Package PyAutoDock :: Module MolecularSystem :: Class MolecularSystem

Class MolecularSystem

AbstractMolecularSystem --+
                          |
                         MolecularSystem

concrete subclass implementation of AbstractMolecularSystem

Instance Methods

[hide private]

__init__(self, e_set=None, coords_access_func=None)

get_entity_set_index(self, entity_set)

_validate_entity_set_index(self, entity_set_ix)

get_supported_attributes(self)

check_required_attributes(self, entity_set_index, attribute_list)
Check that all the elements of the given entity_set have all the attributes in the attribute_list.

_compute_distance_matrix(self, ix, jx)
Compute the distance matrix for the given sets

check_distance_cutoff(self, ix, jx, cutoff)
check if a distance in the distance matrix for the specified sets is below a user specified cutoff.

get_dist_mat(self, ix, jx)
return the distance matrix for the given two sets

clear_dist_mat(self, ix)
clear all distance-squared matrices for the given entity_set

set_configuration(self, ix=None, jx=None)
For now this is a 2-tuple of entity_set_index that describes for a scorer which two entity sets are being considered with respect to one another.

add_entities(self, entity_set, coords_access_func=None)
add a MolKit.EntitySet to the MolecularSystem

get_entities(self, entity_set_ix=0)
return the specified entity_set.

set_coords(self, entity_set_ix, coords, coords_set_func=None)
provide new coords for the specified entitySet.

get_coords(self, entity_set_ix=0)
return the coordinates of the specified entity_set.

Method Details

[hide private]

init(self, e_set=None, coords_access_func=None)
(Constructor)

source code

None

Overrides: AbstractMolecularSystem.__init__

get_entity_set_index(self, entity_set)

source code

None

Overrides: AbstractMolecularSystem.get_entity_set_index

_validate_entity_set_index(self, entity_set_ix)

source code

None

get_supported_attributes(self)

source code

None

Overrides: AbstractMolecularSystem.get_supported_attributes

check_required_attributes(self, entity_set_index, attribute_list)

source code

Check that all the elements of the given entity_set have all the attributes in the attribute_list.

Overrides: AbstractMolecularSystem.check_required_attributes

_compute_distance_matrix(self, ix, jx)

source code

Compute the distance matrix for the given sets

This method should be called from within the class by get_dist_mat which knows when it's really necessary.

check_distance_cutoff(self, ix, jx, cutoff)

source code

check if a distance in the distance matrix for the specified sets is below a user specified cutoff.

If the distance matrix does not exist if is computed up to the first encounter of a distance below the cutoff. If such a distance is encountered it is returned. If the matrix exists the minimum distance is returned if it is below the cutoff. If distance are all above the cutoff, None is returned.

get_dist_mat(self, ix, jx)

source code

return the distance matrix for the given two sets

Overrides: AbstractMolecularSystem.get_dist_mat

clear_dist_mat(self, ix)

source code

clear all distance-squared matrices for the given entity_set

Overrides: AbstractMolecularSystem.clear_dist_mat

set_configuration(self, ix=None, jx=None)

source code

For now this is a 2-tuple of entity_set_index that describes for a scorer which two entity sets are being considered with respect to one another.

Overrides: AbstractMolecularSystem.set_configuration

add_entities(self, entity_set, coords_access_func=None)

source code

add a MolKit.EntitySet to the MolecularSystem

Returns the entity_set_num for the new EntitySet. First two calls to add_entities set the configuration to use those EntitySets.

Overrides: AbstractMolecularSystem.add_entities

get_entities(self, entity_set_ix=0)

source code

return the specified entity_set.

entity_set_ix is an integer that indexes into self.entity_sets

Overrides: AbstractMolecularSystem.get_entities

set_coords(self, entity_set_ix, coords, coords_set_func=None)

source code

provide new coords for the specified entitySet. entity_set_ix is the index of an existing entitySet. coords is a list (of proper length) of anything you want to use to update coordinate with the coords_set_func you supply.

Overrides: AbstractMolecularSystem.set_coords

get_coords(self, entity_set_ix=0)

source code

return the coordinates of the specified entity_set.

DEPRECATED: use get_entities().coords instead. entity_set_ix is an integer that indexes into self.entity_sets

Overrides: AbstractMolecularSystem.get_coords

Class MolecularSystem

__init__(self, e_set=None, coords_access_func=None) (Constructor)

get_entity_set_index(self, entity_set)

_validate_entity_set_index(self, entity_set_ix)

get_supported_attributes(self)

check_required_attributes(self, entity_set_index, attribute_list)

_compute_distance_matrix(self, ix, jx)

check_distance_cutoff(self, ix, jx, cutoff)

get_dist_mat(self, ix, jx)

clear_dist_mat(self, ix)

set_configuration(self, ix=None, jx=None)

add_entities(self, entity_set, coords_access_func=None)

get_entities(self, entity_set_ix=0)

set_coords(self, entity_set_ix, coords, coords_set_func=None)

get_coords(self, entity_set_ix=0)

init(self, e_set=None, coords_access_func=None)
(Constructor)