public void test3()
{
// Type type = Type.GetType("StringHasseNode");
HasseDiagram HDM = new HasseDiagram(HasseNodeFactory.NodeType.STRING);
System.Random rnd = new System.Random(1);
//HasseNodeCollection Elements1 = new HasseNodeCollection();
//HasseNodeCollection elements = new HasseNodeCollection();
StringHasseNode Node1 = new StringHasseNode("CA*", HasseNode.HasseNodeTypes.REAL, "");
StringHasseNode Node2 = new StringHasseNode("DCCCA*", HasseNode.HasseNodeTypes.REAL, "");
bool test = Node2.IsLargerThan(Node1);
System.Diagnostics.Debug.Assert(test);
System.Collections.Queue q = new System.Collections.Queue();
for (int i = 1; i <= 1000; i++)
{
string buf = "";
int strLen = Convert.ToInt32(rnd.Next(1, 10));
//random string length
for (int j = 1; j <= strLen; j++)
{
float r = rnd.Next(0, 4);
//random character choice '4
switch ((Int32)Math.Truncate(r))
{
case 0:
buf += "A";
break;
case 1:
buf += "B";
break;
case 2:
buf += "C";
break;
case 3:
buf += "D";
break;
default:
throw new Exception("error in Test3");
}
}
HDM.AddNode(buf);
}
System.Diagnostics.Debug.WriteLine(HasseDiagramStats.Report(HDM.HasseDiagramNodes, HDM.RootNode));
}
public void test6()
{
HasseDiagram HDM = new HasseDiagram(HasseNodeFactory.NodeType.STRING);
HasseNodeCollection elements = new HasseNodeCollection();
HDM.AddNode("XA0");
HDM.AddNode("XA1");
HDM.AddNode("XB0");
HDM.AddNode("XB1");
HDM.AddNode("YA0");
HDM.AddNode("YA1");
HDM.AddNode("YB0");
HDM.AddNode("YB1");
// HDM.DeleteNodesWithOneCover();
DotFileWriter DW = new DotFileWriter(HDM.HasseDiagramNodes, "C:\\temp\\testdotfile.dot");
DW.WriteDotFile();
//TopologicalSort.topsort(HDM.AllHasseNodes, true);
HDM.Draw();
}
public void test5()
{
HasseDiagram HDM = new HasseDiagram(HasseNodeFactory.NodeType.STRING);
System.Random rnd = new System.Random(1);
HasseNodeCollection elements = new HasseNodeCollection();
for (int i = 1; i <= 500; i++)
{
string buf = "";
int strLen = Convert.ToInt32(rnd.Next(1, 500));
//8
//random string length
for (int j = 1; j <= strLen; j++)
{
buf += "A";
}
HDM.AddNode(buf);
}
//HDM.BFGTopOrder.DebugReport()
//TopologicalSort.topsort(HDM.AllHasseNodes ,true);
HDM.Draw();
}
public static void chemtest()
{
//IndigoTests T = new IndigoTests();
//T.test1();
Indigo indigo = new Indigo();
/*
* ChemHasseNode L_ALA = new ChemHasseNode("N[C@@H](C)C(=O)O", HasseNode.HasseNodeTypes.REAL, allNodes);
* ChemHasseNode D_ALA = new ChemHasseNode("N[C@H](C)C(=O)O", HasseNode.HasseNodeTypes.REAL, allNodes);
* d=L_ALA.GetDifferenceString (D_ALA);
* d = D_ALA.GetDifferenceString(L_ALA);
*/
// HasseDiagram HDM = new HasseDiagram(HasseNodeFactory.NodeType.CHEM );
HasseDiagram HDM = new HasseDiagram(HasseNodeFactory.NodeType.FINGERPRINTCHEM);
HasseNodeCollection elements = new HasseNodeCollection();
//ChemHasseNode A = (ChemHasseNode)HDM.AddNode("c1ccccccc[nH]1"); // azonine
//ChemHasseNode B = (ChemHasseNode)HDM.AddNode("C12=C(C=NC=C1)NC1=C2C=CC=C1"); // pyrido indol
//ChemHasseNode C = (ChemHasseNode)HDM.AddNode("c1cccc2[nH]ccc21"); // indol
//FingerprintChemHasseNode A = (FingerprintChemHasseNode)HDM.AddNode("C"); //
//FingerprintChemHasseNode B = (FingerprintChemHasseNode)HDM.AddNode("CC"); //
//FingerprintChemHasseNode C = (FingerprintChemHasseNode)HDM.AddNode("CN"); //
// ChemHasseNode A = (ChemHasseNode)HDM.AddNode(@"[NH3+]C");
//ChemHasseNode B = (ChemHasseNode)HDM.AddNode(@"[NH2]CC");
//bool tst = A.IsLargerThan(B);
//tst = B.IsLargerThan(A);
//A.GetMaxCommonFragments(A, B);
//tst = A.IsLargerThan(C);
//tst = C.IsLargerThan(A);
// pyridoindol larger than azonine
System.Threading.Thread.CurrentThread.Priority = System.Threading.ThreadPriority.BelowNormal;
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
sw.Start();
int count = 0;
//foreach (IndigoObject item in indigo.iterateSDFile(@"C:\temp\benzodiazepines.sdf"))
//foreach (IndigoObject item in indigo.iterateSDFile(@"C:\temp\monoamtrain_x.sdf"))
//foreach (IndigoObject item in indigo.iterateSDFile(@"C:\HassePub\Datasets\Jorissen\compounds_1st.sdf"))
//foreach (IndigoObject item in indigo.iterateSDFile(@"C:\HassePub\Datasets\benzodiazepines_v4.sdf"))
// foreach (IndigoObject item in indigo.iterateSDFile(@"C:\HassePub\Datasets\small_set.sdf"))
// foreach (IndigoObject item in indigo.iterateSDFile(@"C:\HassePub\Datasets\chembl_pyridines.sdf"))
//foreach (IndigoObject item in indigo.iterateSDFile(@"C:\HassePub\Datasets\ChEBI_anilines_480-500.sdf"))
//foreach (IndigoObject item in indigo.iterateSDFile(@"C:\HassePub\Datasets\ChEBI_valines.sdf"))
foreach (IndigoObject item in indigo.iterateSDFile(@"C:\HassePub\Datasets\ChEBI_valines_v21.sdf")) // in pub
{
if (item.isChiral() == false)
{
continue;
}
count++;
//System.Diagnostics.Debugger.Break();
if (count > 24)
{
break; //24 for valines in pub
}
// HasseNode N = HDM.CreateNewNode(item);
//if (N.IsValid())
//{
System.Diagnostics.Stopwatch sw2 = new System.Diagnostics.Stopwatch();
sw2.Start();
try
{
HasseNode N = HDM.CreateNewNode(item.molfile());
if (item.hasProperty("CHEMBL ID"))
{
string ChemblID = item.getProperty("CHEMBL ID");
N.SetName(ChemblID);
}
else if (item.hasProperty("ChEBI ID"))
{
string ChebiID = item.getProperty("ChEBI ID");
N.SetName(ChebiID);
}
else
{
N.SetName(count.ToString());
}
HDM.AddNode(N);
System.Diagnostics.Debug.WriteLine("--- " + N.KeyString);
}
catch (Exception ex)
{
System.Diagnostics.Debug.WriteLine("WARNING: could not add node: " + ex.ToString());
}
}
List <HasseNode> subset = new List <HasseNode>();
/*
* foreach (HasseNode N in HDM.HasseDiagramNodes.Values)
* {
* if (N.NodeType != HasseNode.HasseNodeTypes.ROOT)
* {
* float weight = N.Weight();
* N.SetName("w=" + weight.ToString());
* float w = 5F * weight / 29F;
* if (w < 1) w = 1F;
* if (w > 3.5) w = 3.5F;
* // N.CreateImage(w);
* N.CreateImage();
* //if (weight > 20) subset.Add(N);
* }
*
* }
*/
//DotFileWriter DW = new DotFileWriter(HDM.HasseDiagramNodes, subset, "C:\\temp\\testdotfile.dot");
DotFileWriter DW = new DotFileWriter(HDM.HasseDiagramNodes, "C:\\temp\\testdotfile.dot");
int cnt = 0;
foreach (HasseNode N in HDM.HasseDiagramNodes.Values)
{
if ((N.GetType() == typeof(ChemHasseNode) || N.GetType() == typeof(FingerprintChemHasseNode)) && N.NodeType != HasseNode.HasseNodeTypes.ROOT)
{
cnt++;
N.SetName(cnt.ToString());
if (N.GetType() == typeof(ChemHasseNode))
{
((ChemHasseNode )N).CreateImage();
}
if (N.GetType() == typeof(FingerprintChemHasseNode))
{
((FingerprintChemHasseNode)N).CreateImage();
}
}
}
DW.SetLabelsToNumericSequence();
DW.SetDrawingColors();
DW.LabelMode = labelMode.NO_LABELS; // for figure 5
DW.directionMode = graphDirection.RIGHT;
//DW.LabelMode = labelMode.USE_NODE_LABEL;
//DW.LabelMode = labelMode.USE_NODE_ID;
DW.UseImage = true;
DW.WriteEdgeLabels = false;
sw.Stop();
System.Diagnostics.Debug.WriteLine(sw.ElapsedMilliseconds.ToString());
DW.WriteDotFile();
System.Diagnostics.Debug.WriteLine("Nodes: " + HDM.HasseDiagramNodes.Count());
System.Diagnostics.Debug.WriteLine("Diffs: " + HDM.DifferenceNodes.Count());
System.Diagnostics.Debug.WriteLine("Hash: " + HDM.RootNode.HashString());
foreach (HasseNode N in HDM.HasseDiagramNodes.Values)
{
if (N.HasNodeType(HasseNode.HasseNodeTypes.FRAGMENT))
{
;
}
// System.Diagnostics.Debug.WriteLine(N.KeyString + " " + N.Weight().ToString() );
}
System.Diagnostics.Debug.WriteLine(HasseDiagramStats.Report(HDM.HasseDiagramNodes, HDM.RootNode));
}
public static void test4(string filename)
{
HasseDiagram HDM = new HasseDiagram(HasseNodeFactory.NodeType.STRING);
HasseNodeCollection elements = new HasseNodeCollection();
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
sw.Start();
System.IO.FileStream fs = new System.IO.FileStream(filename, System.IO.FileMode.Open, System.IO.FileAccess.Read);
System.IO.TextReader rdr = new System.IO.StreamReader(fs);
int maxCount = 200000;
int count = 0;
List <string> Words = new List <string>();
do
{
//if (count >= maxCount) break;
char[] delim = { ' ', ',', '.' };
string line = rdr.ReadLine();
if (line == null)
{
break;
}
string[] words = line.Split(delim);
for (int i = 0; i < words.Length; i++)
{
count += 1;
string w = words[i];
w = w.Trim();
w = w.ToLower();
w = w.Replace("*", "");
w = w.Replace("(", "");
w = w.Replace(")", "");
w = w.Replace("]", "");
w = w.Replace("[", "");
w = w.Replace("„", "");
w = w.Replace(":", "");
w = w.Replace("\"", "");
if (!string.IsNullOrEmpty(w))
{
Words.Add(w); // Add to list for insertion below
}
}
} while (true);
// 'randomise' order
StringHashComparer shc = new StringHashComparer();
Words.Sort(shc);
//65533
count = 0;
foreach (string Word in Words)
{
count += 1;
System.Diagnostics.Debug.WriteLine(Word);
foreach (char c in Word.ToCharArray())
{
// System.Diagnostics.Debug.WriteLine(((int)c).ToString ());
}
HDM.AddNode(Word);
if (count >= maxCount)
{
break;
}
}
fs.Close();
sw.Stop();
System.Diagnostics.Debug.WriteLine("Total time: " + ((double)sw.ElapsedMilliseconds / 1000).ToString() + " seconds");
System.Diagnostics.Debug.WriteLine("Total time: " + ((double)sw.ElapsedTicks / System.Diagnostics.Stopwatch.Frequency).ToString() + " seconds");
HDM.ContractChains2();
HDM.HasseDiagramNodes.Sort();
foreach (HasseNode n in HDM.HasseDiagramNodes.Values)
{
System.Diagnostics.Debug.WriteLine(n.KeyString);
}
DotFileWriter DW = new DotFileWriter(HDM.HasseDiagramNodes, "C:\\Users\\ssampath\\Documents\\HasseDiagramOutput\\testdotfile.dot");
DW.LabelMode = labelMode.USE_NODE_KEY;
DW.WriteDotFile();
System.Diagnostics.Debug.WriteLine(HDM.RootNode.HashString());
System.Diagnostics.Debug.WriteLine(HDM.HasseDiagramNodes.Count.ToString() + " Diagram objects");
System.Diagnostics.Debug.WriteLine(HDM.DifferenceNodes.Count.ToString() + " Difference objects");
//System.Diagnostics.Debug.WriteLine(HasseDiagramStats.Report(HDM.HasseDiagramNodes));
}
