/// <summary>
/// construct a new reader from a Reader type object
/// <param name="input">reader from which input is read</param>
/// </summary>
public PMPReader(TextReader input)
{
this.input = input;
this.lineNumber = 0;
/* compile patterns */
objHeader = new Regex(".*\\((\\d+)\\s(\\w+)$", RegexOptions.Compiled);
objCommand = new Regex(".*\\(A\\s([CFDIO])\\s(\\w+)\\s+\"?(.*?)\"?\\)$", RegexOptions.Compiled);
atomTypePattern = new Regex("^(\\d+)\\s+(\\w+)$", RegexOptions.Compiled);
rebonder = new RebondTool(2.0, 0.5, 0.5);
}
private bool createBondsWithRebondTool(IBioPolymer pol)
{
RebondTool tool = new RebondTool(2.0, 0.5, 0.5);
try
{
// configure atoms
AtomTypeFactory factory = AtomTypeFactory.getInstance("jmol_atomtypes.txt", pol.Builder);
IAtom[] atoms = pol.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
try
{
IAtomType[] types = factory.getAtomTypes(atoms[i].Symbol);
if (types.Length > 0)
{
// just pick the first one
AtomTypeManipulator.configure(atoms[i], types[0]);
}
else
{
System.Console.Out.WriteLine("Could not configure atom with symbol: " + atoms[i].Symbol);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.Console.Out.WriteLine("Could not configure atom (but don't care): " + e.Message);
//logger.debug(e);
}
}
tool.rebond(pol);
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Could not rebond the polymer: " + e.Message);
//logger.debug(e);
}
return(true);
}
private static bool CreateBondsWithRebondTool(IAtomContainer molecule)
{
var tool = new RebondTool(2.0, 0.5, 0.5);
try
{
foreach (var atom in molecule.Atoms)
{
try
{
var types = factory.GetAtomTypes(atom.Symbol);
var type = types.FirstOrDefault();
if (type != null)
{
// just pick the first one
AtomTypeManipulator.Configure(atom, type);
}
else
{
Trace.TraceWarning("Could not configure atom with symbol: " + atom.Symbol);
}
}
catch (Exception e)
{
Trace.TraceWarning("Could not configure atom (but don't care): " + e.Message);
Debug.WriteLine(e);
}
}
tool.Rebond(molecule);
}
catch (Exception e)
{
Trace.TraceError($"Could not rebond the polymer: {e.Message}");
Debug.WriteLine(e);
}
return(true);
}
