Bundles

A Bundle - A set-enhancement to add filtering and store handling capabilities

Bundles can be accessed like a normal set using iteration. You can add objects using .add(item) if the bundle is not a view

Examples

Some basic functions

bundle = Bundle(['10', '20', 1, 2, 3])
str_view = bundle.c(basestring)  # only how strings
print list(str_view)  # ['10', '20']
fnc_view = bundle.v(lambda x: int(x) < 3)
print list(fnc_view) # [1, 2]

Some File specific functions

import adaptivemd as amd
bundle = Bundle([amd.File('0.dcd'), amd.File('a.pdb')])
file_view = bundle.f('*.dcd')
print list(file_view)  # [File('0.dcd')]

Logic operations produce view on the resulting bundle

and_bundle = str_view & fnc_view
print list(and_bundle)  # []
and_bundle = str_view | fnc_view
print list(and_bundle)  # [1, 2, '10', '20']

A StoredBundle is attached to a mongodb store (a stored object list). Adding will append the object to the store if not stored yet. All iteration and views will always be kept synced with the DB store content.

p = amd.Project('test-project')
store = StoredBundle()  # new bundle
store.set_store(p.storage.trajectories)  # attach to DB
print list(store)  # show all trajectories
len_store = store.v(lambda x: len(x) > 10)  # all trajs with len > 10
print list(len_store)

Set do not have ordering so some functions do not make sense. As long as you are working with storable objects (subclassed from adaptivemd.mongodb.StorableMixin) you have some time-ordering (accurate to seconds)

print store.first  # get the earlist created object
print store.one    # get one (any) single object
print store.last   # get the last created object

A bundle is mostly meant to work with storable objects (but does not have to) To simplify access to certain attributes or apply function to all members you can use the BaseBundle.all() attribute and get a delegator that will apply an attribute or method to all objects

print len_store.all.length  # print all lengths of all objects in len_store
print store.all.path  # print all path of all trajectories
# call `.execute('shutdown') on all workers in the `.workers` bundle
print p.workers.all.execute('shutdown')

Classes

Bundle([iterable])	A container of objects
StoredBundle()	A stored bundle in a mongodb
SortedBundle(bundle, key)	Sorted view of a bundle
ViewBundle(bundle, view)	A view on a bundle where object are filtered by a bool function
BaseBundle	BaseClass for Bundle functionality a special set of storable objects
LogicBundle(bundle1, bundle2)	Implement simple and and or logic for bundles
AndBundle(bundle1, bundle2)	And logic
OrBundle(bundle1, bundle2)	Or logic
BundleDelegator(bundle)	Delegate an attribute call to all elements in a bundle
FunctionDelegator(bundle, item)	Delegate a function call to all elements in a bundle