-in:ignore_unrecognized_res==Do not abort if unknown residues are found in PDB file;  instead, ignore them. default='false' [Boolean].
-in:path:database==Database file input search paths", default=['~/rosetta_database']. [PathVector]
-in:file:residue_type_set==ResidueTypeSet for input files', default = 'fa_standard. [String]
-in:file:s==Name(s) of single PDB file(s) to process. [FileVector]
-in:file:l==File(s) containing list(s) of PDB files to process. [FileVector]
-in:file:native==Native PDB filename. [File]
-in:file:native_exclude_res==Residue numbers to be excluded from RMS calculation. [IntegerVector]
-in:file:fullatom==Enable full-atom input of PDB or centroid structures. [Boolean]
-in:file:centroid_input==Enable centroid inputs of PDBs.  default = 'false' [Boolean]
-in:file:fasta==Fasta-formatted sequence file. [FileVector]
-in:file:frag3==Fragments file with residue length of 3 [String]
-in:file:frag9==Fragments file with residue length of 9 [String]
-in:file:silent==Silent input filename(s). [FileVector]
-in:file:silent_list==Silent input filename list(s) - like -l is to -s. [FileVector]
-in:file:silent_optH==Call optH when reading a silent file. [Boolean]
-in:file:silent_structure_type==Type of SilentStruct object to use in silent-file input'. Default='protein', [String]
-in:file:silent_score_prefix==Prefix that is appended to all scores read in from a silent-file', default='' [String]
-in:file:repair_sidechains==Attempt a repack/minmize to repair sidechain problems. Such as proline geometry and his tautomerization' default = 'false' [Boolean]
