# Data structure classes

## `containers`

A collection of container classes supporting the PDBx/mmCIF storage model.

A base container class is defined which supports common features of data and definition containers. PDBx data files are organized in sections called data blocks which are mapped to data containers. PDBx dictionaries contain definition sections and data sections which are mapped to definition and data containers respectively.

Data in both PDBx data files and dictionaries are organized in data categories. In the PDBx syntax individual items or data identified by labels of the form ‘_categoryName.attribute_name’. The terms category and attribute in PDBx jargon are analogous table and column in relational data model, or class and attribute in an object oriented data model.

The DataCategory class provides base storage container for instance data and definition meta data.

class pdbx.containers.CifName

  Class of utilities for CIF-style data names.

  static attribute_part(name) → str

    Get the attribute part of the name.

    Parameters:

      name (str) – name

    Returns:

      attribute part of name

  static category_part(name) → str

    Get the category part of the name.

    Parameters:

      name (str) – name

    Returns:

      category part of name

class pdbx.containers.ContainerBase(name)

  Container base class for data and definition objects.

  append(obj)

    Add the input object to the current object catalog. An existing object of the same name will be overwritten.

    Parameters:

      obj (`DataCategory`) – input object to catalog

  exists(name) → bool

    Determine if object name exists in object catalog.

    Parameters:

      name (str) – object name

    Returns:

      whether object exists in object catalog

  get_object(name)

    Get object from object catalog.

    Parameters:

      name (str) – object name

    Returns:

      object or None

    Return type:

      `DataCategory`

  get_object_name_list() → list

    Get list of object names.

    Returns:

      list of `DataCategory` objects

  get_type() → str

    Get container type.

    Returns:

      container type

  property name: str

    Get container name.

    Returns:

      container name

  print_it(fobj=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, type_='brief')

    Dump information about container to specified file object.

    Parameters:

      - fobj (file) – file object for writing

      - type (str) – type of summary (“brief” makes it short)

  remove(current_name) → bool

    Remove object by name.

    Parameters:

      current_name (str) – name of object to remove

    Returns:

      True on success or False otherwise.

  rename(current_name, new_name) → bool

    Change the name of an object in place.

    Parameters:

      - current_name (str) – old name for object

      - new_name (str) – new name for object

    Returns:

      indicator of whether renaming was successful

  replace(obj)

    Replace an existing object with the input object.

    Parameters:

      obj (`DataCategory`) – input object to catalog

  set_name(name)

    Set container name.

    Parameters:

      name (str) – container name

  set_type(type_)

    Set container type.

    Parameters:

      type (str) – container type

class pdbx.containers.DataCategory(name, attribute_name_list=None, row_list=None)

  Methods for creating, accessing, formatting PDBx cif data categories.

  append(row)

    Add row to container.

    Parameters:

      row (list) – row to add

  append_attribute(attribute_name)

    Add attribute to container.

    Parameters:

      attribute_name (str) – name of attribute to add

  append_attribute_extend_rows(attribute_name)

    Append attribute and extend rows.

    Parameters:

      attribute_name (str) – name of attribute to add

  property attribute_count: int

    Get number of attributes.

  property attribute_list: list

    Get list of attributes.

  property attribute_list_with_order: list

    Get list of attributes in order.

  property current_attribute: str

    Get current attribute.

  property current_row_index: int

    Get current row index.

  dump_it(file_=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

    Dump contents of container.

    Parameters:

      file (file) – file object ready for writing

  get_attribute_index(attribute_name) → int

    Get index of given attribute.

    Parameters:

      attribute_name (str) – name of attribute

    Returns:

      index of attribute

    Raises:

      IndexError – if attribute not found

  get_format_type_list(steps=1) → str

    Get a formatted type list.

    Parameters:

      steps (int) – step size for iterating through rows

    Returns:

      formatted type list

  property get_format_type_list_x: str

    Alternate version of format type list.

  get_full_row(index) → list

    Return a full row based on the length of the the attribute list.

    Parameters:

      index (int) – index of row to retrieve

    Returns:

      row

  get_max_attribute_list_length(steps=1) → int

    Get maximum length of attribute value list.

    Parameters:

      steps (int) – step size for iterating through rows

    Returns:

      attribute value list max length

  get_row(index) → list

    Get specified row.

    Parameters:

      index (int) – row index

    Returns:

      specified row or empty array if row not found.

  get_value(attribute_name=None, row_index=None)

    Get value for specified attribute and row.

    Parameters:

      - attribute_name (str) – attribute name

      - row_index (int) – row index

    Returns:

      attribute value

    Raises:

      IndexError – if attribute not found

  get_value_formatted(attribute_name=None, row_index=None) → str

    Get formatted version of value.

    Parameters:

      - attribute_name (str) – attribute name

      - row_index (int) – row index

    Returns:

      formatted value

  get_value_formatted_by_index(attribute_index, row_index) → str

    Get value formatted by index.

    Parameters:

      - attribute_name (str) – attribute name

      - row_index (int) – row index

    Returns:

      formatted value

  has_attribute(attribute_name) → bool

    Indicate whether container has attribute.

  invoke_attribute_method(attribute_name, method)

    Invoke method of current attribute.

    Parameters:

      - attribute_name (str) – attribute name

      - method (str) – name of attribute method

  invoke_category_method(method)

    Invoke method of current category.

    Parameters:

      method (str) – name of method

  property item_name_list: list

    List of attribute names as fully qualified item names.

  property max_attribute_list_length: int

    Get maximum attribute list length.

  property name: str

    Get container name.

  print_it(file_=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

    Print container information.

    Parameters:

      file (file) – file object ready for writing

  remove_row(index) → bool

    Remove specified row.

    Parameters:

      index (int) – index of row to remove

    Returns:

      True if successful, False otherwise

  rename_attribute(current_attribute_name, new_attribute_name) → bool

    Change the name of an attribute in place.

    Parameters:

      - current_attribute_name (str) – current attribute name

      - new_attribute_name (str) – new attribute name

    Returns:

      flag indicating renaming success

  replace_substring(old_value, new_value, attribute_name) → bool

    Replace substring of value of given attribute.

    Parameters:

      - old_value – old attribute value

      - new_value – new attribute value

      - attribute_name (str) – name of attribute to replace

    Returns:

      Boolean flag indicating success.

  replace_value(old_value, new_value, attribute_name) → int

    Replace the value of the specified attribute.

    Parameters:

      - old_value – old attribute value

      - new_value – new attribute value

      - attribute_name (str) – name of attribute to replace

    Returns:

      number of replacements

  property row_count: int

    Get number of rows.

  property row_list: list

    Get list of rows.

  set_value(value, attribute_name=None, row_index=None)

    Set value of attribute.

    Parameters:

      - value – value of attribute to set

      - attribute_name (str) – name of attribute

      - row_index (int) – index of row

class pdbx.containers.DataCategoryBase(name, attribute_name_list=None, row_list=None)

  Base object definition for a data category.

  get() → tuple

    Get name, attribute name list, and row list.

    Returns:

      tuple of (name, attribute name list, and row list)

  set_attribute_name_list(attribute_name_list)

    Set attribute name list.

    Parameters:

      attribute_name_list (list) – list of attribute names

  set_name(name)

    Set name.

    Parameters:

      name (str) – object name to set

  set_row_list(row_list)

    Set row list.

    Parameters:

      row_list (list) – list of rows

class pdbx.containers.DataContainer(name)

  Container class for DataCategory objects.

  get_global() → bool

    Return global flag.

  invoke_data_block_method(method)

    Invoke a method for the given data block.

    Parameters:

      method (str) – name of method

  set_global()

    Set global flag to True.

class pdbx.containers.DefinitionContainer(name)

  Container for definitions.

  is_attribute() → bool

    Determine if container contains item objects.

    Returns:

      indicator of whether item objects are in container

  is_category() → bool

    Determine if container contains category objects.

    Returns:

      indicator of whether category objects are in container

  print_it(file_=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, type_='brief')

    Print information about container to file object.

    Parameters:

      - file (file) – file object for writing

      - type (str) – type of summary (“brief” makes it short)