*/
package jalview.ext.rbvi.chimera;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.httpserver.AbstractRequestHandler;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
-import java.awt.Color;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
import java.net.BindException;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.httpserver.AbstractRequestHandler;
+import jalview.io.DataSourceType;
+import jalview.structure.AtomSpec;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
- // Chimera clause to exclude alternate locations in atom selection
- private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
-
- private static final String COLOURING_CHIMERA = MessageManager
- .getString("status.colouring_chimera");
-
- private static final boolean debug = false;
-
- private static final String PHOSPHORUS = "P";
+ public static final String CHIMERA_SESSION_EXTENSION = ".py";
- private static final String ALPHACARBON = "CA";
+ public static final String CHIMERA_FEATURE_GROUP = "Chimera";
/*
* Object through which we talk to Chimera
*/
- private ChimeraManager viewer;
+ private ChimeraManager chimeraManager;
/*
* Object which listens to Chimera notifications
private AbstractRequestHandler chimeraListener;
/*
- * set if chimera state is being restored from some source - instructs binding
- * not to apply default display style when structure set is updated for first
- * time.
- */
- private boolean loadingFromArchive = false;
-
- /*
- * flag to indicate if the Chimera viewer should ignore sequence colouring
- * events from the structure manager because the GUI is still setting up
- */
- private boolean loadingFinished = true;
-
- public String fileLoadingError;
-
- /*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
- private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
-
- /*
- * the default or current model displayed if the model cannot be identified
- * from the selection message
- */
- private int frameNo = 0;
-
- private String lastCommand;
+ protected Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
String lastHighlightCommand;
- /*
- * incremented every time a load notification is successfully handled -
- * lightweight mechanism for other threads to detect when they can start
- * referring to new structures.
+ /**
+ * Returns a model of the structure positions described by the Chimera format atomspec
+ * @param atomSpec
+ * @return
*/
- private long loadNotifiesHandled = 0;
+ protected AtomSpec parseAtomSpec(String atomSpec)
+ {
+ return AtomSpec.fromChimeraAtomspec(atomSpec);
+ }
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
- * We check if the PDB model id is already loaded in Chimera, if so don't
- * reopen it. This is the case if Chimera has opened a saved session file.
+ * We check if the PDB model id is already loaded in Chimera, if so don't reopen
+ * it. This is the case if Chimera has opened a saved session file.
*
* @param pe
* @return
String file = pe.getFile();
try
{
- List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
- List<ChimeraModel> oldList = viewer.getModelList();
+ List<ChimeraModel> modelsToMap = new ArrayList<>();
+ List<ChimeraModel> oldList = chimeraManager.getModelList();
boolean alreadyOpen = false;
/*
*/
if (!alreadyOpen)
{
- viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- List<ChimeraModel> newList = viewer.getModelList();
- // JAL-1728 newList.removeAll(oldList) does not work
- for (ChimeraModel cm : newList)
- {
- if (cm.getModelName().equals(pe.getId()))
- {
- modelsToMap.add(cm);
- }
- }
+ chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+ addChimeraModel(pe, modelsToMap);
}
chimeraMaps.put(file, modelsToMap);
if (getSsm() != null)
{
getSsm().addStructureViewerListener(this);
- // ssm.addSelectionListener(this);
- FeatureRenderer fr = getFeatureRenderer(null);
- if (fr != null)
- {
- fr.featuresAdded();
- }
- refreshGUI();
}
return true;
} catch (Exception q)
}
/**
+ * Adds the ChimeraModel corresponding to the given PDBEntry, based on model
+ * name matching PDB id
+ *
+ * @param pe
+ * @param modelsToMap
+ */
+ protected void addChimeraModel(PDBEntry pe,
+ List<ChimeraModel> modelsToMap)
+ {
+ /*
+ * Chimera: query for actual models and find the one with
+ * matching model name - already set in viewer.openModel()
+ */
+ List<ChimeraModel> newList = chimeraManager.getModelList();
+ // JAL-1728 newList.removeAll(oldList) does not work
+ for (ChimeraModel cm : newList)
+ {
+ if (cm.getModelName().equals(pe.getId()))
+ {
+ modelsToMap.add(cm);
+ }
+ }
+ }
+
+ /**
* Constructor
*
* @param ssm
* @param pdbentry
* @param sequenceIs
- * @param chains
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
+ {
+ super(ssm, pdbentry, sequenceIs, protocol);
+ boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType());
+ chimeraManager = chimeraX ? new ChimeraXManager(new StructureManager(true)) : new ChimeraManager(new StructureManager(true));
+ setStructureCommands(chimeraX ? new ChimeraXCommands() : new ChimeraCommands());
+ }
+
+ @Override
+ protected ViewerType getViewerType()
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
- viewer = new ChimeraManager(
- new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ return ViewerType.CHIMERA;
}
/**
- * Start a dedicated HttpServer to listen for Chimera notifications, and tell
- * it to start listening
+ * Start a dedicated HttpServer to listen for Chimera notifications, and tell it
+ * to start listening
*/
public void startChimeraListener()
{
try
{
chimeraListener = new ChimeraListener(this);
- viewer.startListening(chimeraListener.getUri());
+ startListening(chimeraListener.getUri());
} catch (BindException e)
{
- System.err.println("Failed to start Chimera listener: "
- + e.getMessage());
- }
- }
-
- /**
- * Construct a title string for the viewer window based on the data Jalview
- * knows about
- *
- * @param verbose
- * @return
- */
- public String getViewerTitle(boolean verbose)
- {
- return getViewerTitle("Chimera", verbose);
- }
-
- /**
- * Tells Chimera to display only the specified chains
- *
- * @param toshow
- */
- public void showChains(List<String> toshow)
- {
- /*
- * Construct a chimera command like
- *
- * ~display #*;~ribbon #*;ribbon :.A,:.B
- */
- StringBuilder cmd = new StringBuilder(64);
- boolean first = true;
- for (String chain : toshow)
- {
- if (!first)
- {
- cmd.append(",");
- }
- cmd.append(":.").append(chain);
- first = false;
+ System.err.println(
+ "Failed to start Chimera listener: " + e.getMessage());
}
-
- /*
- * could append ";focus" to this command to resize the display to fill the
- * window, but it looks more helpful not to (easier to relate chains to the
- * whole)
- */
- final String command = "~display #*; ~ribbon #*; ribbon "
- + cmd.toString();
- sendChimeraCommand(command, false);
}
/**
* Close down the Jalview viewer and listener, and (optionally) the associated
* Chimera window.
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
- getSsm().removeStructureViewerListener(this, this.getPdbFile());
- if (closeChimera)
- {
- viewer.exitChimera();
- }
+ super.closeViewer(closeChimera);
if (this.chimeraListener != null)
{
chimeraListener.shutdown();
chimeraListener = null;
}
- lastCommand = null;
- viewer = null;
-
- releaseUIResources();
- }
-
- public void colourByChain()
- {
- colourBySequence = false;
- sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
- }
-
- /**
- * Constructs and sends a Chimera command to colour by charge
- * <ul>
- * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
- * <li>Lysine and Arginine (positive charge) blue</li>
- * <li>Cysteine - yellow</li>
- * <li>all others - white</li>
- * </ul>
- */
- public void colourByCharge()
- {
- colourBySequence = false;
- String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
-
- /**
- * Construct and send a command to align structures against a reference
- * structure, based on one or more sequence alignments
- *
- * @param _alignment
- * an array of alignments to process
- * @param _refStructure
- * an array of corresponding reference structures (index into pdb
- * file array); if a negative value is passed, the first PDB file
- * mapped to an alignment sequence is used as the reference for
- * superposition
- * @param _hiddenCols
- * an array of corresponding hidden columns for each alignment
- */
- public void superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
- {
- StringBuilder allComs = new StringBuilder(128);
- String[] files = getPdbFile();
-
- if (!waitForFileLoad(files))
- {
- return;
- }
-
- refreshPdbEntries();
- StringBuilder selectioncom = new StringBuilder(256);
- for (int a = 0; a < _alignment.length; a++)
- {
- int refStructure = _refStructure[a];
- AlignmentI alignment = _alignment[a];
- ColumnSelection hiddenCols = _hiddenCols[a];
-
- if (refStructure >= files.length)
- {
- System.err.println("Ignoring invalid reference structure value "
- + refStructure);
- refStructure = -1;
- }
-
- /*
- * 'matched' array will hold 'true' for visible alignment columns where
- * all sequences have a residue with a mapping to the PDB structure
- */
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
- {
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
- }
-
- SuperposeData[] structures = new SuperposeData[files.length];
- for (int f = 0; f < files.length; f++)
- {
- structures[f] = new SuperposeData(alignment.getWidth());
- }
-
- /*
- * Calculate the superposable alignment columns ('matched'), and the
- * corresponding structure residue positions (structures.pdbResNo)
- */
- int candidateRefStructure = findSuperposableResidues(alignment,
- matched, structures);
- if (refStructure < 0)
- {
- /*
- * If no reference structure was specified, pick the first one that has
- * a mapping in the alignment
- */
- refStructure = candidateRefStructure;
- }
-
- int nmatched = 0;
- for (boolean b : matched)
- {
- if (b)
- {
- nmatched++;
- }
- }
- if (nmatched < 4)
- {
- // TODO: bail out here because superposition illdefined?
- }
-
- /*
- * Generate select statements to select regions to superimpose structures
- */
- String[] selcom = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- String chainCd = "." + structures[pdbfnum].chain;
- int lpos = -1;
- boolean run = false;
- StringBuilder molsel = new StringBuilder();
- for (int r = 0; r < matched.length; r++)
- {
- if (matched[r])
- {
- int pdbResNum = structures[pdbfnum].pdbResNo[r];
- if (lpos != pdbResNum - 1)
- {
- /*
- * discontiguous - append last residue now
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- molsel.append(chainCd);
- molsel.append(",");
- }
- run = false;
- }
- else
- {
- /*
- * extending a contiguous run
- */
- if (!run)
- {
- /*
- * start the range selection
- */
- molsel.append(String.valueOf(lpos));
- molsel.append("-");
- }
- run = true;
- }
- lpos = pdbResNum;
- }
- }
-
- /*
- * and terminate final selection
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- molsel.append(chainCd);
- }
- if (molsel.length() > 1)
- {
- selcom[pdbfnum] = molsel.toString();
- selectioncom.append("#").append(String.valueOf(pdbfnum))
- .append(":");
- selectioncom.append(selcom[pdbfnum]);
- selectioncom.append(" ");
- if (pdbfnum < files.length - 1)
- {
- selectioncom.append("| ");
- }
- }
- else
- {
- selcom[pdbfnum] = null;
- }
- }
-
- StringBuilder command = new StringBuilder(256);
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- if (pdbfnum == refStructure || selcom[pdbfnum] == null
- || selcom[refStructure] == null)
- {
- continue;
- }
- if (command.length() > 0)
- {
- command.append(";");
- }
-
- /*
- * Form Chimera match command, from the 'new' structure to the
- * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
- *
- * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
- *
- * @see
- * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
- */
- command.append("match ").append(getModelSpec(pdbfnum)).append(":");
- command.append(selcom[pdbfnum]);
- command.append("@").append(
- structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
- // JAL-1757 exclude alternate CA locations
- command.append(NO_ALTLOCS);
- command.append(" ").append(getModelSpec(refStructure)).append(":");
- command.append(selcom[refStructure]);
- command.append("@").append(
- structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
- command.append(NO_ALTLOCS);
- }
- if (selectioncom.length() > 0)
- {
- if (debug)
- {
- System.out.println("Select regions:\n" + selectioncom.toString());
- System.out.println("Superimpose command(s):\n"
- + command.toString());
- }
- allComs.append("~display all; chain @CA|P; ribbon ")
- .append(selectioncom.toString())
- .append(";" + command.toString());
- }
- }
- if (selectioncom.length() > 0)
+
+ /*
+ * the following call is added to avoid a stack trace error in Chimera
+ * after "stop really" is sent; Chimera > 1.14 will not need it; see also
+ * http://plato.cgl.ucsf.edu/trac/chimera/ticket/17597
+ */
+ if (closeChimera && (getViewerType() == ViewerType.CHIMERA))
{
- // TODO: visually distinguish regions that were superposed
- if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
- {
- selectioncom.setLength(selectioncom.length() - 1);
- }
- if (debug)
- {
- System.out.println("Select regions:\n" + selectioncom.toString());
- }
- allComs.append("; ~display all; chain @CA|P; ribbon ")
- .append(selectioncom.toString()).append("; focus");
- sendChimeraCommand(allComs.toString(), false);
+ chimeraManager.getChimeraProcess().destroy();
}
+ chimeraManager.clearOnChimeraExit();
+ chimeraManager = null;
}
/**
{
if (pdbfnum < 0 || pdbfnum >= getPdbCount())
{
- return "";
+ return "#" + pdbfnum; // temp hack for ChimeraX
}
/*
* to the Chimera command 'list models type molecule', see
* ChimeraManager.getModelList().
*/
- List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+ List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
boolean hasSubModels = maps != null && maps.size() > 1;
return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
}
/**
* Launch Chimera, unless an instance linked to this object is already
- * running. Returns true if chimera is successfully launched, or already
+ * running. Returns true if Chimera is successfully launched, or already
* running, else false.
*
* @return
*/
public boolean launchChimera()
{
- if (!viewer.isChimeraLaunched())
- {
- return viewer.launchChimera(StructureManager.getChimeraPaths());
- }
- if (viewer.isChimeraLaunched())
+ if (chimeraManager.isChimeraLaunched())
{
return true;
}
- log("Failed to launch Chimera!");
- return false;
- }
- /**
- * Answers true if the Chimera process is still running, false if ended or not
- * started.
- *
- * @return
- */
- public boolean isChimeraRunning()
- {
- return viewer.isChimeraLaunched();
- }
-
- /**
- * Send a command to Chimera, and optionally log any responses.
- *
- * @param command
- * @param logResponse
- */
- public void sendChimeraCommand(final String command, boolean logResponse)
- {
- if (viewer == null)
+ boolean launched = chimeraManager.launchChimera(getChimeraPaths());
+ if (launched)
{
- // ? thread running after viewer shut down
- return;
+ startExternalViewerMonitor(chimeraManager.getChimeraProcess());
}
- viewerCommandHistory(false);
- if (lastCommand == null || !lastCommand.equals(command))
+ else
{
- // trim command or it may never find a match in the replyLog!!
- List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
- logResponse);
- if (logResponse && debug)
- {
- log("Response from command ('" + command + "') was:\n" + lastReply);
- }
+ log("Failed to launch Chimera!");
}
- viewerCommandHistory(true);
- lastCommand = command;
+ return launched;
}
/**
- * Send a Chimera command asynchronously in a new thread. If the progress
- * message is not null, display this message while the command is executing.
+ * Returns a list of candidate paths to the Chimera program executable
*
- * @param command
- * @param progressMsg
- */
- protected abstract void sendAsynchronousCommand(String command,
- String progressMsg);
-
- /**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * @return
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ protected List<String> getChimeraPaths()
{
- if (!colourBySequence || !loadingFinished)
- {
- return;
- }
- if (getSsm() == null)
- {
- return;
- }
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
- {
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
- StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
- .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
- fr, alignment);
- for (String command : colourBySequenceCommands.commands)
- {
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
+ return StructureManager.getChimeraPaths(false);
}
/**
- * @param command
+ * Answers true if the Chimera process is still running, false if ended or not
+ * started.
+ *
+ * @return
*/
- protected void executeWhenReady(String command)
- {
- waitForChimera();
- sendChimeraCommand(command, false);
- waitForChimera();
- }
-
- private void waitForChimera()
+ @Override
+ public boolean isViewerRunning()
{
- while (viewer != null && viewer.isBusy())
- {
- try
- {
- Thread.sleep(15);
- } catch (InterruptedException q)
- {
- }
- }
+ return chimeraManager.isChimeraLaunched();
}
- // End StructureListener
- // //////////////////////////
-
/**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
+ * Send a command to Chimera, and optionally log and return any responses.
*
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
-
- /**
- * instruct the Jalview binding to update the pdbentries vector if necessary
- * prior to matching the viewer's contents to the list of structure files
- * Jalview knows about.
+ * @param command
+ * @param getResponse
*/
- public abstract void refreshPdbEntries();
-
- private int getModelNum(String modelFileName)
+ @Override
+ public List<String> executeCommand(final StructureCommandI command,
+ boolean getResponse)
{
- String[] mfn = getPdbFile();
- if (mfn == null)
+ if (chimeraManager == null || command == null)
{
- return -1;
+ // ? thread running after viewer shut down
+ return null;
+ }
+ List<String> reply = null;
+ // trim command or it may never find a match in the replyLog!!
+ String cmd = command.getCommand().trim();
+ List<String> lastReply = chimeraManager
+ .sendChimeraCommand(cmd, getResponse);
+ if (getResponse)
+ {
+ reply = lastReply;
+ if (Cache.isDebugEnabled()) {
+ Cache.debug(
+ "Response from command ('" + cmd + "') was:\n" + lastReply);
+ }
}
- for (int i = 0; i < mfn.length; i++)
+ else
{
- if (mfn[i].equalsIgnoreCase(modelFileName))
+ if (Cache.isDebugEnabled())
{
- return i;
+ Cache.debug("Command executed: " + cmd);
}
}
- return -1;
- }
- /**
- * map between index of model filename returned from getPdbFile and the first
- * index of models from this file in the viewer. Note - this is not trimmed -
- * use getPdbFile to get number of unique models.
- */
- private int _modelFileNameMap[];
+ return reply;
+ }
- // ////////////////////////////////
- // /StructureListener
@Override
- public synchronized String[] getPdbFile()
+ public synchronized String[] getStructureFiles()
{
- if (viewer == null)
+ if (chimeraManager == null)
{
return new String[0];
}
- // if (modelFileNames == null)
- // {
- // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
- // _modelFileNameMap = new int[chimodels.size()];
- // int j = 0;
- // for (ChimeraModel chimodel : chimodels)
- // {
- // String mdlName = chimodel.getModelName();
- // }
- // modelFileNames = new String[j];
- // // System.arraycopy(mset, 0, modelFileNames, 0, j);
- // }
- return chimeraMaps.keySet().toArray(
- modelFileNames = new String[chimeraMaps.size()]);
+ return chimeraMaps.keySet()
+ .toArray(modelFileNames = new String[chimeraMaps.size()]);
}
/**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
-
- /**
- * Construct and send a command to highlight zero, one or more atoms. We do
- * this by sending an "rlabel" command to show the residue label at that
- * position.
+ * Construct and send a command to highlight zero, one or more atoms. We do this
+ * by sending an "rlabel" command to show the residue label at that position.
*/
@Override
public void highlightAtoms(List<AtomSpec> atoms)
return;
}
+ boolean forChimeraX = chimeraManager.isChimeraX();
StringBuilder cmd = new StringBuilder(128);
boolean first = true;
boolean found = false;
{
if (first)
{
- cmd.append("rlabel #").append(cms.get(0).getModelNumber())
- .append(":");
+ cmd.append(forChimeraX ? "label #" : "rlabel #");
}
else
{
cmd.append(",");
}
first = false;
- cmd.append(pdbResNum);
- if (!chain.equals(" "))
+ if (forChimeraX)
+ {
+ cmd.append(cms.get(0).getModelNumber())
+ .append("/").append(chain).append(":").append(pdbResNum);
+ }
+ else
{
- cmd.append(".").append(chain);
+ cmd.append(cms.get(0).getModelNumber())
+ .append(":").append(pdbResNum);
+ if (!chain.equals(" ") && !forChimeraX)
+ {
+ cmd.append(".").append(chain);
+ }
}
found = true;
}
{
return;
}
-
+ if (!found)
+ {
+ // not a valid residue label command, so clear
+ cmd.setLength(0);
+ }
/*
- * unshow the label for the previous residue
+ * prepend with command
+ * to unshow the label for the previous residue
*/
if (lastHighlightCommand != null)
{
- viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+ cmd.insert(0, ";");
+ cmd.insert(0,lastHighlightCommand);
+ cmd.insert(0,"~");
+
}
- if (found)
- {
- viewer.sendChimeraCommand(command, false);
+ if (cmd.length()>0) {
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
+ }
+
+ if (found) {
+ this.lastHighlightCommand = command;
}
- this.lastHighlightCommand = command;
}
/**
/*
* Ask Chimera for its current selection
*/
- List<String> selection = viewer.getSelectedResidueSpecs();
-
- /*
- * Parse model number, residue and chain for each selected position,
- * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
- */
- List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
- for (String atomSpec : selection)
+ StructureCommandI command = getCommandGenerator().getSelectedResidues();
+
+ Runnable action = new Runnable()
{
- int colonPos = atomSpec.indexOf(":");
- if (colonPos == -1)
+ @Override
+ public void run()
{
- continue; // malformed
+ List<String> chimeraReply = executeCommand(command, true);
+
+ List<String> selectedResidues = new ArrayList<>();
+ if (chimeraReply != null)
+ {
+ /*
+ * expect 0, 1 or more lines of the format either
+ * Chimera:
+ * residue id #0:43.A type GLY
+ * ChimeraX:
+ * residue id /A:89 name THR index 88
+ * We are only interested in the atomspec (third token of the reply)
+ */
+ for (String inputLine : chimeraReply)
+ {
+ String[] inputLineParts = inputLine.split("\\s+");
+ if (inputLineParts.length >= 5)
+ {
+ selectedResidues.add(inputLineParts[2]);
+ }
+ }
+ }
+
+ /*
+ * Parse model number, residue and chain for each selected position,
+ * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
+ */
+ List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+ selectedResidues);
+
+ /*
+ * Broadcast the selection (which may be empty, if the user just cleared all
+ * selections)
+ */
+ getSsm().mouseOverStructure(atomSpecs);
+
}
+ };
+ new Thread(action).start();
+ }
- int hashPos = atomSpec.indexOf("#");
- String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
- int dotPos = modelSubmodel.indexOf(".");
- int modelId = 0;
+ /**
+ * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the
+ * corresponding residues (if any) in Jalview
+ *
+ * @param structureSelection
+ * @return
+ */
+ protected List<AtomSpec> convertStructureResiduesToAlignment(
+ List<String> structureSelection)
+ {
+ List<AtomSpec> atomSpecs = new ArrayList<>();
+ for (String atomSpec : structureSelection)
+ {
try
{
- modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
- : modelSubmodel.substring(0, dotPos));
- } catch (NumberFormatException e)
+ AtomSpec spec = parseAtomSpec(atomSpec);
+ String pdbfilename = getPdbFileForModel(spec.getModelNumber());
+ spec.setPdbFile(pdbfilename);
+ atomSpecs.add(spec);
+ } catch (IllegalArgumentException e)
{
- // ignore, default to model 0
+ Cache.error("Failed to parse atomspec: " + atomSpec);
}
+ }
+ return atomSpecs;
+ }
- String residueChain = atomSpec.substring(colonPos + 1);
- dotPos = residueChain.indexOf(".");
- int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
- : residueChain.substring(0, dotPos));
-
- String chainId = dotPos == -1 ? "" : residueChain
- .substring(dotPos + 1);
-
- /*
- * Work out the pdbfilename from the model number
- */
- String pdbfilename = modelFileNames[frameNo];
- findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
+ /**
+ * @param modelId
+ * @return
+ */
+ protected String getPdbFileForModel(int modelId)
+ {
+ /*
+ * Work out the pdbfilename from the model number
+ */
+ String pdbfilename = modelFileNames[0];
+ findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
+ {
+ for (ChimeraModel cm : chimeraMaps.get(pdbfile))
{
- for (ChimeraModel cm : chimeraMaps.get(pdbfile))
+ if (cm.getModelNumber() == modelId)
{
- if (cm.getModelNumber() == modelId)
- {
- pdbfilename = pdbfile;
- break findfileloop;
- }
+ pdbfilename = pdbfile;
+ break findfileloop;
}
}
- atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
}
-
- /*
- * Broadcast the selection (which may be empty, if the user just cleared all
- * selections)
- */
- getSsm().mouseOverStructure(atomSpecs);
+ return pdbfilename;
}
private void log(String message)
System.err.println("## Chimera log: " + message);
}
- private void viewerCommandHistory(boolean enable)
- {
- // log("(Not yet implemented) History "
- // + ((debug || enable) ? "on" : "off"));
- }
-
- public long getLoadNotifiesHandled()
- {
- return loadNotifiesHandled;
- }
-
- public void setJalviewColourScheme(ColourSchemeI cs)
+ /**
+ * Constructs and send commands to Chimera to set attributes on residues for
+ * features visible in Jalview.
+ * <p>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * <p>
+ * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ *
+ * @param avp
+ * @return
+ */
+ public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
- colourBySequence = false;
+ // TODO refactor as required to pull up to an interface
- if (cs == null)
+ Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
+ avp);
+ List<StructureCommandI> commands = getCommandGenerator()
+ .setAttributes(featureValues);
+ if (commands.size() > 10)
{
- return;
+ sendCommandsByFile(commands);
}
-
- // Chimera expects RBG values in the range 0-1
- final double normalise = 255D;
- viewerCommandHistory(false);
- StringBuilder command = new StringBuilder(128);
-
- List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
- false);
- for (String res : residueSet)
+ else
{
- Color col = cs.findColour(res.charAt(0));
- command.append("color " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + res + ";");
+ executeCommands(commands, false, null);
}
-
- sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
- viewerCommandHistory(true);
- }
-
- /**
- * called when the binding thinks the UI needs to be refreshed after a Chimera
- * state change. this could be because structures were loaded, or because an
- * error has occurred.
- */
- public abstract void refreshGUI();
-
- @Override
- public void setLoadingFromArchive(boolean loadingFromArchive)
- {
- this.loadingFromArchive = loadingFromArchive;
+ return commands.size();
}
/**
+ * Write commands to a temporary file, and send a command to Chimera to open the
+ * file as a commands script. For use when sending a large number of separate
+ * commands would overload the REST interface mechanism.
*
- * @return true if Chimeral is still restoring state or loading is still going
- * on (see setFinsihedLoadingFromArchive)
+ * @param commands
*/
- @Override
- public boolean isLoadingFromArchive()
+ protected void sendCommandsByFile(List<StructureCommandI> commands)
{
- return loadingFromArchive && !loadingFinished;
+ try
+ {
+ File tmp = File.createTempFile("chim", getCommandFileExtension());
+ tmp.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
+ for (StructureCommandI command : commands)
+ {
+ out.println(command.getCommand());
+ }
+ out.flush();
+ out.close();
+ String path = tmp.getAbsolutePath();
+ StructureCommandI command = getCommandGenerator()
+ .openCommandFile(path);
+ executeCommand(false, null, command);
+ } catch (IOException e)
+ {
+ System.err.println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
+ }
}
/**
- * modify flag which controls if sequence colouring events are honoured by the
- * binding. Should be true for normal operation
- *
- * @param finishedLoading
+ * Returns the file extension required for a file of commands to be read by
+ * the structure viewer
+ * @return
*/
- @Override
- public void setFinishedLoadingFromArchive(boolean finishedLoading)
+ protected String getCommandFileExtension()
{
- loadingFinished = finishedLoading;
+ return ".com";
}
/**
- * Send the Chimera 'background solid <color>" command.
+ * Create features in Jalview for the given attribute name and structure
+ * residues.
*
- * @see https
- * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
- * .html
- * @param col
- */
- public void setBackgroundColour(Color col)
- {
- viewerCommandHistory(false);
- double normalise = 255D;
- final String command = "background solid " + col.getRed() / normalise
- + "," + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + ";";
- viewer.sendChimeraCommand(command, false);
- viewerCommandHistory(true);
- }
-
- /**
- * Ask Chimera to save its session to the given file. Returns true if
- * successful, else false.
+ * <pre>
+ * The residue list should be 0, 1 or more reply lines of the format:
+ * residue id #0:5.A isHelix -155.000836316 index 5
+ * or
+ * residue id #0:6.A isHelix None
+ * </pre>
*
- * @param filepath
- * @return
+ * @param attName
+ * @param residues
+ * @return the number of features added
*/
- public boolean saveSession(String filepath)
+ protected int createFeaturesForAttributes(String attName,
+ List<String> residues)
{
- if (isChimeraRunning())
+ int featuresAdded = 0;
+ String featureGroup = getViewerFeatureGroup();
+
+ for (String residue : residues)
{
- List<String> reply = viewer.sendChimeraCommand("save " + filepath,
- true);
- if (reply.contains("Session written"))
+ AtomSpec spec = null;
+ String[] tokens = residue.split(" ");
+ if (tokens.length < 5)
+ {
+ continue;
+ }
+ String atomSpec = tokens[2];
+ String attValue = tokens[4];
+
+ /*
+ * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
+ */
+ if ("None".equalsIgnoreCase(attValue)
+ || "False".equalsIgnoreCase(attValue))
{
- return true;
+ continue;
}
- else
+
+ try
{
- Cache.log
- .error("Error saving Chimera session: " + reply.toString());
+ spec = parseAtomSpec(atomSpec);
+ } catch (IllegalArgumentException e)
+ {
+ Cache.error("Problem parsing atomspec " + atomSpec);
+ continue;
+ }
+
+ String chainId = spec.getChain();
+ String description = attValue;
+ float score = Float.NaN;
+ try
+ {
+ score = Float.valueOf(attValue);
+ description = chainId;
+ } catch (NumberFormatException e)
+ {
+ // was not a float value
+ }
+
+ String pdbFile = getPdbFileForModel(spec.getModelNumber());
+ spec.setPdbFile(pdbFile);
+
+ List<AtomSpec> atoms = Collections.singletonList(spec);
+
+ /*
+ * locate the mapped position in the alignment (if any)
+ */
+ SearchResultsI sr = getSsm()
+ .findAlignmentPositionsForStructurePositions(atoms);
+
+ /*
+ * expect one matched alignment position, or none
+ * (if the structure position is not mapped)
+ */
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ SequenceI seq = m.getSequence();
+ int start = m.getStart();
+ int end = m.getEnd();
+ SequenceFeature sf = new SequenceFeature(attName, description,
+ start, end, score, featureGroup);
+ // todo: should SequenceFeature have an explicit property for chain?
+ // note: repeating the action shouldn't duplicate features
+ if (seq.addSequenceFeature(sf))
+ {
+ featuresAdded++;
+ }
}
}
- return false;
+ return featuresAdded;
}
/**
- * Ask Chimera to open a session file. Returns true if successful, else false.
- * The filename must have a .py extension for this command to work.
+ * Answers the feature group name to apply to features created in Jalview from
+ * Chimera attributes
*
- * @param filepath
* @return
*/
- public boolean openSession(String filepath)
+ protected String getViewerFeatureGroup()
+ {
+ // todo pull up to interface
+ return CHIMERA_FEATURE_GROUP;
+ }
+
+ @Override
+ public String getModelIdForFile(String pdbFile)
{
- sendChimeraCommand("open " + filepath, true);
- // todo: test for failure - how?
- return true;
+ List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
+ if (foundModels != null && !foundModels.isEmpty())
+ {
+ return String.valueOf(foundModels.get(0).getModelNumber());
+ }
+ return "";
}
/**
- * Returns a list of chains mapped in this viewer. Note this list is not
- * currently scoped per structure.
+ * Answers a (possibly empty) list of attribute names in Chimera[X], excluding
+ * any which were added from Jalview
*
* @return
*/
- public List<String> getChainNames()
+ public List<String> getChimeraAttributes()
{
- List<String> names = new ArrayList<String>();
- String[][] allNames = getChains();
- if (allNames != null)
+ List<String> attributes = new ArrayList<>();
+ StructureCommandI command = getCommandGenerator().listResidueAttributes();
+ final List<String> reply = executeCommand(command, true);
+ if (reply != null)
{
- for (String[] chainsForPdb : allNames)
+ for (String inputLine : reply)
{
- if (chainsForPdb != null)
+ String[] lineParts = inputLine.split("\\s");
+ if (lineParts.length == 2 && lineParts[0].equals("resattr"))
{
- for (String chain : chainsForPdb)
+ String attName = lineParts[1];
+ /*
+ * exclude attributes added from Jalview
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
{
- if (chain != null && !names.contains(chain))
- {
- names.add(chain);
- }
+ attributes.add(attName);
}
}
}
}
- return names;
+ return attributes;
}
/**
- * Send a 'focus' command to Chimera to recentre the visible display
- */
- public void focusView()
- {
- sendChimeraCommand("focus", false);
- }
-
- /**
- * Send a 'show' command for all atoms in the currently selected columns
- *
- * TODO: pull up to abstract structure viewer interface
+ * Returns the file extension to use for a saved viewer session file (.py)
*
- * @param vp
+ * @return
*/
- public void highlightSelection(AlignmentViewPanel vp)
+ @Override
+ public String getSessionFileExtension()
{
- List<Integer> cols = vp.getAlignViewport().getColumnSelection()
- .getSelected();
- AlignmentI alignment = vp.getAlignment();
- StructureSelectionManager sm = getSsm();
- for (SequenceI seq : alignment.getSequences())
- {
- /*
- * convert selected columns into sequence positions
- */
- int[] positions = new int[cols.size()];
- int i = 0;
- for (Integer col : cols)
- {
- positions[i++] = seq.findPosition(col);
- }
- sm.highlightStructure(this, seq, positions);
- }
+ return CHIMERA_SESSION_EXTENSION;
}
- /**
- * Constructs and send commands to Chimera to set attributes on residues for
- * features visible in Jalview
- *
- * @param avp
- */
- public void sendFeaturesToChimera(AlignmentViewPanel avp)
+ @Override
+ public String getHelpURL()
{
- // TODO send a command per feature with the range of residues it applies to
- AlignmentI alignment = avp.getAlignment();
- FeatureRenderer fr = getFeatureRenderer(avp);
-
- /*
- * fr is null if feature display is turned off
- */
- if (fr == null)
- {
- return;
- }
-
- String[] files = getPdbFile();
- if (files == null)
- {
- return;
- }
-
- StructureMappingcommandSet commandSet = ChimeraCommands
- .getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), fr, alignment);
- for (String command : commandSet.commands)
- {
- sendAsynchronousCommand(command, null);
- }
-
+ return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
}
}
git://source.jalview.org / jalview.git / blobdiff