commands = new ArrayList<>();
+ for (Object key : colourMap.keySet())
+ {
+ Color colour = (Color) key;
+ final AtomSpecModel colourData = colourMap.get(colour);
+ commands.add(getColourCommand(colourData, colour));
+ }
+
+ return commands;
+ }
+
+ /**
+ * Returns a viewer command to set the given atom property value on atoms
+ * specified by the AtomSpecModel, for example
+ *
+ *
+ * iterate 4zho//B/12-34,48-55/CA,jv_chain='primary'
+ *
+ *
+ * @param attributeName
+ * @param attributeValue
+ * @param atomSpecModel
+ * @return
+ */
+ protected StructureCommandI setAttribute(String attributeName,
+ String attributeValue, AtomSpecModel atomSpecModel)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("p.").append(attributeName).append("='")
+ .append(attributeValue).append("'");
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
+ return new StructureCommand("iterate", atomSpec, sb.toString());
+ }
+
+ /**
+ * Traverse the map of features/values/models/chains/positions to construct a
+ * list of 'set property' commands (one per distinct feature type and value).
+ * The values are stored in the 'p' dictionary of user-defined properties of
+ * each atom.
+ *
+ * The format of each command is
+ *
+ *
+ * iterate atomspec, p.featureName='value'
+ * e.g. iterate 4zho//A/23,28-29/CA, p.jv_Metal='Fe'
+ *
+ *
+ *
+ * @param featureMap
+ * @return
+ */
+ @Override
+ public List setAttributes(
+ Map> featureMap)
+ {
+ List commands = new ArrayList<>();
+ for (String featureType : featureMap.keySet())
+ {
+ String attributeName = makeAttributeName(featureType);
+
+ /*
+ * todo: clear down existing attributes for this feature?
+ */
+ // commands.add(new StructureCommand("iterate", "all",
+ // "p."+attributeName+"='None'"); //?
+
+ Map values = featureMap.get(featureType);
+ for (Object value : values.keySet())
+ {
+ /*
+ * for each distinct value recorded for this feature type,
+ * add a command to set the attribute on the mapped residues
+ * Put values in single quotes, encoding any embedded single quotes
+ */
+ AtomSpecModel atomSpecModel = values.get(value);
+ String featureValue = value.toString();
+ featureValue = featureValue.replaceAll("\\'", "'");
+ StructureCommandI cmd = setAttribute(attributeName, featureValue,
+ atomSpecModel);
+ commands.add(cmd);
+ }
+ }
+
+ return commands;
+ }
+
+ @Override
+ public StructureCommandI openSession(String filepath)
+ {
+ // https://pymolwiki.org/index.php/Load
+ // this version of the command has no dependency on file extension
+ return new StructureCommand("load", filepath, "", "0", "pse");
+ }
+
+ @Override
+ public StructureCommandI closeViewer()
+ {
+ // https://pymolwiki.org/index.php/Quit
+ return CLOSE_PYMOL;
+ }
+
}