public virtual void TestToArray_Empty()
{
BitArray empty = new BitArray(0);
Assert.IsTrue(Compares.AreDeepEqual(Array.Empty <int>(), JumboCyclicVertexSearch.ToArray(empty)));
}
public virtual void Connected()
{
int[][] g = { new[] { 1 }, new[] { 0, 2 }, new[] { 1, 3 }, new[] { 2 } };
Assert.AreEqual(1, new ConnectedComponents(g).NumberOfComponents);
Assert.IsTrue(Compares.AreEqual(new int[] { 1, 1, 1, 1 }, new ConnectedComponents(g).GetComponents()));
}
public void TestCreate_2D()
{
var m_container = new Mock <IAtomContainer>(); var container = m_container.Object;
m_container.SetupGet(n => n.Atoms.Count).Returns(5);
var m_c1 = new Mock <IAtom>(); var c1 = m_c1.Object;
var m_o2 = new Mock <IAtom>(); var o2 = m_o2.Object;
var m_n3 = new Mock <IAtom>(); var n3 = m_n3.Object;
var m_c4 = new Mock <IAtom>(); var c4 = m_c4.Object;
var m_h5 = new Mock <IAtom>(); var h5 = m_h5.Object;
m_container.SetupGet(n => n.Atoms[0]).Returns(c1);
m_container.SetupGet(n => n.Atoms[1]).Returns(o2);
m_container.SetupGet(n => n.Atoms[2]).Returns(n3);
m_container.SetupGet(n => n.Atoms[3]).Returns(c4);
m_container.SetupGet(n => n.Atoms[4]).Returns(h5);
Vector2 p1 = new Vector2(1.23, -0.29);
Vector2 p2 = new Vector2(-0.30, -0.29);
Vector2 p3 = new Vector2(2.00, -1.63);
Vector2 p4 = new Vector2(2.00, 1.03);
Vector2 p5 = new Vector2(2.32, -0.29);
m_c1.SetupGet(n => n.Point2D).Returns(p1);
m_o2.SetupGet(n => n.Point2D).Returns(p2);
m_n3.SetupGet(n => n.Point2D).Returns(p3);
m_c4.SetupGet(n => n.Point2D).Returns(p4);
m_h5.SetupGet(n => n.Point2D).Returns(p5);
var m_c1c4 = new Mock <IBond>(); var c1c4 = m_c1c4.Object;
var m_c1o2 = new Mock <IBond>(); var c1o2 = m_c1o2.Object;
var m_c1n3 = new Mock <IBond>(); var c1n3 = m_c1n3.Object;
var m_c1h5 = new Mock <IBond>(); var c1h5 = m_c1h5.Object;
int[][] graph = new int[][] { new[] { 1, 2, 3, 4 }, new[] { 0 }, new[] { 0 }, new[] { 0 }, new[] { 0 } };
m_container.Setup(n => n.GetConnectedBonds(c1)).Returns(new[] { c1c4, c1o2, c1n3, c1h5 });
// let's say c1 is a chiral carbon
m_c1.SetupGet(n => n.Hybridization).Returns(Hybridization.SP3);
// with a hatch bond from c1 to n3
m_c1n3.SetupGet(n => n.Stereo).Returns(BondStereo.Down);
m_c1n3.SetupGet(n => n.Begin).Returns(c1);
m_c1n3.SetupGet(n => n.End).Returns(n3);
m_c1o2.SetupGet(n => n.Stereo).Returns(BondStereo.None);
m_c1o2.SetupGet(n => n.Begin).Returns(c1);
m_c1o2.SetupGet(n => n.End).Returns(o2);
m_c1c4.SetupGet(n => n.Stereo).Returns(BondStereo.None);
m_c1c4.SetupGet(n => n.Begin).Returns(c1);
m_c1c4.SetupGet(n => n.End).Returns(c4);
m_c1h5.SetupGet(n => n.Stereo).Returns(BondStereo.None);
m_c1h5.SetupGet(n => n.Begin).Returns(c1);
m_c1h5.SetupGet(n => n.End).Returns(h5);
IStereoEncoder encoder = new GeometricTetrahedralEncoderFactory().Create(container, graph);
Assert.AreEqual(1, ExtractEncoders(encoder).Count);
GeometricParity geometricParity = GetGeometricParity(ExtractEncoders(encoder)[0]);
Assert.IsTrue(geometricParity is Tetrahedral2DParity);
Assert.IsTrue(Compares.AreDeepEqual(new Vector2[] { p2, p3, p4, p5 }, Coords2D(geometricParity)));
}
public void Bug844()
{
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 1, 1 }, SMARTSSearchTest.Match("[*R0]-[$([NRD3][CR]=O)]", "N1(CC)C(=O)CCCC1")));
}
/// <summary>Check the electron contribution is the same as expected.</summary>
static void Test(IAtomContainer m, params int[] expected)
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
Assert.IsTrue(Compares.AreDeepEqual(expected, model.Contribution(m, new RingSearch(m))));
}
public void NestedRecursion()
{
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 2, 2 }, SMARTSSearchTest.Match("[$(*C[$(*C)$(**N)])]", "CCCCN")));
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 1, 1 }, SMARTSSearchTest.Match("[$(*C[$(*C)$(**N)])]", "CCN")));
}
public void RecursiveComponentGrouping()
{
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 1, 1 }, SMARTSSearchTest.Match("[O;D1;$(([a,A]).([A,a]))][CH]=O", "OC=O.c1ccccc1")));
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 0, 0 }, SMARTSSearchTest.Match("[O;D1;$(([a,A]).([A,a]))][CH]=O", "OC=O")));
}
public void TestReadParameterSets()
{
MMFF94BasedParameterSetReader mmff94bpsr = new MMFF94BasedParameterSetReader();
mmff94bpsr.ReadParameterSets();
var parameterSet = mmff94bpsr.GetParamterSet();
//test atom type
var atomtypes = mmff94bpsr.AtomTypes;
IAtomType atomtype = atomtypes[0];
string sid = "C";
Assert.AreEqual(sid, atomtype.AtomTypeName);
string rootType = "C";
Assert.AreEqual(rootType, atomtype.Symbol);
string smaxbond = "4";
Assert.AreEqual(int.Parse(smaxbond, NumberFormatInfo.InvariantInfo), (int)atomtype.FormalNeighbourCount);
string satomNr = "6";
Assert.AreEqual(int.Parse(satomNr, NumberFormatInfo.InvariantInfo), (int)atomtype.AtomicNumber);
//atom
//TODO testing
//bond
// string scode = "0";
string sid1 = "C";
string sid2 = "C";
string slen = "1.508";
string sk2 = "306.432";
string sk3 = "-612.865";
string sk4 = "715.009";
string sbci = "0.0000";
string bondkey = "bond" + sid1 + ";" + sid2;
var bonddata = new List <double>
{
(double)(double.Parse(slen, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(sk2, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(sk3, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(sk4, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(sbci, NumberFormatInfo.InvariantInfo))
};
//strbnd
// scode = "0";
sid1 = "C";
sid2 = "C";
string sid3 = "C";
string value1 = "14.82507";
string value2 = "14.82507";
string strbndkey = "strbnd" + sid1 + ";" + sid2 + ";" + sid3;
var strbnddata = new List <double>
{
(double)(double.Parse(value1, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value2, NumberFormatInfo.InvariantInfo))
};
//angle
// scode = "0";
sid1 = "C=";
sid2 = "C";
sid3 = "N";
value1 = "105.837";
value2 = "86.1429";
string value3 = "-34.5494";
string value4 = "0";
string anglekey = "angle" + sid1 + ";" + sid2 + ";" + sid3;
var angledata = new List <double>
{
(double)(double.Parse(value1, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value2, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value3, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value4, NumberFormatInfo.InvariantInfo))
};
//torsion
// scode = "0";
sid1 = "HC";
sid2 = "C";
sid3 = "C";
string sid4 = "HC";
value1 = "0.142";
value2 = "0.693";
value3 = "0.157";
value4 = "0.000";
string value5 = "0.000";
string torsionkey = "torsion" + ";" + sid1 + ";" + sid2 + ";" + sid3 + ";" + sid4;
var torsiondata = new List <double>
{
(double)(double.Parse(value1, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value2, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value3, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value4, NumberFormatInfo.InvariantInfo)),
(double)(double.Parse(value5, NumberFormatInfo.InvariantInfo))
};
//opbend
// scode = "0";
sid1 = "O=";
sid2 = "C=";
sid3 = "CR4R";
sid4 = "CR4R";
value1 = "10.86681780";
string opbendkey = "opbend" + ";" + sid1 + ";" + sid2 + ";" + sid3 + ";" + sid4;
var opbenddata = new List <double>
{
(double)(double.Parse(value1, NumberFormatInfo.InvariantInfo))
};
//TODO data lines testing
foreach (var e in parameterSet)
{
if (e.Key.Equals(bondkey))
{
Assert.IsTrue(Compares.AreDeepEqual(bonddata, e.Value));
}
else if (e.Key.Equals(strbndkey))
{
Assert.IsTrue(Compares.AreDeepEqual(strbnddata, e.Value));
}
else if (e.Key.Equals(anglekey))
{
Assert.IsTrue(Compares.AreDeepEqual(angledata, e.Value));
}
else if (e.Key.Equals(torsionkey))
{
Assert.IsTrue(Compares.AreDeepEqual(torsiondata, e.Value));
}
else if (e.Key.Equals(opbendkey))
{
Assert.IsTrue(Compares.AreDeepEqual(opbenddata, e.Value));
}
}
}
static void Assert_AreEqual(object expected, object actual)
{
Assert.IsTrue(Compares.AreDeepEqual(expected, actual));
}
public void CalculateSummaryEntity_ListOfSimpleObjects_ReturnsRightSummaryEntity(CalculateSummaryEntityUnitTestsTestsModel dataTest)
{
var actualResult = dataTest.Input.CalculateSummaryEntity();
Assert.That(actualResult, Compares.To(dataTest.Expected));
}
public void FavorCarbonyl()
{
IAtomContainer container = CDK.SmilesParser.ParseSmiles("P([O-])=O");
Assert.IsTrue(Compares.AreEqual(new long[] { 3, 2, 1 }, InChINumbersTools.GetUSmilesNumbers(container)));
}
public void ParseStandard()
{
Assert.IsTrue(Compares.AreEqual(
new long[] { 3, 2, 1 },
InChINumbersTools.ParseUSmilesNumbers("AuxInfo=1/0/N:3,2,1/rA:3OCC/rB:s1;s2;/rC:;;;", Mock(3))));
}
