*/
package jalview.ext.jmol;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.Comparison;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
+import jalview.util.Platform;
/**
* Routines for generating Jmol commands for Jalview/Jmol binding
*/
public class JmolCommands extends StructureCommandsBase
{
- private static final String CMD_COLOUR_BY_CHARGE = "select *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow";
+ private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
+ "select *; cartoons off; backbone");
+
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0");
- private static final String CMD_COLOUR_BY_CHAIN = "select *;color chain";
+ private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
+ "select *;color white;");
+
+ private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
+ "select *;color white;select ASP,GLU;color red;"
+ + "select LYS,ARG;color blue;select CYS;color yellow");
+
+ private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
+ "select *;color chain");
private static final String PIPE = "|";
return 1;
}
- @Override
+ /**
+ * Returns a string representation of the given colour suitable for inclusion
+ * in Jmol commands
+ *
+ * @param c
+ * @return
+ */
protected String getColourString(Color c)
{
return c == null ? null
c.getBlue());
}
+ @Override
+ public StructureCommandI colourByChain()
+ {
+ return COLOUR_BY_CHAIN;
+ }
+
+ @Override
+ public List<StructureCommandI> colourByCharge()
+ {
+ return Arrays.asList(COLOUR_BY_CHARGE);
+ }
+
+ @Override
+ public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
+ {
+ List<StructureCommandI> cmds = super.colourByResidues(colours);
+ cmds.add(0, COLOUR_ALL_WHITE);
+ return cmds;
+ }
+
+ @Override
+ public StructureCommandI setBackgroundColour(Color col)
+ {
+ return new StructureCommand("background " + getColourString(col));
+ }
+
+ @Override
+ public StructureCommandI focusView()
+ {
+ return FOCUS_VIEW;
+ }
+
+ @Override
+ public List<StructureCommandI> showChains(List<String> toShow)
+ {
+ StringBuilder atomSpec = new StringBuilder(128);
+ boolean first = true;
+ for (String chain : toShow)
+ {
+ String[] tokens = chain.split(":");
+ if (tokens.length == 2)
+ {
+ if (!first)
+ {
+ atomSpec.append(" or ");
+ }
+ first = false;
+ atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
+ }
+ }
+
+ String spec = atomSpec.toString();
+ String command = "select *;restrict " + spec + ";cartoon;center "
+ + spec;
+ return Arrays.asList(new StructureCommand(command));
+ }
+
/**
- * Returns commands (one per colour key in the map) like
+ * Returns a command to superpose atoms in {@code atomSpec} to those in
+ * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
+ * For example
*
* <pre>
- * select 2:A/1.1|3-27:B/1.1|9-12:A/2.1;color[173,0,82]
+ * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
+ * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
* </pre>
+ *
+ * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
+ * time in seconds to animate the action. For this example, atoms in model 2
+ * are moved towards atoms in model 1.
+ * <p>
+ * The two atomspecs should each be for one model only, but may have more than
+ * one chain. The number of atoms specified should be the same for both
+ * models, though if not, Jmol may make a 'best effort' at superposition.
+ *
+ * @see https://chemapps.stolaf.edu/jmol/docs/#compare
*/
@Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
+ public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
+ AtomSpecModel atomSpec, AtomSpecType backbone)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ String refModel = refAtoms.getModels().iterator().next();
+ String model2 = atomSpec.getModels().iterator().next();
+ sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
+ sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
+
+ /*
+ * command examples don't include modelspec with atoms, getAtomSpec does;
+ * it works, so leave it as it is for simplicity
+ */
+ sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
+ sb.append(getAtomSpec(refAtoms, backbone)).append("}");
+ sb.append(" ROTATE TRANSLATE ");
+ sb.append(getCommandSeparator());
+
+ /*
+ * show residues used for superposition as ribbon
+ */
+ sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
+ .append("cartoons");
+
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+
+ @Override
+ public StructureCommandI openCommandFile(String path)
+ {
+ /*
+ * https://chemapps.stolaf.edu/jmol/docs/#script
+ * not currently used in Jalview
+ */
+ return new StructureCommand("script " + path);
+ }
+
+ @Override
+ public StructureCommandI saveSession(String filepath)
+ {
+ /*
+ * https://chemapps.stolaf.edu/jmol/docs/#writemodel
+ */
+ return new StructureCommand("write STATE \"" + filepath + "\"");
+ }
+
+ @Override
+ protected StructureCommandI colourResidues(String atomSpec, Color colour)
+ {
+ StringBuilder sb = new StringBuilder(atomSpec.length()+20);
+ sb.append("select ").append(atomSpec).append(getCommandSeparator())
+ .append("color").append(getColourString(colour));
+ return new StructureCommand(sb.toString());
+ }
+
+ @Override
+ protected String getResidueSpec(String residue)
+ {
+ return residue;
+ }
+
+ /**
+ * Generates a Jmol atomspec string like
+ *
+ * <pre>
+ * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
+ * </pre>
+ *
+ * Parameter {@code alphaOnly} is not used here - this restriction is made by
+ * a separate clause in the {@code compare} (superposition) command.
+ */
+ @Override
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
+ {
+ StringBuilder sb = new StringBuilder(128);
+
+ boolean first = true;
+ for (String modelNo : model.getModels())
+ {
+ for (String chain : model.getChains(modelNo))
+ {
+ for (int[] range : model.getRanges(modelNo, chain))
+ {
+ if (!first)
+ {
+ sb.append(PIPE);
+ }
+ first = false;
+ if (range[0] == range[1])
+ {
+ sb.append(range[0]);
+ }
+ else
+ {
+ sb.append(range[0]).append(HYPHEN).append(range[1]);
+ }
+ sb.append(COLON).append(chain.trim()).append(SLASH);
+ sb.append(String.valueOf(modelNo)).append(".1");
+ }
+ }
+ }
+
+ return sb.toString();
+ }
+
+ @Override
+ public List<StructureCommandI> showBackbone()
{
- List<String> colourCommands = buildColourCommands(colourMap);
+ return Arrays.asList(SHOW_BACKBONE);
+ }
- return colourCommands.toArray(new String[colourCommands.size()]);
+ @Override
+ public StructureCommandI loadFile(String file)
+ {
+ // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
+ return new StructureCommand("load FILES \"" +
+ Platform.escapeBackslashes(file) + "\"");
}
+ /**
+ * Obsolete method, only referenced from
+ * jalview.javascript.MouseOverStructureListener
+ *
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param viewPanel
+ * @return
+ */
+ @Deprecated
public String[] colourBySequence(StructureSelectionManager ssm,
- String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
+ String[] files, SequenceI[][] sequence, SequenceRenderer sr,
AlignmentViewPanel viewPanel)
{
- // TODO refactor to call buildColoursMap() first...
+ // TODO delete method
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
return cset.toArray(new String[cset.size()]);
}
- public static StringBuilder condenseCommand(StringBuilder command,
+ /**
+ * Helper method
+ *
+ * @param command
+ * @param pos
+ * @return
+ */
+ @Deprecated
+ private static StringBuilder condenseCommand(
+ StringBuilder command,
int pos)
{
}
@Override
- public String colourByChain()
- {
- return CMD_COLOUR_BY_CHAIN;
- }
-
- @Override
- public String colourByCharge()
- {
- return CMD_COLOUR_BY_CHARGE;
- }
-
- @Override
- public String colourByResidues(Map<String, Color> colours)
- {
- StringBuilder cmd = new StringBuilder(128);
- cmd.append("select *;color white;");
- cmd.append(super.colourByResidues(colours));
-
- return cmd.toString();
- }
-
- @Override
- public String setBackgroundColour(Color col)
- {
- return "background " + getColourString(col);
- }
-
- @Override
- public String focusView()
- {
- return "zoom 0";
- }
-
- @Override
- public String showChains(List<String> toShow)
- {
- StringBuilder atomSpec = new StringBuilder(128);
- boolean first = true;
- for (String chain : toShow)
- {
- String[] tokens = chain.split(":");
- if (tokens.length == 2)
- {
- if (!first)
- {
- atomSpec.append(" or ");
- }
- first = false;
- atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
- }
- }
-
- String spec = atomSpec.toString();
- String command = "select *;restrict " + spec + ";cartoon;center "
- + spec;
- return command;
- }
-
- /**
- * Returns a command to superpose atoms in {@code atomSpec} to those in
- * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
- * For example
- *
- * <pre>
- * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
- * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
- * </pre>
- *
- * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
- * time in seconds to animate the action. For this example, atoms in model 2
- * are moved towards atoms in model 1.
- * <p>
- * The two atomspecs should each be for one model only, but may have more than
- * one chain. The number of atoms specified should be the same for both
- * models, though if not, Jmol may make a 'best effort' at superposition.
- *
- * @see https://chemapps.stolaf.edu/jmol/docs/#compare
- */
- @Override
- public String superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ public StructureCommandI openSession(String filepath)
{
- StringBuilder sb = new StringBuilder(64);
- int refModel = refAtoms.getModels().iterator().next();
- int model2 = atomSpec.getModels().iterator().next();
- sb.append(String.format("compare {%d.1} {%d.1}", model2, refModel));
- sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
-
- /*
- * command examples don't include modelspec with atoms, getAtomSpec does;
- * it works, so leave it as it is for simplicity
- */
- sb.append(getAtomSpec(atomSpec, true)).append("}{");
- sb.append(getAtomSpec(refAtoms, true)).append("}");
- sb.append(" ROTATE TRANSLATE ");
- sb.append(getCommandSeparator());
-
- /*
- * show residues used for superposition as ribbon
- */
- sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
- sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
- .append("cartoons");
-
- return sb.toString();
- }
-
- @Override
- public String openCommandFile(String path)
- {
- /*
- * https://chemapps.stolaf.edu/jmol/docs/#script
- * not currently used in Jalview
- */
- return "script " + path;
- }
-
- @Override
- public String saveSession(String filepath)
- {
- /*
- * https://chemapps.stolaf.edu/jmol/docs/#write
- * not currently used in Jalview
- */
- return "write \"" + filepath + "\"";
- }
-
- @Override
- protected String getColourCommand(String atomSpec, Color colour)
- {
- StringBuilder sb = new StringBuilder(atomSpec.length()+20);
- sb.append("select ").append(atomSpec).append(getCommandSeparator())
- .append("color").append(getColourString(colour));
- return sb.toString();
- }
-
- @Override
- protected String getResidueSpec(String residue)
- {
- return residue;
- }
-
- /**
- * Generates a Jmol atomspec string like
- *
- * <pre>
- * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
- * </pre>
- *
- * Parameter {@code alphaOnly} is not used here - this restriction is made by
- * a separate clause in the {@code compare} (superposition) command.
- */
- @Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
- {
- StringBuilder sb = new StringBuilder(128);
-
- boolean first = true;
- for (int modelNo : model.getModels())
- {
- for (String chain : model.getChains(modelNo))
- {
- for (int[] range : model.getRanges(modelNo, chain))
- {
- if (!first)
- {
- sb.append(PIPE);
- }
- first = false;
- if (range[0] == range[1])
- {
- sb.append(range[0]);
- }
- else
- {
- sb.append(range[0]).append(HYPHEN).append(range[1]);
- }
- sb.append(COLON).append(chain.trim()).append(SLASH);
- sb.append(String.valueOf(modelNo)).append(".1");
- }
- }
- }
-
- return sb.toString();
+ return loadFile(filepath);
}
@Override
- public String showBackbone()
+ public StructureCommandI closeViewer()
{
- return "select *; cartoons off; backbone";
+ return null; // not an external viewer
}
}
git://source.jalview.org / jalview.git / blobdiff