private void createMinimumCycleBasis()
{
org._3pq.jgrapht.Graph subgraph = new Subgraph(graph, null, null);
CSGraphT.SupportClass.SetSupport remainingEdges = new CSGraphT.SupportClass.HashSetSupport(graph.edgeSet());
//UPGRADE_TODO: Class 'java.util.HashSet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashSet'"
CSGraphT.SupportClass.SetSupport selectedEdges = new CSGraphT.SupportClass.HashSetSupport();
while (!(remainingEdges.Count == 0))
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
Edge edge = (Edge)remainingEdges.GetEnumerator().Current;
subgraph.removeEdge(edge);
// Compute a shortest cycle through edge
System.Collections.IList path = BFSShortestPath.findPathBetween(subgraph, edge.Source, edge.Target);
path.Add(edge);
SimpleCycle cycle = new SimpleCycle(graph, path);
subgraph.addEdge(edge);
selectedEdges.Add(edge);
cycles_Renamed_Field.Insert(0, cycle);
edgeList.Insert(0, edge);
SupportClass.ICollectionSupport.RemoveAll(remainingEdges, path);
}
subgraph.removeAllEdges(selectedEdges);
// The cycles just created are already minimal, so we can start minimizing at startIndex
int startIndex = cycles_Renamed_Field.Count;
// Now we perform a breadth first traversal and build a fundamental tree base
// ("Kirchhoff base") of the remaining subgraph
System.Object currentVertex = graph.vertexSet()[0];
// We build a spanning tree as a directed graph to easily find the parent of a
// vertex in the tree. This means however that we have to create new Edge objects
// for the tree and can't just use the Edge objects of the graph, since the
// the edge in the graph might have a wrong or no direction.
DirectedGraph spanningTree = new SimpleDirectedGraph();
//UPGRADE_TODO: Class 'java.util.HashSet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashSet'"
CSGraphT.SupportClass.SetSupport visitedEdges = new CSGraphT.SupportClass.HashSetSupport();
// FIFO for the BFS
//UPGRADE_TODO: Class 'java.util.LinkedList' was converted to 'System.Collections.ArrayList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilLinkedList'"
System.Collections.ArrayList vertexQueue = new System.Collections.ArrayList();
// currentVertex is the root of the spanning tree
spanningTree.addVertex(currentVertex);
vertexQueue.Insert(vertexQueue.Count, currentVertex);
// We need to remember the tree edges so we can add them at once to the
// index list for the incidence matrix
System.Collections.IList treeEdges = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
while (!(vertexQueue.Count == 0))
{
System.Object tempObject;
tempObject = vertexQueue[0];
vertexQueue.RemoveAt(0);
currentVertex = tempObject;
System.Collections.IEnumerator edges = subgraph.edgesOf(currentVertex).GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (edges.MoveNext())
{
// find a neighbour vertex of the current vertex
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
Edge edge = (Edge)edges.Current;
if (!visitedEdges.Contains(edge))
{
// mark edge as visited
visitedEdges.Add(edge);
System.Object nextVertex = edge.oppositeVertex(currentVertex);
if (!spanningTree.containsVertex(nextVertex))
{
// tree edge
treeEdges.Add(edge);
spanningTree.addVertex(nextVertex);
// create a new (directed) Edge object (as explained above)
spanningTree.addEdge(currentVertex, nextVertex);
// add the next vertex to the BFS-FIFO
vertexQueue.Insert(vertexQueue.Count, nextVertex);
}
else
{
// non-tree edge
// This edge defines a cycle together with the edges of the spanning tree
// along the path to the root of the tree. We create a new cycle containing
// these edges (not the tree edges, but the corresponding edges in the graph)
System.Collections.IList edgesOfCycle = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
// follow the path to the root of the tree
System.Object vertex = currentVertex;
// get parent of vertex
System.Collections.IList incomingEdgesOfVertex = spanningTree.incomingEdgesOf(vertex);
System.Object parent = (incomingEdgesOfVertex.Count == 0) ? null : ((Edge)incomingEdgesOfVertex[0]).oppositeVertex(vertex);
while (parent != null)
{
// add the corresponding edge to the cycle
edgesOfCycle.Add(subgraph.getEdge(vertex, parent));
// go up the tree
vertex = parent;
// get parent of vertex
incomingEdgesOfVertex = spanningTree.incomingEdgesOf(vertex);
parent = (incomingEdgesOfVertex.Count == 0) ? null : ((Edge)incomingEdgesOfVertex[0]).oppositeVertex(vertex);
}
// do the same thing for nextVertex
vertex = nextVertex;
// get parent of vertex
incomingEdgesOfVertex = spanningTree.incomingEdgesOf(vertex);
parent = (incomingEdgesOfVertex.Count == 0) ? null : ((Edge)incomingEdgesOfVertex[0]).oppositeVertex(vertex);
while (parent != null)
{
edgesOfCycle.Add(subgraph.getEdge(vertex, parent));
vertex = parent;
// get parent of vertex
incomingEdgesOfVertex = spanningTree.incomingEdgesOf(vertex);
parent = (incomingEdgesOfVertex.Count == 0) ? null : ((Edge)incomingEdgesOfVertex[0]).oppositeVertex(vertex);
}
// finally, add the non-tree edge to the cycle
edgesOfCycle.Add(edge);
// add the edge to the index list for the incidence matrix
edgeList.Add(edge);
SimpleCycle newCycle = new SimpleCycle(graph, edgesOfCycle);
cycles_Renamed_Field.Add(newCycle);
}
}
}
}
// Add all the tree edges to the index list for the incidence matrix
SupportClass.ICollectionSupport.AddAll(edgeList, treeEdges);
edgeIndexMap = createEdgeIndexMap(edgeList);
// Now the index list is ordered: first the non-tree edges, then the tree edge.
// Moreover, since the cycles and the corresponding non-tree edge have been added
// to their lists in the same order, the incidence matrix is in upper triangular form.
// Now we can minimize the cycles created from the tree base
minimize(startIndex);
}
/// <summary> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="container"> Molecule that is written to an OutputStream
/// </param>
/// <param name="isVisible">Should a certain atom be written to mdl?
/// </param>
public virtual void writeMolecule(IMolecule container, bool[] isVisible)
{
System.String line = "";
// taking care of the $$$$ signs:
// we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
if (moleculeNumber == 2)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
// write header block
// lines get shortened to 80 chars, that's in the spec
System.String title = (System.String)container.getProperty(CDKConstants.TITLE);
if (title == null)
{
title = "";
}
if (title.Length > 80)
{
title = title.Substring(0, (80) - (0));
}
writer.Write(title + "\n");
/* From CTX spec
* This line has the format:
* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
* (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
* User's first and last initials (l), program name (P),
* date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input, internal registry number (R)
* if input through MDL form.
* A blank line can be substituted for line 2.
*/
writer.Write(" CDK ");
//UPGRADE_ISSUE: Constructor 'java.text.SimpleDateFormat.SimpleDateFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextSimpleDateFormat'"
//UPGRADE_TODO: The equivalent in .NET for method 'java.util.Calendar.getTime' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.TimeZone generatedAux3 = System.TimeZone.CurrentTimeZone;
//writer.Write(SupportClass.FormatDateTime(new SimpleDateFormat("M/d/y,H:m", new System.Globalization.CultureInfo("en-US")), SupportClass.CalendarManager.manager.GetDateTime(new System.Globalization.GregorianCalendar())));
writer.Write('\n');
System.String comment = (System.String)container.getProperty(CDKConstants.REMARK);
if (comment == null)
{
comment = "";
}
if (comment.Length > 80)
{
comment = comment.Substring(0, (80) - (0));
}
writer.Write(comment + "\n");
// write Counts line
int upToWhichAtom = 0;
for (int i = 0; i < isVisible.Length; i++)
{
if (isVisible[i])
{
upToWhichAtom++;
}
}
line += formatMDLInt(upToWhichAtom, 3);
int numberOfBonds = 0;
if (upToWhichAtom < container.AtomCount)
{
for (int i = 0; i < container.getBondCount(); i++)
{
if (isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[1])])
{
numberOfBonds++;
}
}
}
else
{
numberOfBonds = container.getBondCount();
}
line += formatMDLInt(numberOfBonds, 3);
line += " 0 0 0 0 0 0 0 0999 V2000\n";
writer.Write(line);
// write Atom block
IAtom[] atoms = container.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
if (isVisible[f])
{
IAtom atom = atoms[f];
line = "";
if (atom.getPoint3d() != null)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.X3d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.Y3d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += (formatMDLFloat((float)atom.Z3d) + " ");
}
else if (atom.getPoint2d() != null)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.X2d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.Y2d);
line += " 0.0000 ";
}
else
{
// if no coordinates available, then output a number
// of zeros
line += formatMDLFloat((float)0.0);
line += formatMDLFloat((float)0.0);
line += (formatMDLFloat((float)0.0) + " ");
}
if (container.getAtomAt(f) is IPseudoAtom)
{
line += formatMDLString(((IPseudoAtom)container.getAtomAt(f)).Label, 3);
}
else
{
line += formatMDLString(container.getAtomAt(f).Symbol, 3);
}
line += " 0 0 0 0 0 0 0 0 0 0 0 0";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write Bond block
IBond[] bonds = container.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
if (upToWhichAtom == container.AtomCount || (isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[1])]))
{
IBond bond = bonds[g];
if (bond.getAtoms().Length != 2)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.warn("Skipping bond with more/less than two atoms: " + bond);
}
else
{
if (bond.Stereo == CDKConstants.STEREO_BOND_UP_INV || bond.Stereo == CDKConstants.STEREO_BOND_DOWN_INV)
{
// turn around atom coding to correct for inv stereo
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
}
else
{
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
}
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLInt((int)bond.Order, 3);
line += " ";
switch (bond.Stereo)
{
case CDKConstants.STEREO_BOND_UP:
line += "1";
break;
case CDKConstants.STEREO_BOND_UP_INV:
line += "1";
break;
case CDKConstants.STEREO_BOND_DOWN:
line += "6";
break;
case CDKConstants.STEREO_BOND_DOWN_INV:
line += "6";
break;
default:
line += "0";
break;
}
line += " 0 0 0 ";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// write formal atomic charges
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
int charge = atom.getFormalCharge();
if (charge != 0)
{
writer.Write("M CHG 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(charge, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write formal isotope information
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
if (!(atom is IPseudoAtom))
{
int atomicMass = atom.MassNumber;
int majorMass = IsotopeFactory.getInstance(atom.Builder).getMajorIsotope(atom.Symbol).MassNumber;
if (atomicMass != 0 && atomicMass != majorMass)
{
writer.Write("M ISO 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(atomicMass, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// close molecule
writer.Write("M END");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//write sdfields, if any
if (sdFields != null)
{
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
CSGraphT.SupportClass.SetSupport set_Renamed = new CSGraphT.SupportClass.HashSetSupport(sdFields.Keys);
System.Collections.IEnumerator iterator = set_Renamed.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (iterator.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
System.Object element = iterator.Current;
writer.Write("> <" + ((System.String)element) + ">");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
writer.Write(sdFields[element].ToString());
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// taking care of the $$$$ signs:
// we write such a sign at the end of all except the first molecule
if (moleculeNumber != 1)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
moleculeNumber++;
writer.Flush();
}
/// <summary> Returns the atoms which are closes to an atom in an AtomContainer by
/// distance in 3d.
///
/// </summary>
/// <param name="ac"> The AtomContainer to examine
/// </param>
/// <param name="a"> the atom to start from
/// </param>
/// <param name="max"> the number of neighbours to return
/// </param>
/// <returns> the average bond length
/// </returns>
/// <exception cref="CDKException"> Description of the Exception
/// </exception>
public static System.Collections.ArrayList findClosestInSpace(IAtomContainer ac, IAtom a, int max)
{
IAtom[] atoms = ac.Atoms;
Point3d originalPoint = a.getPoint3d();
if (originalPoint == null)
{
throw new CDKException("No point3d, but findClosestInSpace is working on point3ds");
}
//UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
//UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
System.Collections.IDictionary hm = new System.Collections.SortedList();
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != a)
{
if (atoms[i].getPoint3d() == null)
{
throw new CDKException("No point3d, but findClosestInSpace is working on point3ds");
}
double distance = atoms[i].getPoint3d().distance(originalPoint);
hm[(double)distance] = atoms[i];
}
}
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
CSGraphT.SupportClass.SetSupport ks = new CSGraphT.SupportClass.HashSetSupport(hm.Keys);
System.Collections.IEnumerator it = ks.GetEnumerator();
System.Collections.ArrayList returnValue = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
int i2 = 0;
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (it.MoveNext() && i2 < max)
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
returnValue.Add(hm[it.Current]);
i2++;
}
return (returnValue);
}
/// <summary> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="container"> Molecule that is written to an OutputStream
/// </param>
/// <param name="isVisible">Should a certain atom be written to mdl?
/// </param>
public virtual void writeMolecule(IMolecule container, bool[] isVisible)
{
System.String line = "";
// taking care of the $$$$ signs:
// we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
if (moleculeNumber == 2)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
// write header block
// lines get shortened to 80 chars, that's in the spec
System.String title = (System.String)container.getProperty(CDKConstants.TITLE);
if (title == null)
title = "";
if (title.Length > 80)
title = title.Substring(0, (80) - (0));
writer.Write(title + "\n");
/* From CTX spec
* This line has the format:
* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
* (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
* User's first and last initials (l), program name (P),
* date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input, internal registry number (R)
* if input through MDL form.
* A blank line can be substituted for line 2.
*/
writer.Write(" CDK ");
//UPGRADE_ISSUE: Constructor 'java.text.SimpleDateFormat.SimpleDateFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextSimpleDateFormat'"
//UPGRADE_TODO: The equivalent in .NET for method 'java.util.Calendar.getTime' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.TimeZone generatedAux3 = System.TimeZone.CurrentTimeZone;
//writer.Write(SupportClass.FormatDateTime(new SimpleDateFormat("M/d/y,H:m", new System.Globalization.CultureInfo("en-US")), SupportClass.CalendarManager.manager.GetDateTime(new System.Globalization.GregorianCalendar())));
writer.Write('\n');
System.String comment = (System.String)container.getProperty(CDKConstants.REMARK);
if (comment == null)
comment = "";
if (comment.Length > 80)
comment = comment.Substring(0, (80) - (0));
writer.Write(comment + "\n");
// write Counts line
int upToWhichAtom = 0;
for (int i = 0; i < isVisible.Length; i++)
{
if (isVisible[i])
upToWhichAtom++;
}
line += formatMDLInt(upToWhichAtom, 3);
int numberOfBonds = 0;
if (upToWhichAtom < container.AtomCount)
{
for (int i = 0; i < container.getBondCount(); i++)
{
if (isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[1])])
numberOfBonds++;
}
}
else
{
numberOfBonds = container.getBondCount();
}
line += formatMDLInt(numberOfBonds, 3);
line += " 0 0 0 0 0 0 0 0999 V2000\n";
writer.Write(line);
// write Atom block
IAtom[] atoms = container.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
if (isVisible[f])
{
IAtom atom = atoms[f];
line = "";
if (atom.getPoint3d() != null)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.X3d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.Y3d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += (formatMDLFloat((float)atom.Z3d) + " ");
}
else if (atom.getPoint2d() != null)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.X2d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.Y2d);
line += " 0.0000 ";
}
else
{
// if no coordinates available, then output a number
// of zeros
line += formatMDLFloat((float)0.0);
line += formatMDLFloat((float)0.0);
line += (formatMDLFloat((float)0.0) + " ");
}
if (container.getAtomAt(f) is IPseudoAtom)
line += formatMDLString(((IPseudoAtom)container.getAtomAt(f)).Label, 3);
else
line += formatMDLString(container.getAtomAt(f).Symbol, 3);
line += " 0 0 0 0 0 0 0 0 0 0 0 0";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write Bond block
IBond[] bonds = container.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
if (upToWhichAtom == container.AtomCount || (isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[1])]))
{
IBond bond = bonds[g];
if (bond.getAtoms().Length != 2)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.warn("Skipping bond with more/less than two atoms: " + bond);
}
else
{
if (bond.Stereo == CDKConstants.STEREO_BOND_UP_INV || bond.Stereo == CDKConstants.STEREO_BOND_DOWN_INV)
{
// turn around atom coding to correct for inv stereo
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
}
else
{
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
}
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLInt((int)bond.Order, 3);
line += " ";
switch (bond.Stereo)
{
case CDKConstants.STEREO_BOND_UP:
line += "1";
break;
case CDKConstants.STEREO_BOND_UP_INV:
line += "1";
break;
case CDKConstants.STEREO_BOND_DOWN:
line += "6";
break;
case CDKConstants.STEREO_BOND_DOWN_INV:
line += "6";
break;
default:
line += "0";
break;
}
line += " 0 0 0 ";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// write formal atomic charges
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
int charge = atom.getFormalCharge();
if (charge != 0)
{
writer.Write("M CHG 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(charge, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write formal isotope information
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
if (!(atom is IPseudoAtom))
{
int atomicMass = atom.MassNumber;
int majorMass = IsotopeFactory.getInstance(atom.Builder).getMajorIsotope(atom.Symbol).MassNumber;
if (atomicMass != 0 && atomicMass != majorMass)
{
writer.Write("M ISO 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(atomicMass, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// close molecule
writer.Write("M END");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//write sdfields, if any
if (sdFields != null)
{
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
CSGraphT.SupportClass.SetSupport set_Renamed = new CSGraphT.SupportClass.HashSetSupport(sdFields.Keys);
System.Collections.IEnumerator iterator = set_Renamed.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (iterator.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
System.Object element = iterator.Current;
writer.Write("> <" + ((System.String)element) + ">");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
writer.Write(sdFields[element].ToString());
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// taking care of the $$$$ signs:
// we write such a sign at the end of all except the first molecule
if (moleculeNumber != 1)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
moleculeNumber++;
writer.Flush();
}
