mmLib.mmCIFDB.mmCIFDB

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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