public void TestRebond_IAtomContainer()
{
var rebonder = new RebondTool(2.0, 0.5, 0.5);
var methane = builder.NewAtomContainer();
methane.Atoms.Add(builder.NewAtom("C", new Vector3(0.0, 0.0, 0.0)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(0.6, 0.6, 0.6)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(-0.6, -0.6, 0.6)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(0.6, -0.6, -0.6)));
methane.Atoms.Add(builder.NewAtom("H", new Vector3(-0.6, 0.6, -0.6)));
// configure atoms
var factory = AtomTypeFactory.GetInstance("NCDK.Config.Data.jmol_atomtypes.txt");
//IAtom[] atoms = methane.GetAtoms();
for (int i = 0; i < methane.Atoms.Count; i++)
{
factory.Configure(methane.Atoms[i]);
}
// rebond
rebonder.Rebond(methane);
Assert.AreEqual(5, methane.Atoms.Count);
Assert.AreEqual(4, methane.Bonds.Count);
}
/// <summary>
/// Method which assigns van der Waals radii to the biopolymer
/// default org/openscience/cdk/config/data/pdb_atomtypes.xml
/// stored in the variable string vanDerWaalsFile.
/// </summary>
public void AssignVdWRadiiToProtein()
{
AtomTypeFactory atf = null;
var atoms = Protein.Atoms.ToArray();
try
{
atf = AtomTypeFactory.GetInstance(VanDerWaalsFile);
}
catch (Exception ex1)
{
Console.Out.WriteLine($"Problem with AtomTypeFactory due to:{ex1.ToString()}");
}
for (int i = 0; i < atoms.Length; i++)
{
try
{
atf.Configure(atoms[i]);
}
catch (Exception ex2)
{
Trace.TraceError($"Problem with atf.configure due to:{ex2.ToString()}");
}
}
}
/// <summary>
/// Contructs a new PDBReader that can read Molecules from a given
/// Reader.
///
/// </summary>
/// <param name="oIn"> The Reader to read from
///
/// </param>
//UPGRADE_ISSUE: Class hierarchy differences between 'java.io.Reader' and 'System.IO.StreamReader' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
public PDBReader(System.IO.StreamReader oIn)
{
//logger = new LoggingTool(this.GetType());
//UPGRADE_TODO: The differences in the expected value of parameters for constructor 'java.io.BufferedReader.BufferedReader' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
_oInput = oIn;
initIOSettings();
pdbFactory = null;
}
private SybylAtomTypeMatcher()
{
var stream = ResourceLoader.GetAsStream(SYBYL_ATOM_TYPE_LIST);
factory = AtomTypeFactory.GetInstance(stream, "owl");
cdkMatcher = CDK.AtomTypeMatcher;
var mapStream = ResourceLoader.GetAsStream(CDK_TO_SYBYL_MAP);
mapper = AtomTypeMapper.GetInstance(CDK_TO_SYBYL_MAP, mapStream);
}
public void TestToString()
{
var factory = AtomTypeFactory.GetInstance("NCDK.Dict.Data.cdk-atom-types.owl");
var type = factory.GetAtomType("C.sp3");
Assert.IsTrue(type is ImmutableAtomType);
var output = type.ToString();
Assert.IsTrue(output.Contains("ImmutableAtomType("));
Assert.IsTrue(output.Contains("MBO:"));
}
public static void Script12_1()
{
var factory = AtomTypeFactory.GetInstance("NCDK.Dict.Data.cdk-atom-types.owl");
var atomType = factory.GetAtomType("C.sp3");
Console.WriteLine($"element: {atomType.Symbol}");
Console.WriteLine($"formal charge: {atomType.FormalCharge}");
Console.WriteLine($"hybridization: {atomType.Hybridization}");
Console.WriteLine($"neighbors: {atomType.FormalNeighbourCount}");
Console.WriteLine($"lone pairs: {atomType.GetProperty<int>(NCDK.CDKPropertyName.LonePairCount)}");
Console.WriteLine($"pi bonds: {atomType.GetProperty<int>(NCDK.CDKPropertyName.PiBondCount)}");
}
protected internal virtual AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder)
{
if (structgenATF == null)
{
try
{
structgenATF = AtomTypeFactory.getInstance(atomTypeList, builder);
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Could not instantiate AtomTypeFactory!", exception);
}
}
return(structgenATF);
}
public void TestCloseEnoughToBond_IAtom_IAtom_Double()
{
var filename = "NCDK.Data.XYZ.viagra.xyz";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new XYZReader(ins);
var atf = AtomTypeFactory.GetInstance("NCDK.Config.Data.jmol_atomtypes.txt");
var chemFile = reader.Read(builder.NewChemFile());
var mol = chemFile[0][0].MoleculeSet[0];
foreach (var atom in mol.Atoms)
{
atf.Configure(atom);
}
Assert.IsTrue(BondTools.CloseEnoughToBond(mol.Atoms[0], mol.Atoms[1], 1));
Assert.IsFalse(BondTools.CloseEnoughToBond(mol.Atoms[0], mol.Atoms[8], 1));
}
/// <param name="builder">the ChemObjectBuilder implementation used to construct the AtomType's.
/// </param>
protected internal virtual AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder)
{
if (structgenATF == null)
{
try
{
structgenATF = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/structgen_atomtypes.xml", builder);
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Could not instantiate AtomTypeFactory!", exception);
}
}
return(structgenATF);
}
private bool createBondsWithRebondTool(IBioPolymer pol)
{
RebondTool tool = new RebondTool(2.0, 0.5, 0.5);
try
{
// configure atoms
AtomTypeFactory factory = AtomTypeFactory.getInstance("jmol_atomtypes.txt", pol.Builder);
IAtom[] atoms = pol.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
try
{
IAtomType[] types = factory.getAtomTypes(atoms[i].Symbol);
if (types.Length > 0)
{
// just pick the first one
AtomTypeManipulator.configure(atoms[i], types[0]);
}
else
{
System.Console.Out.WriteLine("Could not configure atom with symbol: " + atoms[i].Symbol);
}
}
catch (System.Exception e)
{
//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'"
System.Console.Out.WriteLine("Could not configure atom (but don't care): " + e.Message);
//logger.debug(e);
}
}
tool.rebond(pol);
}
catch (System.Exception e)
{
//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("Could not rebond the polymer: " + e.Message);
//logger.debug(e);
}
return(true);
}
/// <summary>
/// Takes an object which subclasses IChemObject, e.g. Molecule, and will
/// read this (from file, database, internet etc). If the specific
/// implementation does not support a specific IChemObject it will throw
/// an Exception.
///
/// </summary>
/// <param name="oObj"> The object that subclasses IChemObject
/// </param>
/// <returns> The IChemObject read
/// </returns>
/// <exception cref="CDKException">
///
/// </exception>
public override IChemObject read(IChemObject oObj)
{
if (oObj is IChemFile)
{
if (pdbFactory == null)
{
try
{
pdbFactory = AtomTypeFactory.getInstance("pdb_atomtypes.xml", ((IChemFile)oObj).Builder);
}
catch (System.Exception exception)
{
//logger.debug(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'"
throw new CDKException("Could not setup list of PDB atom types! " + exception.Message);
}
}
return(readChemFile((IChemFile)oObj));
}
else
{
throw new CDKException("Only supported is reading of ChemFile objects.");
}
}
/// <summary> Read a Reaction from a file in MDL RXN format
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IMolecule readMolecule(IMolecule molecule)
{
AtomTypeFactory atFactory = null;
try
{
atFactory = AtomTypeFactory.getInstance("mol2_atomtypes.xml", molecule.Builder);
}
catch (System.Exception exception)
{
System.String error = "Could not instantiate an AtomTypeFactory";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
try
{
System.String line = input.ReadLine();
int atomCount = 0;
int bondCount = 0;
while (line != null)
{
if (line.StartsWith("@<TRIPOS>MOLECULE"))
{
//logger.info("Reading molecule block");
// second line has atom/bond counts?
input.ReadLine(); // disregard the name line
System.String counts = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(counts);
try
{
atomCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom count from MOLECULE block";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
if (tokenizer.HasMoreTokens())
{
try
{
bondCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom and bond counts";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
else
{
bondCount = 0;
}
//logger.info("Reading #atoms: ", atomCount);
//logger.info("Reading #bonds: ", bondCount);
//logger.warn("Not reading molecule qualifiers");
}
else if (line.StartsWith("@<TRIPOS>ATOM"))
{
//logger.info("Reading atom block");
for (int i = 0; i < atomCount; i++)
{
line = input.ReadLine().Trim();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String nameStr = tokenizer.NextToken();
System.String xStr = tokenizer.NextToken();
System.String yStr = tokenizer.NextToken();
System.String zStr = tokenizer.NextToken();
System.String atomTypeStr = tokenizer.NextToken();
IAtomType atomType = atFactory.getAtomType(atomTypeStr);
if (atomType == null)
{
atomType = atFactory.getAtomType("X");
//logger.error("Could not find specified atom type: ", atomTypeStr);
}
IAtom atom = molecule.Builder.newAtom("X");
atom.ID = nameStr;
atom.AtomTypeName = atomTypeStr;
atFactory.configure(atom);
try
{
double x = System.Double.Parse(xStr);
double y = System.Double.Parse(yStr);
double z = System.Double.Parse(zStr);
atom.setPoint3d(new Point3d(x, y, z));
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom coordinates";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
molecule.addAtom(atom);
}
}
else if (line.StartsWith("@<TRIPOS>BOND"))
{
//logger.info("Reading bond block");
for (int i = 0; i < bondCount; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String atom1Str = tokenizer.NextToken();
System.String atom2Str = tokenizer.NextToken();
System.String orderStr = tokenizer.NextToken();
try
{
int atom1 = System.Int32.Parse(atom1Str);
int atom2 = System.Int32.Parse(atom2Str);
double order = 0;
if ("1".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("2".Equals(orderStr))
{
order = CDKConstants.BONDORDER_DOUBLE;
}
else if ("3".Equals(orderStr))
{
order = CDKConstants.BONDORDER_TRIPLE;
}
else if ("am".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("ar".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("du".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("un".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("nc".Equals(orderStr))
{
// not connected
order = 0;
}
if (order != 0)
{
molecule.addBond(atom1 - 1, atom2 - 1, order);
}
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading bond information";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
}
line = input.ReadLine();
}
}
catch (System.IO.IOException exception)
{
System.String error = "Error while reading general structure";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
return(molecule);
}
public SmilesValencyChecker(string atomTypeList)
{
structgenATF = AtomTypeFactory.GetInstance(atomTypeList);
Trace.TraceInformation($"Using configuration file: {atomTypeList}");
}
public SmilesValencyChecker()
{
structgenATF = CDK.CdkAtomTypeFactory;
}
