basic::options::OptionKeys::cluster::energy_based_clustering Namespace Reference

Variables
BooleanOptionKey const	energy_based_clustering
BooleanOptionKey const	prerelax
IntegerOptionKey const	relax_rounds
StringOptionKey const	cluster_by
BooleanOptionKey const	use_CB
RealOptionKey const	cluster_radius
IntegerVectorOptionKey const	residues_to_ignore
IntegerVectorOptionKey const	chains_to_ignore
IntegerOptionKey const	limit_structures_per_cluster
IntegerOptionKey const	limit_clusters
BooleanOptionKey const	cyclic
IntegerOptionKey const	cyclic_symmetry
BooleanOptionKey const	cyclic_symmetry_mirroring
RealOptionKey const	cyclic_symmetry_threshold
BooleanOptionKey const	cluster_cyclic_permutations
IntegerOptionKey const	cyclic_permutation_offset
BooleanOptionKey const	perform_ABOXYZ_bin_analysis
BooleanOptionKey const	mutate_to_ala
IntegerVectorOptionKey const	disulfide_positions
BooleanOptionKey const	homooligomer_swap
BooleanOptionKey const	silent_output
FileVectorOptionKey const	cst_file
StringVectorOptionKey const	extra_rms_atoms
BooleanOptionKey const	rebuild_all_in_dihedral_mode
FileOptionKey const	alternative_score_file

Variable Documentation

alternative_score_file

FileOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::alternative_score_file

extern

chains_to_ignore

IntegerVectorOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::chains_to_ignore

extern

cluster_by

StringOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cluster_by

extern

cluster_cyclic_permutations

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cluster_cyclic_permutations

extern

cluster_radius

RealOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius

extern

Referenced by base_pair_to_base_pair_test(), cluster_outfile_test(), cluster_silent_file_data(), cluster_test(), define_states_test(), main(), make_fragments(), and modeler_closure_test().

cst_file

FileVectorOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cst_file

extern

Referenced by ConstraintToolMover::apply(), build_template(), coarse_rna_denovo_test(), RelaxJobQueen::complete_larval_job_maturation(), cst_relax_test(), easy_target_test(), get_stepwise_score_function(), TestQuickRelaxMover::init_from_cmd(), main(), MSA_design(), print_pep_csts(), rebuild_centroid_test(), rebuild_test(), TestQuickRelaxMover::register_options(), rna_assemble_all_combinations_test(), rna_assemble_test(), run(), RunPepSpec(), and stepwise_template_test().

cyclic

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cyclic

extern

cyclic_permutation_offset

IntegerOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_permutation_offset

extern

cyclic_symmetry

IntegerOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_symmetry

extern

cyclic_symmetry_mirroring

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_symmetry_mirroring

extern

cyclic_symmetry_threshold

RealOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_symmetry_threshold

extern

disulfide_positions

IntegerVectorOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::disulfide_positions

extern

energy_based_clustering

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::energy_based_clustering

extern

Referenced by main().

extra_rms_atoms

StringVectorOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::extra_rms_atoms

extern

Referenced by get_distance_measure(), main(), and scoreall().

homooligomer_swap

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::homooligomer_swap

extern

limit_clusters

IntegerOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::limit_clusters

extern

limit_structures_per_cluster

IntegerOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::limit_structures_per_cluster

extern

mutate_to_ala

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::mutate_to_ala

extern

perform_ABOXYZ_bin_analysis

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::perform_ABOXYZ_bin_analysis

extern

prerelax

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::prerelax

extern

rebuild_all_in_dihedral_mode

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::rebuild_all_in_dihedral_mode

extern

relax_rounds

IntegerOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::relax_rounds

extern

residues_to_ignore

IntegerVectorOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::residues_to_ignore

extern

silent_output

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::silent_output

extern

Referenced by distribute_jobs().

use_CB

BooleanOptionKey const basic::options::OptionKeys::cluster::energy_based_clustering::use_CB

extern