PaStO documentation

RSRef

fitting atomic structures into maps.

Embedded RSRef

adding CNS stereochemistry & simulated annealing.

Phi, Psi restraints

added to CNS.

Superpose

flexible structure alignment.

Symexp

Expansion of molecular (non-crystallographic) and/or crystal-lattice symmetry.

Usage: input, syntax

rsref.py [options] <input.pdb> (for example) will invoke the python3 interpreter from $PATH. Use python -u -m pasto.rsref [options] <input.pdb> to invoke a specific interpreter.

Environment Command parser

Model parameterization Atom selection

Atom naming Symmetry operators

Download & Installation

Instructions

Dependencies

Colophon

1.0.6 change log

Examples

Contents, Indices & Tables

Full contents

• Installation & Getting Started
  • Synoposis
  • Dependencies
    • CNS
    • mrcfile
    • Bsoft
    • Python & modules
  • RSRef Installation
    • Python environment
    • pip install
    • tar extraction
    • Validation:
    • Windows
  • Distribution - developers only
  • Environment
    • Unix:
    • Windows
  • Documentation
  • Getting started
    • Running from a pip installation
    • Running from source
    • Examples
  • Version History
  • Ongoing issues
    • SciPy bug in some Windows versions:
    • OpenMP Multi-Processing on unix platforms:
    • Crystallographic symmetry:
  • Colophon
  • Credits
• argparser module
  • ArgumentParser
    • ArgumentParser.dotfile()
    • ArgumentParser.finalize()
    • ArgumentParser.parse_args()
    • ArgumentParser.remaining()
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • ArgumentsSubClass
    • ArgumentsSubClass.domestic()
    • ArgumentsSubClass.export()
  • CommonOptions
    • CommonOptions.asdict()
  • Namespace
    • Namespace.asdict()
  • Options
  • protectedSplit()
  • quoted()
  • token()
• atoms module
  • Anisotropics
    • Anisotropics.alignment()
    • Anisotropics.analyze()
    • Anisotropics.axes()
    • Anisotropics.cciso()
    • Anisotropics.ccuij()
    • Anisotropics.check()
    • Anisotropics.divergence()
    • Anisotropics.iso_like()
    • Anisotropics.isotropic()
    • Anisotropics.isotropize()
    • Anisotropics.join()
    • Anisotropics.rotate()
    • Anisotropics.scale()
    • Anisotropics.scale_individual()
    • Anisotropics.scale_uniform()
    • Anisotropics.selection()
    • Anisotropics.shuffle()
    • Anisotropics.subset()
    • Anisotropics.suij()
    • Anisotropics.triangular()
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • Atoms
    • Atoms.ChainName
      • Atoms.ChainName.warning
    • Atoms.altloc_in_segid()
    • Atoms.angle()
    • Atoms.angle_cos()
    • Atoms.angle_cterm_dc()
    • Atoms.angle_dc()
    • Atoms.are_close()
    • Atoms.are_neighbors()
    • Atoms.bonded
    • Atoms.bounds()
    • Atoms.checks_off()
    • Atoms.checks_on()
    • Atoms.conformer
    • Atoms.connectivity()
    • Atoms.connectivityOld()
    • Atoms.covalentRadius
    • Atoms.diff()
    • Atoms.difference()
    • Atoms.difference_vector_sym()
    • Atoms.differences()
    • Atoms.distance()
    • Atoms.distance_sym()
    • Atoms.from_file()
    • Atoms.from_list()
    • Atoms.from_reader()
    • Atoms.init_non_pdb()
    • Atoms.is_alt()
    • Atoms.is_close()
    • Atoms.is_corresponding()
    • Atoms.is_cterm()
    • Atoms.join()
    • Atoms.label()
    • Atoms.labels()
    • Atoms.labels_close()
    • Atoms.link_torsion()
    • Atoms.max_diff()
    • Atoms.neighbors()
    • Atoms.next_residue()
    • Atoms.next_residue_atoms()
    • Atoms.pdb_coord_records
    • Atoms.randomize()
    • Atoms.residue()
    • Atoms.residueID()
    • Atoms.same()
    • Atoms.same_conformer()
    • Atoms.select()
    • Atoms.sort()
    • Atoms.subset()
    • Atoms.unlink_torsion()
    • Atoms.update_pdb()
    • Atoms.write()
    • Atoms.xyz
  • Collection
  • Commands
    • Commands.ap1
    • Commands.ap2
    • Commands.do_pdbout()
    • Commands.do_select()
    • Commands.help_SELECTION_EXPR()
  • Documentation
    • Documentation.Selection_Group
      • Documentation.Selection_Group.introduction
  • Group
    • Group.check()
    • Group.checks
    • Group.count()
    • Group.duplicates()
    • Group.empty()
    • Group.expand()
    • Group.expand_items()
    • Group.from_criteria()
    • Group.from_selections()
    • Group.inAny()
    • Group.labels()
    • Group.names()
    • Group.nonRedundant()
    • Group.selections()
    • Group.stats()
  • OldArguments
    • OldArguments.export()
  • Selection
    • Selection.asSelection()
    • Selection.attribute()
    • Selection.boundary()
    • Selection.boundary_links()
    • Selection.center()
    • Selection.copy()
    • Selection.empty()
    • Selection.expand()
    • Selection.expand_items()
    • Selection.following()
    • Selection.fop2py
    • Selection.fortran()
    • Selection.get()
    • Selection.inAny()
    • Selection.is_amino_acid()
    • Selection.is_of_atoms()
    • Selection.key
    • Selection.labels()
    • Selection.name
    • Selection.next_residue_atoms()
    • Selection.operators
    • Selection.prefix_set
    • Selection.previous()
    • Selection.select()
    • Selection.split()
    • Selection.synonyms
    • Selection.test()
    • Selection.u
    • Selection.unique_set
    • Selection.v2
    • Selection.value
    • Selection.whichAttr()
    • Selection.x
  • Tasks
    • Tasks.getselect()
    • Tasks.read_coords()
    • Tasks.read_coords_prereq()
    • Tasks.select()
    • Tasks.select_attr()
    • Tasks.select_attr_prereq()
    • Tasks.select_prereq()
    • Tasks.update_coords()
    • Tasks.write_coords()
    • Tasks.write_coords_prereq()
  • Vec
    • Vec.comp()
    • Vec.dot()
    • Vec.length()
    • Vec.norm
    • Vec.proj()
    • Vec.udot()
    • Vec.unit
    • Vec.vec
  • VecList
    • VecList.align()
    • VecList.align_to_vec()
    • VecList.align_unique()
    • VecList.align_vecs()
    • VecList.append()
    • VecList.extend()
    • VecList.extend_svd()
    • VecList.insert()
    • VecList.mean()
    • VecList.norms
    • VecList.permute()
    • VecList.reordered()
    • VecList.sort()
    • VecList.sum()
    • VecList.sumproduct()
    • VecList.sumsq()
  • dummy_chain
  • is_number()
  • is_quoted_string()
  • is_triple_quoted_string()
  • iso_like()
  • isotropic()
  • masked_determinants()
  • masked_inverses()
  • masked_norm()
  • matmul()
  • number_selections()
  • quoteString()
  • startup()
  • triangular()
  • where()
• calling_program module
  • main()
• cmd2nest module
  • Cmd
    • Cmd.ancestory()
    • Cmd.base_keywords
    • Cmd.children
    • Cmd.do_help()
    • Cmd.do_parrot()
    • Cmd.do_set()
    • Cmd.do_test()
    • Cmd.help_parser
    • Cmd.instances
    • Cmd.old_cmdloop()
    • Cmd.old_do_load()
    • Cmd.onfailure()
    • Cmd.parent
    • Cmd.parrot_parser
    • Cmd.postloop()
    • Cmd.preloop()
    • Cmd.set_description
    • Cmd.set_parser
    • Cmd.set_parser_parent
    • Cmd.test_parser
    • Cmd.undocumented
  • Documentation
    • Documentation.general
  • ProgCmd
  • ProgSubCmd
    • ProgSubCmd.do_callee()
    • ProgSubCmd.help_callee()
  • ProgTopCmd
    • ProgTopCmd.do_caller()
    • ProgTopCmd.help_caller()
  • Statekeeper
    • Statekeeper.restore()
    • Statekeeper.save()
  • SubCmd
    • SubCmd.do_done()
  • TestControl
  • TopCmd
    • TopCmd.do_exit()
  • unquote()
• cmd_extensions module
  • Extensions
    • Extensions.do_cmd_file()
    • Extensions.do_echo()
    • Extensions.do_help_all()
    • Extensions.do_null()
    • Extensions.do_parrot()
    • Extensions.do_test()
    • Extensions.do_value()
    • Extensions.emptyline()
    • Extensions.help_cmd_file()
    • Extensions.help_echo()
    • Extensions.help_help_all()
    • Extensions.help_parrot()
    • Extensions.help_test()
    • Extensions.help_value()
    • Extensions.parseargs()
    • Extensions.parseopt()
    • Extensions.parseopts()
    • Extensions.precmd()
    • Extensions.preloop()
    • Extensions.protectedSplit()
    • Extensions.quoted()
    • Extensions.token()
• cmp_grp module
  • GroupTransform
    • GroupTransform.diff()
    • GroupTransform.str_diff()
  • GroupTransforms
    • GroupTransforms.compare()
    • GroupTransforms.mx
    • GroupTransforms.open()
    • GroupTransforms.read()
    • GroupTransforms.readall()
• CNS-RSRef package (Real-space refinement within CNS).
  • Synopsis
  • Usage
  • Division of Labor / Control input
    • Input files
    • Command-line parameters:
  • Installation
    • Background on Implementation
    • Choice of Python Interpreter
    • Glossary
    • Quickstart
    • Complications
    • Underlying CNS installation
    • libpasto_wrap
    • Installation Script: pasto/cns/patch.py
  • Performance guidelines
  • Troubleshooting
    • Coordinates
      • PDB output
  • History
  • Credits
• Command interpreter
  • Syntax:
  • Shell:
  • Hierachical structure:
  • Just-in-time calculation & pre-requisites:
  • Error recovery:
  • Selected commands - implementation-specific extensions & limitations.
    • @FILE or run_script FILE
    • Command-line commands
    • done, exit and quit
    • python interpreter
      • Limitations, bugs & work-arounds
  • Other commands available in all applications
• crystallography module
  • MapOrthogonal
    • MapOrthogonal.deorthogonalize()
    • MapOrthogonal.deorthogonalize_vec()
    • MapOrthogonal.from_unit_cell()
    • MapOrthogonal.getIsOrthogonal()
    • MapOrthogonal.getOrigin()
    • MapOrthogonal.getOrthog()
    • MapOrthogonal.getOrthoxyz()
    • MapOrthogonal.getSpacing()
    • MapOrthogonal.getVolume()
    • MapOrthogonal.isorthogonal
    • MapOrthogonal.new()
    • MapOrthogonal.origin
    • MapOrthogonal.orthog
    • MapOrthogonal.orthogonalize()
    • MapOrthogonal.orthogonalize_vec()
    • MapOrthogonal.orthoxyz
    • MapOrthogonal.spacing
    • MapOrthogonal.volume
  • OrthogonalizationMatrix
    • OrthogonalizationMatrix.getOrthog()
    • OrthogonalizationMatrix.getVolume()
    • OrthogonalizationMatrix.orthog
    • OrthogonalizationMatrix.volume
  • resolutions()
• density module
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • ArrayBoundsError
  • AtomicDensity
    • AtomicDensity.cache_init()
    • AtomicDensity.cache_off()
    • AtomicDensity.cache_on()
    • AtomicDensity.cache_reset()
    • AtomicDensity.density()
    • AtomicDensity.density_array
    • AtomicDensity.density_wo_cache()
    • AtomicDensity.distances()
    • AtomicDensity.filter_resolution
    • AtomicDensity.profile()
    • AtomicDensity.three_d_transform_weights()
  • ModelMap
    • ModelMap.AtomMask
      • ModelMap.AtomMask.distances()
    • ModelMap.atom_box()
    • ModelMap.atomic_partials_current
    • ModelMap.calculate()
    • ModelMap.changed()
    • ModelMap.correlation()
    • ModelMap.distances()
    • ModelMap.distances_assume_orthonormal()
    • ModelMap.dmagnification()
    • ModelMap.getVolume()
    • ModelMap.image_refine()
    • ModelMap.inbounds()
    • ModelMap.indices_near_index()
    • ModelMap.magnify()
    • ModelMap.new_comparison()
    • ModelMap.partial_stats
    • ModelMap.partials()
    • ModelMap.refine_magnification()
    • ModelMap.refine_magnification_no_atomic_partials()
    • ModelMap.rfactor()
    • ModelMap.rms()
    • ModelMap.scale_model_to_observed
    • ModelMap.sorted_correlation()
    • ModelMap.sq_diff()
    • ModelMap.threshold_correlation()
    • ModelMap.togrid()
    • ModelMap.tolerance
    • ModelMap.warnings_issued
    • ModelMap.write_calculated()
    • ModelMap.write_comparison()
    • ModelMap.write_difference()
  • OldArguments
    • OldArguments.export()
  • correl_coeff()
  • scale()
• documentation module
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • Module
    • Module.explain()
    • Module.help()
    • Module.list()
  • apidoc()
  • checkfiles()
  • copyrst()
  • directory_setup()
  • epy2rst()
  • extract()
  • help()
  • main()
  • make()
  • startup()
  • translate()
  • unpackage()
• filter_summarize module
  • main()
  • parse()
  • startup()
• form_factor_table module
  • FormFactorTable
    • FormFactorTable.Counter
      • FormFactorTable.Counter.increment()
    • FormFactorTable.at_dstar()
    • FormFactorTable.at_dstar_array
    • FormFactorTable.at_dstar_sq()
    • FormFactorTable.at_dstar_sq_array
    • FormFactorTable.at_s()
    • FormFactorTable.at_s_array
    • FormFactorTable.at_s_sq()
    • FormFactorTable.at_s_sq_array
    • FormFactorTable.findtype()
    • FormFactorTable.name2type()
    • FormFactorTable.recognized()
    • FormFactorTable.type_number()
• impact module
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
    • Arguments.finalize()
  • Commands
    • Commands.do_show()
    • Commands.help_show()
  • CommandsAdded
    • CommandsAdded.do_color()
    • CommandsAdded.do_histogram()
    • CommandsAdded.do_plot()
    • CommandsAdded.help_color()
    • CommandsAdded.help_histogram()
    • CommandsAdded.help_plot()
  • ControlAdded
    • ControlAdded.color()
    • ControlAdded.histogram()
  • OldArguments
    • OldArguments.export()
    • OldArguments.finalize()
  • ResidueInfo
  • ResidueInfoAdded
    • ResidueInfoAdded.map2structure()
  • Tasks
    • Tasks.impact()
  • TopCommands
  • arrow_range()
  • parseLog()
  • plotImpactHistogram()
  • printImpactHistogram()
  • startup()
  • text_at()
• local_symmetry
• map module
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • Map
    • Map.local_view()
    • Map.zeros_like()
  • ReadMap
    • ReadMap.Scale
      • ReadMap.Scale.input()
      • ReadMap.Scale.output()
    • ReadMap.allow_no_file
    • ReadMap.compare()
    • ReadMap.from_bsoft()
    • ReadMap.from_ccpem()
    • ReadMap.from_file()
    • ReadMap.from_xplor()
    • ReadMap.magnify()
    • ReadMap.to_file()
    • ReadMap.to_xplor()
    • ReadMap.use_mrcfile
• PaStO
  • argparser module
    • ArgumentParser
      • ArgumentParser.dotfile()
      • ArgumentParser.finalize()
      • ArgumentParser.parse_args()
      • ArgumentParser.remaining()
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • ArgumentsSubClass
      • ArgumentsSubClass.domestic()
      • ArgumentsSubClass.export()
    • CommonOptions
      • CommonOptions.asdict()
    • Namespace
      • Namespace.asdict()
    • Options
    • protectedSplit()
    • quoted()
    • token()
  • atoms module
    • Anisotropics
      • Anisotropics.alignment()
      • Anisotropics.analyze()
      • Anisotropics.axes()
      • Anisotropics.cciso()
      • Anisotropics.ccuij()
      • Anisotropics.check()
      • Anisotropics.divergence()
      • Anisotropics.iso_like()
      • Anisotropics.isotropic()
      • Anisotropics.isotropize()
      • Anisotropics.join()
      • Anisotropics.rotate()
      • Anisotropics.scale()
      • Anisotropics.scale_individual()
      • Anisotropics.scale_uniform()
      • Anisotropics.selection()
      • Anisotropics.shuffle()
      • Anisotropics.subset()
      • Anisotropics.suij()
      • Anisotropics.triangular()
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • Atoms
      • Atoms.ChainName
        • Atoms.ChainName.warning
      • Atoms.altloc_in_segid()
      • Atoms.angle()
      • Atoms.angle_cos()
      • Atoms.angle_cterm_dc()
      • Atoms.angle_dc()
      • Atoms.are_close()
      • Atoms.are_neighbors()
      • Atoms.bonded
      • Atoms.bounds()
      • Atoms.checks_off()
      • Atoms.checks_on()
      • Atoms.conformer
      • Atoms.connectivity()
      • Atoms.connectivityOld()
      • Atoms.covalentRadius
      • Atoms.diff()
      • Atoms.difference()
      • Atoms.difference_vector_sym()
      • Atoms.differences()
      • Atoms.distance()
      • Atoms.distance_sym()
      • Atoms.from_file()
      • Atoms.from_list()
      • Atoms.from_reader()
      • Atoms.init_non_pdb()
      • Atoms.is_alt()
      • Atoms.is_close()
      • Atoms.is_corresponding()
      • Atoms.is_cterm()
      • Atoms.join()
      • Atoms.label()
      • Atoms.labels()
      • Atoms.labels_close()
      • Atoms.link_torsion()
      • Atoms.max_diff()
      • Atoms.neighbors()
      • Atoms.next_residue()
      • Atoms.next_residue_atoms()
      • Atoms.pdb_coord_records
      • Atoms.randomize()
      • Atoms.residue()
      • Atoms.residueID()
      • Atoms.same()
      • Atoms.same_conformer()
      • Atoms.select()
      • Atoms.sort()
      • Atoms.subset()
      • Atoms.unlink_torsion()
      • Atoms.update_pdb()
      • Atoms.write()
      • Atoms.xyz
    • Collection
    • Commands
      • Commands.ap1
      • Commands.ap2
      • Commands.do_pdbout()
      • Commands.do_select()
      • Commands.help_SELECTION_EXPR()
    • Documentation
      • Documentation.Selection_Group
        • Documentation.Selection_Group.introduction
    • Group
      • Group.check()
      • Group.checks
      • Group.count()
      • Group.duplicates()
      • Group.empty()
      • Group.expand()
      • Group.expand_items()
      • Group.from_criteria()
      • Group.from_selections()
      • Group.inAny()
      • Group.labels()
      • Group.names()
      • Group.nonRedundant()
      • Group.selections()
      • Group.stats()
    • OldArguments
      • OldArguments.export()
    • Selection
      • Selection.asSelection()
      • Selection.attribute()
      • Selection.boundary()
      • Selection.boundary_links()
      • Selection.center()
      • Selection.copy()
      • Selection.empty()
      • Selection.expand()
      • Selection.expand_items()
      • Selection.following()
      • Selection.fop2py
      • Selection.fortran()
      • Selection.get()
      • Selection.inAny()
      • Selection.is_amino_acid()
      • Selection.is_of_atoms()
      • Selection.key
      • Selection.labels()
      • Selection.name
      • Selection.next_residue_atoms()
      • Selection.operators
      • Selection.prefix_set
      • Selection.previous()
      • Selection.select()
      • Selection.split()
      • Selection.synonyms
      • Selection.test()
      • Selection.u
      • Selection.unique_set
      • Selection.v2
      • Selection.value
      • Selection.whichAttr()
      • Selection.x
    • Tasks
      • Tasks.getselect()
      • Tasks.read_coords()
      • Tasks.read_coords_prereq()
      • Tasks.select()
      • Tasks.select_attr()
      • Tasks.select_attr_prereq()
      • Tasks.select_prereq()
      • Tasks.update_coords()
      • Tasks.write_coords()
      • Tasks.write_coords_prereq()
    • Vec
      • Vec.comp()
      • Vec.dot()
      • Vec.length()
      • Vec.norm
      • Vec.proj()
      • Vec.udot()
      • Vec.unit
      • Vec.vec
    • VecList
      • VecList.align()
      • VecList.align_to_vec()
      • VecList.align_unique()
      • VecList.align_vecs()
      • VecList.append()
      • VecList.extend()
      • VecList.extend_svd()
      • VecList.insert()
      • VecList.mean()
      • VecList.norms
      • VecList.permute()
      • VecList.reordered()
      • VecList.sort()
      • VecList.sum()
      • VecList.sumproduct()
      • VecList.sumsq()
    • dummy_chain
    • is_number()
    • is_quoted_string()
    • is_triple_quoted_string()
    • iso_like()
    • isotropic()
    • masked_determinants()
    • masked_inverses()
    • masked_norm()
    • matmul()
    • number_selections()
    • quoteString()
    • startup()
    • triangular()
    • where()
  • calling_program module
    • main()
  • cmd2nest module
    • Cmd
      • Cmd.ancestory()
      • Cmd.base_keywords
      • Cmd.children
      • Cmd.do_help()
      • Cmd.do_parrot()
      • Cmd.do_set()
      • Cmd.do_test()
      • Cmd.help_parser
      • Cmd.instances
      • Cmd.old_cmdloop()
      • Cmd.old_do_load()
      • Cmd.onfailure()
      • Cmd.parent
      • Cmd.parrot_parser
      • Cmd.postloop()
      • Cmd.preloop()
      • Cmd.set_description
      • Cmd.set_parser
      • Cmd.set_parser_parent
      • Cmd.test_parser
      • Cmd.undocumented
    • Documentation
      • Documentation.general
    • ProgCmd
    • ProgSubCmd
      • ProgSubCmd.do_callee()
      • ProgSubCmd.help_callee()
    • ProgTopCmd
      • ProgTopCmd.do_caller()
      • ProgTopCmd.help_caller()
    • Statekeeper
      • Statekeeper.restore()
      • Statekeeper.save()
    • SubCmd
      • SubCmd.do_done()
    • TestControl
    • TopCmd
      • TopCmd.do_exit()
    • unquote()
  • cmd_extensions module
    • Extensions
      • Extensions.do_cmd_file()
      • Extensions.do_echo()
      • Extensions.do_help_all()
      • Extensions.do_null()
      • Extensions.do_parrot()
      • Extensions.do_test()
      • Extensions.do_value()
      • Extensions.emptyline()
      • Extensions.help_cmd_file()
      • Extensions.help_echo()
      • Extensions.help_help_all()
      • Extensions.help_parrot()
      • Extensions.help_test()
      • Extensions.help_value()
      • Extensions.parseargs()
      • Extensions.parseopt()
      • Extensions.parseopts()
      • Extensions.precmd()
      • Extensions.preloop()
      • Extensions.protectedSplit()
      • Extensions.quoted()
      • Extensions.token()
  • cmp_grp module
    • GroupTransform
      • GroupTransform.diff()
      • GroupTransform.str_diff()
    • GroupTransforms
      • GroupTransforms.compare()
      • GroupTransforms.mx
      • GroupTransforms.open()
      • GroupTransforms.read()
      • GroupTransforms.readall()
  • crystallography module
    • MapOrthogonal
      • MapOrthogonal.deorthogonalize()
      • MapOrthogonal.deorthogonalize_vec()
      • MapOrthogonal.from_unit_cell()
      • MapOrthogonal.getIsOrthogonal()
      • MapOrthogonal.getOrigin()
      • MapOrthogonal.getOrthog()
      • MapOrthogonal.getOrthoxyz()
      • MapOrthogonal.getSpacing()
      • MapOrthogonal.getVolume()
      • MapOrthogonal.isorthogonal
      • MapOrthogonal.new()
      • MapOrthogonal.origin
      • MapOrthogonal.orthog
      • MapOrthogonal.orthogonalize()
      • MapOrthogonal.orthogonalize_vec()
      • MapOrthogonal.orthoxyz
      • MapOrthogonal.spacing
      • MapOrthogonal.volume
    • OrthogonalizationMatrix
      • OrthogonalizationMatrix.getOrthog()
      • OrthogonalizationMatrix.getVolume()
      • OrthogonalizationMatrix.orthog
      • OrthogonalizationMatrix.volume
    • resolutions()
  • density module
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • ArrayBoundsError
    • AtomicDensity
      • AtomicDensity.cache_init()
      • AtomicDensity.cache_off()
      • AtomicDensity.cache_on()
      • AtomicDensity.cache_reset()
      • AtomicDensity.density()
      • AtomicDensity.density_array
      • AtomicDensity.density_wo_cache()
      • AtomicDensity.distances()
      • AtomicDensity.filter_resolution
      • AtomicDensity.profile()
      • AtomicDensity.three_d_transform_weights()
    • ModelMap
      • ModelMap.AtomMask
        • ModelMap.AtomMask.distances()
      • ModelMap.atom_box()
      • ModelMap.atomic_partials_current
      • ModelMap.calculate()
      • ModelMap.changed()
      • ModelMap.correlation()
      • ModelMap.distances()
      • ModelMap.distances_assume_orthonormal()
      • ModelMap.dmagnification()
      • ModelMap.getVolume()
      • ModelMap.image_refine()
      • ModelMap.inbounds()
      • ModelMap.indices_near_index()
      • ModelMap.magnify()
      • ModelMap.new_comparison()
      • ModelMap.partial_stats
      • ModelMap.partials()
      • ModelMap.refine_magnification()
      • ModelMap.refine_magnification_no_atomic_partials()
      • ModelMap.rfactor()
      • ModelMap.rms()
      • ModelMap.scale_model_to_observed
      • ModelMap.sorted_correlation()
      • ModelMap.sq_diff()
      • ModelMap.threshold_correlation()
      • ModelMap.togrid()
      • ModelMap.tolerance
      • ModelMap.warnings_issued
      • ModelMap.write_calculated()
      • ModelMap.write_comparison()
      • ModelMap.write_difference()
    • OldArguments
      • OldArguments.export()
    • correl_coeff()
    • scale()
  • documentation module
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • Module
      • Module.explain()
      • Module.help()
      • Module.list()
    • apidoc()
    • checkfiles()
    • copyrst()
    • directory_setup()
    • epy2rst()
    • extract()
    • help()
    • main()
    • make()
    • startup()
    • translate()
    • unpackage()
  • filter_summarize module
    • main()
    • parse()
    • startup()
  • form_factor_table module
    • FormFactorTable
      • FormFactorTable.Counter
        • FormFactorTable.Counter.increment()
      • FormFactorTable.at_dstar()
      • FormFactorTable.at_dstar_array
      • FormFactorTable.at_dstar_sq()
      • FormFactorTable.at_dstar_sq_array
      • FormFactorTable.at_s()
      • FormFactorTable.at_s_array
      • FormFactorTable.at_s_sq()
      • FormFactorTable.at_s_sq_array
      • FormFactorTable.findtype()
      • FormFactorTable.name2type()
      • FormFactorTable.recognized()
      • FormFactorTable.type_number()
  • impact module
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
      • Arguments.finalize()
    • Commands
      • Commands.do_show()
      • Commands.help_show()
    • CommandsAdded
      • CommandsAdded.do_color()
      • CommandsAdded.do_histogram()
      • CommandsAdded.do_plot()
      • CommandsAdded.help_color()
      • CommandsAdded.help_histogram()
      • CommandsAdded.help_plot()
    • ControlAdded
      • ControlAdded.color()
      • ControlAdded.histogram()
    • OldArguments
      • OldArguments.export()
      • OldArguments.finalize()
    • ResidueInfo
    • ResidueInfoAdded
      • ResidueInfoAdded.map2structure()
    • Tasks
      • Tasks.impact()
    • TopCommands
    • arrow_range()
    • parseLog()
    • plotImpactHistogram()
    • printImpactHistogram()
    • startup()
    • text_at()
  • map module
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • Map
      • Map.local_view()
      • Map.zeros_like()
    • ReadMap
      • ReadMap.Scale
        • ReadMap.Scale.input()
        • ReadMap.Scale.output()
      • ReadMap.allow_no_file
      • ReadMap.compare()
      • ReadMap.from_bsoft()
      • ReadMap.from_ccpem()
      • ReadMap.from_file()
      • ReadMap.from_xplor()
      • ReadMap.magnify()
      • ReadMap.to_file()
      • ReadMap.to_xplor()
      • ReadMap.use_mrcfile
  • numpyExt module
    • Flagged
      • Flagged.inactive
      • Flagged.iteritems()
      • Flagged.set_unused_values()
      • Flagged.set_used_values()
      • Flagged.skip
      • Flagged.skipped
      • Flagged.use
      • Flagged.used
      • Flagged.value
    • testFlagged()
  • optimize module
    • AnalyzeSubCommands
      • AnalyzeSubCommands.convergence_parser
      • AnalyzeSubCommands.do_convergence()
      • AnalyzeSubCommands.do_dihedrals()
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • AtomicParameterization
      • AtomicParameterization.bfactor
      • AtomicParameterization.changing
      • AtomicParameterization.nothing()
      • AtomicParameterization.occupancy
      • AtomicParameterization.position
      • AtomicParameterization.sorted_keys()
      • AtomicParameterization.width
    • AtomicRefinement
      • AtomicRefinement.selectionPair()
    • BGrouping
    • CallBackEmulator
      • CallBackEmulator.argument()
      • CallBackEmulator.queryCallBack()
      • CallBackEmulator.whenCall
    • Commands
      • Commands.analyze_parser
      • Commands.do_analyze()
    • DihedralsSubSubCommands
      • DihedralsSubSubCommands.do_hinges()
      • DihedralsSubSubCommands.do_impact()
      • DihedralsSubSubCommands.do_paint()
      • DihedralsSubSubCommands.hinges_parser
      • DihedralsSubSubCommands.impact_parser
      • DihedralsSubSubCommands.paint_parser
    • Documentation
      • Documentation.Parameterize
        • Documentation.Parameterize.input
    • ExtendedParameterization
    • Fit
    • GroupGp
      • GroupGp.expand()
      • GroupGp.max_items
      • GroupGp.parse()
      • GroupGp.selections
    • Grouping
      • Grouping.append()
      • Grouping.as_count
      • Grouping.assign()
      • Grouping.boolabbrev()
      • Grouping.boolabbrev_old()
      • Grouping.changing
      • Grouping.check_type()
      • Grouping.default()
      • Grouping.default_selection()
      • Grouping.max_len
      • Grouping.nothing()
      • Grouping.parse()
      • Grouping.selections
      • Grouping.value
    • Groupings
      • Groupings.changed()
      • Groupings.changing
      • Groupings.default()
      • Groupings.group
      • Groupings.individual
      • Groupings.nothing()
      • Groupings.overall
      • Groupings.own()
      • Groupings.torsion
      • Groupings.update()
    • History
      • History.deriv
      • History.impact
      • History.info
      • History.normalizeImpact
      • History.param
      • History.residual
      • History.saveGradients()
      • History.saveParameters()
      • History.saveResidual()
      • History.trackImpact()
      • History.update()
      • History.wrapUp()
    • ImpactSubSubSubCommands
      • ImpactSubSubSubCommands.color_parser
      • ImpactSubSubSubCommands.do_color()
      • ImpactSubSubSubCommands.do_pickle()
      • ImpactSubSubSubCommands.do_plot()
      • ImpactSubSubSubCommands.do_print()
      • ImpactSubSubSubCommands.pickle_parser
      • ImpactSubSubSubCommands.plot_parser
      • ImpactSubSubSubCommands.print_parser
    • IndividualGp
      • IndividualGp.default()
    • OGrouping
    • Objective
      • Objective.add_torsion_restraint()
      • Objective.callback()
      • Objective.depends_on_anisou
      • Objective.f()
      • Objective.fprime()
      • Objective.function_detail
      • Objective.progress
      • Objective.step_detail
    • OldArguments
      • OldArguments.export()
    • Optimization
      • Optimization.analyze()
      • Optimization.refine()
      • Optimization.use_minimize
    • OverallGp
      • OverallGp.default()
      • OverallGp.nothing()
      • OverallGp.parse()
    • ParameterizeSubCommands
      • ParameterizeSubCommands.clear_parser
      • ParameterizeSubCommands.do_SELECTION()
      • ParameterizeSubCommands.do_clear()
      • ParameterizeSubCommands.do_group()
      • ParameterizeSubCommands.do_individual()
      • ParameterizeSubCommands.do_overall()
      • ParameterizeSubCommands.do_print()
      • ParameterizeSubCommands.do_torsion()
      • ParameterizeSubCommands.group_parser
      • ParameterizeSubCommands.help_SELECTION()
      • ParameterizeSubCommands.individual_parser
      • ParameterizeSubCommands.overall_parser
      • ParameterizeSubCommands.param_type
      • ParameterizeSubCommands.print_group
      • ParameterizeSubCommands.print_parser
      • ParameterizeSubCommands.torsion_parser
      • ParameterizeSubCommands.which()
    • Parameters
      • Parameters.analyze()
      • Parameters.check_support()
      • Parameters.check_supported()
      • Parameters.debug_instances
      • Parameters.extract()
      • Parameters.grouping
      • Parameters.pack_like()
      • Parameters.param
      • Parameters.partials
      • Parameters.scale_rotation
      • Parameters.supported_modes
      • Parameters.torsion_change()
      • Parameters.value
    • RSParameterization
      • RSParameterization.magnification
      • RSParameterization.resolution
    • ResidueInfo
      • ResidueInfo.angleEntry
      • ResidueInfo.changeArray()
      • ResidueInfo.color()
      • ResidueInfo.combine()
      • ResidueInfo.combined
      • ResidueInfo.combined_bond_ids()
      • ResidueInfo.copy()
      • ResidueInfo.empty()
      • ResidueInfo.emptyID()
      • ResidueInfo.emptyLikeAtom()
      • ResidueInfo.flatten()
      • ResidueInfo.fromParameters()
      • ResidueInfo.getCombined()
      • ResidueInfo.impactArray()
      • ResidueInfo.impactDelta()
      • ResidueInfo.impactHistory()
      • ResidueInfo.impactSequential()
      • ResidueInfo.load()
      • ResidueInfo.name
      • ResidueInfo.neighbors()
      • ResidueInfo.overall
      • ResidueInfo.pickle()
      • ResidueInfo.pickles
      • ResidueInfo.plot()
      • ResidueInfo.print_all
      • ResidueInfo.rankImpact()
      • ResidueInfo.read()
      • ResidueInfo.residue
      • ResidueInfo.residueEntry
      • ResidueInfo.save()
      • ResidueInfo.saved
    • Superimposition
    • Tasks
      • Tasks.analyze()
      • Tasks.analyze_prereq()
      • Tasks.convergence()
      • Tasks.dihedral_hinges()
      • Tasks.dihedral_paint()
      • Tasks.fix_dihedrals()
      • Tasks.impact()
      • Tasks.impact_paint()
      • Tasks.impact_paint_prereq()
      • Tasks.impact_pickle()
      • Tasks.impact_pickle_prereq()
      • Tasks.impact_plot()
      • Tasks.impact_plot_prereq()
      • Tasks.impact_prereq()
      • Tasks.impact_print()
      • Tasks.impact_print_prereq()
      • Tasks.select_dihedrals()
    • TorsionGp
      • TorsionGp.changing
      • TorsionGp.default()
      • TorsionGp.default_selection()
      • TorsionGp.dihedrals_within
      • TorsionGp.linkOverlapWarningMsg
      • TorsionGp.linkOverlapWarnings
      • TorsionGp.movable
      • TorsionGp.nothing()
      • TorsionGp.parse()
      • TorsionGp.selections
    • TorsionParameterization
      • TorsionParameterization.append()
      • TorsionParameterization.changed()
      • TorsionParameterization.changing
      • TorsionParameterization.check()
      • TorsionParameterization.connect
      • TorsionParameterization.connected
      • TorsionParameterization.connectivity
      • TorsionParameterization.default_selection_expr
      • TorsionParameterization.defaults()
      • TorsionParameterization.dihedrals_within
      • TorsionParameterization.efficiency_check
      • TorsionParameterization.efficiency_level
      • TorsionParameterization.extend()
      • TorsionParameterization.insert()
      • TorsionParameterization.movable
      • TorsionParameterization.parse_selection()
      • TorsionParameterization.variable
    • Unit
    • XYZGrouping
    • zero()
  • qsort module
    • qsort()
    • qsort_without_duplicates()
  • restraints module
    • Ala
    • AminoAcid
      • AminoAcid.types
    • Anchor
      • Anchor.check()
      • Anchor.end_atoms
      • Anchor.stats()
    • Arg
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • Asn
    • Asp
    • Brestraint
      • Brestraint.df()
      • Brestraint.f()
      • Brestraint.rms()
    • ClassHolder
      • ClassHolder.add_class()
    • Commands
      • Commands.ap1
      • Commands.do_restraints()
    • CovalentRestraint
      • CovalentRestraint.angle
      • CovalentRestraint.angleDeviants()
      • CovalentRestraint.angleGrad()
      • CovalentRestraint.angleGrad_dc()
      • CovalentRestraint.angleResidual()
      • CovalentRestraint.angleStats()
      • CovalentRestraint.angle_sigma
      • CovalentRestraint.f()
      • CovalentRestraint.f_grad()
      • CovalentRestraint.get_history()
      • CovalentRestraint.length
      • CovalentRestraint.lengthDeviants()
      • CovalentRestraint.lengthGrad()
      • CovalentRestraint.lengthResidual()
      • CovalentRestraint.lengthStats()
      • CovalentRestraint.length_sigma
      • CovalentRestraint.torsionGrad()
      • CovalentRestraint.update()
    • Cys
    • Distance_id
      • Distance_id.childless()
      • Distance_id.deviation()
      • Distance_id.deviation_str()
      • Distance_id.distance()
      • Distance_id.family()
      • Distance_id.partial()
      • Distance_id.residual()
      • Distance_id.vector()
    • Distance_input
    • Distance_selection
      • Distance_selection.deviation()
      • Distance_selection.deviation1()
      • Distance_selection.deviation_sym()
    • Distances
      • Distances.add()
      • Distances.calculate()
      • Distances.doc
      • Distances.entry
    • Geometry
      • Geometry.angle()
      • Geometry.bond()
    • Gln
    • Glu
    • Gly
    • His
    • Ile
    • Leu
    • Lys
    • Met
    • OldArguments
      • OldArguments.export()
    • PairIDs
    • Phe
    • Pro
    • RestraintsSubCommands
      • RestraintsSubCommands.ap2
      • RestraintsSubCommands.do_distance()
      • RestraintsSubCommands.do_information()
    • Ser
    • Tasks
      • Tasks.restraints()
      • Tasks.restraints_distance()
      • Tasks.restraints_distance_prereq()
      • Tasks.restraints_information()
      • Tasks.restraints_information_prereq()
      • Tasks.restraints_prereq()
    • Thr
    • Trp
    • Tyr
    • VDWRestraint
      • VDWRestraint.Status
      • VDWRestraint.connectivityExclusion
      • VDWRestraint.distance
      • VDWRestraint.f()
      • VDWRestraint.f_grad()
      • VDWRestraint.get_history()
      • VDWRestraint.get_neighbors()
      • VDWRestraint.matrix_bonded()
      • VDWRestraint.power
      • VDWRestraint.radius
      • VDWRestraint.status()
      • VDWRestraint.update()
      • VDWRestraint.weightFactor
    • Val
    • distance_arg_parse()
    • ss()
  • rotamer module
    • Rotamer
      • Rotamer.Z
      • Rotamer.all_atoms
      • Rotamer.chi()
      • Rotamer.error
      • Rotamer.extendIndex()
      • Rotamer.index
      • Rotamer.rotate()
    • flip()
  • rotamer_chi_lib module
    • Rotamer_library
      • Rotamer_library.most_probable_rotamer()
      • Rotamer_library.residue_types()
      • Rotamer_library.rotamers()
      • Rotamer_library.rotamers_dictionary()
      • Rotamer_library.rotamers_list()
  • rseval module
    • rseval()
  • rsref module
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
      • Arguments.finalize()
    • OldArguments
      • OldArguments.export()
    • RSRef
    • Tasks
      • Tasks.analyze()
      • Tasks.analyze_prereq()
      • Tasks.atoms_being_evaluated
      • Tasks.atoms_refined
      • Tasks.calculate_map()
      • Tasks.calculate_map_prereq()
      • Tasks.default_group
      • Tasks.diagnostics()
      • Tasks.evaluate()
      • Tasks.evaluate_prereq()
      • Tasks.image_refine()
      • Tasks.image_refine_prereq()
      • Tasks.implied_parameterization()
      • Tasks.import_coord()
      • Tasks.neighbors_deprecated()
      • Tasks.neighbors_prereq()
      • Tasks.parameterization_init()
      • Tasks.parameterization_init_prereq()
      • Tasks.parameterize()
      • Tasks.parameterize_prereq()
      • Tasks.perturb()
      • Tasks.perturb_prereq()
      • Tasks.profile()
      • Tasks.randomize()
      • Tasks.randomize_prereq()
      • Tasks.reconcile_types()
      • Tasks.reconcile_types_prereq()
      • Tasks.refine()
      • Tasks.refine_magnification()
      • Tasks.refine_prereq()
      • Tasks.residual
      • Tasks.residual_db
      • Tasks.residual_do
      • Tasks.residual_dx
      • Tasks.residual_dxyz
      • Tasks.residual_dy
      • Tasks.residual_dz
      • Tasks.restrain_to_reference
      • Tasks.rotamer()
      • Tasks.rotamer_prereq()
      • Tasks.run_test()
      • Tasks.symmetry_current
      • Tasks.symmetry_expand()
      • Tasks.symmetry_expand_prereq()
      • Tasks.symmetry_init()
      • Tasks.symmetry_init_prereq()
      • Tasks.verbose
      • Tasks.write_map()
      • Tasks.write_map_prereq()
    • TopCommands
      • TopCommands.do_evaluate()
      • TopCommands.do_image_refine()
      • TopCommands.do_map()
      • TopCommands.do_neighbors()
      • TopCommands.do_parameterize()
      • TopCommands.do_perturb()
      • TopCommands.do_profile()
      • TopCommands.do_randomize()
      • TopCommands.do_refine()
      • TopCommands.do_rotamer()
      • TopCommands.do_test()
      • TopCommands.evaluate_parser
      • TopCommands.help_test()
      • TopCommands.image_refine_group
      • TopCommands.image_refine_parser
      • TopCommands.map_parser
      • TopCommands.neighbors_parser
      • TopCommands.parameterize_parser
      • TopCommands.perturb_parser
      • TopCommands.profile_parser
      • TopCommands.randomize_parser
      • TopCommands.refine_convergence
      • TopCommands.refine_parser
      • TopCommands.rotamer_parser
    • main()
    • startup()
  • sidechain module
    • Side_chains
      • Side_chains.rota_match()
      • Side_chains.rota_print()
  • space_group module
    • SpaceGroups
      • SpaceGroups.build()
      • SpaceGroups.jar
      • SpaceGroups.pickle()
      • SpaceGroups.which()
    • lattice_operators()
  • stereochemistry module
    • CovalentRadii
      • CovalentRadii.bonds
      • CovalentRadii.checkRadii()
      • CovalentRadii.curated()
      • CovalentRadii.element
      • CovalentRadii.fitBondTypes()
      • CovalentRadii.halfLength()
      • CovalentRadii.number
      • CovalentRadii.optimizeProteinAmide()
      • CovalentRadii.optimizeProteinAromatic()
      • CovalentRadii.optimizeProteinBackbone()
      • CovalentRadii.optimizeProteinCarboxylate()
      • CovalentRadii.optimizeProteinGuanidinium()
      • CovalentRadii.optimizeProteinHis()
      • CovalentRadii.optimizeProteinHisAve()
      • CovalentRadii.optimizeProteinPhe()
      • CovalentRadii.optimizeProteinPheAve()
      • CovalentRadii.optimizeProteinPheH()
      • CovalentRadii.optimizeProteinTrp()
      • CovalentRadii.optimizeProteinTrpAve()
      • CovalentRadii.optimizeProteinTyr()
      • CovalentRadii.optimizeProteinTyrAve()
      • CovalentRadii.protein()
      • CovalentRadii.radius
  • superpose module
    • Accumulator
      • Accumulator.add()
      • Accumulator.mean()
      • Accumulator.std()
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
      • Arguments.finalize()
    • Objective
      • Objective.add_torsion_restraint()
      • Objective.callback()
      • Objective.depends_on_anisou
      • Objective.f()
      • Objective.fprime()
      • Objective.function_detail
      • Objective.progress
      • Objective.step_detail
    • OldArguments
      • OldArguments.export()
      • OldArguments.finalize()
    • PairItem
      • PairItem.copy()
      • PairItem.from_pair()
      • PairItem.index
      • PairItem.matched_to
      • PairItem.reordered
      • PairItem.reordered_paired
    • PairSubCommands
      • PairSubCommands.do_match()
      • PairSubCommands.do_print()
      • PairSubCommands.do_within()
      • PairSubCommands.help_SELECTION_EXPR()
      • PairSubCommands.match_parser
      • PairSubCommands.within_parser
    • Pairing
      • Pairing.add()
      • Pairing.attributeOrder
      • Pairing.bfactors()
      • Pairing.connectivity
      • Pairing.continuable
      • Pairing.deprecated_3ax
      • Pairing.difference()
      • Pairing.differences()
      • Pairing.differences_vs_bs()
      • Pairing.equivs
      • Pairing.info()
      • Pairing.loquacious
      • Pairing.objective
      • Pairing.overlay()
      • Pairing.parameters
      • Pairing.residueTable
      • Pairing.superpose()
    • Parameters
      • Parameters.grouping
      • Parameters.param
      • Parameters.partials
      • Parameters.supported_modes
      • Parameters.value
    • Tasks
      • Tasks.atoms_being_evaluated
      • Tasks.atoms_refined
      • Tasks.backup()
      • Tasks.backup_prereq()
      • Tasks.bfactors()
      • Tasks.bfactors_prereq()
      • Tasks.default_group
      • Tasks.evaluate()
      • Tasks.evaluate_prereq()
      • Tasks.flip()
      • Tasks.flip_prereq()
      • Tasks.overlay()
      • Tasks.overlay_prereq()
      • Tasks.pair()
      • Tasks.pair_init()
      • Tasks.pair_init_prereq()
      • Tasks.pair_prereq()
      • Tasks.parameterization_init()
      • Tasks.parameterization_init_prereq()
      • Tasks.parameterize()
      • Tasks.parameterize_prereq()
      • Tasks.phipsi_copy()
      • Tasks.phipsi_copy_prereq()
      • Tasks.phipsi_diff()
      • Tasks.phipsi_diff_prereq()
      • Tasks.read_coords()
      • Tasks.read_target()
      • Tasks.read_target_prereq()
      • Tasks.refine()
      • Tasks.refine_prereq()
      • Tasks.restore()
      • Tasks.restore_prereq()
      • Tasks.restrain_to_reference
      • Tasks.run_test()
      • Tasks.verbose
    • Test
      • Test.set_options()
    • TopCommands
      • TopCommands.backup_parser
      • TopCommands.bfactors_parser
      • TopCommands.do_backup()
      • TopCommands.do_bfactors()
      • TopCommands.do_evaluate()
      • TopCommands.do_flip()
      • TopCommands.do_overlay()
      • TopCommands.do_pair()
      • TopCommands.do_parameterize()
      • TopCommands.do_phipsi_copy()
      • TopCommands.do_phipsi_diff()
      • TopCommands.do_refine()
      • TopCommands.do_restore()
      • TopCommands.do_test()
      • TopCommands.evaluate_parser
      • TopCommands.flip_parser
      • TopCommands.help_test()
      • TopCommands.overlay_parser
      • TopCommands.pair_parser
      • TopCommands.parameterize_parser
      • TopCommands.phipsi_copy_parser
      • TopCommands.phipsi_diff_parser
      • TopCommands.refine_convergence
      • TopCommands.refine_parser
      • TopCommands.restore_parser
      • TopCommands.test_parser
    • dissect()
    • findS0()
    • main()
    • startup()
    • std_err_mu()
    • t1_Welch_gt()
    • t1_Welch_lt()
    • z_d()
  • symexp module
    • Tasks
      • Tasks.read_coords()
      • Tasks.read_coords_prereq()
      • Tasks.symmetry_expand()
      • Tasks.symmetry_expand_prereq()
      • Tasks.symmetry_init()
      • Tasks.symmetry_init_prereq()
      • Tasks.write_coords()
      • Tasks.write_coords_prereq()
    • TopCommands
      • TopCommands.do_neighbors()
      • TopCommands.do_pdbout()
      • TopCommands.do_sphere()
      • TopCommands.do_test()
      • TopCommands.help_test()
      • TopCommands.neighbors_parser
      • TopCommands.pdbout_parser
      • TopCommands.sphere_parser
    • startup()
  • symmetry module
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • Cartesian_operator
      • Cartesian_operator.euler()
      • Cartesian_operator.isunit()
    • Documentation
      • Documentation.Input
        • Documentation.Input.local
    • OldArguments
      • OldArguments.export()
    • Symmetry
      • Symmetry.complete()
      • Symmetry.debug
      • Symmetry.equivalent()
      • Symmetry.inverse()
      • Symmetry.neighbors()
      • Symmetry.repr_op()
      • Symmetry.verbose
      • Symmetry.with_neighbors()
    • Target
      • Target.debug
      • Target.isclose()
      • Target.isneighbor()
    • safe_eval()
  • torsion module
    • Graph
      • Graph.addDirectedEdge()
      • Graph.addEdge()
      • Graph.addVertex()
      • Graph.dfs()
      • Graph.dfsVisit()
      • Graph.find_articulation_edges()
      • Graph.find_bridgeless_components()
      • Graph.get_reverse()
      • Graph.removeDirectedEdge()
      • Graph.removeEdge()
      • Graph.scc()
      • Graph.version_ID
    • ImpactRestraint
    • Limit
      • Limit.L1Norm
      • Limit.change()
      • Limit.dfL1Norm()
      • Limit.dfL1sq()
      • Limit.fL1Norm()
      • Limit.fL1sq()
      • Limit.mod360()
      • Limit.stats()
    • TAProtein
      • TAProtein.all_dependents
      • TAProtein.apply_torsion()
      • TAProtein.apply_torsion_deprecated()
      • TAProtein.bond_dependents
      • TAProtein.compare()
      • TAProtein.copy()
      • TAProtein.debug
      • TAProtein.edit_links()
      • TAProtein.generate_rotation_masks()
      • TAProtein.generate_structure()
      • TAProtein.get_all_backbone_atoms()
      • TAProtein.get_all_backbone_bonds()
      • TAProtein.get_all_bonds_crossing_cut()
      • TAProtein.get_all_bonds_in_selection()
      • TAProtein.get_all_omega()
      • TAProtein.get_all_phi()
      • TAProtein.get_all_phi_psi()
      • TAProtein.get_all_psi()
      • TAProtein.get_edge_set()
      • TAProtein.get_rotation_mask()
      • TAProtein.get_selected_phi()
      • TAProtein.get_selected_psi()
      • TAProtein.join_all()
      • TAProtein.join_atoms()
      • TAProtein.phi_psi_selection()
      • TAProtein.print_bonds()
      • TAProtein.print_connectivity()
      • TAProtein.quartet()
      • TAProtein.save_selection()
      • TAProtein.saved_selection()
      • TAProtein.separate_all()
      • TAProtein.separate_atoms()
      • TAProtein.vs_old_apply
      • TAProtein.warnings
    • dihedral_atoms()
    • dihedral_name()
    • dihedral_value()
    • getResIDKeys()
    • get_dihedral()
    • hinges()
    • warn()
  • transform module
    • AugmentedOperator
      • AugmentedOperator.augment()
      • AugmentedOperator.dfbydv()
      • AugmentedOperator.dpbydv()
      • AugmentedOperator.eulerAxis()
      • AugmentedOperator.eulerX0Y0Z0()
      • AugmentedOperator.isunit()
      • AugmentedOperator.rotTrans()
      • AugmentedOperator.sphericalPolarAngles()
    • EulerX0Y0Z0
      • EulerX0Y0Z0.dObydv
      • EulerX0Y0Z0.dfbydv()
      • EulerX0Y0Z0.dpbydv()
    • Vector
    • compute_rigid_alignment_deriv()
    • compute_rigid_alignment_matrix()
    • compute_rotation_about_origin()
    • compute_rotation_matrix()
    • compute_transformation_matrix()
    • displacements()
    • dot()
    • general_transformation_matrix()
    • groupPartials()
    • groupTransformations()
    • multiply_matrix_array()
    • non_zero()
    • random_rotation_about_origin()
    • screw()
    • testFunction()
    • trial()
    • zero()
  • translate module
    • Synopsis
    • Command line options
    • Arguments
      • Arguments.domestic()
      • Arguments.export()
    • Dictionary
      • Dictionary.alphabetical
      • Dictionary.convention
      • Dictionary.d
      • Dictionary.dialect()
      • Dictionary.lang
      • Dictionary.repr()
      • Dictionary.res
      • Dictionary.to1
      • Dictionary.to3
      • Dictionary.translate()
      • Dictionary.unknown()
    • startup()
  • tskmgr module
    • Prerequisite
      • Prerequisite.quiet
      • Prerequisite.verbose
    • ReqExpr
    • ReqObj
      • ReqObj.getattr_or_eval()
      • ReqObj.is_met()
      • ReqObj.verbose
    • Task
      • Task.getattr_or_eval()
      • Task.verbose
    • TaskError
    • UnMetPrerequisite
    • errmsg()
    • get_namespace()
    • get_namespaces()
    • public()
    • unexpected()
  • vector module
    • assertOneD()
    • assertSameSize()
    • crossDeriv()
    • crossNorm()
    • crossNormDeriv()
    • crossUnit()
    • crossUnitDeriv()
    • dotDeriv()
    • normDeriv()
  • version module
• numpyExt module
  • Flagged
    • Flagged.inactive
    • Flagged.iteritems()
    • Flagged.set_unused_values()
    • Flagged.set_used_values()
    • Flagged.skip
    • Flagged.skipped
    • Flagged.use
    • Flagged.used
    • Flagged.value
  • testFlagged()
• optimize module
  • AnalyzeSubCommands
    • AnalyzeSubCommands.convergence_parser
    • AnalyzeSubCommands.do_convergence()
    • AnalyzeSubCommands.do_dihedrals()
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • AtomicParameterization
    • AtomicParameterization.bfactor
    • AtomicParameterization.changing
    • AtomicParameterization.nothing()
    • AtomicParameterization.occupancy
    • AtomicParameterization.position
    • AtomicParameterization.sorted_keys()
    • AtomicParameterization.width
  • AtomicRefinement
    • AtomicRefinement.selectionPair()
  • BGrouping
  • CallBackEmulator
    • CallBackEmulator.argument()
    • CallBackEmulator.queryCallBack()
    • CallBackEmulator.whenCall
  • Commands
    • Commands.analyze_parser
    • Commands.do_analyze()
  • DihedralsSubSubCommands
    • DihedralsSubSubCommands.do_hinges()
    • DihedralsSubSubCommands.do_impact()
    • DihedralsSubSubCommands.do_paint()
    • DihedralsSubSubCommands.hinges_parser
    • DihedralsSubSubCommands.impact_parser
    • DihedralsSubSubCommands.paint_parser
  • Documentation
    • Documentation.Parameterize
      • Documentation.Parameterize.input
  • ExtendedParameterization
  • Fit
  • GroupGp
    • GroupGp.expand()
    • GroupGp.max_items
    • GroupGp.parse()
    • GroupGp.selections
  • Grouping
    • Grouping.append()
    • Grouping.as_count
    • Grouping.assign()
    • Grouping.boolabbrev()
    • Grouping.boolabbrev_old()
    • Grouping.changing
    • Grouping.check_type()
    • Grouping.default()
    • Grouping.default_selection()
    • Grouping.max_len
    • Grouping.nothing()
    • Grouping.parse()
    • Grouping.selections
    • Grouping.value
  • Groupings
    • Groupings.changed()
    • Groupings.changing
    • Groupings.default()
    • Groupings.group
    • Groupings.individual
    • Groupings.nothing()
    • Groupings.overall
    • Groupings.own()
    • Groupings.torsion
    • Groupings.update()
  • History
    • History.deriv
    • History.impact
    • History.info
    • History.normalizeImpact
    • History.param
    • History.residual
    • History.saveGradients()
    • History.saveParameters()
    • History.saveResidual()
    • History.trackImpact()
    • History.update()
    • History.wrapUp()
  • ImpactSubSubSubCommands
    • ImpactSubSubSubCommands.color_parser
    • ImpactSubSubSubCommands.do_color()
    • ImpactSubSubSubCommands.do_pickle()
    • ImpactSubSubSubCommands.do_plot()
    • ImpactSubSubSubCommands.do_print()
    • ImpactSubSubSubCommands.pickle_parser
    • ImpactSubSubSubCommands.plot_parser
    • ImpactSubSubSubCommands.print_parser
  • IndividualGp
    • IndividualGp.default()
  • OGrouping
  • Objective
    • Objective.add_torsion_restraint()
    • Objective.callback()
    • Objective.depends_on_anisou
    • Objective.f()
    • Objective.fprime()
    • Objective.function_detail
    • Objective.progress
    • Objective.step_detail
  • OldArguments
    • OldArguments.export()
  • Optimization
    • Optimization.analyze()
    • Optimization.refine()
    • Optimization.use_minimize
  • OverallGp
    • OverallGp.default()
    • OverallGp.nothing()
    • OverallGp.parse()
  • ParameterizeSubCommands
    • ParameterizeSubCommands.clear_parser
    • ParameterizeSubCommands.do_SELECTION()
    • ParameterizeSubCommands.do_clear()
    • ParameterizeSubCommands.do_group()
    • ParameterizeSubCommands.do_individual()
    • ParameterizeSubCommands.do_overall()
    • ParameterizeSubCommands.do_print()
    • ParameterizeSubCommands.do_torsion()
    • ParameterizeSubCommands.group_parser
    • ParameterizeSubCommands.help_SELECTION()
    • ParameterizeSubCommands.individual_parser
    • ParameterizeSubCommands.overall_parser
    • ParameterizeSubCommands.param_type
    • ParameterizeSubCommands.print_group
    • ParameterizeSubCommands.print_parser
    • ParameterizeSubCommands.torsion_parser
    • ParameterizeSubCommands.which()
  • Parameters
    • Parameters.analyze()
    • Parameters.check_support()
    • Parameters.check_supported()
    • Parameters.debug_instances
    • Parameters.extract()
    • Parameters.grouping
    • Parameters.pack_like()
    • Parameters.param
    • Parameters.partials
    • Parameters.scale_rotation
    • Parameters.supported_modes
    • Parameters.torsion_change()
    • Parameters.value
  • RSParameterization
    • RSParameterization.magnification
    • RSParameterization.resolution
  • ResidueInfo
    • ResidueInfo.angleEntry
    • ResidueInfo.changeArray()
    • ResidueInfo.color()
    • ResidueInfo.combine()
    • ResidueInfo.combined
    • ResidueInfo.combined_bond_ids()
    • ResidueInfo.copy()
    • ResidueInfo.empty()
    • ResidueInfo.emptyID()
    • ResidueInfo.emptyLikeAtom()
    • ResidueInfo.flatten()
    • ResidueInfo.fromParameters()
    • ResidueInfo.getCombined()
    • ResidueInfo.impactArray()
    • ResidueInfo.impactDelta()
    • ResidueInfo.impactHistory()
    • ResidueInfo.impactSequential()
    • ResidueInfo.load()
    • ResidueInfo.name
    • ResidueInfo.neighbors()
    • ResidueInfo.overall
    • ResidueInfo.pickle()
    • ResidueInfo.pickles
    • ResidueInfo.plot()
    • ResidueInfo.print_all
    • ResidueInfo.rankImpact()
    • ResidueInfo.read()
    • ResidueInfo.residue
    • ResidueInfo.residueEntry
    • ResidueInfo.save()
    • ResidueInfo.saved
  • Superimposition
  • Tasks
    • Tasks.analyze()
    • Tasks.analyze_prereq()
    • Tasks.convergence()
    • Tasks.dihedral_hinges()
    • Tasks.dihedral_paint()
    • Tasks.fix_dihedrals()
    • Tasks.impact()
    • Tasks.impact_paint()
    • Tasks.impact_paint_prereq()
    • Tasks.impact_pickle()
    • Tasks.impact_pickle_prereq()
    • Tasks.impact_plot()
    • Tasks.impact_plot_prereq()
    • Tasks.impact_prereq()
    • Tasks.impact_print()
    • Tasks.impact_print_prereq()
    • Tasks.select_dihedrals()
  • TorsionGp
    • TorsionGp.changing
    • TorsionGp.default()
    • TorsionGp.default_selection()
    • TorsionGp.dihedrals_within
    • TorsionGp.linkOverlapWarningMsg
    • TorsionGp.linkOverlapWarnings
    • TorsionGp.movable
    • TorsionGp.nothing()
    • TorsionGp.parse()
    • TorsionGp.selections
  • TorsionParameterization
    • TorsionParameterization.append()
    • TorsionParameterization.changed()
    • TorsionParameterization.changing
    • TorsionParameterization.check()
    • TorsionParameterization.connect
    • TorsionParameterization.connected
    • TorsionParameterization.connectivity
    • TorsionParameterization.default_selection_expr
    • TorsionParameterization.defaults()
    • TorsionParameterization.dihedrals_within
    • TorsionParameterization.efficiency_check
    • TorsionParameterization.efficiency_level
    • TorsionParameterization.extend()
    • TorsionParameterization.insert()
    • TorsionParameterization.movable
    • TorsionParameterization.parse_selection()
    • TorsionParameterization.variable
  • Unit
  • XYZGrouping
  • zero()
• Parameterize:
  • Parameterize sub-commands & selections:
• PhiPsi_restraints (CNS; backbone torsion angle).
  • Synopsis
  • Usage
  • Example
  • History
• qsort module
  • qsort()
  • qsort_without_duplicates()
• restraints module
  • Ala
  • AminoAcid
    • AminoAcid.types
  • Anchor
    • Anchor.check()
    • Anchor.end_atoms
    • Anchor.stats()
  • Arg
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • Asn
  • Asp
  • Brestraint
    • Brestraint.df()
    • Brestraint.f()
    • Brestraint.rms()
  • ClassHolder
    • ClassHolder.add_class()
  • Commands
    • Commands.ap1
    • Commands.do_restraints()
  • CovalentRestraint
    • CovalentRestraint.angle
    • CovalentRestraint.angleDeviants()
    • CovalentRestraint.angleGrad()
    • CovalentRestraint.angleGrad_dc()
    • CovalentRestraint.angleResidual()
    • CovalentRestraint.angleStats()
    • CovalentRestraint.angle_sigma
    • CovalentRestraint.f()
    • CovalentRestraint.f_grad()
    • CovalentRestraint.get_history()
    • CovalentRestraint.length
    • CovalentRestraint.lengthDeviants()
    • CovalentRestraint.lengthGrad()
    • CovalentRestraint.lengthResidual()
    • CovalentRestraint.lengthStats()
    • CovalentRestraint.length_sigma
    • CovalentRestraint.torsionGrad()
    • CovalentRestraint.update()
  • Cys
  • Distance_id
    • Distance_id.childless()
    • Distance_id.deviation()
    • Distance_id.deviation_str()
    • Distance_id.distance()
    • Distance_id.family()
    • Distance_id.partial()
    • Distance_id.residual()
    • Distance_id.vector()
  • Distance_input
  • Distance_selection
    • Distance_selection.deviation()
    • Distance_selection.deviation1()
    • Distance_selection.deviation_sym()
  • Distances
    • Distances.add()
    • Distances.calculate()
    • Distances.doc
    • Distances.entry
  • Geometry
    • Geometry.angle()
    • Geometry.bond()
  • Gln
  • Glu
  • Gly
  • His
  • Ile
  • Leu
  • Lys
  • Met
  • OldArguments
    • OldArguments.export()
  • PairIDs
  • Phe
  • Pro
  • RestraintsSubCommands
    • RestraintsSubCommands.ap2
    • RestraintsSubCommands.do_distance()
    • RestraintsSubCommands.do_information()
  • Ser
  • Tasks
    • Tasks.restraints()
    • Tasks.restraints_distance()
    • Tasks.restraints_distance_prereq()
    • Tasks.restraints_information()
    • Tasks.restraints_information_prereq()
    • Tasks.restraints_prereq()
  • Thr
  • Trp
  • Tyr
  • VDWRestraint
    • VDWRestraint.Status
    • VDWRestraint.connectivityExclusion
    • VDWRestraint.distance
    • VDWRestraint.f()
    • VDWRestraint.f_grad()
    • VDWRestraint.get_history()
    • VDWRestraint.get_neighbors()
    • VDWRestraint.matrix_bonded()
    • VDWRestraint.power
    • VDWRestraint.radius
    • VDWRestraint.status()
    • VDWRestraint.update()
    • VDWRestraint.weightFactor
  • Val
  • distance_arg_parse()
  • ss()
• rotamer module
  • Rotamer
    • Rotamer.Z
    • Rotamer.all_atoms
    • Rotamer.chi()
    • Rotamer.error
    • Rotamer.extendIndex()
    • Rotamer.index
    • Rotamer.rotate()
  • flip()
• rotamer_chi_lib module
  • Rotamer_library
    • Rotamer_library.most_probable_rotamer()
    • Rotamer_library.residue_types()
    • Rotamer_library.rotamers()
    • Rotamer_library.rotamers_dictionary()
    • Rotamer_library.rotamers_list()
• rseval module
  • rseval()
• rsref module
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
    • Arguments.finalize()
  • OldArguments
    • OldArguments.export()
  • RSRef
  • Tasks
    • Tasks.analyze()
    • Tasks.analyze_prereq()
    • Tasks.atoms_being_evaluated
    • Tasks.atoms_refined
    • Tasks.calculate_map()
    • Tasks.calculate_map_prereq()
    • Tasks.default_group
    • Tasks.diagnostics()
    • Tasks.evaluate()
    • Tasks.evaluate_prereq()
    • Tasks.image_refine()
    • Tasks.image_refine_prereq()
    • Tasks.implied_parameterization()
    • Tasks.import_coord()
    • Tasks.neighbors_deprecated()
    • Tasks.neighbors_prereq()
    • Tasks.parameterization_init()
    • Tasks.parameterization_init_prereq()
    • Tasks.parameterize()
    • Tasks.parameterize_prereq()
    • Tasks.perturb()
    • Tasks.perturb_prereq()
    • Tasks.profile()
    • Tasks.randomize()
    • Tasks.randomize_prereq()
    • Tasks.reconcile_types()
    • Tasks.reconcile_types_prereq()
    • Tasks.refine()
    • Tasks.refine_magnification()
    • Tasks.refine_prereq()
    • Tasks.residual
    • Tasks.residual_db
    • Tasks.residual_do
    • Tasks.residual_dx
    • Tasks.residual_dxyz
    • Tasks.residual_dy
    • Tasks.residual_dz
    • Tasks.restrain_to_reference
    • Tasks.rotamer()
    • Tasks.rotamer_prereq()
    • Tasks.run_test()
    • Tasks.symmetry_current
    • Tasks.symmetry_expand()
    • Tasks.symmetry_expand_prereq()
    • Tasks.symmetry_init()
    • Tasks.symmetry_init_prereq()
    • Tasks.verbose
    • Tasks.write_map()
    • Tasks.write_map_prereq()
  • TopCommands
    • TopCommands.do_evaluate()
    • TopCommands.do_image_refine()
    • TopCommands.do_map()
    • TopCommands.do_neighbors()
    • TopCommands.do_parameterize()
    • TopCommands.do_perturb()
    • TopCommands.do_profile()
    • TopCommands.do_randomize()
    • TopCommands.do_refine()
    • TopCommands.do_rotamer()
    • TopCommands.do_test()
    • TopCommands.evaluate_parser
    • TopCommands.help_test()
    • TopCommands.image_refine_group
    • TopCommands.image_refine_parser
    • TopCommands.map_parser
    • TopCommands.neighbors_parser
    • TopCommands.parameterize_parser
    • TopCommands.perturb_parser
    • TopCommands.profile_parser
    • TopCommands.randomize_parser
    • TopCommands.refine_convergence
    • TopCommands.refine_parser
    • TopCommands.rotamer_parser
  • main()
  • startup()
• RSRef Real space refinement: atomic structure vs. map
  • Synopsis
  • Sources of Documentation
  • Concepts
    • Image Refinement
      • Magnification
      • Overall B or Envelope Function
      • Contrast Transfer Function (CTF)
      • Low-pass filter / Resolution
      • Image Parameter Refinement with image_refine
    • Model parameterization
      • Individual atom
      • Group
      • Torsion
  • Command-line options
    • Deviations for RSRef embedded in other programs
      • CNS-embedded version
  • Input files
    • local_symmetry
  • Command interpreter
    • Syntax:
    • Shell:
    • Hierachical structure:
    • Just-in-time calculation & pre-requisites:
    • Error recovery:
    • Selected commands - implementation-specific extensions & limitations.
      • @FILE or run_script FILE
      • Command-line commands
      • done, exit and quit
      • python interpreter
        • Limitations, bugs & work-arounds
    • Other commands available in all applications
  • Command list
  • Command Help
    • alias
    • analyze
      • analyze sub-commands
        • convergence
        • dihedrals
          • dihedrals sub-commands
            • hinges
            • impact
              • impact sub-commands
              • color
              • pickle
              • plot
              • print
            • paint
        • done
    • edit
    • evaluate
    • exit
    • help
    • history
    • image_refine
    • macro
    • map
    • neighbors
    • parameterize
      • parameterize sub-commands
        • clear
        • done
        • group
        • individual
        • overall
        • print
        • torsion
    • parrot
    • pdbout
    • perturb
    • profile
    • py
    • quit
    • randomize
    • refine
    • restraints
      • restraints sub-commands
        • distance
        • done
    • rotamer
    • run_pyscript
    • run_script
    • select
    • set
    • shell
    • shortcuts
    • Additional considerations
      • Analyze
      • Evaluate
      • Image_refine
        • Parameters:
        • Options
      • Parrot
      • Pdbout
      • Perturb
        • Output (stdout)
      • Refine
        • Options
      • Restraints
    • Python Interpreter for advanced functionality
  • Performance
    • Radii
    • B-factors
  • Atom selections and groups
    • Selections
    • Groups
  • Troubleshooting
    • Density calculation
      • Form factors
    • Coordinates
      • PDB output
    • Selections
      • Run-time exceptions
    • Parameterization
      • Torsion
    • Refinement
  • Credits
    • Citations
  • Colophon
• Atom selections and groups
  • Selections
  • Groups
• sidechain module
  • Side_chains
    • Side_chains.rota_match()
    • Side_chains.rota_print()
• space_group module
  • SpaceGroups
    • SpaceGroups.build()
    • SpaceGroups.jar
    • SpaceGroups.pickle()
    • SpaceGroups.which()
  • lattice_operators()
• stereochemistry module
  • CovalentRadii
    • CovalentRadii.bonds
    • CovalentRadii.checkRadii()
    • CovalentRadii.curated()
    • CovalentRadii.element
    • CovalentRadii.fitBondTypes()
    • CovalentRadii.halfLength()
    • CovalentRadii.number
    • CovalentRadii.optimizeProteinAmide()
    • CovalentRadii.optimizeProteinAromatic()
    • CovalentRadii.optimizeProteinBackbone()
    • CovalentRadii.optimizeProteinCarboxylate()
    • CovalentRadii.optimizeProteinGuanidinium()
    • CovalentRadii.optimizeProteinHis()
    • CovalentRadii.optimizeProteinHisAve()
    • CovalentRadii.optimizeProteinPhe()
    • CovalentRadii.optimizeProteinPheAve()
    • CovalentRadii.optimizeProteinPheH()
    • CovalentRadii.optimizeProteinTrp()
    • CovalentRadii.optimizeProteinTrpAve()
    • CovalentRadii.optimizeProteinTyr()
    • CovalentRadii.optimizeProteinTyrAve()
    • CovalentRadii.protein()
    • CovalentRadii.radius
• superpose module
  • Accumulator
    • Accumulator.add()
    • Accumulator.mean()
    • Accumulator.std()
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
    • Arguments.finalize()
  • Objective
    • Objective.add_torsion_restraint()
    • Objective.callback()
    • Objective.depends_on_anisou
    • Objective.f()
    • Objective.fprime()
    • Objective.function_detail
    • Objective.progress
    • Objective.step_detail
  • OldArguments
    • OldArguments.export()
    • OldArguments.finalize()
  • PairItem
    • PairItem.copy()
    • PairItem.from_pair()
    • PairItem.index
    • PairItem.matched_to
    • PairItem.reordered
    • PairItem.reordered_paired
  • PairSubCommands
    • PairSubCommands.do_match()
    • PairSubCommands.do_print()
    • PairSubCommands.do_within()
    • PairSubCommands.help_SELECTION_EXPR()
    • PairSubCommands.match_parser
    • PairSubCommands.within_parser
  • Pairing
    • Pairing.add()
    • Pairing.attributeOrder
    • Pairing.bfactors()
    • Pairing.connectivity
    • Pairing.continuable
    • Pairing.deprecated_3ax
    • Pairing.difference()
    • Pairing.differences()
    • Pairing.differences_vs_bs()
    • Pairing.equivs
    • Pairing.info()
    • Pairing.loquacious
    • Pairing.objective
    • Pairing.overlay()
    • Pairing.parameters
    • Pairing.residueTable
    • Pairing.superpose()
  • Parameters
    • Parameters.grouping
    • Parameters.param
    • Parameters.partials
    • Parameters.supported_modes
    • Parameters.value
  • Tasks
    • Tasks.atoms_being_evaluated
    • Tasks.atoms_refined
    • Tasks.backup()
    • Tasks.backup_prereq()
    • Tasks.bfactors()
    • Tasks.bfactors_prereq()
    • Tasks.default_group
    • Tasks.evaluate()
    • Tasks.evaluate_prereq()
    • Tasks.flip()
    • Tasks.flip_prereq()
    • Tasks.overlay()
    • Tasks.overlay_prereq()
    • Tasks.pair()
    • Tasks.pair_init()
    • Tasks.pair_init_prereq()
    • Tasks.pair_prereq()
    • Tasks.parameterization_init()
    • Tasks.parameterization_init_prereq()
    • Tasks.parameterize()
    • Tasks.parameterize_prereq()
    • Tasks.phipsi_copy()
    • Tasks.phipsi_copy_prereq()
    • Tasks.phipsi_diff()
    • Tasks.phipsi_diff_prereq()
    • Tasks.read_coords()
    • Tasks.read_target()
    • Tasks.read_target_prereq()
    • Tasks.refine()
    • Tasks.refine_prereq()
    • Tasks.restore()
    • Tasks.restore_prereq()
    • Tasks.restrain_to_reference
    • Tasks.run_test()
    • Tasks.verbose
  • Test
    • Test.set_options()
  • TopCommands
    • TopCommands.backup_parser
    • TopCommands.bfactors_parser
    • TopCommands.do_backup()
    • TopCommands.do_bfactors()
    • TopCommands.do_evaluate()
    • TopCommands.do_flip()
    • TopCommands.do_overlay()
    • TopCommands.do_pair()
    • TopCommands.do_parameterize()
    • TopCommands.do_phipsi_copy()
    • TopCommands.do_phipsi_diff()
    • TopCommands.do_refine()
    • TopCommands.do_restore()
    • TopCommands.do_test()
    • TopCommands.evaluate_parser
    • TopCommands.flip_parser
    • TopCommands.help_test()
    • TopCommands.overlay_parser
    • TopCommands.pair_parser
    • TopCommands.parameterize_parser
    • TopCommands.phipsi_copy_parser
    • TopCommands.phipsi_diff_parser
    • TopCommands.refine_convergence
    • TopCommands.refine_parser
    • TopCommands.restore_parser
    • TopCommands.test_parser
  • dissect()
  • findS0()
  • main()
  • startup()
  • std_err_mu()
  • t1_Welch_gt()
  • t1_Welch_lt()
  • z_d()
• Superpose: Rigid-group / Flexible Structure Overlay
  • Synopsis
  • Sources of Documentation
  • Command-line options
  • Command interpreter
    • Syntax:
    • Shell:
    • Hierachical structure:
    • Just-in-time calculation & pre-requisites:
    • Error recovery:
    • Selected commands - implementation-specific extensions & limitations.
      • @FILE or run_script FILE
      • Command-line commands
      • done, exit and quit
      • python interpreter
        • Limitations, bugs & work-arounds
    • Other commands available in all applications
  • Command list
  • Command Help
    • alias
    • analyze
      • analyze sub-commands
        • convergence
        • dihedrals
          • dihedrals sub-commands
            • hinges
            • impact
              • impact sub-commands
              • color
              • pickle
              • plot
              • print
            • paint
        • done
    • backup
    • bfactors
    • edit
    • evaluate
    • exit
    • flip
    • help
    • history
    • macro
    • overlay
    • pair
      • pair sub-commands
        • done
        • match
        • print
        • within
    • parameterize
      • parameterize sub-commands
        • clear
        • done
        • group
        • individual
        • overall
        • print
        • torsion
    • parrot
    • pdbout
    • phipsi_copy
    • phipsi_diff
    • py
    • quit
    • refine
    • restore
    • run_pyscript
    • run_script
    • select
    • set
    • shell
    • shortcuts
    • test
    • Python Interpreter for advanced functionality
  • Atom selections and groups
    • Selections
    • Groups
  • Troubleshooting
    • Pairing
    • Refinement
  • Installation:
  • Credits
  • Citations
  • Colophon
• symexp module
  • Tasks
    • Tasks.read_coords()
    • Tasks.read_coords_prereq()
    • Tasks.symmetry_expand()
    • Tasks.symmetry_expand_prereq()
    • Tasks.symmetry_init()
    • Tasks.symmetry_init_prereq()
    • Tasks.write_coords()
    • Tasks.write_coords_prereq()
  • TopCommands
    • TopCommands.do_neighbors()
    • TopCommands.do_pdbout()
    • TopCommands.do_sphere()
    • TopCommands.do_test()
    • TopCommands.help_test()
    • TopCommands.neighbors_parser
    • TopCommands.pdbout_parser
    • TopCommands.sphere_parser
  • startup()
• SymExp: Symmetry expansion of molecular coordinates
  • Synopsis
  • Sources of Documentation
  • Command-line options
  • Input files
    • local_symmetry
  • Command interpreter
    • Syntax:
    • Shell:
    • Hierachical structure:
    • Just-in-time calculation & pre-requisites:
    • Error recovery:
    • Selected commands - implementation-specific extensions & limitations.
      • @FILE or run_script FILE
      • Command-line commands
      • done, exit and quit
      • python interpreter
        • Limitations, bugs & work-arounds
    • Other commands available in all applications
  • Command list
  • Command Help
    • alias
    • edit
    • exit
    • help
    • history
    • macro
    • neighbors
    • parrot
    • pdbout
    • py
    • quit
    • run_pyscript
    • run_script
    • set
    • shell
    • shortcuts
    • sphere
    • Python Interpreter for advanced functionality
  • Credits
  • Colophon
• symmetry module
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • Cartesian_operator
    • Cartesian_operator.euler()
    • Cartesian_operator.isunit()
  • Documentation
    • Documentation.Input
      • Documentation.Input.local
  • OldArguments
    • OldArguments.export()
  • Symmetry
    • Symmetry.complete()
    • Symmetry.debug
    • Symmetry.equivalent()
    • Symmetry.inverse()
    • Symmetry.neighbors()
    • Symmetry.repr_op()
    • Symmetry.verbose
    • Symmetry.with_neighbors()
  • Target
    • Target.debug
    • Target.isclose()
    • Target.isneighbor()
  • safe_eval()
• torsion module
  • Graph
    • Graph.addDirectedEdge()
    • Graph.addEdge()
    • Graph.addVertex()
    • Graph.dfs()
    • Graph.dfsVisit()
    • Graph.find_articulation_edges()
    • Graph.find_bridgeless_components()
    • Graph.get_reverse()
    • Graph.removeDirectedEdge()
    • Graph.removeEdge()
    • Graph.scc()
    • Graph.version_ID
  • ImpactRestraint
  • Limit
    • Limit.L1Norm
    • Limit.change()
    • Limit.dfL1Norm()
    • Limit.dfL1sq()
    • Limit.fL1Norm()
    • Limit.fL1sq()
    • Limit.mod360()
    • Limit.stats()
  • TAProtein
    • TAProtein.all_dependents
    • TAProtein.apply_torsion()
    • TAProtein.apply_torsion_deprecated()
    • TAProtein.bond_dependents
    • TAProtein.compare()
    • TAProtein.copy()
    • TAProtein.debug
    • TAProtein.edit_links()
    • TAProtein.generate_rotation_masks()
    • TAProtein.generate_structure()
    • TAProtein.get_all_backbone_atoms()
    • TAProtein.get_all_backbone_bonds()
    • TAProtein.get_all_bonds_crossing_cut()
    • TAProtein.get_all_bonds_in_selection()
    • TAProtein.get_all_omega()
    • TAProtein.get_all_phi()
    • TAProtein.get_all_phi_psi()
    • TAProtein.get_all_psi()
    • TAProtein.get_edge_set()
    • TAProtein.get_rotation_mask()
    • TAProtein.get_selected_phi()
    • TAProtein.get_selected_psi()
    • TAProtein.join_all()
    • TAProtein.join_atoms()
    • TAProtein.phi_psi_selection()
    • TAProtein.print_bonds()
    • TAProtein.print_connectivity()
    • TAProtein.quartet()
    • TAProtein.save_selection()
    • TAProtein.saved_selection()
    • TAProtein.separate_all()
    • TAProtein.separate_atoms()
    • TAProtein.vs_old_apply
    • TAProtein.warnings
  • dihedral_atoms()
  • dihedral_name()
  • dihedral_value()
  • getResIDKeys()
  • get_dihedral()
  • hinges()
  • warn()
• transform module
  • AugmentedOperator
    • AugmentedOperator.augment()
    • AugmentedOperator.dfbydv()
    • AugmentedOperator.dpbydv()
    • AugmentedOperator.eulerAxis()
    • AugmentedOperator.eulerX0Y0Z0()
    • AugmentedOperator.isunit()
    • AugmentedOperator.rotTrans()
    • AugmentedOperator.sphericalPolarAngles()
  • EulerX0Y0Z0
    • EulerX0Y0Z0.dObydv
    • EulerX0Y0Z0.dfbydv()
    • EulerX0Y0Z0.dpbydv()
  • Vector
  • compute_rigid_alignment_deriv()
  • compute_rigid_alignment_matrix()
  • compute_rotation_about_origin()
  • compute_rotation_matrix()
  • compute_transformation_matrix()
  • displacements()
  • dot()
  • general_transformation_matrix()
  • groupPartials()
  • groupTransformations()
  • multiply_matrix_array()
  • non_zero()
  • random_rotation_about_origin()
  • screw()
  • testFunction()
  • trial()
  • zero()
• translate module
  • Synopsis
  • Command line options
  • Arguments
    • Arguments.domestic()
    • Arguments.export()
  • Dictionary
    • Dictionary.alphabetical
    • Dictionary.convention
    • Dictionary.d
    • Dictionary.dialect()
    • Dictionary.lang
    • Dictionary.repr()
    • Dictionary.res
    • Dictionary.to1
    • Dictionary.to3
    • Dictionary.translate()
    • Dictionary.unknown()
  • startup()
• tskmgr module
  • Prerequisite
    • Prerequisite.quiet
    • Prerequisite.verbose
  • ReqExpr
  • ReqObj
    • ReqObj.getattr_or_eval()
    • ReqObj.is_met()
    • ReqObj.verbose
  • Task
    • Task.getattr_or_eval()
    • Task.verbose
  • TaskError
  • UnMetPrerequisite
  • errmsg()
  • get_namespace()
  • get_namespaces()
  • public()
  • unexpected()
• vector module
  • assertOneD()
  • assertSameSize()
  • crossDeriv()
  • crossNorm()
  • crossNormDeriv()
  • crossUnit()
  • crossUnitDeriv()
  • dotDeriv()
  • normDeriv()
• version module

Indices and tables

• Index

• Module Index

• Search Page