private void processAtomLoopBlock(System.String firstLine)
{
int atomLabel = -1; // -1 means not found in this block
int atomSymbol = -1;
int atomFractX = -1;
int atomFractY = -1;
int atomFractZ = -1;
int atomRealX = -1;
int atomRealY = -1;
int atomRealZ = -1;
System.String line = firstLine.Trim();
int headerCount = 0;
bool hasParsableInformation = false;
while (line != null && line[0] == '_')
{
headerCount++;
if (line.Equals("_atom_site_label") || line.Equals("_atom_site_label_atom_id"))
{
atomLabel = headerCount;
hasParsableInformation = true;
//logger.info("label found in col: " + atomLabel);
}
else if (line.StartsWith("_atom_site_fract_x"))
{
atomFractX = headerCount;
hasParsableInformation = true;
//logger.info("frac x found in col: " + atomFractX);
}
else if (line.StartsWith("_atom_site_fract_y"))
{
atomFractY = headerCount;
hasParsableInformation = true;
//logger.info("frac y found in col: " + atomFractY);
}
else if (line.StartsWith("_atom_site_fract_z"))
{
atomFractZ = headerCount;
hasParsableInformation = true;
//logger.info("frac z found in col: " + atomFractZ);
}
else if (line.Equals("_atom_site.Cartn_x"))
{
atomRealX = headerCount;
hasParsableInformation = true;
//logger.info("cart x found in col: " + atomRealX);
}
else if (line.Equals("_atom_site.Cartn_y"))
{
atomRealY = headerCount;
hasParsableInformation = true;
//logger.info("cart y found in col: " + atomRealY);
}
else if (line.Equals("_atom_site.Cartn_z"))
{
atomRealZ = headerCount;
hasParsableInformation = true;
//logger.info("cart z found in col: " + atomRealZ);
}
else if (line.Equals("_atom_site.type_symbol"))
{
atomSymbol = headerCount;
hasParsableInformation = true;
//logger.info("type_symbol found in col: " + atomSymbol);
}
else
{
//logger.warn("Ignoring atom loop block field: " + line);
}
line = input.ReadLine().Trim();
}
if (hasParsableInformation == false)
{
//logger.info("No parsable info found");
skipUntilEmptyOrCommentLine(line);
}
else
{
// now that headers are parsed, read the data
while (line != null && line.Length > 0 && line[0] != '#')
{
//logger.debug("new row");
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
if (tokenizer.Count < headerCount)
{
//logger.warn("Column count mismatch; assuming continued on next line");
//logger.debug("Found #expected, #found: " + headerCount + ", " + tokenizer.Count);
tokenizer = new SupportClass.Tokenizer(line + input.ReadLine());
}
int colIndex = 0;
// process one row
IAtom atom = crystal.Builder.newAtom("C");
Point3d frac = new Point3d();
Point3d real = new Point3d();
bool hasFractional = false;
bool hasCartesian = false;
while (tokenizer.HasMoreTokens())
{
colIndex++;
System.String field = tokenizer.NextToken();
//logger.debug("Parsing col,token: " + colIndex + "=" + field);
if (colIndex == atomLabel)
{
if (atomSymbol == -1)
{
// no atom symbol found, use label
System.String element = extractFirstLetters(field);
atom.Symbol = element;
}
atom.ID = field;
}
else if (colIndex == atomFractX)
{
hasFractional = true;
frac.x = parseIntoDouble(field);
}
else if (colIndex == atomFractY)
{
hasFractional = true;
frac.y = parseIntoDouble(field);
}
else if (colIndex == atomFractZ)
{
hasFractional = true;
frac.z = parseIntoDouble(field);
}
else if (colIndex == atomSymbol)
{
atom.Symbol = field;
}
else if (colIndex == atomRealX)
{
hasCartesian = true;
//logger.debug("Adding x3: " + parseIntoDouble(field));
real.x = parseIntoDouble(field);
}
else if (colIndex == atomRealY)
{
hasCartesian = true;
//logger.debug("Adding y3: " + parseIntoDouble(field));
real.y = parseIntoDouble(field);
}
else if (colIndex == atomRealZ)
{
hasCartesian = true;
//logger.debug("Adding x3: " + parseIntoDouble(field));
real.z = parseIntoDouble(field);
}
}
if (hasCartesian)
{
Vector3d a = crystal.A;
Vector3d b = crystal.B;
Vector3d c = crystal.C;
frac = CrystalGeometryTools.cartesianToFractional(a, b, c, real);
atom.setFractionalPoint3d(frac);
}
if (hasFractional)
{
atom.setFractionalPoint3d(frac);
}
//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("Adding atom: " + atom);
crystal.addAtom(atom);
// look up next row
line = input.ReadLine().Trim();
}
}
}
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);
}