public static void ToFile(string filepath
, IList <Atom> atoms
, IList <Vector> coords = null
, IList <MatrixByArr> anisous = null
, double?anisouScale = null
, IList <double> bfactors = null
, bool append = false
, IList <string> headers = null
, int?modelidx = null
)
{
List <string> lines = new List <string>();
int size = atoms.Count;
if (coords != null)
{
HDebug.Assert(size == coords.Count);
}
if (anisous != null)
{
HDebug.Assert(size == anisous.Count);
}
//if(anisouScale != null) Debug.Assert(size == anisouScale.Count);
if (headers != null)
{
lines.AddRange(headers);
}
{
// 1 2 3 4 5 6 7 8
// 12345678901234567890123456789012345678901234567890123456789012345678901234567890
// "MODEL 1 "
string line = "MODEL 1 ";
if (modelidx != null)
{
line.Replace("1", modelidx.Value.ToString());
}
line = line.Substring(0, 80);
lines.Add(line);
}
for (int i = 0; i < size; i++)
{
Atom atom = atoms[i];
if (atom == null)
{
continue;
}
{
if (coords != null)
{
double x = coords[i][0];
double y = coords[i][1];
double z = coords[i][2];
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
}
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[i]));
}
lines.Add(atom.line);
}
{
if (anisous != null)
{
MatrixByArr U = anisous[i];
if (anisouScale != null)
{
U = U * anisouScale.Value;
}
Anisou anisou = Anisou.FromAtom(atom, U.ToArray().HToInt());
string line = anisou.line; //anisou.GetUpdatedU(anisous[i])
lines.Add(line);
}
}
}
lines.Add("ENDMDL ");
//int idx = 0;
//foreach(Element element in elements)
//{
// string line = element.line;
// if(typeof(Atom).IsInstanceOfType(element))
// {
// double x = coords[idx][0];
// double y = coords[idx][1];
// double z = coords[idx][2];
// Atom atom = (Atom)element;
// line = atom.GetUpdatedLine(x, y, z);
// idx++;
// }
// lines.Add(line);
//}
if (append == false)
{
HFile.WriteAllLines(filepath, lines);
}
else
{
StringBuilder text = new StringBuilder();
foreach (string line in lines)
{
text.AppendLine(line);
}
HFile.AppendAllText(filepath, text.ToString());
}
}
public void ToFile(string filepath, IList <Vector> coords = null, IList <double> bfactors = null, IList <MatrixByArr> anisous = null, double anisous_scale = 1, bool append = false)
{
List <string> lines = new List <string>();
if (coords == null)
{
coords = this.atoms.ListCoord();
}
//Debug.Assert(atoms.Length == coords.Count);
int idx = 0;
foreach (Element element in elements)
{
//string line = element.line;
if (typeof(Atom).IsInstanceOfType(element))
{
double x = coords[idx][0];
double y = coords[idx][1];
double z = coords[idx][2];
Atom atom = (Atom)element;
atom = Atom.FromString(atom.GetUpdatedLine(x, y, z));
if (bfactors != null)
{
atom = Atom.FromString(atom.GetUpdatedLineTempFactor(bfactors[idx]));
}
lines.Add(atom.line);
if (anisous != null)
{
MatrixByArr anisoui = anisous[idx] * anisous_scale;
int[,] U = new int[3, 3] {
{ (int)anisoui[0, 0], (int)anisoui[0, 1], (int)anisoui[0, 2], },
{ (int)anisoui[1, 0], (int)anisoui[1, 1], (int)anisoui[1, 2], },
{ (int)anisoui[2, 0], (int)anisoui[2, 1], (int)anisoui[2, 2], },
};
Anisou anisou = Anisou.FromAtom(atom, U);
lines.Add(anisou.line);
}
idx++;
}
else if (typeof(Anisou).IsInstanceOfType(element) && anisous != null)
{
// skip because it is handled in the "Atom" part
}
else
{
lines.Add(element.line);
}
}
if (append == false)
{
HFile.WriteAllLines(filepath, lines);
}
else
{
StringBuilder text = new StringBuilder();
foreach (string line in lines)
{
text.AppendLine(line);
}
HFile.AppendAllText(filepath, text.ToString());
}
}
