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# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Class that maps (chain_id, residue_id) to a residue property."""
from __future__ import print_function
class AbstractPropertyMap(object):
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 __contains__(self, id):
"""True if the mapping has a property for this residue.
Example:
>>> if (chain_id, res_id) in apmap:
... res, prop = apmap[(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 (translated_id in self.property_dict)
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):
"""True if the mapping has a property for this residue.
(Obsolete; use "id in mapping" instead.)
Example:
>>> if apmap.has_key((chain_id, res_id)):
... res, prop = apmap[(chain_id, res_id)]
Is equivalent to:
>>> if (chain_id, res_id) in apmap:
... res, prop = apmap[(chain_id, res_id)]
@param chain_id: chain id
@type chain_id: char
@param res_id: residue id
@type res_id: char
"""
import warnings
from Bio import BiopythonDeprecationWarning
warnings.warn("This function is deprecated; use 'id in mapping' instead", BiopythonDeprecationWarning)
return (id in self)
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 isinstance(res_id, int):
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 isinstance(res_id, int):
ent_id = (chain_id, (' ', res_id, ' '), atom_name, icode)
return ent_id
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