/// <summary> writes a single frame in XYZ format to the Writer.</summary>
/// <param name="mol">the Molecule to write
/// </param>
public virtual void writeMolecule(IMolecule mol)
{
System.String st = "";
bool writecharge = true;
try
{
System.String s1 = ((System.Int32)mol.AtomCount).ToString();
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(s1.ToCharArray(), 0, s1.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
System.String s2 = null; // FIXME: add some interesting comment
if (s2 != null)
{
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(s2.ToCharArray(), 0, s2.Length);
}
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
// Loop through the atoms and write them out:
IAtom[] atoms = mol.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
IAtom a = atoms[i];
st = a.Symbol;
Point3d p3 = a.getPoint3d();
if (p3 != null)
{
st = st + "\t" + p3.x.ToString() + "\t" + p3.y.ToString() + "\t" + p3.z.ToString();
}
if (writecharge)
{
double ct = a.getCharge();
st = st + "\t" + ct;
}
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(st.ToCharArray(), 0, st.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
}
catch (System.IO.IOException e)
{
// throw e;
//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 writing file: ", e.Message);
//logger.debug(e);
}
}
/// <summary> Writes a single frame to the Writer.
///
/// <p>Format:
/// <pre>
/// line data
/// ------- --------------------------
/// 1 spacegroup
/// 2,3,4 cell parameter: a
/// 5,6,7 b
/// 8,9,10 c
/// 11 number of atoms
/// 12 number of asym. units
/// 13-16 atomtype: charge, atomcoord x, y, z
/// 17-20 idem second atom
/// 21-24 idem third atom etc
/// </pre>
///
/// </summary>
/// <param name="crystal">the Crystal to serialize
/// </param>
//UPGRADE_NOTE: Access modifiers of method 'write' were changed to 'public'. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1204'"
public void write(ICrystal crystal)
{
System.String sg = crystal.SpaceGroup;
if ("P 2_1 2_1 2_1".Equals(sg))
{
write("P 21 21 21 (1)\n");
}
else
{
write("P 1 (1)\n");
}
// output unit cell axes
writeVector3d(crystal.A);
writeVector3d(crystal.B);
writeVector3d(crystal.C);
// output number of atoms
int noatoms = crystal.AtomCount;
write(((System.Int32)noatoms).ToString());
write("\n");
// output number of asym. units (Z)
if (sg.Equals("P1"))
{
write("1\n");
}
else
{
// duno
write("1\n");
}
// output atoms
for (int i = 0; i < noatoms; i++)
{
// output atom sumbol
IAtom atom = crystal.getAtomAt(i);
write(atom.Symbol);
write(":");
// output atom charge
write(((double)atom.getCharge()).ToString() + "\n");
// output coordinates
write(((double)atom.X3d).ToString() + "\n");
write(((double)atom.Y3d).ToString() + "\n");
write(((double)atom.Z3d).ToString() + "\n");
}
}
/// <summary> writes all the molecules supplied in a SetOfMolecules class to
/// a single HIN file. You can also supply a single Molecule object
/// as well
/// </summary>
/// <param name="mol">the Molecule to write
/// </param>
private void writeMolecule(ISetOfMolecules som)
{
//int na = 0;
//String info = "";
System.String sym = "";
double chrg = 0.0;
//boolean writecharge = true;
for (int molnum = 0; molnum < som.MoleculeCount; molnum++)
{
IMolecule mol = som.getMolecule(molnum);
try
{
int natom = mol.AtomCount;
int nbond = mol.getBondCount();
System.String molname = "mol " + (molnum + 1) + " " + ((System.String)mol.getProperty(CDKConstants.TITLE));
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(molname.ToCharArray(), 0, molname.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
// Loop through the atoms and write them out:
IAtom[] atoms = mol.Atoms;
IBond[] bonds = mol.Bonds;
for (int i = 0; i < natom; i++)
{
System.String line = "atom ";
IAtom a = atoms[i];
sym = a.Symbol;
chrg = a.getCharge();
Point3d p3 = a.getPoint3d();
line = line + ((System.Int32)(i + 1)).ToString() + " - " + sym + " ** - " + ((double)chrg).ToString() + " " + p3.x.ToString() + " " + p3.y.ToString() + " " + p3.z.ToString() + " ";
System.String buf = "";
int ncon = 0;
for (int j = 0; j < nbond; j++)
{
IBond b = bonds[j];
if (b.contains(a))
{
// current atom is in the bond so lets get the connected atom
IAtom ca = b.getConnectedAtom(a);
double bo = b.Order;
int serial = -1;
System.String bt = "";
// get the serial no for this atom
serial = mol.getAtomNumber(ca);
if (bo == 1)
{
bt = new System.Text.StringBuilder("s").ToString();
}
else if (bo == 2)
{
bt = new System.Text.StringBuilder("d").ToString();
}
else if (bo == 3)
{
bt = new System.Text.StringBuilder("t").ToString();
}
else if (bo == 1.5)
{
bt = new System.Text.StringBuilder("a").ToString();
}
buf = buf + ((System.Int32)(serial + 1)).ToString() + " " + bt + " ";
ncon++;
}
}
line = line + " " + ((System.Int32)ncon).ToString() + " " + buf;
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(line.ToCharArray(), 0, line.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
System.String buf2 = "endmol " + (molnum + 1);
//UPGRADE_NOTE: Exceptions thrown by the equivalent in .NET of method 'java.io.BufferedWriter.write' may be different. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1099'"
writer.Write(buf2.ToCharArray(), 0, buf2.Length);
//UPGRADE_TODO: Method 'java.io.BufferedWriter.newLine' was converted to 'System.IO.TextWriter.WriteLine' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073'"
writer.WriteLine();
}
catch (System.IO.IOException e)
{
throw e;
}
}
}
