Package mmLib :: Module mmCIFDB :: Class mmCIFDB
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Type mmCIFDB

object --+        
         |        
      list --+    
             |    
     mmCIFData --+
                 |
                mmCIFDB


Database class for the storage and access of structural data. This database is organized according to mmCIF data tags. Methods to lookup common structure items are included.
Method Summary
  __str__(self)
  add_table(self, table)
  add_tables(self, tables)
  confirm_table(self, table_name)
Return table table_name, create the table if necessary.
  get_deposition_date(self)
Return the origional depositoin date as stored in _database_pdb_ref.date_original.
  get_entry_id(self)
Methods to get/set the structure ID.
  get_single(self, table_name, col_name)
Utility function for getting a table where there should only be a single row of data.
  get_struct_keywords(self)
Return structure keywords as stored in _struct_keywords.text
  set_deposition_date(self, date)
  set_entry_id(self, idcode)
  set_single(self, table_name, col_name, val)
Utility function for setting a table where there should only be a single row of data.
  set_struct_keywords(self, text)
    Inherited from mmCIFData
  __init__(self, name)
  __deepcopy__(self, memo)
  __delitem__(self, x)
Remove a mmCIFTable by index or table name.
  __eq__(self, other)
  __getattr__(self, name)
  __getitem__(self, x)
  __setitem__(self, x, table)
  append(self, table)
Append a mmCIFTable.
  get(self, x, default)
  get_table(self, name)
Looks up and returns a stored mmCIFTable class by it's name.
  get_tag(self, tag)
Get.
  has_key(self, x)
  has_table(self, x)
  insert(self, i, table)
  join_tag(self, cif_table_name, cif_column_name)
  new_table(self, name, columns)
Creates and returns a mmCIFTable object with the given name.
  remove(self, table)
  set_tag(self, tag, value)
Set.x
  split_tag(self, tag)
    Inherited from list
  __add__(x, y)
x.__add__(y) <==> x+y
  __contains__(x, y)
x.__contains__(y) <==> y in x
  __delslice__(x, i, j)
Use of negative indices is not supported.
  __ge__(x, y)
x.__ge__(y) <==> x>=y
  __getattribute__(...)
x.__getattribute__('name') <==> x.name
  __getslice__(x, i, j)
Use of negative indices is not supported.
  __gt__(x, y)
x.__gt__(y) <==> x>y
  __hash__(x)
x.__hash__() <==> hash(x)
  __iadd__(x, y)
x.__iadd__(y) <==> x+=y
  __imul__(x, y)
x.__imul__(y) <==> x*=y
  __iter__(x)
x.__iter__() <==> iter(x)
  __le__(x, y)
x.__le__(y) <==> x<=y
  __len__(x)
x.__len__() <==> len(x)
  __lt__(x, y)
x.__lt__(y) <==> x<y
  __mul__(x, n)
x.__mul__(n) <==> x*n
  __ne__(x, y)
x.__ne__(y) <==> x!=y
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T
  __repr__(x)
x.__repr__() <==> repr(x)
  __reversed__(...)
L.__reversed__() -- return a reverse iterator over the list
  __rmul__(x, n)
x.__rmul__(n) <==> n*x
  __setslice__(x, i, j, y)
Use of negative indices is not supported.
  count(L, value)
L.count(value) -> integer -- return number of occurrences of value
  extend(...)
L.extend(iterable) -- extend list by appending elements from the iterable
  index(...)
L.index(value, [start, [stop]]) -> integer -- return first index of value
  pop(L, index)
L.pop([index]) -> item -- remove and return item at index (default last)
  reverse(...)
L.reverse() -- reverse *IN PLACE*
  sort(...)
L.sort(cmp=None, key=None, reverse=False) -- stable sort *IN PLACE*; cmp(x, y) -> -1, 0, 1
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name
  __reduce__(...)
helper for pickle
  __reduce_ex__(...)
helper for pickle
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value

Class Variable Summary
    Inherited from mmCIFData
list __slots__ = ['name', 'file']
member_descriptor file = <member 'file' of 'mmCIFData' objects>
member_descriptor name = <member 'name' of 'mmCIFData' objects>

Method Details

confirm_table(self, table_name)

Return table table_name, create the table if necessary.

get_deposition_date(self)

Return the origional depositoin date as stored in _database_pdb_ref.date_original.

get_entry_id(self)

Methods to get/set the structure ID.

get_single(self, table_name, col_name)

Utility function for getting a table where there should only be a single row of data.

get_struct_keywords(self)

Return structure keywords as stored in _struct_keywords.text

set_single(self, table_name, col_name, val)

Utility function for setting a table where there should only be a single row of data.

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