new public static IEnumerable <string> GetUsageOptions()
{
IEnumerable <string> options = FusionFlags.GetUsageOptions();
List <string> additionalOptions = new List <string>();
List <string> symmetries = SymmetryBuilderFactory.GetKnownSymmetryNames().Where(sym => !sym.StartsWith("C")).ToList();
// architecture options
additionalOptions.Add(GetFormattedOptionString("-arch <architecture>", "desired symmetry architecture, options are:"));
additionalOptions.Add(GetFormattedOptionString("", symmetries.Aggregate((a, b) => a + ", " + b)));
// axis1 options
additionalOptions.Add(GetFormattedOptionString("-axis1 <axis>", "first axis name corresponding to selected architecture"));
foreach (string symmetry in symmetries)
{
additionalOptions.Add(GetFormattedOptionString("", String.Format("\t{0} available in architecture {1}", GetAxesOptionsString(symmetry), symmetry)));
}
// axis2 options
additionalOptions.Add(GetFormattedOptionString("-axis2 <axis>", "first axis name corresponding to selected architecture"));
foreach (string symmetry in symmetries)
{
additionalOptions.Add(GetFormattedOptionString("", String.Format("\t{0} available in architecture {1}", GetAxesOptionsString(symmetry), symmetry)));
}
// oligomer selection
additionalOptions.Add(GetFormattedOptionString("-regex_oligomer1 <regex>", "oligomer1 pdb search pattern"));
additionalOptions.Add(GetFormattedOptionString("-regex_oligomer2 <regex>", "oligomer2 pdb search pattern"));
return(options.Concat(additionalOptions));
}
new public static IEnumerable <string> GetUsageOptions()
{
return(FusionFlags.GetUsageOptions().Concat(new String[]
{
GetFormattedOptionString("-multiplicity", "An integer 2 or greater; the number of times the assembly should be patterned."),
GetFormattedOptionString("-regex_assembly <regex>", "Regular expression naming at least one multi-chain assembly. All scaffold directories are searched by default."),
GetFormattedOptionString("-regex_repeat <regex>", "Regular expression naming repeat proteins. The DHR scaffold directory is searched by default."),
GetFormattedOptionString("-chain_index1 <char>", "Assembly chain index to use at the N-terminus of the final fusion."),
GetFormattedOptionString("-chain_index2 <char>", "Assembly chain index to use at the C-terminus of the final fusion."),
}));
}
new public static IEnumerable <string> GetUsageOptions()
{
return(FusionFlags.GetUsageOptions().Concat(new String[]
{
GetFormattedOptionString("-regex_n <path>", "Full path (or optionally regular expression) of one or more pdbs"),
GetFormattedOptionString("-regex_c <path>", "Full path (or optionally regular expression) of one or more pdbs"),
GetFormattedOptionString("-range_n <int> <int>", "Limit the allowed alignment ranges to the indicated inclusive range"),
GetFormattedOptionString("", "Only for use with a single N-terminal peptide - not a set"),
GetFormattedOptionString("-range_c <int> <int>", "Limit the allowed alignment ranges to the indicated inclusive range"),
GetFormattedOptionString("", "Only for use with a single C-terminal peptide - not a set"),
}));
}