* PDB input:
------------
-in:file:s *.pdb or
-in:file:l list_of_pdbs
-no_optH Dont change positions of Hydrogen atoms. [Boolean]
*Silent input:
--------------
-in:file:silent Silent input filesname.[String]
-in:file:s specify specific tags to be extracted, if left out all will be taken
-in:file:fullatom For full atom structures. [Boolean]
*Native:
--------
-in:file:native Native PDB if CaRMS is required
*Scorefunction:
-score:weights Name of weight set or weights file, default is 'standard'. [String]
-score:patch Name of patch file (without extension)" , default="". [String]
-rescore:verbose Full break down of weights, raw scores and weighted scores. [Boolean]
-rescore:output_only
*Output:
-------
-nooutput Don't print PDB structures (default false) [Boolean]
-out:prefix Prefix the output structures with a string.[String]
*Clustering:
------------
-input_score_filter Ignore structures above certain energy
-exclude_res Exclude residue numbers
-radius Cluster radius
-limit_cluster_size Maximal cluster size
-limit_clusters Maximal number of clusters
-limit_total_structures Maximal number of structures in total
-limit_dist_matrix <defunc> only pre cluster N structures, then redo.
-sort_groups_by_energy Sort clusters by energy.
-remove_highest_energy_member Remove highest energy member of each cluster
-cluster:radius RMSD in Angstrom
