import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.gui.Preferences;
import jalview.gui.StructureViewer.ViewerType;
import jalview.httpserver.AbstractRequestHandler;
import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureCommandsI.SuperposeData;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
/*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
- private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
+ protected Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
String lastHighlightCommand;
if (!alreadyOpen)
{
chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- if (chimeraManager.isChimeraX())
- {
- /*
- * ChimeraX hack: force chimera model name to pdbId
- */
- int modelNumber = chimeraMaps.size() + 1;
- String command = "setattr #" + modelNumber + " models name "
- + pe.getId();
- executeCommand(command, false);
- modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
- modelNumber, 0));
- }
- else
- {
- /*
- * Chimera: query for actual models and find the one with
- * matching model name - 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);
- }
- }
- }
+ addChimeraModel(pe, modelsToMap);
}
chimeraMaps.put(file, modelsToMap);
}
/**
+ * 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
{
super(ssm, pdbentry, sequenceIs, protocol);
chimeraManager = new ChimeraManager(new StructureManager(true));
- String viewerType = Cache.getProperty(Preferences.STRUCTURE_DISPLAY);
- chimeraManager.setChimeraX(ViewerType.CHIMERAX.name().equals(viewerType));
+ chimeraManager.setChimeraX(ViewerType.CHIMERAX.equals(getViewerType()));
setStructureCommands(new ChimeraCommands());
}
+ @Override
+ protected ViewerType getViewerType()
+ {
+ return ViewerType.CHIMERA;
+ }
+
/**
* Starts a thread that waits for the Chimera process to finish, so that we can
* then close the associated resources. This avoids leaving orphaned Chimera
}
/**
- * {@inheritDoc}
- */
- @Override
- public String superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, HiddenColumns[] _hiddenCols)
- {
- StringBuilder allComs = new StringBuilder(128);
- String[] files = getStructureFiles();
-
- if (!waitForFileLoad(files))
- {
- return null;
- }
-
- refreshPdbEntries();
- StringBuilder selectioncom = new StringBuilder(256);
- boolean chimeraX = chimeraManager.isChimeraX();
- for (int a = 0; a < _alignment.length; a++)
- {
- int refStructure = _refStructure[a];
- AlignmentI alignment = _alignment[a];
- HiddenColumns hiddenCols = _hiddenCols[a];
-
- if (refStructure >= files.length)
- {
- System.err.println("Ignoring invalid reference structure value "
- + refStructure);
- refStructure = -1;
- }
-
- /*
- * 'matched' bit i will be set for visible alignment columns i where
- * all sequences have a residue with a mapping to the PDB structure
- */
- BitSet matched = new BitSet();
- for (int m = 0; m < alignment.getWidth(); m++)
- {
- if (hiddenCols == null || hiddenCols.isVisible(m))
- {
- matched.set(m);
- }
- }
-
- 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 = matched.cardinality();
- if (nmatched < 4)
- {
- return MessageManager.formatMessage("label.insufficient_residues",
- nmatched);
- }
-
- /*
- * Generate select statements to select regions to superimpose structures
- */
- String[] selcom = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- final int modelNo = pdbfnum + (chimeraX ? 1 : 0);
- // todo correct resolution to model number
- String chainCd = "." + structures[pdbfnum].chain;
- int lpos = -1;
- boolean run = false;
- StringBuilder molsel = new StringBuilder();
- if (chimeraX)
- {
- molsel.append("/" + structures[pdbfnum].chain + ":");
- }
-
- int nextColumnMatch = matched.nextSetBit(0);
- while (nextColumnMatch != -1)
- {
- int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
- if (lpos != pdbResNum - 1)
- {
- /*
- * discontiguous - append last residue now
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- if (!chimeraX)
- {
- 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;
- nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
- }
-
- /*
- * and terminate final selection
- */
- if (lpos != -1)
- {
- molsel.append(String.valueOf(lpos));
- if (!chimeraX)
- {
- molsel.append(chainCd);
- }
- }
- if (molsel.length() > 1)
- {
- selcom[pdbfnum] = molsel.toString();
- selectioncom.append("#").append(String.valueOf(modelNo));
- if (!chimeraX)
- {
- selectioncom.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++)
- {
- final int modelNo = pdbfnum + (chimeraX ? 1 : 0);
- 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(chimeraX ? "align " : "match ");
- command.append(getModelSpec(modelNo));
- if (!chimeraX)
- {
- command.append(":");
- }
- command.append(selcom[pdbfnum]);
- command.append("@").append(
- structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
- // JAL-1757 exclude alternate CA locations - ChimeraX syntax tbd
- if (!chimeraX)
- {
- command.append(NO_ALTLOCS);
- }
- command.append(chimeraX ? " toAtoms " : " ")
- .append(getModelSpec(refStructure + (chimeraX ? 1 : 0)));
- if (!chimeraX)
- {
- command.append(":");
- }
- command.append(selcom[refStructure]);
- command.append("@").append(
- structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
- if (!chimeraX)
- {
- 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; ");
- // if (chimeraX)
- // {
- // allComs.append("show ").append(selectioncom.toString())
- // .append(" pbonds");
- // }
- // else
- // {
- // allComs.append("chain @CA|P; ribbon ");
- // allComs.append(selectioncom.toString());
- // }
- if (allComs.length() > 0) {
- allComs.append(";");
- }
- allComs.append(command.toString());
- }
- }
-
- String error = null;
- if (selectioncom.length() > 0)
- {
- // 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; ");
- if (chimeraX)
- {
- allComs.append("show @CA|P pbonds; show ")
- .append(selectioncom.toString()).append(" ribbons; view");
- }
- else
- {
- allComs.append("chain @CA|P; ribbon ; focus");
- allComs.append(selectioncom.toString());
- }
- // allComs.append("; ~display all; chain @CA|P; ribbon ")
- // .append(selectioncom.toString()).append("; focus");
- List<String> chimeraReplies = executeCommand(allComs.toString(),
- true);
- for (String reply : chimeraReplies)
- {
- if (reply.toLowerCase().contains("unequal numbers of atoms"))
- {
- error = reply;
- }
- }
- }
- return error;
- }
-
- /**
* Helper method to construct model spec in Chimera format:
* <ul>
* <li>#0 (#1 etc) for a PDB file with no sub-models</li>
return true;
}
- boolean launched = chimeraManager.launchChimera(
- StructureManager.getChimeraPaths(chimeraManager.isChimeraX()));
+ boolean launched = chimeraManager.launchChimera(getChimeraPaths());
if (launched)
{
startChimeraProcessMonitor();
}
/**
+ * Returns a list of candidate paths to the Chimera program executable
+ *
+ * @return
+ */
+ protected List<String> getChimeraPaths()
+ {
+ return StructureManager.getChimeraPaths(false);
+ }
+
+ /**
* Answers true if the Chimera process is still running, false if ended or not
* started.
*
}
/**
- * Send a Chimera command asynchronously in a new thread. If the progress
- * message is not null, display this message while the command is executing.
- *
- * @param command
- * @param progressMsg
- */
- protected abstract void sendAsynchronousCommand(String command,
- String progressMsg);
-
- /**
* @param command
*/
protected void executeWhenReady(String command)
* Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
* ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
*/
- String command = isChimeraX() ? "save session " : "save ";
- List<String> reply = chimeraManager.sendChimeraCommand(command + filepath,
- true);
+ String command = getCommandGenerator().saveSession(filepath);
+ List<String> reply = chimeraManager.sendChimeraCommand(command, true);
if (reply.contains("Session written"))
{
return true;
return 0;
}
- StructureMappingcommandSet commandSet = ChimeraCommands
- .getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), avp, chimeraManager.isChimeraX());
- String[] commands = commandSet.commands;
+ String[] commands = getCommandGenerator()
+ .setAttributesForFeatures(getSsm(), files, getSequence(), avp);
if (commands.length > 10)
{
sendCommandsByFile(commands);
*/
protected void sendCommandsByFile(String[] commands)
{
- boolean toChimeraX = chimeraManager.isChimeraX();
try
{
- File tmp = File.createTempFile("chim", toChimeraX ? ".cxc" : ".com");
+ File tmp = File.createTempFile("chim", getCommandFileExtension());
tmp.deleteOnExit();
PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
for (String command : commands)
out.flush();
out.close();
String path = tmp.getAbsolutePath();
- String command = "open " + (toChimeraX ? "" : "cmd:") + path;
+ String command = getCommandGenerator().openCommandFile(path);
sendAsynchronousCommand(command, null);
} catch (IOException e)
{
}
/**
+ * Returns the file extension required for a file of commands to be read by
+ * the structure viewer
+ * @return
+ */
+ protected String getCommandFileExtension()
+ {
+ return ".com";
+ }
+
+ /**
* Get Chimera residues which have the named attribute, find the mapped
* positions in the Jalview sequence(s), and set as sequence features
*
return atts;
}
- public boolean isChimeraX()
+ /**
+ * Returns the file extension to use for a saved viewer session file
+ *
+ * @return
+ */
+ public String getSessionFileExtension()
+ {
+ return ".py";
+ }
+
+ public String getHelpURL()
{
- return chimeraManager.isChimeraX();
+ return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
}
}
git://source.jalview.org / jalview.git / blobdiff