public void LoadFromFile()
{
var factory = new Abbreviations();
//Assert.AreEqual(27, factory.LoadFromFile("obabel_superatoms.smi"));
Assert.AreEqual(27, factory.LoadFromFile("NCDK.Depict.obabel_superatoms.smi"));
}
public void SnCl2()
{
var factory = new Abbreviations();
var mol = Smi("Cl[Sn]Cl");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("SnCl2", sgroups[0].Subscript);
}
public void HOOH()
{
var factory = new Abbreviations();
var mol = Smi("OO");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("HOOH", sgroups[0].Subscript);
}
public void AvoidOverZealousAbbreviations()
{
var factory = new Abbreviations {
"*c1ccccc1 Ph"
};
var mol = Smi("Clc1ccccc1");
Assert.AreEqual(0, factory.Apply(mol));
}
public void PhenylShouldNotMatchBenzene()
{
var factory = new Abbreviations {
"*c1ccccc1 Ph"
};
var mol = Smi("c1ccccc1");
var sgroups = factory.Generate(mol);
Assert.AreEqual(0, sgroups.Count);
}
public void HclSaltOfEdci()
{
var factory = new Abbreviations {
"CCN=C=NCCCN(C)C EDCI"
};
var mol = Smi("CCN=C=NCCCN(C)C.Cl");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("EDCI·HCl", sgroups[0].Subscript);
}
public void SO3minusFromHeteroCollapseNone()
{
var factory = new Abbreviations {
"*S(=O)(=O)[O-] SO3-"
};
var mol = Smi("c1ccccc1N(S(=O)(=O)[O-])S(=O)(=O)[O-]");
var sgroups = factory.Generate(mol);
Assert.AreEqual(2, sgroups.Count);
Assert.AreEqual("SO3-", sgroups[0].Subscript);
Assert.AreEqual("SO3-", sgroups[1].Subscript);
}
public void PotassiumCarbonate()
{
var mol = Smi("[K+].[O-]C(=O)[O-].[K+]");
var factory = new Abbreviations {
"[K+].[O-]C(=O)[O-].[K+] K2CO3"
};
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("K2CO3", sgroups[0].Subscript);
Assert.AreEqual(6, sgroups[0].Atoms.Count);
}
public void IPrFromHeteroCollapse()
{
var factory = new Abbreviations {
"*C(C)C iPr"
};
var mol = Smi("[CH3:27][CH:19]([CH3:28])[C:20]1=[N:26][C:23](=[CH:22][S:21]1)[C:24](=[O:25])O");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("iPr", sgroups[0].Subscript);
Assert.AreEqual(1, sgroups[0].Bonds.Count);
Assert.AreEqual(3, sgroups[0].Atoms.Count);
}
public void PhenylShouldMatchKekuleForm()
{
var factory = new Abbreviations {
"*c1ccccc1 Ph"
};
var mol = Smi("CCCCC1=CC=CC=C1");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("Ph", sgroups[0].Subscript);
Assert.AreEqual(6, sgroups[0].Atoms.Count);
Assert.AreEqual(1, sgroups[0].Bonds.Count);
}
public void PhenylShouldAbbreviateExplicitHydrogens()
{
var factory = new Abbreviations {
"*c1ccccc1 Ph"
};
var mol = Smi("CCCCc1ccc([H])cc1");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("Ph", sgroups[0].Subscript);
Assert.AreEqual(7, sgroups[0].Atoms.Count);
Assert.AreEqual(1, sgroups[0].Bonds.Count);
}
public void DcmAndTfaNoSingleFrag()
{
var factory = new Abbreviations();
var mol = Smi("ClCCl.FC(F)(F)C(=O)O");
factory.Add("ClCCl DCM");
factory.Add("FC(F)(F)C(=O)O TFA");
factory.ContractToSingleLabel = false;
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("DCM", sgroups[0].Subscript);
}
public void NBocFromHeteroCollapseExplicitH()
{
var factory = new Abbreviations {
"*C(=O)OC(C)(C)C Boc"
};
var mol = Smi("c1cc2ccccc2ccn1C(=O)OC(C)(C)C");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("NBoc", sgroups[0].Subscript);
Assert.AreEqual(2, sgroups[0].Bonds.Count);
Assert.AreEqual(8, sgroups[0].Atoms.Count);
}
public void TFASaltDisconnected()
{
Abbreviations factory = new Abbreviations();
IAtomContainer mol = Smi("c1ccccc1c1ccccc1.FC(F)(F)C(=O)O");
factory.Add("*C(F)(F)F CF3");
factory.Add("*C(=O)O CO2H");
factory.Add("FC(F)(F)C(=O)O TFA");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("TFA", sgroups[0].Subscript);
}
public void AvoidAmbiguity()
{
var smi = "C1CCCCC1=NC(C)C";
var factory = new Abbreviations
{
"*C(C)C iPr"
};
var mol = Smi(smi);
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("iPr", sgroups[0].Subscript);
}
public void AbbreviationsHavePriority()
{
var factory = new Abbreviations
{
"*CCC Pr",
"*CC Et"
};
var mol = Smi("c1ccccc1CCC");
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("Pr", sgroups[0].Subscript);
}
public void MultipleDisconnectedAbbreviations2()
{
var smi = "ClCCl.Cl[Pd]Cl.[Fe+2].c1ccc(P([c-]2cccc2)c2ccccc2)cc1.c1ccc(P([c-]2cccc2)c2ccccc2)cc1";
var factory = new Abbreviations
{
"Cl[Pd]Cl.[Fe+2].c1ccc(P([c-]2cccc2)c2ccccc2)cc1.c1ccc(P([c-]2cccc2)c2ccccc2)cc1 Pd(dppf)Cl2",
"Cl[Pd]Cl PdCl2"
};
var mol = Smi(smi);
var sgroups = factory.Generate(mol);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual("Pd(dppf)Cl2", sgroups[0].Subscript);
}
public void TFASaltConnected()
{
var factory = new Abbreviations();
var mol = Smi("FC(F)(F)C(=O)O");
factory.Add("*C(F)(F)F CF3");
factory.Add("*C(=O)O CO2H");
factory.Add("FC(F)(F)C(=O)O TFA");
var sgroups = factory.Generate(mol);
Assert.AreEqual(2, sgroups.Count);
for (int i = 0; i < 2; i++)
{
var sgroup = sgroups[i];
Assert.IsTrue(sgroup.Subscript.Contains("CF3") || sgroup.Subscript.Contains("CO2H"));
}
Assert.AreNotEqual(sgroups[0].Subscript, sgroups[1].Subscript);
}
public void NitroGroups()
{
var factory = new Abbreviations
{
"*N(=O)(=O) NO2",
"*[N+]([O-])(=O) NO2"
};
var mol = Smi("O=N(=O)CCCC[N+]([O-])=O");
var sgroups = factory.Generate(mol);
Assert.AreEqual(2, sgroups.Count);
Assert.AreEqual("NO2", sgroups[0].Subscript);
Assert.AreEqual(3, sgroups[0].Atoms.Count);
Assert.AreEqual(1, sgroups[0].Bonds.Count);
Assert.AreEqual("NO2", sgroups[1].Subscript);
Assert.AreEqual(3, sgroups[1].Atoms.Count);
Assert.AreEqual(1, sgroups[1].Bonds.Count);
}
public void DontOverwriteExistingSgroups()
{
var factory = new Abbreviations {
"*CCC Bu"
};
var mol = Smi("c1ccccc1CCC");
var sgroup = new Sgroup();
sgroup.Atoms.Add(mol.Atoms[6]);
sgroup.Atoms.Add(mol.Atoms[7]);
sgroup.Atoms.Add(mol.Atoms[8]);
sgroup.Type = SgroupType.CtabAbbreviation;
sgroup.Subscript = "n-Bu";
mol.SetCtabSgroups(new[] { sgroup });
var sgroups = factory.Generate(mol);
Assert.AreEqual(0, sgroups.Count);
}
public void Phenyl()
{
var factory = new Abbreviations {
"*c1ccccc1 Ph"
};
var mol = Smi("CCCCCCC(c1ccccc1)(c1ccccc1)c1ccccc1");
var sgroups = factory.Generate(mol);
Assert.AreEqual(3, sgroups.Count);
Assert.AreEqual("Ph", sgroups[0].Subscript);
Assert.AreEqual(6, sgroups[0].Atoms.Count);
Assert.AreEqual(1, sgroups[0].Bonds.Count);
Assert.AreEqual("Ph", sgroups[1].Subscript);
Assert.AreEqual(6, sgroups[1].Atoms.Count);
Assert.AreEqual(1, sgroups[1].Bonds.Count);
Assert.AreEqual("Ph", sgroups[2].Subscript);
Assert.AreEqual(6, sgroups[2].Atoms.Count);
Assert.AreEqual(1, sgroups[2].Bonds.Count);
}