Index

A

aa2ace (symmetry.Symmetry.Cap attribute) aa2nme (symmetry.Symmetry.Cap attribute) Accumulator (class in superpose) add() (restraints.Distances method) (superpose.Accumulator method) (superpose.Pairing method) add_class() (restraints.ClassHolder method) add_torsion_restraint() (optimize.Objective method) (superpose.Objective method) addDirectedEdge() (torsion.Graph method) addEdge() (torsion.Graph method) addVertex() (torsion.Graph method) Ala (class in restraints) all_atoms (rotamer.Rotamer attribute) all_dependents (torsion.TAProtein property) allow_no_file (map.ReadMap attribute) alphabetical (translate.Dictionary attribute) AminoAcid (class in restraints) analyze() (optimize.Optimization method) (optimize.Parameters method) (optimize.Tasks method) (rsref.Tasks method) analyze_parser (optimize.Commands attribute) analyze_prereq() (optimize.Tasks method) (rsref.Tasks method) AnalyzeSubCommands (class in optimize) ancestory() (cmd2nest.Cmd method) Anchor (class in restraints) angle (restraints.CovalentRestraint attribute) angle() (restraints.Geometry method) angle_sigma (restraints.CovalentRestraint attribute) angleDeviants() (restraints.CovalentRestraint method) angleEntry (optimize.ResidueInfo attribute) angleGrad() (restraints.CovalentRestraint method) angleGrad_dc() (restraints.CovalentRestraint method) angleResidual() (restraints.CovalentRestraint method) angleStats() (restraints.CovalentRestraint method) ap1 (restraints.Commands attribute) ap2 (restraints.RestraintsSubCommands attribute) apidoc() (in module documentation) append() (optimize.Grouping method) (optimize.TorsionParameterization method) apply_torsion() (torsion.TAProtein method) apply_torsion_deprecated() (torsion.TAProtein method) Arg (class in restraints) argparser module

argument() (optimize.CallBackEmulator method) ArgumentParser (class in argparser) Arguments (class in argparser) (class in density) (class in documentation) (class in energy) (class in impact) (class in map) (class in optimize) (class in restraints) (class in rsref) (class in superpose) (class in symmetry) (class in translate) ArgumentsSubClass (class in argparser) ArrayBoundsError arrow_range() (in module impact) as_count (optimize.Grouping attribute) asdict() (argparser.CommonOptions method) (argparser.Namespace method) Asn (class in restraints) Asp (class in restraints) assertOneD() (in module vector) assertSameSize() (in module vector) 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 property) AtomicDensity (class in density) AtomicParameterization (class in optimize) AtomicRefinement (class in optimize) atoms_being_evaluated (rsref.Tasks property) (superpose.Tasks property) atoms_refined (rsref.Tasks property) (superpose.Tasks property) Attenuation, [1] attenuation Gaussian attributeOrder (superpose.Pairing attribute) augment() (transform.AugmentedOperator method) AugmentedOperator (class in transform)

B

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

bfactors_parser (superpose.TopCommands attribute) bfactors_prereq() (superpose.Tasks method) BGrouping (class in optimize) bond() (restraints.Geometry method) bond_dependents (torsion.TAProtein property) bonds (stereochemistry.CovalentRadii attribute) boolabbrev() (optimize.Grouping method) boolabbrev_old() (optimize.Grouping 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) (restraints.Distances 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) change() (torsion.Limit method) changeArray() (optimize.ResidueInfo method) changed() (density.ModelMap method) (optimize.Groupings method) (optimize.TorsionParameterization method) changing (optimize.AtomicParameterization property) (optimize.Grouping property) (optimize.Groupings property) (optimize.TorsionGp property) (optimize.TorsionParameterization property) check() (optimize.TorsionParameterization method) (restraints.Anchor method) check_support() (optimize.Parameters method) check_supported() (optimize.Parameters static method) check_type() (optimize.Grouping method) checkfiles() (in module documentation) checkRadii() (stereochemistry.CovalentRadii method) chi() (rotamer.Rotamer method) childless() (restraints.Distance_id method) children (cmd2nest.Cmd attribute) ClassHolder (class in restraints) clear_parser (optimize.ParameterizeSubCommands attribute) Cmd (class in cmd2nest) cmd2nest module cmd_extensions module cmp_grp module color() (impact.ControlAdded method) (optimize.ResidueInfo method) color_parser (optimize.ImpactSubSubSubCommands attribute) combine() (optimize.ResidueInfo method) combined (optimize.ResidueInfo attribute)

combined_bond_ids() (optimize.ResidueInfo method) Commands (class in impact) (class in optimize) (class in restraints) CommandsAdded (class in impact) CommonOptions (class in argparser) compare() (cmp_grp.GroupTransforms method) (map.ReadMap method) (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) connect (optimize.TorsionParameterization property) connected (optimize.TorsionParameterization property) connectivity (optimize.TorsionParameterization attribute) (superpose.Pairing property) connectivityExclusion (restraints.VDWRestraint attribute) continuable (superpose.Pairing attribute) Contrast Transfer Function CTF, [1] ControlAdded (class in impact) convention (translate.Dictionary attribute) convergence() (optimize.Tasks method) convergence_parser (optimize.AnalyzeSubCommands attribute) 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) CovalentRadii (class in stereochemistry) CovalentRestraint (class in restraints) crossDeriv() (in module vector) crossNorm() (in module vector) crossNormDeriv() (in module vector) crossUnit() (in module vector) crossUnitDeriv() (in module vector) Crystallography crystallography module CTF Contrast Transfer Function, [1] curated() (stereochemistry.CovalentRadii method) cyclesB4debugStop (optimize.Objective attribute) Cys (class in restraints)

D

d (translate.Dictionary attribute) 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 property) (superpose.Tasks property) 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) deviation() (restraints.Distance_id method) (restraints.Distance_selection method) deviation1() (restraints.Distance_selection method) deviation_str() (restraints.Distance_id method) deviation_sym() (restraints.Distance_selection method) 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) dialect() (translate.Dictionary method) Dictionary (class in translate) diff() (cmp_grp.GroupTransform method) difference() (superpose.Pairing method) differences() (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 property) (optimize.TorsionParameterization property) DihedralsSubSubCommands (class in optimize) directory_setup() (in module documentation) displacements() (in module transform) dissect() (in module superpose) distance (restraints.VDWRestraint attribute) distance() (restraints.Distance_id method) distance_arg_parse() (in module restraints) Distance_id (class in restraints) Distance_input (class in restraints) Distance_selection (class in restraints) Distances (class in restraints) distances() (density.AtomicDensity method) (density.ModelMap method) (density.ModelMap.AtomMask method) distances_assume_orthonormal() (density.ModelMap method) dmagnification() (density.ModelMap 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_distance() (restraints.RestraintsSubCommands method) do_done() (cmd2nest.SubCmd method)

do_echo() (cmd_extensions.Extensions method) do_evaluate() (rsref.TopCommands method) (superpose.TopCommands method) do_exit() (cmd2nest.TopCmd 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_information() (restraints.RestraintsSubCommands 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() (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() (restraints.Commands method) do_rotamer() (rsref.TopCommands method) do_SELECTION() (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 property) doc (restraints.Distances attribute) documentation module Documentation (class in cmd2nest) (class in optimize) (class in symmetry) Documentation.Input (class in symmetry) Documentation.Parameterize (class in optimize) domestic() (argparser.Arguments method) (argparser.ArgumentsSubClass method) (density.Arguments method) (documentation.Arguments method) (energy.Arguments method) (impact.Arguments method) (map.Arguments method) (optimize.Arguments method) (restraints.Arguments method) (rsref.Arguments method) (superpose.Arguments method) (symmetry.Arguments method) (translate.Arguments method) dot() (in module transform) dotDeriv() (in module vector) dotfile() (argparser.ArgumentParser method) dpbydv() (transform.AugmentedOperator method) (transform.EulerX0Y0Z0 method)

E

edit_links() (torsion.TAProtein method) efficiency_check (optimize.TorsionParameterization attribute) efficiency_level (optimize.TorsionParameterization attribute) Electron Microscopy element (stereochemistry.CovalentRadii attribute) EMBfactor empty() (optimize.ResidueInfo method) emptyID() (optimize.ResidueInfo method) emptyLikeAtom() (optimize.ResidueInfo method) emptyline() (cmd_extensions.Extensions method) end_atoms (restraints.Anchor attribute) energy module Energy (class in energy) energy (energy.Energy property) EnergyRestraint (class in energy) entry (restraints.Distances attribute) 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_parser (rsref.TopCommands attribute) (superpose.TopCommands attribute) evaluate_prereq() (rsref.Tasks method) (superpose.Tasks method) expand() (optimize.GroupGp method) explain() (documentation.Module method) export() (argparser.Arguments method) (argparser.ArgumentsSubClass method) (density.Arguments method) (density.OldArguments static method) (documentation.Arguments method) (energy.Arguments method) (impact.Arguments method) (impact.OldArguments static method) (map.Arguments method) (optimize.Arguments method) (restraints.Arguments method) (rsref.Arguments method) (rsref.OldArguments static method) (superpose.Arguments method) (symmetry.Arguments method) (translate.Arguments method) extend() (optimize.TorsionParameterization method) ExtendedParameterization (class in optimize) extendIndex() (rotamer.Rotamer method) Extensions (class in cmd_extensions) extract() (in module documentation) (optimize.Parameters method)

F

f() (energy.Energy method) (energy.EnergyRestraint method) (optimize.Objective method) (restraints.Brestraint method) (restraints.CovalentRestraint method) (restraints.VDWRestraint method) (superpose.Objective method) f_grad() (energy.EnergyRestraint method) (restraints.CovalentRestraint method) (restraints.VDWRestraint method) family() (restraints.Distance_id method) filter low-pass, [1] Weiner filter_resolution (density.AtomicDensity property) filter_summarize module finalize() (argparser.ArgumentParser method) (impact.Arguments method) (impact.OldArguments method) (rsref.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) fitBondTypes() (stereochemistry.CovalentRadii method) fix_dihedrals() (optimize.Tasks method)

fixed (energy.Energy property) fL1Norm() (torsion.Limit method) fL1sq() (torsion.Limit method) Flagged (class in numpyExt) flatten() (optimize.ResidueInfo method) flip() (in module rotamer) (superpose.Tasks method) flip_parser (superpose.TopCommands attribute) flip_prereq() (superpose.Tasks method) forcefields (energy.Energy attribute) forces (energy.Energy property) form_factor_table module FormFactorTable (class in form_factor_table) FormFactorTable.Counter (class in form_factor_table) fprime() (energy.Energy method) (optimize.Objective method) (superpose.Objective method) from_bsoft() (map.ReadMap method) from_ccpem() (map.ReadMap method) from_file() (map.ReadMap method) from_pair() (superpose.PairItem 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 property) general_transformation_matrix() (in module transform) generate_rotation_masks() (torsion.TAProtein method) generate_structure() (torsion.TAProtein method) Geometry (class in restraints) 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() (energy.EnergyRestraint method) (restraints.CovalentRestraint method) (restraints.VDWRestraint method) get_namespace() (in module tskmgr) get_namespaces() (in module tskmgr) get_neighbors() (energy.EnergyRestraint method) (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) getSpacing() (crystallography.MapOrthogonal method) getVolume() (crystallography.MapOrthogonal method) (crystallography.OrthogonalizationMatrix method) (density.ModelMap method) Gln (class in restraints) Glu (class in restraints) Gly (class in restraints) Graph (class in torsion) group (optimize.Groupings property) group_parser (optimize.ParameterizeSubCommands attribute) GroupGp (class in optimize) Grouping (class in optimize) grouping (optimize.Parameters attribute) (superpose.Parameters attribute) Groupings (class in optimize) groupPartials() (in module transform) GroupTransform (class in cmp_grp) groupTransformations() (in module transform) GroupTransforms (class in cmp_grp)

H

halfLength() (stereochemistry.CovalentRadii method) help() (documentation.Module method) (in module documentation) 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_parser (cmd2nest.Cmd attribute) help_plot() (impact.CommandsAdded method)

help_SELECTION() (optimize.ParameterizeSubCommands method) help_SELECTION_EXPR() (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) hinges_parser (optimize.DihedralsSubSubCommands attribute) His (class in restraints) histogram() (impact.ControlAdded method) History (class in optimize)

I

Ile (class in restraints) image_refine parameter image_refine() (density.ModelMap method) (rsref.Tasks method) image_refine_group (rsref.TopCommands attribute) image_refine_parser (rsref.TopCommands attribute) image_refine_prereq() (rsref.Tasks method) impact module impact (optimize.History property) impact() (impact.Tasks method) (optimize.Tasks method) impact_paint() (optimize.Tasks method) impact_paint_prereq() (optimize.Tasks method) impact_parser (optimize.DihedralsSubSubCommands attribute) 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) inbounds() (density.ModelMap method) increment() (form_factor_table.FormFactorTable.Counter method) index (rotamer.Rotamer attribute) (superpose.PairItem property) indices_near_index() (density.ModelMap method) individual (optimize.Groupings property) individual_parser (optimize.ParameterizeSubCommands attribute) IndividualGp (class in optimize) info (optimize.History attribute) info() (superpose.Pairing method) input (optimize.Documentation.Parameterize property) input() (map.ReadMap.Scale method) insert() (optimize.TorsionParameterization method) instances (cmd2nest.Cmd attribute) Instrumental parameters inverse() (symmetry.Symmetry method) is_met() (tskmgr.ReqObj method) isclose() (symmetry.Target method) isneighbor() (symmetry.Target method) isorthogonal (crystallography.MapOrthogonal property) isunit() (symmetry.Cartesian_operator method) (transform.AugmentedOperator method) iteritems() (numpyExt.Flagged method)

J

jar (space_group.SpaceGroups attribute)

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

L

L1Norm (torsion.Limit attribute) lang (translate.Dictionary attribute) lattice_operators() (in module space_group) length (restraints.CovalentRestraint attribute) length_sigma (restraints.CovalentRestraint attribute) lengthDeviants() (restraints.CovalentRestraint method) lengthGrad() (restraints.CovalentRestraint method) lengthResidual() (restraints.CovalentRestraint method) lengthStats() (restraints.CovalentRestraint method) Leu (class in restraints)

Limit (class in torsion) linkOverlapWarningMsg (optimize.TorsionGp attribute) linkOverlapWarnings (optimize.TorsionGp attribute) list() (documentation.Module method) load() (optimize.ResidueInfo method) local (symmetry.Documentation.Input property) local_view() (map.Map method) loquacious (superpose.Pairing attribute) low-pass filter, [1] Lys (class in restraints)

M

Magnification, [1] magnification (optimize.RSParameterization property) magnify() (density.ModelMap method) (map.ReadMap method) main() (in module calling_program) (in module documentation) (in module energy) (in module filter_summarize) (in module rsref) (in module superpose) (in module symexp) make() (in module documentation) map module Map (class in map) map2structure() (impact.ResidueInfoAdded method) map_parser (rsref.TopCommands attribute) MapOrthogonal (class in crystallography) match_parser (superpose.PairSubCommands attribute) matched_to (superpose.PairItem attribute) matrix_bonded() (restraints.VDWRestraint static method) max_items (optimize.GroupGp attribute) max_len (optimize.Grouping attribute) mean() (superpose.Accumulator method) Met (class in restraints) mod360() (torsion.Limit static method) model_stats() (energy.Energy method) (in module energy) ModelMap (class in density) ModelMap.AtomMask (class in density) module argparser calling_program cmd2nest cmd_extensions cmp_grp crystallography density documentation energy filter_summarize form_factor_table impact map numpyExt optimize qsort restraints rotamer rotamer_chi_lib rseval rsref sidechain space_group stereochemistry superpose symexp symmetry torsion transform translate tskmgr vector version

Module (class in documentation) most_probable_rotamer() (rotamer_chi_lib.Rotamer_library method) movable (optimize.TorsionGp property) (optimize.TorsionParameterization property) multiply_matrix_array() (in module transform) mutate() (symmetry.Symmetry.Cap method) mx (cmp_grp.GroupTransforms attribute)

N

name (optimize.ResidueInfo attribute) name2type() (form_factor_table.FormFactorTable method) Namespace (class in argparser) neighbors() (optimize.ResidueInfo method) (symmetry.Symmetry method) neighbors_deprecated() (rsref.Tasks method) neighbors_parser (rsref.TopCommands attribute) (symexp.TopCommands attribute) neighbors_prereq() (rsref.Tasks method) new() (crystallography.MapOrthogonal method) new_comparison() (density.ModelMap method)

non_zero() (in module transform) normalizeImpact (optimize.History attribute) normDeriv() (in module vector) nothing() (optimize.AtomicParameterization method) (optimize.Grouping method) (optimize.Groupings method) (optimize.OverallGp method) (optimize.TorsionGp method) number (stereochemistry.CovalentRadii attribute) numbers (energy.Energy property) numpyExt module

O

Objective (class in optimize) (class in superpose) objective (superpose.Pairing attribute) occupancy (optimize.AtomicParameterization property) OGrouping (class in optimize) old_cmdloop() (cmd2nest.Cmd method) old_do_load() (cmd2nest.Cmd method) old_with_neighbors() (symmetry.Symmetry method) OldArguments (class in density) (class in impact) (class in rsref) onfailure() (cmd2nest.Cmd method) open() (cmp_grp.GroupTransforms method) Optimization (class in optimize) optimize module optimizeProteinAmide() (stereochemistry.CovalentRadii method) optimizeProteinAromatic() (stereochemistry.CovalentRadii method) optimizeProteinBackbone() (stereochemistry.CovalentRadii method) optimizeProteinCarboxylate() (stereochemistry.CovalentRadii method) optimizeProteinGuanidinium() (stereochemistry.CovalentRadii method) optimizeProteinHis() (stereochemistry.CovalentRadii method) optimizeProteinHisAve() (stereochemistry.CovalentRadii method) optimizeProteinPhe() (stereochemistry.CovalentRadii method) optimizeProteinPheAve() (stereochemistry.CovalentRadii method)

optimizeProteinPheH() (stereochemistry.CovalentRadii method) optimizeProteinTrp() (stereochemistry.CovalentRadii method) optimizeProteinTrpAve() (stereochemistry.CovalentRadii method) optimizeProteinTyr() (stereochemistry.CovalentRadii method) optimizeProteinTyrAve() (stereochemistry.CovalentRadii method) Options (class in argparser) origin (crystallography.MapOrthogonal property) orthog (crystallography.MapOrthogonal property) (crystallography.OrthogonalizationMatrix property) OrthogonalizationMatrix (class in crystallography) orthogonalize() (crystallography.MapOrthogonal method) orthogonalize_vec() (crystallography.MapOrthogonal method) orthoxyz (crystallography.MapOrthogonal property) output() (map.ReadMap.Scale method) overall B overall (optimize.Groupings property) (optimize.ResidueInfo property) Overall_B overall_parser (optimize.ParameterizeSubCommands attribute) OverallGp (class in optimize) overlay() (superpose.Pairing method) (superpose.Tasks method) overlay_parser (superpose.TopCommands attribute) overlay_prereq() (superpose.Tasks method) own() (optimize.Groupings method)

P

pack_like() (optimize.Parameters method) paint_parser (optimize.DihedralsSubSubCommands attribute) pair() (superpose.Tasks method) pair_init() (superpose.Tasks method) pair_init_prereq() (superpose.Tasks method) pair_parser (superpose.TopCommands attribute) pair_prereq() (superpose.Tasks method) PairIDs (class in restraints) 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_parser (rsref.TopCommands attribute) (superpose.TopCommands attribute) 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) parrot_parser (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() (restraints.Distance_id method) partial_stats (density.ModelMap attribute) partials (optimize.Parameters attribute) (superpose.Parameters attribute)

partials() (density.ModelMap method) pdbout_parser (symexp.TopCommands attribute) perturb() (rsref.Tasks method) perturb_parser (rsref.TopCommands attribute) perturb_prereq() (rsref.Tasks method) Phe (class in restraints) phi_psi_selection() (torsion.TAProtein method) phipsi_copy() (superpose.Tasks method) phipsi_copy_parser (superpose.TopCommands attribute) phipsi_copy_prereq() (superpose.Tasks method) phipsi_diff() (superpose.Tasks method) phipsi_diff_parser (superpose.TopCommands attribute) phipsi_diff_prereq() (superpose.Tasks method) pickle() (optimize.ResidueInfo method) (space_group.SpaceGroups method) pickle_parser (optimize.ImpactSubSubSubCommands attribute) pickles (optimize.ResidueInfo attribute) plot() (optimize.ResidueInfo method) plot_parser (optimize.ImpactSubSubSubCommands attribute) plotImpactHistogram() (in module impact) position (optimize.AtomicParameterization property) postloop() (cmd2nest.Cmd method) power (restraints.VDWRestraint attribute) precmd() (cmd_extensions.Extensions method) preloop() (cmd2nest.Cmd method) (cmd_extensions.Extensions method) Prerequisite (class in tskmgr) print_all (optimize.ResidueInfo attribute) print_bonds() (torsion.TAProtein method) print_connectivity() (torsion.TAProtein method) print_group (optimize.ParameterizeSubCommands attribute) print_parser (optimize.ImpactSubSubSubCommands attribute) (optimize.ParameterizeSubCommands attribute) printImpactHistogram() (in module impact) Pro (class in restraints) profile() (density.AtomicDensity method) (rsref.Tasks method) profile_parser (rsref.TopCommands attribute) ProgCmd (class in cmd2nest) progress (optimize.Objective attribute) (superpose.Objective attribute) ProgSubCmd (class in cmd2nest) ProgTopCmd (class in cmd2nest) protectedSplit() (cmd_extensions.Extensions static method) (in module argparser) protein() (stereochemistry.CovalentRadii method) prune() (symmetry.Symmetry.Cap method) 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)

R

radius (restraints.VDWRestraint attribute) (stereochemistry.CovalentRadii attribute) random_rotation_about_origin() (in module transform) randomize() (energy.Energy method) (rsref.Tasks method) randomize_parser (rsref.TopCommands attribute) randomize_prereq() (rsref.Tasks method) rankImpact() (optimize.ResidueInfo method) read() (cmp_grp.GroupTransforms method) (optimize.ResidueInfo method) read_coords() (superpose.Tasks method) (symexp.Tasks method) read_coords_prereq() (symexp.Tasks method) read_target() (superpose.Tasks method) read_target_prereq() (superpose.Tasks method) readall() (cmp_grp.GroupTransforms method) ReadMap (class in map) ReadMap.Scale (class in map) rechain() (symmetry.Symmetry method) recognized() (form_factor_table.FormFactorTable method) reconcile_types() (rsref.Tasks method) reconcile_types_prereq() (rsref.Tasks method) refine() (energy.Energy method) (optimize.Optimization method) (rsref.Tasks method) (superpose.Tasks method) refine_convergence (rsref.TopCommands attribute) (superpose.TopCommands attribute) refine_magnification() (density.ModelMap method) (rsref.Tasks method) refine_magnification_no_atomic_partials() (density.ModelMap method) refine_parser (rsref.TopCommands attribute) (superpose.TopCommands attribute) refine_prereq() (rsref.Tasks method) (superpose.Tasks method) remaining() (argparser.ArgumentParser static method) removeDirectedEdge() (torsion.Graph method) removeEdge() (torsion.Graph method) reordered (superpose.PairItem property) reordered_paired (superpose.PairItem property) repr() (translate.Dictionary static method) repr_op() (symmetry.Symmetry method) ReqExpr (class in tskmgr) ReqObj (class in tskmgr) res (translate.Dictionary attribute) residual (optimize.History attribute) (rsref.Tasks property) residual() (restraints.Distance_id method) residual_db (rsref.Tasks property) residual_do (rsref.Tasks property) residual_dx (rsref.Tasks property) residual_dxyz (rsref.Tasks property) residual_dy (rsref.Tasks property)

residual_dz (rsref.Tasks property) residue (optimize.ResidueInfo attribute) residue_types() (rotamer_chi_lib.Rotamer_library method) residueEntry (optimize.ResidueInfo attribute) ResidueInfo (class in impact) (class in optimize) ResidueInfoAdded (class in impact) residueTable (superpose.Pairing attribute) Resolution, [1], [2] resolution (optimize.RSParameterization property) resolutions() (in module crystallography) restore() (cmd2nest.Statekeeper method) (superpose.Tasks method) restore_parser (superpose.TopCommands attribute) restore_prereq() (superpose.Tasks method) restrain_to_reference (rsref.Tasks attribute) (superpose.Tasks attribute) restraints module restraints() (restraints.Tasks method) restraints_distance() (restraints.Tasks method) restraints_distance_prereq() (restraints.Tasks method) restraints_information() (restraints.Tasks method) restraints_information_prereq() (restraints.Tasks method) restraints_prereq() (restraints.Tasks method) RestraintsSubCommands (class in restraints) rfactor() (density.ModelMap method) rms() (density.ModelMap method) (restraints.Brestraint method) rota_match() (sidechain.Side_chains method) rota_print() (sidechain.Side_chains method) rotamer module Rotamer (class in rotamer) rotamer() (rsref.Tasks method) rotamer_chi_lib module Rotamer_library (class in rotamer_chi_lib) rotamer_parser (rsref.TopCommands attribute) rotamer_prereq() (rsref.Tasks method) rotamers() (rotamer_chi_lib.Rotamer_library method) rotamers_dictionary() (rotamer_chi_lib.Rotamer_library method) rotamers_list() (rotamer_chi_lib.Rotamer_library method) rotate() (rotamer.Rotamer method) rotTrans() (transform.AugmentedOperator method) rseval module rseval() (in module rseval) RSParameterization (class in optimize) rsref module RSRef (in module rsref) run_test() (rsref.Tasks method) (superpose.Tasks method)

S

safe_eval() (in module symmetry) save() (cmd2nest.Statekeeper method) (optimize.ResidueInfo method) save_selection() (torsion.TAProtein method) saved (optimize.ResidueInfo property) saved_selection() (torsion.TAProtein method) saveGradients() (optimize.History method) saveParameters() (optimize.History method) saveResidual() (optimize.History method) scale() (in module density) scale_model_to_observed (density.ModelMap attribute) scale_rotation (optimize.Parameters property) scc() (torsion.Graph method) screw() (in module transform) select_dihedrals() (optimize.Tasks method) selectionPair() (optimize.AtomicRefinement static method) selections (optimize.GroupGp property) (optimize.Grouping property) (optimize.TorsionGp property) separate_all() (torsion.TAProtein method) separate_atoms() (torsion.TAProtein method) Ser (class in restraints) set_description (cmd2nest.Cmd attribute) set_options() (superpose.Test method) set_parser (cmd2nest.Cmd attribute) set_parser_parent (cmd2nest.Cmd attribute) set_unused_values() (numpyExt.Flagged method) set_used_values() (numpyExt.Flagged method) sharpen Side_chains (class in sidechain) sidechain module skip (numpyExt.Flagged property) skipped (numpyExt.Flagged property) sorted_correlation() (density.ModelMap method) sorted_keys() (optimize.AtomicParameterization method) space_group module SpaceGroups (class in space_group) spacing (crystallography.MapOrthogonal property) speed sphere_parser (symexp.TopCommands attribute)

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) (in module translate) Statekeeper (class in cmd2nest) stats() (restraints.Anchor method) (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) stereochemistry module str_diff() (cmp_grp.GroupTransform method) SubCmd (class in cmd2nest) Superimposition (class in optimize) superpose module superpose() (superpose.Pairing method) supported_modes (optimize.Parameters attribute) (superpose.Parameters attribute) symexp module symmetry module Symmetry (class in symmetry) Symmetry.Cap (class in symmetry) symmetry_current (rsref.Tasks property) 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)

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 impact) (class in optimize) (class in restraints) (class in rsref) (class in superpose) (class in symexp) termini() (in module energy) terms() (energy.Energy method) Test (class in superpose) test_parser (cmd2nest.Cmd attribute) (superpose.TopCommands attribute) TestControl (class in cmd2nest) testFlagged() (in module numpyExt) testFunction() (in module transform) testpartial() (energy.Energy method) text_at() (in module impact) Thr (class in restraints) three_d_transform_weights() (density.AtomicDensity method) threshold_correlation() (density.ModelMap method) to1 (translate.Dictionary attribute) to3 (translate.Dictionary attribute) 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 torsion (optimize.Groupings property) torsion_change() (optimize.Parameters method) torsion_parser (optimize.ParameterizeSubCommands attribute) TorsionGp (class in optimize) torsionGrad() (restraints.CovalentRestraint method) TorsionParameterization (class in optimize) trackImpact() (optimize.History method) transform module translate module translate() (in module documentation) (translate.Dictionary method) trial() (in module transform) Trp (class in restraints) tskmgr module type_number() (form_factor_table.FormFactorTable method) types (restraints.AminoAcid attribute) Tyr (class in restraints)

U

undocumented (cmd2nest.Cmd attribute) unexpected() (in module tskmgr) Unit (class in optimize) unknown() (translate.Dictionary method) UnMetPrerequisite unpackage() (in module documentation) unquote() (in module cmd2nest) update() (energy.EnergyRestraint method) (optimize.Groupings method) (optimize.History method) (restraints.CovalentRestraint method) (restraints.VDWRestraint method)

use (numpyExt.Flagged property) use_minimize (energy.Energy attribute) (optimize.Optimization attribute) use_mrcfile (map.ReadMap attribute) used (numpyExt.Flagged property)

V

Val (class in restraints) value (numpyExt.Flagged property) (optimize.Grouping property) (optimize.Parameters attribute) (superpose.Parameters attribute) variable (optimize.TorsionParameterization property) VDWRestraint (class in restraints) VDWRestraint.Status (class in restraints) vector module Vector (class in transform) vector() (restraints.Distance_id method)

verbose (rsref.Tasks attribute) (superpose.Tasks attribute) (symmetry.Symmetry attribute) (tskmgr.Prerequisite attribute) (tskmgr.ReqObj attribute) (tskmgr.Task attribute) version module version_ID (torsion.Graph attribute) volume (crystallography.MapOrthogonal property) (crystallography.OrthogonalizationMatrix property) vs_old_apply (torsion.TAProtein attribute)

W

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

with_neighbors() (symmetry.Symmetry method) within_parser (superpose.PairSubCommands attribute) wrapUp() (optimize.History method) write_calculated() (density.ModelMap method) write_comparison() (density.ModelMap method) write_coords() (symexp.Tasks method) write_coords_prereq() (symexp.Tasks method) write_difference() (density.ModelMap method) write_map() (rsref.Tasks method) write_map_prereq() (rsref.Tasks method) write_pdb() (energy.Energy method)

X

xyz (energy.Energy property)

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)