private void InitIOSettings()
{
useRebondTool = IOSettings.Add(new BooleanIOSetting("UseRebondTool", Importance.Low,
"Should the PDBReader deduce bonding patterns?", "false"));
readConnect = IOSettings.Add(new BooleanIOSetting("ReadConnectSection", Importance.Low,
"Should the CONECT be read?", "true"));
useHetDictionary = IOSettings.Add(new BooleanIOSetting("UseHetDictionary", Importance.Low,
"Should the PDBReader use the HETATM dictionary for atom types?", "false"));
}
private void InitIOSettings()
{
write2DCoordinates = IOSettings.Add(new BooleanIOSetting("write2DCoordinates", Importance.Low,
"Should 2D coordinates be added?", "true"));
write3DCoordinates = IOSettings.Add(new BooleanIOSetting("write3DCoordinates", Importance.Low,
"Should 3D coordinates be added?", "true"));
builder = IOSettings.Add(new StringIOSetting("builder", Importance.Low,
$"Which {nameof(IChemObjectBuilder)} should be used?",
"NCDK.Silent.ChemObjectBuilder"));
}
/// <summary>
/// Creates a PDB writer.
/// </summary>
/// <param name="output">the stream to write the PDB file to.</param>
public PDBWriter(TextWriter output)
{
writer = output;
writeAsHET = IOSettings.Add(new BooleanIOSetting("WriteAsHET", Importance.Low,
"Should the output file use HETATM", "false"));
useElementSymbolAsAtomName = IOSettings.Add(new BooleanIOSetting("UseElementSymbolAsAtomName", Importance.Low,
"Should the element symbol be written as the atom name", "false"));
writeCONECTRecords = IOSettings.Add(new BooleanIOSetting("WriteCONECT", Importance.Low,
"Should the bonds be written as CONECT records?", "true"));
writeTERRecord = IOSettings.Add(new BooleanIOSetting("WriteTER", Importance.Low,
"Should a TER record be put at the end of the atoms?", "false"));
writeENDRecord = IOSettings.Add(new BooleanIOSetting("WriteEND", Importance.Low,
"Should an END record be put at the end of the file?", "true"));
}
private void InitIOSettings()
{
var basisOptions = new List <string>
{
"6-31g",
"6-31g*",
"6-31g(d)",
"6-311g",
"6-311+g**"
};
basis = new OptionIOSetting("Basis", Importance.Medium, "Which basis set do you want to use?",
basisOptions, "6-31g");
var methodOptions = new List <string>
{
"rb3lyp",
"b3lyp",
"rhf"
};
method = new OptionIOSetting("Method", Importance.Medium, "Which method do you want to use?",
methodOptions, "b3lyp");
var commandOptions = new List <string>
{
"energy calculation",
"geometry optimization",
"IR frequency calculation",
"IR frequency calculation (with Raman)"
};
command = IOSettings.Add(new OptionIOSetting("Command", Importance.High,
"What kind of job do you want to perform?", commandOptions, "energy calculation"));
comment = IOSettings.Add(new StringIOSetting("Comment", Importance.Low,
"What comment should be put in the file?", "Created with CDK (http://cdk.sf.net/)"));
memory = IOSettings.Add(new StringIOSetting("Memory", Importance.Low,
"How much memory do you want to use?", "unset"));
shell = IOSettings.Add(new BooleanIOSetting("OpenShell", Importance.Medium,
"Should the calculation be open shell?", "false"));
proccount = IOSettings.Add(new IntegerIOSetting("ProcessorCount", Importance.Low,
"How many processors should be used by Gaussian?", "1"));
usecheckpoint = new BooleanIOSetting("UseCheckPointFile", Importance.Low,
"Should a check point file be saved?", "false");
}
/// <summary>
/// Initializes IO settings.
/// </summary>
/// <remarks>
/// Please note with regards to "writeAromaticBondTypes": bond type values 4 through 8 are for SSS queries only,
/// so a 'query file' is created if the container has aromatic bonds and this settings is true.
/// </remarks>
private void InitIOSettings()
{
programNameOpt = IOSettings.Add(
new StringIOSetting(OptProgramName, Importance.Low,
"Program name to write at the top of the molfile header, should be exactly 8 characters long", "CDK"));
}
private void InitIOSettings()
{
forceReadAs3DCoords = IOSettings.Add(new BooleanIOSetting("ForceReadAs3DCoordinates", Importance.Low,
"Should coordinates always be read as 3D?", "false"));
}