Examples with Keyword ffx.utilities.Keyword used on opensource projects

Example 6 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class KeyFilter method open.

/**
 * <p>
 * open</p>
 *
 * @param keyFile a {@link java.io.File} object.
 * @param keywordHash a {@link java.util.Hashtable} object.
 * @return a {@link java.util.Hashtable} object.
 */
public static Hashtable<String, Keyword> open(File keyFile, Hashtable<String, Keyword> keywordHash) {
    if (keyFile == null || !keyFile.exists() || !keyFile.canRead()) {
        return null;
    }
    if (keywordHash == null) {
        keywordHash = new Hashtable<String, Keyword>();
    }
    FileReader fr = null;
    BufferedReader br = null;
    try {
        fr = new FileReader(keyFile);
        br = new BufferedReader(fr);
        Keyword comments = new Keyword("COMMENTS");
        keywordHash.put("COMMENTS", comments);
        while (br.ready()) {
            String s = br.readLine();
            if (s == null) {
                continue;
            }
            s = s.trim();
            if (s.equals("")) {
                // Skip blank lines
                continue;
            }
            // Store comments together
            if (s.startsWith("#") || s.toUpperCase().startsWith("ECHO")) {
                comments.append(s);
            } else {
                int firstspace = s.indexOf(" ");
                String keyword, data;
                if (firstspace == -1) {
                    // no parameters
                    keyword = s.trim().toUpperCase();
                    // Each of these valid cases mean different things...
                    if (keyword.equalsIgnoreCase("rattle")) {
                        data = "RATTLE";
                    } else {
                        data = null;
                    }
                } else {
                    keyword = s.substring(0, firstspace).toUpperCase();
                    data = s.substring(firstspace).trim();
                }
                Keyword kd = keywordHash.get(keyword);
                if (kd == null) {
                    kd = new Keyword(keyword);
                    keywordHash.put(keyword, kd);
                }
                if (data != null) {
                    kd.append(data);
                }
                /**
                 * Multipoles and TORTORS are the only keywords that span
                 * multiple lines. Editing these from within Force Field X
                 * seems unlikely, so they are treated as comments.
                 */
                if (keyword.equalsIgnoreCase("MULTIPOLE")) {
                    int[] mnum = { 3, 1, 2, 3 };
                    for (int i = 0; i < 4; i++) {
                        if (!br.ready()) {
                            System.out.println("Check for an invalid MULTIPOLE keyword.");
                            return null;
                        }
                        s = br.readLine();
                        if (s == null) {
                            logger.warning("Multipole format error.");
                            return null;
                        }
                        s = s.trim();
                        if (s.split(" +").length != mnum[i]) {
                            logger.warning("Multipole format error.");
                            return null;
                        }
                        kd.append(s);
                    }
                } else if (keyword.equalsIgnoreCase("TORTORS")) {
                    String[] res = data.split(" +");
                    if (res == null || res.length < 7) {
                        logger.warning("TORTOR format error.");
                        return null;
                    }
                    int xres = Integer.parseInt(res[5]);
                    int yres = Integer.parseInt(res[6]);
                    for (int i = 0; i < xres * yres; i++) {
                        if (!br.ready()) {
                            System.out.println("Check for an invalid TORTOR keyword.");
                            return null;
                        }
                        s = br.readLine();
                        if (s == null) {
                            logger.warning("TORTOR format error.");
                            return null;
                        }
                        s = s.trim();
                        if (s.split(" +").length != 3) {
                            logger.warning("TORTOR format error.");
                            return null;
                        }
                        kd.append(s);
                    }
                }
            }
        }
        return keywordHash;
    } catch (IOException e) {
        System.err.println("Error reading Key File: " + e);
        return null;
    } finally {
        if (fr != null) {
            try {
                fr.close();
            } catch (IOException e) {
            }
        }
    }
}

Example 7 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class MainPanel method openKey.

/**
 * Attempt to convert a TINKER *.key file
 *
 * @param newSystem FFXSystem that needs an associated Key File
 * @param createKey flag to create a key file be created
 * @return Key file that was found, or null if nothing could be found
 */
public boolean openKey(FFXSystem newSystem, boolean createKey) {
    String keyFileName = null;
    String temp = newSystem.getFile().getName();
    int dot = temp.lastIndexOf(".");
    if (dot > 0) {
        keyFileName = temp.substring(0, dot) + ".key";
    } else {
        keyFileName = temp + ".key";
    }
    String path = newSystem.getFile().getParent() + File.separator;
    File keyfile = new File(path + keyFileName);
    // System.out.println("" + keyfile);
    if (keyfile.exists()) {
        Hashtable<String, Keyword> keywordHash = KeyFilter.open(keyfile);
        if (keywordHash != null) {
            newSystem.setKeywords(keywordHash);
        } else {
            return false;
        }
        newSystem.setKeyFile(keyfile);
        newSystem.setForceField(null);
        return true;
    }
    keyfile = new File(path + "tinker.key");
    if (keyfile.exists()) {
        logger.info("Using tinker.key: " + keyfile);
        Hashtable<String, Keyword> keywordHash = KeyFilter.open(keyfile);
        if (keywordHash != null) {
            newSystem.setKeywords(keywordHash);
        } else {
            return false;
        }
        newSystem.setKeyFile(keyfile);
        newSystem.setForceField(null);
        return true;
    }
    if (createKey) {
        return createKeyFile(newSystem);
    }
    return false;
}

Example 8 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class KeyFilter method loadSystemKeywords.

/**
 * <p>
 * loadSystemKeywords</p>
 *
 * @return a {@link java.util.Hashtable} object.
 */
public static Hashtable<String, Keyword> loadSystemKeywords() {
    File f = new File("/etc/ffx.conf");
    Hashtable<String, Keyword> systemKeywords = new Hashtable<>();
    if (f.exists() && f.canRead()) {
        logger.info("Reading /etc/ffx.conf");
        systemKeywords = KeyFilter.open(f, systemKeywords);
    }
    String path = System.getProperty("user.home") + File.separator + ".ffx/ffx.conf";
    f = new File(path);
    if (f.exists() && f.canRead()) {
        logger.log(Level.INFO, "Reading {0}", path);
        systemKeywords = KeyFilter.open(f, systemKeywords);
    }
    return systemKeywords;
}

Example 9 with Keyword

use of ffx.utilities.Keyword in project ffx by mjschnie.

the class KeywordPanel method loadActive.

/**
 * <p>
 * loadActive</p>
 *
 * @param newSystem a {@link ffx.ui.FFXSystem} object.
 * @return a boolean.
 */
public boolean loadActive(FFXSystem newSystem) {
    synchronized (this) {
        if (newSystem == null) {
            keyClear();
            return false;
        }
        configToKeywords(newSystem);
        File newKeyFile = newSystem.getKeyFile();
        if (newKeyFile != null) {
        // logger.info(String.format("Key File %s.", newKeyFile.getAbsolutePath()));
        }
        Hashtable<String, Keyword> newKeys = newSystem.getKeywords();
        if (newKeyFile == null && newKeys == null) {
            logger.info(String.format("Loaded %s with no keywords.", newSystem.toString()));
            return false;
        }
        // logger.info(String.format("Loading %s with %d keywords.", newSystem.toString(), newKeys.size()));
        return loadActive(newSystem, newKeys, newKeyFile);
    }
}