import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
-import java.util.Map.Entry;
/**
* Routines for generating Jmol commands for Jalview/Jmol binding
private static final String CMD_COLOUR_BY_CHAIN = "select *;color chain";
- private static String formatRGB(Color c) {
+ private static final String PIPE = "|";
+
+ private static final String HYPHEN = "-";
+
+ private static final String COLON = ":";
+
+ private static final String SLASH = "/";
+
+ /**
+ * {@inheritDoc}
+ *
+ * @return
+ */
+ @Override
+ public int getModelStartNo()
+ {
+ return 1;
+ }
+
+ @Override
+ protected String getColourString(Color c)
+ {
return c == null ? null
: String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
c.getBlue());
}
+ /**
+ * Returns commands (one per colour key in the map) like
+ *
+ * <pre>
+ * select 2:A/1.1|3-27:B/1.1|9-12:A/2.1;color[173,0,82]
+ * </pre>
+ */
@Override
- public String[] colourBySequence(
- StructureSelectionManager ssm, String[] files,
+ public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
+ {
+ List<String> colourCommands = buildColourCommands(colourMap);
+
+ return colourCommands.toArray(new String[colourCommands.size()]);
+ }
+
+ public String[] colourBySequence(StructureSelectionManager ssm,
+ String[] files,
SequenceI[][] sequence, SequenceRenderer sr,
AlignmentViewPanel viewPanel)
{
String newSelcom = (mapping[m].getChain() != " "
? ":" + mapping[m].getChain()
- : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
- + col.getRed() + "," + col.getGreen() + ","
- + col.getBlue() + "]";
+ : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
+ + getColourString(col);
if (command.length() > newSelcom.length() && command
.substring(command.length() - newSelcom.length())
.equals(newSelcom))
{
StringBuilder cmd = new StringBuilder(128);
cmd.append("select *;color white;");
-
- /*
- * concatenate commands like
- * select VAL;color[100,215,55]
- */
- for (Entry<String, Color> entry : colours.entrySet())
- {
- Color col = entry.getValue();
- String resCode = entry.getKey();
- cmd.append("select ").append(resCode).append(";");
- cmd.append("color[");
- cmd.append(formatRGB(col));
- cmd.append("];");
- }
+ cmd.append(super.colourByResidues(colours));
return cmd.toString();
}
@Override
public String setBackgroundColour(Color col)
{
- return "background " + formatRGB(col);
+ return "background " + getColourString(col);
}
@Override
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)
+ {
+ 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();
+ }
+
+ @Override
+ public String showBackbone()
+ {
+ return "select *; cartoons off; backbone";
+ }
}
git://source.jalview.org / jalview.git / blobdiff