2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.rbvi.chimera;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureRenderer;
25 import jalview.api.SequenceRenderer;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SequenceI;
31 import jalview.httpserver.AbstractRequestHandler;
32 import jalview.io.DataSourceType;
33 import jalview.schemes.ColourSchemeI;
34 import jalview.schemes.ResidueProperties;
35 import jalview.structure.AtomSpec;
36 import jalview.structure.StructureMappingcommandSet;
37 import jalview.structure.StructureSelectionManager;
38 import jalview.structures.models.AAStructureBindingModel;
39 import jalview.util.MessageManager;
41 import java.awt.Color;
42 import java.net.BindException;
43 import java.util.ArrayList;
44 import java.util.Hashtable;
45 import java.util.LinkedHashMap;
46 import java.util.List;
49 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
50 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
51 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
52 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
54 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
56 // Chimera clause to exclude alternate locations in atom selection
57 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
59 private static final String COLOURING_CHIMERA = MessageManager
60 .getString("status.colouring_chimera");
62 private static final boolean debug = false;
64 private static final String PHOSPHORUS = "P";
66 private static final String ALPHACARBON = "CA";
68 private List<String> chainNames = new ArrayList<String>();
70 private Hashtable<String, String> chainFile = new Hashtable<String, String>();
73 * Object through which we talk to Chimera
75 private ChimeraManager viewer;
78 * Object which listens to Chimera notifications
80 private AbstractRequestHandler chimeraListener;
83 * set if chimera state is being restored from some source - instructs binding
84 * not to apply default display style when structure set is updated for first
87 private boolean loadingFromArchive = false;
90 * flag to indicate if the Chimera viewer should ignore sequence colouring
91 * events from the structure manager because the GUI is still setting up
93 private boolean loadingFinished = true;
95 public String fileLoadingError;
98 * Map of ChimeraModel objects keyed by PDB full local file name
100 private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
103 * the default or current model displayed if the model cannot be identified
104 * from the selection message
106 private int frameNo = 0;
108 private String lastCommand;
110 String lastHighlightCommand;
113 * incremented every time a load notification is successfully handled -
114 * lightweight mechanism for other threads to detect when they can start
115 * referring to new structures.
117 private long loadNotifiesHandled = 0;
120 * Open a PDB structure file in Chimera and set up mappings from Jalview.
122 * We check if the PDB model id is already loaded in Chimera, if so don't
123 * reopen it. This is the case if Chimera has opened a saved session file.
128 public boolean openFile(PDBEntry pe)
130 String file = pe.getFile();
133 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
134 List<ChimeraModel> oldList = viewer.getModelList();
135 boolean alreadyOpen = false;
138 * If Chimera already has this model, don't reopen it, but do remap it.
140 for (ChimeraModel open : oldList)
142 if (open.getModelName().equals(pe.getId()))
145 modelsToMap.add(open);
150 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
151 * the model name(s) added by Chimera.
155 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
156 List<ChimeraModel> newList = viewer.getModelList();
157 // JAL-1728 newList.removeAll(oldList) does not work
158 for (ChimeraModel cm : newList)
160 if (cm.getModelName().equals(pe.getId()))
167 chimeraMaps.put(file, modelsToMap);
169 if (getSsm() != null)
171 getSsm().addStructureViewerListener(this);
172 // ssm.addSelectionListener(this);
173 FeatureRenderer fr = getFeatureRenderer(null);
181 } catch (Exception q)
183 log("Exception when trying to open model " + file + "\n"
198 public JalviewChimeraBinding(StructureSelectionManager ssm,
199 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
201 super(ssm, pdbentry, sequenceIs, protocol);
202 viewer = new ChimeraManager(
203 new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
207 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
208 * it to start listening
210 public void startChimeraListener()
214 chimeraListener = new ChimeraListener(this);
215 viewer.startListening(chimeraListener.getUri());
216 } catch (BindException e)
218 System.err.println("Failed to start Chimera listener: "
224 * Construct a title string for the viewer window based on the data Jalview
230 public String getViewerTitle(boolean verbose)
232 return getViewerTitle("Chimera", verbose);
236 * Tells Chimera to display only the specified chains
240 public void showChains(List<String> toshow)
243 * Construct a chimera command like
245 * ~display #*;~ribbon #*;ribbon :.A,:.B
247 StringBuilder cmd = new StringBuilder(64);
248 boolean first = true;
249 for (String chain : toshow)
251 int modelNumber = getModelNoForChain(chain);
252 String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
253 + chain.split(":")[1];
258 cmd.append(showChainCmd);
263 * could append ";focus" to this command to resize the display to fill the
264 * window, but it looks more helpful not to (easier to relate chains to the
267 final String command = "~display #*; ~ribbon #*; ribbon :"
269 sendChimeraCommand(command, false);
273 * Close down the Jalview viewer and listener, and (optionally) the associated
276 public void closeViewer(boolean closeChimera)
278 getSsm().removeStructureViewerListener(this, this.getPdbFile());
281 viewer.exitChimera();
283 if (this.chimeraListener != null)
285 chimeraListener.shutdown();
286 chimeraListener = null;
291 releaseUIResources();
294 public void colourByChain()
296 colourBySequence = false;
297 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
301 * Constructs and sends a Chimera command to colour by charge
303 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
304 * <li>Lysine and Arginine (positive charge) blue</li>
305 * <li>Cysteine - yellow</li>
306 * <li>all others - white</li>
309 public void colourByCharge()
311 colourBySequence = false;
312 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
313 sendAsynchronousCommand(command, COLOURING_CHIMERA);
317 * Construct and send a command to align structures against a reference
318 * structure, based on one or more sequence alignments
321 * an array of alignments to process
322 * @param _refStructure
323 * an array of corresponding reference structures (index into pdb
324 * file array); if a negative value is passed, the first PDB file
325 * mapped to an alignment sequence is used as the reference for
328 * an array of corresponding hidden columns for each alignment
330 public void superposeStructures(AlignmentI[] _alignment,
331 int[] _refStructure, ColumnSelection[] _hiddenCols)
333 StringBuilder allComs = new StringBuilder(128);
334 String[] files = getPdbFile();
336 if (!waitForFileLoad(files))
342 StringBuilder selectioncom = new StringBuilder(256);
343 for (int a = 0; a < _alignment.length; a++)
345 int refStructure = _refStructure[a];
346 AlignmentI alignment = _alignment[a];
347 ColumnSelection hiddenCols = _hiddenCols[a];
349 if (refStructure >= files.length)
351 System.err.println("Ignoring invalid reference structure value "
357 * 'matched' array will hold 'true' for visible alignment columns where
358 * all sequences have a residue with a mapping to the PDB structure
360 boolean matched[] = new boolean[alignment.getWidth()];
361 for (int m = 0; m < matched.length; m++)
363 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
366 SuperposeData[] structures = new SuperposeData[files.length];
367 for (int f = 0; f < files.length; f++)
369 structures[f] = new SuperposeData(alignment.getWidth());
373 * Calculate the superposable alignment columns ('matched'), and the
374 * corresponding structure residue positions (structures.pdbResNo)
376 int candidateRefStructure = findSuperposableResidues(alignment,
377 matched, structures);
378 if (refStructure < 0)
381 * If no reference structure was specified, pick the first one that has
382 * a mapping in the alignment
384 refStructure = candidateRefStructure;
388 for (boolean b : matched)
397 // TODO: bail out here because superposition illdefined?
401 * Generate select statements to select regions to superimpose structures
403 String[] selcom = new String[files.length];
404 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
406 String chainCd = "." + structures[pdbfnum].chain;
409 StringBuilder molsel = new StringBuilder();
410 for (int r = 0; r < matched.length; r++)
414 int pdbResNum = structures[pdbfnum].pdbResNo[r];
415 if (lpos != pdbResNum - 1)
418 * discontiguous - append last residue now
422 molsel.append(String.valueOf(lpos));
423 molsel.append(chainCd);
431 * extending a contiguous run
436 * start the range selection
438 molsel.append(String.valueOf(lpos));
448 * and terminate final selection
452 molsel.append(String.valueOf(lpos));
453 molsel.append(chainCd);
455 if (molsel.length() > 1)
457 selcom[pdbfnum] = molsel.toString();
458 selectioncom.append("#").append(String.valueOf(pdbfnum))
460 selectioncom.append(selcom[pdbfnum]);
461 selectioncom.append(" ");
462 if (pdbfnum < files.length - 1)
464 selectioncom.append("| ");
469 selcom[pdbfnum] = null;
473 StringBuilder command = new StringBuilder(256);
474 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
476 if (pdbfnum == refStructure || selcom[pdbfnum] == null
477 || selcom[refStructure] == null)
481 if (command.length() > 0)
487 * Form Chimera match command, from the 'new' structure to the
488 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
490 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
493 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
495 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
496 command.append(selcom[pdbfnum]);
497 command.append("@").append(
498 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
499 // JAL-1757 exclude alternate CA locations
500 command.append(NO_ALTLOCS);
501 command.append(" ").append(getModelSpec(refStructure)).append(":");
502 command.append(selcom[refStructure]);
503 command.append("@").append(
504 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
505 command.append(NO_ALTLOCS);
507 if (selectioncom.length() > 0)
511 System.out.println("Select regions:\n" + selectioncom.toString());
512 System.out.println("Superimpose command(s):\n"
513 + command.toString());
515 allComs.append("~display all; chain @CA|P; ribbon ")
516 .append(selectioncom.toString())
517 .append(";" + command.toString());
520 if (selectioncom.length() > 0)
522 // TODO: visually distinguish regions that were superposed
523 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
525 selectioncom.setLength(selectioncom.length() - 1);
529 System.out.println("Select regions:\n" + selectioncom.toString());
531 allComs.append("; ~display all; chain @CA|P; ribbon ")
532 .append(selectioncom.toString()).append("; focus");
533 sendChimeraCommand(allComs.toString(), false);
539 * Helper method to construct model spec in Chimera format:
541 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
542 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
544 * Note for now we only ever choose the first of multiple models. This
545 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
546 * future if there is a need to select specific sub-models.
551 protected String getModelSpec(int pdbfnum)
553 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
559 * For now, the test for having sub-models is whether multiple Chimera
560 * models are mapped for the PDB file; the models are returned as a response
561 * to the Chimera command 'list models type molecule', see
562 * ChimeraManager.getModelList().
564 List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
565 boolean hasSubModels = maps != null && maps.size() > 1;
566 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
570 * Launch Chimera, unless an instance linked to this object is already
571 * running. Returns true if chimera is successfully launched, or already
572 * running, else false.
576 public boolean launchChimera()
578 if (!viewer.isChimeraLaunched())
580 return viewer.launchChimera(StructureManager.getChimeraPaths());
582 if (viewer.isChimeraLaunched())
586 log("Failed to launch Chimera!");
591 * Answers true if the Chimera process is still running, false if ended or not
596 public boolean isChimeraRunning()
598 return viewer.isChimeraLaunched();
602 * Send a command to Chimera, and optionally log any responses.
607 public void sendChimeraCommand(final String command, boolean logResponse)
611 // ? thread running after viewer shut down
614 viewerCommandHistory(false);
615 if (lastCommand == null || !lastCommand.equals(command))
617 // trim command or it may never find a match in the replyLog!!
618 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
620 if (logResponse && debug)
622 log("Response from command ('" + command + "') was:\n" + lastReply);
625 viewerCommandHistory(true);
626 lastCommand = command;
630 * Send a Chimera command asynchronously in a new thread. If the progress
631 * message is not null, display this message while the command is executing.
636 protected abstract void sendAsynchronousCommand(String command,
640 * colour any structures associated with sequences in the given alignment
641 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
642 * if colourBySequence is enabled.
644 public void colourBySequence(boolean showFeatures,
645 jalview.api.AlignmentViewPanel alignmentv)
647 if (!colourBySequence || !loadingFinished)
651 if (getSsm() == null)
655 String[] files = getPdbFile();
657 SequenceRenderer sr = getSequenceRenderer(alignmentv);
659 FeatureRenderer fr = null;
662 fr = getFeatureRenderer(alignmentv);
664 AlignmentI alignment = alignmentv.getAlignment();
666 for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
667 files, sr, fr, alignment))
669 for (String command : cpdbbyseq.commands)
671 sendAsynchronousCommand(command, COLOURING_CHIMERA);
683 protected StructureMappingcommandSet[] getColourBySequenceCommands(
684 String[] files, SequenceRenderer sr, FeatureRenderer fr,
685 AlignmentI alignment)
687 return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
688 getSequence(), sr, fr, alignment);
694 protected void executeWhenReady(String command)
697 sendChimeraCommand(command, false);
701 private void waitForChimera()
703 while (viewer != null && viewer.isBusy())
708 } catch (InterruptedException q)
714 // End StructureListener
715 // //////////////////////////
718 * returns the current featureRenderer that should be used to colour the
725 public abstract FeatureRenderer getFeatureRenderer(
726 AlignmentViewPanel alignment);
729 * instruct the Jalview binding to update the pdbentries vector if necessary
730 * prior to matching the viewer's contents to the list of structure files
731 * Jalview knows about.
733 public abstract void refreshPdbEntries();
735 private int getModelNum(String modelFileName)
737 String[] mfn = getPdbFile();
742 for (int i = 0; i < mfn.length; i++)
744 if (mfn[i].equalsIgnoreCase(modelFileName))
753 * map between index of model filename returned from getPdbFile and the first
754 * index of models from this file in the viewer. Note - this is not trimmed -
755 * use getPdbFile to get number of unique models.
757 private int _modelFileNameMap[];
759 // ////////////////////////////////
760 // /StructureListener
762 public synchronized String[] getPdbFile()
766 return new String[0];
769 return chimeraMaps.keySet().toArray(
770 modelFileNames = new String[chimeraMaps.size()]);
774 * returns the current sequenceRenderer that should be used to colour the
781 public abstract SequenceRenderer getSequenceRenderer(
782 AlignmentViewPanel alignment);
785 * Construct and send a command to highlight zero, one or more atoms. We do
786 * this by sending an "rlabel" command to show the residue label at that
790 public void highlightAtoms(List<AtomSpec> atoms)
792 if (atoms == null || atoms.size() == 0)
797 StringBuilder cmd = new StringBuilder(128);
798 boolean first = true;
799 boolean found = false;
801 for (AtomSpec atom : atoms)
803 int pdbResNum = atom.getPdbResNum();
804 String chain = atom.getChain();
805 String pdbfile = atom.getPdbFile();
806 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
807 if (cms != null && !cms.isEmpty())
811 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
819 cmd.append(pdbResNum);
820 if (!chain.equals(" "))
822 cmd.append(".").append(chain);
827 String command = cmd.toString();
830 * avoid repeated commands for the same residue
832 if (command.equals(lastHighlightCommand))
838 * unshow the label for the previous residue
840 if (lastHighlightCommand != null)
842 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
846 viewer.sendChimeraCommand(command, false);
848 this.lastHighlightCommand = command;
852 * Query Chimera for its current selection, and highlight it on the alignment
854 public void highlightChimeraSelection()
857 * Ask Chimera for its current selection
859 List<String> selection = viewer.getSelectedResidueSpecs();
862 * Parse model number, residue and chain for each selected position,
863 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
865 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
866 for (String atomSpec : selection)
868 int colonPos = atomSpec.indexOf(":");
871 continue; // malformed
874 int hashPos = atomSpec.indexOf("#");
875 String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
876 int dotPos = modelSubmodel.indexOf(".");
880 modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
881 : modelSubmodel.substring(0, dotPos));
882 } catch (NumberFormatException e)
884 // ignore, default to model 0
887 String residueChain = atomSpec.substring(colonPos + 1);
888 dotPos = residueChain.indexOf(".");
889 int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
890 : residueChain.substring(0, dotPos));
892 String chainId = dotPos == -1 ? "" : residueChain
893 .substring(dotPos + 1);
896 * Work out the pdbfilename from the model number
898 String pdbfilename = modelFileNames[frameNo];
899 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
901 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
903 if (cm.getModelNumber() == modelId)
905 pdbfilename = pdbfile;
910 atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
914 * Broadcast the selection (which may be empty, if the user just cleared all
917 getSsm().mouseOverStructure(atomSpecs);
920 private void log(String message)
922 System.err.println("## Chimera log: " + message);
925 private void viewerCommandHistory(boolean enable)
927 // log("(Not yet implemented) History "
928 // + ((debug || enable) ? "on" : "off"));
931 public long getLoadNotifiesHandled()
933 return loadNotifiesHandled;
936 public void setJalviewColourScheme(ColourSchemeI cs)
938 colourBySequence = false;
945 // Chimera expects RBG values in the range 0-1
946 final double normalise = 255D;
947 viewerCommandHistory(false);
948 StringBuilder command = new StringBuilder(128);
950 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
952 for (String res : residueSet)
954 Color col = cs.findColour(res.charAt(0));
955 command.append("color " + col.getRed() / normalise + ","
956 + col.getGreen() / normalise + "," + col.getBlue()
957 / normalise + " ::" + res + ";");
960 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
961 viewerCommandHistory(true);
965 * called when the binding thinks the UI needs to be refreshed after a Chimera
966 * state change. this could be because structures were loaded, or because an
967 * error has occurred.
969 public abstract void refreshGUI();
972 public void setLoadingFromArchive(boolean loadingFromArchive)
974 this.loadingFromArchive = loadingFromArchive;
979 * @return true if Chimeral is still restoring state or loading is still going
980 * on (see setFinsihedLoadingFromArchive)
983 public boolean isLoadingFromArchive()
985 return loadingFromArchive && !loadingFinished;
989 * modify flag which controls if sequence colouring events are honoured by the
990 * binding. Should be true for normal operation
992 * @param finishedLoading
995 public void setFinishedLoadingFromArchive(boolean finishedLoading)
997 loadingFinished = finishedLoading;
1001 * Send the Chimera 'background solid <color>" command.
1004 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
1008 public void setBackgroundColour(Color col)
1010 viewerCommandHistory(false);
1011 double normalise = 255D;
1012 final String command = "background solid " + col.getRed() / normalise
1013 + "," + col.getGreen() / normalise + "," + col.getBlue()
1015 viewer.sendChimeraCommand(command, false);
1016 viewerCommandHistory(true);
1020 * Ask Chimera to save its session to the given file. Returns true if
1021 * successful, else false.
1026 public boolean saveSession(String filepath)
1028 if (isChimeraRunning())
1030 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1032 if (reply.contains("Session written"))
1039 .error("Error saving Chimera session: " + reply.toString());
1046 * Ask Chimera to open a session file. Returns true if successful, else false.
1047 * The filename must have a .py extension for this command to work.
1052 public boolean openSession(String filepath)
1054 sendChimeraCommand("open " + filepath, true);
1055 // todo: test for failure - how?
1060 * Returns a list of chains mapped in this viewer. Note this list is not
1061 * currently scoped per structure.
1067 * Send a 'focus' command to Chimera to recentre the visible display
1069 public void focusView()
1071 sendChimeraCommand("focus", false);
1075 * Send a 'show' command for all atoms in the currently selected columns
1077 * TODO: pull up to abstract structure viewer interface
1081 public void highlightSelection(AlignmentViewPanel vp)
1083 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1085 AlignmentI alignment = vp.getAlignment();
1086 StructureSelectionManager sm = getSsm();
1087 for (SequenceI seq : alignment.getSequences())
1090 * convert selected columns into sequence positions
1092 int[] positions = new int[cols.size()];
1094 for (Integer col : cols)
1096 positions[i++] = seq.findPosition(col);
1098 sm.highlightStructure(this, seq, positions);
1104 public List<String> getChainNames()
1109 public Hashtable<String, String> getChainFile()
1114 public List<ChimeraModel> getChimeraModelByChain(String chain)
1116 return chimeraMaps.get(chainFile.get(chain));
1119 public int getModelNoForChain(String chain)
1121 List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
1122 if (foundModels != null && !foundModels.isEmpty())
1124 return foundModels.get(0).getModelNumber();