X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=58b69efbb07f9201dec6f1a685f62afd1ee1fa5b;hb=b9b1f47cc74bbec8c28b75776e1d00c258215dfb;hp=c8a54cdca1c6df99fc5353403db7a12326f11249;hpb=2ab7b9b152018bb808693218ad88dc3778166492;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java index c8a54cd..58b69ef 100644 --- a/src/jalview/ext/jmol/JmolCommands.java +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -20,6 +20,12 @@ */ 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; @@ -28,16 +34,15 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; 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 java.util.Map.Entry; +import jalview.util.Platform; /** * Routines for generating Jmol commands for Jalview/Jmol binding @@ -47,24 +52,274 @@ import java.util.Map.Entry; */ 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 = "|"; + + private static final String HYPHEN = "-"; + + private static final String COLON = ":"; + + private static final String SLASH = "/"; + + /** + * {@inheritDoc} + * + * @return + */ + @Override + public int getModelStartNo() + { + return 1; + } - private static String formatRGB(Color c) { + /** + * 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 : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(), c.getBlue()); } @Override - public String[] colourBySequence( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, + public StructureCommandI colourByChain() + { + return COLOUR_BY_CHAIN; + } + + @Override + public List colourByCharge() + { + return Arrays.asList(COLOUR_BY_CHARGE); + } + + @Override + public List colourByResidues( + Map colours) + { + List 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 showChains(List 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 a command to superpose atoms in {@code atomSpec} to those in + * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna). + * For example + * + * 
+   * 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;
+   *
+ * + * 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. + *

+ * 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 List 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 + * + * 

+   * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
+   *
+ * + * 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 showBackbone() + { + return Arrays.asList(SHOW_BACKBONE); + } + + @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, AlignmentViewPanel viewPanel) { - // TODO refactor to call buildColoursMap() first... + // TODO delete method FeatureRenderer fr = viewPanel.getFeatureRenderer(); FeatureColourFinder finder = new FeatureColourFinder(fr); @@ -134,9 +389,8 @@ public class JmolCommands extends StructureCommandsBase 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)) @@ -177,7 +431,15 @@ public class JmolCommands extends StructureCommandsBase 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) { @@ -214,75 +476,14 @@ public class JmolCommands extends StructureCommandsBase } @Override - public String colourByChain() + public StructureCommandI openSession(String filepath) { - return CMD_COLOUR_BY_CHAIN; + return loadFile(filepath); } @Override - public String colourByCharge() + public StructureCommandI closeViewer() { - return CMD_COLOUR_BY_CHARGE; + return null; // not an external viewer } - - @Override - public String colourByResidues(Map colours) - { - StringBuilder cmd = new StringBuilder(128); - cmd.append("select *;color white;"); - - /* - * concatenate commands like - * select VAL;color[100,215,55] - */ - for (Entry 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("];"); - } - - return cmd.toString(); - } - - @Override - public String setBackgroundColour(Color col) - { - return "background " + formatRGB(col); - } - - @Override - public String focusView() - { - return "zoom 0"; - } - - @Override - public String showChains(List 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; - } - }