*/
package jalview.ext.rbvi.chimera;
-import jalview.structure.AtomSpecModel;
-import jalview.util.ColorUtils;
-import jalview.util.IntRangeComparator;
-
import java.awt.Color;
-import java.util.Collections;
-import java.util.Iterator;
+import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+
/**
* Routines for generating ChimeraX commands for Jalview/ChimeraX binding
*/
public class ChimeraXCommands extends ChimeraCommands
{
- private static final String CMD_COLOUR_BY_CHARGE = "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow";
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("info resattr");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
+ private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("info notify stop selection jalview");
+
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
+ private static final StructureCommand GET_SELECTION = new StructureCommand(
+ "info selection level residue");
+
+ private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
+ "~display all;~ribbon;show @CA|P atoms");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "view");
+
+ private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
+ "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
@Override
- public String colourByCharge()
+ public List<StructureCommandI> colourByCharge()
{
- return CMD_COLOUR_BY_CHARGE;
+ return Arrays.asList(COLOUR_BY_CHARGE);
}
@Override
}
@Override
- public String setBackgroundColour(Color col)
- {
- // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/set.html
- return "set bgColor " + ColorUtils.toTkCode(col);
- }
-
- @Override
- public String getColourCommand(String atomSpec, Color colour)
+ public StructureCommandI colourResidues(String atomSpec, Color colour)
{
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
String colourCode = getColourString(colour);
- return "color " + atomSpec + " " + colourCode;
+ return new StructureCommand("color " + atomSpec + " " + colourCode);
}
@Override
- public String focusView()
+ public StructureCommandI focusView()
{
- // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
- return "view";
+ return FOCUS_VIEW;
}
/**
* @return
*/
@Override
- protected String setAttribute(String attributeName,
+ protected StructureCommandI setAttribute(String attributeName,
String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
sb.append(" res ").append(attributeName).append(" '")
.append(attributeValue).append("'");
sb.append(" create true");
- return sb.toString();
+ return new StructureCommand(sb.toString());
}
@Override
- public String openCommandFile(String path)
+ public StructureCommandI openCommandFile(String path)
{
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
- return "open " + path;
+ return new StructureCommand("open " + path);
}
@Override
- public String saveSession(String filepath)
+ public StructureCommandI saveSession(String filepath)
{
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
- return "save session " + filepath;
+ // note ChimeraX will append ".cxs" to the filepath!
+ return new StructureCommand("save " + filepath + " format session");
}
/**
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
- for (Integer model : atomSpec.getModels())
+ for (String model : atomSpec.getModels())
{
if (!firstModel)
{
appendModel(sb, model, atomSpec);
if (alphaOnly)
{
- sb.append("@CA|P");
+ // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
+ sb.append("@CA");
}
// todo: is there ChimeraX syntax to exclude altlocs?
}
* @param model
* @param atomSpec
*/
- protected void appendModel(StringBuilder sb, Integer model,
+ protected void appendModel(StringBuilder sb, String model,
AtomSpecModel atomSpec)
{
sb.append("#").append(model);
boolean firstPositionForChain = true;
sb.append("/").append(chain.trim()).append(":");
List<int[]> rangeList = atomSpec.getRanges(model, chain);
-
- /*
- * sort ranges into ascending start position order
- */
- Collections.sort(rangeList, IntRangeComparator.ASCENDING);
-
- int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
- int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
-
- Iterator<int[]> iterator = rangeList.iterator();
- while (iterator.hasNext())
+ boolean first = true;
+ for (int[] range : rangeList)
{
- int[] range = iterator.next();
- if (range[0] <= end + 1)
- {
- /*
- * range overlaps or is contiguous with the last one
- * - so just extend the end position, and carry on
- * (unless this is the last in the list)
- */
- end = Math.max(end, range[1]);
- }
- else
+ if (!first)
{
- /*
- * we have a break so append the last range
- */
- appendRange(sb, start, end, chain, firstPositionForChain, true);
- start = range[0];
- end = range[1];
- firstPositionForChain = false;
+ sb.append(",");
}
+ first = false;
+ appendRange(sb, range[0], range[1], chain, firstPositionForChain,
+ true);
}
-
- /*
- * and append the last range
- */
- if (!rangeList.isEmpty())
- {
- appendRange(sb, start, end, chain, firstPositionForChain, true);
- }
- firstPositionForChain = false;
}
}
@Override
- public String showBackbone()
+ public List<StructureCommandI> showBackbone()
{
- return "~display all;show @CA|P pbonds";
+ return Arrays.asList(SHOW_BACKBONE);
}
@Override
- public String superposeStructures(AtomSpecModel spec, AtomSpecModel ref)
+ public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
+ AtomSpecModel spec)
{
/*
* Form ChimeraX match command to match spec to ref
*
* match #1/A:2-94 toAtoms #2/A:1-93
*
- * @see
- * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
+ * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
*/
StringBuilder cmd = new StringBuilder();
String atomSpec = getAtomSpec(spec, true);
cmd.append(getAtomSpec(spec, false)).append("|");
cmd.append(getAtomSpec(ref, false)).append("; view");
- return cmd.toString();
+ return Arrays.asList(new StructureCommand(cmd.toString()));
}
+ @Override
+ public StructureCommandI openSession(String filepath)
+ {
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#composite
+ // this version of the command has no dependency on file extension
+ return new StructureCommand("open " + filepath + " format session");
+ }
+
+ @Override
+ public StructureCommandI closeViewer()
+ {
+ return CLOSE_CHIMERAX;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ List<StructureCommandI> cmds = new ArrayList<>();
+ cmds.add(new StructureCommand("info notify start models jalview prefix ModelChanged url " + uri));
+ cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri));
+ return cmds;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ List<StructureCommandI> cmds = new ArrayList<>();
+ cmds.add(STOP_NOTIFY_MODELS);
+ cmds.add(STOP_NOTIFY_SELECTION);
+ return cmds;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return GET_SELECTION;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
}
git://source.jalview.org / jalview.git / blobdiff