*/
package jalview.ext.rbvi.chimera;
-import java.util.Locale;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import jalview.structure.AtomSpecModel;
public class ChimeraCommands extends StructureCommandsBase
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
- private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "focus");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
- private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+ "list resattr");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
- private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
+ private static final StructureCommand CLOSE_CHIMERA = new StructureCommand(
+ "stop really");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
- private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+ "listen stop selection");
- private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+ "listen stop models");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
- private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
+ private static final StructureCommand GET_SELECTION = new StructureCommand(
+ "list selection level residue");
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
"~display all;~ribbon;chain @CA|P");
* @return
*/
protected StructureCommandI setAttribute(String attributeName,
- String attributeValue,
- AtomSpecModel atomSpecModel)
+ String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
- sb.append(getAtomSpec(atomSpecModel, false));
+ sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
return new StructureCommand(sb.toString());
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec, boolean isNucleotide)
+ AtomSpecModel spec, AtomSpecType backbone)
{
/*
* Form Chimera match command to match spec to ref
* @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
StringBuilder cmd = new StringBuilder();
- String atomSpecAlphaOnly = getAtomSpec(spec, true);
- String refSpecAlphaOnly = getAtomSpec(ref, true);
- cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
+ String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
+ String refSpecAlphaOnly = getAtomSpec(ref, backbone);
+ cmd.append("match ").append(atomSpecAlphaOnly).append(" ")
+ .append(refSpecAlphaOnly);
/*
* show superposed residues as ribbon
*/
- String atomSpec = getAtomSpec(spec, false);
- String refSpec = getAtomSpec(ref, false);
+ String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY);
+ String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY);
cmd.append("; ribbon ");
cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
* <pre>
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
* @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*/
@Override
- public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
sb.append("|");
}
firstModel = false;
- appendModel(sb, model, atomSpec, alphaOnly);
+ appendModel(sb, model, atomSpec, specType);
}
return sb.toString();
}
* @param alphaOnly
*/
protected void appendModel(StringBuilder sb, String model,
- AtomSpecModel atomSpec, boolean alphaOnly)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
sb.append("#").append(model).append(":");
firstPositionForModel = false;
}
}
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
/*
* restrict to alpha carbon, no alternative locations
* (needed to ensuring matching atom counts for superposition)
*/
- // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA").append(NO_ALTLOCS);
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("@P").append(NO_ALTLOCS);
+ }
}
@Override
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
List<StructureCommandI> cmds = new ArrayList<>();
cmds.add(new StructureCommand("listen start models url " + uri));
- cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
+ cmds.add(new StructureCommand(
+ "listen start select prefix SelectionChanged url " + uri));
return cmds;
}
return new StructureCommand("list residues attr '" + attName + "'");
}
+ @Override
+ public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}