/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void endDocument()
{
//logger.debug("Closing document");
if (currentSetOfReactions != null && currentSetOfReactions.ReactionCount == 0 && currentReaction != null)
{
//logger.debug("Adding reaction to SetOfReactions");
currentSetOfReactions.addReaction(currentReaction);
}
if (currentSetOfReactions != null && currentChemModel.SetOfReactions == null)
{
//logger.debug("Adding SOR to ChemModel");
currentChemModel.SetOfReactions = currentSetOfReactions;
}
if (currentSetOfMolecules != null && currentSetOfMolecules.MoleculeCount != 0)
{
//logger.debug("Adding reaction to SetOfMolecules");
currentChemModel.SetOfMolecules = currentSetOfMolecules;
}
if (currentChemSequence.ChemModelCount == 0)
{
//logger.debug("Adding ChemModel to ChemSequence");
currentChemSequence.addChemModel(currentChemModel);
}
if (ChemSequenceCount == 0)
{
// assume there is one non-animation ChemSequence
addChemSequence(currentChemSequence);
}
//logger.info("End CDO Object");
//logger.info("Number of sequences:", ChemSequenceCount);
}
/// <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="object"> The object that subclasses
/// IChemObject
/// </param>
/// <returns> The IChemObject read
/// </returns>
/// <exception cref="CDKException">
/// </exception>
public override IChemObject read(IChemObject object_Renamed)
{
if (object_Renamed is IReaction)
{
return((IChemObject)readReaction(object_Renamed.Builder));
}
else if (object_Renamed is IChemModel)
{
IChemModel model = object_Renamed.Builder.newChemModel();
ISetOfReactions reactionSet = object_Renamed.Builder.newSetOfReactions();
reactionSet.addReaction(readReaction(object_Renamed.Builder));
model.SetOfReactions = reactionSet;
return(model);
}
else if (object_Renamed is IChemFile)
{
IChemFile chemFile = object_Renamed.Builder.newChemFile();
IChemSequence sequence = object_Renamed.Builder.newChemSequence();
sequence.addChemModel((IChemModel)read(object_Renamed.Builder.newChemModel()));
chemFile.addChemSequence(sequence);
return(chemFile);
}
else
{
throw new CDKException("Only supported are Reaction and ChemModel, and not " + object_Renamed.GetType().FullName + ".");
}
}
/// <summary> Takes an object which subclasses IChemObject, e.g.Molecule, and will read
/// this from from the Reader. If the specific implementation
/// does not support a specific IChemObject it will throw an Exception.
///
/// </summary>
/// <param name="object">The object that subclasses IChemObject
/// </param>
/// <returns> The IChemObject read
/// </returns>
/// <exception cref="CDKException">
/// </exception>
public override IChemObject read(IChemObject object_Renamed)
{
if (object_Renamed is IChemFile)
{
IChemFile file = (IChemFile)object_Renamed;
IChemSequence sequence = file.Builder.newChemSequence();
IChemModel model = file.Builder.newChemModel();
ISetOfMolecules moleculeSet = file.Builder.newSetOfMolecules();
moleculeSet.addMolecule(readMolecule(model.Builder.newMolecule()));
model.SetOfMolecules = moleculeSet;
sequence.addChemModel(model);
file.addChemSequence(sequence);
return(file);
}
else if (object_Renamed is IChemModel)
{
IChemModel model = (IChemModel)object_Renamed;
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addMolecule(readMolecule(model.Builder.newMolecule()));
model.SetOfMolecules = moleculeSet;
return(model);
}
else
{
throw new CDKException("Only supported is ChemModel, and not " + object_Renamed.GetType().FullName + ".");
}
}
// private functions
/// <summary> Reads a ChemFile object from input.
///
/// </summary>
/// <returns> ChemFile with the content read from the input
/// </returns>
private IChemFile readChemFile(IChemFile cf)
{
// have to do stuff here
try
{
System.String line = input.ReadLine();
while (line != null)
{
if (line.StartsWith("INChI="))
{
// ok, the fun starts
cf = cf.Builder.newChemFile();
// ok, we need to parse things like:
// INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H
//UPGRADE_NOTE: Final was removed from the declaration of 'INChI '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String INChI = line.Substring(6);
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(INChI, "/");
// ok, we expect 4 tokens
//UPGRADE_NOTE: Final was removed from the declaration of 'version '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String version = tokenizer.NextToken(); // 1.12Beta
//UPGRADE_NOTE: Final was removed from the declaration of 'formula '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String formula = tokenizer.NextToken(); // C6H6
//UPGRADE_NOTE: Final was removed from the declaration of 'connections '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String connections = tokenizer.NextToken().Substring(1); // 1-2-4-6-5-3-1
//UPGRADE_NOTE: Final was removed from the declaration of 'hydrogens '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String hydrogens = tokenizer.NextToken().Substring(1); // 1-6H
IAtomContainer parsedContent = inchiTool.processFormula(cf.Builder.newAtomContainer(), formula);
inchiTool.processConnections(connections, parsedContent, -1);
ISetOfMolecules moleculeSet = cf.Builder.newSetOfMolecules();
moleculeSet.addMolecule(cf.Builder.newMolecule(parsedContent));
IChemModel model = cf.Builder.newChemModel();
model.SetOfMolecules = moleculeSet;
IChemSequence sequence = cf.Builder.newChemSequence();
sequence.addChemModel(model);
cf.addChemSequence(sequence);
}
line = input.ReadLine();
}
}
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'"
throw new CDKException("Error while reading INChI file: " + exception.Message, exception);
}
return(cf);
}
/// <summary> Reads data from the "file system" file through the use of the "input"
/// field, parses data and feeds the ChemFile object with the extracted data.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
///
/// </returns>
/// <throws IOException may> be thrown buy the <code>this.input.readLine()</code> instruction. </throws IOException may>
/// <summary>
/// </summary>
/// <seealso cref="org.openscience.cdk.io.GamessReader.input">
/// </seealso>
//TODO Answer the question : Is this method's name appropriate (given the fact that it do not read a ChemFile object, but return it)?
private IChemFile readChemFile(IChemFile file)
{
IChemSequence sequence = file.Builder.newChemSequence(); // TODO Answer the question : Is this line needed ?
IChemModel model = file.Builder.newChemModel(); // TODO Answer the question : Is this line needed ?
ISetOfMolecules moleculeSet = file.Builder.newSetOfMolecules();
model.SetOfMolecules = moleculeSet; //TODO Answer the question : Should I do this?
sequence.addChemModel(model); //TODO Answer the question : Should I do this?
file.addChemSequence(sequence); //TODO Answer the question : Should I do this?
System.String currentReadLine = this.input.ReadLine();
while (this.input.Peek() != -1 == true && (currentReadLine != null))
{
/*
* There are 2 types of coordinate sets:
* - bohr coordinates sets (if statement)
* - angstr???m coordinates sets (else statement)
*/
if (currentReadLine.IndexOf("COORDINATES (BOHR)") >= 0)
{
/*
* The following line do no contain data, so it is ignored.
*/
this.input.ReadLine();
moleculeSet.addMolecule(this.readCoordinates(file.Builder.newMolecule(), GamessReader.BOHR_UNIT));
//break; //<- stops when the first set of coordinates is found.
}
else if (currentReadLine.IndexOf(" COORDINATES OF ALL ATOMS ARE (ANGS)") >= 0)
{
/*
* The following 2 lines do no contain data, so it are ignored.
*/
this.input.ReadLine();
this.input.ReadLine();
moleculeSet.addMolecule(this.readCoordinates(file.Builder.newMolecule(), GamessReader.ANGSTROM_UNIT));
//break; //<- stops when the first set of coordinates is found.
}
currentReadLine = this.input.ReadLine();
}
return(file);
}
private IChemSequence readChemSequence(IChemSequence sequence)
{
IChemModel model = null;
try
{
System.String line = input.ReadLine();
//String levelOfTheory = null;
// Find first set of coordinates
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
model = sequence.Builder.newChemModel();
try
{
readCoordinates(model);
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading coordinates: " + exception.ToString(), exception);
}
break;
}
line = input.ReadLine();
}
if (model != null)
{
// Read all other data
line = input.ReadLine();
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
// Add current frame to file and create a new one.
sequence.addChemModel(model);
fireFrameRead();
model = sequence.Builder.newChemModel();
readCoordinates(model);
}
else if (line.IndexOf("SCF Done:") >= 0)
{
// Found an energy
model.setProperty("org.openscience.cdk.io.Gaussian03Reaer:SCF Done", line.Trim());
}
else if (line.IndexOf("Harmonic frequencies") >= 0)
{
// Found a set of vibrations
try
{
readFrequencies(model);
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading frequencies: " + exception.ToString(), exception);
}
}
else if (line.IndexOf("Mulliken atomic charges") >= 0)
{
readPartialCharges(model);
}
else if (line.IndexOf("Magnetic shielding") >= 0)
{
// Found NMR data
try
{
readNMRData(model, line);
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading NMR data: " + exception.ToString(), exception);
}
}
else if (line.IndexOf("GINC") >= 0)
{
// Found calculation level of theory
//levelOfTheory = parseLevelOfTheory(line);
// FIXME: is doing anything with it?
}
line = input.ReadLine();
}
// Add current frame to file
sequence.addChemModel(model);
fireFrameRead();
}
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading general structure: " + exception.ToString(), exception);
}
return(sequence);
}
/// <summary> Private method that actually parses the input to read a ChemFile
/// object. In its current state it is able to read all the molecules
/// (if more than one is present) in the specified HIN file. These are
/// placed in a SetOfMolecules object which in turn is placed in a ChemModel
/// which in turn is placed in a ChemSequence object and which is finally
/// placed in a ChemFile object and returned to the user.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.newChemSequence();
IChemModel chemModel = file.Builder.newChemModel();
ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();
System.String info;
SupportClass.Tokenizer tokenizer;
try
{
System.String line;
// read in header info
while (true)
{
line = input.ReadLine();
if (line.IndexOf("mol ") == 0)
{
info = getMolName(line);
break;
}
}
// start the actual molecule data - may be multiple molecule
line = input.ReadLine();
while (true)
{
if (line == null)
{
break; // end of file
}
if (line.IndexOf(';') == 0)
{
continue; // comment line
}
if (line.IndexOf("mol ") == 0)
{
info = getMolName(line);
line = input.ReadLine();
}
IMolecule m = file.Builder.newMolecule();
m.setProperty(CDKConstants.TITLE, info);
// Each elemnt of cons is an ArrayList of length 3 which stores
// the start and end indices and bond order of each bond
// found in the HIN file. Before adding bonds we need to reduce
// the number of bonds so as not to count the same bond twice
System.Collections.ArrayList cons = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
// read data for current molecule
int atomSerial = 0;
while (true)
{
if (line.IndexOf("endmol ") >= 0)
{
break;
}
if (line.IndexOf(';') == 0)
{
continue; // comment line
}
tokenizer = new SupportClass.Tokenizer(line, " ");
int ntoken = tokenizer.Count;
System.String[] toks = new System.String[ntoken];
for (int i = 0; i < ntoken; i++)
{
toks[i] = tokenizer.NextToken();
}
System.String sym = new System.Text.StringBuilder(toks[3]).ToString();
double charge = System.Double.Parse(toks[6]);
double x = System.Double.Parse(toks[7]);
double y = System.Double.Parse(toks[8]);
double z = System.Double.Parse(toks[9]);
int nbond = System.Int32.Parse(toks[10]);
IAtom atom = file.Builder.newAtom(sym, new Point3d(x, y, z));
atom.setCharge(charge);
for (int j = 11; j < (11 + nbond * 2); j += 2)
{
double bo = 1;
int s = System.Int32.Parse(toks[j]) - 1; // since atoms start from 1 in the file
char bt = toks[j + 1][0];
switch (bt)
{
case 's':
bo = 1;
break;
case 'd':
bo = 2;
break;
case 't':
bo = 3;
break;
case 'a':
bo = 1.5;
break;
}
System.Collections.ArrayList ar = new System.Collections.ArrayList(3);
ar.Add((System.Int32)atomSerial);
ar.Add((System.Int32)s);
ar.Add((double)bo);
cons.Add(ar);
}
m.addAtom(atom);
atomSerial++;
line = input.ReadLine();
}
// before storing the molecule lets include the connections
// First we reduce the number of bonds stored, since we have
// stored both, say, C1-H1 and H1-C1.
System.Collections.ArrayList blist = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < cons.Count; i++)
{
System.Collections.ArrayList ar = (System.Collections.ArrayList)cons[i];
// make a reversed list
System.Collections.ArrayList arev = new System.Collections.ArrayList(3);
arev.Add(ar[1]);
arev.Add(ar[0]);
arev.Add(ar[2]);
// Now see if ar or arev are already in blist
if (blist.Contains(ar) || blist.Contains(arev))
{
continue;
}
else
{
blist.Add(ar);
}
}
// now just store all the bonds we have
for (int i = 0; i < blist.Count; i++)
{
System.Collections.ArrayList ar = (System.Collections.ArrayList)blist[i];
int s = ((System.Int32)ar[0]);
int e = ((System.Int32)ar[1]);
double bo = ((System.Double)ar[2]);
m.addBond(s, e, bo);
}
setOfMolecules.addMolecule(m);
line = input.ReadLine(); // read in the 'mol N'
}
// got all the molecule in the HIN file (hopefully!)
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
file.addChemSequence(chemSequence);
}
catch (System.IO.IOException e)
{
// should make some noise now
file = null;
}
return(file);
}
// private procedures
/// <summary> Private method that actually parses the input to read a ChemFile
/// object.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.newChemSequence();
int number_of_atoms = 0;
SupportClass.Tokenizer tokenizer;
try
{
System.String line = input.ReadLine();
while (input.Peek() != -1 && line != null)
{
// parse frame by frame
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
System.String token = tokenizer.NextToken();
number_of_atoms = System.Int32.Parse(token);
System.String info = input.ReadLine();
IChemModel chemModel = file.Builder.newChemModel();
ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();
IMolecule m = file.Builder.newMolecule();
m.setProperty(CDKConstants.TITLE, info);
for (int i = 0; i < number_of_atoms; i++)
{
line = input.ReadLine();
if (line == null)
{
break;
}
if (line.StartsWith("#") && line.Length > 1)
{
System.Object comment = m.getProperty(CDKConstants.COMMENT);
if (comment == null)
{
comment = "";
}
//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'"
comment = comment.ToString() + line.Substring(1).Trim();
m.setProperty(CDKConstants.COMMENT, comment);
//logger.debug("Found and set comment: ", comment);
}
else
{
double x = 0.0f, y = 0.0f, z = 0.0f;
double charge = 0.0f;
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
int fields = tokenizer.Count;
if (fields < 4)
{
// this is an error but cannot throw exception
}
else
{
System.String atomtype = tokenizer.NextToken();
//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(tokenizer.NextToken()));
//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(tokenizer.NextToken()));
//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(tokenizer.NextToken()));
if (fields == 8)
{
//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'"
charge = (System.Double.Parse(tokenizer.NextToken()));
}
IAtom atom = file.Builder.newAtom(atomtype, new Point3d(x, y, z));
atom.setCharge(charge);
m.addAtom(atom);
}
}
}
setOfMolecules.addMolecule(m);
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
line = input.ReadLine();
}
file.addChemSequence(chemSequence);
}
catch (System.IO.IOException e)
{
// should make some noise now
file = null;
//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("Error while reading file: ", e.Message);
//logger.debug(e);
}
return(file);
}
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;
}
private IChemSequence readChemSequence(IChemSequence sequence)
{
IChemModel model = null;
try
{
System.String line = input.ReadLine();
//String levelOfTheory = null;
// Find first set of coordinates
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
model = sequence.Builder.newChemModel();
try
{
readCoordinates(model);
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading coordinates: " + exception.ToString(), exception);
}
break;
}
line = input.ReadLine();
}
if (model != null)
{
// Read all other data
line = input.ReadLine();
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
// Add current frame to file and create a new one.
sequence.addChemModel(model);
fireFrameRead();
model = sequence.Builder.newChemModel();
readCoordinates(model);
}
else if (line.IndexOf("SCF Done:") >= 0)
{
// Found an energy
model.setProperty("org.openscience.cdk.io.Gaussian03Reaer:SCF Done", line.Trim());
}
else if (line.IndexOf("Harmonic frequencies") >= 0)
{
// Found a set of vibrations
try
{
readFrequencies(model);
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading frequencies: " + exception.ToString(), exception);
}
}
else if (line.IndexOf("Mulliken atomic charges") >= 0)
{
readPartialCharges(model);
}
else if (line.IndexOf("Magnetic shielding") >= 0)
{
// Found NMR data
try
{
readNMRData(model, line);
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading NMR data: " + exception.ToString(), exception);
}
}
else if (line.IndexOf("GINC") >= 0)
{
// Found calculation level of theory
//levelOfTheory = parseLevelOfTheory(line);
// FIXME: is doing anything with it?
}
line = input.ReadLine();
}
// Add current frame to file
sequence.addChemModel(model);
fireFrameRead();
}
}
catch (System.IO.IOException 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'"
throw new CDKException("Error while reading general structure: " + exception.ToString(), exception);
}
return sequence;
}
/// <summary> Read the Gaussian98 output.
///
/// </summary>
/// <returns> a ChemFile with the coordinates, energies, and
/// vibrations.
/// </returns>
/// <throws> IOException if an I/O error occurs </throws>
/// <throws> CDKException Description of the Exception </throws>
private IChemFile readChemFile(IChemFile chemFile)
{
IChemSequence sequence = chemFile.Builder.newChemSequence();
IChemModel model = null;
System.String line = input.ReadLine();
System.String levelOfTheory;
System.String description;
int modelCounter = 0;
// Find first set of coordinates by skipping all before "Standard orientation"
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
model = chemFile.Builder.newChemModel();
readCoordinates(model);
break;
}
line = input.ReadLine();
}
if (model != null)
{
// Read all other data
line = input.ReadLine().Trim();
while (input.Peek() != -1 && (line != null))
{
if (line.IndexOf("#") == 0)
{
// Found the route section
// Memorizing this for the description of the chemmodel
lastRoute = line;
modelCounter = 0;
}
else if (line.IndexOf("Standard orientation:") >= 0)
{
// Found a set of coordinates
// Add current frame to file and create a new one.
if (!readOptimizedStructureOnly.Set)
{
sequence.addChemModel(model);
}
else
{
//logger.info("Skipping frame, because I was told to do");
}
fireFrameRead();
model = chemFile.Builder.newChemModel();
modelCounter++;
readCoordinates(model);
}
else if (line.IndexOf("SCF Done:") >= 0)
{
// Found an energy
model.setProperty(CDKConstants.REMARK, line.Trim());
}
else if (line.IndexOf("Harmonic frequencies") >= 0)
{
// Found a set of vibrations
// readFrequencies(frame);
}
else if (line.IndexOf("Total atomic charges") >= 0)
{
readPartialCharges(model);
}
else if (line.IndexOf("Magnetic shielding") >= 0)
{
// Found NMR data
readNMRData(model, line);
}
else if (line.IndexOf("GINC") >= 0)
{
// Found calculation level of theory
levelOfTheory = parseLevelOfTheory(line);
//logger.debug("Level of Theory for this model: " + levelOfTheory);
description = lastRoute + ", model no. " + modelCounter;
model.setProperty(CDKConstants.DESCRIPTION, description);
}
else
{
////logger.debug("Skipping line: " + line);
}
line = input.ReadLine();
}
// Add last frame to file
sequence.addChemModel(model);
fireFrameRead();
}
chemFile.addChemSequence(sequence);
return(chemFile);
}
/// <summary> Read the ShelX from input. Each ShelX document is expected to contain
/// one crystal structure.
///
/// </summary>
/// <returns> a ChemFile with the coordinates, charges, vectors, etc.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence seq = file.Builder.newChemSequence();
IChemModel model = file.Builder.newChemModel();
crystal = file.Builder.newCrystal();
System.String line = input.ReadLine();
bool end_found = false;
while (input.Peek() != -1 && line != null && !end_found)
{
if (line.StartsWith("#"))
{
//logger.warn("Skipping comment: " + line);
// skip comment lines
}
else if (line.Length == 0)
{
//logger.debug("Skipping empty line");
// skip empty lines
}
else if (!(line.StartsWith("_") || line.StartsWith("loop_")))
{
//logger.warn("Skipping unrecognized line: " + line);
// skip line
}
else
{
/* determine CIF command */
System.String command = "";
int spaceIndex = line.IndexOf(" ");
if (spaceIndex != -1)
{
// everything upto space is command
try
{
command = new System.Text.StringBuilder(line.Substring(0, (spaceIndex) - (0))).ToString();
}
catch (System.ArgumentOutOfRangeException sioobe)
{
// disregard this line
break;
}
}
else
{
// complete line is command
command = line;
}
//logger.debug("command: " + command);
if (command.StartsWith("_cell"))
{
processCellParameter(command, line);
}
else if (command.Equals("loop_"))
{
processLoopBlock();
}
else if (command.Equals("_symmetry_space_group_name_H-M"))
{
System.String value_Renamed = line.Substring(29).Trim();
crystal.SpaceGroup = value_Renamed;
}
else
{
// skip command
//logger.warn("Skipping command: " + command);
line = input.ReadLine();
if (line.StartsWith(";"))
{
//logger.debug("Skipping block content");
line = input.ReadLine().Trim();
while (!line.Equals(";"))
{
line = input.ReadLine().Trim();
//logger.debug("Skipping block line: " + line);
}
line = input.ReadLine();
}
}
}
line = input.ReadLine();
}
//logger.info("Adding crystal to file with #atoms: " + crystal.AtomCount);
model.Crystal = crystal;
seq.addChemModel(model);
file.addChemSequence(seq);
return(file);
}
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);
}
/// <summary> Read a <code>ChemFile</code> from a file in PDB format. The molecules
/// in the file are stored as <code>BioPolymer</code>s in the
/// <code>ChemFile</code>. The residues are the monomers of the
/// <code>BioPolymer</code>, and their names are the concatenation of the
/// residue, chain id, and the sequence number. Separate chains (denoted by
/// TER records) are stored as separate <code>BioPolymer</code> molecules.
///
/// <p>Connectivity information is not currently read.
///
/// </summary>
/// <returns> The ChemFile that was read from the PDB file.
/// </returns>
private IChemFile readChemFile(IChemFile oFile)
{
int bonds = 0;
// initialize all containers
IChemSequence oSeq = oFile.Builder.newChemSequence();
IChemModel oModel = oFile.Builder.newChemModel();
ISetOfMolecules oSet = oFile.Builder.newSetOfMolecules();
// some variables needed
string cCol;
PDBAtom oAtom;
PDBPolymer oBP = new PDBPolymer();
System.Text.StringBuilder cResidue;
string oObj;
IMonomer oMonomer;
string cRead = "";
char chain = 'A'; // To ensure stringent name giving of monomers
IStrand oStrand;
int lineLength = 0;
atomNumberMap = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
// do the reading of the Input
try
{
do
{
cRead = _oInput.ReadLine();
//logger.debug("Read line: ", cRead);
if (cRead != null)
{
lineLength = cRead.Length;
if (lineLength < 80)
{
//logger.warn("Line is not of the expected length 80!");
}
// make sure the record name is 6 characters long
if (lineLength < 6)
{
cRead = cRead + " ";
}
// check the first column to decide what to do
cCol = cRead.Substring(0, (6) - (0));
if ("ATOM ".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
// construct a string describing the residue
cResidue = new System.Text.StringBuilder(8);
oObj = oAtom.ResName;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
oObj = oAtom.ChainID;
if (oObj != null)
{
// cResidue = cResidue.append(((String)oObj).trim());
cResidue = cResidue.Append(System.Convert.ToString(chain));
}
oObj = oAtom.ResSeq;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
// search for an existing strand or create a new one.
oStrand = oBP.getStrand(System.Convert.ToString(chain));
if (oStrand == null)
{
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
}
// search for an existing monomer or create a new one.
oMonomer = oBP.getMonomer(cResidue.ToString(), System.Convert.ToString(chain));
if (oMonomer == null)
{
PDBMonomer monomer = new PDBMonomer();
monomer.MonomerName = cResidue.ToString();
monomer.MonomerType = oAtom.ResName;
monomer.ChainID = oAtom.ChainID;
monomer.ICode = oAtom.ICode;
oMonomer = monomer;
}
// add the atom
oBP.addAtom(oAtom, oMonomer, oStrand);
System.Object tempObject;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (readConnect.Set && tempObject != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
// //logger.debug("Added ATOM: ", oAtom);
/** As HETATMs cannot be considered to either belong to a certain monomer or strand,
* they are dealt with seperately.*/
}
else if ("HETATM".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
oAtom.HetAtom = true;
oBP.addAtom(oAtom);
System.Object tempObject2;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject2 = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (tempObject2 != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
//logger.debug("Added HETATM: ", oAtom);
}
else if ("TER ".ToUpper().Equals(cCol.ToUpper()))
{
// start new strand
chain++;
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
//logger.debug("Added new STRAND");
}
else if ("END ".ToUpper().Equals(cCol.ToUpper()))
{
atomNumberMap.Clear();
// create bonds and finish the molecule
if (deduceBonding.Set)
{
// OK, try to deduce the bonding patterns
if (oBP.AtomCount != 0)
{
// Create bonds. If bonds could not be created, all bonds are deleted.
try
{
if (useRebondTool.Set)
{
if (!createBondsWithRebondTool(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created using the RebondTool when PDB file was read.");
oBP.removeAllBonds();
}
}
else
{
if (!createBonds(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created when PDB file was read.");
oBP.removeAllBonds();
}
}
}
catch (System.Exception exception)
{
//logger.info("Bonds could not be created when PDB file was read.");
//logger.debug(exception);
}
}
}
oSet.addMolecule(oBP);
// oBP = new BioPolymer();
// } else if (cCol.equals("USER ")) {
// System.out.println(cLine);
// System.out.println(cLine);
// } else if (cCol.equals("ENDMDL")) {
// System.out.println(cLine);
}
else if (cCol.Equals("MODEL "))
{
// OK, start a new model and save the current one first *if* it contains atoms
if (oBP.AtomCount > 0)
{
// save the model
oSet.addAtomContainer(oBP);
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
// setup a new one
oBP = new PDBPolymer();
oModel = oFile.Builder.newChemModel();
oSet = oFile.Builder.newSetOfMolecules();
}
}
else if ("REMARK".ToUpper().Equals(cCol.ToUpper()))
{
System.Object comment = oFile.getProperty(CDKConstants.COMMENT);
if (comment == null)
{
comment = "";
}
if (lineLength > 12)
{
//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'"
comment = comment.ToString() + cRead.Substring(11).Trim() + "\n";
oFile.setProperty(CDKConstants.COMMENT, comment);
}
else
{
//logger.warn("REMARK line found without any comment!");
}
}
else if ("COMPND".ToUpper().Equals(cCol.ToUpper()))
{
string title = cRead.Substring(10).Trim();
oFile.setProperty(CDKConstants.TITLE, title);
}
/*************************************************************
* Read connectivity information from CONECT records.
* Only covalent bonds are dealt with. Perhaps salt bridges
* should be dealt with in the same way..?
*/
else if (readConnect.Set && "CONECT".ToUpper().Equals(cCol.ToUpper()))
{
cRead.Trim();
if (cRead.Length < 16)
{
//logger.debug("Skipping unexpected empty CONECT line! : ", cRead);
}
else
{
string bondAtom = cRead.Substring(7, 5).Trim();
int bondAtomNo = System.Int32.Parse(bondAtom);
for (int b = 0; b < 9; b += (b == 5 ? 2 : 1))
{
string bondedAtom = cRead.Substring((b * 5) + 11, 5).Trim();
int bondedAtomNo;
if (int.TryParse(bondedAtom, out bondedAtomNo))
{
bonds++;
addBond(oBP, bondAtomNo, bondedAtomNo);
}
}
//string bondedAtom = cRead.Substring(12, 5).Trim();
//int bondedAtomNo = -1;
//try
//{
// bondedAtomNo = System.Int32.Parse(bondedAtom);
//}
//catch (System.Exception e)
//{
// bondedAtomNo = -1;
//}
//if (bondedAtomNo != -1)
//{
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
//}
//else
//{
//}
//if (cRead.Length > 17)
//{
// bondedAtom = cRead.Substring(16, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 22)
//{
// bondedAtom = cRead.Substring(22, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 27)
//{
// bondedAtom = cRead.Substring(27, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
}
}
/*************************************************************/
else if ("HELIX ".ToUpper().Equals(cCol.ToUpper()))
{
// HELIX 1 H1A CYS A 11 LYS A 18 1 RESIDUE 18 HAS POSITIVE PHI 1D66 72
// 1 2 3 4 5 6 7
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.HELIX;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(21, (25) - (21)).Trim());
structure.StartInsertionCode = cRead[25];
structure.EndChainID = cRead[31];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("SHEET ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.SHEET;
structure.StartChainID = cRead[21];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(22, (26) - (22)).Trim());
structure.StartInsertionCode = cRead[26];
structure.EndChainID = cRead[32];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("TURN ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.TURN;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(20, (24) - (20)).Trim());
structure.StartInsertionCode = cRead[24];
structure.EndChainID = cRead[30];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(31, (35) - (31)).Trim());
structure.EndInsertionCode = cRead[35];
oBP.addStructure(structure);
} // ignore all other commands
}
}while (_oInput.Peek() != -1 && (cRead != null));
}
catch (System.Exception e)
{
//logger.error("Found a problem at line:\n");
//logger.error(cRead);
//logger.error("01234567890123456789012345678901234567890123456789012345678901234567890123456789");
//logger.error(" 1 2 3 4 5 6 7 ");
//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(" error: " + e.Message);
//logger.debug(e);
}
// try to close the Input
try
{
_oInput.Close();
}
catch (System.Exception e)
{
//logger.debug(e);
}
// Set all the dependencies
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
oFile.addChemSequence(oSeq);
return(oFile);
}
/// <summary> Read a ChemFile from a file in MDL SDF format.
///
/// </summary>
/// <returns> The ChemFile that was read from the MDL file.
/// </returns>
private IChemFile readChemFile(IChemFile chemFile)
{
IChemSequence chemSequence = chemFile.Builder.newChemSequence();
IChemModel chemModel = chemFile.Builder.newChemModel();
ISetOfMolecules setOfMolecules = chemFile.Builder.newSetOfMolecules();
IMolecule m = readMolecule(chemFile.Builder.newMolecule());
if (m != null)
{
setOfMolecules.addMolecule(m);
}
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
setOfMolecules = chemFile.Builder.newSetOfMolecules();
chemModel = chemFile.Builder.newChemModel();
System.String str;
try
{
System.String line;
while ((line = input.ReadLine()) != null)
{
//logger.debug("line: ", line);
// apparently, this is a SDF file, continue with
// reading mol files
str = new System.Text.StringBuilder(line).ToString();
if (str.Equals("$$$$"))
{
m = readMolecule(chemFile.Builder.newMolecule());
if (m != null)
{
setOfMolecules.addMolecule(m);
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
setOfMolecules = chemFile.Builder.newSetOfMolecules();
chemModel = chemFile.Builder.newChemModel();
}
}
else
{
// here the stuff between 'M END' and '$$$$'
if (m != null)
{
// ok, the first lines should start with '>'
System.String fieldName = null;
if (str.StartsWith("> "))
{
// ok, should extract the field name
str.Substring(2); // String content =
int index = str.IndexOf("<");
if (index != -1)
{
int index2 = str.Substring(index).IndexOf(">");
if (index2 != -1)
{
fieldName = str.Substring(index + 1, (index + index2) - (index + 1));
}
}
// end skip all other lines
while ((line = input.ReadLine()) != null && line.StartsWith(">"))
{
//logger.debug("data header line: ", line);
}
}
if (line == null)
{
throw new CDKException("Expecting data line here, but found null!");
}
System.String data = line;
while ((line = input.ReadLine()) != null && line.Trim().Length > 0)
{
if (line.Equals("$$$$"))
{
//logger.error("Expecting data line here, but found end of molecule: ", line);
break;
}
//logger.debug("data line: ", line);
data += line;
}
if (fieldName != null)
{
//logger.info("fieldName, data: ", fieldName, ", ", data);
m.setProperty(fieldName, data);
}
}
}
}
}
catch (CDKException cdkexc)
{
throw cdkexc;
}
catch (System.Exception exception)
{
System.String error = "Error while parsing SDF";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
try
{
input.Close();
}
catch (System.Exception exc)
{
//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 closing file: " + exc.Message;
//logger.error(error);
throw new CDKException(error, exc);
}
chemFile.addChemSequence(chemSequence);
return(chemFile);
}
private IChemFile readChemFile(IChemFile file)
{
IChemSequence seq = file.Builder.newChemSequence();
IChemModel model = file.Builder.newChemModel();
ICrystal crystal = null;
int lineNumber = 0;
Vector3d a, b, c;
try
{
System.String line = input.ReadLine();
while (input.Peek() != -1 && line != null)
{
//logger.debug((lineNumber++) + ": ", line);
if (line.StartsWith("frame:"))
{
//logger.debug("found new frame");
model = file.Builder.newChemModel();
crystal = file.Builder.newCrystal();
// assume the file format is correct
//logger.debug("reading spacegroup");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
crystal.SpaceGroup = line;
//logger.debug("reading unit cell axes");
Vector3d axis = new Vector3d();
//logger.debug("parsing A: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.A = axis;
axis = new Vector3d();
//logger.debug("parsing B: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.B = axis;
axis = new Vector3d();
//logger.debug("parsing C: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.C = axis;
//logger.debug("Crystal: ", crystal);
a = crystal.A;
b = crystal.B;
c = crystal.C;
//logger.debug("Reading number of atoms");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int atomsToRead = System.Int32.Parse(line);
//logger.debug("Reading no molecules in assym unit cell");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int Z = System.Int32.Parse(line);
crystal.Z = Z;
System.String symbol;
double charge;
Point3d cart;
for (int i = 1; i <= atomsToRead; i++)
{
cart = new Point3d();
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
symbol = line.Substring(0, (line.IndexOf(":")) - (0));
charge = System.Double.Parse(line.Substring(line.IndexOf(":") + 1));
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.x = System.Double.Parse(line); // x
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.y = System.Double.Parse(line); // y
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.z = System.Double.Parse(line); // z
IAtom atom = file.Builder.newAtom(symbol);
atom.setCharge(charge);
// convert cartesian coords to fractional
Point3d frac = CrystalGeometryTools.cartesianToFractional(a, b, c, cart);
atom.setFractionalPoint3d(frac);
crystal.addAtom(atom);
//logger.debug("Added atom: ", atom);
}
model.Crystal = crystal;
seq.addChemModel(model);
}
else
{
//logger.debug("Format seems broken. Skipping these lines:");
while (!line.StartsWith("frame:") && input.Peek() != -1 && line != null)
{
line = input.ReadLine();
//logger.debug(lineNumber++ + ": ", line);
}
//logger.debug("Ok, resynched: found new frame");
}
}
file.addChemSequence(seq);
}
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 message = "Error while parsing CrystClust file: " + exception.Message;
//logger.error(message);
//logger.debug(exception);
throw new CDKException(message, exception);
}
return(file);
}
/// <summary> Private method that actually parses the input to read a ChemFile
/// object.
///
/// </summary>
/// <returns> A ChemFile containing the data parsed from input.
/// </returns>
private IChemFile readChemFile(IChemFile file)
{
IChemSequence chemSequence = file.Builder.newChemSequence();
int number_of_atoms = 0;
SupportClass.Tokenizer tokenizer;
try
{
System.String line = input.ReadLine();
while (line.StartsWith("#"))
{
line = input.ReadLine();
}
/*while (input.ready() && line != null)
* {*/
// System.out.println("lauf");
// parse frame by frame
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
System.String token = tokenizer.NextToken();
number_of_atoms = System.Int32.Parse(token);
System.String info = input.ReadLine();
IChemModel chemModel = file.Builder.newChemModel();
ISetOfMolecules setOfMolecules = file.Builder.newSetOfMolecules();
IMolecule m = file.Builder.newMolecule();
m.setProperty(CDKConstants.TITLE, info);
System.String[] types = new System.String[number_of_atoms];
double[] d = new double[number_of_atoms]; int[] d_atom = new int[number_of_atoms]; // Distances
double[] a = new double[number_of_atoms]; int[] a_atom = new int[number_of_atoms]; // Angles
double[] da = new double[number_of_atoms]; int[] da_atom = new int[number_of_atoms]; // Diederangles
//Point3d[] pos = new Point3d[number_of_atoms]; // calculated positions
int i = 0;
while (i < number_of_atoms)
{
line = input.ReadLine();
// System.out.println("line:\""+line+"\"");
if (line == null)
{
break;
}
if (line.StartsWith("#"))
{
// skip comment in file
}
else
{
d[i] = 0d; d_atom[i] = -1;
a[i] = 0d; a_atom[i] = -1;
da[i] = 0d; da_atom[i] = -1;
tokenizer = new SupportClass.Tokenizer(line, "\t ,;");
int fields = tokenizer.Count;
if (fields < System.Math.Min(i * 2 + 1, 7))
{
// this is an error but cannot throw exception
}
else if (i == 0)
{
types[i] = tokenizer.NextToken();
i++;
}
else if (i == 1)
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
else if (i == 2)
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
a[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
else
{
types[i] = tokenizer.NextToken();
d_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
d[i] = (System.Double.Parse(tokenizer.NextToken()));
a_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
a[i] = (System.Double.Parse(tokenizer.NextToken()));
da_atom[i] = (System.Int32.Parse(tokenizer.NextToken())) - 1;
//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'"
da[i] = (System.Double.Parse(tokenizer.NextToken()));
i++;
}
}
}
// calculate cartesian coordinates
Point3d[] cartCoords = ZMatrixTools.zmatrixToCartesian(d, d_atom, a, a_atom, da, da_atom);
for (i = 0; i < number_of_atoms; i++)
{
m.addAtom(file.Builder.newAtom(types[i], cartCoords[i]));
}
// System.out.println("molecule:\n"+m);
setOfMolecules.addMolecule(m);
chemModel.SetOfMolecules = setOfMolecules;
chemSequence.addChemModel(chemModel);
line = input.ReadLine();
file.addChemSequence(chemSequence);
}
catch (System.IO.IOException e)
{
// should make some noise now
file = null;
}
return(file);
}