/* private Dictionary<string,double> SableDist(List<string> refStructures)
* {
* StreamReader sableFile = new StreamReader(textBox3.Text);
* string line = sableFile.ReadLine();
* string prefix=refStructures[0];
* protInfo pr_SS=new protInfo();
* protInfo pr_SA = new protInfo();
* string seq, ss, sa;
* if(prefix.Contains("\\"))
* {
* string []aux=prefix.Split('\\');
* prefix=aux[aux.Length-2];
* }
* while (line !=null)
* {
* if(line.StartsWith("Query:"))
* {
* string[] aux = line.Split(' ');
* aux = aux[1].Split('.');
* if (prefix.Contains(aux[0]))
* {
* pr_SS.sequence = sableFile.ReadLine();
* string ww=sableFile.ReadLine();
* pr_SS.profile = new List<byte>();
* for (int i = 0; i < ww.Length;i++ )
* pr_SS.profile.Add(ww[i].ToString());
* line = sableFile.ReadLine();
* pr_SA.sequence = pr_SS.sequence;
* pr_SA.profile = new List<string>(Regex.Replace(sableFile.ReadLine(),@"\s+"," ").Trim().Split(' '));
* for (int i = 0; i < pr_SA.profile.Count; i++)
* pr_SA.profile[i] = (Convert.ToInt16(pr_SA.profile[i]) / 10).ToString();
*
* }
* }
* line = sableFile.ReadLine();
* }
*
* sableFile.Close();
* Settings set=new Settings();
* set.Load();
* Alignment al=new Alignment(refStructures,set,"H:\\profiels\\SS3_SA9_internal.profiles");
* al.MyAlign(null);
* al.AddStructureToAlignment("sable_res","SS", ref pr_SS);
* al.AddStructureToAlignment("sable_res", "SA", ref pr_SA);
*
* Dictionary<string, Dictionary<string, protInfo>> allProf = new Dictionary<string, Dictionary<string, protInfo>>();
* allProf.Add("SS", new Dictionary<string, protInfo>());
* allProf["SS"].Add("sable_res", pr_SS);
* allProf.Add("SA", new Dictionary<string, protInfo>());
* allProf["SA"].Add("sable_res", pr_SA);
* Dictionary<string,List<string>> protCombineStates = al.CombineProfiles("sable_res", allProf);
*
*
* JuryDistance dist = new JuryDistance(al, false);
*
* Dictionary<string, double> distRes = new Dictionary<string, double>();
*
* foreach (var item in refStructures)
* {
* distRes.Add(Path.GetFileName(item), dist.GetDistance("sable_res",Path.GetFileName(item)));
* currentV++;
* }
*
*
* return distRes;
*
* }*/
private DistanceMeasure PrepareDistanceMeasure(List <string> cluster, DistanceMeasures measure, string dirName)
{
DistanceMeasure distRes = null;
List <string> clustFiles = new List <string>();
foreach (var item in cluster)
{
clustFiles.Add(dirName + Path.DirectorySeparatorChar + item);
}
switch (measure)
{
case DistanceMeasures.HAMMING:
distRes = new JuryDistance(clustFiles, alignFile, true, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
{
distRes = new MaxSub(clustFiles, alignFile, distanceControl1.reference);
}
break;
case DistanceMeasures.RMSD:
distRes = new Rmsd(clustFiles, alignFile, distanceControl1.reference, distanceControl1.CAtoms, distanceControl1.referenceProfile);
break;
}
distRes.InitMeasure();
return(distRes);
}
int GetDist(DistanceMeasures distance,string dirName,string item1,string item2)
{
DistanceMeasure dist = null;
List<string> targets = new List<string>();
if(!item1.Contains(dirName))
targets.Add(dirName + Path.DirectorySeparatorChar + item1);
else
targets.Add(item1);
targets.Add(dirName + Path.DirectorySeparatorChar + item2);
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, "", false, "");
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, "", false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, "", false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, "", false);
break;
}
dist.InitMeasure();
return GetDist(dist, item1, item2);
}
private DistanceMeasure CreateMeasureForDCD(DCDFile dcd, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist = null;
switch (measure)
{
case DistanceMeasures.HAMMING:
if (refJuryProfile == null || !jury1d)
{
throw new Exception("Sorry but for jury measure you have to define 1djury profile to find reference structure");
}
else
{
dist = new JuryDistance(dcd, alignFileName, true, profileName, refJuryProfile);
}
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(dcd, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(dcd, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(dcd, alignFileName, jury1d, refJuryProfile);
break;
}
dist.InitMeasure();
return(dist);
}
static void StartJobsAsymmetricPair(AsymmetricFusionFlags options)
{
List <string> files1 = GetPdbFiles("./", options.PeptideRegex1).ToList();
List <string> files2 = GetPdbFiles("./", options.PeptideRegex2).ToList();
ThreadSafeJobCounter sharedCounter = new ThreadSafeJobCounter();
sharedCounter.Total = files1.Count * files2.Count;
Console.WriteLine("\nUsing the following files for unit 1:");
files1.ForEach(file => Console.WriteLine(file));
Console.WriteLine("\nUsing the following files for unit 2:");
files2.ForEach(file => Console.WriteLine(file));
// Parse n-peptide and offset it to positive Z
foreach (string file1 in files1)
{
string pdbCode1 = PdbQuick.CodeFromFilePath(file1);
IChain peptide1 = PdbQuick.ChainFromFileOrCode(file1);
peptide1.Translate(-Rmsd.GetBackboneCentroid(peptide1));
// Parse c-peptide and offset it to positive Z
foreach (string file2 in files2)
{
string pdbCode2 = PdbQuick.CodeFromFilePath(file2);
IChain peptide2 = PdbQuick.ChainFromFileOrCode(file2);
peptide2.Translate(-Rmsd.GetBackboneCentroid(peptide2));
if (peptide1 == null || peptide2 == null)
{
Console.WriteLine("Pdb parsing failed for one of [{0}, {1}]", file1, file2);
continue;
}
JobStartParamsAsymmetricPair startParams = new JobStartParamsAsymmetricPair();
startParams.OutputPrefix = "PAIR";
startParams.PdbCodeN = pdbCode1;
startParams.PdbCodeC = pdbCode2;
startParams.PeptideN = peptide1;
startParams.PeptideC = peptide2;
startParams.RangeN = options.Range1 != null ? (Range)options.Range1 : new Range(0, peptide1.Count - 1);
startParams.RangeC = options.Range2 != null ? (Range)options.Range2 : new Range(0, peptide2.Count - 1);
startParams.TopX = options.TopX;
startParams.Counter = sharedCounter; // Shared counter across queued jobs
Debug.Assert(startParams.Validate(), "JobStartParamsAsymmetricPair validation failure");
_threadCountSemaphore.WaitOne();
sharedCounter.IncrementQueued();
Console.WriteLine("Queuing triplet [Bundle {0}]:[Bundle {1}], {2:F2} % ({3}/{4})", pdbCode1, pdbCode2, startParams.Counter.PercentQueued, startParams.Counter.Queued, startParams.Counter.Total);
Thread thread = new Thread(new ParameterizedThreadStart(RunJobAsymmetricPair));
thread.Start(startParams);
}
}
}
public static IEnumerable <FusionDesignInfo> GetSplices(IChain nPeptide, Range nAllowedSpliceRange, IChain cPeptide, Range cAllowedSpliceRange, int topX = DefaultTopX)
{
List <FusionDesignInfo> splices = new List <FusionDesignInfo>();
int minAlignmentLength = 8;
float maxRmsd = 0.25f;
// Find all alignments and remove those that are not between the desired ranges
// If this becomes a bottleneck, could specify allowed alignment ranges
List <SequenceAlignment> alignments = Fusion.GetAlignmentsPreservingFullSsBlocks(nPeptide, cPeptide, SS.Helix, minAlignmentLength, maxRmsd);
alignments.RemoveAll(a => !(nAllowedSpliceRange.Start <= a.Range1.Start && a.Range1.End <= nAllowedSpliceRange.End));
alignments.RemoveAll(a => !(cAllowedSpliceRange.Start <= a.Range2.Start && a.Range2.End <= cAllowedSpliceRange.End));
foreach (SequenceAlignment alignment in alignments)
{
Matrix alignmentTransform = Rmsd.GetRmsdTransformForResidues(nPeptide, alignment.Range1.Start, alignment.Range1.End, cPeptide, alignment.Range2.Start, alignment.Range2.End);
IChain copy1 = new Chain(nPeptide);
IChain copy2 = new Chain(cPeptide);
copy1.Transform(alignmentTransform);
IChain[] clashCheckPeptides = new IChain[] { copy1, copy2 };
if (Clash.GetInterSetBackboneClashes(clashCheckPeptides, new int[] { 0, alignment.Range2.End + 1 }, new int[] { alignment.Range1.Start - 1, copy2.Count - 1 }))
{
continue;
}
// Create the spliced peptide
IChain splicedPeptide = Fusion.GetChain(
new IChain[] { copy1, copy2 },
new SequenceAlignment[] { alignment },
new IEnumerable <int>[] { new int[] { }, new int[] { } });
// Save it
FusionDesignInfo spliceInfo = new FusionDesignInfo();
Range[] originalRanges = null;
Range[] finalRanges = null;
Fusion.GetIdentityRanges(clashCheckPeptides, new SequenceAlignment[] { alignment }, out originalRanges, out finalRanges);
spliceInfo.Peptide = splicedPeptide;
spliceInfo.OriginalChains = new IChain[] { nPeptide, cPeptide };
spliceInfo.PdbOutputChains = new IChain[] { splicedPeptide, copy1, copy2 };
spliceInfo.ImmutablePositions = new int[] { };
spliceInfo.IdentityRanges = finalRanges;
spliceInfo.OriginalRanges = originalRanges;
splices.Add(spliceInfo);
splices.Sort((a, b) => b.Score.CompareTo(a.Score));
if (splices.Count > topX)
{
splices.RemoveAt(topX);
}
}
return(splices);
}
DistanceMeasure PrepareDistance(DistanceMeasures distance,List <string> targets,string alignFile,string profileName)
{
DistanceMeasure dist=null;
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, alignFile, false, profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, alignFile, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, alignFile, false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, alignFile, false);
break;
}
dist.InitMeasure();
return dist;
}
private StatClust Calc(ClusterOutput outp, bool flag)
{
List <string> five = new List <string>();
List <string> listFiles = new List <string>();
//if (outp == null || outp.clusters == null)
// return null;
if (outp == null || outp.dirName == null)
{
return(null);
}
string [] aux = outp.dirName.Split(Path.DirectorySeparatorChar);
string native = aux[aux.Length - 1] + ".pdb";
string dirM = "";
for (int i = 0; i < aux.Length - 1; i++)
{
dirM += aux[i] + Path.DirectorySeparatorChar;
}
native = dirM + native;
if (!File.Exists(native))
{
return(null);
}
five.Add(native);
jury1D jury;
if (outp.clusters != null)
{
outp.clusters.Sort((a, b) => b.Count.CompareTo(a.Count));
int end = outp.clusters.Count;
if (outp.clusters.Count > 5)
{
end = 5;
}
for (int i = 0; i < end; i++)
{
listFiles.Clear();
foreach (var item in outp.clusters[i])
{
listFiles.Add(outp.dirName + Path.DirectorySeparatorChar + item);
}
//
//
//Sift sift = new Sift(listFiles);
//ClusterOutput oo = sift.Shape();
if (flag)
{
DistanceMeasure distRmsd = new Rmsd(listFiles, "", false, uQlustCore.PDB.PDBMODE.ONLY_CA);
distRmsd.InitMeasure();
string strName = distRmsd.GetReferenceStructure(outp.clusters[i]);
five.Add(outp.dirName + Path.DirectorySeparatorChar + strName);
}
else
{
jury = new jury1D();
//jury.PrepareJury(listFiles, "", "Z:\\dcd\\SS3_SA9_jury_internal.profiles");
ClusterOutput oo = jury.JuryOptWeights(outp.clusters[i]);
if (oo == null)
{
continue;
}
five.Add(outp.dirName + Path.DirectorySeparatorChar + oo.juryLike[0].Key);
}
//five.Add(outp.dirName + Path.DirectorySeparatorChar + outp.clusters[i][0]);
}
}
if (outp.hNode != null)
{
int end;
List <List <string> > cli = outp.hNode.GetClusters(10);
cli.Sort((a, b) => b.Count.CompareTo(a.Count));
outp.clusters = new List <List <string> >();
end = cli.Count;
if (cli.Count > 5)
{
end = 5;
}
for (int i = 0; i < end; i++)
{
// listFiles.Clear();
//foreach (var item in cli[i])
//{
//listFiles.Add(
//}
listFiles.Clear();
foreach (var item in cli[i])
{
listFiles.Add(outp.dirName + Path.DirectorySeparatorChar + item);
}
jury = new jury1D();
jury.PrepareJury(listFiles, "", "C:\\data\\dcd\\SS8_SA3_jury_internal.profiles");
outp.clusters.Add(cli[0]); //jury
ClusterOutput oo = jury.JuryOptWeights(cli[i]);
if (oo == null)
{
continue;
}
five.Add(outp.dirName + Path.DirectorySeparatorChar + cli[i][0]);
//five.Add(outp.dirName + Path.DirectorySeparatorChar + strName);
}
}
if (outp.juryLike != null)
{
int end = outp.juryLike.Count;
if (outp.juryLike.Count > 5)
{
end = 5;
}
for (int i = 0; i < end; i++)
{
five.Add(outp.dirName + Path.DirectorySeparatorChar + outp.juryLike[i].Key);
}
}
// DistanceMeasure dist;
// dist = new Rmsd(five, "", false, PDB.PDBMODE.ONLY_CA);
// dist = new MaxSub(five, "", false);
Dictionary <string, double> cc = ReadScore(aux[aux.Length - 1]);
if (cc == null)
{
return(null);
}
StatClust stCLust = new StatClust();
string[] tt1 = native.Split(Path.DirectorySeparatorChar);
stCLust.native = tt1[tt1.Length - 1];
for (int i = 1; i < five.Count; i++)
{
string[] tt2 = five[i].Split(Path.DirectorySeparatorChar);
// double rmsd = dist.GetDistance(tt1[tt1.Length-1], tt2[tt2.Length-1]) /100.0;
double rmsd = 0;
if (cc.ContainsKey(tt2[tt2.Length - 1]))
{
rmsd = cc[tt2[tt2.Length - 1]];
}
if (rmsd > stCLust.rmsd)
{
if (outp.juryLike != null)
{
stCLust.size = outp.juryLike.Count;
}
else
{
stCLust.size = outp.clusters[i - 1].Count;
}
stCLust.rmsd = rmsd;
string[] dd = five[i].Split(Path.DirectorySeparatorChar);
stCLust.reference = dd[dd.Length - 1];
}
}
if (stCLust.rmsd < 1000)
{
avrSum += stCLust.rmsd;
avrCount++;
}
if (outp.hNode != null)
{
outp.clusters.Clear();
outp.clusters = null;
}
return(stCLust);
}
static void StartJobsAngleCXRCX(CxrcxFusionFlags options)
{
SymmetryBuilder symmetry = SymmetryBuilderFactory.CreateFromSymmetryName(options.Architecture);
List <string> filesOligomer1 = GetPdbFiles(Directory.GetCurrentDirectory(), options.OligomerRegex1).ToList();
List <string> filesOligomer2 = GetPdbFiles(Directory.GetCurrentDirectory(), options.OligomerRegex2).ToList();
List <string> filesRepeat = GetPdbFiles(Directory.GetCurrentDirectory(), options.RepeatRegex).ToList();
ThreadSafeJobCounter sharedCounter = new ThreadSafeJobCounter();
sharedCounter.Total = filesOligomer1.Count * filesOligomer2.Count * filesRepeat.Count;
Console.WriteLine("Using the following spacer repeat proteins:");
filesRepeat.ForEach(file => Console.WriteLine(file));
Console.WriteLine("\nUsing the following files for h**o-oligomer 1:");
filesOligomer1.ForEach(file => Console.WriteLine(file));
Console.WriteLine("\nUsing the following files for h**o-oligomer 2:");
filesOligomer2.ForEach(file => Console.WriteLine(file));
float angleDegrees = (float)VectorMath.GetAngleDegrees(symmetry.GetPrincipalCoordinateSystem(options.UnitId1).UnitX, Vector3.Zero, symmetry.GetPrincipalCoordinateSystem(options.UnitId2).UnitX);
Console.WriteLine("Angle for {0}:{1}:{2} calculated to: {3:F4}", options.Architecture, options.UnitId1, options.UnitId2, angleDegrees);
// Parse oligomer 1 and offset it to positive Z
foreach (string fileOligomer1 in filesOligomer1)
{
string pdbCodeOligomer1 = PdbQuick.CodeFromFilePath(fileOligomer1);
IChain peptide1 = PdbQuick.ChainFromFileOrCode(fileOligomer1);
if (peptide1 == null)
{
Console.WriteLine("Pdb parsing failed for {0}", fileOligomer1);
continue;
}
peptide1.Translate(new Vector3(0, 0, 20 - Rmsd.GetBackboneCentroid(peptide1).Z));
// Parse oligomer 2 and offset it to positive Z
foreach (string fileOligomer2 in filesOligomer2)
{
string pdbCodeOligomer2 = PdbQuick.CodeFromFilePath(fileOligomer2);
IChain peptide2 = PdbQuick.ChainFromFileOrCode(fileOligomer2);
if (peptide2 == null)
{
Console.WriteLine("Pdb parsing failed for {0}", fileOligomer2);
continue;
}
peptide2.Translate(new Vector3(0, 0, 20 - Rmsd.GetBackboneCentroid(peptide2).Z));
// Parse the repeat and offset it to positive Z
foreach (string fileRepeat in filesRepeat)
{
IChain repeat = PdbQuick.ChainFromFileOrCode(fileRepeat);
string pdbCodeRepeat = PdbQuick.CodeFromFilePath(fileRepeat);
if (repeat == null)
{
Console.WriteLine("Pdb parsing failed for {0}", repeat);
continue;
}
repeat.Translate(new Vector3(0, 0, 20 - Rmsd.GetBackboneCentroid(repeat).Z));
JobStartParamsCXRCX startParams = new JobStartParamsCXRCX();
// things taken directly from user options
startParams.OutputPrefix = options.Architecture + "-" + options.UnitId1 + "-" + options.UnitId2;
startParams.UnitId1 = options.UnitId1;
startParams.UnitId2 = options.UnitId2;
startParams.ChainCount1 = options.Oligomerization1;
startParams.ChainCount2 = options.Oligomerization2;
startParams.TopX = options.TopX;
// everything else:
startParams.Symmetry = SymmetryBuilderFactory.CreateFromSymmetryName(options.Architecture);
startParams.PdbCodeBundle1 = pdbCodeOligomer1;
startParams.PdbCodeBundle2 = pdbCodeOligomer2;
startParams.PdbCodeRepeat = pdbCodeRepeat;
startParams.Cx1 = peptide1;
startParams.Cx2 = peptide2;
startParams.Repeat = repeat;
startParams.AngleDegrees = angleDegrees;
startParams.Counter = sharedCounter; // Shared counter across queued jobs
Debug.Assert(startParams.Validate(), "JobStartParamsCXRCX validation failure");
// Wait for free threads
_threadCountSemaphore.WaitOne();
sharedCounter.IncrementQueued();
// Start the job
Thread thread = new Thread(new ParameterizedThreadStart(RunJobAngleCXRCX));
thread.Start(startParams);
Console.WriteLine("Queuing triplet [Bundle {0}]:[Repeat {1}]:[Bundle {2}], {3:F2} degrees, {4:F2} % ({5}/{6})", pdbCodeOligomer1, pdbCodeRepeat, pdbCodeOligomer2, angleDegrees, startParams.Counter.PercentQueued, startParams.Counter.Queued, startParams.Counter.Total);
}
}
}
}
private void SaveAll()
{
DistanceMeasure dist = null;
Settings set = new Settings();
set.Load();
string[] files;
if (set.extension.Length > 0)
{
files = Directory.GetFiles(directory, set.extension);
}
else
{
files = Directory.GetFiles(directory);
}
List <string> fileList = new List <string>(2);
StreamWriter r = new StreamWriter(saveFile);
maxV = files.Length;
foreach (var item in files)
{
fileList.Clear();
fileList.Add(item);
fileList.Add(markStructure);
switch (distanceControl1.distDef)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileList, null, false, distanceControl1.profileName, distanceControl1.referenceProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileList, null, false, distanceControl1.CAtoms, null);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileList, null, false, null);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(fileList, null, false, null);
break;
}
dist.InitMeasure();
try
{
int val = dist.GetDistance(Path.GetFileName(fileList[1]), Path.GetFileName(fileList[0]));
currentV++;
if (val < int.MaxValue)
{
r.WriteLine(fileList[0] + " " + (double)val / 100);
}
else
{
r.WriteLine(fileList[0] + " NaN");
}
}
catch (Exception ex)
{
exc = ex;
}
}
r.Close();
currentV = maxV;
}
private void button2_Click(object sender, EventArgs e)
{
string[] aux;
if (checkBox1.Checked)
{
if (jury1DSetup1.profileName == null || jury1DSetup1.profileName.Length == 0)
{
MessageBox.Show("Profile name for 1djury must be specified!");
this.DialogResult = DialogResult.None;
return;
}
jury1D jury = new jury1D();
jury.PrepareJury(structures, "", jury1DSetup1.profileName);
List <string> prep = new List <string>();
foreach (var item in structures)
{
aux = item.Split(Path.DirectorySeparatorChar);
prep.Add(aux[aux.Length - 1]);
}
ClusterOutput oc = jury.JuryOptWeights(prep);
for (int i = 0; i < selectBest1.bestNumber; i++)
{
bestJuryStructures.Add(oc.juryLike[i].Key);
}
}
this.DialogResult = DialogResult.OK;
if (selectBest1.getFileName != null && File.Exists(selectBest1.getFileName))
{
DistanceMeasures measure = selectBest1.measure;
structures.Add(selectBest1.getFileName);
DistanceMeasure dist = null;
switch (measure)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(structures, "", false, selectBest1.hammingProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(structures, "", false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(structures, "", false, selectBest1.CAtoms);
break;
}
List <KeyValuePair <string, int> > distList = new List <KeyValuePair <string, int> >();
aux = selectBest1.getFileName.Split(Path.DirectorySeparatorChar);
dist.InitMeasure();
string native = aux[aux.Length - 1];
foreach (var item in structures)
{
aux = item.Split(Path.DirectorySeparatorChar);
int val = dist.GetDistance(native, aux[aux.Length - 1]);
distList.Add(new KeyValuePair <string, int>(aux[aux.Length - 1], val));
}
distList.Sort((firstPair, nextPair) =>
{
return(firstPair.Value.CompareTo(nextPair.Value));
});
for (int i = 0; i < selectBest1.bestNumber; i++)
{
bestStructures.Add(distList[i].Key);
}
}
}
private DistanceMeasure CreateMeasure(string processName, string dirName, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist = null;
switch (measure)
{
case DistanceMeasures.HAMMING:
if (alignFileName != null)
{
dist = new JuryDistance(alignFileName, jury1d, profileName, refJuryProfile);
}
else
{
dist = new JuryDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
}
break;
case DistanceMeasures.TANIMOTO:
if (alignFileName != null)
{
dist = new Tanimoto(alignFileName, jury1d, profileName, refJuryProfile);
}
else
{
dist = new Tanimoto(dirName, alignFileName, jury1d, profileName, refJuryProfile);
}
break;
case DistanceMeasures.COSINE:
if (alignFileName != null)
{
dist = new CosineDistance(alignFileName, jury1d, profileName, refJuryProfile);
}
else
{
dist = new CosineDistance(dirName, alignFileName, jury1d, profileName, refJuryProfile);
}
break;
case DistanceMeasures.RMSD:
if (dirName == null)
{
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
}
dist = new Rmsd(dirName, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
if (dirName == null)
{
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
}
dist = new MaxSub(dirName, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
if (dirName == null)
{
throw new Exception("RMSD and MAXSUB measures cannot be used for aligned profiles!");
}
dist = new GDT_TS(dirName, alignFileName, jury1d, refJuryProfile);
break;
}
return(dist);
}
