public IndigoInchi(Indigo indigo)
{
String dllpath = indigo.getDllPath();
string libraryName;
IndigoDllLoader dll_loader = IndigoDllLoader.Instance;
switch (Environment.OSVersion.Platform)
{
case PlatformID.Win32NT:
libraryName = "indigo-inchi.dll";
dll_loader.loadLibrary(dllpath, libraryName, "com.ggasoftware.indigo.Properties.ResourcesWin", false);
break;
case PlatformID.Unix:
if (IndigoDllLoader.isMac())
{
libraryName = "libindigo-inchi.dylib";
dll_loader.loadLibrary(dllpath, libraryName, "com.ggasoftware.indigo.Properties.ResourcesMac", false);
}
else
{
libraryName = "libindigo-inchi.so";
dll_loader.loadLibrary(dllpath, libraryName, "com.ggasoftware.indigo.Properties.ResourcesLinux", false);
}
break;
default:
throw new PlatformNotSupportedException(String.Format("Unsupported platform: {0}", Environment.OSVersion.Platform));
}
_inchi_lib = dll_loader.getInterface <IndigoInchiLib> (libraryName);
_indigo = indigo;
}
internal BingoObject(int id, Indigo indigo, BingoLib bingo_lib)
{
this._id = id;
this._indigo = indigo;
this._bingoLib = bingo_lib;
this._dllLoader = IndigoDllLoader.Instance;
}
private Bingo(Indigo indigo, int id, BingoLib lib)
{
_indigo = indigo;
_lib = lib;
_id = id;
_dllLoader = IndigoDllLoader.Instance;
}
public IndigoObject(Indigo dispatcher, object parent, int id)
{
this.dispatcher = dispatcher;
this.self = id;
this.parent = parent;
_indigo_lib = dispatcher._indigo_lib;
}
public IndigoRenderer(Indigo indigo)
{
String dllpath = indigo.getDllPath ();
string libraryName;
IndigoDllLoader dll_loader = IndigoDllLoader.Instance;
switch (Environment.OSVersion.Platform) {
case PlatformID.Win32NT:
libraryName = "indigo-renderer.dll";
dll_loader.loadLibrary (dllpath, libraryName, "com.ggasoftware.indigo.Properties.ResourcesWin", false);
break;
case PlatformID.Unix:
if (IndigoDllLoader.isMac()) {
libraryName = "libindigo-renderer.dylib";
dll_loader.loadLibrary (dllpath, libraryName, "com.ggasoftware.indigo.Properties.ResourcesMac", false);
} else {
libraryName = "libindigo-renderer.so";
dll_loader.loadLibrary (dllpath, libraryName, "com.ggasoftware.indigo.Properties.ResourcesLinux", false);
}
break;
default:
throw new PlatformNotSupportedException (String.Format ("Unsupported platform: {0}", Environment.OSVersion.Platform));
}
_renderer_lib = dll_loader.getInterface<IndigoRendererLib> (libraryName);
_indigo = indigo;
}
private Bingo(Indigo indigo, int id, BingoLib lib)
{
_indigo = indigo;
_lib = lib;
_id = id;
_dllLoader = IndigoDllLoader.Instance;
}
internal BingoObject(int id, Indigo indigo, BingoLib bingo_lib)
{
this._id = id;
this._indigo = indigo;
this._bingoLib = bingo_lib;
this._dllLoader = IndigoDllLoader.Instance;
}
public IndigoObject(Indigo dispatcher, object parent, int id)
{
this.dispatcher = dispatcher;
this.self = id;
this.parent = parent;
_indigo_lib = dispatcher._indigo_lib;
}
public IndigoObject(Indigo dispatcher, int id, object parent)
{
this.dispatcher = dispatcher;
this.self = id;
this.parent = parent;
_indigo_lib = dispatcher._indigo_lib;
dll_loader = IndigoDllLoader.Instance;
}
internal static string checkResult(Indigo indigo, string result)
{
if (result == null)
{
throw new BingoException(new String(indigo._indigo_lib.indigoGetLastError()));
}
return result;
}
internal static float checkResult(Indigo indigo, float result)
{
if (result < 0.0)
{
throw new BingoException(new String(indigo._indigo_lib.indigoGetLastError()));
}
return result;
}
internal static float checkResult(Indigo indigo, float result)
{
if (result < 0.0)
{
throw new BingoException(new String(indigo._indigo_lib.indigoGetLastError()));
}
return(result);
}
internal static string checkResult(Indigo indigo, string result)
{
if (result == null)
{
throw new BingoException(new String(indigo._indigo_lib.indigoGetLastError()));
}
return(result);
}
public IndigoRenderer(Indigo indigo)
{
String dllpath = indigo.getDllPath();
IndigoDllLoader dll_loader = IndigoDllLoader.Instance;
dll_loader.loadLibrary(dllpath, "indigo-renderer.dll",
"com.ggasoftware.indigo.Properties.Resources", false);
_renderer_lib = dll_loader.getInterface<IndigoRendererLib>("indigo-renderer.dll");
_indigo = indigo;
}
public IndigoInchi(Indigo indigo)
{
String dllpath = indigo.getDllPath();
IndigoDllLoader dll_loader = IndigoDllLoader.Instance;
dll_loader.loadLibrary(dllpath, "indigo-inchi.dll",
"com.ggasoftware.indigo.Properties.Resources", false);
_inchi_lib = dll_loader.getInterface <IndigoInchiLib>("indigo-inchi.dll");
_indigo = indigo;
}
/// <summary>
/// Creates a chemical storage of a specifed type in a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <param name="type">"molecule" or "reaction"</param>
/// <param name="options">Additional options separated with a semicolon. See the Bingo documentation for more details.</param>
/// <returns>Bingo database instance</returns>
public static Bingo createDatabaseFile(Indigo indigo, string location, string type, string options)
{
indigo.setSessionID();
if (options == null)
{
options = "";
}
BingoLib lib = Bingo.getLib(indigo);
int databaseID = Bingo.checkResult(indigo, lib.bingoCreateDatabaseFile(location, type, options));
return(new Bingo(indigo, databaseID, lib));
}
public void removeAtoms(ICollection vertices)
{
removeAtoms(Indigo.toIntArray(vertices));
}
public IndigoChemistryDepiction(Indigo _indigo)
{
indigo = _indigo;
renderer = new IndigoRenderer(indigo);
}
private static void _handleError(sbyte* message, Indigo self)
{
throw new IndigoException(new String(message));
}
/// <summary>
/// Creates a chemical storage of a specifed type in a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <param name="type">"molecule" or "reaction"</param>
/// <returns>Bingo database instance</returns>
public static Bingo createDatabaseFile(Indigo indigo, string location, string type)
{
return createDatabaseFile(indigo, location, type, null);
}
/// <summary>
/// Loads a chemical storage of a specifed type from a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <param name="options">Additional options separated with a semicolon. See the Bingo documentation for more details.</param>
/// <returns>Bingo database instance</returns>
public static Bingo loadDatabaseFile(Indigo indigo, string location, string options)
{
if (options == null)
{
options = "";
}
BingoLib lib = Bingo.getLib(indigo);
indigo.setSessionID();
int databaseID = Bingo.checkResult(indigo, lib.bingoLoadDatabaseFile(location, options));
return new Bingo(indigo, databaseID, lib);
}
/// <summary>
/// Loads a chemical storage of a specifed type from a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <returns>Bingo database instance</returns>
public static Bingo loadDatabaseFile(Indigo indigo, string location)
{
return loadDatabaseFile(indigo, location, null);
}
/// <summary>
/// Loads a chemical storage of a specifed type from a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <returns>Bingo database instance</returns>
public static Bingo loadDatabaseFile(Indigo indigo, string location)
{
return(loadDatabaseFile(indigo, location, null));
}
/// <summary>
/// Creates a chemical storage of a specifed type in a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <param name="type">"molecule" or "reaction"</param>
/// <returns>Bingo database instance</returns>
public static Bingo createDatabaseFile(Indigo indigo, string location, string type)
{
return(createDatabaseFile(indigo, location, type, null));
}
public IndigoObject addDataSGroup(ICollection atoms, ICollection bonds, String description, String data)
{
return(addDataSGroup(Indigo.toIntArray(atoms), Indigo.toIntArray(bonds), description, data));
}
public IndigoObject addSuperatom(ICollection atoms, String name)
{
return(addSuperatom(Indigo.toIntArray(atoms), name));
}
public IndigoObject(Indigo dispatcher, int id) : this(dispatcher, id, null)
{
dll_loader = IndigoDllLoader.Instance;
}
private static void _handleError(sbyte *message, Indigo self)
{
throw new IndigoException(new String(message));
}
public ChemHasseFingerprint(Indigo _indigo, BitArray _fp)
{
indigo = _indigo;
fp = _fp;
base.bitCount = base.CountBits();
}
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();
}
public IndigoObject getSubmolecule(ICollection vertices)
{
return(getSubmolecule(Indigo.toIntArray(vertices)));
}
public ChemHasseFingerprint(Indigo _indigo)
{
indigo = _indigo;
}
public IndigoObject(Indigo dispatcher, int id) : this(dispatcher, null, id)
{
}
public float alignAtoms(ICollection atom_ids, ICollection desired_xyz)
{
return(alignAtoms(Indigo.toIntArray(atom_ids), Indigo.toFloatArray(desired_xyz)));
}
public IndigoObject(Indigo dispatcher, int id)
: this(dispatcher, null, id)
{
}