public GaussianParserTest() throws Exception {
IBIOMESConfiguration.getInstance(TestCommon.TEST_IBIOMES_CONFIG_FILE, true);
}
/**
* Parse CHARMM parameter file
*
* @param filePath
* @throws Exception
*/
private void parseFile() throws Exception {
ArrayList<String> lines = new ArrayList<String>();
IBIOMESFileReader br = null;
String line = null;
boolean append = false;
boolean appendCurrent = false;
int nLines = 0;
try {
br = new IBIOMESFileReader(this);
while ((line = br.readLine()) != null) {
line = line.trim();
if (!line.startsWith("!") && !line.startsWith("*") && line.length() > 0) {
int indexComment = line.indexOf('!');
if (indexComment != -1) line = line.substring(0, indexComment).trim();
appendCurrent = append;
if (line.endsWith(" -")) {
line = line.substring(0, line.lastIndexOf(" -")).trim();
append = true;
} else append = false;
if (!appendCurrent) {
lines.add(line);
nLines++;
} else {
String concatLine = lines.get(nLines - 1) + " " + line;
lines.remove(nLines - 1);
lines.add(concatLine);
}
}
}
br.close();
for (String entry : lines) {
entry = entry.toLowerCase();
int index = entry.indexOf(' ');
if (index > 0) {
// use first word as keyword
String key = entry.substring(0, index);
// put rest of values in array
String[] values = entry.substring(index + 1).split("\\s+");
List<String> valueList = Arrays.asList(values);
parameters.put(key, valueList);
}
}
ExperimentTask task = CHARMMKeywordMapper.mapKeysToTask(parameters);
this.tasks = new ArrayList<ExperimentTask>();
this.tasks.add(task);
} catch (Exception e) {
this.format = LocalFile.FORMAT_UNKNOWN;
if (IBIOMESConfiguration.getInstance().isOutputToConsole())
System.out.println(
"WARNING: cannot parse '" + this.getAbsolutePath() + "' as a CHARMM input file.");
if (IBIOMESConfiguration.getInstance().isOutputErrorStackToConsole()) e.printStackTrace();
if (br != null) {
try {
br.close();
} catch (Exception e2) {
e.printStackTrace();
}
}
throw e;
}
}