/// <summary>
/// Creates a QueryAtomContainer with the following settings:
/// <c>QueryAtomContainer.Create(container,
/// ExprType.ELEMENT,
/// ExprType.IS_AROMATIC,
/// ExprType.ALIPHATIC_ORDER);
/// </c>>
/// </summary>
/// <param name="container">The AtomContainer that stands as model</param>
/// <returns>The new QueryAtomContainer created from container.</returns>
public static QueryAtomContainer CreateAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)
{
return(QueryAtomContainer.Create(container,
ExprType.Element,
ExprType.IsAromatic,
ExprType.AliphaticOrder));
}
/// <summary>
/// Creates a <see cref="QueryAtomContainer"/> with the following settings:
/// <c>QueryAtomContainer.Create(container,
/// ExprType.ELEMENT,
/// ExprType.FORMAL_CHARGE,
/// ExprType.IS_AROMATIC,
/// ExprType.ORDER);</c>
/// </summary>
/// <param name="container">The <see cref="IAtomContainer"/> that stands as model</param>
/// <returns>The new <see cref="QueryAtomContainer"/> created from container.</returns>
public static QueryAtomContainer CreateSymbolAndChargeQueryContainer(IAtomContainer container)
{
return(QueryAtomContainer.Create(container,
ExprType.Element,
ExprType.FormalCharge,
ExprType.IsAromatic,
ExprType.Order));
}
/// <summary>
/// Creates a <see cref="QueryAtomContainer"/> with the following settings:
/// <c>QueryAtomContainer.Create(container,
/// Expr.Type.ALIPHATIC_ELEMENT,
/// Expr.Type.AROMATIC_ELEMENT,
/// Expr.Type.IS_AROMATIC,
/// Expr.Type.ALIPHATIC_ORDER,
/// Expr.Type.STEREOCHEMISTRY);</c>
/// </summary>
/// <param name="container">The <see cref="IAtomContainer"/> that stands as model</param>
/// <returns>The new <see cref="QueryAtomContainer"/> created from container.</returns>
public static QueryAtomContainer CreateBasicQueryContainer(IAtomContainer container)
{
return(QueryAtomContainer.Create(container,
ExprType.AliphaticElement,
ExprType.AromaticElement,
ExprType.IsAromatic,
ExprType.AliphaticOrder,
ExprType.Stereochemistry));
}
private void Test(string expected, string smi, params ExprType[] opts)
{
var mol = smipar.ParseSmiles(smi);
Cycles.MarkRingAtomsAndBonds(mol);
var query = QueryAtomContainer.Create(mol, opts);
var actual = Smarts.Generate(query);
Assert.AreEqual(expected, actual);
}
/// <summary>
/// Creates a QueryAtomContainer with the following settings:
/// <c>
/// // aromaticity = true
/// QueryAtomContainer.Create(container, ExprType.IS_AROMATIC);
/// // aromaticity = false
/// QueryAtomContainer.Create(container);
/// </c>
/// </summary>
/// <remarks>
/// This method thus allows the user to search based only on connectivity.
/// </remarks>
/// <param name="container">The AtomContainer that stands as the model</param>
/// <param name="aromaticity">option flag</param>
/// <returns>The new QueryAtomContainer</returns>
public static QueryAtomContainer CreateAnyAtomAnyBondContainer(IAtomContainer container, bool aromaticity)
{
if (aromaticity)
{
return(QueryAtomContainer.Create(container, ExprType.IsAromatic));
}
else
{
return(QueryAtomContainer.Create(container));
}
}
/// <summary>
/// Create a pattern which can be used to find molecules which contain the <paramref name="query"/>
/// structure. If a 'real' molecule is provided is is converted
/// with <see cref="QueryAtomContainer.Create(IAtomContainer, ExprType[])"/>
/// matching elements, aromaticity status, and bond orders.
/// </summary>
/// <param name="query">the substructure to find</param>
/// <returns>a pattern for finding the <paramref name="query"/></returns>
/// <see cref="QueryAtomContainer.Create(IAtomContainer, ExprType[])"/>
public static new DfPattern FindSubstructure(IAtomContainer query)
{
if (query is IQueryAtomContainer)
{
return(new DfPattern((IQueryAtomContainer)query));
}
else
{
return(new DfPattern(QueryAtomContainer.Create(query,
ExprType.AliphaticElement,
ExprType.AromaticElement,
ExprType.SingleOrAromatic,
ExprType.AliphaticOrder,
ExprType.Stereochemistry)));
}
}
void Main()
{
IAtomContainer mol = null;
#region Create1
// [nH]1ccc(=O)cc1 => n1:c:c:c(=O):c:c:1
QueryAtomContainer.Create(mol,
ExprType.AliphaticElement,
ExprType.AromaticElement,
ExprType.SingleOrAromatic,
ExprType.AliphaticOrder,
ExprType.Stereochemistry);
#endregion
#region Create2
// [nH]1ccc(=O)cc1 => [nD2]1:[cD2]:[cD2]:[cD2](=[OD1]):[cD2]:[cD2]:1
QueryAtomContainer.Create(mol,
ExprType.AliphaticElement,
ExprType.AromaticElement,
ExprType.Degree,
ExprType.SingleOrAromatic,
ExprType.AliphaticOrder);
#endregion
#region Create3
// [nH]1ccc(=O)cc1 => [nx2+0]1:[cx2+0]:[cx2+0]:[cx2+0](=[O&x0+0]):[cx2+0]:[cx2+0]:1
// IMPORTANT! use Cycles.MarkRingAtomsAndBonds(mol) to set ring status
QueryAtomContainer.Create(mol,
ExprType.AliphaticElement,
ExprType.AromaticElement,
ExprType.FormalCharge,
ExprType.Isotope,
ExprType.RingBondCount,
ExprType.SingleOrAromatic,
ExprType.AliphaticOrder);
#endregion
#region Create4
// [nH]1ccc(=O)cc1 => [0n+0]1:[0c+0]:[0c+0]:[0c+0](=[O+0]):[0c+0]:[0c+0]:1
QueryAtomContainer.Create(mol,
ExprType.AliphaticElement,
ExprType.AromaticElement,
ExprType.FormalCharge,
ExprType.Isotope,
ExprType.RingBondCount,
ExprType.SingleOrAromatic,
ExprType.AliphaticOrder);
#endregion
}
/// <summary>
/// Creates a <see cref="QueryAtomContainer"/> with the following settings:
/// <c>QueryAtomContainer.Create(container,
/// ExprType.ELEMENT,
/// ExprType.ORDER);</c>
/// </summary>
/// <param name="container">The AtomContainer that stands as model</param>
/// <returns>The new QueryAtomContainer created from container.</returns>
public static QueryAtomContainer CreateSymbolAndBondOrderQueryContainer(IAtomContainer container)
{
return(QueryAtomContainer.Create(container,
ExprType.Element,
ExprType.Order));
}
