public override bool IsLargerThan(HasseNode smallobj)
{
if (this.HasNodeType(HasseNodeTypes.ROOT))
{
return(false);
}
if (smallobj.HasNodeType(HasseNodeTypes.ROOT))
{
return(true);
}
bool retval = this.hFingerprint.IsLargerThan(((FingerprintChemHasseNode )smallobj).hFingerprint);
// if (retval == true) System.Diagnostics.Debugger.Break();
return(retval);
}
public override bool IsLargerThan(HasseNode smallobj)
{
if (smallobj.HasNodeType(HasseNode.HasseNodeTypes.MAX_COMMON_FRAGMENT))
{
System.Diagnostics.Debugger.Break();
}
if (smallobj.NodeType == HasseNode.HasseNodeTypes.ROOT)
{
return(true);
}
if (this.NodeType == HasseNode.HasseNodeTypes.ROOT)
{
return(false);
}
bool IsPossiblyLargerThanByFingerprint = ContainsFingerprintOf(((ChemHasseNode)smallobj).fingerprint());
if (TrustFingerprints)
{
if (IsPossiblyLargerThanByFingerprint)
{
;
} // is likely to be larger, but we are not sure, needs to be checked
else
{
return(false); // if fingerprints work as they should we are guaranteed that IsLargerThan must be false
}
}
// todo take a away those checks that fingerprints work
if (IsPossiblyLargerThanByFingerprint)
{ // can be a substructure match but need not be
//if (matcher.countMatches(smallMol) == 0)
//{
// System.Diagnostics.Debug.WriteLine("a fingerprint contained in b fingerprint - but a was not substruc of b");
// System.Diagnostics.Debug.WriteLine("a\t" + smallMol.smiles());
// System.Diagnostics.Debug.WriteLine("b\t" + molecule.smiles());
//}
}
else
{
//if (matcher.countMatches(smallMol) != 0)
// System.Diagnostics.Debugger.Break(); //we have a match where fp says we certainly have not!
}
return(ChemObject.IsLargerThan(smallobj));
}
public override bool IsLargerThan(HasseNode smallobj)
{
if (this.HasNodeType(HasseNodeTypes.ROOT)) { return false; }
if (smallobj.HasNodeType(HasseNodeTypes.ROOT)) { return true; }
bool retval= this.hFingerprint.IsLargerThan(((FingerprintChemHasseNode )smallobj).hFingerprint );
// if (retval == true) System.Diagnostics.Debugger.Break();
return retval;
}
private bool addNode(HasseNode newNode, HasseNode[] AboveTheseNodes, HasseNode[] BelowTheseNodes)
{
// should return true if node was inserted
// or false if corresponding node already exist
bool debug = Convert.ToBoolean(DEBUGLEVEL & LOG_INSERTIONS);
bool dbgTimings = Convert.ToBoolean(DEBUGLEVEL & LOG_ALL_TIMINGS);
sw.Reset();
sw.Start();
if (newNode.Size() < MINIMUM_FRAGMENT_SIZE) return false;
// do not add identical objects
if (HasseDiagramNodes.ContainsKey(newNode.KeyString))
{
// is already there - we will update type, set name, redraw image, then return.
HasseDiagramNodes[newNode.KeyString].AddNodeType(newNode.NodeType);
if(newNode.HasNodeType ( HasseNode.HasseNodeTypes.REAL )){
string n = newNode.GetName();
HasseDiagramNodes[newNode.KeyString].SetName(n);
//if (CREATE_NODE_IMAGE) HasseDiagramNodes[newNode.KeyString].CreateImage();
System.Diagnostics.Debug.WriteLineIf(debug, " Skipping add of " + newNode.KeyString);
}
return false;
}
//if (CREATE_NODE_IMAGE) newNode.CreateImage();
CountAdditions += 1;
if (DEBUGLEVEL > 0)
{
System.Diagnostics.Debug.WriteLine("Add Node " + newNode.KeyString + " " + CountAdditions.ToString());
}
// loop elements of new object
/*
foreach (HasseNode Element in newNode.getElementarySubobjects().Values)
{
if (USE_ELEMENTS)
{
// add to diagram nodes list if not already there
if (!HasseDiagramNodes.ContainsKey(Element.KeyString))
{
HasseDiagramNodes.Add(Element.KeyString, Element);
//Element.CreateImage();
this.MakeEdge(RootNode, Element);
}
}
// add to elements collection if not there already
if (!ElementaryHasseNodes.ContainsKey(Element.KeyString))
ElementaryHasseNodes.Add(Element.KeyString, Element);
}
*/
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks add 1 (init) " + sw.ElapsedTicks.ToString());
sw.Reset();
sw.Start();
System.Diagnostics.Debug.WriteLineIf(debug, "=== Start LUB and GLB for " + newNode.KeyString + " ===");
if (CountAdditions == -1)
System.Diagnostics.Debugger.Break();
HasseNodeCollection NodesInGreatestLowerBound = null;
HasseNodeCollection NodesInLeastUpperBound = null;
FindLUBAndGLB(newNode, ref NodesInLeastUpperBound, ref NodesInGreatestLowerBound);
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 2 (got lub and glb) " + sw.ElapsedTicks.ToString());
sw.Reset();
sw.Start();
System.Diagnostics.Debug.WriteLineIf(debug, "=== Done LUB and GLB =======");
List<HasseEdge> NewlyFormedEdges = InsertNodeBetweenGlbAndLub(
newNode, NodesInLeastUpperBound, NodesInGreatestLowerBound, debug);
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 3 (inserted new) " + sw.ElapsedTicks.ToString());
sw.Reset();
sw.Start();
if (Convert.ToBoolean(CHECK_LEVEL & CHECK_ALL))
newNode.validate();
if (MAKE_MCS_AT_ONCE) { FindCommonFragments(newNode); }
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 4 (made MCS)" + sw.ElapsedTicks.ToString());
// The node may be there already, just added, as element if it is both element and real
// if (!newNode.HasNodeType(HasseNode.HasseNodeTypes.ELEMENT))
HasseDiagramNodes.Add(newNode.KeyString, newNode);
return true;
}
private bool addNode(HasseNode newNode, HasseNode[] AboveTheseNodes, HasseNode[] BelowTheseNodes)
{
// should return true if node was inserted
// or false if corresponding node already exist
bool debug = Convert.ToBoolean(DEBUGLEVEL & LOG_INSERTIONS);
bool dbgTimings = Convert.ToBoolean(DEBUGLEVEL & LOG_ALL_TIMINGS);
sw.Reset();
sw.Start();
if (newNode.Size() < MINIMUM_FRAGMENT_SIZE)
{
return(false);
}
// do not add identical objects
if (HasseDiagramNodes.ContainsKey(newNode.KeyString))
{
// is already there - we will update type, set name, redraw image, then return.
HasseDiagramNodes[newNode.KeyString].AddNodeType(newNode.NodeType);
if (newNode.HasNodeType(HasseNode.HasseNodeTypes.REAL))
{
string n = newNode.GetName();
HasseDiagramNodes[newNode.KeyString].SetName(n);
//if (CREATE_NODE_IMAGE) HasseDiagramNodes[newNode.KeyString].CreateImage();
System.Diagnostics.Debug.WriteLineIf(debug, " Skipping add of " + newNode.KeyString);
}
return(false);
}
//if (CREATE_NODE_IMAGE) newNode.CreateImage();
CountAdditions += 1;
if (DEBUGLEVEL > 0)
{
System.Diagnostics.Debug.WriteLine("Add Node " + newNode.KeyString + " " + CountAdditions.ToString());
}
// loop elements of new object
/*
* foreach (HasseNode Element in newNode.getElementarySubobjects().Values)
* {
* if (USE_ELEMENTS)
* {
* // add to diagram nodes list if not already there
* if (!HasseDiagramNodes.ContainsKey(Element.KeyString))
* {
* HasseDiagramNodes.Add(Element.KeyString, Element);
* //Element.CreateImage();
* this.MakeEdge(RootNode, Element);
* }
* }
* // add to elements collection if not there already
* if (!ElementaryHasseNodes.ContainsKey(Element.KeyString))
* ElementaryHasseNodes.Add(Element.KeyString, Element);
* }
*/
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks add 1 (init) " + sw.ElapsedTicks.ToString());
sw.Reset();
sw.Start();
System.Diagnostics.Debug.WriteLineIf(debug, "=== Start LUB and GLB for " + newNode.KeyString + " ===");
if (CountAdditions == -1)
{
System.Diagnostics.Debugger.Break();
}
HasseNodeCollection NodesInGreatestLowerBound = null;
HasseNodeCollection NodesInLeastUpperBound = null;
FindLUBAndGLB(newNode, ref NodesInLeastUpperBound, ref NodesInGreatestLowerBound);
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 2 (got lub and glb) " + sw.ElapsedTicks.ToString());
sw.Reset();
sw.Start();
System.Diagnostics.Debug.WriteLineIf(debug, "=== Done LUB and GLB =======");
List <HasseEdge> NewlyFormedEdges = InsertNodeBetweenGlbAndLub(
newNode, NodesInLeastUpperBound, NodesInGreatestLowerBound, debug);
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 3 (inserted new) " + sw.ElapsedTicks.ToString());
sw.Reset();
sw.Start();
if (Convert.ToBoolean(CHECK_LEVEL & CHECK_ALL))
{
newNode.validate();
}
if (MAKE_MCS_AT_ONCE)
{
FindCommonFragments(newNode);
}
System.Diagnostics.Debug.WriteLineIf(dbgTimings, " ticks 4 (made MCS)" + sw.ElapsedTicks.ToString());
// The node may be there already, just added, as element if it is both element and real
// if (!newNode.HasNodeType(HasseNode.HasseNodeTypes.ELEMENT))
HasseDiagramNodes.Add(newNode.KeyString, newNode);
return(true);
}
private void WriteNode(HasseNode N)
{
//System.Diagnostics.Debug.WriteLine(((ChemHasseNode)N).GetName());
//DotFile.WriteLine("node[shape = rounded];");
DotFile.Write(DoubleQuoted(N.KeyString));
DotFile.Write(" ["); // start node attributes
switch (LabelMode)
{
case labelMode.NO_LABELS:
DotFile.Write(" label=\"\" "); //empty label
break;
case labelMode.USE_NODE_ID:
DotFile.Write(" label=" + DoubleQuoted(N.GetID().ToString()));
break;
case labelMode.USE_MOLNAME:
if (((ChemHasseNode)N).GetName() != "")
{
DotFile.Write(" label=" + DoubleQuoted(((ChemHasseNode)N).GetName()));
}
else
{
DotFile.Write(" label=" + DoubleQuoted(N.GetID().ToString()));
}
break;
case labelMode.USE_NODE_KEY:
// need not do anything, the node key is shown by default
break;
case labelMode.USE_NODE_LABEL:
DotFile.Write(" label=" + DoubleQuoted(N.LabelText));
break;
default:
throw new Exception("unhandled labelmode");
}
if (N.DrawingColor!="" ) DotFile.Write(" color=" + N.DrawingColor + " ");
if (UseImage && N.ImageFileName.Length > 0)
{
DotFile.Write(" image=\"" + N.ImageFileName + "\"");
}
if (N.HasNodeType (HasseNode.HasseNodeTypes.REAL) || N.NodeType == HasseNode.HasseNodeTypes.ROOT )
{ DotFile.Write(" shape=ellipse "); }
else
{ DotFile.Write(" shape=none "); }
DotFile.Write("] "); // end node attributes
DotFile.WriteLine(";");
}
private void WriteNode(HasseNode N)
{
//System.Diagnostics.Debug.WriteLine(((ChemHasseNode)N).GetName());
//DotFile.WriteLine("node[shape = rounded];");
DotFile.Write(DoubleQuoted(N.KeyString));
DotFile.Write(" ["); // start node attributes
switch (LabelMode)
{
case labelMode.NO_LABELS:
DotFile.Write(" label=\"\" "); //empty label
break;
case labelMode.USE_NODE_ID:
DotFile.Write(" label=" + DoubleQuoted(N.GetID().ToString()));
break;
case labelMode.USE_MOLNAME:
if (((ChemHasseNode)N).GetName() != "")
{
DotFile.Write(" label=" + DoubleQuoted(((ChemHasseNode)N).GetName()));
}
else
{
DotFile.Write(" label=" + DoubleQuoted(N.GetID().ToString()));
}
break;
case labelMode.USE_NODE_KEY:
// need not do anything, the node key is shown by default
break;
case labelMode.USE_NODE_LABEL:
DotFile.Write(" label=" + DoubleQuoted(N.LabelText));
break;
default:
throw new Exception("unhandled labelmode");
}
if (N.DrawingColor != "")
{
DotFile.Write(" color=" + N.DrawingColor + " ");
}
if (UseImage && N.ImageFileName.Length > 0)
{
DotFile.Write(" image=\"" + N.ImageFileName + "\"");
}
if (N.HasNodeType(HasseNode.HasseNodeTypes.REAL) || N.NodeType == HasseNode.HasseNodeTypes.ROOT)
{
DotFile.Write(" shape=ellipse ");
}
else
{
DotFile.Write(" shape=none ");
}
DotFile.Write("] "); // end node attributes
DotFile.WriteLine(";");
}
public override bool IsLargerThan(HasseNode smallobj)
{
if (smallobj.HasNodeType(HasseNode.HasseNodeTypes.MAX_COMMON_FRAGMENT))
System.Diagnostics.Debugger.Break();
if (smallobj.NodeType == HasseNode.HasseNodeTypes.ROOT)
{
return true;
}
if (this.NodeType == HasseNode.HasseNodeTypes.ROOT)
{
return false;
}
bool IsPossiblyLargerThanByFingerprint = ContainsFingerprintOf(((ChemHasseNode)smallobj).fingerprint());
if (TrustFingerprints)
{
if (IsPossiblyLargerThanByFingerprint)
{
;
} // is likely to be larger, but we are not sure, needs to be checked
else
{
return false; // if fingerprints work as they should we are guaranteed that IsLargerThan must be false
}
}
// todo take a away those checks that fingerprints work
if (IsPossiblyLargerThanByFingerprint)
{ // can be a substructure match but need not be
//if (matcher.countMatches(smallMol) == 0)
//{
// System.Diagnostics.Debug.WriteLine("a fingerprint contained in b fingerprint - but a was not substruc of b");
// System.Diagnostics.Debug.WriteLine("a\t" + smallMol.smiles());
// System.Diagnostics.Debug.WriteLine("b\t" + molecule.smiles());
//}
}
else
{
//if (matcher.countMatches(smallMol) != 0)
// System.Diagnostics.Debugger.Break(); //we have a match where fp says we certainly have not!
}
return ChemObject.IsLargerThan(smallobj);
}
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));
}
