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")); }