/// <summary>
/// Get all combinatorial chemical isotopes given a structure.
/// </summary>
/// <param name="molFor">The IMolecularFormula to start</param>
/// <returns>A IsotopePattern object containing the different combinations</returns>
public IsotopePattern GetIsotopes(IMolecularFormula molFor)
{
if (builder == null)
{
try
{
isoFactory = CDK.IsotopeFactory;
builder = molFor.Builder;
}
catch (Exception e)
{
Console.WriteLine(e.StackTrace);
}
}
var mf = MolecularFormulaManipulator.GetString(molFor, true);
var molecularFormula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula(mf, builder);
IsotopePattern abundance_Mass = null;
foreach (var isos in molecularFormula.Isotopes)
{
var elementSymbol = isos.Symbol;
var atomCount = molecularFormula.GetCount(isos);
// Generate possible isotope containers for the current atom's
// these will then me 'multiplied' with the existing patten
var additional = new List <IsotopeContainer>();
foreach (var isotope in isoFactory.GetIsotopes(elementSymbol))
{
double mass = isotope.ExactMass.Value;
double abundance = isotope.Abundance.Value;
if (abundance <= 0.000000001)
{
continue;
}
IsotopeContainer container = new IsotopeContainer(mass, abundance);
if (storeFormula)
{
container.Formula = AsFormula(isotope);
}
additional.Add(container);
}
for (int i = 0; i < atomCount; i++)
{
abundance_Mass = CalculateAbundanceAndMass(abundance_Mass, additional);
}
}
var isoP = IsotopePatternManipulator.SortAndNormalizedByIntensity(abundance_Mass);
isoP = CleanAbundance(isoP, minIntensity);
var isoPattern = IsotopePatternManipulator.SortByMass(isoP);
return(isoPattern);
}
public MolecularFormulaCheckerTest()
: base()
{
try
{
ifac = BODRIsotopeFactory.Instance;
}
catch (IOException e)
{
Console.Error.WriteLine(e.StackTrace);
}
}
public static void Main(string[] args)
{
{
#region
IsotopeFactory f = XMLIsotopeFactory.Instance;
ChemicalElement e1 = f.GetElement("C");
ChemicalElement e2 = f.GetElement(12);
#endregion
}
{
#region AtomicNumber
IAtom element = new Atom("C");
IsotopeFactory f = XMLIsotopeFactory.Instance;
f.Configure(element);
#endregion
}
}
/// <summary>
/// Get the major isotope mass number for an element
/// </summary>
/// <param name="atomicNumber"></param>
/// <returns></returns>
public static int GetMajorIsotopeMassNumber(int atomicNumber)
{
int mass = 0;
IsotopeFactory factory = XMLIsotopeFactory.Instance;
IIsotope major = factory.GetMajorIsotope(atomicNumber);
if (major.MassNumber != null)
{
return((int)major.MassNumber);
}
else
{
return(0);
}
}
/// <summary> Method that saturates an atom in a molecule by adding explicit hydrogens.
///
/// </summary>
/// <param name="atom"> Atom to saturate
/// </param>
/// <param name="container">AtomContainer containing the atom
/// </param>
/// <param name="count"> Number of hydrogens to add
/// </param>
/// <param name="totalContainer">In case you have a container containing multiple structures, this is the total container, whereas container is a partial structure
///
/// </param>
/// <cdk.keyword> hydrogen, adding </cdk.keyword>
/// <cdk.keyword> explicit hydrogen </cdk.keyword>
public virtual IAtomContainer addExplicitHydrogensToSatisfyValency(IAtomContainer container, IAtom atom, int count, IAtomContainer totalContainer)
{
//boolean create2DCoordinates = GeometryTools.has2DCoordinates(container);
IIsotope isotope = IsotopeFactory.getInstance(container.Builder).getMajorIsotope("H");
atom.setHydrogenCount(0);
IAtomContainer changedAtomsAndBonds = container.Builder.newAtomContainer();
for (int i = 1; i <= count; i++)
{
IAtom hydrogen = container.Builder.newAtom("H");
IsotopeFactory.getInstance(container.Builder).configure(hydrogen, isotope);
totalContainer.addAtom(hydrogen);
IBond newBond = container.Builder.newBond((IAtom)atom, hydrogen, 1.0);
totalContainer.addBond(newBond);
changedAtomsAndBonds.addAtom(hydrogen);
changedAtomsAndBonds.addBond(newBond);
}
return(changedAtomsAndBonds);
}
/// <summary>
///
/// </summary>
/// <param name="builder"></param>
/// <exception cref="System.IO.IOException">if there is error in getting the <see cref="IsotopeFactory"/></exception>
public PubChemXMLHelper(IChemObjectBuilder builder)
{
this.builder = builder;
factory = CDK.IsotopeFactory;
}
/// <summary> Writes a Molecule to an OutputStream in MDL sdf format.
///
/// </summary>
/// <param name="container"> Molecule that is written to an OutputStream
/// </param>
/// <param name="isVisible">Should a certain atom be written to mdl?
/// </param>
public virtual void writeMolecule(IMolecule container, bool[] isVisible)
{
System.String line = "";
// taking care of the $$$$ signs:
// we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
if (moleculeNumber == 2)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
// write header block
// lines get shortened to 80 chars, that's in the spec
System.String title = (System.String)container.getProperty(CDKConstants.TITLE);
if (title == null)
{
title = "";
}
if (title.Length > 80)
{
title = title.Substring(0, (80) - (0));
}
writer.Write(title + "\n");
/* From CTX spec
* This line has the format:
* IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
* (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
* User's first and last initials (l), program name (P),
* date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s),
* energy (E) if modeling program input, internal registry number (R)
* if input through MDL form.
* A blank line can be substituted for line 2.
*/
writer.Write(" CDK ");
//UPGRADE_ISSUE: Constructor 'java.text.SimpleDateFormat.SimpleDateFormat' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javatextSimpleDateFormat'"
//UPGRADE_TODO: The equivalent in .NET for method 'java.util.Calendar.getTime' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.TimeZone generatedAux3 = System.TimeZone.CurrentTimeZone;
//writer.Write(SupportClass.FormatDateTime(new SimpleDateFormat("M/d/y,H:m", new System.Globalization.CultureInfo("en-US")), SupportClass.CalendarManager.manager.GetDateTime(new System.Globalization.GregorianCalendar())));
writer.Write('\n');
System.String comment = (System.String)container.getProperty(CDKConstants.REMARK);
if (comment == null)
{
comment = "";
}
if (comment.Length > 80)
{
comment = comment.Substring(0, (80) - (0));
}
writer.Write(comment + "\n");
// write Counts line
int upToWhichAtom = 0;
for (int i = 0; i < isVisible.Length; i++)
{
if (isVisible[i])
{
upToWhichAtom++;
}
}
line += formatMDLInt(upToWhichAtom, 3);
int numberOfBonds = 0;
if (upToWhichAtom < container.AtomCount)
{
for (int i = 0; i < container.getBondCount(); i++)
{
if (isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[1])])
{
numberOfBonds++;
}
}
}
else
{
numberOfBonds = container.getBondCount();
}
line += formatMDLInt(numberOfBonds, 3);
line += " 0 0 0 0 0 0 0 0999 V2000\n";
writer.Write(line);
// write Atom block
IAtom[] atoms = container.Atoms;
for (int f = 0; f < atoms.Length; f++)
{
if (isVisible[f])
{
IAtom atom = atoms[f];
line = "";
if (atom.getPoint3d() != null)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.X3d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.Y3d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += (formatMDLFloat((float)atom.Z3d) + " ");
}
else if (atom.getPoint2d() != null)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.X2d);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLFloat((float)atom.Y2d);
line += " 0.0000 ";
}
else
{
// if no coordinates available, then output a number
// of zeros
line += formatMDLFloat((float)0.0);
line += formatMDLFloat((float)0.0);
line += (formatMDLFloat((float)0.0) + " ");
}
if (container.getAtomAt(f) is IPseudoAtom)
{
line += formatMDLString(((IPseudoAtom)container.getAtomAt(f)).Label, 3);
}
else
{
line += formatMDLString(container.getAtomAt(f).Symbol, 3);
}
line += " 0 0 0 0 0 0 0 0 0 0 0 0";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write Bond block
IBond[] bonds = container.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
if (upToWhichAtom == container.AtomCount || (isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[1])]))
{
IBond bond = bonds[g];
if (bond.getAtoms().Length != 2)
{
//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.warn("Skipping bond with more/less than two atoms: " + bond);
}
else
{
if (bond.Stereo == CDKConstants.STEREO_BOND_UP_INV || bond.Stereo == CDKConstants.STEREO_BOND_DOWN_INV)
{
// turn around atom coding to correct for inv stereo
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
}
else
{
line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1, 3);
line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1, 3);
}
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
line += formatMDLInt((int)bond.Order, 3);
line += " ";
switch (bond.Stereo)
{
case CDKConstants.STEREO_BOND_UP:
line += "1";
break;
case CDKConstants.STEREO_BOND_UP_INV:
line += "1";
break;
case CDKConstants.STEREO_BOND_DOWN:
line += "6";
break;
case CDKConstants.STEREO_BOND_DOWN_INV:
line += "6";
break;
default:
line += "0";
break;
}
line += " 0 0 0 ";
writer.Write(line);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// write formal atomic charges
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
int charge = atom.getFormalCharge();
if (charge != 0)
{
writer.Write("M CHG 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(charge, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// write formal isotope information
for (int i = 0; i < atoms.Length; i++)
{
IAtom atom = atoms[i];
if (!(atom is IPseudoAtom))
{
int atomicMass = atom.MassNumber;
int majorMass = IsotopeFactory.getInstance(atom.Builder).getMajorIsotope(atom.Symbol).MassNumber;
if (atomicMass != 0 && atomicMass != majorMass)
{
writer.Write("M ISO 1 ");
writer.Write(formatMDLInt(i + 1, 3));
writer.Write(" ");
writer.Write(formatMDLInt(atomicMass, 3));
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
}
// close molecule
writer.Write("M END");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//write sdfields, if any
if (sdFields != null)
{
//UPGRADE_TODO: Method 'java.util.Map.keySet' was converted to 'CSGraphT.SupportClass.HashSetSupport' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilMapkeySet'"
CSGraphT.SupportClass.SetSupport set_Renamed = new CSGraphT.SupportClass.HashSetSupport(sdFields.Keys);
System.Collections.IEnumerator iterator = set_Renamed.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' 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_javautilIteratorhasNext'"
while (iterator.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' 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_javautilIteratornext'"
System.Object element = iterator.Current;
writer.Write("> <" + ((System.String)element) + ">");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//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'"
writer.Write(sdFields[element].ToString());
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
// taking care of the $$$$ signs:
// we write such a sign at the end of all except the first molecule
if (moleculeNumber != 1)
{
writer.Write("$$$$");
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
moleculeNumber++;
writer.Flush();
}
private IChemModel readChemModel(IChemModel model)
{
int[] atoms = new int[1];
double[] atomxs = new double[1];
double[] atomys = new double[1];
double[] atomzs = new double[1];
double[] atomcharges = new double[1];
int[] bondatomid1 = new int[1];
int[] bondatomid2 = new int[1];
int[] bondorder = new int[1];
int numberOfAtoms = 0;
int numberOfBonds = 0;
try
{
System.String line = input.ReadLine();
while (line != null)
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line);
System.String command = st.NextToken();
if ("!Header".Equals(command))
{
//logger.warn("Ignoring header");
}
else if ("!Info".Equals(command))
{
//logger.warn("Ignoring info");
}
else if ("!Atoms".Equals(command))
{
//logger.info("Reading atom block");
// determine number of atoms to read
try
{
numberOfAtoms = System.Int32.Parse(st.NextToken());
//logger.debug(" #atoms: " + numberOfAtoms);
atoms = new int[numberOfAtoms];
atomxs = new double[numberOfAtoms];
atomys = new double[numberOfAtoms];
atomzs = new double[numberOfAtoms];
atomcharges = new double[numberOfAtoms];
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
atoms[atomID] = System.Int32.Parse(atomInfoFields.NextToken());
//logger.debug("Set atomic number of atom (" + atomID + ") to: " + atoms[atomID]);
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Atoms block");
//logger.debug(exception);
}
}
else if ("!Bonds".Equals(command))
{
//logger.info("Reading bond block");
try
{
// determine number of bonds to read
numberOfBonds = System.Int32.Parse(st.NextToken());
bondatomid1 = new int[numberOfAtoms];
bondatomid2 = new int[numberOfAtoms];
bondorder = new int[numberOfAtoms];
for (int i = 0; i < numberOfBonds; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer bondInfoFields = new SupportClass.Tokenizer(line);
bondatomid1[i] = System.Int32.Parse(bondInfoFields.NextToken());
bondatomid2[i] = System.Int32.Parse(bondInfoFields.NextToken());
System.String order = bondInfoFields.NextToken();
if ("D".Equals(order))
{
bondorder[i] = 2;
}
else if ("S".Equals(order))
{
bondorder[i] = 1;
}
else if ("T".Equals(order))
{
bondorder[i] = 3;
}
else
{
// ignore order, i.e. set to single
//logger.warn("Unrecognized bond order, using single bond instead. Found: " + order);
bondorder[i] = 1;
}
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Bonds block");
//logger.debug(exception);
}
}
else if ("!Coord".Equals(command))
{
//logger.info("Reading coordinate block");
try
{
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
double x = System.Double.Parse(atomInfoFields.NextToken());
double y = System.Double.Parse(atomInfoFields.NextToken());
double z = System.Double.Parse(atomInfoFields.NextToken());
atomxs[atomID] = x;
atomys[atomID] = y;
atomzs[atomID] = z;
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Coord block");
//logger.debug(exception);
}
}
else if ("!Charges".Equals(command))
{
//logger.info("Reading charges block");
try
{
for (int i = 0; i < numberOfAtoms; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer atomInfoFields = new SupportClass.Tokenizer(line);
int atomID = System.Int32.Parse(atomInfoFields.NextToken());
double charge = System.Double.Parse(atomInfoFields.NextToken());
atomcharges[atomID] = charge;
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading Charges block");
//logger.debug(exception);
}
}
else if ("!End".Equals(command))
{
//logger.info("Found end of file");
// Store atoms
IAtomContainer container = model.Builder.newAtomContainer();
for (int i = 0; i < numberOfAtoms; i++)
{
try
{
IAtom atom = model.Builder.newAtom(IsotopeFactory.getInstance(container.Builder).getElementSymbol(atoms[i]));
atom.AtomicNumber = atoms[i];
atom.setPoint3d(new Point3d(atomxs[i], atomys[i], atomzs[i]));
atom.setCharge(atomcharges[i]);
container.addAtom(atom);
//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("Stored atom: " + atom);
}
catch (System.Exception exception)
{
//logger.error("Cannot create an atom with atomic number: " + atoms[i]);
//logger.debug(exception);
}
}
// Store bonds
for (int i = 0; i < numberOfBonds; i++)
{
container.addBond(bondatomid1[i], bondatomid2[i], bondorder[i]);
}
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addMolecule(model.Builder.newMolecule(container));
model.SetOfMolecules = moleculeSet;
return(model);
}
else
{
//logger.warn("Skipping line: " + line);
}
line = input.ReadLine();
}
}
catch (System.Exception exception)
{
//logger.error("Error while reading file");
//logger.debug(exception);
}
// this should not happen, file is lacking !End command
return(null);
}
/// <summary> Reads a set of coordinates into ChemFrame.
///
/// </summary>
/// <param name="model">Description of the Parameter
/// </param>
/// <throws> IOException if an I/O error occurs </throws>
/// <throws> CDKException Description of the Exception </throws>
private void readCoordinates(IChemModel model)
{
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
IMolecule molecule = model.Builder.newMolecule();
System.String line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
line = input.ReadLine();
while (input.Peek() != -1)
{
line = input.ReadLine();
if ((line == null) || (line.IndexOf("-----") >= 0))
{
break;
}
int atomicNumber;
System.IO.StringReader sr = new System.IO.StringReader(line);
SupportClass.StreamTokenizerSupport token = new SupportClass.StreamTokenizerSupport(sr);
token.NextToken();
// ignore first token
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
atomicNumber = (int)token.nval;
if (atomicNumber == 0)
{
// Skip dummy atoms. Dummy atoms must be skipped
// if frequencies are to be read because Gaussian
// does not report dummy atoms in frequencies, and
// the number of atoms is used for reading frequencies.
continue;
}
}
else
{
throw new CDKException("Error while reading coordinates: expected integer.");
}
token.NextToken();
// ignore third token
double x;
double y;
double z;
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
x = token.nval;
}
else
{
throw new System.IO.IOException("Error reading x coordinate");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
y = token.nval;
}
else
{
throw new System.IO.IOException("Error reading y coordinate");
}
if (token.NextToken() == SupportClass.StreamTokenizerSupport.TT_NUMBER)
{
z = token.nval;
}
else
{
throw new System.IO.IOException("Error reading z coordinate");
}
System.String symbol = "Du";
try
{
symbol = IsotopeFactory.getInstance(model.Builder).getElementSymbol(atomicNumber);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine element symbol!", exception);
}
IAtom atom = model.Builder.newAtom(symbol);
atom.setPoint3d(new Point3d(x, y, z));
molecule.addAtom(atom);
}
/*
* this is the place where we store the atomcount to
* be used as a counter in the nmr reading
*/
atomCount = molecule.AtomCount;
moleculeSet.addMolecule(molecule);
model.SetOfMolecules = moleculeSet;
}
/// <summary> Reads the atoms, coordinates and charges.
///
/// <p>IMPORTANT: it does not support the atom list and its negation!
/// </summary>
public virtual void readAtomBlock(IAtomContainer readData)
{
bool foundEND = false;
while (Ready && !foundEND)
{
System.String command = readCommand();
if ("END ATOM".Equals(command))
{
// FIXME: should check wether 3D is really 2D
foundEND = true;
}
else
{
//logger.debug("Parsing atom from: " + command);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
IAtom atom = readData.Builder.newAtom("C");
// parse the index
try
{
System.String indexString = tokenizer.NextToken();
atom.ID = indexString;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom index";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// parse the element
System.String element = tokenizer.NextToken();
bool isElement = false;
try
{
isElement = IsotopeFactory.getInstance(atom.Builder).isElement(element);
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine if element exists!", exception);
}
if (isPseudoAtom(element))
{
atom = readData.Builder.newPseudoAtom(atom);
}
else if (isElement)
{
atom.Symbol = element;
}
else
{
System.String error = "Cannot parse element of type: " + element;
//logger.error(error);
throw new CDKException("(Possible CDK bug) " + error);
}
// parse atom coordinates (in Angstrom)
try
{
System.String xString = tokenizer.NextToken();
System.String yString = tokenizer.NextToken();
System.String zString = tokenizer.NextToken();
double x = System.Double.Parse(xString);
double y = System.Double.Parse(yString);
double z = System.Double.Parse(zString);
atom.setPoint3d(new Point3d(x, y, z));
atom.setPoint2d(new Point2d(x, y)); // FIXME: dirty!
}
catch (System.Exception exception)
{
System.String error = "Error while parsing atom coordinates";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
// atom-atom mapping
System.String mapping = tokenizer.NextToken();
if (!mapping.Equals("0"))
{
//logger.warn("Skipping atom-atom mapping: " + mapping);
} // else: default 0 is no mapping defined
// the rest are key value things
if (command.IndexOf("=") != -1)
{
System.Collections.Hashtable options = parseOptions(exhaustStringTokenizer(tokenizer));
System.Collections.IEnumerator keys = options.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 (keys.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.String key = (System.String)keys.Current;
System.String value_Renamed = (System.String)options[key];
try
{
if (key.Equals("CHG"))
{
int charge = System.Int32.Parse(value_Renamed);
if (charge != 0)
{
// zero is no charge specified
atom.setFormalCharge(charge);
}
}
else
{
//logger.warn("Not parsing key: " + key);
}
}
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'"
System.String error = "Error while parsing key/value " + key + "=" + value_Renamed + ": " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
}
// store atom
readData.addAtom(atom);
//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("Added atom: " + atom);
}
}
}
/// <summary>
/// Gets the paulingElectronegativities attribute of the
/// InductivePartialCharges object.
/// </summary>
/// <param name="ac">AtomContainer</param>
/// <param name="modified">if true, some values are modified by following the reference</param>
/// <returns>The pauling electronegativities</returns>
public double[] GetPaulingElectronegativities(IAtomContainer ac, bool modified)
{
var paulingElectronegativities = new double[ac.Atoms.Count];
string symbol = null;
int atomicNumber = 0;
try
{
ifac = CDK.IsotopeFactory;
for (int i = 0; i < ac.Atoms.Count; i++)
{
var atom = ac.Atoms[i];
symbol = ac.Atoms[i].Symbol;
var element = ifac.GetElement(symbol);
atomicNumber = element.AtomicNumber;
if (modified)
{
switch (atom.AtomicNumber)
{
case AtomicNumbers.Cl:
paulingElectronegativities[i] = 3.28;
break;
case AtomicNumbers.Br:
paulingElectronegativities[i] = 3.13;
break;
case AtomicNumbers.I:
paulingElectronegativities[i] = 2.93;
break;
case AtomicNumbers.H:
paulingElectronegativities[i] = 2.10;
break;
case AtomicNumbers.C:
if (ac.GetMaximumBondOrder(atom) == BondOrder.Single)
{
// Csp3
paulingElectronegativities[i] = 2.20;
}
else if (ac.GetMaximumBondOrder(atom) == BondOrder.Double)
{
paulingElectronegativities[i] = 2.31;
}
else
{
paulingElectronegativities[i] = 3.15;
}
break;
case AtomicNumbers.O:
if (ac.GetMaximumBondOrder(atom) == BondOrder.Single)
{
// Osp3
paulingElectronegativities[i] = 3.20;
}
else if (ac.GetMaximumBondOrder(atom) != BondOrder.Single)
{
paulingElectronegativities[i] = 4.34;
}
break;
case AtomicNumbers.Si:
paulingElectronegativities[i] = 1.99;
break;
case AtomicNumbers.S:
paulingElectronegativities[i] = 2.74;
break;
case AtomicNumbers.N:
paulingElectronegativities[i] = 2.59;
break;
default:
paulingElectronegativities[i] = pauling[atomicNumber];
break;
}
}
else
{
paulingElectronegativities[i] = pauling[atomicNumber];
}
}
return(paulingElectronegativities);
}
catch (Exception ex1)
{
Debug.WriteLine(ex1);
throw new CDKException($"Problems with IsotopeFactory due to {ex1.Message}", ex1);
}
}
/// <summary> Read a Molecule from a file in MDL sd format
///
/// </summary>
/// <returns> The Molecule that was read from the MDL file.
/// </returns>
private IMolecule readMolecule(IMolecule molecule)
{
//logger.debug("Reading new molecule");
int linecount = 0;
int atoms = 0;
int bonds = 0;
int atom1 = 0;
int atom2 = 0;
int order = 0;
int stereo = 0;
int RGroupCounter = 1;
int Rnumber = 0;
System.String[] rGroup = null;
double x = 0.0;
double y = 0.0;
double z = 0.0;
double totalZ = 0.0;
//int[][] conMat = new int[0][0];
//String help;
IBond bond;
IAtom atom;
System.String line = "";
try
{
//logger.info("Reading header");
line = input.ReadLine(); linecount++;
if (line == null)
{
return(null);
}
//logger.debug("Line " + linecount + ": " + line);
if (line.StartsWith("$$$$"))
{
//logger.debug("File is empty, returning empty molecule");
return(molecule);
}
if (line.Length > 0)
{
molecule.setProperty(CDKConstants.TITLE, line);
}
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
if (line.Length > 0)
{
molecule.setProperty(CDKConstants.REMARK, line);
}
//logger.info("Reading rest of file");
line = input.ReadLine(); linecount++;
//logger.debug("Line " + linecount + ": " + line);
atoms = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
//logger.debug("Atomcount: " + atoms);
bonds = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
//logger.debug("Bondcount: " + bonds);
// read ATOM block
//logger.info("Reading atom block");
for (int f = 0; f < atoms; f++)
{
line = input.ReadLine(); linecount++;
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
x = System.Double.Parse(line.Substring(0, (10) - (0)).Trim());
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
y = System.Double.Parse(line.Substring(10, (20) - (10)).Trim());
//UPGRADE_TODO: The differences in the format of parameters for constructor 'java.lang.Double.Double' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1092'"
z = System.Double.Parse(line.Substring(20, (30) - (20)).Trim());
totalZ += System.Math.Abs(z); // *all* values should be zero, not just the sum
//logger.debug("Coordinates: " + x + "; " + y + "; " + z);
System.String element = line.Substring(31, (34) - (31)).Trim();
//logger.debug("Atom type: ", element);
if (IsotopeFactory.getInstance(molecule.Builder).isElement(element))
{
atom = IsotopeFactory.getInstance(molecule.Builder).configure(molecule.Builder.newAtom(element));
}
else
{
//logger.debug("Atom ", element, " is not an regular element. Creating a PseudoAtom.");
//check if the element is R
rGroup = element.Split(new char[] { '^', 'R' }); // ????
if (rGroup.Length > 1)
{
try
{
Rnumber = System.Int32.Parse(rGroup[(rGroup.Length - 1)]);
RGroupCounter = Rnumber;
}
catch (System.Exception ex)
{
Rnumber = RGroupCounter;
RGroupCounter++;
}
element = "R" + Rnumber;
}
atom = molecule.Builder.newPseudoAtom(element);
}
// store as 3D for now, convert to 2D (if totalZ == 0.0) later
atom.setPoint3d(new Point3d(x, y, z));
// parse further fields
System.String massDiffString = line.Substring(34, (36) - (34)).Trim();
//logger.debug("Mass difference: ", massDiffString);
if (!(atom is IPseudoAtom))
{
try
{
int massDiff = System.Int32.Parse(massDiffString);
if (massDiff != 0)
{
IIsotope major = IsotopeFactory.getInstance(molecule.Builder).getMajorIsotope(element);
atom.AtomicNumber = major.AtomicNumber + massDiff;
}
}
catch (System.Exception exception)
{
//logger.error("Could not parse mass difference field");
}
}
else
{
//logger.error("Cannot set mass difference for a non-element!");
}
System.String chargeCodeString = line.Substring(36, (39) - (36)).Trim();
//logger.debug("Atom charge code: ", chargeCodeString);
int chargeCode = System.Int32.Parse(chargeCodeString);
if (chargeCode == 0)
{
// uncharged species
}
else if (chargeCode == 1)
{
atom.setFormalCharge(+3);
}
else if (chargeCode == 2)
{
atom.setFormalCharge(+2);
}
else if (chargeCode == 3)
{
atom.setFormalCharge(+1);
}
else if (chargeCode == 4)
{
}
else if (chargeCode == 5)
{
atom.setFormalCharge(-1);
}
else if (chargeCode == 6)
{
atom.setFormalCharge(-2);
}
else if (chargeCode == 7)
{
atom.setFormalCharge(-3);
}
try
{
// read the mmm field as position 61-63
System.String reactionAtomIDString = line.Substring(60, (63) - (60)).Trim();
//logger.debug("Parsing mapping id: ", reactionAtomIDString);
try
{
int reactionAtomID = System.Int32.Parse(reactionAtomIDString);
if (reactionAtomID != 0)
{
atom.ID = reactionAtomIDString;
}
}
catch (System.Exception exception)
{
//logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");
//logger.debug(exception);
}
}
catch (System.Exception exception)
{
// older mol files don't have all these fields...
//logger.warn("A few fields are missing. Older MDL MOL file?");
}
molecule.addAtom(atom);
}
// convert to 2D, if totalZ == 0
if (totalZ == 0.0 && !forceReadAs3DCoords.Set)
{
//logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");
IAtom[] atomsToUpdate = molecule.Atoms;
for (int f = 0; f < atomsToUpdate.Length; f++)
{
IAtom atomToUpdate = atomsToUpdate[f];
Point3d p3d = atomToUpdate.getPoint3d();
atomToUpdate.setPoint2d(new Point2d(p3d.x, p3d.y));
atomToUpdate.setPoint3d(null);
}
}
// read BOND block
//logger.info("Reading bond block");
for (int f = 0; f < bonds; f++)
{
line = input.ReadLine(); linecount++;
atom1 = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
atom2 = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
order = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
if (line.Length > 12)
{
stereo = System.Int32.Parse(line.Substring(9, (12) - (9)).Trim());
}
else
{
//logger.warn("Missing expected stereo field at line: " + line);
}
//if (//logger.DebugEnabled)
//{
// //logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order);
//}
if (stereo == 1)
{
// MDL up bond
stereo = CDKConstants.STEREO_BOND_UP;
}
else if (stereo == 6)
{
// MDL down bond
stereo = CDKConstants.STEREO_BOND_DOWN;
}
else if (stereo == 4)
{
//MDL bond undefined
stereo = CDKConstants.STEREO_BOND_UNDEFINED;
}
// interpret CTfile's special bond orders
IAtom a1 = molecule.getAtomAt(atom1 - 1);
IAtom a2 = molecule.getAtomAt(atom2 - 1);
if (order == 4)
{
// aromatic bond
bond = molecule.Builder.newBond(a1, a2, CDKConstants.BONDORDER_AROMATIC, stereo);
// mark both atoms and the bond as aromatic
bond.setFlag(CDKConstants.ISAROMATIC, true);
a1.setFlag(CDKConstants.ISAROMATIC, true);
a2.setFlag(CDKConstants.ISAROMATIC, true);
molecule.addBond(bond);
}
else
{
bond = molecule.Builder.newBond(a1, a2, (double)order, stereo);
molecule.addBond(bond);
}
}
// read PROPERTY block
//logger.info("Reading property block");
while (true)
{
line = input.ReadLine(); linecount++;
if (line == null)
{
throw new CDKException("The expected property block is missing!");
}
if (line.StartsWith("M END"))
{
break;
}
bool lineRead = false;
if (line.StartsWith("M CHG"))
{
// FIXME: if this is encountered for the first time, all
// atom charges should be set to zero first!
int infoCount = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
System.String token = st.NextToken();
int atomNumber = System.Int32.Parse(token.Trim());
token = st.NextToken();
int charge = System.Int32.Parse(token.Trim());
molecule.getAtomAt(atomNumber - 1).setFormalCharge(charge);
}
}
else if (line.StartsWith("M ISO"))
{
try
{
System.String countString = line.Substring(6, (9) - (6)).Trim();
int infoCount = System.Int32.Parse(countString);
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
int atomNumber = System.Int32.Parse(st.NextToken().Trim());
int absMass = System.Int32.Parse(st.NextToken().Trim());
if (absMass != 0)
{
IAtom isotope = molecule.getAtomAt(atomNumber - 1);
isotope.MassNumber = absMass;
}
}
}
catch (System.FormatException 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'"
System.String error = "Error (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in isotope information on line: " + line, exception);
}
}
else if (line.StartsWith("M RAD"))
{
try
{
System.String countString = line.Substring(6, (9) - (6)).Trim();
int infoCount = System.Int32.Parse(countString);
SupportClass.Tokenizer st = new SupportClass.Tokenizer(line.Substring(9));
for (int i = 1; i <= infoCount; i++)
{
int atomNumber = System.Int32.Parse(st.NextToken().Trim());
int spinMultiplicity = System.Int32.Parse(st.NextToken().Trim());
if (spinMultiplicity > 1)
{
IAtom radical = molecule.getAtomAt(atomNumber - 1);
for (int j = 2; j <= spinMultiplicity; j++)
{
// 2 means doublet -> one unpaired electron
// 3 means triplet -> two unpaired electron
molecule.addElectronContainer(molecule.Builder.newSingleElectron(radical));
}
}
}
}
catch (System.FormatException 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'"
System.String error = "Error (" + exception.Message + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in radical information on line: " + line, exception);
}
}
else if (line.StartsWith("G "))
{
try
{
System.String atomNumberString = line.Substring(3, (6) - (3)).Trim();
int atomNumber = System.Int32.Parse(atomNumberString);
//String whatIsThisString = line.substring(6,9).trim();
System.String atomName = input.ReadLine();
// convert Atom into a PseudoAtom
IAtom prevAtom = molecule.getAtomAt(atomNumber - 1);
IPseudoAtom pseudoAtom = molecule.Builder.newPseudoAtom(atomName);
if (prevAtom.getPoint2d() != null)
{
pseudoAtom.setPoint2d(prevAtom.getPoint2d());
}
if (prevAtom.getPoint3d() != null)
{
pseudoAtom.setPoint3d(prevAtom.getPoint3d());
}
AtomContainerManipulator.replaceAtomByAtom(molecule, prevAtom, pseudoAtom);
}
catch (System.FormatException exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String error = "Error (" + exception.ToString() + ") while parsing line " + linecount + ": " + line + " in property block.";
//logger.error(error);
throw new CDKException("NumberFormatException in group information on line: " + line, exception);
}
}
if (!lineRead)
{
//logger.warn("Skipping line in property block: ", line);
}
}
}
catch (CDKException 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'"
System.String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw exception;
}
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'"
System.String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
return(molecule);
}
private IChemSequence readChemSequence(IChemSequence sequence)
{
IChemModel chemModel = sequence.Builder.newChemModel();
ICrystal crystal = null;
// Get the info line (first token of the first line)
//UPGRADE_ISSUE: Method 'java.io.BufferedReader.mark' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReadermark_int'"
//inputBuffer.mark(255);
//long pos = inputBuffer.BaseStream.Position;
info = nextVASPToken(false);
//System.out.println(info);
//UPGRADE_ISSUE: Method 'java.io.BufferedReader.reset' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderreset'"
//inputBuffer.reset();
// Get the number of different atom "NCLASS=X"
//UPGRADE_ISSUE: Method 'java.io.BufferedReader.mark' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReadermark_int'"
//inputBuffer.mark(255);
nextVASPTokenFollowing("NCLASS");
ntype = System.Int32.Parse(fieldVal);
//System.out.println("NCLASS= " + ntype);
//UPGRADE_ISSUE: Method 'java.io.BufferedReader.reset' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaioBufferedReaderreset'"
//inputBuffer.reset();
// Get the different atom names
anames = new System.String[ntype];
nextVASPTokenFollowing("ATOM");
for (int i = 0; i < ntype; i++)
{
anames[i] = fieldVal;
nextVASPToken(false);
}
// Get the number of atom of each type
int[] natom_type = new int[ntype];
natom = 0;
for (int i = 0; i < ntype; i++)
{
natom_type[i] = System.Int32.Parse(fieldVal);
nextVASPToken(false);
natom = natom + natom_type[i];
}
// Get the representation type of the primitive vectors
// only "Direct" is recognize now.
representation = fieldVal;
if (representation.Equals("Direct"))
{
//logger.info("Direct representation");
// DO NOTHING
}
else
{
throw new CDKException("This VASP file is not supported. Please contact the Jmol developpers");
}
while (nextVASPToken(false) != null)
{
//logger.debug("New crystal started...");
crystal = sequence.Builder.newCrystal();
chemModel = sequence.Builder.newChemModel();
// Get acell
for (int i = 0; i < 3; i++)
{
acell[i] = FortranFormat.atof(fieldVal); // all the same FIX?
}
// Get primitive vectors
for (int i = 0; i < 3; i++)
{
for (int j = 0; j < 3; j++)
{
nextVASPToken(false);
rprim[i][j] = FortranFormat.atof(fieldVal);
}
}
// Get atomic position
int[] atomType = new int[natom];
double[][] xred = new double[natom][];
for (int i2 = 0; i2 < natom; i2++)
{
xred[i2] = new double[3];
}
int atomIndex = 0;
for (int i = 0; i < ntype; i++)
{
for (int j = 0; j < natom_type[i]; j++)
{
try
{
atomType[atomIndex] = IsotopeFactory.getInstance(sequence.Builder).getElement(anames[i]).AtomicNumber;
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine atomic number!", exception);
}
//logger.debug("aname: " + anames[i]);
//logger.debug("atomType: " + atomType[atomIndex]);
nextVASPToken(false);
xred[atomIndex][0] = FortranFormat.atof(fieldVal);
nextVASPToken(false);
xred[atomIndex][1] = FortranFormat.atof(fieldVal);
nextVASPToken(false);
xred[atomIndex][2] = FortranFormat.atof(fieldVal);
atomIndex = atomIndex + 1;
// FIXME: store atom
}
}
crystal.A = new Vector3d(rprim[0][0] * acell[0], rprim[0][1] * acell[0], rprim[0][2] * acell[0]);
crystal.B = new Vector3d(rprim[1][0] * acell[1], rprim[1][1] * acell[1], rprim[1][2] * acell[1]);
crystal.C = new Vector3d(rprim[2][0] * acell[2], rprim[2][1] * acell[2], rprim[2][2] * acell[2]);
for (int i = 0; i < atomType.Length; i++)
{
System.String symbol = "Du";
try
{
symbol = IsotopeFactory.getInstance(sequence.Builder).getElement(atomType[i]).Symbol;
}
catch (System.Exception exception)
{
throw new CDKException("Could not determine element symbol!", exception);
}
IAtom atom = sequence.Builder.newAtom(symbol);
atom.AtomicNumber = atomType[i];
// convert fractional to cartesian
double[] frac = new double[3];
frac[0] = xred[i][0];
frac[1] = xred[i][1];
frac[2] = xred[i][2];
atom.setFractionalPoint3d(new Point3d(frac[0], frac[1], frac[2]));
crystal.addAtom(atom);
}
crystal.setProperty(CDKConstants.REMARK, info);
chemModel.Crystal = crystal;
//logger.info("New Frame set!");
sequence.addChemModel(chemModel);
} //end while
return(sequence);
}
