public MoleculeBuilder FromSmiles(string smiles)
{
var builder = new StringBuilder();
// Switch the current directory to the application's bin directory so
// it can find all the related Open Babel files
using(new TemporarilySwitchCurrentDirectory(new DirectoryInfo(AppDomain.CurrentDomain.RelativeSearchPath)))
{
var process = new Process
{
StartInfo =
{
FileName = @".\obabel.exe",
Arguments = string.Format("-:\"{0}\" -omol --gen3d", smiles),
UseShellExecute = false,
RedirectStandardOutput = true
}
};
process.OutputDataReceived += (sender, args) => builder.AppendLine(args.Data);
process.Start();
process.BeginOutputReadLine();
process.WaitForExit();
}
var mol = builder.ToString();
var reader = new MolReader(() => new StringReader(mol));
atomData = reader.AtomData;
bondData = reader.BondData;
return this;
}
public void MedianTest()
{
Assert.AreEqual(Benzene.BalabanJ, Math.Round(this._molSet.Median("BalabanJ"), 4));
Assert.AreEqual(Benzene.Kappa3, Math.Round(this._molSet.Median("Kappa3"), 4));
Assert.AreEqual(Benzene.LabuteASA, Math.Round(this._molSet.Median("Labute ASA"), 4));
Assert.AreEqual(Benzene.Chi0, Math.Round(this._molSet.Median("Chi0"), 4));
var propane = new MolReader(FileNames.PropaneFilePath).GetMol();
var benzene = new MolReader(FileNames.BenzeneFilePath).GetMol();
var cyclosporin = new MolReader(FileNames.CyclosporineFilePath).GetMol();
var phenylPyridine = new MolReader(FileNames.PyridineFilePath).GetMol();
this._molSet = new MolDescriptorSet(new List <MolDescriptor>
{
new MolDescriptor(propane),
new MolDescriptor(benzene),
new MolDescriptor(cyclosporin),
new MolDescriptor(phenylPyridine)
});
var BalabanJMedian = (PhenylPyridine.BalabanJ + Benzene.BalabanJ) / 2;
var Kappa3Median = (PhenylPyridine.Kappa3 + Benzene.Kappa3) / 2;
var LabuteASAMedian = (PhenylPyridine.LabuteASA + Benzene.LabuteASA) / 2;
var Chi0Median = (PhenylPyridine.Chi0 + Benzene.Chi0) / 2;
Assert.AreEqual(Math.Round(BalabanJMedian, 4), Math.Round(this._molSet.Median("BalabanJ"), 4));
Assert.AreEqual(Math.Round(Kappa3Median, 4), Math.Round(this._molSet.Median("Kappa3"), 4));
Assert.AreEqual(Math.Round(LabuteASAMedian, 4), Math.Round(this._molSet.Median("Labute ASA"), 4));
Assert.AreEqual(Math.Round(Chi0Median, 4), Math.Round(this._molSet.Median("Chi0"), 4));
}
public void TestSetup()
{
var propane = new MolReader(FileNames.PropaneFilePath).GetMol();
var benzene = new MolReader(FileNames.BenzeneFilePath).GetMol();
var cyclosporin = new MolReader(FileNames.CyclosporineFilePath).GetMol();
this._molSet = new MolDescriptorSet(new List <MolDescriptor> {
new MolDescriptor(propane), new MolDescriptor(benzene), new MolDescriptor(cyclosporin)
});
}
public void PostedFileTest()
{
using (var stream = new FileStream(FileNames.MultiMolFilePath, FileMode.Open))
{
var postedFile = new Mock <HttpPostedFileBase>();
postedFile.Setup(f => f.ContentLength).Returns((int)stream.Length).Verifiable();
postedFile.Setup(f => f.FileName).Returns(FileNames.MultiMolFilePath.Split('/').Last()).Verifiable();
postedFile.Setup(f => f.InputStream).Returns(stream).Verifiable();
var reader = new MolReader(postedFile.Object);
this._molCollection = reader.Open();
Assert.AreEqual <int>(1597, this._molCollection.Count(), string.Format("PostedFileTest: {0} does not equal 1597", this._molCollection.Count()));
File.Delete(reader.FilePath);
}
}
public void GasteigerChargeTest()
{
var mol = new MolReader(FileNames.BenzeneFilePath).GetMol();
var chargedMol = mol.AssignGasteigerCharges();
Assert.IsTrue(chargedMol.Atoms().Count() > 0);
foreach (var atom in chargedMol.Atoms())
{
if (atom.IsCarbon())
{
Assert.AreEqual(-0.0618, Math.Round(atom.GetPartialCharge(), 4));
}
else
{
Assert.AreEqual(0.0618, Math.Round(atom.GetPartialCharge(), 4));
}
}
mol = new MolReader(FileNames.PropaneFilePath).GetMol();
chargedMol = mol.AssignGasteigerCharges();
Assert.IsTrue(chargedMol.Atoms().Count() > 0);
foreach (var atom in chargedMol.Atoms())
{
if (atom.IsCarbon() && (atom.GetIdx() == 1 || atom.GetIdx() == 3))
{
Assert.AreEqual(-0.0655, Math.Round(atom.GetPartialCharge(), 4));
}
else if (atom.IsCarbon() && atom.GetIdx() == 2)
{
Assert.AreEqual(-0.0588, Math.Round(atom.GetPartialCharge(), 4));
}
else if (atom.IsHydrogen() && atom.Neighbors().First().IsCarbon() && (atom.Neighbors().First().GetIdx() == 1 || atom.Neighbors().First().GetIdx() == 3))
{
Assert.AreEqual(0.0230, Math.Round(atom.GetPartialCharge(), 4));
}
else if (atom.IsHydrogen() && atom.Neighbors().First().IsCarbon() && atom.Neighbors().First().GetIdx() == 2)
{
Assert.AreEqual(0.0260, Math.Round(atom.GetPartialCharge(), 4));
}
}
}
public void FeatureNamesTest()
{
var mol = new MolReader(FileNames.PropaneFilePath).GetMol();
this._descriptor = new MolDescriptor(mol);
Assert.AreEqual(_featureNames.Length, MolDescriptor.FeatureCount());
foreach (var name in this._featureNames)
{
Assert.IsTrue(MolDescriptor.GetFeatureNames().Contains(name));
}
try
{
this._descriptor.FeatureValue("Fenske Descriptor");
Assert.Fail("Fenske Descriptor is not a valid feature");
}
catch (ArgumentException)
{
// Expected
}
}
public void FormalChargeTest()
{
var mol = new MolReader(FileNames.AceticAcidFilePath).GetMol();
this._descriptor = new MolDescriptor(mol);
Assert.AreEqual(0, this._descriptor.TotalCharge);
var newMol = mol.AssignGasteigerCharges();
Assert.AreEqual(0, Math.Round(newMol.Atoms().Sum(a => a.GetPartialCharge()), 4));
mol = new MolReader(FileNames.AcetateFilePath).GetMol();
this._descriptor = new MolDescriptor(mol);
Assert.AreEqual(-1, this._descriptor.TotalCharge);
newMol = mol.AssignGasteigerCharges();
this._descriptor = new MolDescriptor(newMol);
Assert.AreEqual(-1, Math.Round(newMol.Atoms().Sum(a => a.GetPartialCharge()), 4));
mol = new MolReader(FileNames.CyclosporineFilePath).GetMol();
this._descriptor = new MolDescriptor(mol);
Assert.AreEqual(0d, Math.Round(this._descriptor.TotalCharge, 4));
}
public void PropaneTest()
{
var mol = new MolReader(FileNames.PropaneFilePath).GetMol();
this._descriptor = new MolDescriptor(mol);
Assert.AreEqual(Propane.Title, this._descriptor.Title);
Assert.AreEqual(Propane.Smiles, this._descriptor.Smiles);
Assert.AreEqual(Propane.SingleCarbonCount, this._descriptor.FragmentCount("C"));
Assert.AreEqual(Propane.DoubleCarbonCount, this._descriptor.FragmentCount("CC"));
Assert.AreEqual(Propane.TripleCarbonCount, this._descriptor.FragmentCount("CCC"));
Assert.AreEqual(0, this._descriptor.FragmentCount("c"));
Assert.AreEqual(Propane.LabuteASA, Math.Round(this._descriptor.LabuteASA, 4));
var frags = this._descriptor.FragmentCounts;
foreach (var key in frags.Keys)
{
int count;
var hasCount = frags.TryGetValue(key, out count);
if (!hasCount)
{
throw new KeyNotFoundException(string.Format("{0} is not a valid key", key));
}
Assert.AreEqual(0, count);
}
Assert.AreEqual(Propane.NumHeavyAtoms, this._descriptor.FeatureValue("Number Heavy Atoms").Value);
Assert.AreEqual(Propane.PeoeVSA1, this._descriptor.PeoeVSA1);
Assert.AreEqual(Propane.PeoeVSA2, this._descriptor.PeoeVSA2);
Assert.AreEqual(Propane.PeoeVSA3, this._descriptor.PeoeVSA3);
Assert.AreEqual(Propane.PeoeVSA4, this._descriptor.PeoeVSA4);
Assert.AreEqual(Propane.PeoeVSA5, this._descriptor.PeoeVSA5);
Assert.AreEqual(Propane.PeoeVSA6, Math.Round(this._descriptor.PeoeVSA6, 4));
Assert.AreEqual(Propane.PeoeVSA7, this._descriptor.PeoeVSA7);
Assert.AreEqual(Propane.PeoeVSA8, this._descriptor.PeoeVSA8);
Assert.AreEqual(Propane.PeoeVSA9, this._descriptor.PeoeVSA9);
Assert.AreEqual(Propane.PeoeVSA10, this._descriptor.PeoeVSA10);
Assert.AreEqual(Propane.PeoeVSA11, this._descriptor.PeoeVSA11);
Assert.AreEqual(Propane.PeoeVSA12, this._descriptor.PeoeVSA12);
Assert.AreEqual(Propane.SmrVSA1, this._descriptor.SmrVSA1);
Assert.AreEqual(Propane.SmrVSA2, this._descriptor.SmrVSA2);
Assert.AreEqual(Propane.SmrVSA3, this._descriptor.SmrVSA3);
Assert.AreEqual(Propane.SmrVSA4, this._descriptor.SmrVSA4);
Assert.AreEqual(Propane.SmrVSA5, Math.Round(this._descriptor.SmrVSA5, 4));
Assert.AreEqual(Propane.SmrVSA6, this._descriptor.SmrVSA6);
Assert.AreEqual(Propane.SmrVSA7, this._descriptor.SmrVSA7);
Assert.AreEqual(Propane.SmrVSA8, this._descriptor.SmrVSA8);
Assert.AreEqual(Propane.SmrVSA9, this._descriptor.SmrVSA9);
Assert.AreEqual(Propane.SmrVSA10, this._descriptor.SmrVSA10);
Assert.AreEqual(Propane.SLogPVSA1, this._descriptor.SLogPVSA1);
Assert.AreEqual(Propane.SLogPVSA2, this._descriptor.SLogPVSA2);
Assert.AreEqual(Propane.SLogPVSA3, this._descriptor.SLogPVSA3);
Assert.AreEqual(Propane.SLogPVSA4, this._descriptor.SLogPVSA4);
Assert.AreEqual(Propane.SLogPVSA5, Math.Round(this._descriptor.SLogPVSA5, 4));
Assert.AreEqual(Propane.SLogPVSA6, this._descriptor.SLogPVSA6);
Assert.AreEqual(Propane.SLogPVSA7, this._descriptor.SLogPVSA7);
Assert.AreEqual(Propane.SLogPVSA8, this._descriptor.SLogPVSA8);
Assert.AreEqual(Propane.SLogPVSA9, this._descriptor.SLogPVSA9);
Assert.AreEqual(Propane.SLogPVSA10, this._descriptor.SLogPVSA10);
Assert.AreEqual(Propane.SLogPVSA11, this._descriptor.SLogPVSA11);
Assert.AreEqual(Propane.SLogPVSA12, this._descriptor.SLogPVSA12);
Assert.AreEqual(Propane.VsaEState9, Math.Round(this._descriptor.VsaEState9, 1));
Assert.AreEqual(Propane.EStateVsa5, Math.Round(this._descriptor.EStateVsa5, 4));
Assert.AreEqual(Propane.EStateVsa8, Math.Round(this._descriptor.EStateVsa8, 4));
Assert.AreEqual(Propane.Chi0, Math.Round(this._descriptor.Chi0, 4));
Assert.AreEqual(Propane.Chi1, Math.Round(this._descriptor.Chi1, 4));
Assert.AreEqual(Propane.Chi0v, Math.Round(this._descriptor.Chi0v, 4));
Assert.AreEqual(Propane.Chi1v, Math.Round(this._descriptor.Chi1v, 4));
Assert.AreEqual(Propane.Chi2v, Math.Round(this._descriptor.Chi2v, 4));
Assert.AreEqual(Propane.Chi3v, Math.Round(this._descriptor.Chi3v, 4));
Assert.AreEqual(Propane.Chi4v, Math.Round(this._descriptor.Chi4v, 4));
Assert.AreEqual(Propane.Chi0n, Math.Round(this._descriptor.Chi0n, 4));
Assert.AreEqual(Propane.Chi1n, Math.Round(this._descriptor.Chi1n, 4));
Assert.AreEqual(Propane.Chi2n, Math.Round(this._descriptor.Chi2n, 4));
Assert.AreEqual(Propane.Chi3n, Math.Round(this._descriptor.Chi3n, 4));
Assert.AreEqual(Propane.Chi4n, Math.Round(this._descriptor.Chi4n, 4));
Assert.AreEqual(Propane.HallKierAlpha, Math.Round(this._descriptor.HallKierAlpha, 1));
Assert.AreEqual(Propane.Kappa1, Math.Round(this._descriptor.Kappa1, 1));
Assert.AreEqual(Propane.Kappa2, Math.Round(this._descriptor.Kappa2, 1));
Assert.AreEqual(Propane.Kappa3, Math.Round(this._descriptor.Kappa3, 1));
Assert.AreEqual(Propane.Ipc, Math.Round(this._descriptor.Ipc, 4));
Assert.AreEqual(Propane.BalabanJ, Math.Round(this._descriptor.BalabanJ, 4));
}
public void CyclosporineTest()
{
var mol = new MolReader(FileNames.CyclosporineFilePath).GetMol();
this._descriptor = new MolDescriptor(mol);
Assert.AreEqual(Cyclosporine.Title, this._descriptor.Title);
Assert.AreEqual(Cyclosporine.CarbonylCount, this._descriptor.FragmentCount(Fragments.Collection["fr_C=O"]));
Assert.AreEqual(Cyclosporine.LabuteASA, Math.Round(this._descriptor.LabuteASA, 4));
Assert.AreEqual(Cyclosporine.NumHeavyAtoms, this._descriptor.NumHeavyAtoms);
/** These test are not run because the values given by RDKit (used as the truth argument in
* the asserts) appear to be incorrect. This is based upon the fact that the total charge
* calculated by RDKit after computing the Gasteiger charges for cyclosporine gives -4.55
* and the actual total charge for cyclosporine should be close to 0. In comparison, the
* total charge given by OpenBabel (after assigning Gasteiger charges) was close to 0.
*
* Since the binning of the PEOE VSA algorithm is dependent upon Gasteiger charges, this
* leads me to believe that the binning given by RDKit is incorrect and hence is leading
* to false fails for these tests.
* Assert.AreEqual(Cyclosporine.PeoeVSA1, Math.Round(this._descriptor.PeoeVSA1, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA2, Math.Round(this._descriptor.PeoeVSA2, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA3, Math.Round(this._descriptor.PeoeVSA3, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA4, Math.Round(this._descriptor.PeoeVSA4, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA5, Math.Round(this._descriptor.PeoeVSA5, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA6, Math.Round(this._descriptor.PeoeVSA6, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA7, Math.Round(this._descriptor.PeoeVSA7, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA8, Math.Round(this._descriptor.PeoeVSA8, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA9, Math.Round(this._descriptor.PeoeVSA9, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA10, Math.Round(this._descriptor.PeoeVSA10, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA11, Math.Round(this._descriptor.PeoeVSA11, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA12, Math.Round(this._descriptor.PeoeVSA12, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA13, Math.Round(this._descriptor.PeoeVSA13, 4));
* Assert.AreEqual(Cyclosporine.PeoeVSA14, Math.Round(this._descriptor.PeoeVSA14, 4));
* */
Assert.AreEqual(Cyclosporine.SmrVSA1, Math.Round(this._descriptor.SmrVSA1, 4));
Assert.AreEqual(Cyclosporine.SmrVSA2, Math.Round(this._descriptor.SmrVSA2, 4));
Assert.AreEqual(Cyclosporine.SmrVSA3, Math.Round(this._descriptor.SmrVSA3, 4));
Assert.AreEqual(Cyclosporine.SmrVSA4, Math.Round(this._descriptor.SmrVSA4, 4));
Assert.AreEqual(Cyclosporine.SmrVSA5, Math.Round(this._descriptor.SmrVSA5, 4));
Assert.AreEqual(Cyclosporine.SmrVSA6, Math.Round(this._descriptor.SmrVSA6, 4));
Assert.AreEqual(Cyclosporine.SmrVSA7, Math.Round(this._descriptor.SmrVSA7, 4));
Assert.AreEqual(Cyclosporine.SmrVSA8, Math.Round(this._descriptor.SmrVSA8, 4));
Assert.AreEqual(Cyclosporine.SmrVSA9, Math.Round(this._descriptor.SmrVSA9, 4));
Assert.AreEqual(Cyclosporine.SmrVSA10, Math.Round(this._descriptor.SmrVSA10, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA1, Math.Round(this._descriptor.SLogPVSA1, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA2, Math.Round(this._descriptor.SLogPVSA2, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA3, Math.Round(this._descriptor.SLogPVSA3, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA4, Math.Round(this._descriptor.SLogPVSA4, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA5, Math.Round(this._descriptor.SLogPVSA5, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA6, Math.Round(this._descriptor.SLogPVSA6, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA7, Math.Round(this._descriptor.SLogPVSA7, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA8, Math.Round(this._descriptor.SLogPVSA8, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA9, Math.Round(this._descriptor.SLogPVSA9, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA10, Math.Round(this._descriptor.SLogPVSA10, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA11, Math.Round(this._descriptor.SLogPVSA11, 4));
Assert.AreEqual(Cyclosporine.SLogPVSA12, Math.Round(this._descriptor.SLogPVSA12, 4));
Assert.AreEqual(Cyclosporine.VsaEState9, Math.Round(this._descriptor.VsaEState9, 4));
Assert.AreEqual(Cyclosporine.EStateVsa1, Math.Round(this._descriptor.EStateVsa1, 4));
Assert.AreEqual(Cyclosporine.EStateVsa2, Math.Round(this._descriptor.EStateVsa2, 4));
Assert.AreEqual(Cyclosporine.EStateVsa3, Math.Round(this._descriptor.EStateVsa3, 4));
Assert.AreEqual(Cyclosporine.EStateVsa4, Math.Round(this._descriptor.EStateVsa4, 4));
Assert.AreEqual(Cyclosporine.EStateVsa5, Math.Round(this._descriptor.EStateVsa5, 4));
Assert.AreEqual(Cyclosporine.EStateVsa6, Math.Round(this._descriptor.EStateVsa6, 4));
Assert.AreEqual(Cyclosporine.EStateVsa7, Math.Round(this._descriptor.EStateVsa7, 4));
Assert.AreEqual(Cyclosporine.EStateVsa8, Math.Round(this._descriptor.EStateVsa8, 4));
Assert.AreEqual(Cyclosporine.EStateVsa9, Math.Round(this._descriptor.EStateVsa9, 4));
Assert.AreEqual(Cyclosporine.EStateVsa10, Math.Round(this._descriptor.EStateVsa10, 4));
Assert.AreEqual(Cyclosporine.EStateVsa11, Math.Round(this._descriptor.EStateVsa11, 4));
Assert.AreEqual(Cyclosporine.Chi0, Math.Round(this._descriptor.Chi0, 4));
Assert.AreEqual(Cyclosporine.Chi1, Math.Round(this._descriptor.Chi1, 4));
Assert.AreEqual(Cyclosporine.Chi0v, Math.Round(this._descriptor.Chi0v, 4));
Assert.AreEqual(Cyclosporine.Chi1v, Math.Round(this._descriptor.Chi1v, 4));
Assert.AreEqual(Cyclosporine.Chi2v, Math.Round(this._descriptor.Chi2v, 4));
Assert.AreEqual(Cyclosporine.Chi3v, Math.Round(this._descriptor.Chi3v, 4));
Assert.AreEqual(Cyclosporine.Chi4v, Math.Round(this._descriptor.Chi4v, 4));
Assert.AreEqual(Cyclosporine.Chi0n, Math.Round(this._descriptor.Chi0n, 4));
Assert.AreEqual(Cyclosporine.Chi1n, Math.Round(this._descriptor.Chi1n, 4));
Assert.AreEqual(Cyclosporine.Chi2n, Math.Round(this._descriptor.Chi2n, 4));
Assert.AreEqual(Cyclosporine.Chi3n, Math.Round(this._descriptor.Chi3n, 4));
Assert.AreEqual(Cyclosporine.Chi4n, Math.Round(this._descriptor.Chi4n, 4));
Assert.AreEqual(Cyclosporine.HallKierAlpha, Math.Round(this._descriptor.HallKierAlpha, 4));
Assert.AreEqual(Cyclosporine.Kappa1, Math.Round(this._descriptor.Kappa1, 4));
Assert.AreEqual(Cyclosporine.Kappa2, Math.Round(this._descriptor.Kappa2, 4));
Assert.AreEqual(Cyclosporine.Kappa3, Math.Round(this._descriptor.Kappa3, 4));
Assert.AreEqual(Cyclosporine.Ipc.ToString("E4"), this._descriptor.Ipc.ToString("E4"));
Assert.AreEqual(Cyclosporine.BalabanJ, Math.Round(this._descriptor.BalabanJ, 4));
}
