Bio.PDB.AbstractPropertyMap module

Class that maps (chain_id, residue_id) to a residue property.

class Bio.PDB.AbstractPropertyMap.AbstractPropertyMap(property_dict, property_keys, property_list)

Bases: object

Define base class, map holder of residue properties.

__init__(property_dict, property_keys, property_list)

Initialize the class.

__contains__(id)

Check if the mapping has a property for this residue.

Parameters:

• chain_id (char) – chain id

• res_id (char) – residue id

Examples

This is an incomplete but illustrative example:

if (chain_id, res_id) in apmap:
    res, prop = apmap[(chain_id, res_id)]

__getitem__(key)

Return property for a residue.

Parameters:

• chain_id (char) – chain id

• res_id (int or (char, int, char)) – residue id

Returns:

some residue property

Return type:

anything (can be a tuple)

__len__()

Return number of residues for which the property is available.

Returns:

number of residues

Return type:

int

keys()

Return the list of residues.

Returns:

list of residues for which the property was calculated

Return type:

[(chain_id, res_id), (chain_id, res_id),…]

__iter__()

Iterate over the (entity, property) list.

Handy alternative to the dictionary-like access.

Returns:

iterator

Examples

>>> entity_property_list = [
...     ('entity_1', 'property_1'),
...     ('entity_2', 'property_2')
... ]
>>> map = AbstractPropertyMap({}, [], entity_property_list)
>>> for (res, property) in iter(map):
...     print(res, property)
entity_1 property_1
entity_2 property_2

class Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap(property_dict, property_keys, property_list)

Bases: AbstractPropertyMap

Define class for residue properties map.

__init__(property_dict, property_keys, property_list)

Initialize the class.

class Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap(property_dict, property_keys, property_list)

Bases: AbstractPropertyMap

Define class for atom properties map.

__init__(property_dict, property_keys, property_list)

Initialize the class.