public void Isotopes()
{
// FIXME SMARTS Grammar needs fixing/replacing [12] is not considered valid
Assert.IsFalse(SmartsPattern.Create("[12*]").Matches(Smi("C")));
Assert.IsFalse(SmartsPattern.Create("[12*]").Matches(Smi("[CH4]")));
Assert.IsTrue(SmartsPattern.Create("[12*]").Matches(Smi("[12CH4]")));
Assert.IsFalse(SmartsPattern.Create("[12*]").Matches(Smi("[13CH4]")));
Assert.IsFalse(SmartsPattern.Create("[13*]").Matches(Smi("C")));
Assert.IsFalse(SmartsPattern.Create("[13*]").Matches(Smi("[CH4]")));
Assert.IsFalse(SmartsPattern.Create("[13*]").Matches(Smi("[12CH4]")));
Assert.IsTrue(SmartsPattern.Create("[13*]").Matches(Smi("[13CH4]")));
Assert.IsTrue(SmartsPattern.Create("[0*]").Matches(Smi("C")));
Assert.IsTrue(SmartsPattern.Create("[0*]").Matches(Smi("[CH4]")));
Assert.IsFalse(SmartsPattern.Create("[0*]").Matches(Smi("[12CH4]")));
Assert.IsFalse(SmartsPattern.Create("[0*]").Matches(Smi("[13CH4]")));
// Not possible with current grammar
// assertFalse(SmartsPattern.create("[!0*]").matches(smi("C")));
// assertFalse(SmartsPattern.create("[!0*]").matches(smi("[CH4]")));
// assertTrue(SmartsPattern.create("[!0*]").matches(smi("[12CH4]")));
// assertTrue(SmartsPattern.create("[!0*]").matches(smi("[13CH4]")));
}
public void SmartsMatchingReaction()
{
Assert.IsTrue(SmartsPattern.Create("CC").Matches(Rsmi("CC>>")));
Assert.IsTrue(SmartsPattern.Create("CC").Matches(Rsmi(">>CC")));
Assert.IsTrue(SmartsPattern.Create("CC").Matches(Rsmi(">CC>")));
Assert.IsFalse(SmartsPattern.Create("CO").Matches(Rsmi(">>CC")));
}
public void HIsotope()
{
var ptrn = SmartsPattern.Create("[2#1,3#1]");
Assert.IsFalse(ptrn.Matches(Smi("[H][H]")));
Assert.IsTrue(ptrn.Matches(Smi("[2H]")));
Assert.IsTrue(ptrn.Matches(Smi("[3H]")));
}
public void HasIsotope()
{
var ptrn = SmartsPattern.Create("[!0]");
Assert.IsFalse(ptrn.Matches(Smi("C")));
Assert.IsTrue(ptrn.Matches(Smi("[12C]")));
Assert.IsTrue(ptrn.Matches(Smi("[13C]")));
}
public void ReactionGrouping()
{
Assert.IsTrue(SmartsPattern.Create("[Na+].[OH-]>>").Matches(Rsmi("[Na+].[OH-]>>")));
Assert.IsTrue(SmartsPattern.Create("[Na+].[OH-]>>").Matches(Rsmi("[Na+].[OH-]>> |f:0.1|")));
Assert.IsTrue(SmartsPattern.Create("([Na+].[OH-])>>").Matches(Rsmi("[Na+].[OH-]>> |f:0.1|")));
// this one can't match because we don't know if NaOH is one component from the input smiles
Assert.IsFalse(SmartsPattern.Create("([Na+].[OH-])>>").Matches(Rsmi("[Na+].[OH-]>>")));
}
public void Stereochemistry()
{
Assert.IsTrue(SmartsPattern.Create("C[C@H](O)CC").Matches(Smi("C[C@H](O)CC")));
Assert.IsFalse(SmartsPattern.Create("C[C@H](O)CC").Matches(Smi("C[C@@H](O)CC")));
Assert.IsFalse(SmartsPattern.Create("C[C@H](O)CC").Matches(Smi("CC(O)CC")));
}
public void Components()
{
Assert.IsTrue(SmartsPattern.Create("(O).(O)").Matches(Smi("O.O")));
Assert.IsFalse(SmartsPattern.Create("(O).(O)").Matches(Smi("OO")));
}
public void Stereo_ring_closures()
{
var ptrn = SmartsPattern.Create("[C@@]1(O[C@@]([C@@]([C@]([C@]1(C)O)(C)O)(O)C)(O)C)(O)C");
Assert.IsTrue(ptrn.Matches(Smi("[C@@]1(O[C@@]([C@@]([C@]([C@]1(C)O)(C)O)(O)C)(O)C)(O)C")));
}
public void NoMapsInQueryMapsInTargetIgnored()
{
Assert.AreEqual(4, SmartsPattern.Create("C>>C").MatchAll(Rsmi("[C:7][C:8]>>[C:7][C:8]")).Count());
}
public void CCBondForming()
{
Assert.AreEqual(2, SmartsPattern.Create("([C:1]).([C:2])>>[C:1][C:2]").MatchAll(Rsmi("[C-:13]#[N:14].[K+].[CH:3]1=[CH:4][C:5](=[CH:11][CH:12]=[C:2]1[CH2:1]Br)[C:6](=[O:10])[CH:7]2[CH2:8][CH2:9]2>>[CH:3]1=[CH:4][C:5](=[CH:11][CH:12]=[C:2]1[CH2:1][C:13]#[N:14])[C:6](=[O:10])[CH:7]2[CH2:8][CH2:9]2 |f:0.1|")).Count());
}
public void AtomMapsWithOrLogic3()
{
Assert.AreEqual(2, SmartsPattern.Create("[C:1][C:1]>>[C:1]").MatchAll(Rsmi("[CH3:7][CH3:7]>>[CH3:7][CH3:8]")).Count());
}
public void MismatchedQueryMapsIgnored()
{
Assert.AreEqual(4, SmartsPattern.Create("[C:1]>>[C:2]").MatchAll(Rsmi("[CH3:7][CH3:8]>>[CH3:7][CH3:8]")).Count());
}
public void MappedMatch()
{
Assert.AreEqual(2, SmartsPattern.Create("[C:1]>>[C:1]").MatchAll(Rsmi("[CH3:7][CH3:8]>>[CH3:7][CH3:8]")).Count());
}
[TestMethod(), Ignore()] // Not supported yet
public void OptionalMapping()
{
Assert.AreEqual(2, SmartsPattern.Create("[C:?1]>>[C:?1]").MatchAll(Rsmi("[CH3:7][CH3:8]>>[CH3:7][CH3:8]")).Count());
Assert.AreEqual(4, SmartsPattern.Create("[C:?1]>>[C:?1]").MatchAll(Rsmi("CC>>CC")).Count());
}
public void NoMapsInTarget()
{
Assert.AreEqual(0, SmartsPattern.Create("[C:1]>>[C:1]").MatchAll(Rsmi("C>>C")).Count());
}
public void UnpairedMapIsQueryIsIgnored()
{
Assert.AreEqual(4, SmartsPattern.Create("[C:1]>>C").MatchAll(Rsmi("[CH3:7][CH3:8]>>[CH3:7][CH3:8]")).Count());
Assert.AreEqual(4, SmartsPattern.Create("C>>[C:1]").MatchAll(Rsmi("[CH3:7][CH3:8]>>[CH3:7][CH3:8]")).Count());
}
public void MatchProductStereo()
{
Assert.AreEqual(1, SmartsPattern.Create(">>C[C@H](CC)[C@H](CC)O")
.MatchAll(Rsmi(">>C[C@H](CC)[C@H](CC)O"))
.CountUnique());
}
public void NoMaps()
{
Assert.AreEqual(4, SmartsPattern.Create("C>>C").MatchAll(Rsmi("CC>>CC")).Count());
}