-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+/*
+ * 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
- *******************************************************************************/
-/**\r
- * \r
- */\r
-package jalview.ext.jmol;\r
-\r
-import jalview.api.FeatureRenderer;\r
-import jalview.api.SequenceRenderer;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.structure.StructureMapping;\r
-import jalview.structure.StructureMappingcommandSet;\r
-import jalview.structure.StructureSelectionManager;\r
-import jalview.util.Comparison;\r
-\r
-import java.awt.Color;\r
-import java.util.ArrayList;\r
-/**\r
- * Routines for generating Jmol commands for Jalview/Jmol binding\r
- * another cruisecontrol test.\r
- * \r
- * @author JimP\r
- *\r
- */\r
-public class JmolCommands\r
-{\r
-\r
- /**\r
- * Jmol utility which constructs the commands to colour chains by the given alignment\r
- * @returns Object[] { Object[] { <model being coloured>, \r
- * \r
- */\r
- public static StructureMappingcommandSet[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
- {\r
- \r
- ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();\r
- \r
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
- {\r
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
- StringBuffer command = new StringBuffer();\r
- StructureMappingcommandSet smc;\r
- ArrayList<String> str = new ArrayList<String>();\r
- \r
- if (mapping == null || mapping.length < 1)\r
- continue;\r
- \r
- int lastPos = -1;\r
- for (int s = 0; s < sequence[pdbfnum].length; s++)\r
- {\r
- for (int sp, m = 0; m < mapping.length; m++)\r
- {\r
- if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
- {\r
- SequenceI asp = alignment.getSequenceAt(sp);\r
- for (int r = 0; r < asp.getLength(); r++)\r
- {\r
- // no mapping to gaps in sequence\r
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
- {\r
- continue;\r
- }\r
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));\r
- \r
- if (pos < 1 || pos == lastPos)\r
- continue;\r
- \r
- lastPos = pos;\r
- \r
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);\r
- \r
- if (fr != null)\r
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);\r
- String newSelcom = (mapping[m].getChain() != " " ? ":"\r
- + mapping[m].getChain() : "")\r
- + "/"\r
- + (pdbfnum + 1)\r
- + ".1"\r
- + ";color["\r
- + col.getRed()\r
- + ","\r
- + col.getGreen()\r
- + ","\r
- + col.getBlue() + "]";\r
- if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))\r
- {\r
- command = JmolCommands.condenseCommand(command, pos);\r
- continue;\r
- }\r
- // TODO: deal with case when buffer is too large for Jmol to parse\r
- // - execute command and flush\r
- \r
- command.append(";");\r
- if (command.length()>51200)\r
- {\r
- // add another chunk\r
- str.add(command.toString());\r
- command.setLength(0);\r
- }\r
- command.append("select " + pos);\r
- command.append(newSelcom);\r
- }\r
- break;\r
- }\r
- }\r
- }\r
- {\r
- // add final chunk\r
- str.add(command.toString());\r
- command.setLength(0);\r
- }\r
- // Finally, add the command set ready to be returned.\r
- cset.add(new StructureMappingcommandSet(JmolCommands.class,files[pdbfnum], str.toArray(new String[str.size()])));\r
-\r
- }\r
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);\r
- }\r
-\r
- public static StringBuffer condenseCommand(StringBuffer command, int pos)\r
- {\r
- \r
- // work back to last 'select'\r
- int p=command.length(),q=p;\r
- do {\r
- p-=6;\r
- if (p<1) { p=0; };\r
- } while ((q=command.indexOf("select",p))==-1 && p>0);\r
- \r
- StringBuffer sb = new StringBuffer(command.substring(0,q+7));\r
- \r
- command = command.delete(0,q+7);\r
- \r
- String start;\r
- \r
- if (command.indexOf("-") > -1)\r
- {\r
- start = command.substring(0, command.indexOf("-"));\r
- }\r
- else\r
- {\r
- start = command.substring(0, command.indexOf(":"));\r
- }\r
- \r
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));\r
- \r
- return sb;\r
- }\r
-\r
-}\r
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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;
+import jalview.util.Platform;
+
+/**
+ * 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<StructureCommandI> colourByCharge()
+ {
+ return Arrays.asList(COLOUR_BY_CHARGE);
+ }
+
+ @Override
+ public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
+ {
+ List<StructureCommandI> 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<StructureCommandI> showChains(List<String> 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
+ *
+ * <pre>
+ * 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;
+ * </pre>
+ *
+ * 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.
+ * <p>
+ * 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<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
+ AtomSpecModel atomSpec, boolean isNucleotide)
+ {
+ 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 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
+ *
+ * <pre>
+ * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
+ * </pre>
+ *
+ * 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<StructureCommandI> 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 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<String> cset = new ArrayList<>();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ StringBuilder command = new StringBuilder(128);
+ List<String> 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;
+ }
+
+ @Override
+ public StructureCommandI openSession(String filepath)
+ {
+ return loadFile(filepath);
+ }
+
+ @Override
+ public StructureCommandI closeViewer()
+ {
+ return null; // not an external viewer
+ }
+}
git://source.jalview.org / jalview.git / blobdiff