Package csb :: Package bio :: Package fragments :: Class FragmentCluster |
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# Class FragmentCluster

source code

    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)