Rosetta 3.3
Functions
in::file Namespace Reference

Functions

BooleanOptionKey const file ("in:file")
FileVectorOptionKey const s ("in:file:s")
FileVectorOptionKey const l ("in:file:l")
FileVectorOptionKey const list ("in:file:list")
FileOptionKey const native ("in:file:native")
FileOptionKey const torsion_bin_probs ("in:file:torsion_bin_probs")
FileOptionKey const PCS_frag_cst ("in:file:PCS_frag_cst")
FileOptionKey const talos_phi_psi ("in:file:talos_phi_psi")
FileOptionKey const talos_cs ("in:file:talos_cs")
FileOptionKey const ambig_talos_cs_A ("in:file:ambig_talos_cs_A")
FileOptionKey const ambig_talos_cs_B ("in:file:ambig_talos_cs_B")
IntegerVectorOptionKey const native_exclude_res ("in:file:native_exclude_res")
StringVectorOptionKey const tags ("in:file:tags")
StringVectorOptionKey const user_tags ("in:file:user_tags")
FileOptionKey const tagfile ("in:file:tagfile")
FileVectorOptionKey const frag_files ("in:file:frag_files")
IntegerVectorOptionKey const frag_sizes ("in:file:frag_sizes")
FileVectorOptionKey const extra_res_fa ("in:file:extra_res_fa")
FileVectorOptionKey const extra_res_mol ("in:file:extra_res_mol")
FileVectorOptionKey const extra_res_cen ("in:file:extra_res_cen")
PathVectorOptionKey const extra_res_path ("in:file:extra_res_path")
StringOptionKey const frag3 ("in:file:frag3")
StringOptionKey const frag9 ("in:file:frag9")
StringOptionKey const fragA ("in:file:fragA")
StringOptionKey const fragB ("in:file:fragB")
StringOptionKey const xyz ("in:file:xyz")
IntegerOptionKey const fragA_size ("in:file:fragA_size")
BooleanOptionKey const keep_input_scores ("in:file:keep_input_scores")
BooleanOptionKey const lazy_silent ("in:file:lazy_silent")
FileVectorOptionKey const silent ("in:file:silent")
FileVectorOptionKey const atom_tree_diff ("in:file:atom_tree_diff")
StringOptionKey const zip ("in:file:zip")
FileVectorOptionKey const boinc_wu_zip ("in:file:boinc_wu_zip")
BooleanOptionKey const fullatom ("in:file:fullatom")
StringOptionKey const residue_type_set ("in:file:residue_type_set")
FileOptionKey const pca ("in:file:pca")
RealOptionKey const silent_energy_cut ("in:file:silent_energy_cut")
FileVectorOptionKey const silent_list ("in:file:silent_list")
BooleanOptionKey const silent_renumber ("in:file:silent_renumber")
BooleanOptionKey const silent_optH ("in:file:silent_optH")
StringOptionKey const silent_struct_type ("in:file:silent_struct_type")
BooleanOptionKey const silent_read_through_errors ("in:file:silent_read_through_errors")
StringOptionKey const silent_score_prefix ("in:file:silent_score_prefix")
IntegerOptionKey const silent_select_random ("in:file:silent_select_random")
StringVectorOptionKey const silent_scores_wanted ("in:file:silent_scores_wanted")
BooleanOptionKey const centroid_input ("in:file:centroid_input")
FileVectorOptionKey const fasta ("in:file:fasta")
FileVectorOptionKey const pssm ("in:file:pssm")
StringVectorOptionKey const seq ("in:file:seq")
FileOptionKey const checkpoint ("in:file:checkpoint")
FileVectorOptionKey const alignment ("in:file:alignment")
FileVectorOptionKey const alignment2 ("in:file:alignment2")
FileOptionKey const rama2b_map ("in:file:rama2b_map")
FileOptionKey const psipred_ss2 ("in:file:psipred_ss2")
FileOptionKey const dssp ("in:file:dssp")
BooleanOptionKey const fail_on_bad_hbond ("in:file:fail_on_bad_hbond")
FileOptionKey const movemap ("in:file:movemap")
BooleanOptionKey const repair_sidechains ("in:file:repair_sidechains")
BooleanOptionKey const no_binary_dunlib ("in:file:no_binary_dunlib")
IntegerOptionKey const extended_pose ("in:file:extended_pose")
FileVectorOptionKey const template_pdb ("in:file:template_pdb")
FileOptionKey const template_silent ("in:file:template_silent")
FileVectorOptionKey const rdc ("in:file:rdc")
FileVectorOptionKey const vall ("in:file:vall")
BooleanOptionKey const rescore ("in:file:rescore")
StringOptionKey const spanfile ("in:file:spanfile")
StringOptionKey const lipofile ("in:file:lipofile")
FileOptionKey const sucker_params ("in:file:sucker_params")
FileOptionKey const fold_tree ("in:file:fold_tree")
BooleanOptionKey const obey_ENDMDL ("in:file:obey_ENDMDL")
BooleanOptionKey const new_chain_order ("in:file:new_chain_order")
FileOptionKey const ddg_predictions_file ("in:file:ddg_predictions_file")

Function Documentation

FileVectorOptionKey const in::file::alignment ( "in:file:alignment"  )
FileVectorOptionKey const in::file::alignment2 ( "in:file:alignment2"  )
FileOptionKey const in::file::ambig_talos_cs_A ( "in:file:ambig_talos_cs_A"  )
FileOptionKey const in::file::ambig_talos_cs_B ( "in:file:ambig_talos_cs_B"  )
FileVectorOptionKey const in::file::atom_tree_diff ( "in:file:atom_tree_diff"  )
FileVectorOptionKey const in::file::boinc_wu_zip ( "in:file:boinc_wu_zip"  )

Referenced by main().

BooleanOptionKey const in::file::centroid_input ( "in:file:centroid_input"  )

Referenced by distribute_jobs(), main(), and my_main().

FileOptionKey const in::file::checkpoint ( "in:file:checkpoint"  )

Referenced by register_options().

FileOptionKey const in::file::ddg_predictions_file ( "in:file:ddg_predictions_file"  )
FileOptionKey const in::file::dssp ( "in:file:dssp"  )
IntegerOptionKey const in::file::extended_pose ( "in:file:extended_pose"  )
FileVectorOptionKey const in::file::extra_res_cen ( "in:file:extra_res_cen"  )
FileVectorOptionKey const in::file::extra_res_fa ( "in:file:extra_res_fa"  )

Referenced by main().

FileVectorOptionKey const in::file::extra_res_mol ( "in:file:extra_res_mol"  )
PathVectorOptionKey const in::file::extra_res_path ( "in:file:extra_res_path"  )
BooleanOptionKey const in::file::fail_on_bad_hbond ( "in:file:fail_on_bad_hbond"  )
FileVectorOptionKey const in::file::fasta ( "in:file:fasta"  )

Referenced by main(), and register_options().

BooleanOptionKey const in::file::file ( "in:file"  )
FileOptionKey const in::file::fold_tree ( "in:file:fold_tree"  )
StringOptionKey const in::file::frag3 ( "in:file:frag3"  )
StringOptionKey const in::file::frag9 ( "in:file:frag9"  )
FileVectorOptionKey const in::file::frag_files ( "in:file:frag_files"  )
IntegerVectorOptionKey const in::file::frag_sizes ( "in:file:frag_sizes"  )
StringOptionKey const in::file::fragA ( "in:file:fragA"  )
IntegerOptionKey const in::file::fragA_size ( "in:file:fragA_size"  )
StringOptionKey const in::file::fragB ( "in:file:fragB"  )
BooleanOptionKey const in::file::fullatom ( "in:file:fullatom"  )
BooleanOptionKey const in::file::keep_input_scores ( "in:file:keep_input_scores"  )
FileVectorOptionKey const in::file::l ( "in:file:l"  )

Referenced by main(), and register_options().

BooleanOptionKey const in::file::lazy_silent ( "in:file:lazy_silent"  )
StringOptionKey const in::file::lipofile ( "in:file:lipofile"  )
FileVectorOptionKey const in::file::list ( "in:file:list"  )
FileOptionKey const in::file::movemap ( "in:file:movemap"  )

Referenced by main(), and my_main().

FileOptionKey const in::file::native ( "in:file:native"  )
IntegerVectorOptionKey const in::file::native_exclude_res ( "in:file:native_exclude_res"  )
BooleanOptionKey const in::file::new_chain_order ( "in:file:new_chain_order"  )
BooleanOptionKey const in::file::no_binary_dunlib ( "in:file:no_binary_dunlib"  )
BooleanOptionKey const in::file::obey_ENDMDL ( "in:file:obey_ENDMDL"  )
FileOptionKey const in::file::pca ( "in:file:pca"  )
FileOptionKey const in::file::PCS_frag_cst ( "in:file:PCS_frag_cst"  )
FileOptionKey const in::file::psipred_ss2 ( "in:file:psipred_ss2"  )
FileVectorOptionKey const in::file::pssm ( "in:file:pssm"  )

Referenced by main(), and register_options().

FileOptionKey const in::file::rama2b_map ( "in:file:rama2b_map"  )
FileVectorOptionKey const in::file::rdc ( "in:file:rdc"  )
BooleanOptionKey const in::file::repair_sidechains ( "in:file:repair_sidechains"  )

Referenced by main().

BooleanOptionKey const in::file::rescore ( "in:file:rescore"  )

Referenced by main().

StringOptionKey const in::file::residue_type_set ( "in:file:residue_type_set"  )

Referenced by main().

FileVectorOptionKey const in::file::s ( "in:file:s"  )
StringVectorOptionKey const in::file::seq ( "in:file:seq"  )

Referenced by main().

FileVectorOptionKey const in::file::silent ( "in:file:silent"  )
RealOptionKey const in::file::silent_energy_cut ( "in:file:silent_energy_cut"  )
FileVectorOptionKey const in::file::silent_list ( "in:file:silent_list"  )
BooleanOptionKey const in::file::silent_optH ( "in:file:silent_optH"  )
BooleanOptionKey const in::file::silent_read_through_errors ( "in:file:silent_read_through_errors"  )
BooleanOptionKey const in::file::silent_renumber ( "in:file:silent_renumber"  )

Referenced by main().

StringOptionKey const in::file::silent_score_prefix ( "in:file:silent_score_prefix"  )
StringVectorOptionKey const in::file::silent_scores_wanted ( "in:file:silent_scores_wanted"  )
IntegerOptionKey const in::file::silent_select_random ( "in:file:silent_select_random"  )
StringOptionKey const in::file::silent_struct_type ( "in:file:silent_struct_type"  )

Referenced by main(), and rna_denovo_test().

StringOptionKey const in::file::spanfile ( "in:file:spanfile"  )
FileOptionKey const in::file::sucker_params ( "in:file:sucker_params"  )
FileOptionKey const in::file::tagfile ( "in:file:tagfile"  )
StringVectorOptionKey const in::file::tags ( "in:file:tags"  )

Referenced by extract_pdbs_test(), and main().

FileOptionKey const in::file::talos_cs ( "in:file:talos_cs"  )
FileOptionKey const in::file::talos_phi_psi ( "in:file:talos_phi_psi"  )

Referenced by register_options().

FileVectorOptionKey const in::file::template_pdb ( "in:file:template_pdb"  )

Referenced by main().

FileOptionKey const in::file::template_silent ( "in:file:template_silent"  )
FileOptionKey const in::file::torsion_bin_probs ( "in:file:torsion_bin_probs"  )

Referenced by register_options().

StringVectorOptionKey const in::file::user_tags ( "in:file:user_tags"  )
FileVectorOptionKey const in::file::vall ( "in:file:vall"  )
StringOptionKey const in::file::xyz ( "in:file:xyz"  )

Referenced by register_options().

StringOptionKey const in::file::zip ( "in:file:zip"  )

Referenced by main().

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