-lopps:input_pdb==Template pdb file. default='input_pdb' [File]
-loops:loop_file==Loop definition file. default='loop_file' [File]
-loops:mm_loop_file==Loop definition file. default='loop_file' [File]
-loops:fix_natsc==Fix sidechains in template region in loop modeling. Default='false' [Boolean]
-loops:refine_only==Perform full atom refinement only on loops. Default='false' [Boolean]
-loops:fa_input==Input structures are in full atom format. Default='false' [Boolean]
-loops:fast==Reduce number of simulation cycles in loop modeling. Default='false' [Boolean]
-loops:frag_sizes==(non-kic modes only) Length of fragments to be used in loop modeling (in other words, number of amino acids/residues for each segment. For each type of fragment). defaults to 9 3 1 [IntegerVector]
-loops:frag_files==(non-kic modes only) Path/Name of fragment libraries files, defaults to frag9 frag3 frag1. [FileVector]
-loops:build_initial==Preceed loopmodelling with a initial round of just removing the missing densities and building simple loop. Default = 'false'. [Boolean]
-loops:extended==Force extended on loops, independent of loop input file. Default='false' [Boolean]
-loops:idealize_before_relax==Idealize the structure before going into fa relax. Default='false' [Boolean]
-loops:select_best_loop_from==Keep building loops until N and choose best (by score). Default='1' [Integer]
-loops:build_attempts==Build attempts per growth attempt. Default='3' [Integer]
-loops:neighbor_dist==Distance in angstroms to optimize side-chains near segment moved by KIC. Default='10.0' [Real]
-loops:vicinity_sampling==Sample non-pivot torsions within a vicinity of their input values. Default='false' [Boolean]
-loops:vicinity_degree== Number of degrees to deviate from (current) non-pivot torsions. Default='1.0' [Real]
-loops:kic_max_seglen==Maximum number residues in a KIC move segment. Default='12' [Integer]
-loops:remodel_init_temp==Initial temperature for simulated annealing for perturb_kic
-loops:remodel_final_temp==Final temperature for simulated annealing for perturb_kic
-loops:refine_init_temp==Initial temperature for simulated annealing for refine_kic
-loops:refine_final_temp==Final temperature for simulated annealing for refine_kic
-loops:grow_attempts==Total loop growth attempts. Default='7' [Integer]
-loops:random_grow_loops_by==Randomly grow loops by up to this number of residues on either side.Default='0.0' [Real]
-loops:accept_aborted_loops==Accept aborted loops. Default='false' [Boolean]
-loops:strict_loops==Do not allow growing of loops. Default='false' [Boolean]
-loops:build_specific_loops==Numbers of the loops to be built. [IntegerVector]
-loops:random_order==Build in random order. Default='false' [Boolean]
-loops:build_all_loops==Build all loops(no skip). Default='false' [Boolean]
-loops:combine_rate==Combine successive loops at this rate. Default='0.0' [Real]
-loops:remodel==Legal values: 'no','perturb_ccd','perturb_kic'. This option controls the centroid-stage loop remodeling (where large perturbations are attempted). Default = 'quick_ccd' [String]
-loops:intermedrelax==Currently not used; Eventually may provide for a full-pose relax between centroid and fullatom modeling. default = 'no' [String]
-loops:refine==Legal values: 'no','refine_ccd','refine_kic'. This option controls the fullatom refinement stage of loop. modeling. Default = 'no' [String]
-loops:relax==Legal values: 'no','fastrelax','shortrelax','fullrelax'    [String] Controls whether a full-structure relax occurs after loop modeling.  Defaults to "no".
