private ICrystal ReadCrystal(ICrystal crystal)
{
string line = input.ReadLine();
bool end_found = false;
while (line != null && !end_found)
{
/* is line continued? */
if (line.Length > 0 && line.Substring(line.Length - 1).Equals("=", StringComparison.Ordinal))
{
/* yes, line is continued */
line = line + input.ReadLine();
}
/* determine ShelX command */
string command;
try
{
command = line.Substring(0, 4);
}
catch (ArgumentOutOfRangeException)
{
// disregard this line
break;
}
Debug.WriteLine($"command: {command}");
var u_command = command.ToUpperInvariant();
if (u_command.StartsWith("REM", StringComparison.Ordinal))
{
/* line is comment, disregard */
/* 7.1 Crystal data and general instructions */
}
else if (u_command.StartsWith("END", StringComparison.Ordinal))
{
end_found = true;
}
else
{
switch (u_command)
{
case "TITL":
break;
case "CELL":
{
// example: CELL 1.54184 23.56421 7.13203 18.68928 90.0000
// 109.3799 90.0000 CELL 1.54184 7.11174 21.71704 30.95857
// 90.000 90.000 90.000
var st = Strings.Tokenize(line);
//st[0]; // string command_again
//st[1]; // string wavelength
string sa = st[2];
string sb = st[3];
string sc = st[4];
string salpha = st[5];
string sbeta = st[6];
string sgamma = st[7];
Debug.WriteLine($"a: {sa}");
Debug.WriteLine($"b: {sb}");
Debug.WriteLine($"c: {sc}");
Debug.WriteLine($"alpha: {salpha}");
Debug.WriteLine($"beta : {sbeta}");
Debug.WriteLine($"gamma: {sgamma}");
double a = FortranFormat.Atof(sa);
double b = FortranFormat.Atof(sb);
double c = FortranFormat.Atof(sc);
double alpha = FortranFormat.Atof(salpha);
double beta = FortranFormat.Atof(sbeta);
double gamma = FortranFormat.Atof(sgamma);
Vector3[] axes = CrystalGeometryTools.NotionalToCartesian(a, b, c, alpha, beta, gamma);
crystal.A = axes[0];
crystal.B = axes[1];
crystal.C = axes[2];
}
break;
case "ZERR":
case "LATT":
case "SYMM":
case "SFAC":
case "DISP":
case "UNIT":
case "LAUE":
case "REM ":
case "MORE":
case "TIME":
/* 7.2 Reflection data input */
case "HKLF":
case "OMIT":
case "SHEL":
case "BASF":
case "TWIN":
case "EXTI":
case "SWAT":
case "HOPE":
case "MERG":
/* 7.3 Atom list and least-squares constraints */
case "SPEC":
case "RESI":
case "MOVE":
case "ANIS":
case "AFIX":
case "HFIX":
case "FRAG":
case "FEND":
case "EXYZ":
//case "EXTI":
case "EADP":
case "EQIV":
/* 7.4 The connectivity list */
case "CONN":
case "PART":
case "BIND":
case "FREE":
/* 7.5 Least-squares restraints */
case "DFIX":
case "DANG":
case "BUMP":
case "SAME":
case "SADI":
case "CHIV":
case "FLAT":
case "DELU":
case "SIMU":
case "DEFS":
case "ISOR":
case "NCSY":
case "SUMP":
/* 7.6 Least-squares organization */
case "L.S.":
case "CGLS":
case "BLOC":
case "DAMP":
case "STIR":
case "WGHT":
case "FVAR":
/* 7.7 Lists and tables */
case "BOND":
case "CONF":
case "MPLA":
case "RTAB":
case "HTAB":
case "LIST":
case "ACTA":
case "SIZE":
case "TEMP":
case "WPDB":
/* 7.8 Fouriers, peak search and lineprinter plots */
case "FMAP":
case "GRID":
case "PLAN":
break;
case "MOLE":
/* NOT DOCUMENTED BUT USED BY PLATON */
break;
case "SPGR":
{
// Line added by PLATON stating the spacegroup
var st = Strings.Tokenize(line);
//st[0]; // string command_again
string spacegroup = st[1];
crystal.SpaceGroup = spacegroup;
}
break;
case " ":
{
Debug.WriteLine($"Disrgarding line assumed to be added by PLATON: {line}");
/* All other is atom */
}
break;
default:
{
//Debug.WriteLine($"Assumed to contain an atom: {line}");
// this line gives an atom, because all lines not starting with
// a ShelX command is an atom (that sucks!)
var st = Strings.Tokenize(line);
string atype = st[0];
//st[1]; // string scatt_factor
string sa = st[2];
string sb = st[3];
string sc = st[4];
// skip the rest
if (char.IsDigit(atype[1]))
{
// atom type has a one letter code
atype = atype.Substring(0, 1);
}
else
{
var sb2 = new StringBuilder();
sb2.Append(atype[1]);
atype = atype.Substring(0, 1) + sb2.ToString().ToLowerInvariant();
}
double[] frac = new double[3];
frac[0] = FortranFormat.Atof(sa); // fractional coordinates
frac[1] = FortranFormat.Atof(sb);
frac[2] = FortranFormat.Atof(sc);
Debug.WriteLine("fa,fb,fc: " + frac[0] + ", " + frac[1] + ", " + frac[2]);
if (string.Equals(atype, "Q", StringComparison.OrdinalIgnoreCase))
{
// ingore atoms named Q
}
else
{
Trace.TraceInformation("Adding atom: " + atype + ", " + frac[0] + ", " + frac[1] + ", " + frac[2]);
IAtom atom = crystal.Builder.NewAtom(atype);
atom.FractionalPoint3D = new Vector3(frac[0], frac[1], frac[2]);
crystal.Atoms.Add(atom);
Debug.WriteLine($"Atom added: {atom}");
}
}
break;
}
}
line = input.ReadLine();
}
return(crystal);
}
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);
}
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 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);
}
