public void AvoidWedgingRingBond()
{
var smi = "CC(C)[C@@H]1CCCCO1";
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles(smi);
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
int wedgeCount = 0;
foreach (var bond in mol.Bonds)
{
switch (bond.Stereo)
{
case BondStereo.Up:
case BondStereo.Down:
case BondStereo.UpInverted:
case BondStereo.DownInverted:
Assert.IsFalse(bond.IsInRing);
++wedgeCount;
break;
}
}
Assert.AreEqual(1, wedgeCount);
}
public void AtropisomerWedgeBonds()
{
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles("OC1=CC=C2C=CC=CC2=C1C1=C(O)C=CC2=C1C=CC=C2");
var focus = mol.GetBond(mol.Atoms[10], mol.Atoms[11]);
var carriers = new List <IAtom>();
carriers.AddRange(mol.GetConnectedAtoms(focus.Begin));
carriers.AddRange(mol.GetConnectedAtoms(focus.End));
carriers.Remove(focus.Begin);
carriers.Remove(focus.End);
mol.StereoElements.Add(new Atropisomeric(focus, carriers, StereoConfigurations.Left));
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
var bond1 = mol.GetBond(focus.Begin, carriers[1]);
var bond2 = mol.GetBond(focus.End, carriers[3]);
Assert.AreEqual(BondOrder.Single, bond1.Order);
Assert.AreEqual(BondOrder.Single, bond2.Order);
Assert.IsTrue(bond1.Stereo == BondStereo.Down || bond2.Stereo == BondStereo.Down, "One of the single bonds should have been wedged");
}
private bool ShowIt(IAtomContainer molecule, string name)
{
StructureDiagramGenerator sdg = new StructureDiagramGenerator {
Molecule = (IAtomContainer)molecule.Clone()
};
sdg.GenerateCoordinates(new Vector2(0, 1));
return(true);
}
/// <summary>
/// Automatically generate coordinates if a user has provided a molecule without them.
/// </summary>
/// <param name="container">a molecule</param>
/// <returns>if coordinates needed to be generated</returns>
/// <exception cref="CDKException">coordinates could not be generated</exception>
private static bool Ensure2DLayout(IAtomContainer container)
{
if (!GeometryUtil.Has2DCoordinates(container))
{
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(container);
return(true);
}
return(false);
}
/// <summary>
/// Automatically generate coordinates if a user has provided reaction without them.
/// </summary>
/// <param name="rxn">reaction</param>
/// <exception cref="CDKException">coordinates could not be generated</exception>
private void Ensure2DLayout(IReaction rxn)
{
if (!GeometryUtil.Has2DCoordinates(rxn))
{
var sdg = new StructureDiagramGenerator {
AlignMappedReaction = alignMappedReactions
};
sdg.GenerateCoordinates(rxn);
}
}
/// <summary>
/// Generate coordinates for a molecule
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public IAtomContainer GenerateCoordinates(
IAtomContainer mol)
{
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.Molecule = mol;
sdg.GenerateCoordinates();
IAtomContainer mol2 = sdg.Molecule;
return(mol2);
}
void Main()
{
IAtomContainer someMolecule = null;
#region
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.Molecule = someMolecule;
sdg.GenerateCoordinates();
IAtomContainer layedOutMol = sdg.Molecule;
#endregion
}
private bool EverythingOk(IEnumerable <IAtomContainer> structures)
{
Debug.WriteLine($"number of structures in vector: {structures.Count()}");
foreach (var mol in structures)
{
var sdg = new StructureDiagramGenerator {
Molecule = mol
};
sdg.GenerateCoordinates(new Vector2(0, 1));
}
return(true);
}
public void NoWavyBondForCisTransNv5()
{
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles("CN(C)(C)=CC");
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
foreach (IBond bond in mol.Bonds)
{
Assert.AreNotEqual(BondStereo.UpOrDown, bond.Stereo);
Assert.AreNotEqual(BondStereo.UpOrDownInverted, bond.Stereo);
}
}
private bool everythingOk(IEnumerable <IAtomContainer> structures)
{
StructureDiagramGenerator sdg;
if (debug)
{
Console.Out.WriteLine("number of structures in vector: " + structures.Count());
}
foreach (var mol in structures)
{
sdg = new StructureDiagramGenerator {
Molecule = mol
};
sdg.GenerateCoordinates(new Vector2(0, 1));
}
return(true);
}
public void InconsistentStereoState()
{
try
{
var smi = "O[C@]([H])(C)CCC";
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles(smi);
mol.Remove(mol.Bonds[1]);
mol.Atoms.RemoveAt(2); // unsafe-removes
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
Assert.Fail();
}
catch (ArgumentException)
{
}
}
public void Testosterone()
{
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles("O=C4C=C2[C@]([C@@]1([H])CC[C@@]3([C@@]([H])(O)CC[C@@]3([H])[C@]1([H])CC2)C)(C)CC4");
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
int wedgeCount = 0;
foreach (IBond bond in mol.Bonds)
{
if (bond.Stereo == BondStereo.Up || bond.Stereo == BondStereo.Down)
{
wedgeCount++;
}
}
Assert.AreEqual(7, wedgeCount);
}
public void MinWedges()
{
var smi = "[C@](([C@@H](C)Cl)([C@H](C)Cl)[C@H](O)[C@](([C@@H](C)Cl)[C@H](C)Cl)[H])[H]";
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles(smi);
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
int wedgeCount = 0;
foreach (var bond in mol.Bonds)
{
switch (bond.Stereo)
{
case BondStereo.Up:
case BondStereo.Down:
case BondStereo.UpInverted:
case BondStereo.DownInverted:
++wedgeCount;
break;
}
}
Assert.AreEqual(7, wedgeCount);
}
public void WedgeExtendedTetrahedral()
{
var smi = "C(=C=C=[C@@]=C=C=CC)C";
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles(smi);
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
int wedgeCount = 0;
foreach (var bond in mol.Bonds)
{
switch (bond.Stereo)
{
case BondStereo.Up:
case BondStereo.Down:
case BondStereo.UpInverted:
case BondStereo.DownInverted:
++wedgeCount;
break;
}
}
Assert.AreEqual(2, wedgeCount);
}
public void AvoidBondsToOtherStereoCentres()
{
var smi = "[H][C@@]([C@H](C)N)([C@@H](C)O)[C@@H](C)OC";
var smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles(smi);
var sdg = new StructureDiagramGenerator();
sdg.GenerateCoordinates(mol);
int wedgeCount = 0;
foreach (var bond in mol.Bonds)
{
switch (bond.Stereo)
{
case BondStereo.Up:
case BondStereo.Down:
case BondStereo.UpInverted:
case BondStereo.DownInverted:
wedgeCount++;
break;
}
}
Assert.AreEqual(4, wedgeCount);
}
public void TestModel3D_bug_1610997()
{
//bool notCalculatedResults = false;
var inputList = new List <IAtomContainer>();
////////////////////////////////////////////////////////////////////////////////////////////
//generate the input molecules. This are molecules without x, y, z coordinates
string[] smiles = new string[] { "CC", "OCC", "O(C)CCC", "c1ccccc1", "C(=C)=C", "OCC=CCc1ccccc1(C=C)",
"O(CC=C)CCN", "CCCCCCCCCCCCCCC", "OCC=CCO", "NCCCCN" };
var sp = CDK.SmilesParser;
IAtomContainer[] atomContainer = new IAtomContainer[smiles.Length];
for (int i = 0; i < smiles.Length; i++)
{
atomContainer[i] = sp.ParseSmiles(smiles[i]);
inputList.Add(atomContainer[i]);
}
///////////////////////////////////////////////////////////////////////////////////////////
// Generate 2D coordinates for the input molecules with the Structure Diagram Generator
StructureDiagramGenerator str;
List <IAtomContainer> resultList = new List <IAtomContainer>();
foreach (var molecule in inputList)
{
str = new StructureDiagramGenerator()
{
Molecule = molecule
};
str.GenerateCoordinates();
resultList.Add(str.Molecule);
}
inputList = resultList;
/////////////////////////////////////////////////////////////////////////////////////////////
// Delete x and y coordinates
foreach (var molecule in inputList)
{
foreach (var atom in molecule.Atoms)
{
atom.Point2D = null;
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////
// Test for the method Model3DBuildersWithMM2ForceField
var builder = CDK.Builder;
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
for (var i = 0; i < inputList.Count; i++)
{
var input = inputList[i];
{
// shallow copy
IAtomContainer mol = builder.NewAtomContainer(input);
try
{
mol = mb3d.Generate3DCoordinates(mol, false);
foreach (var a in mol.Atoms)
{
Assert.IsNotNull(a.Point3D, $"{smiles[0]} has unplaced atom");
}
CheckAverageBondLength(mol);
}
catch (Exception e)
{
if (e is CDKException || e is IOException)
{
Assert.Fail($"3D coordinated could not be generator for {smiles[i]}: {e.StackTrace}");
}
else
{
throw;
}
}
}
}
}
static TemplateHandlerTest()
{
sdg = new StructureDiagramGenerator();
sp = CDK.SmilesParser;
}
