out::file Namespace Reference

Functions
BooleanOptionKey const	file ("out:file")
StringOptionKey const	o ("out:file:o")
FileOptionKey const	design_contrast ("out:file:design_contrast")
StringOptionKey const	residue_type_set ("out:file:residue_type_set")
BooleanOptionKey const	srlz ("out:file:srlz")
StringOptionKey const	atom_tree_diff ("out:file:atom_tree_diff")
IntegerOptionKey const	atom_tree_diff_bb ("out:file:atom_tree_diff_bb")
IntegerOptionKey const	atom_tree_diff_sc ("out:file:atom_tree_diff_sc")
IntegerOptionKey const	atom_tree_diff_bl ("out:file:atom_tree_diff_bl")
StringOptionKey const	alignment ("out:file:alignment")
StringOptionKey const	score_only ("out:file:score_only")
StringOptionKey const	scorefile ("out:file:scorefile")
StringOptionKey const	scorefile_format ("out:file:scorefile_format")
StringOptionKey const	silent ("out:file:silent")
StringOptionKey const	silent_struct_type ("out:file:silent_struct_type")
BooleanOptionKey const	silent_print_all_score_headers ("out:file:silent_print_all_score_headers")
BooleanOptionKey const	raw ("out:file:raw")
BooleanOptionKey const	weight_silent_scores ("out:file:weight_silent_scores")
BooleanOptionKey const	silent_preserve_H ("out:file:silent_preserve_H")
BooleanOptionKey const	fullatom ("out:file:fullatom")
BooleanOptionKey const	suppress_zero_occ_pdb_output ("out:file:suppress_zero_occ_pdb_output")
BooleanOptionKey const	output_ligands_as_separate_chains ("out:file:output_ligands_as_separate_chains")
BooleanOptionKey const	output_virtual ("out:file:output_virtual")
BooleanOptionKey const	output_virtual_zero_occ ("out:file:output_virtual_zero_occ")
BooleanOptionKey const	no_chainend_ter ("out:file:no_chainend_ter")
BooleanOptionKey const	no_output_cen ("out:file:no_output_cen")
BooleanOptionKey const	output_orbitals ("out:file:output_orbitals")
BooleanOptionKey const	renumber_pdb ("out:file:renumber_pdb")
BooleanOptionKey const	pdb_parents ("out:file:pdb_parents")
BooleanOptionKey const	per_chain_renumbering ("out:file:per_chain_renumbering")
BooleanOptionKey const	output_secondary_structure ("out:file:output_secondary_structure")
BooleanOptionKey const	do_not_autoassign_SS ("out:file:do_not_autoassign_SS")
BooleanOptionKey const	output_torsions ("out:file:output_torsions")
BooleanOptionKey const	use_occurrence_data ("out:file:use_occurrence_data")
BooleanOptionKey const	pdb_comments ("out:file:pdb_comments")
BooleanOptionKey const	force_nonideal_structure ("out:file:force_nonideal_structure")
BooleanOptionKey const	write_pdb_link_records ("out:file:write_pdb_link_records")
BooleanOptionKey const	use_pdb_format_HETNAM_records ("out:file:use_pdb_format_HETNAM_records")
BooleanOptionKey const	write_pdb_parametric_info ("out:file:write_pdb_parametric_info")
BooleanOptionKey const	write_glycan_pdb_codes ("out:file:write_glycan_pdb_codes")
BooleanOptionKey const	write_seqres_records ("out:file:write_seqres_records")
BooleanOptionKey const	output_pose_energies_table ("out:file:output_pose_energies_table")
BooleanOptionKey const	output_pose_cache_data ("out:file:output_pose_cache_data")
BooleanOptionKey const	output_pose_fold_tree ("out:file:output_pose_fold_tree")
BooleanOptionKey const	output_only_asymmetric_unit ("out:file:output_only_asymmetric_unit")
BooleanOptionKey const	cif_extra_data_separate_file ("out:file:cif_extra_data_separate_file")
BooleanOptionKey const	dont_rewrite_dunbrack_database ("out:file:dont_rewrite_dunbrack_database")
StringOptionKey const	frag_prefix ("out:file:frag_prefix")
BooleanOptionKey const	no_extra_sdf_data ("out:file:no_extra_sdf_data")
BooleanOptionKey const	no_scores_in_pdb ("out:file:no_scores_in_pdb")

Function Documentation

StringOptionKey const out::file::alignment

(

"out:file:alignment"

)

Referenced by main().

StringOptionKey const out::file::atom_tree_diff

(

"out:file:atom_tree_diff"

)

IntegerOptionKey const out::file::atom_tree_diff_bb

(

"out:file:atom_tree_diff_bb"

)

IntegerOptionKey const out::file::atom_tree_diff_bl

(

"out:file:atom_tree_diff_bl"

)

IntegerOptionKey const out::file::atom_tree_diff_sc

(

"out:file:atom_tree_diff_sc"

)

BooleanOptionKey const out::file::cif_extra_data_separate_file

(

"out:file:cif_extra_data_separate_file"

)

FileOptionKey const out::file::design_contrast

(

"out:file:design_contrast"

)

Referenced by main().

BooleanOptionKey const out::file::do_not_autoassign_SS

(

"out:file:do_not_autoassign_SS"

)

BooleanOptionKey const out::file::dont_rewrite_dunbrack_database

(

"out:file:dont_rewrite_dunbrack_database"

)

BooleanOptionKey const out::file::file

(

"out:file"

)

BooleanOptionKey const out::file::force_nonideal_structure

(

"out:file:force_nonideal_structure"

)

StringOptionKey const out::file::frag_prefix

(

"out:file:frag_prefix"

)

Referenced by register_options().

BooleanOptionKey const out::file::fullatom

(

"out:file:fullatom"

)

BooleanOptionKey const out::file::no_chainend_ter

(

"out:file:no_chainend_ter"

)

BooleanOptionKey const out::file::no_extra_sdf_data

(

"out:file:no_extra_sdf_data"

)

BooleanOptionKey const out::file::no_output_cen

(

"out:file:no_output_cen"

)

BooleanOptionKey const out::file::no_scores_in_pdb

(

"out:file:no_scores_in_pdb"

)

StringOptionKey const out::file::o

(

"out:file:o"

)

Referenced by create_bp_jump_database_test(), create_rna_vall_torsions_test(), graft_pdb(), main(), mg_modeler_test(), print_pep_csts(), rhiju_pdbstats(), rna_build_helix_test(), rna_thread_test(), run_pep_prep(), and RunPepSpec().

BooleanOptionKey const out::file::output_ligands_as_separate_chains

(

"out:file:output_ligands_as_separate_chains"

)

BooleanOptionKey const out::file::output_only_asymmetric_unit

(

"out:file:output_only_asymmetric_unit"

)

BooleanOptionKey const out::file::output_orbitals

(

"out:file:output_orbitals"

)

BooleanOptionKey const out::file::output_pose_cache_data

(

"out:file:output_pose_cache_data"

)

BooleanOptionKey const out::file::output_pose_energies_table

(

"out:file:output_pose_energies_table"

)

BooleanOptionKey const out::file::output_pose_fold_tree

(

"out:file:output_pose_fold_tree"

)

BooleanOptionKey const out::file::output_secondary_structure

(

"out:file:output_secondary_structure"

)

BooleanOptionKey const out::file::output_torsions

(

"out:file:output_torsions"

)

BooleanOptionKey const out::file::output_virtual

(

"out:file:output_virtual"

)

BooleanOptionKey const out::file::output_virtual_zero_occ

(

"out:file:output_virtual_zero_occ"

)

BooleanOptionKey const out::file::pdb_comments

(

"out:file:pdb_comments"

)

BooleanOptionKey const out::file::pdb_parents

(

"out:file:pdb_parents"

)

BooleanOptionKey const out::file::per_chain_renumbering

(

"out:file:per_chain_renumbering"

)

BooleanOptionKey const out::file::raw

(

"out:file:raw"

)

BooleanOptionKey const out::file::renumber_pdb

(

"out:file:renumber_pdb"

)

StringOptionKey const out::file::residue_type_set

(

"out:file:residue_type_set"

)

Referenced by main().

StringOptionKey const out::file::score_only

(

"out:file:score_only"

)

StringOptionKey const out::file::scorefile

(

"out:file:scorefile"

)

Referenced by main().

StringOptionKey const out::file::scorefile_format

(

"out:file:scorefile_format"

)

StringOptionKey const out::file::silent

(

"out:file:silent"

)

Referenced by analyze_base_pair_test(), build_full_model_test(), BuildFullModel::BuildFullModel(), calc_rms_test(), cluster_outfile_test(), cluster_test(), StepWiseJobQueen::complete_larval_job_maturation(), RNA_DeNovoJobQueen::complete_larval_job_maturation(), BuildFullModel::fill_and_sample_full_model(), main(), mg_modeler_test(), minimize_with_constraints(), my_main(), nucleobase_probe_score_test(), post_rebuild_bulge_assembly(), rebuild_test(), rna_build_helix_test(), rna_sample_virtual_sugar(), rna_score_test(), DockFragmentsMover::run(), FragmentAssemblyMover::run(), run_mc(), stepwise_monte_carlo_legacy(), swa_rna_cluster(), and swa_rna_sample().

BooleanOptionKey const out::file::silent_preserve_H

(

"out:file:silent_preserve_H"

)

BooleanOptionKey const out::file::silent_print_all_score_headers

(

"out:file:silent_print_all_score_headers"

)

StringOptionKey const out::file::silent_struct_type

(

"out:file:silent_struct_type"

)

BooleanOptionKey const out::file::srlz

(

"out:file:srlz"

)

BooleanOptionKey const out::file::suppress_zero_occ_pdb_output

(

"out:file:suppress_zero_occ_pdb_output"

)

BooleanOptionKey const out::file::use_occurrence_data

(

"out:file:use_occurrence_data"

)

BooleanOptionKey const out::file::use_pdb_format_HETNAM_records

(

"out:file:use_pdb_format_HETNAM_records"

)

BooleanOptionKey const out::file::weight_silent_scores

(

"out:file:weight_silent_scores"

)

BooleanOptionKey const out::file::write_glycan_pdb_codes

(

"out:file:write_glycan_pdb_codes"

)

BooleanOptionKey const out::file::write_pdb_link_records

(

"out:file:write_pdb_link_records"

)

BooleanOptionKey const out::file::write_pdb_parametric_info

(

"out:file:write_pdb_parametric_info"

)

BooleanOptionKey const out::file::write_seqres_records

(

"out:file:write_seqres_records"

)