/// <summary>
/// Method which assigns van der Waals radii to the biopolymer
/// default org/openscience/cdk/config/data/pdb_atomtypes.xml
/// stored in the variable string vanDerWaalsFile.
/// </summary>
public void AssignVdWRadiiToProtein()
{
AtomTypeFactory atf = null;
var atoms = Protein.Atoms.ToArray();
try
{
atf = AtomTypeFactory.GetInstance(VanDerWaalsFile);
}
catch (Exception ex1)
{
Console.Out.WriteLine($"Problem with AtomTypeFactory due to:{ex1.ToString()}");
}
for (int i = 0; i < atoms.Length; i++)
{
try
{
atf.Configure(atoms[i]);
}
catch (Exception ex2)
{
Trace.TraceError($"Problem with atf.configure due to:{ex2.ToString()}");
}
}
}
/// <summary>
/// Creates an <see cref="PDBAtom"/> and sets properties to their values from
/// the ATOM or HETATM record. If the line is shorter than 80 characters, the
/// information past 59 characters is treated as optional. If the line is
/// shorter than 59 characters, a <see cref="ApplicationException"/> is thrown.
/// </summary>
/// <param name="cLine">the PDB ATOM or HEATATM record.</param>
/// <param name="lineLength"></param>
/// <returns>the <see cref="PDBAtom"/>created from the record.</returns>
/// <exception cref="InvalidDataException">if the line is too short (less than 59 characters).</exception>
private PDBAtom ReadAtom(string cLine, int lineLength)
{
// a line can look like (two in old format, then two in new format):
//
// 1 2 3 4 5 6 7
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
// ATOM 1 O5* C A 1 20.662 36.632 23.475 1.00 10.00 114D 45
// ATOM 1186 1H ALA 1 10.105 5.945 -6.630 1.00 0.00 1ALE1288
// ATOM 31 CA SER A 3 -0.891 17.523 51.925 1.00 28.64 C
// HETATM 3486 MG MG A 302 24.885 14.008 59.194 1.00 29.42 MG+2
//
// note: the first two examples have the PDBID in col 72-75
// note: the last two examples have the element symbol in col 76-77
// note: the last (Mg hetatm) has a charge in col 78-79
if (lineLength < 59)
{
throw new InvalidDataException("PDBReader error during ReadAtom(): line too short");
}
var isHetatm = cLine.StartsWith("HETATM", StringComparison.Ordinal);
var atomName = cLine.Substring(12, 4).Trim();
var resName = cLine.Substring(17, 3).Trim();
var symbol = ParseAtomSymbol(cLine);
if (symbol == null)
{
HandleError($"Cannot parse symbol from {atomName}");
}
var oAtom = new PDBAtom(symbol, new Vector3(double.Parse(cLine.Substring(30, 8), NumberFormatInfo.InvariantInfo),
double.Parse(cLine.Substring(38, 8), NumberFormatInfo.InvariantInfo), double.Parse(cLine.Substring(46, 8), NumberFormatInfo.InvariantInfo)));
if (useHetDictionary.IsSet && isHetatm)
{
var cdkType = TypeHetatm(resName, atomName);
oAtom.AtomTypeName = cdkType;
if (cdkType != null)
{
try
{
cdkAtomTypeFactory.Configure(oAtom);
}
catch (CDKException)
{
Trace.TraceWarning("Could not configure", resName, " ", atomName);
}
}
}
oAtom.Record = cLine;
oAtom.Serial = int.Parse(cLine.Substring(6, 5).Trim(), NumberFormatInfo.InvariantInfo);
oAtom.Name = atomName.Trim();
oAtom.AltLoc = cLine.Substring(16, 1).Trim();
oAtom.ResName = resName;
oAtom.ChainID = cLine.Substring(21, 1).Trim();
oAtom.ResSeq = cLine.Substring(22, 4).Trim();
oAtom.ICode = cLine.Substring(26, 1).Trim();
if (useHetDictionary.IsSet && isHetatm)
{
oAtom.Id = oAtom.ResName + "." + atomName;
}
else
{
oAtom.AtomTypeName = oAtom.ResName + "." + atomName;
}
if (lineLength >= 59)
{
var frag = cLine.Substring(54, Math.Min(lineLength - 54, 6)).Trim();
if (frag.Length > 0)
{
oAtom.Occupancy = double.Parse(frag, NumberFormatInfo.InvariantInfo);
}
}
if (lineLength >= 65)
{
var frag = cLine.Substring(60, Math.Min(lineLength - 60, 6)).Trim();
if (frag.Length > 0)
{
oAtom.TempFactor = double.Parse(frag, NumberFormatInfo.InvariantInfo);
}
}
if (lineLength >= 75)
{
oAtom.SegID = cLine.Substring(72, Math.Min(lineLength - 72, 4)).Trim();
}
if (lineLength >= 79)
{
string frag;
if (lineLength >= 80)
{
frag = cLine.Substring(78, 2).Trim();
}
else
{
frag = cLine.Substring(78);
}
if (frag.Length > 0)
{
// see Format_v33_A4.pdf, p. 178
if (frag.EndsWithChar('-') || frag.EndsWithChar('+'))
{
var aa = frag.ToCharArray();
Array.Reverse(aa);
oAtom.Charge = double.Parse(new string(aa), NumberFormatInfo.InvariantInfo);
}
else
{
oAtom.Charge = double.Parse(frag, NumberFormatInfo.InvariantInfo);
}
}
}
// ***********************************************************************************
// It sets a flag in the property content of an atom, which is used when
// bonds are created to check if the atom is an OXT-record => needs
// special treatment.
var oxt = cLine.Substring(13, 3).Trim();
if (string.Equals(oxt, "OXT", StringComparison.Ordinal))
{
oAtom.Oxt = true;
}
else
{
oAtom.Oxt = false;
}
// **********************************************************************************
return(oAtom);
}