Package csb :: Package bio :: Package fragments :: Class FragmentCluster

Class FragmentCluster

object --+
         |
        FragmentCluster

Provides clustering/filtering of the fragments, covering a common residue in the target. Clustering is done via iterative shrinking of the cluster. At each iteration, node rejection (deletion) is attempted for each node. The node rejection, causing the most significant drop in the average pairwise distance (RMSD) in the cluster, is retained. This procedure is repeated until: 1) the average pairwise RMSD drops below the threshold (converged), 2) the cluster gets exhausted or 3) node rejection no longer causes a drop in the average distance (not converging).

Instance Methods

__init__(self, items, threshold=1.5, connectedness=0.5)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

ClusterRep

centroid(self)
Returns: the current representative fragment

source code

float

mean(self, skip=None)
Returns: the current mean distance in the cluster

source code

reject(self, item)
Remove item from the cluster. source code

ClusterRep

shrink(self, minitems=2)
Start automatic shrinking.

source code

bool

shrinkone(self)
Shrink the cluster by a single node.

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables
	MIN_LENGTH = `6`

Properties
	connectedness
	count
	fragments
	items
	threshold
Inherited from `object`: `__class__`

Method Details

init(self, items, threshold=1.5, connectedness=0.5)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

items (iterable of ClusterNodes) - cluster members
threshold (float) - RMSD threshold; continue shrinking until the mean distance drops below this value (default=1.5)
connectedness (float) - when calculating centroids, consider only nodes connected to at least c% of all surviving vertices (default=0.5)

Overrides: object.__init__

(inherited documentation)

centroid(self)

source code

Returns: ClusterRep: the current representative fragment

Note: the cluster rep is the node with the lowest average distance to all other nodes. If a fixed fragment exists, structurally similar to the rep, but longer, this fragment may be suggested as an alternative (see also ClusterRep).

mean(self, skip=None)

source code

Returns: float: the current mean distance in the cluster

reject(self, item)

source code

Remove item from the cluster.

Parameters:

item (ClusterNode)

Raises:

ClusterExhaustedError - if this is the last remaining item

shrink(self, minitems=2)

source code

Start automatic shrinking.

Parameters:

minitems (int) - absolute minimum of the number of nodes in the cluster

Returns: ClusterRep

cluster's representative: the node with the lowest average distance to all other nodes in the cluster

Raises:

ClusterExhaustedError - if self.count < minitems and still not converged

shrinkone(self)

source code

Shrink the cluster by a single node.

Returns: bool

True on successful shrink, False otherwise (e.g. if already converged)

Raises:

ClusterExhaustedError - if exhausted
ClusterDivergingError - if not converging

Property Details

connectedness

Get Method:: unreachable.connectedness(self)

count

Get Method:: unreachable.count(self)

fragments

Get Method:: unreachable.fragments(self)

items

Get Method:: unreachable.items(self)

threshold

Get Method:: unreachable.threshold(self)
Set Method:: unreachable.threshold(self, value)

Class FragmentCluster

__init__(self, items, threshold=1.5, connectedness=0.5) (Constructor)

centroid(self)

mean(self, skip=None)

reject(self, item)

shrink(self, minitems=2)

shrinkone(self)

connectedness

count

fragments

items

threshold

init(self, items, threshold=1.5, connectedness=0.5)
(Constructor)