1 package jalview.ext.pymol;
4 import java.util.ArrayList;
5 import java.util.Arrays;
9 import jalview.structure.AtomSpecModel;
10 import jalview.structure.StructureCommand;
11 import jalview.structure.StructureCommandI;
12 import jalview.structure.StructureCommandsBase;
15 * A class that generates commands to send to PyMol over its XML-RPC interface.
17 * Note that because the xml-rpc interface can only accept one command at a
18 * time, we can't concatenate commands, and must instead form and send them
21 * @see https://pymolwiki.org/index.php/Category:Commands
22 * @see https://pymolwiki.org/index.php/RPC
24 public class PymolCommands extends StructureCommandsBase
26 // https://pymol.org/dokuwiki/doku.php?id=command:zoom
27 // not currently documented on
28 // https://pymolwiki.org/index.php/Category:Commands
29 private static final StructureCommand FOCUS_VIEW = new StructureCommand(
32 // https://pymolwiki.org/index.php/Quit
33 private static final StructureCommand CLOSE_PYMOL = new StructureCommand(
36 // not currently documented on
37 // https://pymolwiki.org/index.php/Category:Commands
38 private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand(
41 private static final List<StructureCommandI> COLOR_BY_CHARGE = Arrays
42 .asList(new StructureCommand("color", "white", "*"),
43 new StructureCommand("color", "red", "resn ASP resn GLU"),
44 new StructureCommand("color", "blue",
46 new StructureCommand("color", "yellow", "resn CYS"));
48 private static final List<StructureCommandI> SHOW_BACKBONE = Arrays
49 .asList(new StructureCommand("hide", "everything"),
50 new StructureCommand("show", "ribbon"));
53 public StructureCommandI colourByChain()
55 return COLOUR_BY_CHAIN;
59 public List<StructureCommandI> colourByCharge()
61 return COLOR_BY_CHARGE;
65 public StructureCommandI setBackgroundColour(Color col)
67 // https://pymolwiki.org/index.php/Bg_Color
68 return new StructureCommand("bg_color", getColourString(col));
72 * Returns a colour formatted suitable for use in viewer command syntax. For
73 * example, red is {@code "0xff0000"}.
78 protected String getColourString(Color c)
80 return String.format("0x%02x%02x%02x", c.getRed(), c.getGreen(),
85 public StructureCommandI focusView()
91 public List<StructureCommandI> showChains(List<String> toShow)
93 // https://pymolwiki.org/index.php/Show
94 List<StructureCommandI> commands = new ArrayList<>();
95 commands.add(new StructureCommand("hide", "everything"));
96 commands.add(new StructureCommand("show", "lines"));
97 StringBuilder chains = new StringBuilder();
98 for (String chain : toShow)
100 chains.append(" chain ").append(chain);
103 new StructureCommand("show", "cartoon", chains.toString()));
108 public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
109 AtomSpecModel atomSpec)
111 // https://pymolwiki.org/index.php/Super
112 List<StructureCommandI> commands = new ArrayList<>();
113 String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
114 String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
115 commands.add(new StructureCommand("super", refAtomsAlphaOnly,
116 atomSpec2AlphaOnly));
119 * and show superposed residues as cartoon
121 String refAtomsAll = getAtomSpec(refAtoms, false);
122 String atomSpec2All = getAtomSpec(atomSpec, false);
123 commands.add(new StructureCommand("show", "cartoon",
124 refAtomsAll + " " + atomSpec2All));
130 public StructureCommandI openCommandFile(String path)
132 // https://pymolwiki.org/index.php/Run
133 return new StructureCommand("run", path); // should be .pml
137 public StructureCommandI saveSession(String filepath)
139 // https://pymolwiki.org/index.php/Save#EXAMPLES
140 return new StructureCommand("save", filepath); // should be .pse
144 * Returns a selection string in PyMOL 'selection macro' format:
147 * modelId// chain/residues/
150 * If more than one chain, makes a selection expression for each, and they are
151 * separated by spaces.
153 * @see https://pymolwiki.org/index.php/Selection_Macros
156 public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
158 StringBuilder sb = new StringBuilder(64);
159 boolean first = true;
160 for (String modelId : model.getModels())
162 for (String chain : model.getChains(modelId))
169 List<int[]> rangeList = model.getRanges(modelId, chain);
170 chain = chain.trim();
171 sb.append(modelId).append("//").append(chain).append("/");
172 boolean firstRange = true;
173 for (int[] range : rangeList)
180 sb.append(String.valueOf(range[0]));
181 if (range[0] != range[1])
183 sb.append("-").append(String.valueOf(range[1]));
193 return sb.toString();
197 public List<StructureCommandI> showBackbone()
199 return SHOW_BACKBONE;
203 protected StructureCommandI colourResidues(String atomSpec, Color colour)
205 // https://pymolwiki.org/index.php/Color
206 return new StructureCommand("color", getColourString(colour), atomSpec);
210 protected String getResidueSpec(String residue)
212 // https://pymolwiki.org/index.php/Selection_Algebra
213 return "resn " + residue;
217 public StructureCommandI loadFile(String file)
219 return new StructureCommand("load", file);
223 * Overrides the default implementation (which generates concatenated
224 * commands) to generate one per colour (because the XML-RPC interface to
225 * PyMOL only accepts one command at a time)
231 public List<StructureCommandI> colourBySequence(
232 Map<Object, AtomSpecModel> colourMap)
234 List<StructureCommandI> commands = new ArrayList<>();
235 for (Object key : colourMap.keySet())
237 Color colour = (Color) key;
238 final AtomSpecModel colourData = colourMap.get(colour);
239 commands.add(getColourCommand(colourData, colour));
246 * Returns a viewer command to set the given atom property value on atoms
247 * specified by the AtomSpecModel, for example
250 * iterate 4zho//B/12-34,48-55/CA,jv_chain='primary'
253 * @param attributeName
254 * @param attributeValue
255 * @param atomSpecModel
258 protected StructureCommandI setAttribute(String attributeName,
259 String attributeValue, AtomSpecModel atomSpecModel)
261 StringBuilder sb = new StringBuilder(128);
262 sb.append("p.").append(attributeName).append("='")
263 .append(attributeValue).append("'");
264 String atomSpec = getAtomSpec(atomSpecModel, false);
265 return new StructureCommand("iterate", atomSpec, sb.toString());
269 * Traverse the map of features/values/models/chains/positions to construct a
270 * list of 'set property' commands (one per distinct feature type and value).
271 * The values are stored in the 'p' dictionary of user-defined properties of
274 * The format of each command is
277 * <blockquote> iterate atomspec, p.featureName='value'
278 * e.g. iterate 4zho//A/23,28-29/CA, p.jv_Metal='Fe'
286 public List<StructureCommandI> setAttributes(
287 Map<String, Map<Object, AtomSpecModel>> featureMap)
289 List<StructureCommandI> commands = new ArrayList<>();
290 for (String featureType : featureMap.keySet())
292 String attributeName = makeAttributeName(featureType);
295 * todo: clear down existing attributes for this feature?
297 // commands.add(new StructureCommand("iterate", "all",
298 // "p."+attributeName+"='None'"); //?
300 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
301 for (Object value : values.keySet())
304 * for each distinct value recorded for this feature type,
305 * add a command to set the attribute on the mapped residues
306 * Put values in single quotes, encoding any embedded single quotes
308 AtomSpecModel atomSpecModel = values.get(value);
309 String featureValue = value.toString();
310 featureValue = featureValue.replaceAll("\\'", "'");
311 StructureCommandI cmd = setAttribute(attributeName, featureValue,
321 public StructureCommandI openSession(String filepath)
323 // https://pymolwiki.org/index.php/Load
324 // this version of the command has no dependency on file extension
325 return new StructureCommand("load", filepath, "", "0", "pse");
329 public StructureCommandI closeViewer()
331 // https://pymolwiki.org/index.php/Quit