public void TestInvalidPcoreXML()
{
var filename = "NCDK.Data.PCore.invalid1.xml";
var ins = ResourceLoader.GetAsStream(filename);
PharmacophoreUtils.ReadPharmacophoreDefinitions(ins);
}
void Main()
{
#region ReadPharmacophoreDefinitions
using (var srm = new FileStream("mydefs.xml", FileMode.Open))
{
IList <PharmacophoreQuery> defs = PharmacophoreUtils.ReadPharmacophoreDefinitions(srm);
Console.Out.WriteLine("Number of definitions = " + defs.Count);
for (int i = 0; i < defs.Count; i++)
{
Console.Out.WriteLine($"Desc: {defs[i].GetProperty<string>("description")}");
}
}
#endregion
}
public void TestPCoreWrite()
{
var filename = "NCDK.Data.PCore.pcore.xml";
var ins = ResourceLoader.GetAsStream(filename);
var defs = PharmacophoreUtils.ReadPharmacophoreDefinitions(ins);
PharmacophoreQuery[] defarray = defs.ToArray();
var baos = new MemoryStream();
PharmacophoreUtils.WritePharmacophoreDefinition(defarray, baos);
Assert.IsTrue(baos.ToArray().Length > 0);
string[] lines;
using (var sr = new StreamReader(new MemoryStream(baos.ToArray()), true))
{
var list = new List <string>();
string line;
while ((line = sr.ReadLine()) != null)
{
list.Add(line);
}
lines = list.ToArray();
}
Assert.AreEqual("<?xml version=\"1.0\" encoding=\"utf-8\"?>", lines[0].Trim());
int ndef = 0;
int ndist = 0;
int nangle = 0;
foreach (var line in lines)
{
if (line.IndexOf("</pharmacophore>") != -1)
{
ndef++;
}
if (line.IndexOf("</distanceConstraint>") != -1)
{
ndist++;
}
if (line.IndexOf("</angleConstraint>") != -1)
{
nangle++;
}
}
Assert.AreEqual(2, ndef);
Assert.AreEqual(5, ndist);
Assert.AreEqual(0, nangle);
}
public void TestReadPcoreAngleDef()
{
var filename = "NCDK.Data.PCore.pcoreangle.xml";
var ins = ResourceLoader.GetAsStream(filename);
var defs = PharmacophoreUtils.ReadPharmacophoreDefinitions(ins);
Assert.AreEqual(1, defs.Count);
var def1 = defs[0];
Assert.AreEqual(3, def1.Atoms.Count);
Assert.AreEqual(2, def1.Bonds.Count);
Assert.AreEqual("A modified definition for the D1 receptor", def1.GetProperty <string>("description"));
string[] ids = { "Aromatic", "Hydroxyl", "BasicAmine" };
foreach (var atom in def1.Atoms)
{
string sym = atom.Symbol;
bool found = false;
foreach (var s in ids)
{
if (sym.Equals(s))
{
found = true;
break;
}
}
Assert.IsTrue(found, "'" + sym + "' in pcore.xml is invalid");
}
foreach (var bond in def1.Bonds)
{
IAtom[] a;
switch (bond)
{
case PharmacophoreQueryBond cons:
a = GetAtoms(cons);
Assert.AreEqual(2, a.Length);
break;
case PharmacophoreQueryAngleBond cons:
a = GetAtoms(cons);
Assert.AreEqual(3, a.Length);
break;
}
}
}
public void TestReadPcoreDef()
{
var filename = "NCDK.Data.PCore.pcore.xml";
var ins = ResourceLoader.GetAsStream(filename);
var defs = PharmacophoreUtils.ReadPharmacophoreDefinitions(ins);
Assert.AreEqual(2, defs.Count);
var def1 = defs[0];
Assert.AreEqual(4, def1.Atoms.Count);
Assert.AreEqual(2, def1.Bonds.Count);
Assert.AreEqual("An imaginary pharmacophore definition", def1.GetProperty <string>("description"));
Assert.AreEqual("Imaginary", def1.Title);
var def2 = defs[1];
Assert.AreEqual(3, def2.Atoms.Count);
Assert.AreEqual(3, def2.Bonds.Count);
Assert.IsNull(def2.Title);
string[] ids = { "Aromatic", "Hydroxyl", "BasicAmine" };
foreach (var atom in def2.Atoms)
{
string sym = atom.Symbol;
bool found = false;
foreach (var s in ids)
{
if (sym.Equals(s))
{
found = true;
break;
}
}
Assert.IsTrue(found, "'" + sym + "' in pcore.xml is invalid");
}
}
