public override void StartDocument()
{
ChemFile = new ChemFile();
chemSequence = new ChemSequence();
chemModel = new ChemModel();
setOfMolecules = new ChemObjectSet <IAtomContainer>();
}
public void TestAlign()
{
{
IAtomContainer ac;
var filename = "NCDK.Data.HIN.gravindex.hin";
var ins = ResourceLoader.GetAsStream(filename);
ISimpleChemObjectReader reader = new HINReader(ins);
ChemFile content = (ChemFile)reader.Read((ChemObject) new ChemFile());
var cList = ChemFileManipulator.GetAllAtomContainers(content);
ac = cList.First();
KabschAlignment ka = new KabschAlignment(ac, ac);
Assert.IsNotNull(ka);
ka.Align();
double rmsd = ka.RMSD;
Assert.IsTrue(1e-8 > rmsd);
Assert.IsNotNull(ka.RotationMatrix);
}
{
double[][] p1 = new[] { new[] { 16.754, 20.462, 45.049 }, new[] { 19.609, 18.145, 46.011 }, new[] { 17.101, 17.256, 48.707 },
new[] { 13.963, 18.314, 46.820 }, new[] { 14.151, 15.343, 44.482 }, new[] { 14.959, 12.459, 46.880 }, new[] { 11.987, 13.842, 48.862 },
new[] { 9.586, 12.770, 46.123 }, new[] { 11.006, 9.245, 46.116 }, new[] { 10.755, 9.090, 49.885 } };
double[][] p2 = new[] { new[] { 70.246, 317.510, 188.263 }, new[] { 73.457, 317.369, 190.340 }, new[] { 71.257, 318.976, 193.018 },
new[] { 68.053, 317.543, 191.651 }, new[] { 68.786, 313.954, 192.637 }, new[] { 70.248, 314.486, 196.151 },
new[] { 67.115, 316.584, 196.561 }, new[] { 64.806, 313.610, 196.423 }, new[] { 66.804, 311.735, 199.035 },
new[] { 66.863, 314.832, 201.113 } };
Atom[] a1 = new Atom[10];
Atom[] a2 = new Atom[10];
for (int i = 0; i < 10; i++)
{
a1[i] = new Atom("C");
Vector3 newCoord = new Vector3
{
X = p1[i][0],
Y = p1[i][1],
Z = p1[i][2]
};
a1[i].Point3D = newCoord;
a2[i] = new Atom("C");
newCoord = new Vector3
{
X = p2[i][0],
Y = p2[i][1],
Z = p2[i][2]
};
a2[i].Point3D = newCoord;
}
var ka = new KabschAlignment(a1, a2);
ka.Align();
var rmsd = ka.RMSD;
Assert.AreEqual(0.13479726, rmsd, 0.00000001);
}
}
public void TestBug2846213()
{
var filename = "NCDK.Data.MDL.bug2846213.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
ChemFile chemFile = (ChemFile)reader.Read((ChemObject) new ChemFile());
IAtomContainer ac = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
long[] morganNumbers = MorganNumbersTools.GetMorganNumbers(ac);
Assert.IsFalse(morganNumbers[7] == morganNumbers[8]);
}
public void TestIsConnectedFromSDFile()
{
var filename = "NCDK.Data.MDL.mdeotest.sdf";
var ins = ResourceLoader.GetAsStream(filename);
ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
ChemFile content = (ChemFile)reader.Read((ChemObject) new ChemFile());
var cList = ChemFileManipulator.GetAllAtomContainers(content);
IAtomContainer ac = cList.First();
Assert.IsTrue(ConnectivityChecker.IsConnected(ac), "Molecule appears not to be connected");
}
public void TestAtomProperties()
{
var filename = "NCDK.Data.CML.custompropertiestest.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
ChemFile chemFile = (ChemFile)reader.Read((ChemFile) new ChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
IAtomContainer container = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
for (int i = 0; i < container.Atoms.Count; i++)
{
Assert.AreEqual(2, container.Atoms[i].GetProperties().Count);
}
}
public void TestNMRReading()
{
IAtomContainer atomContainer = null;
//bool foundOneShieldingEntry = false;
//Double shielding = null;
object obj = null;
int shieldingCounter = 0;
var filename = "NCDK.Data.Gaussian.g98ReaderNMRTest.log";
var ins = ResourceLoader.GetAsStream(filename);
var inputReader = new StreamReader(ins);
Gaussian98Reader g98Reader = new Gaussian98Reader(inputReader);
ChemFile chemFile = (ChemFile)g98Reader.Read(new ChemFile());
g98Reader.Close();
var atomContainersList = ChemFileManipulator.GetAllAtomContainers(chemFile);
Assert.IsNotNull(atomContainersList);
Assert.IsTrue(atomContainersList.Count() == 54);
//Debug.WriteLine("Found " + atomContainers.Length + " atomContainers");
int counter = 0;
foreach (var ac in atomContainersList)
{
shieldingCounter = 0;
atomContainer = ac;
for (int g = 0; g < atomContainer.Atoms.Count; g++)
{
obj = atomContainer.Atoms[g].GetProperty <double?>(CDKPropertyName.IsotropicShielding);
if (obj != null)
{
//shielding = (double)object;
shieldingCounter++;
}
}
if (counter < 53)
{
Assert.IsTrue(shieldingCounter == 0);
}
else
{
Assert.IsTrue(shieldingCounter == ac.Atoms.Count);
}
//Debug.WriteLine("AtomContainer " + (f + 1) + " has " + atomContainers[f].Atoms.Count + " atoms and " + shieldingCounter + " shielding entries");
counter++;
}
}
public override void EndDocument()
{
ChemFile.Add(chemSequence);
}
/// <summary> Creates amino acid AminoAcid objects.
///
/// </summary>
/// <returns> aminoAcids, a HashMap containing the amino acids as AminoAcids.
/// </returns>
public static AminoAcid[] createAAs()
{
if (aminoAcids != null)
{
return aminoAcids;
}
// Create set of AtomContainers
aminoAcids = new AminoAcid[20];
IChemFile list = new ChemFile();
//UPGRADE_ISSUE: Method 'java.lang.ClassLoader.getResourceAsStream' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassLoader'"
//UPGRADE_ISSUE: Method 'java.lang.Class.getClassLoader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassgetClassLoader'"
CMLReader reader = new CMLReader(Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + "list_aminoacids.cml"));//typeof(AminoAcids).getClassLoader().getResourceAsStream("data/templates/list_aminoacids.cml"));
try
{
list = (IChemFile)reader.read(list);
IAtomContainer[] containers = ChemFileManipulator.getAllAtomContainers(list);
for (int i = 0; i < containers.Length; i++)
{
//logger.debug("Adding AA: ", containers[i]);
// convert into an AminoAcid
AminoAcid aminoAcid = new AminoAcid();
IAtom[] atoms = containers[i].Atoms;
System.Collections.IEnumerator props = containers[i].Properties.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (props.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.Object next = props.Current;
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Class.getName' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Prop class: " + next.GetType().FullName);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Prop: " + next.ToString());
if (next is DictRef)
{
DictRef dictRef = (DictRef)next;
// System.out.println("DictRef type: " + dictRef.getType());
if (dictRef.Type.Equals("pdb:residueName"))
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
aminoAcid.setProperty(RESIDUE_NAME, containers[i].getProperty(dictRef).ToString().ToUpper());
}
else if (dictRef.Type.Equals("pdb:oneLetterCode"))
{
aminoAcid.setProperty(RESIDUE_NAME_SHORT, containers[i].getProperty(dictRef));
}
else if (dictRef.Type.Equals("pdb:id"))
{
aminoAcid.setProperty(ID, containers[i].getProperty(dictRef));
//logger.debug("Set AA ID to: ", containers[i].getProperty(dictRef));
}
else
{
//logger.error("Cannot deal with dictRef!");
}
}
}
for (int atomCount = 0; atomCount < atoms.Length; atomCount++)
{
IAtom atom = atoms[atomCount];
System.String dictRef = (System.String)atom.getProperty("org.openscience.cdk.dict");
if (dictRef != null && dictRef.Equals("pdb:nTerminus"))
{
aminoAcid.addNTerminus(atom);
}
else if (dictRef != null && dictRef.Equals("pdb:cTerminus"))
{
aminoAcid.addCTerminus(atom);
}
else
{
aminoAcid.addAtom(atom);
}
}
IBond[] bonds = containers[i].Bonds;
for (int bondCount = 0; bondCount < bonds.Length; bondCount++)
{
aminoAcid.addBond(bonds[bondCount]);
}
AminoAcidManipulator.removeAcidicOxygen(aminoAcid);
aminoAcid.setProperty(NO_ATOMS, "" + aminoAcid.AtomCount);
aminoAcid.setProperty(NO_BONDS, "" + aminoAcid.getBondCount());
if (i < aminoAcids.Length)
{
aminoAcids[i] = aminoAcid;
}
else
{
//logger.error("Could not store AminoAcid! Array too short!");
}
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Failed reading file: ", exception.Message);
//logger.debug(exception);
}
return aminoAcids;
}
#pragma warning disable CA1810 // Initialize reference type static fields inline
static AminoAcids()
#pragma warning restore CA1810 // Initialize reference type static fields inline
{
// Create set of AtomContainers
proteinogenics = new AminoAcid[20];
#region Create proteinogenics
{
IChemFile list = new ChemFile();
using (var reader = new CMLReader(ResourceLoader.GetAsStream("NCDK.Templates.Data.list_aminoacids.cml")))
{
try
{
list = (IChemFile)reader.Read(list);
var containersList = ChemFileManipulator.GetAllAtomContainers(list);
int counter = 0;
foreach (var ac in containersList)
{
Debug.WriteLine($"Adding AA: {ac}");
// convert into an AminoAcid
var aminoAcid = new AminoAcid();
foreach (var next in ac.GetProperties().Keys)
{
Debug.WriteLine("Prop: " + next.ToString());
if (next is DictRef dictRef)
{
// Debug.WriteLine("DictRef type: " + dictRef.Type}");
if (string.Equals(dictRef.Type, "pdb:residueName", StringComparison.Ordinal))
{
aminoAcid.SetProperty(ResidueNameKey, ac.GetProperty <string>(next).ToUpperInvariant());
aminoAcid.MonomerName = ac.GetProperty <string>(next);
}
else if (string.Equals(dictRef.Type, "pdb:oneLetterCode", StringComparison.Ordinal))
{
aminoAcid.SetProperty(ResidueNameShortKey, ac.GetProperty <string>(next));
}
else if (string.Equals(dictRef.Type, "pdb:id", StringComparison.Ordinal))
{
aminoAcid.SetProperty(IdKey, ac.GetProperty <string>(next));
Debug.WriteLine($"Set AA ID to: {ac.GetProperty<string>(next)}");
}
else
{
Trace.TraceError("Cannot deal with dictRef!");
}
}
}
foreach (var atom in ac.Atoms)
{
string dictRef = atom.GetProperty <string>("org.openscience.cdk.dict");
switch (dictRef)
{
case "pdb:nTerminus":
aminoAcid.AddNTerminus(atom);
break;
case "pdb:cTerminus":
aminoAcid.AddCTerminus(atom);
break;
default:
aminoAcid.Atoms.Add(atom);
break;
}
}
foreach (var bond in ac.Bonds)
{
aminoAcid.Bonds.Add(bond);
}
AminoAcidManipulator.RemoveAcidicOxygen(aminoAcid);
aminoAcid.SetProperty(NoAtomsKey, "" + aminoAcid.Atoms.Count);
aminoAcid.SetProperty(NoBoundsKey, "" + aminoAcid.Bonds.Count);
if (counter < proteinogenics.Length)
{
proteinogenics[counter] = aminoAcid;
}
else
{
Trace.TraceError("Could not store AminoAcid! Array too short!");
}
counter++;
}
}
catch (Exception exception)
{
if (exception is CDKException | exception is IOException)
{
Trace.TraceError($"Failed reading file: {exception.Message}");
Debug.WriteLine(exception);
}
else
{
throw;
}
}
}
}
#endregion
int count = proteinogenics.Length;
singleLetterCodeMap = new Dictionary <string, IAminoAcid>(count);
threeLetterCodeMap = new Dictionary <string, IAminoAcid>(count);
singleLetterToThreeLetter = new Dictionary <string, string>(count);
threeLetterToSingleLetter = new Dictionary <string, string>(count);
foreach (IAminoAcid aa in proteinogenics)
{
var single = aa.GetProperty <string>(ResidueNameShortKey);
var three = aa.GetProperty <string>(ResidueNameKey);
singleLetterCodeMap[single] = aa;
threeLetterCodeMap[three] = aa;
singleLetterToThreeLetter[single] = three;
threeLetterToSingleLetter[three] = single;
}
}
/// <summary> Creates amino acid AminoAcid objects.
///
/// </summary>
/// <returns> aminoAcids, a HashMap containing the amino acids as AminoAcids.
/// </returns>
public static AminoAcid[] createAAs()
{
if (aminoAcids != null)
{
return(aminoAcids);
}
// Create set of AtomContainers
aminoAcids = new AminoAcid[20];
IChemFile list = new ChemFile();
//UPGRADE_ISSUE: Method 'java.lang.ClassLoader.getResourceAsStream' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassLoader'"
//UPGRADE_ISSUE: Method 'java.lang.Class.getClassLoader' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javalangClassgetClassLoader'"
CMLReader reader = new CMLReader(Assembly.GetExecutingAssembly().GetManifestResourceStream("NuGenCDKSharp." + "list_aminoacids.cml"));//typeof(AminoAcids).getClassLoader().getResourceAsStream("data/templates/list_aminoacids.cml"));
try
{
list = (IChemFile)reader.read(list);
IAtomContainer[] containers = ChemFileManipulator.getAllAtomContainers(list);
for (int i = 0; i < containers.Length; i++)
{
//logger.debug("Adding AA: ", containers[i]);
// convert into an AminoAcid
AminoAcid aminoAcid = new AminoAcid();
IAtom[] atoms = containers[i].Atoms;
System.Collections.IEnumerator props = containers[i].Properties.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (props.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
System.Object next = props.Current;
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Class.getName' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Prop class: " + next.GetType().FullName);
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.debug("Prop: " + next.ToString());
if (next is DictRef)
{
DictRef dictRef = (DictRef)next;
// System.out.println("DictRef type: " + dictRef.getType());
if (dictRef.Type.Equals("pdb:residueName"))
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
aminoAcid.setProperty(RESIDUE_NAME, containers[i].getProperty(dictRef).ToString().ToUpper());
}
else if (dictRef.Type.Equals("pdb:oneLetterCode"))
{
aminoAcid.setProperty(RESIDUE_NAME_SHORT, containers[i].getProperty(dictRef));
}
else if (dictRef.Type.Equals("pdb:id"))
{
aminoAcid.setProperty(ID, containers[i].getProperty(dictRef));
//logger.debug("Set AA ID to: ", containers[i].getProperty(dictRef));
}
else
{
//logger.error("Cannot deal with dictRef!");
}
}
}
for (int atomCount = 0; atomCount < atoms.Length; atomCount++)
{
IAtom atom = atoms[atomCount];
System.String dictRef = (System.String)atom.getProperty("org.openscience.cdk.dict");
if (dictRef != null && dictRef.Equals("pdb:nTerminus"))
{
aminoAcid.addNTerminus(atom);
}
else if (dictRef != null && dictRef.Equals("pdb:cTerminus"))
{
aminoAcid.addCTerminus(atom);
}
else
{
aminoAcid.addAtom(atom);
}
}
IBond[] bonds = containers[i].Bonds;
for (int bondCount = 0; bondCount < bonds.Length; bondCount++)
{
aminoAcid.addBond(bonds[bondCount]);
}
AminoAcidManipulator.removeAcidicOxygen(aminoAcid);
aminoAcid.setProperty(NO_ATOMS, "" + aminoAcid.AtomCount);
aminoAcid.setProperty(NO_BONDS, "" + aminoAcid.getBondCount());
if (i < aminoAcids.Length)
{
aminoAcids[i] = aminoAcid;
}
else
{
//logger.error("Could not store AminoAcid! Array too short!");
}
}
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Failed reading file: ", exception.Message);
//logger.debug(exception);
}
return(aminoAcids);
}
