X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalviewChimeraXBindingModel.java;h=737e72a740b23e1b1179d1cbe06fe3859887cca3;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=e2aaa65e81448e8967a5f7faae81c1108ee2b117;hpb=2ab7b9b152018bb808693218ad88dc3778166492;p=jalview.git
diff --git a/src/jalview/gui/JalviewChimeraXBindingModel.java b/src/jalview/gui/JalviewChimeraXBindingModel.java
index e2aaa65..737e72a 100644
--- a/src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
@@ -1,18 +1,124 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
+import java.util.List;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.ChimeraXCommands;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
{
+ public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, DataSourceType protocol)
{
super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
+ setStructureCommands(new ChimeraXCommands());
+ }
+
+ @Override
+ protected List getChimeraPaths()
+ {
+ return StructureManager.getChimeraPaths(true);
+ }
+
+ @Override
+ protected void addChimeraModel(PDBEntry pe,
+ List modelsToMap)
+ {
+ /*
+ * ChimeraX hack: force chimera model name to pdbId here
+ */
+ int modelNumber = chimeraMaps.size() + 1;
+ String command = "setattr #" + modelNumber + " models name "
+ + pe.getId();
+ executeCommand(new StructureCommand(command), false);
+ modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
+ modelNumber, 0));
+ }
+
+ /**
+ * {@inheritDoc}
+ *
+ * @return
+ */
+ @Override
+ protected String getCommandFileExtension()
+ {
+ return ".cxc";
+ }
+
+ /**
+ * Returns the file extension to use for a saved viewer session file (.cxs)
+ *
+ * @return
+ * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#sesformat
+ */
+ @Override
+ public String getSessionFileExtension()
+ {
+ return CHIMERAX_SESSION_EXTENSION;
+ }
+
+ @Override
+ public String getHelpURL()
+ {
+ return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
+ }
+
+ @Override
+ protected ViewerType getViewerType()
+ {
+ return ViewerType.CHIMERAX;
+ }
+
+ @Override
+ protected String getModelId(int pdbfnum, String file)
+ {
+ return String.valueOf(pdbfnum + 1);
+ }
+
+ /**
+ * Returns a model of the structure positions described by the ChimeraX format
+ * atomspec
+ *
+ * @param atomSpec
+ * @return
+ */
+ @Override
+ protected AtomSpec parseAtomSpec(String atomSpec)
+ {
+ return AtomSpec.fromChimeraXAtomspec(atomSpec);
}
}