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Namespaces | Functions
stepwise Namespace Reference

Namespaces

 monte_carlo
 
 polar_hydrogens
 
 protein
 
 rna
 

Functions

BooleanOptionKey const stepwise ("stepwise")
 
StringVectorOptionKey const s1 ("stepwise:s1")
 
StringVectorOptionKey const s2 ("stepwise:s2")
 
StringVectorOptionKey const silent1 ("stepwise:silent1")
 
StringVectorOptionKey const silent2 ("stepwise:silent2")
 
StringVectorOptionKey const tags1 ("stepwise:tags1")
 
StringVectorOptionKey const tags2 ("stepwise:tags2")
 
IntegerVectorOptionKey const slice_res1 ("stepwise:slice_res1")
 
IntegerVectorOptionKey const slice_res2 ("stepwise:slice_res2")
 
IntegerVectorOptionKey const input_res1 ("stepwise:input_res1")
 
IntegerVectorOptionKey const input_res2 ("stepwise:input_res2")
 
BooleanOptionKey const backbone_only1 ("stepwise:backbone_only1")
 
BooleanOptionKey const backbone_only2 ("stepwise:backbone_only2")
 
IntegerVectorOptionKey const fixed_res ("stepwise:fixed_res")
 
BooleanOptionKey const test_encapsulation ("stepwise:test_encapsulation")
 
BooleanOptionKey const choose_random ("stepwise:choose_random")
 
IntegerOptionKey const num_random_samples ("stepwise:num_random_samples")
 
IntegerOptionKey const max_tries_multiplier_for_ccd ("stepwise:max_tries_multiplier_for_ccd")
 
IntegerOptionKey const num_pose_minimize ("stepwise:num_pose_minimize")
 
BooleanOptionKey const atr_rep_screen ("stepwise:atr_rep_screen")
 
BooleanOptionKey const atr_rep_screen_for_docking ("stepwise:atr_rep_screen_for_docking")
 
StringOptionKey const align_pdb ("stepwise:align_pdb")
 
StringOptionKey const new_align_pdb ("stepwise:new_align_pdb")
 
BooleanOptionKey const enumerate ("stepwise:enumerate")
 
BooleanOptionKey const preminimize ("stepwise:preminimize")
 
BooleanOptionKey const skip_preminimize ("stepwise:skip_preminimize")
 
BooleanOptionKey const minimize_waters ("stepwise:minimize_waters")
 
BooleanOptionKey const test_all_moves ("stepwise:test_all_moves")
 
BooleanOptionKey const new_move_selector ("stepwise:new_move_selector")
 
BooleanOptionKey const dump ("stepwise:dump")
 
BooleanOptionKey const VERBOSE ("stepwise:VERBOSE")
 
BooleanOptionKey const use_green_packer ("stepwise:use_green_packer")
 
RealOptionKey const rmsd_screen ("stepwise:rmsd_screen")
 
BooleanOptionKey const skip_minimize ("stepwise:skip_minimize")
 
BooleanOptionKey const virtualize_packable_moieties_in_screening_pose ("stepwise:virtualize_packable_moieties_in_screening_pose")
 
StringOptionKey const minimizer_mode ("stepwise:minimizer_mode")
 
StringOptionKey const sampler_silent_file ("stepwise:sampler_silent_file")
 
BooleanOptionKey const superimpose_over_all ("stepwise:superimpose_over_all")
 
ResidueChainVectorOptionKey const alignment_anchor_res ("stepwise:alignment_anchor_res")
 
StringVectorOptionKey const move ("stepwise:move")
 
StringOptionKey const min_type ("stepwise:min_type")
 
RealOptionKey const min_tolerance ("stepwise:min_tolerance")
 
BooleanOptionKey const output_minimized_pose_list ("stepwise:output_minimized_pose_list")
 
BooleanOptionKey const virtualize_free_moieties_in_native ("stepwise:virtualize_free_moieties_in_native")
 
BooleanOptionKey const output_cluster_size ("stepwise:output_cluster_size")
 
BooleanOptionKey const lores ("stepwise:lores")
 
BooleanOptionKey const verbose_sampler ("stepwise:verbose_sampler")
 
BooleanOptionKey const pack_protein_side_chains ("stepwise:pack_protein_side_chains")
 
IntegerVectorOptionKey const definitely_virtualize ("stepwise:definitely_virtualize")
 
BooleanOptionKey const force_moving_res_for_erraser ("stepwise:force_moving_res_for_erraser")
 
BooleanOptionKey const boltzmann_choice_post_enumerated_minimize ("stepwise:boltzmann_choice_post_enumerated_minimize")
 

Function Documentation

StringOptionKey const stepwise::align_pdb ( "stepwise:align_pdb"  )
ResidueChainVectorOptionKey const stepwise::alignment_anchor_res ( "stepwise:alignment_anchor_res"  )
BooleanOptionKey const stepwise::atr_rep_screen ( "stepwise:atr_rep_screen"  )
BooleanOptionKey const stepwise::atr_rep_screen_for_docking ( "stepwise:atr_rep_screen_for_docking"  )
BooleanOptionKey const stepwise::backbone_only1 ( "stepwise:backbone_only1"  )
BooleanOptionKey const stepwise::backbone_only2 ( "stepwise:backbone_only2"  )
BooleanOptionKey const stepwise::boltzmann_choice_post_enumerated_minimize ( "stepwise:boltzmann_choice_post_enumerated_minimize"  )
BooleanOptionKey const stepwise::choose_random ( "stepwise:choose_random"  )
IntegerVectorOptionKey const stepwise::definitely_virtualize ( "stepwise:definitely_virtualize"  )
BooleanOptionKey const stepwise::dump ( "stepwise:dump"  )
BooleanOptionKey const stepwise::enumerate ( "stepwise:enumerate"  )
IntegerVectorOptionKey const stepwise::fixed_res ( "stepwise:fixed_res"  )
BooleanOptionKey const stepwise::force_moving_res_for_erraser ( "stepwise:force_moving_res_for_erraser"  )
IntegerVectorOptionKey const stepwise::input_res1 ( "stepwise:input_res1"  )
IntegerVectorOptionKey const stepwise::input_res2 ( "stepwise:input_res2"  )
BooleanOptionKey const stepwise::lores ( "stepwise:lores"  )
IntegerOptionKey const stepwise::max_tries_multiplier_for_ccd ( "stepwise:max_tries_multiplier_for_ccd"  )
RealOptionKey const stepwise::min_tolerance ( "stepwise:min_tolerance"  )
StringOptionKey const stepwise::min_type ( "stepwise:min_type"  )
BooleanOptionKey const stepwise::minimize_waters ( "stepwise:minimize_waters"  )
StringOptionKey const stepwise::minimizer_mode ( "stepwise:minimizer_mode"  )
StringVectorOptionKey const stepwise::move ( "stepwise:move"  )
StringOptionKey const stepwise::new_align_pdb ( "stepwise:new_align_pdb"  )
BooleanOptionKey const stepwise::new_move_selector ( "stepwise:new_move_selector"  )
IntegerOptionKey const stepwise::num_pose_minimize ( "stepwise:num_pose_minimize"  )
IntegerOptionKey const stepwise::num_random_samples ( "stepwise:num_random_samples"  )
BooleanOptionKey const stepwise::output_cluster_size ( "stepwise:output_cluster_size"  )
BooleanOptionKey const stepwise::output_minimized_pose_list ( "stepwise:output_minimized_pose_list"  )
BooleanOptionKey const stepwise::pack_protein_side_chains ( "stepwise:pack_protein_side_chains"  )
BooleanOptionKey const stepwise::preminimize ( "stepwise:preminimize"  )
RealOptionKey const stepwise::rmsd_screen ( "stepwise:rmsd_screen"  )
StringVectorOptionKey const stepwise::s1 ( "stepwise:s1"  )
StringVectorOptionKey const stepwise::s2 ( "stepwise:s2"  )
StringOptionKey const stepwise::sampler_silent_file ( "stepwise:sampler_silent_file"  )
StringVectorOptionKey const stepwise::silent1 ( "stepwise:silent1"  )
StringVectorOptionKey const stepwise::silent2 ( "stepwise:silent2"  )
BooleanOptionKey const stepwise::skip_minimize ( "stepwise:skip_minimize"  )
BooleanOptionKey const stepwise::skip_preminimize ( "stepwise:skip_preminimize"  )
IntegerVectorOptionKey const stepwise::slice_res1 ( "stepwise:slice_res1"  )
IntegerVectorOptionKey const stepwise::slice_res2 ( "stepwise:slice_res2"  )
BooleanOptionKey const stepwise::stepwise ( "stepwise"  )
BooleanOptionKey const stepwise::superimpose_over_all ( "stepwise:superimpose_over_all"  )
StringVectorOptionKey const stepwise::tags1 ( "stepwise:tags1"  )
StringVectorOptionKey const stepwise::tags2 ( "stepwise:tags2"  )
BooleanOptionKey const stepwise::test_all_moves ( "stepwise:test_all_moves"  )
BooleanOptionKey const stepwise::test_encapsulation ( "stepwise:test_encapsulation"  )
BooleanOptionKey const stepwise::use_green_packer ( "stepwise:use_green_packer"  )
BooleanOptionKey const stepwise::VERBOSE ( "stepwise:VERBOSE"  )
BooleanOptionKey const stepwise::verbose_sampler ( "stepwise:verbose_sampler"  )
BooleanOptionKey const stepwise::virtualize_free_moieties_in_native ( "stepwise:virtualize_free_moieties_in_native"  )
BooleanOptionKey const stepwise::virtualize_packable_moieties_in_screening_pose ( "stepwise:virtualize_packable_moieties_in_screening_pose"  )