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from types import IntType
__doc__="Class that maps (chain_id, residue_id) to a residue property"
class AbstractPropertyMap:
def __init__(self, property_dict, property_keys, property_list):
self.property_dict=property_dict
self.property_keys=property_keys
self.property_list=property_list
def _translate_id(self, entity_id):
return entity_id
def __getitem__(self, key):
"""
Return property for a residue.
@param chain_id: chain id
@type chain_id: char
@param res_id: residue id
@type res_id: int or (char, int, char)
@return: some residue property
@rtype: anything (can be a tuple)
"""
translated_id=self._translate_id(key)
return self.property_dict[translated_id]
def __len__(self):
"""
Return number of residues for which the property is available.
@return: number of residues
@rtype: int
"""
return len(self.property_dict)
def has_key(self, id):
"""
Return 1 if the map has a property for this residue, 0 otherwise.
Example:
>>> if map.has_key((chain_id, res_id)):
>>> res, property=map[(chain_id, res_id)]
@param chain_id: chain id
@type chain_id: char
@param res_id: residue id
@type res_id: char
"""
translated_id=self._translate_id(id)
return self.property_dict.has_key(translated_id)
def keys(self):
"""
Return the list of residues.
@return: list of residues for which the property was calculated
@rtype: [(chain_id, res_id), (chain_id, res_id),...]
"""
return self.property_keys
def __iter__(self):
"""
Iterate over the (entity, property) list. Handy alternative to
the dictionary-like access.
Example:
>>> for (res, property) in iter(map):
>>> print res, property
@return: iterator
"""
for i in range(0, len(self.property_list)):
yield self.property_list[i]
class AbstractResiduePropertyMap(AbstractPropertyMap):
def __init__(self, property_dict, property_keys, property_list):
AbstractPropertyMap.__init__(self, property_dict, property_keys,
property_list)
def _translate_id(self, ent_id):
chain_id, res_id=ent_id
if type(res_id)==IntType:
ent_id=(chain_id, (' ', res_id, ' '))
return ent_id
class AbstractAtomPropertyMap(AbstractPropertyMap):
def __init__(self, property_dict, property_keys, property_list):
AbstractPropertyMap.__init__(self, property_dict, property_keys,
property_list)
def _translate_id(self, ent_id):
if len(ent_id)==4:
chain_id, res_id, atom_name, icode=ent_id
else:
chain_id, res_id, atom_name=ent_id
icode=None
if type(res_id)==IntType:
ent_id=(chain_id, (' ', res_id, ' '), atom_name, icode)
return ent_id
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