIDisplayMenu The Display menu items mostly act by changing variables in the KinCanvas S Engine instance Now for a few loose ends The u1Text class manages the kinemage text window and allows the user to edit that text HTMLHelp is an ultra simple HTML browser intended for displaying help information like the user manual Note that the Java HTML viewer component only supports the HTML 3 2 standard so you can t do anything too fancy GridBagPanel is the predecessor to driftwood gui TablePane but harder to use I would remove it entirely except that some parts of the GUI still haven t been upgraded to TablePane ReflectiveRunnable works just like ReflectiveAction except that it lets any arbitrary function stand in for the Runnable interface This
23. ething happens to them e g a button is pressed Each component is monitored by a class implementing ActionListener which then responds appropriately Unfortunately this typically means creating one small class for every event that can happen in the UI which for large programs is very expensive both in terms of disk space and run time memory By using the Java reflection API ReflectiveAction allows one to redirect ActionEvents froma specific component to a named function in some arbitrary class usually this This is much more efficient although you do lose some compile time safety because you could name a function that doesn t really exist AngleDial is a custom widget that allows the user to graphically select an angle by dragging a pointer around the circular dial It s used in several of the tools in KiNG and is fairly configurable FoldingBox and its ancestors IndentBox AlignBox and SwapBox allow for fold out sections of the GUI that are de activated by a checkbox This is how the recessiveon property is implemented in KiNG TablePane makes the process of hand coding a GUI much like using TABLE tags in HTML It s actually just a wrapper on top of the standard GridBagLayout but I find it makes layout code much more compact and comprehensible driftwood isosurface This package contains all the code for loading and contouring electron density It s named isosurface because in principle it i
24. feeds the EdgePlotter a series of kinemage style move draw commands that define either a wireframe mesh or a series of triangle strips depending on how MarchingCubes was configured Three input formats are currently supported O maps DSN6 or Brix XPLOR maps and CCP4 maps Each map type is read by its own class all of which are descended from CrystalVertexSource Only primitive output capabilities are provided in this package KinfileEdgePlotter writes a kinemage file from the mesh output of MarchingCubes KiNG implements its own EdgePlotter that constructs the contours directly in memory rather than first writing a kinemage file and then parsing it driftwood moldb2 This package implements data structures for working with macromolecules ModelGroup represents the contents of a PDB file and contains one or more Models These in turn contain Residues which contain Atoms The information in this tree is only the naming and relatedness parent child information To store coordinates B factors occupancies etc each Atom has one or more AtomStates The AtomStates for a particular Model are collected together into one or more ModelStates each of which represents e g a particular alternate conformation Each ModelState contains either zero or one AtomStates for each Atom in the Model and thus represents a single unique unambiguous conformation with the possibility that some Atoms are undefined usually leading to an AtomE
25. give different kinds of renderings The last major functionality in king core is reading and writing kinemages KinfileParser is responsible for reading the kinemages though it delegates the low level parsing tokenizing to KinfileTokenizer The parser is rather large but is pretty simple It s recursive decent except without the recursive part because kinemages don t have any recursive parenthesized sorts of expressions in them You feed the parser a stream and it returns to you 1 a Collection of Kinemage objects and 2 all of the text and caption sections of the kinemage concatenated together Note that before using the kinemages you must call initAl1 on them which does things like calculate the bounding box and initialize the views masters and animations KinWriter is also very straightforward you feed it a Collection of Kinemages some text and a stream All that s left in this package are a few loose ends KinemageSignal and KinemageSignalSubscriber are modeled after TransformSignal and TransformSignalSubscriber but to inform listeners about changes to the kinemage creating and deleting groups efc Unfortunately I built it rather late so it s not used by much of anything most of KiNG relies on a more primitive notifyChange method in king KingMain RecursivePointIterator is a utility class for visiting all of the KPoints in a kinemage it gets used by the Find command king The king package itself contain
26. h Ca difference distance plots vector and unsigned sum methods of collapsing the difference distance information and Lesk s method of choosing an optimal subset of atoms to superimpose on It s pretty limited in usability because it requires two PDBs with the same number of alpha carbons in them It seems relatively straightforward to enhance it with the ability to select ranges align on something other than Ca s etc However I wrote it in a hurry so the code s kind of a mess and the design would probably require substantial reworking So far I don t see the payoff in reinventing the wheel ProFit and LSQMAN I just edit my PDBs to be the same length then run the alignment that way chiropraxis minimize This is sort of a toy package written so I could learn about steepest descent and conjugate gradient minimizers GradientMinimizer supports both modes of operation but the implementation is far from optimal and may not even be correct If you want to use this for a serious application you should study something like the Numerical Recipes books or the GNU Scientific Library to learn the ins amp outs of doing conjugate gradients robustly I don t see how I could mess up steepest descent that badly but I may have The minimizer accepts a PotentialFunction SequenceSpacer uses a SimpleHarmonicPotential in the minimizer to do a 3 D graph layout of a bunch of amino acid sequences We used this tool to look at the evolution
27. having each ace keep a list of master names that affect it when a master is turned on off the whole kinemage tree is traversed and groups are flipped on off as necessary AnimationGroup is the remains of my grand scheme to enhance the kinemage format with an arbitrary number of highly configurable animations of which the traditional animate and 2animate would merely be a subset Unfortunately it was rather awkward and relied on the original non standard behavior of the masters I still haven t decided whether I m going to remove it entirely along with the Animations menu or whether I want to take another crack at creating more complex animations Now we come to KPoint and its subclasses Bal1lPoint also responsible for spheres DotPoint LabelPoint MarkerPoint TrianglePoint also responsible for ribbons and VectorPoint They implement the standard point properties like color aspects via the Aspect class unpickable ness and width radius that they don t get from AHE but their main function is to store an lt x y z gt coordinate This is another place where I went tragically wrong Points store both their original location and their transformed location after rotation scaling etc Among other things this means that implementing stereo is nearly impossible because you need to track two transformed locations for each point I got around this by doing two transform draw cycles the downside is that you can then only pick po
28. in Kinfile1o which may either present a dialog box or not depending on the method chosen It tracks the name of the last file opened and provides automatic versioned naming foo kin foo 1 kin foo 2 kin It also displays the progress dialog KinfileIo implements KinLoadListener so that it can use a KinfileLoader to do the actual parsing in a background thread this is what makes the progress dialog possible Clients that don t want to use Kinfileto directly but still want background thread file loading can implement KinLoadListener themselves and use their own KinfileLoader Several other classes are also involved in I O operations ImageExport saves the current graphics display to disk in bitmap form as a PNG or a JPEG PdfExport saves the display in Adobe s Portable Document Format for 2 D vector graphics xknWriter tries to save the currently open kinemages as XML and vrm197Writer tries to save them as VRML2 VRML97 Both xknwriter and vrm197Writer are incomplete out of date and not maintained they are kept on with the thought that they may one day be fleshed out All of these classes except vrm197Writer use libraries that may not be present on all systems javax imageio the iText PDF library and javax xm1 Thus they are instantiated by reflection so that systems with Java 1 3 or without iText can still run KiNG ContentPane is the root of the GUI hierarchy It divides the main GUI space into graphics display kinemage checkboxes
29. ing point numbers which is overkill for this application The Ramachandran and Rotamer classes are bare bones evaluators KiNG uses these to score the results of interactive modeling However the evaluations and kinemages produced on MolProbity come from completely separate code in my old hless package so named because models didn t need Hs to be processed That code uses a very different set of classes to represent macromolecular models and since it works just fine I haven t bothered to port it all over to the modern driftwood moldb2 system Finally TauByPhiPsi uses data from a 1996 paper by P A Karplus to predict the ideal or at least average tau angle for a given backbone conformation chiropraxis sc This package contains all the functions for working with protein sidechain conformations RotamerDef is a simple data structure for storing rotamer definitions from the Penultimate Rotamer Library name frequency of occurance canonical x angles SidechainAngles2 is the class that allows measuring and adjusting all the sidechain dihedrals both x angles and rotatable methyls etc It s somewhat fragile in that it relies on atom names being absolutely uniform rather than trying to make decisions based on spatial data too Both RotamerDef and SidechainAngles2 use the angle props resource file that defines all the rotamers and all the angles SidechainIdealizer contains code both for idealizing whole sidechains and fo
30. ing through themselves with each point knowing who it s predecessor is Other types of points know which list they belong to but not what order they re in The vectors and triangles use this information to draw themselves if they have a predecessor they draw from that point to themselves and are thus L points if their predecessor is nu11 they draw nothing and are thus P points The advantage to this scheme relative to having each point know its index in an array is that it requires little or no updating to insert and remove points from the list The downside is that traversing the list for other purposes is more difficult you have to retrieve the full list of children from the list search for the starting point and then explore up and down the list from there I m almost ready to discuss the rendering engine but first need to introduce a few utility classes A KPaint object represents each named kinemage color like green or lilactint It keeps the java awt Color objects used for painting points with various depth cueing levels on white and black backgrounds in full color and in monochrome It also does all the calculations for how colors are depth cued and how lighting interacts with the triangle and ribbon normals KPalette actually defines all the different colors in terms of a hue saturation value HSV model and maintains the various pens used for depth cueing line thickness KingView defi
31. ints on whichever side was transformed last It also makes it very hard to use the nice linear algebra functions from driftwood r3 because sometimes you want them to apply to the original coordinates and sometimes to the transformed ones The upside and original motivation for this decision is that it s an efficiency gain because storing the transformed coordinates outside of the points themselves requires frequently creating and then discarding thousands of short lived objects which can be expensive My understanding is that modern Java VMs have been extensively optimized so that this isn t much of a concern any more It would be very difficult to accomplish this change because it s so fundamental but if it didn t degrade performance much it would really improve the design Closely related is the fact that each specialized point type contains all the code for actually drawing it to the screen This was fine when there was only one way to draw each point but as I introduced different quality settings for the rendering I realized this was a bad idea A better arrangement would be to have pluggable drawing engines that know how to draw each type of point so that you could even have for example an OpenGL option without having to change the point code which should be primarily a very long lived and slow changing data structure It s also worth mentioning that the VectorPoint and TrianglePoint classes maintain a singly linked list runn
32. ither of these functions may return null to indicate that they don t have an associated menu item getToolsMenuItem must be implemented from scratch for each plugin but there is already an infrastructure in place for the default Help behavior If the plugin s documentation resides in the KiNG manual you need only return an HTML anchor from getHelpAnchor If the help is in a different HTML file you can instead override getHelpURL to return that address Note that the Java browser only supports HTML 3 2 If you re going to use this default help system instead of overriding getHelpMenultem you should override toString to return a reasonable name for your plugin Since it s so easy to add plugin documentation please provide help pages for your plugins More complex plugins may want to implement some additional methods Overriding isAppletSafe to return false will ensure that KiNG does not try to load that plugin when running as an applet This is useful for plugins that access the file system use native libraries and so on The getDependencies method returns a list of the fully qualified class names of other tools or plugins on which this plugin depends KiNG will only load this plugin if it can successfully load all of its dependencies first Complex chains can be resolved but be careful not to introduce circular dependencies as this will prevent all the plugins involved from being loaded Tools must be deriv
33. ll the functions I don t worry so much about variables though I should pay more attention to them One thing that s currently lacking is package overview documentation in the Javadocs but that s basically the purpose of this document so I may not do much more there Resource data and user documentation The resource directory for each top level package has a structure parallel to that of src again named by sub package name The resource directory is incorporated directly into the JAR file so that the compiled Java class files and their necessary resources end up in the same directory of the JAR The code can retrieve this resource data with Class getResource and similar functions For example the smoothed rotamer and Ramachandran distributions are stored this way in chiropraxis KING keeps its icons configuration files and HTML help in the resource tree Most of the command line utilities also keep their help information in plain text he1lp files this way It is my goal to provide all end user documentation in HTML format always and in PDF format when it makes sense As mentioned command line utilities often contain their own plain text help summaries as well There are no really great tools that I ve ever run across for producing clean and attractive HTML and PDFs from the same source document Microsoft Word is a possibility but it writes atrocious HTML that the Java viewer could never handle and it doesn t run on Lin
34. log box from scratch There are two more important methods in BasicTool signalTransform and overpaintCanvas Yes just like the active kinemage the ToolBox ToolServices and the active tool are part of the TransformSignal driven drawing hierarchy Plugins must register themselves explicitly to be included but they can if they want to By having the tool s signalTransform call the signalTransform method of a group subgroup or list that it owns that graphics element can be rendered to the screen or printer without being saved as part of the kinemage This is how ToolServices manages markers and is analogous to how electron density is displayed The overpaintCanvas method allows the tool to draw directly on the canvas after all the 3 D graphics are rendered this is how ToolServices paints point ID labels measurement distances etc The best way to learn about writing tools and plugins is to explore the existing code in the king tool package and its subpackages See below for more description of the existing tool set There is actually one plugin that lives in the king package which is the electron density displayer EDMapPlugin It s a simple shell that allows the user to select a file and then opens a EDMapWindow for it As mentioned above in its constructor the window subscribes to the ToolBox s TransformSignal so that it can display the maps without them necessarily being part of the kinemage EDMapPlotter implements
35. low a service provider model which is partially reflected in this document some of the changes may not have made it in though All the structural biology specific tools that used to be in the king tool packages have been moved into chiropraxis kingtools This effectively inverts the dependency relationship KiNG no longer depends on Chiropraxis to compile but compiling Chiropraxis now requires that KiNG be present Last updated 6 June 2004 by IWD for KiNG 1 28 Overview of the code Packages driftwood and Jama This group of classes defines a lot of the low level highly reusable functions I needed to build KiNG and the various macromolecular modeling tools Most of the classes have few dependencies and fall into small clusters of related functionalties Some of the sub packages do depend on the others e g driftwood moldb2 uses the data structures from driftwood data but I try to keep these to a minimum In no case will any class in this group of packages depend on anything outside the group except for the standard Java libraries Thus it should be easy to reuse these classes in whole or in part in other projects OK I lied a little I realized I was going to need some standard linear algebra operations and I didn t want to write them So I incorporated the JAMA Java Matrix Libraries into the driftwood tree and some of the things in driftwood r3 depend on them JAMA is public domain code released by the U S government
36. ndo system ModelManager2 also drives all the interactive model visualizations A better design of would be to factor the visualizations out of this class and make them operate as registered clients of the model manager instead more like the tools do However I haven t gotten to this yet So at the moment the manager uses ModelPlotter to make kinemage drawings of the entire frozen state in sky and yellowtint and the molten parts of the molten state in shades of orange ModelPlotter operates only on proteins and goes strictly by atom names so its pretty easy to break it Still it works most of the time Its connectivity database is stored in the sc connect props resource file ModelManager2 also calls the command line C programs probe and noe display to generate more visualizations although most of the noe display logic and interface has been isolated in the NoePanel and ExpectedNoePanel Classes The calls to probe and noe display are done by BgkKinRunner These programs can take several seconds to run and then KiNG still has to parse the textual kinemage data they output Furthermore running external programs from Java seems to be a little dicey sometimes they hang indefinitely for no apparent reason in a random and irreproducible fashion For all these reasons BgKinRunner launches such programs in a background thread and kills them off if they run for too long It then parses the kinemage data and adds it to the display replacing
37. nes a view in the kinemage sense center rotation matrix zoom or span and is also used to track the current viewpoint as the kinemage is moved with the mouse It s all straightforward matrix multiplication and so forth but it was done way before driftwood r3 Transform and is quite quirky It s made even worse by the fact that it s thread safe so it worries about synchronization I originally anticipated that I wanted a background thread to be able to update the view so I could get automatic rocking for presentations However I ended up using a Timer and doing the actual updates on the main thread anyway so it s all for naught The drawing process now just pulls the information out and builds a driftwood r3 Transform to actually work with I should also mention that the zoom can be stored as either a zoom value or a span value because that s the way it is in the kinemage format However the first time a KingView is used for drawing it converts everything to a span based on the current size of the bounding box of the kinemage I find spans to be more robust because a view defined in terms of span doesn t change if you change the size of the kinemage For instance if you define a view of your model s active site and then merge in a larger tetramer of the same structure for comparison you don t want the active site view to get zoomed out just because the kinemage now occupies a larger volume Points are actually rendered in two pa
38. olecular modeling operations that provide a lot of the core functionality of the modeling tools in KiNG They are intermediate in complexity and in number of dependencies between those of driftwood and those of king In particular they depend heavily on driftwood r3 and driftwood moldb2 so using chiropraxis in another project will mandate including the driftwood code as well However nothing in this package depends on anything in KiNG Chiropraxis is a general name for remodeling the backbone of macromolecular structures and was dreamed up by Laura Weston Murray and David Richardson chiropraxis mc This package implements functions for re modeling protein mainchains If we develop tools to refit RNA backbone in the future they would likely go here caRotation implements the Backrub motion a simple rigid body rotation around an imaginary axis between two alpha carbons It can handle either a single rotation for two Ca s that are any distance apart or all the peptide rotations between those two Ca s The math is straightforward but tedious and somewhat error prone so it s nice to have it all packaged up here The package also includes two utility programs HingeFit tries to iteratively superimpose two loop conformations using only Backrub like moves by selecting the hinge motion that most improves the Ca RMSD at each iteration Suppose is a utility for doing least squares superpositions It was a test bed for me to play wit
39. ore sophisticated tool It overrides BasicTool getToolPanel to provide an accessory dialog box and it has its own data structure for storing picked points It also overrides signalTransform to display the numbered markers that describe the alignment to be performed Its transformAllVisible method demonstrates how to go about changing the coordinates of kinemage objects using a driftwood r3 Transform Finally it uses driftwood r3 Builder to do the geometric calculations necessary for the superposition DockLsqTool is quite similar except that is uses driftwood r3 SuperPoser to do the least squares superposition calculation ViewpointPlugin Is fairly boring except that it illustrates how to modify the current view directly rather than through the ToolServices rotate zoom etc functions CrossWindowPickTool shows how two or more KiNG instances in the same Java VM can communicate Multiple instances are created with the File New command Each new KiNG instance has its own instance of CrossWindowPickTool and these all share a static class list of all the crossWindowPickTool instances The list is implemented using SoftReferences to avoid memory leaks Thus each instance of the tool is able to find out about and communicate with all the others SolidObj Plugin is interesting in that it does some non trivial geometric calculations and creates fairly intricate surfaces from TrianglePoints It also does the cute trick of tra
40. r idealizing just the CB position and Ha s It uses singlesc pdb and singleres pdb which are slightly adapted versions of the ideal geometry data hard coded into Prekin The algorithm for Cf idealization is basically the one in Prekin which constructs ideal positions from both directions and averages them However I treat all amino acids like alanine whereas in fact the ideals are slightly different for the branched betas etc This is due to sheer laziness and could be fixed RotamerSampler is just a quick hack to generate the sampled sidechain conformation libraries that Homme wanted for Dezymer Packages king The code for KiNG is larger and more interconnected than that for driftwood or chiropraxis Note that most of this code depends on the driftwood libraries as well as on some third party libraries regular expressions PostScript export However only the king tool model package which contains the rebuilding functions depends on chiropraxis Thus it s relatively easy to eliminate all the molecular modeling stuff if you just want a 3 D graphics program Also a lot of the math in KiNG was done before I had written driftwood r3 so there s some duplication of effort dot products cross products matrix multiplication etc P ve slowly been trying to replace the original code with calls to standard stuff in driftwood r3 but the transition is incomplete Incidentally the name KiNG isn t me being conceit
41. re short There s a fair bit of lore in the CS world that comprehensibility of any chunk suffers badly as soon as you can t see the whole thing at once and my own experience bears this out Since I leave a line of space between folded segments for readability that puts an upper limit of about 20 segments 40 lines 800 lines of code in any one file Beyond this point you can t even fit the folded overview of a single class on screen at once Indeed I find it hard to keep track of all the things going on in a class with 1000 lines of code and sometimes end of stepping on my own toes With few exceptions I believe that classes this big are trying to do too much and should be split into several more focused and modular components The same philosophy extends to package organization 10 to 20 classes is a nice number Finer divisions seem silly unless you expect future growth as I do for many of the packages documented here but beyond about 20 classes I find that it s hard to get a handle on what a package does and how its parts interrelate Libraries with hundreds of public classes in a package are just plain poorly organized in my opinion The main king package is pushing 40 classes now and I think that s a little unwieldy On the other hand king core is about 30 classes and I can t see any good way to segment it further so I won t I make a real effort to document my source code using Javadoc comments for a
42. registered but free basic version of Install Anywhere http www zerog com does a very nice job of distributing Java applications bundled with a private copy of the Java VM and runtime libraries This makes for some large ten megabytes and up downloads but great convenience I use this method for Windows and Linux where a Java VM is not part of the standard installation For the Macintosh I used the included OS X developer tools to make an application bundle for my JARs Once you ve created that once you can easily update it just by replacing the JARs inside without having to go through the whole song and dance again
43. s all the code that makes up KiNG the program largely the graphical user interface GUI and its trappings It also contains the foundations of the tool plugin system discussed below but most of the actual tools and plugins are sequestered in king tool and its subpackages king does not depend on them and can easily be compiled without them KingMain provides the entry point for KiNG running as an application it contains the main method and it serves as a control center throughout the lifetime of a run KingMain parses the command line instantiates the major subsystems and lets them find each other via the get___ methods coordinates the event notification system via notifyChange and manages multiple instances Most message event passing is done by clients calling KingMain notifyChange which then trickles down into the notifyChange methods of all the subsystems When multiple instances are created in the same Java VM using the File New command a new KingMain instance is created and a static counter is incremented When a KiNG window and its associated KingMain die File Exit or close the window the counter is decremented When it reaches zero System exit is called to ensure clean termination of the program Kinglet provides the entry point for KiNG running as a web page applet It does very little except to decide which of three modes its running in embedded free floating window or launcher button and ins
44. s capable of generating isosurfaces for any function sampled in three dimensions However the focus so far has been on electron density The core functionality is in the MarchingCubes class which implements the marching cubes algorithm The basic idea is that you have a grid of data samples and you see that grid as lots of little cubes that have one data sample at each corner Classifying each corner or vertex as above or below the contour level a k a isosurface threshold yields 256 different patterns which can be reduced to 15 unique cases by rotation etc The algorithm marches through the cubes one at a time and contours each one individually The remarkable thing is that these pieces almost always fit together to make the correct surface One occasionally gets holes but the truly topologically correct algorithms are much harder to implement My code is capable of generating either wireframe mesh or triangle solid surfaces Data samples are identified by three integer indices Thus the MarchingCubes class needs two kinds of input a class that implements VertexLocator to translates the indices into a point in Cartesian coordinates and a class that implements VertexEvaluator to look up the actual data value at the specified indices In practice a single data source usually implements both interfaces Output of the marching cubes algorithm can be directed to anything that implements the EdgePlotter interface MarchingCubes
45. sses in the first pass they are transformed rotated scaled etc and register themselves to be painted and in the second pass they are actually painted to the screen TransformSignal drives that first pass with a publish subscribe model Various TransformSignalSubscribers register with the TransformSignal to be notified when a new rendering is initiated When someone then publishes a rendering request to the TransformSignal all subscribers are given the opportunity to transform themselves via a matrix multiplication and or to register to be drawn in the next pass As mentioned above all anes implement TransformSignalSubscriber However typically only the kinemage is registered as a subscriber with TransformSignal because the aces kinemage groups subgroups lists respond to a signal by simply passing it on to all their children Thus the signal trickles down from the kinemage down through its groups to all its points which are then actually rotated and registered to be drawn In addition to kinemages many tools subscribe to a transform signal so that they can render objects that are not actually part of the current kinemage such as markers or electron density contours Finally TransformSignal is itself a TransformSignalSubscriber so that you could hook up several of them to create a sort of signaling cascade I guess that means I ve taken to many molecular biology courses huh The Engine class coordinates most of the secon
46. tantiate a KingMain object All remaining tasks are delegated to KingMain even the processing of applet lt PARAM gt tags The first task for KingMain is configuration including parsing the command line or applet lt PARAM gt tags These tasks are performed in the KingMain constructor whereas the other subsystems are not created until later in the Main method an instance method called after the constructor not to be confused with the static function main where execution starts for the application It first creates a KingPrefs object to hold all the configuration data KingPrefs is a souped up java util Properties Class that holds lots of key value pairs e g fontMagnification 1 0 The default values for all the keys are loaded from king_prefs in the JAR file but may be overridden by entries the user s king prefs file located in his her home directory as defined by the underlying OS or by command line switches The allowed configuration keys are documented in the king prefs file and will not be repeated here KingPrefs is also responsible for loading other resources from the JAR file e g icons for identifying the location of other programs distributed with KiNG e g Probe and for querying kinemage biochem duke edu to find out if a newer version of the software is available The query is just an HTTP GET and can be disabled by the user it reveals no information about the user except their IP address and that they re running
47. the program s previous output if any Thus the probe and noe display visualizations often lag a few seconds behind the moving molten model but the UI remains responsive and crashes don t seem to have any adverse destabilizing effect on KiNG Finally to the tools of which there are three HingeTool implements the generalized version of the Backrub backbone motion and uses the PeptideTwister2 component to manage peptide rotations Both use chiropraxis mc CaRotation to do the actual rotation calculations ScMutTool is entirely self contained and is the only one that actually changes the Model as well as the ModelState ScRotTool spawns lots of SidechainRotator windows that do the actual work of reconfiguring sidechains Organizational principles Source code All of the Java source code is stored in the src directory of each top level package s distribution driftwood chiropraxis king Subdirectories are named by sub package name according to the Java convention When editing code I prefer to use the jEdit text editor http www jedit org One of its features is explicit folding of the source code driven by the triple curly brace markers and I try to keep these folded sections to about 40 lines so that one of them fits comfortably on the screen when expanded Thus whenever possible I work hard to keep my function definitions to about 40 lines as well Multiple functions may go in the same fold if they
48. ux The best alternative I found is LyX http www lyx org a what you see is what you mean cross platform document processor that uses LaTeX as its underlying formatting engine It produces pretty clean HTML and nice PDFs and it s really good about helping maintain a hierarchical structure chapters sections subsections and cross references Every project also has a CHANGELOG html file which is really just an HTML wrapper around a plain text file It records an overview of the changes made for each version along with notes and ideas for future features to dos and bug reports that are still outstanding I take care to make sure the nominal current version number from the changelog tracks with the actual version number stored in the resource tree as version props Build system The build system is driven by Apache Ant http ant apache org which is the Java standard Ant stores its build instructions in build xml files one per top level project The major targets are compile run javac to compile the source build construct the JAR file dist build source and executable distribution bundles and clean remove products of the other three The compiled class files are placed into the build directory and the distribution bundles are built up in the dist directory Both directories are removed by clean and recreated as needed There are also other targets like backup and deploy xxx that exist only for my conveni
49. versing the kinemage and finding all of the currently visible vector lists DrawingTool has a whole host of interesting tricks Its undo mechanism saves the state of a KList by making a copy of its children variable with the additional complication of saving connectedness information at the end of Vector and TriangleLists The undo system also uses SoftReferences to make the undo cache memory sensitive it s cleared out in response to memory demand by the Java VM DrawingTool uses driftwood gui FoldingBox With a JRadioButton for a slight twist on the GUI segment that drops down in response to a checkbox It demonstrates the use of a Kinemage s metadata field for storing kinemage specific information with the kinemage rather than within the tool This helps avoid memory leaks when kinemages are closed The other solution is to use a SoftReference again The prune and punch commands demonstrate traversing a KList and making modifications to a line segment or polyline The auger command shows how to use Engine to pick all the points in a region and the spherical crop demonstrates the use of king RecursivePointIterator Auger also does some interesting work in mouseMoved to do XOR drawing of its beach ball of death rather than trying to install a large custom mouse cursor The RNA tools in king tool xtal were developed by Vincent Chen during his rotation in the Richardson lab in the fall of 2003 They were derived from EDMapPlugin and
50. xception ModelStates inherit from one another to avoid duplication of information so that for instance the B conformation only needs to define positions that differ from A This also makes it easy to model a change to one residue as a small mask that rides on top of the original conformation ModelStates are implemented using hash tables often driftwood data UberMap in fact so that look up of the state for a particular Atom is a fast constant time operation AminoAcid provides some static functions for evaluating Residues that happen to be amino acids You can measure 9 p and t determine if the residue is pre Pro etc Things like Ramachandran and rotamer evaluations are done in the chiropraxis rotarama package I m still not entirely satisfied with this library although it s the best I ve managed so far AtomException really should have been a checked exception because uncaught AtomExceptions are always crashing my code somewhere Still it would put a fairly substantial burden on clients of the library because a lot of fundamental operations can throw this exception I don t particularly like the way all the original conformations read in from the PDB file are bundled with the Model but I don t have a good alternative yet And I don t have any support yet for bonds CONECT records and traversing a network of bonded atoms or for ANISOU records driftwood r3 The x3 package provides basic support
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