public void test1()
{
string strQmol = "[H]/N=C(C)/N1CCCCC1"; //shows problem!
//string strQmol = "[H]/N=C(C)/N"; // still shows problem
//string strQmol = "[H]/N=C(C)/C"; // no problem
//string strQmol = "[H]/N=C(C)/C(C)(C)"; // no problem again
// string strLmol = "[H]/N=C(C)/N1CCCCC1CCC";
string strLmol = "N(C(=N([H])[H])c1cccc(C=CCN(C(=O)CCC(=O)OCC)c2ccc(OC3CCN(C(=N[H])C)CC3)c(C(F)(F)F)c2)c1)([H])[H]";
IndigoObject qmol = indigo.loadQueryMolecule(strQmol);
IndigoObject mol = indigo.loadMolecule(strLmol);
System.Diagnostics.Debug.WriteLine("QueryMol 1: " + qmol.smiles());
//qmol.clearCisTrans();
//
string problem = mol.checkAmbiguousH();
problem = mol.checkBadValence();
System.Diagnostics.Debug.WriteLine("QueryMol 2: " + qmol.smiles());
System.Diagnostics.Debug.WriteLine("Largermol is : " + mol.smiles());
IndigoObject matcher = indigo.substructureMatcher(mol);
indigo.setOption("embedding-uniqueness", "atoms");
foreach (IndigoObject m in matcher.iterateMatches(qmol))
{
System.Diagnostics.Debug.WriteLine(m.highlightedTarget().smiles());
}
}
/// <summary>
/// Returns whether the chemical structure contains a specified substructure.
/// </summary>
/// <param name="substructureQuery">The specified substructure to search for.</param>
/// <returns>True if this chemical structure contains the specified substructure.</returns>
public bool HasSubstructure(ChemicalStructure substructureQuery)
{
bool hasSubstructure = false;
using (Indigo indigo = new Indigo())
{
// Load inputs.
IndigoObject structure = CreateIndigoStructure(indigo);
IndigoObject substructure = indigo.loadQueryMolecule(substructureQuery.MolfileContents);
// Perform the match.
IndigoObject substructureMatcher = indigo.substructureMatcher(structure);
hasSubstructure = (substructureMatcher.match(substructure) != null);
// Dispose.
structure.Dispose();
substructure.Dispose();
substructureMatcher.Dispose();
}
return(hasSubstructure);
}
static void Main(string[] args)
{
Indigo indigo = new Indigo();
// By default Bingo loads a database and stores all the data in RAM for faster operations
// But if the application is limited in the memory usage Bingo can work
// in a file mode with loading only minor parts of data into the memory
Bingo database = Bingo.createDatabaseFile(indigo, "db1", "molecule", "storage:file");
// Insert structures from the file
using (IndigoObject input = indigo.iterateSmilesFile("input.smi"))
foreach (IndigoObject obj in input)
{
Console.WriteLine(" Object: {0}", obj.name());
// When loading from SMILES the only information that we have is an object name
// that is stored on the same line with the SMILES in the file
int id = int.Parse(obj.name());
// Insert loaded object into the database
database.insert(obj, id);
// Dispose native Indigo object as .NET object is much smaller than native object
// and GC can postpone disposing of this object resulting in a large memory
// consumption
obj.Dispose();
}
// Bingo can also assign structure ID automatically
int autoId1 = database.insert(indigo.loadMolecule("OC1C(C(=O)O)=CC=CC1O"));
Console.WriteLine("Automatic id = {0}", autoId1);
int autoId2 = database.insert(indigo.loadMolecule("OC1C(C(=O)O)=CC=CC1O"));
Console.WriteLine("Automatic id = {0}", autoId2);
// Search over the database
Console.WriteLine("Search Benzene:");
IndigoObject query = indigo.loadQueryMolecule("C1=CC=CC=C1");
BingoObject search = database.searchSub(query);
while (search.next())
{
Console.WriteLine(" Found id = {0}", search.getCurrentId());
}
// You can close and reopen database at any moment
database.close();
// Load Bingo in a RAM mode with caching all data into the memory
// Search operations works faster in this mode
database = Bingo.loadDatabaseFile(indigo, "db1", "molecule", "storage:ram");
// Search the same query but in the aromatic form
// Results are the same
Console.WriteLine("Search Benzene in the aromatic form:");
query = indigo.loadQueryMolecule("c1ccccc1");
search = database.searchSub(query);
while (search.next())
{
Console.WriteLine(" Found id = {0}", search.getCurrentId());
}
Console.WriteLine("Search C=O");
query = indigo.loadQueryMolecule("C=O");
// Using block will automatically call search.Dispose() that calls search.close()
// to terminate further search
using (search = database.searchSub(query))
{
int count = 0;
while (search.next())
{
Console.WriteLine(" Found id = {0}", search.getCurrentId());
count++;
if (count == 4)
{
break;
}
}
}
// Similarity search
Console.WriteLine("Similarity search:");
query = indigo.loadMolecule("NC1C=CC=C(C1O)C(O)=O");
search = database.searchSim(query, 0.7f, 1.0f);
while (search.next())
{
Console.WriteLine(" Found id = {0}", search.getCurrentId());
}
// Database will be closed automatically in the object destructor
// but we can close it manually to dispose memory
database.close();
}
