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 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); }
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); }
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 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); }