Examples with MolecularAssembly ffx.potential.MolecularAssembly used on opensource projects

Example 16 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class TitrationUtils method openFullyProtonated.

public static MolecularAssembly openFullyProtonated(File structure) {
    String name = format("%s-prot", FilenameUtils.removeExtension(structure.getName()));
    MolecularAssembly mola = new MolecularAssembly(name);
    mola.setFile(structure);
    List<Mutation> mutations = new ArrayList<>();
    List<Residue> residues = mola.getResidueList();
    for (Residue res : residues) {
        char chain = res.getChainID();
        int resID = res.getResidueNumber();
        Titration titration = Titration.lookup(res);
        if (res.getAminoAcid3() != titration.protForm) {
            String protName = titration.protForm.name();
            mutations.add(new PDBFilter.Mutation(chain, resID, protName));
        }
    }
    PotentialsUtils utils = new PotentialsUtils();
    return utils.openWithMutations(structure, mutations);
}

Example 17 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class GraphicsEvents method processMouseEvent.

/**
 * <p>
 * processMouseEvent</p>
 *
 * @param evt a {@link java.awt.event.MouseEvent} object.
 */
public void processMouseEvent(MouseEvent evt) {
    buttonPress = false;
    leftButton = false;
    middleButton = false;
    rightButton = false;
    int mod = evt.getModifiersEx();
    if (evt.getID() == MouseEvent.MOUSE_PRESSED) {
        buttonPress = true;
    }
    // Left Button
    if ((mod & MouseEvent.BUTTON1_DOWN_MASK) == MouseEvent.BUTTON1_DOWN_MASK) {
        leftButton = true;
    }
    // Middle Button
    if ((mod & MouseEvent.BUTTON2_DOWN_MASK) == MouseEvent.BUTTON2_DOWN_MASK) {
        middleButton = true;
    }
    // Alternatively, map "alt + button1" to the middle button
    if ((mod & MouseEvent.ALT_DOWN_MASK) == MouseEvent.ALT_DOWN_MASK) {
        if (leftButton) {
            middleButton = true;
            leftButton = false;
        }
    }
    // Right Button
    if ((mod & MouseEvent.BUTTON3_DOWN_MASK) == MouseEvent.BUTTON3_DOWN_MASK) {
        rightButton = true;
    }
    // Alternatively, map "shift + button1" to the right button
    if ((mod & MouseEvent.SHIFT_DOWN_MASK) == MouseEvent.SHIFT_DOWN_MASK) {
        if (leftButton) {
            rightButton = true;
            leftButton = false;
        }
    }
    x = evt.getX();
    y = evt.getY();
    atom = null;
    axisSelected = false;
    if (buttonPress) {
        // Picking Results
        pickCanvas.setShapeLocation(x, y);
        // Catch and ignore this until a fix is determined...
        try {
            pickResult = pickCanvas.pickClosest();
        } catch (Exception e) {
            pickResult = null;
        }
        if (pickResult != null) {
            SceneGraphPath sgp = pickResult.getSceneGraphPath();
            Node node = sgp.getObject();
            if (node instanceof Shape3D) {
                Shape3D s = (Shape3D) node;
                Object o = s.getUserData();
                if (o instanceof MolecularAssembly) {
                    MolecularAssembly sys = (MolecularAssembly) o;
                    if (pickResult.numIntersections() > 0) {
                        PickIntersection pi = pickResult.getIntersection(0);
                        int[] coords = pi.getPrimitiveCoordinateIndices();
                        atom = sys.getAtomFromWireVertex(coords[0]);
                    }
                } else if (o instanceof Atom) {
                    atom = (Atom) o;
                } else if (o instanceof GraphicsAxis) {
                    axisSelected = true;
                }
            }
        }
    }
}

Example 18 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class MainPanel method convertWait.

/**
 * Converts a non-Force Field X data structure into an array of FFXSystem[].
 * Presently does not yet have support for array- or list-based data
 * structures, only singular objects.
 *
 * @param data Outside data structure
 * @param file Source file
 * @return An array of FFXSystem
 */
public synchronized FFXSystem[] convertWait(Object data, File file) {
    if (file == null) {
        try {
            file = PotentialsDataConverter.getDefaultFile(data);
        } catch (FileNotFoundException | IllegalArgumentException ex) {
            logger.warning(String.format(" Exception in finding file for data structure: %s", ex.toString()));
            return null;
        }
    }
    String name = file.getName();
    Thread thread = convert(data, file, null);
    while (thread != null && thread.isAlive()) {
        try {
            wait(1);
        } catch (InterruptedException e) {
            String message = "Exception waiting for " + name + " to open.";
            logger.log(Level.WARNING, message, e);
            return null;
        }
    }
    MolecularAssembly[] systems = activeConvFilter.getMolecularAssemblys();
    if (systems != null) {
        int n = systems.length;
        FFXSystem[] ffxSystems = new FFXSystem[n];
        FFXSystem[] allSystems = getHierarchy().getSystems();
        int total = allSystems.length;
        for (int i = 0; i < n; i++) {
            ffxSystems[i] = allSystems[total - n + i];
        }
        return ffxSystems;
    } else {
        return null;
    }
}

Example 19 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class PDBFilter method readNext.

@Override
public boolean readNext(boolean resetPosition) {
    // ^ is beginning of line, \\s+ means "one or more whitespace", (\\d+) means match and capture one or more digits.
    Pattern modelPatt = Pattern.compile("^MODEL\\s+(\\d+)");
    modelsRead = resetPosition ? 1 : modelsRead + 1;
    boolean eof = true;
    for (MolecularAssembly system : systems) {
        File file = system.getFile();
        currentFile = file;
        try {
            BufferedReader currentReader;
            if (readers.containsKey(system)) {
                currentReader = readers.get(system);
                if (!currentReader.ready()) {
                    currentReader = new BufferedReader(new FileReader(currentFile));
                    readers.put(system, currentReader);
                }
            } else {
                currentReader = new BufferedReader(new FileReader(currentFile));
                readers.put(system, currentReader);
            }
            // Skip to appropriate model.
            String line = currentReader.readLine();
            while (line != null) {
                line = line.trim();
                Matcher m = modelPatt.matcher(line);
                if (m.find()) {
                    int modelNum = Integer.parseInt(m.group(1));
                    if (modelNum == modelsRead) {
                        logger.log(Level.INFO, String.format(" Reading model %d for %s", modelNum, currentFile));
                        eof = false;
                        break;
                    }
                }
                line = currentReader.readLine();
            }
            if (eof) {
                logger.log(Level.INFO, String.format(" End of file reached for %s", file));
                currentReader.close();
                return false;
            }
            // Begin parsing the model.
            boolean modelDone = false;
            line = currentReader.readLine();
            while (line != null) {
                line = line.trim();
                String recID = line.substring(0, Math.min(6, line.length())).trim();
                try {
                    Record record = Record.valueOf(recID);
                    boolean hetatm = true;
                    switch(record) {
                        // ATOM      2  CA  ILE A  16      60.793  72.149  -9.511  1.00  6.91           C
                        case ATOM:
                            hetatm = false;
                        case HETATM:
                            if (!line.substring(17, 20).trim().equals("HOH")) {
                                // int serial = Hybrid36.decode(5, line.substring(6, 11));
                                String name = line.substring(12, 16).trim();
                                if (name.toUpperCase().contains("1H") || name.toUpperCase().contains("2H") || name.toUpperCase().contains("3H")) {
                                    // VERSION3_2 is presently just a placeholder for "anything non-standard".
                                    fileStandard = VERSION3_2;
                                }
                                Character altLoc = line.substring(16, 17).toUpperCase().charAt(0);
                                if (!altLoc.equals(' ') && !altLoc.equals('A') && !altLoc.equals(currentAltLoc)) {
                                    break;
                                }
                                String resName = line.substring(17, 20).trim();
                                Character chainID = line.substring(21, 22).charAt(0);
                                List<String> segIDList = segidMap.get(chainID);
                                if (segIDList == null) {
                                    logger.log(Level.WARNING, String.format(" No " + "known segment ID corresponds to " + "chain ID %s", chainID.toString()));
                                    break;
                                }
                                String segID = segIDList.get(0);
                                if (segIDList.size() > 1) {
                                    logger.log(Level.WARNING, String.format(" " + "Multiple segment IDs correspond to" + "chain ID %s; assuming %s", chainID.toString(), segID));
                                }
                                int resSeq = Hybrid36.decode(4, line.substring(22, 26));
                                double[] d = new double[3];
                                d[0] = new Double(line.substring(30, 38).trim());
                                d[1] = new Double(line.substring(38, 46).trim());
                                d[2] = new Double(line.substring(46, 54).trim());
                                double occupancy = 1.0;
                                double tempFactor = 1.0;
                                Atom newAtom = new Atom(0, name, altLoc, d, resName, resSeq, chainID, occupancy, tempFactor, segID);
                                newAtom.setHetero(hetatm);
                                // Check if this is a modified residue.
                                if (modres.containsKey(resName.toUpperCase())) {
                                    newAtom.setModRes(true);
                                }
                                Atom returnedAtom = activeMolecularAssembly.findAtom(newAtom);
                                if (returnedAtom != null) {
                                    returnedAtom.setXYZ(d);
                                    double[] retXYZ = new double[3];
                                    returnedAtom.getXYZ(retXYZ);
                                } else {
                                    String message = String.format(" " + "Could not find atom %s in assembly", newAtom.toString());
                                    if (dieOnMissingAtom) {
                                        logger.severe(message);
                                    } else {
                                        logger.warning(message);
                                    }
                                }
                                break;
                            }
                        case ENDMDL:
                        case // Technically speaking, END should be at the end of the file, not end of the model.
                        END:
                            logger.log(Level.FINE, String.format(" Model %d successfully read", modelsRead));
                            modelDone = true;
                        default:
                            break;
                    }
                } catch (Exception ex) {
                // Do nothing; it's not an ATOM/HETATM line.
                }
                if (modelDone) {
                    break;
                }
                line = currentReader.readLine();
            }
            return true;
        } catch (IOException ex) {
            logger.info(String.format(" Exception in parsing frame %d of %s:" + " %s", modelsRead, system.toString(), ex.toString()));
        }
    }
    return false;
}

Example 20 with MolecularAssembly

use of ffx.potential.MolecularAssembly in project ffx by mjschnie.

the class PotentialsDataConverter method run.

/**
 * Converts the data structure to MolecularAssembly(s).
 */
@Override
public void run() {
    if (dataStructure == null || dataType.equals(Utilities.DataType.UNK)) {
        throw new IllegalArgumentException("Object passed was not recognized.");
    }
    assemblies = new ArrayList<>();
    propertyList = new ArrayList<>();
    switch(dataType) {
        case BIOJAVA:
            Structure struct = (Structure) dataStructure;
            String name = struct.getPDBCode();
            CompositeConfiguration properties = Keyword.loadProperties(file);
            MolecularAssembly assembly = new MolecularAssembly(name);
            assembly.setFile(file);
            ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
            ForceField forceField = forceFieldFilter.parse();
            assembly.setForceField(forceField);
            BiojavaFilter filter = new BiojavaFilter(struct, assembly, forceField, properties);
            if (filter.convert()) {
                filter.applyAtomProperties();
                assembly.finalize(true, forceField);
                ForceFieldEnergy energy = ForceFieldEnergy.energyFactory(assembly, filter.getCoordRestraints());
                assembly.setPotential(energy);
                assemblies.add(assembly);
                propertyList.add(properties);
                List<Character> altLocs = filter.getAltLocs();
                if (altLocs.size() > 1 || altLocs.get(0) != ' ') {
                    StringBuilder altLocString = new StringBuilder("\n Alternate locations found [ ");
                    for (Character c : altLocs) {
                        // Do not report the root conformer.
                        if (c == ' ') {
                            continue;
                        }
                        altLocString.append(format("(%s) ", c));
                    }
                    altLocString.append("]\n");
                    logger.info(altLocString.toString());
                }
                /**
                 * Alternate conformers may have different chemistry, so
                 * they each need to be their own MolecularAssembly.
                 */
                for (Character c : altLocs) {
                    if (c.equals(' ') || c.equals('A')) {
                        continue;
                    }
                    MolecularAssembly newAssembly = new MolecularAssembly(name);
                    newAssembly.setForceField(assembly.getForceField());
                    filter.setAltID(newAssembly, c);
                    filter.clearSegIDs();
                    if (filter.convert()) {
                        String fileName = assembly.getFile().getAbsolutePath();
                        newAssembly.setName(FilenameUtils.getBaseName(fileName) + " " + c);
                        filter.applyAtomProperties();
                        newAssembly.finalize(true, assembly.getForceField());
                        energy = ForceFieldEnergy.energyFactory(newAssembly, filter.getCoordRestraints());
                        newAssembly.setPotential(energy);
                        assemblies.add(newAssembly);
                        properties.addConfiguration(properties);
                    }
                }
            } else {
                logger.warning(String.format(" Failed to convert structure %s", dataStructure.toString()));
            }
            activeAssembly = assembly;
            activeProperties = properties;
            break;
        case UNK:
        default:
            throw new IllegalArgumentException("Object passed was not recognized.");
    }
}