/// <summary>
/// Convert to an identity template library.
/// </summary>
/// <returns>identity template library</returns>
internal IdentityTemplateLibrary ToIdentityTemplateLibrary()
{
var lib = IdentityTemplateLibrary.Empty();
foreach (var mol in templates)
{
lib.Add(AtomContainerManipulator.Anonymise(mol));
}
return(lib);
}
/// <summary>
/// Layout a macro cycle (the rest of the ring set is untouched).
/// </summary>
/// <param name="macrocycle">the macrocycle</param>
/// <param name="ringset">the ring set the macrocycle belongs to (may only be it's self)</param>
/// <returns>layout was successfully, if false caller fall-back to regular polygons</returns>
public static bool Layout(IRing macrocycle, IRingSet ringset)
{
var anon = RoundUpIfNeeded(AtomContainerManipulator.Anonymise(macrocycle));
var coords = TEMPLATES.GetCoordinates(anon);
if (coords.Count == 0)
{
return(false);
}
var best = new Vector2[anon.Atoms.Count];
var bestOffset = SelectCoords(coords, best, macrocycle, ringset);
for (int i = 0; i < macrocycle.Atoms.Count; i++)
{
macrocycle.Atoms[i].Point2D = best[(bestOffset + i) % macrocycle.Atoms.Count];
macrocycle.Atoms[i].IsPlaced = true;
macrocycle.Atoms[i].SetProperty(MACROCYCLE_ATOM_HINT, true);
}
macrocycle.IsPlaced = true;
return(true);
}
public static IReadOnlyList <IBitFingerprint> MakeFingerprintsFromSdf(bool anyAtom, bool anyAtomAnyBond, Dictionary <string, int> timings, TextReader fin, int limit)
{
var fingerPrinter = new HybridizationFingerprinter(HybridizationFingerprinter.DefaultSize, HybridizationFingerprinter.DefaultSearchDepth);
fingerPrinter.SetHashPseudoAtoms(true);
IAtomContainer query = null;
var data = new List <IBitFingerprint>();
try
{
Trace.TraceInformation("Read data file in ...");
using (var imdl = new EnumerableSDFReader(fin, builder))
{
Trace.TraceInformation("ready");
int moleculeCounter = 0;
int fingerprintCounter = 0;
Trace.TraceInformation($"Generated Fingerprints: {fingerprintCounter} ");
foreach (var m in imdl)
{
if (!(moleculeCounter < limit || limit == -1))
{
break;
}
moleculeCounter++;
if (anyAtom && !anyAtomAnyBond)
{
query = QueryAtomContainerCreator.CreateAnyAtomContainer(m, false);
}
else
{
query = AtomContainerManipulator.Anonymise(m);
}
try
{
var time = -DateTime.Now.Ticks / 10000;
if (anyAtom || anyAtomAnyBond)
{
data.Add(fingerPrinter.GetBitFingerprint(query));
fingerprintCounter = fingerprintCounter + 1;
}
else
{
data.Add(fingerPrinter.GetBitFingerprint(query));
fingerprintCounter = fingerprintCounter + 1;
}
time += (DateTime.Now.Ticks / 10000);
// store the time
var bin = ((int)Math.Floor(time / 10.0)).ToString(NumberFormatInfo.InvariantInfo);
if (timings.ContainsKey(bin))
{
timings[bin] = (timings[bin]) + 1;
}
else
{
timings[bin] = 1;
}
}
catch (Exception exc1)
{
Trace.TraceInformation($"QueryFingerprintError: from molecule:{moleculeCounter} due to:{exc1.Message}");
// OK, just adds a fingerprint with all ones, so that any
// structure will match this template, and leave it up
// to substructure match to figure things out
var allOnesFingerprint = new BitSetFingerprint(fingerPrinter.Length);
for (int i = 0; i < fingerPrinter.Length; i++)
{
allOnesFingerprint.Set(i);
}
data.Add(allOnesFingerprint);
fingerprintCounter = fingerprintCounter + 1;
}
if (fingerprintCounter % 2 == 0)
{
Trace.TraceInformation("\b" + "/");
}
else
{
Trace.TraceInformation("\b" + "\\");
}
if (fingerprintCounter % 100 == 0)
{
Trace.TraceInformation("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b"
+ "Generated Fingerprints: " + fingerprintCounter + " \n");
}
}// while
Trace.TraceInformation($"...ready with:{moleculeCounter} molecules\nWrite data...of data vector:{data.Count} fingerprintCounter:{fingerprintCounter}");
}
}
catch (Exception exc)
{
Console.Out.WriteLine("Could not read Molecules from file" + " due to: " + exc.Message);
}
return(data);
}
