Package PyAutoDock :: Module MolecularSystem :: Class AbstractMolecularSystem

Class AbstractMolecularSystem

Known Subclasses:: MolecularSystem

This class defines the interface that a MolecularSystem must support for use with a Scorer or other object(s). This class maintains a list of sets of entities (like Atoms).

The get_supported_attributes method returns the list of attributes that each Entity supports.

A distance matrix is maintained pairwise by set and pairwise by entities within the set. NB: is actually the distance, **not** distance-squared. The reason for this is that for clients (like WeightedMultiTerm scorers) who must get_dist_mat repeatedly, forcing them to take the sqrt for each term is a false economy.

An index is returned when adding a set of entities (by the add_entities method). This index for an entity set can also be found using the get_entity_set_index method. The molecular system attribute configuration is a 2-tuple of validated entity_set_index. In its use, the Autodock scorer uses the first as the Receptor and second as the Ligand.

This class is intended to abstract any number of underlying molecular representations such as MolKit, mmLib, MMTK, or just a PDB file. The underlying molecular representation is abstracted as a list of entities which support the 'supported_attributes'. So, for instance, if your molecular representation doesn't have charges, its abstraction as a specialized implementation of this interface (ie the subclass of MolecularSystemBase) may have to calculate per entity charges.

Instance Methods

[hide private]

__init__(self)

add_entities(self, entity_set, coords_access_func=None)

get_entity_set_index(self, entity_set)

set_coords(self, entity_set_index, coords)

get_dist_mat(self, ix, jx)

clear_dist_mat(self, ix)

get_supported_attributes(self)

check_required_attributes(self, entity_set_index, attribute_list)

get_coords(self, entity_set_index)

get_entities(self, entity_set_num)