public void SetMMFF94Parameters()
{
if (mmff94 == null)
{
mmff94 = new MMFF94BasedParameterSetReader();
}
mmff94.ReadParameterSets();
parameterSet = mmff94.GetParamterSet();
atomTypes = mmff94.AtomTypes;
}
/// <summary>
///Constructor for the ForceFieldConfigurator object
/// </summary>
/// <param name="ffname">name of the force field data file</param>
public void SetForceFieldConfigurator(string ffname)
{
ffname = ffname.ToLowerInvariant();
bool check = false;
if (ffname == ffName && parameterSet != null)
{
}
else
{
check = this.CheckForceFieldType(ffname);
ffName = ffname;
if (string.Equals(ffName, "mm2", StringComparison.Ordinal))
{
ins = ResourceLoader.GetAsStream("NCDK.Modelings.ForceField.Data.mm2.prm");
mm2 = new MM2BasedParameterSetReader();
mm2.SetInputStream(ins);
try
{
this.SetMM2Parameters();
}
catch (Exception ex1)
{
throw new CDKException("Problems with set MM2Parameters due to " + ex1.ToString(), ex1);
}
}
else if (ffName.Equals("mmff94", StringComparison.Ordinal) || !check)
{
ins = ResourceLoader.GetAsStream("NCDK.Modelings.ForceField.Data.mmff94.prm");
mmff94 = new MMFF94BasedParameterSetReader();
mmff94.SetInputStream(ins);
try
{
this.SetMMFF94Parameters();
}
catch (Exception ex2)
{
throw new CDKException("Problems with set MM2Parameters due to" + ex2.ToString(), ex2);
}
}
}
}
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));
}
}
}
