public void RadicalCanon()
{
var builder = CDK.Builder;
IAtomContainer mola = builder.NewAtomContainer();
mola.Atoms.Add(builder.NewAtom("CH3"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH1"));
mola.Atoms.Add(builder.NewAtom("CH3"));
mola.AddBond(mola.Atoms[1], mola.Atoms[2], BondOrder.Single);
mola.AddBond(mola.Atoms[2], mola.Atoms[3], BondOrder.Single);
mola.AddBond(mola.Atoms[3], mola.Atoms[4], BondOrder.Single);
mola.AddBond(mola.Atoms[4], mola.Atoms[5], BondOrder.Single);
mola.AddBond(mola.Atoms[5], mola.Atoms[6], BondOrder.Single);
mola.AddBond(mola.Atoms[0], mola.Atoms[5], BondOrder.Single);
mola.AddSingleElectronTo(mola.Atoms[1]);
SmilesParser smipar = new SmilesParser(builder);
var molb = smipar.ParseSmiles("CC(CCC[CH2])C |^1:5|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.Canonical | SmiFlavors.CxRadical);
Assert.AreEqual(smigen.Create(molb), smigen.Create(mola));
}
public void CanonicalReactionAtomLabelsAndFragmentGroups()
{
IReaction rxn1 = smipar.ParseReactionSmiles("CC(C)c1ccccc1.ClC([*])=O>[Al+3].[Cl-].[Cl-].[Cl-].ClCCl>CC(C)c1ccc(cc1)C([*])=O |$;;;;;;;;;;;R1;;;;;;;;;;;;;;;;;;;R1;$,f:2.3.4.5|");
IReaction rxn2 = smipar.ParseReactionSmiles("ClC([*])=O.CC(C)c1ccccc1>[Al+3].[Cl-].[Cl-].[Cl-].ClCCl>CC(C)c1ccc(cc1)C([*])=O |$;;R1;;;;;;;;;;;;;;;;;;;;;;;;;;;;R1;$,f:2.3.5.4|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxAtomLabel |
SmiFlavors.CxFragmentGroup |
SmiFlavors.Canonical);
Assert.AreEqual(smigen.Create(rxn2), smigen.Create(rxn1));
}
public void CanonAtomLabels()
{
var mol = smipar.ParseSmiles("c1ccccc1O |$_AV:0;1;2;3;4;5;6$|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.Canonical | SmiFlavors.CxAtomValue);
Assert.AreEqual("OC=1C=CC=CC1 |$_AV:6;5;0;1;2;3;4$|", smigen.Create(mol));
}
public void RoundTripRadicals()
{
var mol = smipar.ParseSmiles("[C]1C[CH][CH]OC1 |^1:2,3,^2:0|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxRadical);
string smi = smigen.Create(mol);
Assert.AreEqual("[C]1C[CH][CH]OC1 |^1:2,3,^2:0|", smi);
}
public void NoCoordsInEtOH()
{
var mol = smipar.ParseSmiles("CCO");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxCoordinates);
string smi = smigen.Create(mol);
Assert.AreEqual("CCO", smi);
}
public void NoCoordsOptEtOH()
{
var mol = smipar.ParseSmiles("CCO |(,,;1,1,;2,2,)|");
SmilesGenerator smigen = new SmilesGenerator(0);
string smi = smigen.Create(mol);
Assert.AreEqual("CCO", smi);
}
public void CoordsEtOH()
{
var mol = smipar.ParseSmiles("CCO |(,,;1,1,;2,2,)|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxCoordinates);
string smi = smigen.Create(mol);
Assert.AreEqual("CCO |(,,;1,1,;2,2,)|", smi);
}
public void RoundTripPEGn()
{
var mol = smipar.ParseSmiles("CCCOCCO |Sg:n:1,2,3::ht|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxPolymer);
string smi = smigen.Create(mol);
Assert.AreEqual("CCCOCCO |Sg:n:1,2,3:n:ht|", smi);
}
public void RoundTripMulticenter()
{
var mol = smipar.ParseSmiles("c1ccccc1.*Cl |m:6:0.1.2.3.4.5|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.UseAromaticSymbols |
SmiFlavors.CxMulticenter);
string smi = smigen.Create(mol);
Assert.AreEqual("c1ccccc1.*Cl |m:6:0.1.2.3.4.5|", smi);
}
public void CanonMulticenter()
{
var mol = smipar.ParseSmiles("c1ccccc1.*Cl |m:6:0.1.2.3.4.5|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.UseAromaticSymbols |
SmiFlavors.CxMulticenter |
SmiFlavors.Canonical);
string smi = smigen.Create(mol);
Assert.AreEqual("*Cl.c1ccccc1 |m:0:2.3.4.5.6.7|", smi);
}
public void GenerateLabelledSmiles()
{
var mol = new AtomContainer();
mol.Atoms.Add(new Atom("C"));
mol.Atoms[0].ImplicitHydrogenCount = 3;
mol.Atoms.Add(new Atom("C"));
mol.Atoms[1].ImplicitHydrogenCount = 2;
mol.Atoms.Add(new PseudoAtom("R1"));
mol.Atoms[2].ImplicitHydrogenCount = 0;
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Single);
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxAtomLabel);
string smi = smigen.Create(mol);
Assert.AreEqual("CC* |$;;R1$|", smi);
}
public void RoundTripReactionAtomLabelsAndFragmentGroups()
{
IReaction rxn = smipar.ParseReactionSmiles("CC(C)c1ccccc1.ClC([*])=O>ClCCl.[Al+3].[Cl-].[Cl-].[Cl-]>CC(C)c1ccc(cc1)C([*])=O |$;;;;;;;;;;;R1;;;;;;;;;;;;;;;;;;;R1;$,f:3.4.5.6|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxAtomLabel |
SmiFlavors.CxFragmentGroup);
Assert.AreEqual("CC(C)C1=CC=CC=C1.ClC(*)=O>ClCCl.[Al+3].[Cl-].[Cl-].[Cl-]>CC(C)C1=CC=C(C=C1)C(*)=O |f:3.4.5.6,$;;;;;;;;;;;R1;;;;;;;;;;;;;;;;;;;R1$|", smigen.Create(rxn));
}
public void Chembl367774()
{
using (MDLV2000Reader mdlr = new MDLV2000Reader(GetType().Assembly.GetManifestResourceStream(GetType(), "CHEMBL367774.mol")))
{
IAtomContainer container = mdlr.Read(builder.NewAtomContainer());
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxSmiles);
Assert.AreEqual("OC(=O)C1=CC(F)=CC=2NC(=NC12)C3=CC=C(C=C3F)C4=CC=CC=C4", smigen.Create(container));
}
}
public void Chebi53695()
{
using (var ins = GetType().Assembly.GetManifestResourceStream(GetType(), "CHEBI_53695.mol"))
using (var mdlr = new MDLV2000Reader(ins))
{
IAtomContainer mol = mdlr.Read(CDK.Builder.NewAtomContainer());
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxSmiles | SmiFlavors.AtomicMassStrict);
Assert.AreEqual("C(C(=O)OC)(C*)*C(C(C1=C(C(=C(C(=C1[2H])[2H])[2H])[2H])[2H])(*)[2H])([2H])[2H] |Sg:n:0,1,2,3,4,5:n:ht,Sg:n:8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24:m:ht|", smigen.Create(mol));
}
}
static void Main()
{
{
#region SmiFlavors
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.Isomeric);
#endregion
}
{
#region SmiFlavor_Isomeric
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.Stereo | SmiFlavors.AtomicMass);
#endregion
}
{
string smi = null;
SmilesGenerator sg = null;
{
#region 1
IAtomContainer ethanol = TestMoleculeFactory.MakeEthanol();
sg = new SmilesGenerator(SmiFlavors.Generic);
smi = sg.Create(ethanol); // CCO, C(C)O, C(O)C, or OCC
sg = SmilesGenerator.Unique;
smi = sg.Create(ethanol); // only CCO
#endregion
#region 2
IAtomContainer benzene = TestMoleculeFactory.MakeBenzene();
// 'benzene' molecule has no arom flags, we always get Kekulé output
sg = new SmilesGenerator(SmiFlavors.Generic);
smi = sg.Create(benzene); // C1=CC=CC=C1
sg = new SmilesGenerator(SmiFlavors.Generic | SmiFlavors.UseAromaticSymbols);
smi = sg.Create(benzene); // C1=CC=CC=C1 flags not set!
// Note, in practice we'd use an aromaticity algorithm
foreach (IAtom a in benzene.Atoms)
{
a.IsAromatic = true;
}
foreach (IBond b in benzene.Bonds)
{
b.IsAromatic = true;
}
// 'benzene' molecule now has arom flags, we always get aromatic SMILES if we request it
sg = new SmilesGenerator(SmiFlavors.Generic);
smi = sg.Create(benzene); // C1=CC=CC=C1
sg = new SmilesGenerator(SmiFlavors.Generic | SmiFlavors.UseAromaticSymbols);
smi = sg.Create(benzene); // c1ccccc1
#endregion
}
}
{
#region 4
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
SmilesGenerator sg = new SmilesGenerator(SmiFlavors.Generic);
int n = mol.Atoms.Count;
int[] order = new int[n];
// the order array is filled up as the SMILES is generated
string smi = sg.Create(mol, order);
// load the coordinates array such that they are in the order the atoms
// are read when parsing the SMILES
Vector2[] coords = new Vector2[mol.Atoms.Count];
for (int i = 0; i < coords.Length; i++)
{
coords[order[i]] = mol.Atoms[i].Point2D.Value;
}
// SMILES string suffixed by the coordinates
string smi2d = smi + " " + Arrays.ToJavaString(coords);
#endregion
}
{
#region 5 ctor_SmiFlavor
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.Stereo | SmiFlavors.Canonical);
#endregion
}
{
#region Aromatic
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.UseAromaticSymbols);
#endregion
}
{
IAtomContainer container = null;
#region WithAtomClasses
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.AtomAtomMap);
smigen.CreateSMILES(container); // C[CH2:4]O second atom has class = 4
#endregion
}
{
#region WithAtomClasses
IAtomContainer container = TestMoleculeFactory.MakeAlphaPinene();
SmilesGenerator smilesGen = SmilesGenerator.Unique.WithAtomClasses();
smilesGen.CreateSMILES(container); // C[CH2:4]O second atom has class = 4
#endregion
}
{
#region Create_IAtomContainer_int
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
SmilesGenerator sg = new SmilesGenerator();
int n = mol.Atoms.Count;
int[] order = new int[n];
// the order array is filled up as the SMILES is generated
string smi = sg.Create(mol, order);
// load the coordinates array such that they are in the order the atoms
// are read when parsing the SMILES
Vector2[] coords = new Vector2[mol.Atoms.Count];
for (int i = 0; i < coords.Length; i++)
{
coords[order[i]] = mol.Atoms[i].Point2D.Value;
}
// SMILES string suffixed by the coordinates
string smi2d = smi + " " + Arrays.ToJavaString(coords);
#endregion
}
{
IAtomContainer container = null;
#region Create_IAtomContainer_int_int
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
SmilesGenerator sg = new SmilesGenerator();
int n = mol.Atoms.Count;
int[] order = new int[n];
// the order array is filled up as the SMILES is generated
string smi = sg.Create(mol, order);
// load the coordinates array such that they are in the order the atoms
// are read when parsing the SMILES
Vector2[] coords = new Vector2[mol.Atoms.Count];
for (int i = 0; i < coords.Length; i++)
{
coords[order[i]] = container.Atoms[i].Point2D.Value;
}
// SMILES string suffixed by the coordinates
string smi2d = smi + " " + Arrays.ToJavaString(coords);
#endregion
}
}