biotite.structure
=================
.. currentmodule:: biotite.structure

.. automodule:: biotite.structure

.. currentmodule:: biotite.structure


Structure types
---------------

.. autosummary::
   :nosignatures:
   :toctree:

   Atom
   AtomArray
   AtomArrayStack
   array
   stack
   repeat
   from_template

Boxes and unit cells
--------------------

.. autosummary::
   :nosignatures:
   :toctree:

   vectors_from_unitcell
   unitcell_from_vectors
   box_volume
   repeat_box
   repeat_box_coord
   move_inside_box
   remove_pbc
   remove_pbc_from_coord
   coord_to_fraction
   fraction_to_coord
   is_orthogonal

Bonds
-----

.. autosummary::
   :nosignatures:
   :toctree:

   BondList
   BondType
   connect_via_residue_names
   connect_via_distances
   find_connected
   find_rotatable_bonds

Geometry
--------

.. autosummary::
   :nosignatures:
   :toctree:

   displacement
   index_displacement
   distance
   index_distance
   angle
   index_angle
   dihedral
   index_dihedral
   centroid
   mass_center
   gyration_radius
   rdf

Transformations
---------------

.. autosummary::
   :nosignatures:
   :toctree:

   translate
   rotate
   rotate_centered
   rotate_about_axis
   align_vectors
   orient_principal_components
   superimpose
   superimpose_apply

Filters
-------

.. autosummary::
   :nosignatures:
   :toctree:

   filter_canonical_nucleotides
   filter_nucleotides
   filter_canonical_amino_acids
   filter_amino_acids
   filter_carbohydrates
   filter_backbone
   filter_peptide_backbone
   filter_phosphate_backbone
   filter_linear_bond_continuity
   filter_polymer
   filter_solvent
   filter_monoatomic_ions
   filter_intersection
   filter_first_altloc
   filter_highest_occupancy_altloc

Checks
------

.. autosummary::
   :nosignatures:
   :toctree:

   check_id_continuity
   check_atom_id_continuity
   check_res_id_continuity
   check_backbone_continuity
   check_duplicate_atoms
   check_bond_continuity
   check_linear_continuity

Residue level utility
---------------------

.. autosummary::
   :nosignatures:
   :toctree:

   get_residue_starts
   get_residues
   apply_residue_wise
   spread_residue_wise
   get_residue_masks
   get_residue_starts_for
   get_residue_positions
   get_residue_count
   residue_iter

Chain level utility
-------------------

.. autosummary::
   :nosignatures:
   :toctree:

   get_chain_starts
   apply_chain_wise
   spread_chain_wise
   get_chain_masks
   get_chain_starts_for
   get_chain_positions
   chain_iter
   get_chains
   get_chain_count
   chain_iter

Molecule level utility
----------------------

.. autosummary::
   :nosignatures:
   :toctree:

   get_molecule_indices
   get_molecule_masks
   molecule_iter

Structure comparison
--------------------

.. autosummary::
   :nosignatures:
   :toctree:

   average
   rmsd
   rmspd
   rmsf

General analysis
----------------

.. autosummary::
   :nosignatures:
   :toctree:

   sasa
   hbond
   hbond_frequency
   partial_charges
   density

Proteins
--------

.. autosummary::
   :nosignatures:
   :toctree:

   dihedral_backbone
   annotate_sse

Nucleic acids
-------------

.. autosummary::
   :nosignatures:
   :toctree:

   Edge
   GlycosidicBond
   map_nucleotide
   base_pairs
   base_stacking
   pseudoknots
   base_pairs_edge
   base_pairs_glycosidic_bond
   dot_bracket
   dot_bracket_from_structure
   base_pairs_from_dot_bracket

Miscellaneous
-------------

.. autosummary::
   :nosignatures:
   :toctree:

   AffineTransformation
   BadStructureError
   CellList
   IncompleteStructureWarning
   UnexpectedStructureWarning
   coord
   renumber_atom_ids
   renumber_res_ids


Subpackages
-----------

.. autosummary::

   biotite.structure.io
   biotite.structure.io.netcdf
   biotite.structure.io.mol
   biotite.structure.io.dcd
   biotite.structure.io.trr
   biotite.structure.io.pdbx
   biotite.structure.io.pdbqt
   biotite.structure.io.xtc
   biotite.structure.io.npz
   biotite.structure.io.mmtf
   biotite.structure.io.gro
   biotite.structure.io.pdb
   biotite.structure.io.tng
   biotite.structure.info
   biotite.structure.graphics