예제 #1
0
        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));
        }
예제 #2
0
 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."),
     }));
 }
예제 #3
0
 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"),
     }));
 }