+++ /dev/null
-/*
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ext.jmol;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
-import jalview.util.Format;
-import jalview.util.MessageManager;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import javajs.awt.Dimension;
-
-import org.jmol.api.JmolStatusListener;
-import org.jmol.api.JmolViewer;
-import org.jmol.c.CBK;
-import org.jmol.c.STR;
-import org.jmol.modelset.ModelSet;
-import org.jmol.viewer.Viewer;
-
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.Residue;
-
-/**
- * Import and process files with Jmol for file like PDB, mmCIF
- *
- * @author jprocter
- *
- */
-public class JmolParser extends StructureFile implements JmolStatusListener
-{
- Viewer viewer = null;
-
- public JmolParser(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
- public JmolParser(FileParse fp) throws IOException
- {
- super(fp);
- }
-
- public JmolParser()
- {
- }
-
- /**
- * Calls the Jmol library to parse the PDB/mmCIF file, and then inspects the
- * resulting object model to generate Jalview-style sequences, with secondary
- * structure annotation added where available (i.e. where it has been computed
- * by Jmol using DSSP).
- *
- * @see jalview.io.AlignFile#parse()
- */
- @Override
- public void parse() throws IOException
- {
- setChains(new Vector<PDBChain>());
- Viewer jmolModel = getJmolData();
- jmolModel.openReader(getDataName(), getDataName(), getReader());
- waitForScript(jmolModel);
-
- /*
- * Convert one or more Jmol Model objects to Jalview sequences
- */
- if (jmolModel.ms.mc > 0)
- {
- // ideally we do this
- // try
- // {
- // setStructureFileType(jmolModel.evalString("show _fileType"));
- // } catch (Exception q)
- // {
- // }
- // ;
- // instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
- .toString() : "PDB");
-
- transformJmolModelToJalview(jmolModel.ms);
- }
- }
-
- /**
- * create a headless jmol instance for dataprocessing
- *
- * @return
- */
- private Viewer getJmolData()
- {
- if (viewer == null)
- {
- try
- {
- /*
- * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
- * see http://wiki.jmol.org/index.php/Jmol_Application
- */
- viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n", this);
- // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
- viewer.setBooleanProperty("defaultStructureDSSP", true);
- } catch (ClassCastException x)
- {
- throw new Error(MessageManager.formatMessage(
- "error.jmol_version_not_compatible_with_jalview_version",
- new String[] { JmolViewer.getJmolVersion() }), x);
- }
- }
- return viewer;
- }
-
- public void transformJmolModelToJalview(ModelSet ms) throws IOException
- {
- try
- {
- String lastID = "";
- List<SequenceI> rna = new ArrayList<SequenceI>();
- List<SequenceI> prot = new ArrayList<SequenceI>();
- PDBChain tmpchain;
- String pdbId = (String) ms.getInfo(0, "title");
-
- if (pdbId == null)
- {
- setId(safeName(getDataName()));
- setPDBIdAvailable(false);
- }
- else
- {
- setId(pdbId);
- setPDBIdAvailable(true);
- }
- List<Atom> significantAtoms = convertSignificantAtoms(ms);
- for (Atom tmpatom : significantAtoms)
- {
- try
- {
- tmpchain = findChain(tmpatom.chain);
- if (tmpatom.resNumIns.trim().equals(lastID))
- {
- // phosphorylated protein - seen both CA and P..
- continue;
- }
- tmpchain.atoms.addElement(tmpatom);
- } catch (Exception e)
- {
- tmpchain = new PDBChain(getId(), tmpatom.chain);
- getChains().add(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
- }
- lastID = tmpatom.resNumIns.trim();
- }
- xferSettings();
-
- makeResidueList();
- makeCaBondList();
-
-<<<<<<< HEAD
-=======
- if (getId() == null)
- {
- // always use resource name, not the hardwired file
- // Does the value of ID get used ? Behaviour needs to be
- // documented and tested
- setId(getDataName());
- }
->>>>>>> spike/JAL-2040_JAL-2137_phyre2
- for (PDBChain chain : getChains())
- {
- SequenceI chainseq = postProcessChain(chain);
- if (isRNA(chainseq))
- {
- rna.add(chainseq);
- }
- else
- {
- prot.add(chainseq);
- }
-
- if (StructureImportSettings.isProcessSecondaryStructure())
- {
- createAnnotation(chainseq, chain, ms.at);
- }
- }
- } catch (OutOfMemoryError er)
- {
- System.out
- .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_mmcif_file"));
- }
- }
-
- private List<Atom> convertSignificantAtoms(ModelSet ms)
- {
- List<Atom> significantAtoms = new ArrayList<Atom>();
- HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
- org.jmol.modelset.Atom prevAtom = null;
- for (org.jmol.modelset.Atom atom : ms.at)
- {
- if (atom.getAtomName().equalsIgnoreCase("CA")
- || atom.getAtomName().equalsIgnoreCase("P"))
- {
- if (!atomValidated(atom, prevAtom, chainTerMap))
- {
- continue;
- }
- Atom curAtom = new Atom(atom.x, atom.y, atom.z);
- curAtom.atomIndex = atom.getIndex();
- curAtom.chain = atom.getChainIDStr();
- curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
- : atom.group.getInsertionCode();
- curAtom.name = atom.getAtomName();
- curAtom.number = atom.getAtomNumber();
- curAtom.resName = atom.getGroup3(true);
- curAtom.resNumber = atom.getResno();
- curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
- .getIndex()] : Float.valueOf(atom.getOccupancy100());
- String fmt = new Format("%4i").form(curAtom.resNumber);
- curAtom.resNumIns = (fmt + curAtom.insCode);
- curAtom.tfactor = atom.getBfactor100() / 100f;
- curAtom.type = 0;
- // significantAtoms.add(curAtom);
- // ignore atoms from subsequent models
- if (!significantAtoms.contains(curAtom))
- {
- significantAtoms.add(curAtom);
- }
- prevAtom = atom;
- }
- }
- return significantAtoms;
- }
-
- private boolean atomValidated(org.jmol.modelset.Atom curAtom,
- org.jmol.modelset.Atom prevAtom,
- HashMap<String, org.jmol.modelset.Atom> chainTerMap)
- {
- // System.out.println("Atom: " + curAtom.getAtomNumber()
- // + " Last atom index " + curAtom.group.lastAtomIndex);
- if (chainTerMap == null || prevAtom == null)
- {
- return true;
- }
- String curAtomChId = curAtom.getChainIDStr();
- String prevAtomChId = prevAtom.getChainIDStr();
- // new chain encoutered
- if (!prevAtomChId.equals(curAtomChId))
- {
- // On chain switch add previous chain termination to xTerMap if not exists
- if (!chainTerMap.containsKey(prevAtomChId))
- {
- chainTerMap.put(prevAtomChId, prevAtom);
- }
- // if current atom belongs to an already terminated chain and the resNum
- // diff < 5 then mark as valid and update termination Atom
- if (chainTerMap.containsKey(curAtomChId))
- {
- if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
- {
- return false;
- }
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
- {
- chainTerMap.put(curAtomChId, curAtom);
- return true;
- }
- return false;
- }
- }
- // atom with previously terminated chain encountered
- else if (chainTerMap.containsKey(curAtomChId))
- {
- if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
- {
- return false;
- }
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
- {
- chainTerMap.put(curAtomChId, curAtom);
- return true;
- }
- return false;
- }
- // HETATM with resNum jump > 2
- return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
- .getResno()) > 2));
- }
-
- private void createAnnotation(SequenceI sequence, PDBChain chain,
- org.jmol.modelset.Atom[] jmolAtoms)
- {
- char[] secstr = new char[sequence.getLength()];
- char[] secstrcode = new char[sequence.getLength()];
-
- // Ensure Residue size equals Seq size
- if (chain.residues.size() != sequence.getLength())
- {
- return;
- }
- int annotIndex = 0;
- for (Residue residue : chain.residues)
- {
- Atom repAtom = residue.getAtoms().get(0);
- STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group
- .getProteinStructureSubType();
- setSecondaryStructure(proteinStructureSubType, annotIndex, secstr,
- secstrcode);
- ++annotIndex;
- }
- addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
- secstrcode, chain.id, sequence.getStart());
- }
-
- /**
- * Helper method that adds an AlignmentAnnotation for secondary structure to
- * the sequence, provided at least one secondary structure prediction has been
- * made
- *
- * @param modelTitle
- * @param seq
- * @param secstr
- * @param secstrcode
- * @param chainId
- * @param firstResNum
- * @return
- */
- protected void addSecondaryStructureAnnotation(String modelTitle,
- SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
- int firstResNum)
- {
- char[] seq = sq.getSequence();
- boolean ssFound = false;
- Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
- for (int p = 0; p < seq.length; p++)
- {
- if (secstr[p] >= 'A' && secstr[p] <= 'z')
- {
- try
- {
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
- } catch (Exception e)
- {
- // e.printStackTrace();
- }
- }
- }
-
- if (ssFound)
- {
- String mt = modelTitle == null ? getDataName() : modelTitle;
- mt += chainId;
- AlignmentAnnotation ann = new AlignmentAnnotation(
- "Secondary Structure", "Secondary Structure for " + mt,
- asecstr);
- ann.belowAlignment = true;
- ann.visible = true;
- ann.autoCalculated = false;
- ann.setCalcId(getClass().getName());
- ann.adjustForAlignment();
- ann.validateRangeAndDisplay();
- annotations.add(ann);
- sq.addAlignmentAnnotation(ann);
- }
- }
-
- private void waitForScript(Viewer jmd)
- {
- while (jmd.isScriptExecuting())
- {
- try
- {
- Thread.sleep(50);
-
- } catch (InterruptedException x)
- {
- }
- }
- }
-
- /**
- * Convert Jmol's secondary structure code to Jalview's, and stored it in the
- * secondary structure arrays at the given sequence position
- *
- * @param proteinStructureSubType
- * @param pos
- * @param secstr
- * @param secstrcode
- */
- protected void setSecondaryStructure(STR proteinStructureSubType,
- int pos, char[] secstr, char[] secstrcode)
- {
- switch (proteinStructureSubType)
- {
- case HELIX310:
- secstr[pos] = '3';
- break;
- case HELIX:
- case HELIXALPHA:
- secstr[pos] = 'H';
- break;
- case HELIXPI:
- secstr[pos] = 'P';
- break;
- case SHEET:
- secstr[pos] = 'E';
- break;
- default:
- secstr[pos] = 0;
- }
-
- switch (proteinStructureSubType)
- {
- case HELIX310:
- case HELIXALPHA:
- case HELIXPI:
- case HELIX:
- secstrcode[pos] = 'H';
- break;
- case SHEET:
- secstrcode[pos] = 'E';
- break;
- default:
- secstrcode[pos] = 0;
- }
- }
-
- /**
- * Convert any non-standard peptide codes to their standard code table
- * equivalent. (Initial version only does Selenomethionine MSE->MET.)
- *
- * @param threeLetterCode
- * @param seq
- * @param pos
- */
- protected void replaceNonCanonicalResidue(String threeLetterCode,
- char[] seq, int pos)
- {
- String canonical = ResidueProperties
- .getCanonicalAminoAcid(threeLetterCode);
- if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode))
- {
- seq[pos] = ResidueProperties.getSingleCharacterCode(canonical);
- }
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public String print()
- {
- return null;
- }
-
- /**
- * Not implemented
- */
- @Override
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {
- }
-
- @Override
- public void notifyCallback(CBK cbType, Object[] data)
- {
- String strInfo = (data == null || data[1] == null ? null : data[1]
- .toString());
- switch (cbType)
- {
- case ECHO:
- sendConsoleEcho(strInfo);
- break;
- case SCRIPT:
- notifyScriptTermination((String) data[2],
- ((Integer) data[3]).intValue());
- break;
- case MEASURE:
- String mystatus = (String) data[3];
- if (mystatus.indexOf("Picked") >= 0
- || mystatus.indexOf("Sequence") >= 0)
- {
- // Picking mode
- sendConsoleMessage(strInfo);
- }
- else if (mystatus.indexOf("Completed") >= 0)
- {
- sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
- strInfo.length() - 1));
- }
- break;
- case MESSAGE:
- sendConsoleMessage(data == null ? null : strInfo);
- break;
- case PICK:
- sendConsoleMessage(strInfo);
- break;
- default:
- break;
- }
- }
-
- String lastConsoleEcho = "";
-
- private void sendConsoleEcho(String string)
- {
- lastConsoleEcho += string;
- lastConsoleEcho += "\n";
- }
-
- String lastConsoleMessage = "";
-
- private void sendConsoleMessage(String string)
- {
- lastConsoleMessage += string;
- lastConsoleMessage += "\n";
- }
-
- int lastScriptTermination = -1;
-
- String lastScriptMessage = "";
-
- private void notifyScriptTermination(String string, int intValue)
- {
- lastScriptMessage += string;
- lastScriptMessage += "\n";
- lastScriptTermination = intValue;
- }
-
- @Override
- public boolean notifyEnabled(CBK callbackPick)
- {
- switch (callbackPick)
- {
- case MESSAGE:
- case SCRIPT:
- case ECHO:
- case LOADSTRUCT:
- case ERROR:
- return true;
- default:
- return false;
- }
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public String eval(String strEval)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public float[][] functionXY(String functionName, int x, int y)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public String createImage(String fileName, String imageType,
- Object text_or_bytes, int quality)
- {
- return null;
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public Map<String, Object> getRegistryInfo()
- {
- return null;
- }
-
- /**
- * Not implemented
- */
- @Override
- public void showUrl(String url)
- {
- }
-
- /**
- * Not implemented - returns null
- */
- @Override
- public Dimension resizeInnerPanel(String data)
- {
- return null;
- }
-
- @Override
- public Map<String, Object> getJSpecViewProperty(String arg0)
- {
- return null;
- }
-
- public boolean isPredictSecondaryStructure()
- {
- return predictSecondaryStructure;
- }
-
- public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
- {
- this.predictSecondaryStructure = predictSecondaryStructure;
- }
-
- public boolean isVisibleChainAnnotation()
- {
- return visibleChainAnnotation;
- }
-
- public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
- {
- this.visibleChainAnnotation = visibleChainAnnotation;
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff