private IChemFile ReadChemFile(IChemFile file)
{
IChemSequence seq = file.Builder.NewChemSequence();
IChemModel model = file.Builder.NewChemModel();
ICrystal crystal = null;
int lineNumber = 0;
Vector3 a, b, c;
try
{
string line = input.ReadLine();
while (line != null)
{
Debug.WriteLine($"{lineNumber++}: {line}");
if (line.StartsWith("frame:", StringComparison.Ordinal))
{
Debug.WriteLine("found new frame");
model = file.Builder.NewChemModel();
crystal = file.Builder.NewCrystal();
// assume the file format is correct
Debug.WriteLine("reading spacegroup");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
crystal.SpaceGroup = line;
Debug.WriteLine("reading unit cell axes");
Vector3 axis = new Vector3();
Debug.WriteLine("parsing A: ");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.X = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Y = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Z = FortranFormat.Atof(line);
crystal.A = axis;
axis = new Vector3();
Debug.WriteLine("parsing B: ");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.X = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Y = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Z = FortranFormat.Atof(line);
crystal.B = axis;
axis = new Vector3();
Debug.WriteLine("parsing C: ");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.X = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Y = FortranFormat.Atof(line);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
axis.Z = FortranFormat.Atof(line);
crystal.C = axis;
Debug.WriteLine($"Crystal: {crystal}");
a = crystal.A;
b = crystal.B;
c = crystal.C;
Debug.WriteLine("Reading number of atoms");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
int atomsToRead = int.Parse(line, NumberFormatInfo.InvariantInfo);
Debug.WriteLine("Reading no molecules in assym unit cell");
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
int Z = int.Parse(line, NumberFormatInfo.InvariantInfo);
crystal.Z = Z;
string symbol;
double charge;
Vector3 cart;
for (int i = 1; i <= atomsToRead; i++)
{
cart = new Vector3();
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
symbol = line.Substring(0, line.IndexOf(':'));
charge = double.Parse(line.Substring(line.IndexOf(':') + 1), NumberFormatInfo.InvariantInfo);
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
cart.X = double.Parse(line, NumberFormatInfo.InvariantInfo); // x
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
cart.Y = double.Parse(line, NumberFormatInfo.InvariantInfo); // y
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
cart.Z = double.Parse(line, NumberFormatInfo.InvariantInfo); // z
IAtom atom = file.Builder.NewAtom(symbol);
atom.Charge = charge;
// convert Cartesian coords to fractional
Vector3 frac = CrystalGeometryTools.CartesianToFractional(a, b, c, cart);
atom.FractionalPoint3D = frac;
crystal.Atoms.Add(atom);
Debug.WriteLine($"Added atom: {atom}");
}
model.Crystal = crystal;
seq.Add(model);
}
else
{
Debug.WriteLine("Format seems broken. Skipping these lines:");
while (line != null && !line.StartsWith("frame:", StringComparison.Ordinal))
{
line = input.ReadLine();
Debug.WriteLine($"{lineNumber++}: {line}");
}
Debug.WriteLine("Ok, resynched: found new frame");
}
}
file.Add(seq);
}
catch (Exception exception)
{
if (!(exception is IOException || exception is ArgumentException))
{
throw;
}
string message = "Error while parsing CrystClust file: " + exception.Message;
Trace.TraceError(message);
Debug.WriteLine(exception);
throw new CDKException(message, exception);
}
return(file);
}
private string ProcessAtomLoopBlock(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;
string line = firstLine.Trim();
int headerCount = 0;
bool hasParsableInformation = false;
while (line != null && line[0] == '_')
{
headerCount++;
if (line.Equals("_atom_site_label", StringComparison.Ordinal) || line.Equals("_atom_site_label_atom_id", StringComparison.Ordinal))
{
atomLabel = headerCount;
hasParsableInformation = true;
Trace.TraceInformation($"label found in col: {atomLabel}");
}
else if (line.StartsWith("_atom_site_fract_x", StringComparison.Ordinal))
{
atomFractX = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("frac x found in col: " + atomFractX);
}
else if (line.StartsWith("_atom_site_fract_y", StringComparison.Ordinal))
{
atomFractY = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("frac y found in col: " + atomFractY);
}
else if (line.StartsWith("_atom_site_fract_z", StringComparison.Ordinal))
{
atomFractZ = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("frac z found in col: " + atomFractZ);
}
else if (string.Equals(line, "_atom_site.Cartn_x", StringComparison.Ordinal))
{
atomRealX = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("cart x found in col: " + atomRealX);
}
else if (string.Equals(line, "_atom_site.Cartn_y", StringComparison.Ordinal))
{
atomRealY = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("cart y found in col: " + atomRealY);
}
else if (string.Equals(line, "_atom_site.Cartn_z", StringComparison.Ordinal))
{
atomRealZ = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("cart z found in col: " + atomRealZ);
}
else if (string.Equals(line, "_atom_site.type_symbol", StringComparison.Ordinal))
{
atomSymbol = headerCount;
hasParsableInformation = true;
Trace.TraceInformation("type_symbol found in col: " + atomSymbol);
}
else
{
Trace.TraceWarning("Ignoring atom loop block field: " + line);
}
line = input.ReadLine().Trim();
}
if (!hasParsableInformation)
{
Trace.TraceInformation("No parsable info found");
return(SkipLoopBody(line));
}
else
{
// now that headers are parsed, read the data
while (line != null && line.Length > 0 &&
line[0] != '#' &&
line[0] != '_' &&
!line.StartsWith("loop_", StringComparison.Ordinal) &&
!line.StartsWith("data_", StringComparison.Ordinal))
{
Debug.WriteLine("new row");
var tokenizer = Strings.Tokenize(line);
if (tokenizer.Count < headerCount)
{
Trace.TraceWarning("Column count mismatch; assuming continued on next line");
Debug.WriteLine($"Found #expected, #found:{headerCount}, {tokenizer.Count}");
tokenizer = Strings.Tokenize(line + input.ReadLine());
}
int colIndex = 0;
// process one row
IAtom atom = crystal.Builder.NewAtom("C");
Vector3 frac = new Vector3();
Vector3 real = new Vector3();
bool hasFractional = false;
bool hasCartesian = false;
foreach (var field in tokenizer)
{
colIndex++;
Debug.WriteLine("Parsing col,token: " + colIndex + "=" + field);
if (colIndex == atomLabel)
{
if (atomSymbol == -1)
{
// no atom symbol found, use label
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;
Debug.WriteLine("Adding x3: " + ParseIntoDouble(field));
real.X = ParseIntoDouble(field);
}
else if (colIndex == atomRealY)
{
hasCartesian = true;
Debug.WriteLine("Adding y3: " + ParseIntoDouble(field));
real.Y = ParseIntoDouble(field);
}
else if (colIndex == atomRealZ)
{
hasCartesian = true;
Debug.WriteLine("Adding x3: " + ParseIntoDouble(field));
real.Z = ParseIntoDouble(field);
}
}
if (hasCartesian)
{
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
frac = CrystalGeometryTools.CartesianToFractional(a, b, c, real);
atom.FractionalPoint3D = frac;
}
if (hasFractional)
{
atom.FractionalPoint3D = frac;
}
Debug.WriteLine($"Adding atom: {atom}");
crystal.Atoms.Add(atom);
// look up next row
line = input.ReadLine();
if (line != null)
{
line = line.Trim();
}
}
}
return(line);
}
// Private procedures
private void WriteCrystal(ICrystal crystal)
{
var title = crystal.Title;
if (title != null && title.Trim().Length > 0)
{
Writeln($"TITL {title.Trim()}");
}
else
{
Writeln("TITL Produced with CDK (http://cdk.sf.net/)");
}
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
double alength = a.Length();
double blength = b.Length();
double clength = c.Length();
double alpha = Vectors.RadianToDegree(Vectors.Angle(b, c));
double beta = Vectors.RadianToDegree(Vectors.Angle(a, c));
double gamma = Vectors.RadianToDegree(Vectors.Angle(a, b));
Write("CELL " + 1.54184.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(blength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(clength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alpha.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(beta.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(gamma.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Writeln("ZERR " + ((double)crystal.Z).ToString("F5", NumberFormatInfo.InvariantInfo)
+ " 0.01000 0.01000 0.01000 0.0100 0.0100 0.0100");
string spaceGroup = crystal.SpaceGroup;
if (string.Equals("P1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
}
else if (string.Equals("P 2_1 2_1 2_1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
Writeln("SYMM 1/2+X , 1/2-Y , -Z");
Writeln("SYMM -X , 1/2+Y , 1/2-Z");
Writeln("SYMM 1/2-X , -Y , 1/2+Z");
}
string elemNames = "";
string elemCounts = "";
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula(crystal);
var asortedElements = MolecularFormulaManipulator.Elements(formula).ToReadOnlyList();
foreach (var element in asortedElements)
{
string symbol = element.Symbol;
elemNames += symbol + " ".Substring(symbol.Length);
string countS = MolecularFormulaManipulator.GetElementCount(formula, element).ToString(NumberFormatInfo.InvariantInfo);
elemCounts += countS + " ".Substring(countS.Length);
}
Writeln("SFAC " + elemNames);
Writeln("UNIT " + elemCounts);
/* write atoms */
for (int i = 0; i < crystal.Atoms.Count; i++)
{
IAtom atom = crystal.Atoms[i];
Vector3 cartCoord = atom.Point3D.Value;
Vector3 fracCoord = CrystalGeometryTools.CartesianToFractional(a, b, c, cartCoord);
string symbol = atom.Symbol;
string output = symbol + (i + 1);
Write(output);
for (int j = 1; j < 5 - output.Length; j++)
{
Write(" ");
}
Write(" ");
string elemID = null;
for (int elemidx = 0; elemidx < asortedElements.Count; elemidx++)
{
var elem = asortedElements[elemidx];
if (elem.Symbol.Equals(symbol, StringComparison.Ordinal))
{
elemID = (elemidx + 1).ToString(NumberFormatInfo.InvariantInfo);
break;
}
}
Write(elemID);
Write(" ".Substring(elemID.Length));
Write(fracCoord.X.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Writeln(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " 11.00000 0.05000");
}
Writeln("END");
}
