parmed.topologyobjects.AtomList

class parmed.topologyobjects.AtomList(*args)

Array of Atoms

Notes

Deleting an atom from the AtomList also deletes that atom from the residue it belongs to.

Methods

assign_nbidx_from_types()	Assigns the nb_idx attribute of every atom inside here from the atom_type definition.
claim()	This method causes this list to “claim” all of the items it contains and subsequently indexes all of its items.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
find_original_index(idx)	Finds an atom with the given original index.
index(value[, start, stop])	Return first index of value.
index_members()	Assigns the idx variable for every member of this list to its place in the list, if the members of this list permit
prune_unused()	This method inspects the used attribute of all of its members, if it has one, and deletes any item in which it is set to False
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
unmark()	Unmark all atoms in this list

append
extend
insert
pop
remove

__init__(*args)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(*args)	Initialize self.
append(*args, **kwargs)	Append object to the end of the list.
assign_nbidx_from_types()	Assigns the nb_idx attribute of every atom inside here from the atom_type definition.
claim()	This method causes this list to “claim” all of the items it contains and subsequently indexes all of its items.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(*args, **kwargs)	Extend list by appending elements from the iterable.
find_original_index(idx)	Finds an atom with the given original index.
index(value[, start, stop])	Return first index of value.
index_members()	Assigns the idx variable for every member of this list to its place in the list, if the members of this list permit
insert(*args, **kwargs)	Insert object before index.
pop(*args, **kwargs)	Remove and return item at index (default last).
prune_unused()	This method inspects the used attribute of all of its members, if it has one, and deletes any item in which it is set to False
remove(*args, **kwargs)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
unmark()	Unmark all atoms in this list