Index

A

Accumulator (class in superpose) add() (superpose.Accumulator method) (superpose.Pairing method) add_torsion_restraint() (optimize.Objective method) (superpose.Objective method) addDirectedEdge() (torsion.Graph method) addEdge() (torsion.Graph method) addVertex() (torsion.Graph method) align() (atoms.VecList method) align_to_vec() (atoms.VecList method) align_unique() (atoms.VecList method) align_vecs() (atoms.VecList method) alignment() (atoms.Anisotropics method) all_atoms (rotamer.Rotamer attribute) all_dependents (torsion.TAProtein attribute) allow_no_file (map.ReadMap attribute) analyze() (atoms.Anisotropics method) (optimize.Optimization method) (optimize.Parameters method) (optimize.Tasks method) (rsref.Tasks method) analyze_prereq() (optimize.Tasks method) (rsref.Tasks method) AnalyzeSubCommands (class in optimize) ancestory() (cmd2nest.Cmd method) angleEntry (optimize.ResidueInfo attribute) Anisotropics (class in atoms) apidoc() (in module documentation) append() (atoms.VecList method) (optimize.TorsionParameterization method) apply_torsion() (torsion.TAProtein method) apply_torsion_deprecated() (torsion.TAProtein method) are_close() (atoms.Atoms method) are_neighbors() (atoms.Atoms method) argparser (module) argument() (optimize.CallBackEmulator method) ArgumentParser (class in argparser) Arguments (class in argparser) (class in atoms) (class in density) (class in documentation) (class in impact) (class in map) (class in optimize) (class in restraints) (class in rsref) (class in superpose) (class in symmetry) ArrayBoundsError

arrow_range() (in module impact) as_count (optimize.Grouping attribute) asdict() (argparser.CommonOptions method) asSelection() (atoms.Selection method) assign() (optimize.Grouping method) at_dstar() (form_factor_table.FormFactorTable method) at_dstar_array (form_factor_table.FormFactorTable attribute) at_dstar_sq() (form_factor_table.FormFactorTable method) at_dstar_sq_array (form_factor_table.FormFactorTable attribute) at_s() (form_factor_table.FormFactorTable method) at_s_array (form_factor_table.FormFactorTable attribute) at_s_sq() (form_factor_table.FormFactorTable method) at_s_sq_array (form_factor_table.FormFactorTable attribute) atom_box() (density.ModelMap method) atomic_partials_current (density.ModelMap attribute) AtomicDensity (class in density) AtomicParameterization (class in optimize) AtomicRefinement (class in optimize) Atoms (class in atoms) atoms (module) Atoms.ChainName (class in atoms) atoms_being_evaluated (rsref.Tasks attribute) (superpose.Tasks attribute) atoms_refined (rsref.Tasks attribute) (superpose.Tasks attribute) Attenuation, [1] attenuation Gaussian attribute() (atoms.Selection static method) attributeOrder (superpose.Pairing attribute) augment() (transform.AugmentedOperator method) AugmentedOperator (class in transform) axes() (atoms.Anisotropics method)

B

B overall B-factor, [1] backup() (superpose.Tasks method) backup_prereq() (superpose.Tasks method) base_keywords (cmd2nest.Cmd attribute) bfactor (optimize.AtomicParameterization attribute) bfactors() (superpose.Pairing method) (superpose.Tasks method)

bfactors_prereq() (superpose.Tasks method) BGrouping (class in optimize) bond_dependents (torsion.TAProtein attribute) boolabbrev() (optimize.Grouping static method) bounds() (atoms.Atoms method) Brestraint (class in restraints) build() (space_group.SpaceGroups method)

C

cache_init() (density.AtomicDensity method) cache_off() (density.AtomicDensity method) cache_on() (density.AtomicDensity method) cache_reset() (density.AtomicDensity method) calculate() (density.ModelMap method) calculate_map() (rsref.Tasks method) calculate_map_prereq() (rsref.Tasks method) callback() (optimize.Objective method) (superpose.Objective method) CallBackEmulator (class in optimize) calling_program (module) Cartesian_operator (class in symmetry) cciso() (atoms.Anisotropics method) ccuij() (atoms.Anisotropics method) center() (atoms.Selection method) change() (torsion.Limit method) changeArray() (optimize.ResidueInfo method) changed() (density.ModelMap method) (optimize.Groupings method) (optimize.TorsionParameterization method) changing (optimize.AtomicParameterization attribute) (optimize.Grouping attribute) (optimize.Groupings attribute) (optimize.TorsionGp attribute) (optimize.TorsionParameterization attribute) check() (atoms.Anisotropics method) (atoms.Group method) (optimize.TorsionParameterization method) check_support() (optimize.Parameters method) check_supported() (optimize.Parameters static method) check_type() (optimize.Grouping method) checkfiles() (in module documentation) checks_off() (atoms.Atoms method) checks_on() (atoms.Atoms method) chi() (rotamer.Rotamer method) children (cmd2nest.Cmd attribute) Cmd (class in cmd2nest) cmd2nest (module) cmd_extensions (module) cmdloop() (cmd2nest.Cmd method) Collection (class in atoms) color() (impact.ControlAdded method) (optimize.ResidueInfo method)

combine() (optimize.ResidueInfo method) combined (optimize.ResidueInfo attribute) combined_bond_ids() (optimize.ResidueInfo method) Commands (class in atoms) (class in impact) (class in optimize) CommandsAdded (class in impact) CommonOptions (class in argparser) comp() (atoms.Vec method) compare() (torsion.TAProtein method) complete() (symmetry.Symmetry method) compute_rigid_alignment_deriv() (in module transform) compute_rigid_alignment_matrix() (in module transform) compute_rotation_about_origin() (in module transform) compute_rotation_matrix() (in module transform) compute_transformation_matrix() (in module transform) conformer (atoms.Atoms attribute) connect (optimize.TorsionParameterization attribute) connected (optimize.TorsionParameterization attribute) connectivity (optimize.TorsionParameterization attribute) (superpose.Pairing attribute) connectivity() (atoms.Atoms method) connectivityExclusion (restraints.VDWRestraint attribute) continuable (superpose.Pairing attribute) Contrast Transfer Function CTF, [1] ControlAdded (class in impact) convergence() (optimize.Tasks method) copy() (optimize.ResidueInfo method) (superpose.PairItem method) (torsion.TAProtein method) copyrst() (in module documentation) Correction, [1] correl_coeff() (in module density) correlation() (density.ModelMap method) Crystallography crystallography (module) CTF Contrast Transfer Function, [1]

D

debug (symmetry.Symmetry attribute) (symmetry.Target attribute) (torsion.TAProtein attribute) debug_instances (optimize.Parameters attribute) default() (optimize.Grouping method) (optimize.Groupings method) (optimize.IndividualGp method) (optimize.OverallGp method) (optimize.TorsionGp method) default_group (rsref.Tasks attribute) (superpose.Tasks attribute) default_selection() (optimize.Grouping method) (optimize.TorsionGp method) default_selection_expr (optimize.TorsionParameterization attribute) defaults() (optimize.TorsionParameterization method) density (module) density() (density.AtomicDensity method) density_array (density.AtomicDensity attribute) density_wo_cache() (density.AtomicDensity method) deorthogonalize() (crystallography.MapOrthogonal method) deorthogonalize_vec() (crystallography.MapOrthogonal method) depends_on_anisou (optimize.Objective attribute) (superpose.Objective attribute) deprecated_3ax (superpose.Pairing attribute) deriv (optimize.History attribute) df() (restraints.Brestraint method) dfbydv() (transform.AugmentedOperator method) (transform.EulerX0Y0Z0 method) dfL1Norm() (torsion.Limit method) dfL1sq() (torsion.Limit method) dfs() (torsion.Graph method) dfsVisit() (torsion.Graph method) diagnostics() (rsref.Tasks method) difference() (atoms.Atoms method) (superpose.Pairing method) differences() (atoms.Atoms method) (superpose.Pairing method) differences_vs_bs() (superpose.Pairing method) dihedral_atoms() (in module torsion) dihedral_hinges() (optimize.Tasks method) dihedral_name() (in module torsion) dihedral_paint() (optimize.Tasks method) dihedral_value() (in module torsion) dihedrals_within (optimize.TorsionGp attribute) (optimize.TorsionParameterization attribute) DihedralsSubSubCommands (class in optimize) directory_setup() (in module documentation) displacements() (in module transform) dissect() (in module superpose) distance (restraints.VDWRestraint attribute) distances() (density.AtomicDensity method) (density.ModelMap method) (density.ModelMap.AtomMask method) distances_assume_orthonormal() (density.ModelMap method) divergence() (atoms.Anisotropics method) dmagnification() (density.ModelMap method) do__load() (cmd2nest.Cmd method) do_analyze() (optimize.Commands method) do_backup() (superpose.TopCommands method) do_bfactors() (superpose.TopCommands method) do_callee() (cmd2nest.ProgSubCmd method) do_caller() (cmd2nest.ProgTopCmd method) do_clear() (optimize.ParameterizeSubCommands method) do_cmd_file() (cmd_extensions.Extensions method) do_color() (impact.CommandsAdded method) (optimize.ImpactSubSubSubCommands method) do_convergence() (optimize.AnalyzeSubCommands method) do_dihedrals() (optimize.AnalyzeSubCommands method) do_done() (cmd2nest.SubCmd method)

do_echo() (cmd_extensions.Extensions method) do_evaluate() (rsref.TopCommands method) (superpose.TopCommands method) do_flip() (superpose.TopCommands method) do_group() (optimize.ParameterizeSubCommands method) do_help() (cmd2nest.Cmd method) do_help_all() (cmd_extensions.Extensions method) do_hinges() (optimize.DihedralsSubSubCommands method) do_histogram() (impact.CommandsAdded method) do_image_refine() (rsref.TopCommands method) do_impact() (optimize.DihedralsSubSubCommands method) do_individual() (optimize.ParameterizeSubCommands method) do_load() (cmd2nest.Cmd method) do_map() (rsref.TopCommands method) do_match() (superpose.PairSubCommands method) do_neighbors() (rsref.TopCommands method) (symexp.TopCommands method) do_null() (cmd_extensions.Extensions method) do_overall() (optimize.ParameterizeSubCommands method) do_overlay() (superpose.TopCommands method) do_paint() (optimize.DihedralsSubSubCommands method) do_pair() (superpose.TopCommands method) do_parameterize() (rsref.TopCommands method) (superpose.TopCommands method) do_parrot() (cmd2nest.Cmd method) (cmd_extensions.Extensions method) do_pdbout() (atoms.Commands method) (symexp.TopCommands method) do_perturb() (rsref.TopCommands method) do_phipsi_copy() (superpose.TopCommands method) do_phipsi_diff() (superpose.TopCommands method) do_pickle() (optimize.ImpactSubSubSubCommands method) do_plot() (impact.CommandsAdded method) (optimize.ImpactSubSubSubCommands method) do_print() (optimize.ImpactSubSubSubCommands method) (optimize.ParameterizeSubCommands method) (superpose.PairSubCommands method) do_profile() (rsref.TopCommands method) do_randomize() (rsref.TopCommands method) do_refine() (rsref.TopCommands method) (superpose.TopCommands method) do_restore() (superpose.TopCommands method) do_restraints() (rsref.TopCommands method) do_select() (atoms.Commands method) do_SELECTION_EXPR() (optimize.ParameterizeSubCommands method) do_set() (cmd2nest.Cmd method) do_show() (impact.Commands method) do_sphere() (symexp.TopCommands method) do_test() (cmd2nest.Cmd method) (cmd_extensions.Extensions method) (rsref.TopCommands method) (superpose.TopCommands method) (symexp.TopCommands method) do_torsion() (optimize.ParameterizeSubCommands method) do_value() (cmd_extensions.Extensions method) do_within() (superpose.PairSubCommands method) dObydv (transform.EulerX0Y0Z0 attribute) Documentation (class in atoms) (class in cmd2nest) (class in optimize) (class in symmetry) documentation (module) Documentation.Input (class in symmetry) Documentation.Parameterize (class in optimize) Documentation.Selection_Group (class in atoms) dot() (atoms.Vec method) (in module transform) dotfile() (argparser.ArgumentParser method) dpbydv() (transform.AugmentedOperator method) (transform.EulerX0Y0Z0 method) dummy_chain (class in atoms)

E

edit_links() (torsion.TAProtein method) efficiency_check (optimize.TorsionParameterization attribute) efficiency_level (optimize.TorsionParameterization attribute) Electron Microscopy EMBfactor empty() (atoms.Group method) (atoms.Selection method) (optimize.ResidueInfo method) emptyID() (optimize.ResidueInfo method) emptyLikeAtom() (optimize.ResidueInfo method) emptyline() (cmd_extensions.Extensions method) Envelope, [1], [2], [3] function epy2rst() (in module documentation) equivalent() (symmetry.Symmetry method) equivs (superpose.Pairing attribute) errmsg() (in module tskmgr) error (rotamer.Rotamer attribute) euler() (symmetry.Cartesian_operator method)

eulerAxis() (transform.AugmentedOperator method) EulerX0Y0Z0 (class in transform) eulerX0Y0Z0() (transform.AugmentedOperator method) evaluate() (rsref.Tasks method) (superpose.Tasks method) evaluate_prereq() (rsref.Tasks method) (superpose.Tasks method) expand() (atoms.Group method) (atoms.Selection method) (optimize.GroupGp method) expand_items() (atoms.Group method) (atoms.Selection method) explain() (documentation.Module method) export() (argparser.Arguments static method) (atoms.Arguments static method) (density.Arguments static method) (documentation.Arguments static method) (impact.Arguments static method) (map.Arguments static method) (optimize.Arguments static method) (restraints.Arguments static method) (rsref.Arguments static method) (superpose.Arguments static method) (symmetry.Arguments static method) extend() (atoms.VecList method) (optimize.TorsionParameterization method) extend_svd() (atoms.VecList method) ExtendedParameterization (class in optimize) extendIndex() (rotamer.Rotamer method) Extensions (class in cmd_extensions) extract() (in module documentation) (optimize.Parameters method)

F

f() (optimize.Objective method) (restraints.Brestraint method) (restraints.VDWRestraint method) (superpose.Objective method) f_grad() (restraints.VDWRestraint method) filter Weiner low-pass, [1] filter_resolution (density.AtomicDensity attribute) filter_summarize (module) finalize() (argparser.ArgumentParser method) (impact.Arguments method) (superpose.Arguments method) find_articulation_edges() (torsion.Graph method) find_bridgeless_components() (torsion.Graph method) findS0() (in module superpose) findtype() (form_factor_table.FormFactorTable method) Fit (class in optimize) fix_dihedrals() (optimize.Tasks method) fL1Norm() (torsion.Limit method) fL1sq() (torsion.Limit method) Flagged (class in numpyExt) flatten() (optimize.ResidueInfo method) flip() (in module rotamer) (superpose.Tasks method) flip_prereq() (superpose.Tasks method)

following() (atoms.Selection method) form_factor_table (module) FormFactorTable (class in form_factor_table) FormFactorTable.Counter (class in form_factor_table) fprime() (optimize.Objective method) (superpose.Objective method) from_bsoft() (map.ReadMap method) from_criteria() (atoms.Group method) from_file() (atoms.Atoms method) (map.ReadMap method) from_list() (atoms.Atoms method) from_pair() (superpose.PairItem method) from_reader() (atoms.Atoms method) from_selections() (atoms.Group method) from_unit_cell() (crystallography.MapOrthogonal method) from_xplor() (map.ReadMap method) fromParameters() (optimize.ResidueInfo method) function Envelope function_detail (optimize.Objective attribute) (superpose.Objective attribute)

G

Gaussian attenuation general (cmd2nest.Documentation attribute) general_transformation_matrix() (in module transform) generate_rotation_masks() (torsion.TAProtein method) generate_structure() (torsion.TAProtein method) get() (atoms.Selection method) get_all_backbone_atoms() (torsion.TAProtein method) get_all_backbone_bonds() (torsion.TAProtein method) get_all_bonds_crossing_cut() (torsion.TAProtein method) get_all_bonds_in_selection() (torsion.TAProtein method) get_all_omega() (torsion.TAProtein method) get_all_phi() (torsion.TAProtein method) get_all_phi_psi() (torsion.TAProtein method) get_all_psi() (torsion.TAProtein method) get_dihedral() (in module torsion) get_edge_set() (torsion.TAProtein method) get_history() (restraints.VDWRestraint method) get_namespace() (in module tskmgr) get_namespaces() (in module tskmgr) get_neighbors() (restraints.VDWRestraint method) get_reverse() (torsion.Graph method) get_rotation_mask() (torsion.TAProtein method)

get_selected_phi() (torsion.TAProtein method) get_selected_psi() (torsion.TAProtein method) getattr_or_eval() (tskmgr.ReqObj method) (tskmgr.Task method) getCombined() (optimize.ResidueInfo method) getIsOrthogonal() (crystallography.MapOrthogonal method) getOrigin() (crystallography.MapOrthogonal method) getOrthog() (crystallography.MapOrthogonal method) (crystallography.OrthogonalizationMatrix method) getOrthoxyz() (crystallography.MapOrthogonal method) getResIDKeys() (in module torsion) getselect() (atoms.Tasks method) getSpacing() (crystallography.MapOrthogonal method) getVolume() (crystallography.MapOrthogonal method) (crystallography.OrthogonalizationMatrix method) (density.ModelMap method) Graph (class in torsion) Group (class in atoms) group (optimize.Groupings attribute) GroupGp (class in optimize) Grouping (class in optimize) grouping (optimize.Parameters attribute) (superpose.Parameters attribute) Groupings (class in optimize) groupPartials() (in module transform) groupTransformations() (in module transform)

H

help() (documentation.Module method) (in module documentation) help_backup() (superpose.TopCommands method) help_callee() (cmd2nest.ProgSubCmd method) help_caller() (cmd2nest.ProgTopCmd method) help_cmd_file() (cmd_extensions.Extensions method) help_color() (impact.CommandsAdded method) help_echo() (cmd_extensions.Extensions method) help_help_all() (cmd_extensions.Extensions method) help_histogram() (impact.CommandsAdded method) help_parrot() (cmd_extensions.Extensions method)

help_plot() (impact.CommandsAdded method) help_restore() (superpose.TopCommands method) help_SELECTION_EXPR() (atoms.Commands method) (optimize.ParameterizeSubCommands method) (superpose.PairSubCommands method) help_show() (impact.Commands method) help_test() (cmd_extensions.Extensions method) (rsref.TopCommands method) (superpose.TopCommands method) (symexp.TopCommands method) help_value() (cmd_extensions.Extensions method) hinges() (in module torsion) histogram() (impact.ControlAdded method) History (class in optimize) homepage() (in module documentation)

I

image_refine parameter image_refine() (density.ModelMap method) (rsref.Tasks method) image_refine_prereq() (rsref.Tasks method) impact (module) (optimize.History attribute) impact() (impact.Tasks method) (optimize.Tasks method) impact_paint() (optimize.Tasks method) impact_paint_prereq() (optimize.Tasks method) impact_pickle() (optimize.Tasks method) impact_pickle_prereq() (optimize.Tasks method) impact_plot() (optimize.Tasks method) impact_plot_prereq() (optimize.Tasks method) impact_prereq() (optimize.Tasks method) impact_print() (optimize.Tasks method) impact_print_prereq() (optimize.Tasks method) impactArray() (optimize.ResidueInfo method) impactDelta() (optimize.ResidueInfo method) impactHistory() (optimize.ResidueInfo method) ImpactRestraint (class in torsion) impactSequential() (optimize.ResidueInfo method) ImpactSubSubSubCommands (class in optimize) implied_parameterization() (rsref.Tasks method) import_coord() (rsref.Tasks method) inactive (numpyExt.Flagged attribute) inAny() (atoms.Group method) (atoms.Selection method) inbounds() (density.ModelMap method) increment() (form_factor_table.FormFactorTable.Counter method) index (rotamer.Rotamer attribute) (superpose.PairItem attribute) indices_near_index() (density.ModelMap method) individual (optimize.Groupings attribute)

IndividualGp (class in optimize) info (optimize.History attribute) info() (superpose.Pairing method) init_non_pdb() (atoms.Atoms method) input (optimize.Documentation.Parameterize attribute) input() (map.ReadMap.Scale method) insert() (atoms.VecList method) (optimize.TorsionParameterization method) instances (cmd2nest.Cmd attribute) Instrumental parameters introduction (atoms.Documentation.Selection_Group attribute) is_alt() (atoms.Atoms method) is_amino_acid() (atoms.Selection method) is_close() (atoms.Atoms method) is_corresponding() (atoms.Atoms method) is_cterm() (atoms.Atoms method) is_met() (tskmgr.ReqObj method) is_number() (in module atoms) is_of_atoms() (atoms.Selection method) is_quoted_string() (in module atoms) is_triple_quoted_string() (in module atoms) isclose() (symmetry.Target method) isneighbor() (symmetry.Target method) iso_like() (atoms.Anisotropics method) (in module atoms) isorthogonal (crystallography.MapOrthogonal attribute) isotropic() (atoms.Anisotropics method) (in module atoms) isotropize() (atoms.Anisotropics method) isunit() (symmetry.Cartesian_operator method) (transform.AugmentedOperator method) iteritems() (numpyExt.Flagged method)

J

jar (space_group.SpaceGroups attribute) join() (atoms.Anisotropics method) (atoms.Atoms method)

join_all() (torsion.TAProtein method) join_atoms() (torsion.TAProtein method)

K

key (atoms.Selection attribute)

L

L1Norm (torsion.Limit attribute) label() (atoms.Atoms method) labels() (atoms.Atoms method) labels_close() (atoms.Atoms method) lattice_operators() (in module space_group) length() (atoms.Vec method) Limit (class in torsion)

link_torsion() (atoms.Atoms method) list() (documentation.Module method) load() (optimize.ResidueInfo method) local (symmetry.Documentation.Input attribute) local_view() (map.Map method) loquacious (superpose.Pairing attribute) low-pass filter, [1]

M

Magnification, [1] magnification (optimize.RSParameterization attribute) magnify() (density.ModelMap method) (map.ReadMap method) main() (in module calling_program) make() (in module documentation) Map (class in map) map (module) map2structure() (impact.ResidueInfoAdded method) MapOrthogonal (class in crystallography) masked_determinants() (in module atoms) masked_inverses() (in module atoms) masked_norm() (in module atoms)

matched_to (superpose.PairItem attribute) matmul() (in module atoms) matrix_bonded() (restraints.VDWRestraint static method) max_diff() (atoms.Atoms method) max_len (optimize.Grouping attribute) mean() (atoms.VecList method) (superpose.Accumulator method) mod360() (torsion.Limit static method) ModelMap (class in density) ModelMap.AtomMask (class in density) Module (class in documentation) movable (optimize.TorsionGp attribute) (optimize.TorsionParameterization attribute) multiply_matrix_array() (in module transform)

N

name (atoms.Selection attribute) (optimize.ResidueInfo attribute) name2type() (form_factor_table.FormFactorTable method) names() (atoms.Group static method) neighbors() (atoms.Atoms method) (optimize.ResidueInfo method) (symmetry.Symmetry method) neighbors_deprecated() (rsref.Tasks method) neighbors_prereq() (rsref.Tasks method) nested_help() (in module documentation) new() (crystallography.MapOrthogonal method)

new_comparison() (density.ModelMap method) non_zero() (in module transform) norm (atoms.Vec attribute) normalizeImpact (optimize.History attribute) norms (atoms.VecList attribute) nothing() (optimize.AtomicParameterization method) (optimize.Grouping method) (optimize.Groupings method) (optimize.OverallGp method) (optimize.TorsionGp method) number_selections() (in module atoms) numpyExt (module)

O

Objective (class in optimize) (class in superpose) objective (superpose.Pairing attribute) occupancy (optimize.AtomicParameterization attribute) OGrouping (class in optimize) onfailure() (cmd2nest.Cmd method) operators (atoms.Selection attribute) Optimization (class in optimize) optimize (module) Options (class in argparser) origin (crystallography.MapOrthogonal attribute) orthog (crystallography.MapOrthogonal attribute) (crystallography.OrthogonalizationMatrix attribute) OrthogonalizationMatrix (class in crystallography)

orthogonalize() (crystallography.MapOrthogonal method) orthogonalize_vec() (crystallography.MapOrthogonal method) orthoxyz (crystallography.MapOrthogonal attribute) output() (map.ReadMap.Scale method) overall B overall (optimize.Groupings attribute) (optimize.ResidueInfo attribute) Overall_B OverallGp (class in optimize) overlay() (superpose.Pairing method) (superpose.Tasks method) overlay_prereq() (superpose.Tasks method) own() (optimize.Groupings method)

P

pack_like() (optimize.Parameters method) pair() (superpose.Tasks method) pair_init() (superpose.Tasks method) pair_init_prereq() (superpose.Tasks method) pair_prereq() (superpose.Tasks method) Pairing (class in superpose) PairItem (class in superpose) PairSubCommands (class in superpose) param (optimize.History attribute) (optimize.Parameters attribute) (superpose.Parameters attribute) param_type (optimize.ParameterizeSubCommands attribute) parameter image_refine parameterization_init() (rsref.Tasks method) (superpose.Tasks method) parameterization_init_prereq() (rsref.Tasks method) (superpose.Tasks method) parameterize() (rsref.Tasks method) (superpose.Tasks method) parameterize_prereq() (rsref.Tasks method) (superpose.Tasks method) ParameterizeSubCommands (class in optimize) Parameters (class in optimize) (class in superpose) parameters (superpose.Pairing attribute) parent (cmd2nest.Cmd attribute) parse() (in module filter_summarize) (optimize.GroupGp method) (optimize.Grouping method) (optimize.OverallGp method) (optimize.TorsionGp method) parse_args() (argparser.ArgumentParser method) parse_selection() (optimize.TorsionParameterization method) parseargs() (cmd_extensions.Extensions static method) parseLog() (in module impact) parseopt() (cmd_extensions.Extensions static method) parseopts() (cmd_extensions.Extensions static method) partial_stats (density.ModelMap attribute) partials (optimize.Parameters attribute) (superpose.Parameters attribute) partials() (density.ModelMap method) pdb_coord_records (atoms.Atoms attribute) permute() (atoms.VecList method)

perturb() (rsref.Tasks method) perturb_prereq() (rsref.Tasks method) phi_psi_selection() (torsion.TAProtein method) phipsi_copy() (superpose.Tasks method) phipsi_copy_prereq() (superpose.Tasks method) phipsi_diff() (superpose.Tasks method) phipsi_diff_prereq() (superpose.Tasks method) pickle() (optimize.ResidueInfo method) (space_group.SpaceGroups method) pickles (optimize.ResidueInfo attribute) plot() (optimize.ResidueInfo method) plotImpactHistogram() (in module impact) position (optimize.AtomicParameterization attribute) postloop() (cmd2nest.Cmd method) (optimize.ParameterizeSubCommands method) power (restraints.VDWRestraint attribute) precmd() (cmd_extensions.Extensions method) prefix_set (atoms.Selection attribute) preloop() (cmd2nest.Cmd method) (cmd_extensions.Extensions method) (optimize.ParameterizeSubCommands method) Prerequisite (class in tskmgr) previous() (atoms.Selection method) print_all (optimize.ResidueInfo attribute) print_bonds() (torsion.TAProtein method) print_connectivity() (torsion.TAProtein method) printImpactHistogram() (in module impact) profile() (density.AtomicDensity method) (rsref.Tasks method) ProgCmd (class in cmd2nest) progress (optimize.Objective attribute) (superpose.Objective attribute) ProgSubCmd (class in cmd2nest) ProgTopCmd (class in cmd2nest) proj() (atoms.Vec method) protectedSplit() (cmd_extensions.Extensions static method) (in module argparser) public() (in module tskmgr)

Q

qsort (module) qsort() (in module qsort) qsort_without_duplicates() (in module qsort) quartet() (torsion.TAProtein method)

queryCallBack() (optimize.CallBackEmulator method) quiet (tskmgr.Prerequisite attribute) quoted() (cmd_extensions.Extensions static method) (in module argparser) quoteString() (in module atoms)

R

radius (restraints.VDWRestraint attribute) random_rotation_about_origin() (in module transform) randomize() (atoms.Atoms method) (rsref.Tasks method) randomize_prereq() (rsref.Tasks method) rankImpact() (optimize.ResidueInfo method) read() (optimize.ResidueInfo method) read_coords() (atoms.Tasks method) (superpose.Tasks method) (symexp.Tasks method) read_coords_prereq() (atoms.Tasks method) (symexp.Tasks method) read_target() (superpose.Tasks method) read_target_prereq() (superpose.Tasks method) ReadMap (class in map) ReadMap.Scale (class in map) recognized() (form_factor_table.FormFactorTable method) reconcile_types() (rsref.Tasks method) reconcile_types_prereq() (rsref.Tasks method) refine() (optimize.Optimization method) (rsref.Tasks method) (superpose.Tasks method) refine_magnification() (density.ModelMap method) (rsref.Tasks method) refine_magnification_no_atomic_partials() (density.ModelMap method) refine_prereq() (rsref.Tasks method) (superpose.Tasks method) remaining() (argparser.ArgumentParser static method) removeDirectedEdge() (torsion.Graph method) removeEdge() (torsion.Graph method) reordered (superpose.PairItem attribute) reordered() (atoms.VecList method) reordered_paired (superpose.PairItem attribute) repr_op() (symmetry.Symmetry method) ReqExpr (class in tskmgr) ReqObj (class in tskmgr) residual (optimize.History attribute) (rsref.Tasks attribute) residual_db (rsref.Tasks attribute) residual_do (rsref.Tasks attribute) residual_dx (rsref.Tasks attribute)

residual_dxyz (rsref.Tasks attribute) residual_dy (rsref.Tasks attribute) residual_dz (rsref.Tasks attribute) residue (optimize.ResidueInfo attribute) residue() (atoms.Atoms method) residueEntry (optimize.ResidueInfo attribute) residueID() (atoms.Atoms method) ResidueInfo (class in impact) (class in optimize) ResidueInfoAdded (class in impact) residueTable (superpose.Pairing attribute) Resolution, [1], [2] resolution (optimize.RSParameterization attribute) resolutions() (in module crystallography) restore() (superpose.Tasks method) restore_prereq() (superpose.Tasks method) restrain_to_reference (rsref.Tasks attribute) (superpose.Tasks attribute) restraints (module) restraints() (rsref.Tasks method) restraints_prereq() (rsref.Tasks method) rfactor() (density.ModelMap method) rms() (density.ModelMap method) (restraints.Brestraint method) Rotamer (class in rotamer) rotamer (module) rotate() (atoms.Anisotropics method) (rotamer.Rotamer method) rotTrans() (transform.AugmentedOperator method) rseval (module) rseval() (in module rseval) RSParameterization (class in optimize) RSRef (in module rsref) rsref (module) run_test() (rsref.Tasks method) (superpose.Tasks method)

S

safe_eval() (in module symmetry) same() (atoms.Atoms method) same_conformer() (atoms.Atoms method) save() (optimize.ResidueInfo method) save_selection() (torsion.TAProtein method) saved (optimize.ResidueInfo attribute) saved_selection() (torsion.TAProtein method) saveGradients() (optimize.History method) saveParameters() (optimize.History method) saveResidual() (optimize.History method) scale() (atoms.Anisotropics method) (in module density) scale_individual() (atoms.Anisotropics method) scale_model_to_observed (density.ModelMap attribute) scale_rotation (optimize.Parameters attribute) scale_uniform() (atoms.Anisotropics method) scc() (torsion.Graph method) select() (atoms.Atoms method) (atoms.Selection method) (atoms.Tasks method) select_attr() (atoms.Tasks method) select_attr_prereq() (atoms.Tasks method) select_dihedrals() (optimize.Tasks method) select_prereq() (atoms.Tasks method) Selection (class in atoms) selection() (atoms.Anisotropics method) selectionPair() (optimize.AtomicRefinement static method) selections (optimize.GroupGp attribute) (optimize.Grouping attribute) (optimize.TorsionGp attribute) selections() (atoms.Group static method) separate_all() (torsion.TAProtein method) separate_atoms() (torsion.TAProtein method) set_options() (superpose.Test method) set_unused_values() (numpyExt.Flagged method) set_used_values() (numpyExt.Flagged method) sharpen shuffle() (atoms.Anisotropics method) skip (numpyExt.Flagged attribute) skipped (numpyExt.Flagged attribute)

sort() (atoms.Atoms method) (atoms.VecList method) sorted_correlation() (density.ModelMap method) sorted_keys() (optimize.AtomicParameterization method) space_group (module) SpaceGroups (class in space_group) spacing (crystallography.MapOrthogonal attribute) speed sphericalPolarAngles() (transform.AugmentedOperator method) sq_diff() (density.ModelMap method) ss() (in module restraints) startup() (in module documentation) (in module filter_summarize) (in module impact) (in module rsref) (in module superpose) (in module symexp) stats() (torsion.Limit method) status() (restraints.VDWRestraint method) std() (superpose.Accumulator method) std_err_mu() (in module superpose) step_detail (optimize.Objective attribute) (superpose.Objective attribute) SubCmd (class in cmd2nest) subset() (atoms.Anisotropics method) (atoms.Atoms method) suij() (atoms.Anisotropics method) sum() (atoms.VecList method) sumproduct() (atoms.VecList method) sumsq() (atoms.VecList method) Superimposition (class in optimize) superpose (module) superpose() (superpose.Pairing method) supported_modes (optimize.Parameters attribute) (superpose.Parameters attribute) symexp (module) Symmetry (class in symmetry) symmetry (module) symmetry_current (rsref.Tasks attribute) symmetry_expand() (rsref.Tasks method) (symexp.Tasks method) symmetry_expand_prereq() (rsref.Tasks method) (symexp.Tasks method) symmetry_init() (rsref.Tasks method) (symexp.Tasks method) symmetry_init_prereq() (rsref.Tasks method) (symexp.Tasks method) synonyms (atoms.Selection attribute)

T

t1_Welch_gt() (in module superpose) t1_Welch_lt() (in module superpose) TAProtein (class in torsion) Target (class in symmetry) Task (class in tskmgr) TaskError Tasks (class in atoms) (class in impact) (class in optimize) (class in rsref) (class in superpose) (class in symexp) Test (class in superpose) test() (atoms.Selection method) TestControl (class in cmd2nest) testFlagged() (in module numpyExt) testFunction() (in module transform) text_at() (in module impact) three_d_transform_weights() (density.AtomicDensity method) threshold_correlation() (density.ModelMap method) to_file() (map.ReadMap method) to_xplor() (map.ReadMap method)

togrid() (density.ModelMap method) token() (cmd_extensions.Extensions static method) (in module argparser) tolerance (density.ModelMap attribute) TopCmd (class in cmd2nest) TopCommands (class in impact) (class in rsref) (class in superpose) (class in symexp) torsion (module) (optimize.Groupings attribute) torsion_change() (optimize.Parameters method) TorsionGp (class in optimize) TorsionParameterization (class in optimize) trackImpact() (optimize.History method) transform (module) translate() (in module documentation) trial() (in module transform) triangular() (atoms.Anisotropics method) (in module atoms) tskmgr (module) type_number() (form_factor_table.FormFactorTable method)

U

u (atoms.Selection attribute) udot() (atoms.Vec method) undocumented (cmd2nest.Cmd attribute) unexpected() (in module tskmgr) unique_set (atoms.Selection attribute) unit (atoms.Vec attribute) Unit (class in optimize) unlink_torsion() (atoms.Atoms method)

UnMetPrerequisite unpackage() (in module documentation) unquote() (in module cmd2nest) update() (optimize.Groupings method) (optimize.History method) (restraints.VDWRestraint method) update_coords() (atoms.Tasks method) update_pdb() (atoms.Atoms method) use (numpyExt.Flagged attribute) used (numpyExt.Flagged attribute)

V

v2 (atoms.Selection attribute) value (atoms.Selection attribute) (numpyExt.Flagged attribute) (optimize.Grouping attribute) (optimize.Parameters attribute) (superpose.Parameters attribute) variable (optimize.TorsionParameterization attribute) VDWRestraint (class in restraints) VDWRestraint.Status (class in restraints) vec (atoms.Vec attribute) Vec (class in atoms)

VecList (class in atoms) Vector (class in transform) verbose (rsref.Tasks attribute) (superpose.Tasks attribute) (symmetry.Symmetry attribute) (tskmgr.Prerequisite attribute) (tskmgr.ReqObj attribute) (tskmgr.Task attribute) version_ID (torsion.Graph attribute) volume (crystallography.MapOrthogonal attribute) (crystallography.OrthogonalizationMatrix attribute) vs_old_apply (torsion.TAProtein attribute)

W

warn() (in module torsion) warning (atoms.Atoms.ChainName attribute) warnings (torsion.TAProtein attribute) warnings_issued (density.ModelMap attribute) weightFactor (restraints.VDWRestraint attribute) Weiner filter whenCall (optimize.CallBackEmulator attribute) where() (in module atoms) which() (optimize.ParameterizeSubCommands method) (space_group.SpaceGroups method) whichAttr() (atoms.Selection method) width (optimize.AtomicParameterization attribute)

with_neighbors() (symmetry.Symmetry method) wrapUp() (optimize.History method) write() (atoms.Atoms method) write_calculated() (density.ModelMap method) write_comparison() (density.ModelMap method) write_coords() (atoms.Tasks method) (symexp.Tasks method) write_coords_prereq() (atoms.Tasks method) (symexp.Tasks method) write_difference() (density.ModelMap method) write_map() (rsref.Tasks method) write_map_prereq() (rsref.Tasks method)

X

x (atoms.Selection attribute) xyz (atoms.Atoms attribute)

XYZGrouping (class in optimize)

Z

Z (rotamer.Rotamer attribute) z_d() (in module superpose)

zero() (in module optimize) (in module transform) zeros_like() (map.Map method)