static void SaveXyzCoordinates(TextWriter stream, Vector3[] coordinates, ref int residueNumber, ref int atomNumber)
{
foreach (Vector3 coordinate in coordinates)
{
AtomRecord record = new AtomRecord();
record.XYZ = coordinate;
record.Name = "XYZ";
record.ResidueName = "XYZ";
record.Element = Element.H;
record.ResidueSequenceNumber = residueNumber++;
record.Serial = atomNumber++;
stream.WriteLine(record.Text);
}
}
static void Save(TextWriter stream, char chainId, IAa residue, ref int atomNumber, ref int residueSequenceNumber)
{
foreach (IAtom atom in residue)
{
if (float.IsNaN(atom.Xyz.Length()) || atom.Element == Element.H && atom.Xyz == Vector3.Zero)
{
continue;
}
AtomRecord record = new AtomRecord(atom, chainId, residue.Name.ToString(), residueSequenceNumber, atomNumber++);
atomNumber %= 100000;
switch (OutputPdbFormat)
{
case PdbFormat.DefaultPdbV3: break;
case PdbFormat.BMRB: break;
case PdbFormat.RosettaPdbV1:
string name = record.Name;
if (alternateAtomNamesByFormat_[OutputPdbFormat].TryGetValue(residue.Letter + "_" + name, out name) ||
alternateAtomNamesByFormat_[OutputPdbFormat].TryGetValue("X_" + name, out name))
{
record.Name = name;
}
break;
default: throw new InvalidDataException();
}
stream.WriteLine(record.Text);
}
residueSequenceNumber++;
residueSequenceNumber %= 10000;
if (residueSequenceNumber == 0)
{
residueSequenceNumber++;
}
}