public void EscapedAtomLabels()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|$R';;;;;;$|", state));
Assert.IsTrue(state.atomLabels[0] == "R'");
}
public void HydrogenBondingTruncated()
{
CxSmilesState state = new CxSmilesState();
Assert.AreEqual(-1, CxSmilesParser.ProcessCx("|H:0.1,2.3", state));
Assert.AreEqual(-1, CxSmilesParser.ProcessCx("|H:0.1,2.", state));
}
public void AtomLabelsEmpty()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|$$|", state));
Assert.AreEqual(0, state.atomLabels.Count);
}
public void EscapedAtomLabels2()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|$;;;(C(R41)(R41))n;;R41;R41;R41;;_AP1;R41;R41;;_AP1$|", state));
Assert.IsTrue(state.atomLabels[3] == "(C(R41)(R41))n");
}
public void AtomLabelsTruncated1()
{
CxSmilesState state = new CxSmilesState();
Assert.AreEqual(-1, CxSmilesParser.ProcessCx("|$;;;Het", state));
Assert.AreEqual(-1, CxSmilesParser.ProcessCx("|$;;;Het;", state));
}
public void RemoveUnderscore()
{
CxSmilesState state = new CxSmilesState();
CxSmilesParser.ProcessCx("|$;;;_R1;$|", state);
Assert.AreEqual("R1", state.atomLabels[3]);
}
public void AtomLabels()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|$;;;Het;;;;;A$|", state));
Assert.IsTrue(state.atomLabels.Contains(new KeyValuePair <int, string>(3, "Het")));
Assert.IsTrue(state.atomLabels.Contains(new KeyValuePair <int, string>(8, "A")));
}
public void AtomValues()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|$_AV:;;;5;;;;;8$|", state));
Assert.IsTrue(state.atomValues.Contains(new KeyValuePair <int, string>(3, "5")));
Assert.IsTrue(state.atomValues.Contains(new KeyValuePair <int, string>(8, "8")));
}
public void RelativeStereoMolecule()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|r|", state));
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|r,$_R1$|", state));
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|$_R1$,r|", state));
}
public void FragmentGrouping()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|f:0.1.2.3,4.5.6|", state));
Assert.IsTrue(Compares.AreDeepEqual(
new[] { new[] { 0, 1, 2, 3 }, new[] { 4, 5, 6 } },
state.fragGroups));
}
public void MultiAtomSRU()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|Sg:n:1,2,3:m:ht|", state));
Assert.IsTrue(Compares.DeepContains(
state.sgroups,
new CxSmilesState.PolymerSgroup("n", new[] { 1, 2, 3 }, "m", "ht")));
}
public void DataSgroups()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|SgD::cdk:ReactionConditions:Heat Hv|", state));
Assert.IsTrue(Compares.DeepContains(
state.dataSgroups,
new CxSmilesState.DataSgroup(new List <int>(), "cdk:ReactionConditions", "Heat\nHv", "", "", "")));
}
public void FragmentGroupingFollowedByAtomLabels()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|f:0.1.2.3,4.5.6,$;;;R$|", state));
Assert.IsTrue(Compares.AreDeepEqual(
new[] { new[] { 0, 1, 2, 3 }, new[] { 4, 5, 6 } },
state.fragGroups));
Assert.IsTrue(state.atomLabels.Contains(new KeyValuePair <int, string>(3, "R")));
}
public void Coords()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|(.0,-1.5,;-1.3,-.75,;-2.6,-1.5,;-3.9,-.75,;-3.9,.75,)|", state));
Assert.IsTrue(new AprxDoubleArray(0, -1.5, 0).Matches(state.atomCoords[0]));
Assert.IsTrue(new AprxDoubleArray(-1.3, -.75, 0).Matches(state.atomCoords[1]));
Assert.IsTrue(new AprxDoubleArray(-2.6, -1.5, 0).Matches(state.atomCoords[2]));
Assert.IsTrue(new AprxDoubleArray(-3.9, -.75, 0).Matches(state.atomCoords[3]));
Assert.IsTrue(new AprxDoubleArray(-3.9, .75, 0).Matches(state.atomCoords[4]));
}
public void PositionalVariationImpliedLayer()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|m:2:5.6.7.8.9.10,4:5.6.7.8.9|", state));
Assert.IsTrue(Compares.DeepContains(
state.positionVar,
new KeyValuePair <int, IList <int> >(2, new[] { 5, 6, 7, 8, 9, 10 })));
Assert.IsTrue(Compares.DeepContains(
state.positionVar,
new KeyValuePair <int, IList <int> >(4, new[] { 5, 6, 7, 8, 9 })));
}
/// <summary>
/// Parses CXSMILES layer and set attributes for atoms and bonds on the provided reaction.
/// </summary>
/// <param name="title">SMILES title field</param>
/// <param name="rxn">parsed reaction</param>
private void ParseRxnCXSMILES(string title, IReaction rxn)
{
if (title != null && title.StartsWithChar('|'))
{
int pos;
CxSmilesState cxstate;
if ((pos = CxSmilesParser.ProcessCx(title, cxstate = new CxSmilesState())) >= 0)
{
// set the correct title
rxn.SetProperty(CDKPropertyName.Title, title.Substring(pos));
var atomToMol = new Dictionary <IAtom, IAtomContainer>(100);
var atoms = new List <IAtom>();
HandleFragmentGrouping(rxn, cxstate);
// merge all together
foreach (var mol in rxn.Reactants)
{
foreach (var atom in mol.Atoms)
{
atoms.Add(atom);
atomToMol[atom] = mol;
}
}
foreach (var mol in rxn.Agents)
{
foreach (var atom in mol.Atoms)
{
atoms.Add(atom);
atomToMol[atom] = mol;
}
}
foreach (var mol in rxn.Products)
{
foreach (var atom in mol.Atoms)
{
atoms.Add(atom);
atomToMol[atom] = mol;
}
}
AssignCxSmilesInfo(rxn.Builder, rxn, atoms, atomToMol, cxstate);
}
}
}
/// <summary>
/// Parses CXSMILES layer and set attributes for atoms and bonds on the provided molecule.
/// </summary>
/// <param name="title">SMILES title field</param>
/// <param name="mol">molecule</param>
private void ParseMolCXSMILES(string title, IAtomContainer mol)
{
if (title != null && title.StartsWithChar('|'))
{
int pos;
CxSmilesState cxstate;
if ((pos = CxSmilesParser.ProcessCx(title, cxstate = new CxSmilesState())) >= 0)
{
// set the correct title
mol.Title = title.Substring(pos);
var atomToMol = new Dictionary <IAtom, IAtomContainer>(mol.Atoms.Count);
var atoms = new List <IAtom>(mol.Atoms.Count);
foreach (var atom in mol.Atoms)
{
atoms.Add(atom);
atomToMol.Add(atom, mol);
}
AssignCxSmilesInfo(mol.Builder, mol, atoms, atomToMol, cxstate);
}
}
}
public void SkipCisTransUnspec()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|c:2,6,8,ctu:10,t:1,4,5|", state));
}
public void SkipLonePairDefinitions()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|c:6,8,t:4,lp:2:2,4:1,11:1,m:1:8.9|", state));
}
public void HydrogenBondingSkipped()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|H:0.1,2.3|", state));
}
public void HydrogenAndCoordinationBondingSkipped()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|H:0.1,2.3,C:6.7,3.4|", state));
}
public void RelativeStereoReaction()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|r:2,4,5|", state));
}
public void SkipTrans()
{
CxSmilesState state = new CxSmilesState();
Assert.AreNotEqual(-1, CxSmilesParser.ProcessCx("|t:1,4,5|", state));
}