public static ProteinHelper getHelperInstance()
{
if (instance == null)
{
instance = new ProteinHelper();
}
return(instance);
}
/// <summary>
/// Extract the content from the UnitInfo.txt file produced by the folding
/// console
/// </summary>
/// <param name="LogFileName">Full path to local copy of UnitInfo.txt</param>
/// <param name="Instance">Reference back to the instance to which the
/// UnitInfo file belongs</param>
public Boolean ParseUnitInfo(String LogFileName, Base Instance)
{
if (!System.IO.File.Exists(LogFileName))
{
return(false);
}
DateTime Start = Debug.ExecStart;
TextReader tr;
try
{
tr = File.OpenText(LogFileName);
}
catch (Exception Ex)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw exception {1}.", Debug.FunctionName, Ex.Message), null);
ClassLogger.Log(LogLevel.Trace, Debug.FunctionName, String.Format("Execution Time: {0}", Debug.GetExecTime(Start)));
return(false);
}
while (tr.Peek() != -1)
{
String sData = tr.ReadLine();
if (sData.StartsWith("Name: "))
{
Instance.UnitInfo.ProteinID = ProteinHelper.ExtractProteinID(sData.Substring(6));
Instance.UnitInfo.ProteinName = sData.Substring(6);
}
else if (sData.StartsWith("Download time: "))
{
Instance.UnitInfo.DownloadTime = DateTime.ParseExact(sData.Substring(15), "MMMM d H:mm:ss", System.Globalization.DateTimeFormatInfo.InvariantInfo, System.Globalization.DateTimeStyles.AssumeUniversal);
}
else if (sData.StartsWith("Progress: "))
{
Instance.UnitInfo.PercentComplete = Int32.Parse(sData.Substring(10, sData.IndexOf("%") - 10));
}
}
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
return(true);
}
/// <summary>
/// Parses one line from a UnitInfo file to the correct class property
/// </summary>
/// <param name="sData">Line from UnitInfo.txt</param>
private void ParseUI(String sData)
{
DateTime Start = Debug.ExecStart;
if (sData.StartsWith("Name:"))
{
// Dammit, Stanford trims the protein name to 24 characters and some are much longer!
// Still, grab it as it's a good start, extract the ID and use it
_ProteinName = sData.Split(' ')[1].Trim();
_ProteinID = ProteinHelper.ExtractProteinID(_ProteinName);
}
else if (sData.StartsWith("Download time:"))
{
String sDate = sData.Substring(15).Trim();
this.DownloadTime = DateTime.ParseExact(sDate, "MMMM d HH:mm:ss", System.Globalization.DateTimeFormatInfo.InvariantInfo, System.Globalization.DateTimeStyles.AssumeUniversal);
}
else if (sData.StartsWith("Progress:"))
{
String sProgress = sData.Split(' ')[1].Replace("%", "");
this.PercentComplete = Int32.Parse(sProgress);
}
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
}
public void makeProtein(string filename)
{
//Uses PDBReader to read a file
//Then extracts the information needed to instantiate the protein
PDBReader reader = new PDBReader();
reader.readFile(filename);
AtomData[] proteinAtoms = reader.getProteinAtoms();
AtomData[] extraAtoms = reader.getExtraAtoms();
string[] aminoAcidCodes = reader.getAminoAcidCodes();
BondData[] extraBonds = reader.getExtraBonds();
//Gets instance of ProteinHelper
helper = ProteinHelper.getHelperInstance();
//Initalizes array of atoms
atoms = new GameObject[proteinAtoms.Length + extraAtoms.Length];
int i = 0;
//Instantiates atoms present in amino acids and adds object to array of Atoms
foreach (AtomData atom in proteinAtoms)
{
atoms[i++] = createAtom(atom.x, atom.y, atom.z, helper.getColor(atom.element));
}
//Instantiates atoms not present in amino acids and adds object to array of Atoms
foreach (AtomData atom in extraAtoms)
{
atoms[i++] = createAtom(atom.x, atom.y, atom.z, helper.getColor(atom.element));
}
//Instantiates bonds present in amino acid sequence and adds them to array of bonds
List <GameObject> bonds = new List <GameObject>();
BondData[] bondData;
i = 0;
int previousEnd = 0;
foreach (string aminoAcid in aminoAcidCodes)
{
//Instantiates bonds in the backbone of the amino acid
bonds.Add(createBond(atoms[i], atoms[i + 1]));
bonds.Add(createBond(atoms[i + 1], atoms[i + 2]));
bonds.Add(createBond(atoms[i + 2], atoms[i + 3])); //should be a double bond in future
//Instantiates bond connecting current amino acid to previous one
if (previousEnd != 0)
{
bonds.Add(createBond(atoms[previousEnd], atoms[i]));
}
//Grabs bonds in R group of current amino acid
bondData = helper.getRGroupBonds(aminoAcid);
//Instantiates each of the bonds in the R group
foreach (BondData bond in bondData)
{
bonds.Add(createBond(atoms[i + bond.atom1Index], atoms[i + bond.atom2Index]));
}
//Increases iterator and stores carboxyl end for next amino acid
previousEnd = i + 2;
i += helper.getNumAtoms(aminoAcid);
}
//Instantiates bonds not present in amino acid sequence and adds them to list of bonds
foreach (BondData bond in extraBonds)
{
bonds.Add(createBond(atoms[bond.atom1Index], atoms[bond.atom2Index]));
}
this.bonds = bonds.ToArray();
}
/// <summary>
/// Reads through the FAH log file and grabs desired information
/// </summary>
/// <param name="LogFileName">Full path to the FAH log file</param>
/// <param name="Instance">Instance to which the log file data is
/// attached</param>
/// <returns></returns>
public Boolean ParseFAHLog(String LogFileName, Base Instance)
{
if (!System.IO.File.Exists(LogFileName))
{
return(false);
}
DateTime Start = Debug.ExecStart;
TextReader FAHlog;
try
{
FAHlog = File.OpenText(LogFileName);
}
catch (Exception Ex)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw exception {1}.", Debug.FunctionName, Ex.Message), null);
return(false);
}
String s;
//Regex rCoreVersion =
// new Regex("Folding@Home (?<CoreVer>.*) Core", RegexOptions.Compiled | RegexOptions.ExplicitCapture | RegexOptions.Singleline);
//Regex rProjectNumber =
// new Regex("Project: (?<ProjectNumber>.*)", RegexOptions.Compiled | RegexOptions.ExplicitCapture | RegexOptions.Singleline);
Regex rFramesCompleted =
new Regex("\\[(?<Timestamp>.*)\\] Completed (?<Completed>.*) out of (?<Total>.*) steps ((?<Percent>.*))", RegexOptions.Compiled | RegexOptions.ExplicitCapture | RegexOptions.Singleline);
Regex rProtein =
new Regex("Protein: (?<Protein>.*)", RegexOptions.Compiled | RegexOptions.ExplicitCapture | RegexOptions.Singleline);
Regex rCompletedWUs =
new Regex("Number of Units Completed: (?<Completed>.*)$", RegexOptions.Compiled | RegexOptions.ExplicitCapture | RegexOptions.Singleline);
DateTime time1 = new DateTime(1900, 1, 1, 0, 0, 0); // Placeholder date
DateTime time2 = new DateTime(1900, 1, 1, 0, 0, 0); // Placeholder date
DateTime time3 = new DateTime(1900, 1, 1, 0, 0, 0); // Placeholder date
while (FAHlog.Peek() != -1)
{
s = FAHlog.ReadLine();
//Match mCoreVer = rCoreVersion.Match(s);
//Match mProjectNumber = rProjectNumber.Match(s);
Match mFramesCompleted = rFramesCompleted.Match(s);
Match mProtein = rProtein.Match(s);
Match mCompletedWUs = rCompletedWUs.Match(s);
if (mProtein.Success)
{
Instance.UnitInfo.ProteinID = ProteinHelper.ExtractProteinID(mProtein.Result("${Protein}"));
Instance.UnitInfo.ProteinName = mProtein.Result("${Protein}");
}
if (mFramesCompleted.Success)
{
Instance.UnitInfo.RawFramesComplete = Int32.Parse(mFramesCompleted.Result("${Completed}"));
Instance.UnitInfo.RawFramesTotal = Int32.Parse(mFramesCompleted.Result("${Total}"));
time1 = time2;
time2 = time3;
time3 = DateTime.ParseExact(mFramesCompleted.Result("${Timestamp}"), "H:mm:ss", System.Globalization.DateTimeFormatInfo.InvariantInfo, System.Globalization.DateTimeStyles.AssumeUniversal);
if (time1.Year != 1900)
{
// time1 is valid for 2 "sets" ago
TimeSpan tDelta = time3.Subtract(time1);
Instance.UnitInfo.RawTimePerSection = Convert.ToInt32((tDelta.TotalSeconds) / 2);
}
else if (time2.Year != 1900)
{
// time2 is valid for 1 "set" ago
TimeSpan tDelta = time3.Subtract(time2);
Instance.UnitInfo.RawTimePerSection = Convert.ToInt32(tDelta.TotalSeconds);
}
}
if (mCompletedWUs.Success)
{
Instance.TotalUnits = Int32.Parse(mCompletedWUs.Result("${Completed}"));
}
Application.DoEvents();
}
FAHlog.Close();
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
return(true);
}
