X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=3e0afd705a2c14e56d8054cbdcd6e3912c4e69ac;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=acf27f62dcfbc346d31baa68d3c73c0a0aadedb6;hpb=b4f141d24f090c73e5608214cef2e1dd2c3e21ad;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java index acf27f6..3e0afd7 100644 --- a/src/jalview/ext/jmol/JmolCommands.java +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -1,135 +1,469 @@ -/** - * - */ -package jalview.ext.jmol; - -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceI; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; -import jalview.util.Comparison; - -import java.awt.Color; -import java.util.ArrayList; - -/** - * Routines for generating Jmol commands for Jalview/Jmol binding - * @author JimP - * - */ -public class JmolCommands -{ - - /** - * Jmol utility which constructs the commands to colour chains by the given alignment - * - */ - public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) - { - ArrayList str = new ArrayList(); - StringBuffer command = new StringBuffer(); - - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - continue; - - int lastPos = -1; - for (int s = 0; s < sequence[pdbfnum].length; s++) - { - for (int sp, m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) - { - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < asp.getLength(); r++) - { - // no mapping to gaps in sequence - if (jalview.util.Comparison.isGap(asp.getCharAt(r))) - { - continue; - } - int pos = mapping[m].getPDBResNum(asp.findPosition(r)); - - if (pos < 1 || pos == lastPos) - continue; - - lastPos = pos; - - Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); - - if (fr != null) - col = fr.findFeatureColour(col, sequence[pdbfnum][s], r); - String newSelcom = (mapping[m].getChain() != " " ? ":" - + mapping[m].getChain() : "") - + "/" - + (pdbfnum + 1) - + ".1" - + ";color[" - + col.getRed() - + "," - + col.getGreen() - + "," - + col.getBlue() + "]"; - if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom)) - { - command = JmolCommands.condenseCommand(command, pos); - continue; - } - // TODO: deal with case when buffer is too large for Jmol to parse - // - execute command and flush - - command.append(";"); - if (command.length()>51200) - { - // add another chunk - str.add(command.toString()); - command.setLength(0); - } - command.append("select " + pos); - command.append(newSelcom); - } - break; - } - } - } - } - return str.toArray(new String[str.size()]); - } - - public static StringBuffer condenseCommand(StringBuffer command, int pos) - { - - // work back to last 'select' - int p=command.length(),q=p; - do { - p-=6; - if (p<1) { p=0; }; - } while ((q=command.indexOf("select",p))==-1 && p>0); - - StringBuffer sb = new StringBuffer(command.substring(0,q+7)); - - command = command.delete(0,q+7); - - String start; - - if (command.indexOf("-") > -1) - { - start = command.substring(0, command.indexOf("-")); - } - else - { - start = command.substring(0, command.indexOf(":")); - } - - sb.append(start + "-" + pos + command.substring(command.indexOf(":"))); - - return sb; - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +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; +import jalview.api.SequenceRenderer; +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.util.Comparison; + +/** + * Routines for generating Jmol commands for Jalview/Jmol binding + * + * @author JimP + * + */ +public class JmolCommands extends StructureCommandsBase +{ + 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 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; + } + + /** + * 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 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) + { + 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, 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 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 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 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, boolean alphaOnly) + { + 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) + { + return null; + } + + /** + * 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 delete method + + FeatureRenderer fr = viewPanel.getFeatureRenderer(); + FeatureColourFinder finder = new FeatureColourFinder(fr); + AlignViewportI viewport = viewPanel.getAlignViewport(); + HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); + AlignmentI al = viewport.getAlignment(); + List cset = new ArrayList<>(); + + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + StringBuilder command = new StringBuilder(128); + List str = new ArrayList<>(); + + if (mapping == null || mapping.length < 1) + { + continue; + } + + for (int s = 0; s < sequence[pdbfnum].length; s++) + { + for (int sp, m = 0; m < mapping.length; m++) + { + if (mapping[m].getSequence() == sequence[pdbfnum][s] + && (sp = al.findIndex(sequence[pdbfnum][s])) > -1) + { + int lastPos = StructureMapping.UNASSIGNED_VALUE; + SequenceI asp = al.getSequenceAt(sp); + for (int r = 0; r < asp.getLength(); r++) + { + // no mapping to gaps in sequence + if (Comparison.isGap(asp.getCharAt(r))) + { + continue; + } + int pos = mapping[m].getPDBResNum(asp.findPosition(r)); + + if (pos == lastPos) + { + continue; + } + if (pos == StructureMapping.UNASSIGNED_VALUE) + { + // terminate current colour op + if (command.length() > 0 + && command.charAt(command.length() - 1) != ';') + { + command.append(";"); + } + // reset lastPos + lastPos = StructureMapping.UNASSIGNED_VALUE; + continue; + } + + lastPos = pos; + + Color col = sr.getResidueColour(sequence[pdbfnum][s], r, + finder); + + /* + * shade hidden regions darker + */ + if (!cs.isVisible(r)) + { + col = Color.GRAY; + } + + String newSelcom = (mapping[m].getChain() != " " + ? ":" + mapping[m].getChain() + : "") + "/" + (pdbfnum + 1) + ".1" + ";color" + + getColourString(col); + if (command.length() > newSelcom.length() && command + .substring(command.length() - newSelcom.length()) + .equals(newSelcom)) + { + command = JmolCommands.condenseCommand(command, pos); + continue; + } + // TODO: deal with case when buffer is too large for Jmol to parse + // - execute command and flush + + if (command.length() > 0 + && command.charAt(command.length() - 1) != ';') + { + command.append(";"); + } + + if (command.length() > 51200) + { + // add another chunk + str.add(command.toString()); + command.setLength(0); + } + command.append("select " + pos); + command.append(newSelcom); + } + // break; + } + } + } + { + // add final chunk + str.add(command.toString()); + command.setLength(0); + } + cset.addAll(str); + + } + return cset.toArray(new String[cset.size()]); + } + + /** + * Helper method + * + * @param command + * @param pos + * @return + */ + @Deprecated + private static StringBuilder condenseCommand( + StringBuilder command, + int pos) + { + + // work back to last 'select' + int p = command.length(), q = p; + do + { + p -= 6; + if (p < 1) + { + p = 0; + } + ; + } while ((q = command.indexOf("select", p)) == -1 && p > 0); + + StringBuilder sb = new StringBuilder(command.substring(0, q + 7)); + + command = command.delete(0, q + 7); + + String start; + + if (command.indexOf("-") > -1) + { + start = command.substring(0, command.indexOf("-")); + } + else + { + start = command.substring(0, command.indexOf(":")); + } + + sb.append(start + "-" + pos + command.substring(command.indexOf(":"))); + + return sb; + } +}