- fileLoadingError = null;
-
- if (fileName != null)
- {
- // FILE LOADED OK
- jmolpopup.updateComputedMenus();
- viewer
- .evalStringQuiet("select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdb;
- if (loadedInline)
- {
- pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
- AppletFormatAdapter.PASTE);
- pdbentry.setFile("INLINE" + pdb.id);
- }
- else
- {
- // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs
- // to be tested. See mantis bug
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-
- pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
- AppletFormatAdapter.URL);
-
- }
-
- pdbentry.setId(pdb.id);
-
- ssm.addStructureViewerListener(this);
-
- Vector chains = new Vector();
- for (int i = 0; i < pdb.chains.size(); i++)
- {
- chains.addElement(((MCview.PDBChain) pdb.chains.elementAt(i)).id);
- }
- setChainMenuItems(chains);
-
- colourBySequence(ap);
-
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
- + pdbentry.getId());
-
- if (pdbentry.getProperty() != null)
- {
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
- }
- }
-
- this.setTitle(title.toString());
-
- }
- else
- return;
- }
-
- public void notifyFrameChanged(int frameNo)
- {
- boolean isAnimationRunning = (frameNo <= -2);
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo)
- {
- }
-
- public void sendConsoleEcho(String strEcho)
- {
- if (scriptWindow == null)
- showConsole(true);
-
- history.append("\n" + strEcho);
- }
-
- public void sendConsoleMessage(String strStatus)
- {
- if (history != null && strStatus != null
- && !strStatus.equals("Script completed"))
- {
- history.append("\n" + strStatus);
- }
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- }
-
- public void handlePopupMenu(int x, int y)
- {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
- {
- notifyAtomPicked(iatom, strMeasure);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo)
- {
-
- int chainSeparator = strInfo.indexOf(":");
-
- if (chainSeparator == -1)
- chainSeparator = strInfo.indexOf(".");
-
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,
- chainSeparator);
-
- if (strInfo.indexOf(":") > -1)
- picked += strInfo.substring(strInfo.indexOf(":") + 1, strInfo
- .indexOf("."));
-
- picked += ".CA";
-
- if (!atomsPicked.contains(picked))
- {
- viewer.evalString("select " + picked + ";label %n %r:%c");
- atomsPicked.addElement(picked);
- }
- else
- {
- viewer.evalString("select " + picked + ";label off");
- atomsPicked.removeElement(picked);
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo)
- {
- mouseOverStructure(atomIndex, strInfo);
- }
-
- public void sendSyncScript(String script, String appletName)
- {