in::file Namespace Reference

Functions
BooleanOptionKey const	file ("in:file")
FileVectorOptionKey const	s ("in:file:s")
FileVectorOptionKey const	t ("in:file:t")
FileVectorOptionKey const	l ("in:file:l")
FileOptionKey const	job_definition_file ("in:file:job_definition_file")
FileVectorOptionKey const	list ("in:file:list")
BooleanOptionKey const	srlz ("in:file:srlz")
BooleanOptionKey const	srlz_override ("in:file:srlz_override")
FileVectorOptionKey const	screening_list ("in:file:screening_list")
FileOptionKey const	screening_job_file ("in:file:screening_job_file")
BooleanOptionKey const	shuffle_screening_jobs ("in:file:shuffle_screening_jobs")
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")
BooleanOptionKey const	no_detect_pseudobonds ("in:file:no_detect_pseudobonds")
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")
StringVectorOptionKey const	remap_pdb_atom_names_for ("in:file:remap_pdb_atom_names_for")
FileVectorOptionKey const	extra_res ("in:file:extra_res")
FileVectorOptionKey const	extra_res_fa ("in:file:extra_res_fa")
FileVectorOptionKey const	extra_res_mol ("in:file:extra_res_mol")
FileVectorOptionKey const	extra_res_mmCIF ("in:file:extra_res_mmCIF")
BooleanOptionKey const	load_PDB_components ("in:file:load_PDB_components")
StringOptionKey const	PDB_components_directory ("in:file:PDB_components_directory")
StringVectorOptionKey const	PDB_components_overrides ("in:file:PDB_components_overrides")
BooleanOptionKey const	check_all_PDB_components ("in:file:check_all_PDB_components")
StringOptionKey const	extra_res_database ("in:file:extra_res_database")
StringOptionKey const	extra_res_pq_schema ("in:file:extra_res_pq_schema")
StringOptionKey const	extra_res_database_mode ("in:file:extra_res_database_mode")
FileOptionKey const	extra_res_database_resname_list ("in:file:extra_res_database_resname_list")
FileVectorOptionKey const	extra_res_cen ("in:file:extra_res_cen")
PathVectorOptionKey const	extra_res_path ("in:file:extra_res_path")
PathVectorOptionKey const	extra_rot_lib_path ("in:file:extra_rot_lib_path")
PathVectorOptionKey const	override_rot_lib_path ("in:file:override_rot_lib_path")
PathVectorOptionKey const	extra_res_batch_path ("in:file:extra_res_batch_path")
FileVectorOptionKey const	extra_patch_fa ("in:file:extra_patch_fa")
FileVectorOptionKey const	extra_patch_cen ("in:file:extra_patch_cen")
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	surface_vectors ("in:file:surface_vectors")
StringOptionKey const	xyz ("in:file:xyz")
BooleanOptionKey const	keep_input_scores ("in:file:keep_input_scores")
BooleanOptionKey const	lazy_silent ("in:file:lazy_silent")
FileVectorOptionKey const	silent ("in:file:silent")
BooleanOptionKey const	force_silent_bitflip_on_read ("in:file:force_silent_bitflip_on_read")
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")
BooleanOptionKey const	centroid_input ("in:file:centroid_input")
BooleanOptionKey const	centroid ("in:file:centroid")
BooleanOptionKey const	assign_gasteiger_atom_types ("in:file:assign_gasteiger_atom_types")
StringOptionKey const	treat_residues_in_these_chains_as_separate_chemical_entities ("in:file:treat_residues_in_these_chains_as_separate_chemical_entities")
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")
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")
IntegerOptionKey const	silent_select_range_start ("in:file:silent_select_range_start")
IntegerOptionKey const	silent_select_range_mul ("in:file:silent_select_range_mul")
IntegerOptionKey const	silent_select_range_len ("in:file:silent_select_range_len")
BooleanOptionKey const	skip_failed_simulations ("in:file:skip_failed_simulations")
StringVectorOptionKey const	silent_scores_wanted ("in:file:silent_scores_wanted")
FileVectorOptionKey const	fasta ("in:file:fasta")
FileVectorOptionKey const	pssm ("in:file:pssm")
StringVectorOptionKey const	seq ("in:file:seq")
FileOptionKey const	checkpoint ("in:file:checkpoint")
FileOptionKey const	binary_chk ("in:file:binary_chk")
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	csa ("in:file:csa")
FileVectorOptionKey const	dc ("in:file:dc")
FileVectorOptionKey const	burial ("in:file:burial")
FileOptionKey const	hrf_ms_labeling ("in:file:hrf_ms_labeling")
FileVectorOptionKey const	vall ("in:file:vall")
BooleanOptionKey const	rescore ("in:file:rescore")
StringOptionKey const	spanfile ("in:file:spanfile")
StringOptionKey const	lipofile ("in:file:lipofile")
StringOptionKey const	HDX ("in:file:HDX")
RealOptionKey const	d2h_sa_reweight ("in:file:d2h_sa_reweight")
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")
ResidueChainVectorOptionKey const	input_res ("in:file:input_res")
IntegerVectorOptionKey const	minimize_res ("in:file:minimize_res")
StringOptionKey const	md_schfile ("in:file:md_schfile")
FileOptionKey const	native_contacts ("in:file:native_contacts")

Function Documentation

FileVectorOptionKey const in::file::alignment

(

"in:file:alignment"

)

Referenced by main().

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"

)

BooleanOptionKey const in::file::assign_gasteiger_atom_types

(

"in:file:assign_gasteiger_atom_types"

)

FileVectorOptionKey const in::file::atom_tree_diff

(

"in:file:atom_tree_diff"

)

FileOptionKey const in::file::binary_chk

(

"in:file:binary_chk"

)

FileVectorOptionKey const in::file::boinc_wu_zip

(

"in:file:boinc_wu_zip"

)

FileVectorOptionKey const in::file::burial

(

"in:file:burial"

)

BooleanOptionKey const in::file::centroid

(

"in:file:centroid"

)

Referenced by main().

BooleanOptionKey const in::file::centroid_input

(

"in:file:centroid_input"

)

Referenced by main().

BooleanOptionKey const in::file::check_all_PDB_components

(

"in:file:check_all_PDB_components"

)

FileOptionKey const in::file::checkpoint

(

"in:file:checkpoint"

)

Referenced by register_options().

FileVectorOptionKey const in::file::csa

(

"in:file:csa"

)

RealOptionKey const in::file::d2h_sa_reweight

(

"in:file:d2h_sa_reweight"

)

FileVectorOptionKey const in::file::dc

(

"in:file:dc"

)

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_patch_cen

(

"in:file:extra_patch_cen"

)

FileVectorOptionKey const in::file::extra_patch_fa

(

"in:file:extra_patch_fa"

)

FileVectorOptionKey const in::file::extra_res

(

"in:file:extra_res"

)

Referenced by main().

PathVectorOptionKey const in::file::extra_res_batch_path

(

"in:file:extra_res_batch_path"

)

FileVectorOptionKey const in::file::extra_res_cen

(

"in:file:extra_res_cen"

)

Referenced by main().

StringOptionKey const in::file::extra_res_database

(

"in:file:extra_res_database"

)

StringOptionKey const in::file::extra_res_database_mode

(

"in:file:extra_res_database_mode"

)

FileOptionKey const in::file::extra_res_database_resname_list

(

"in:file:extra_res_database_resname_list"

)

FileVectorOptionKey const in::file::extra_res_fa

(

"in:file:extra_res_fa"

)

Referenced by main().

FileVectorOptionKey const in::file::extra_res_mmCIF

(

"in:file:extra_res_mmCIF"

)

FileVectorOptionKey const in::file::extra_res_mol

(

"in:file:extra_res_mol"

)

PathVectorOptionKey const in::file::extra_res_path

(

"in:file:extra_res_path"

)

StringOptionKey const in::file::extra_res_pq_schema

(

"in:file:extra_res_pq_schema"

)

PathVectorOptionKey const in::file::extra_rot_lib_path

(

"in:file:extra_rot_lib_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(), my_main(), Prepare(), rebuild_test(), register_options(), rna_build_helix_test(), rna_score_test(), rna_thread_test(), and DockFragmentsMover::run().

BooleanOptionKey const in::file::file

(

"in:file"

)

FileOptionKey const in::file::fold_tree

(

"in:file:fold_tree"

)

Referenced by do_erraser2().

BooleanOptionKey const in::file::force_silent_bitflip_on_read

(

"in:file:force_silent_bitflip_on_read"

)

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"

)

StringOptionKey const in::file::fragA

(

"in:file:fragA"

)

StringOptionKey const in::file::fragB

(

"in:file:fragB"

)

BooleanOptionKey const in::file::fullatom

(

"in:file:fullatom"

)

Referenced by Minimize::apply(), main(), Minimize::Minimize(), and MyScoreMover::MyScoreMover().

StringOptionKey const in::file::HDX

(

"in:file:HDX"

)

FileOptionKey const in::file::hrf_ms_labeling

(

"in:file:hrf_ms_labeling"

)

ResidueChainVectorOptionKey const in::file::input_res

(

"in:file:input_res"

)

Referenced by main(), and mg_modeler_test().

FileOptionKey const in::file::job_definition_file

(

"in:file:job_definition_file"

)

BooleanOptionKey const in::file::keep_input_scores

(

"in:file:keep_input_scores"

)

Referenced by MyScoreMover::MyScoreMover().

FileVectorOptionKey const in::file::l

(

"in:file:l"

)

Referenced by main(), and rhiju_pdbstats().

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"

)

BooleanOptionKey const in::file::load_PDB_components

(

"in:file:load_PDB_components"

)

StringOptionKey const in::file::md_schfile

(

"in:file:md_schfile"

)

IntegerVectorOptionKey const in::file::minimize_res

(

"in:file:minimize_res"

)

FileOptionKey const in::file::movemap

(

"in:file:movemap"

)

Referenced by main().

FileOptionKey const in::file::native

(

"in:file:native"

)

Referenced by align_pdbs(), analyze_base_pair_test(), ExposedStrandMover::apply(), HDdesignMover::apply(), BuildFullModel::BuildFullModel(), calc_rms_test(), calculate_pairwise_RMSD(), initialize_native_pose(), main(), minimize_test(), pep_phipsi_analysis(), pep_rmsd_analysis(), register_options(), repack_test(), rna_score_test(), run(), DockFragmentsMover::run(), and swa_rna_sample().

FileOptionKey const in::file::native_contacts

(

"in:file:native_contacts"

)

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::no_detect_pseudobonds

(

"in:file:no_detect_pseudobonds"

)

BooleanOptionKey const in::file::obey_ENDMDL

(

"in:file:obey_ENDMDL"

)

PathVectorOptionKey const in::file::override_rot_lib_path

(

"in:file:override_rot_lib_path"

)

FileOptionKey const in::file::pca

(

"in:file:pca"

)

FileOptionKey const in::file::PCS_frag_cst

(

"in:file:PCS_frag_cst"

)

StringOptionKey const in::file::PDB_components_directory

(

"in:file:PDB_components_directory"

)

StringVectorOptionKey const in::file::PDB_components_overrides

(

"in:file:PDB_components_overrides"

)

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"

)

StringVectorOptionKey const in::file::remap_pdb_atom_names_for

(

"in:file:remap_pdb_atom_names_for"

)

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"

)

Referenced by align_pdbs(), analyze_base_pair_test(), calculate_pairwise_RMSD(), calculate_sasa(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), densityTools(), do_erraser2(), drrafter_error_estimation(), erraser2_test(), fill_input_poses_based_on_possible_checkpoints(), find_close_motifs(), import_and_dump_pdb(), main(), mg_modeler_test(), mutate_residues_wrapper(), my_main(), nucleobase_probe_score_test(), o2prime_packer(), obtain_start_pose(), pdb_to_silent_file(), predict_chem_map_test(), quick_score_test(), register_options(), resample_full_model_test(), rhiju_pdbstats(), rna_design_test(), rna_score_test(), rna_suitename(), rna_superimpose_and_graft_test(), rna_thread_test(), sequence_tolerance_main(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), and ss_ds_ts_assign_test().

FileOptionKey const in::file::screening_job_file

(

"in:file:screening_job_file"

)

FileVectorOptionKey const in::file::screening_list

(

"in:file:screening_list"

)

StringVectorOptionKey const in::file::seq

(

"in:file:seq"

)

BooleanOptionKey const in::file::shuffle_screening_jobs

(

"in:file:shuffle_screening_jobs"

)

FileVectorOptionKey const in::file::silent

(

"in:file:silent"

)

Referenced by analyze_base_pair_test(), build_full_model_test(), calc_rms_test(), calc_rmsf_and_avrg(), cluster_outfile_test(), cluster_test(), drrafter_error_estimation(), extract_pdbs_test(), filter_combine_long_loop(), main(), post_rebuild_bulge_assembly(), read_structures(), register_options(), rna_sample_virtual_sugar(), rna_score_test(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), and swa_rna_cluster().

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_read_through_errors

(

"in:file:silent_read_through_errors"

)

Referenced by main().

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"

)

IntegerOptionKey const in::file::silent_select_range_len

(

"in:file:silent_select_range_len"

)

IntegerOptionKey const in::file::silent_select_range_mul

(

"in:file:silent_select_range_mul"

)

IntegerOptionKey const in::file::silent_select_range_start

(

"in:file:silent_select_range_start"

)

StringOptionKey const in::file::silent_struct_type

(

"in:file:silent_struct_type"

)

Referenced by main().

BooleanOptionKey const in::file::skip_failed_simulations

(

"in:file:skip_failed_simulations"

)

StringOptionKey const in::file::spanfile

(

"in:file:spanfile"

)

BooleanOptionKey const in::file::srlz

(

"in:file:srlz"

)

BooleanOptionKey const in::file::srlz_override

(

"in:file:srlz_override"

)

FileOptionKey const in::file::sucker_params

(

"in:file:sucker_params"

)

StringOptionKey const in::file::surface_vectors

(

"in:file:surface_vectors"

)

FileVectorOptionKey const in::file::t

(

"in:file:t"

)

FileOptionKey const in::file::tagfile

(

"in:file:tagfile"

)

Referenced by main().

StringVectorOptionKey const in::file::tags

(

"in:file:tags"

)

Referenced by analyze_base_pair_test(), build_full_model_test(), drrafter_error_estimation(), extract_pdbs_test(), main(), post_rebuild_bulge_assembly(), and rna_score_test().

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 calc_rmsf_and_avrg(), get_exclid(), and 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().

StringOptionKey const in::file::treat_residues_in_these_chains_as_separate_chemical_entities

(

"in:file:treat_residues_in_these_chains_as_separate_chemical_entities"

)

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"

)