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, AtomSpecType specType)
112 // https://pymolwiki.org/index.php/Super
113 List<StructureCommandI> commands = new ArrayList<>();
114 String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
115 String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" and (altloc '' or altloc 'a'))";
116 // pair_fit mobile -> reference
117 commands.add(new StructureCommand("pair_fit",
118 atomSpec2AlphaOnly, refAtomsAlphaOnly));
121 * and show superposed residues as cartoon
123 String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
124 String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
125 commands.add(new StructureCommand("show", "cartoon",
126 refAtomsAll + " " + atomSpec2All));
132 public StructureCommandI openCommandFile(String path)
134 // https://pymolwiki.org/index.php/Run
135 return new StructureCommand("run", path); // should be .pml
139 public StructureCommandI saveSession(String filepath)
141 // https://pymolwiki.org/index.php/Save#EXAMPLES
142 return new StructureCommand("save", filepath); // should be .pse
146 * Returns a selection string in PyMOL 'selection macro' format:
149 * modelId// chain/residues/
152 * If more than one chain, makes a selection expression for each, and they are
153 * separated by spaces.
155 * @see https://pymolwiki.org/index.php/Selection_Macros
158 public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
160 StringBuilder sb = new StringBuilder(64);
161 boolean first = true;
162 for (String modelId : model.getModels())
164 for (String chain : model.getChains(modelId))
171 List<int[]> rangeList = model.getRanges(modelId, chain);
172 chain = chain.trim();
173 sb.append(modelId).append("//").append(chain).append("/");
174 boolean firstRange = true;
175 for (int[] range : rangeList)
182 sb.append(String.valueOf(range[0]));
183 if (range[0] != range[1])
185 sb.append("-").append(String.valueOf(range[1]));
189 if (specType == AtomSpecType.ALPHA)
193 if (specType == AtomSpecType.PHOSPHATE)
199 return sb.toString();
203 public List<StructureCommandI> showBackbone()
205 return SHOW_BACKBONE;
209 protected StructureCommandI colourResidues(String atomSpec, Color colour)
211 // https://pymolwiki.org/index.php/Color
212 return new StructureCommand("color", getColourString(colour), atomSpec);
216 protected String getResidueSpec(String residue)
218 // https://pymolwiki.org/index.php/Selection_Algebra
219 return "resn " + residue;
223 public StructureCommandI loadFile(String file)
225 return new StructureCommand("load", file);
229 * Overrides the default implementation (which generates concatenated
230 * commands) to generate one per colour (because the XML-RPC interface to
231 * PyMOL only accepts one command at a time)
237 public List<StructureCommandI> colourBySequence(
238 Map<Object, AtomSpecModel> colourMap)
240 List<StructureCommandI> commands = new ArrayList<>();
241 for (Object key : colourMap.keySet())
243 Color colour = (Color) key;
244 final AtomSpecModel colourData = colourMap.get(colour);
245 commands.add(getColourCommand(colourData, colour));
252 * Returns a viewer command to set the given atom property value on atoms
253 * specified by the AtomSpecModel, for example
256 * iterate 4zho//B/12-34,48-55/CA,jv_chain='primary'
259 * @param attributeName
260 * @param attributeValue
261 * @param atomSpecModel
264 protected StructureCommandI setAttribute(String attributeName,
265 String attributeValue, AtomSpecModel atomSpecModel)
267 StringBuilder sb = new StringBuilder(128);
268 sb.append("p.").append(attributeName).append("='")
269 .append(attributeValue).append("'");
270 String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
271 return new StructureCommand("iterate", atomSpec, sb.toString());
275 * Traverse the map of features/values/models/chains/positions to construct a
276 * list of 'set property' commands (one per distinct feature type and value).
277 * The values are stored in the 'p' dictionary of user-defined properties of
280 * The format of each command is
283 * <blockquote> iterate atomspec, p.featureName='value'
284 * e.g. iterate 4zho//A/23,28-29/CA, p.jv_Metal='Fe'
292 public List<StructureCommandI> setAttributes(
293 Map<String, Map<Object, AtomSpecModel>> featureMap)
295 List<StructureCommandI> commands = new ArrayList<>();
296 for (String featureType : featureMap.keySet())
298 String attributeName = makeAttributeName(featureType);
301 * todo: clear down existing attributes for this feature?
303 // commands.add(new StructureCommand("iterate", "all",
304 // "p."+attributeName+"='None'"); //?
306 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
307 for (Object value : values.keySet())
310 * for each distinct value recorded for this feature type,
311 * add a command to set the attribute on the mapped residues
312 * Put values in single quotes, encoding any embedded single quotes
314 AtomSpecModel atomSpecModel = values.get(value);
315 String featureValue = value.toString();
316 featureValue = featureValue.replaceAll("\\'", "'");
317 StructureCommandI cmd = setAttribute(attributeName, featureValue,
327 public StructureCommandI openSession(String filepath)
329 // https://pymolwiki.org/index.php/Load
330 // this version of the command has no dependency on file extension
331 return new StructureCommand("load", filepath, "", "0", "pse");
335 public StructureCommandI closeViewer()
337 // https://pymolwiki.org/index.php/Quit