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Biskit :: TrajCluster :: TrajCluster :: Class TrajCluster
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Class TrajCluster

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Instance Methods [hide private]
  __init__(self, traj, verbose=1)
  __raveled(self)
Apply current atom mask and return list of raveled frames.
  cluster(self, n_clusters, weight=1.13, converged=1e-11, aMask=None, force=0)
Calculate new clusters.
int calcClusterNumber(self, min_clst=5, max_clst=30, rmsLimit=1.0, weight=1.13, converged=1e-11, aMask=None, force=0)
Calculate the approximate number of clusters needed to pass the average intra-cluster rmsd limit.
array memberships(self)
Get degree of membership of each frame to each cluster.
[float] maxMemberships(self)
Get maximum membership value for each frame.
array centers(self)
Get 'center structure' for each cluster.
[int] centerFrames(self)
Get indices for frame nearest to each cluster center.
[[int]] memberFrames(self, threshold=0.)
Get indices of all frames belonging to each cluster.
[int] membershipSort(self, frames, cluster)
Sort given list of frame indices by their membership in cluster.
Trajectory memberTraj(self, cluster, threshold=0.)
Get trajectory with all frames belonging to this cluster, sorted by their membership-degree (highest first).
[Trajectory] memberTrajs(self, threshold=0.)
Get member Trajectories for each cluster.
float, float avgRmsd(self, cluster, aMask=None, threshold=0.)
Claculate the average pairwise rmsd (in Angstrom) for members of a cluter.
  avgRmsd2Ref(self, cluster, ref, avg=1)
Claculate the rmsd (or average rmsd) of all frames belonging to a cluster to a reference structure (in Angstrom).

Method Details [hide private]

__init__(self, traj, verbose=1)
(Constructor)

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Parameters:
  • traj (Trajectory) - Trajectory to cluster (has to be fitted before hand)

__raveled(self)

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Apply current atom mask and return list of raveled frames.

cluster(self, n_clusters, weight=1.13, converged=1e-11, aMask=None, force=0)

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Calculate new clusters.
Parameters:
  • n_clusters (int) - number of clusters
  • weight (float (default: 1.13)) - fuzziness weigth
  • converged (float) - stop iteration if min dist changes less than converged (default: 1e-11)
  • aMask ([1|0]) - atom mask applied before clustering
  • force (1|0) - re-calculate even if parameters haven't changed (default:0)

calcClusterNumber(self, min_clst=5, max_clst=30, rmsLimit=1.0, weight=1.13, converged=1e-11, aMask=None, force=0)

source code 

Calculate the approximate number of clusters needed to pass the average intra-cluster rmsd limit.
Parameters:
  • min_clst (int) - lower limit for clusters (default: 5)
  • max_clst (int) - upper limit for clusters (default: 30 )
  • rmsLimit (float) - rmsd criteria that the average of all clusters must meet in Angstrom (default: 1.0)
  • weight (float) - fuzziness weigth (default: 1.13)
  • converged (float) - stop iteration if min dist changes less than converged (default: 1e-11)
  • force (1|0) - re-calculate even if parameters haven't changed (default: 0)
Returns: int
number of clusters
Raises:

memberships(self)

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Get degree of membership of each frame to each cluster.
Returns: array
N.array( n_clusters x n_frames )

maxMemberships(self)

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Get maximum membership value for each frame.
Returns: [float]
list of float

centers(self)

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Get 'center structure' for each cluster.
Returns: array
N.array( n_clusters x n_atoms_masked x 3 )

centerFrames(self)

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Get indices for frame nearest to each cluster center.
Returns: [int]
list of cluster center indecies

memberFrames(self, threshold=0.)

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Get indices of all frames belonging to each cluster. Each frame is guaranteed to belong, at least, to the cluster for which it has its maximum membership. If threshold > 0, it can additionally pop up in other clusters.
Parameters:
  • threshold (float) - minimal cluster membership or 0 to consider only max membership (default: 0)
Returns: [[int]]
n_cluster, lst of lst of int, frame indices

membershipSort(self, frames, cluster)

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Sort given list of frame indices by their membership in cluster.
Parameters:
  • frames ([int]) - list of frame indecies
  • cluster (int) - cluster number
Returns: [int]
indecies sorted by ther membership to cluster

memberTraj(self, cluster, threshold=0.)

source code 

Get trajectory with all frames belonging to this cluster, sorted by their membership-degree (highest first).
Parameters:
  • cluster (int) - cluster number
  • threshold (float) - float 0-1, minimal cluster membership, see memberFrames()
Returns: Trajectory
Trajectory with all members of a cluster, sorted by membership

memberTrajs(self, threshold=0.)

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Get member Trajectories for each cluster. Frames are sorted by their membership-degree (highest first).
Parameters:
  • threshold () - float 0-1, minimal cluster membership, see memberFrames()
Returns: [Trajectory]
lst of Trajectories, with members of each cluster, sorted by membership

avgRmsd(self, cluster, aMask=None, threshold=0.)

source code 

Claculate the average pairwise rmsd (in Angstrom) for members of a cluter.
Parameters:
  • cluster (int) - cluster number
  • aMask ([1|0]) - atom mask applied before calculation
  • threshold (float) - float 0-1, minimal cluster membership, see memberTraj()
Returns: float, float
average rmsd and the standard deviation

avgRmsd2Ref(self, cluster, ref, avg=1)

source code 

Claculate the rmsd (or average rmsd) of all frames belonging to a cluster to a reference structure (in Angstrom).
Parameters:
  • cluster (int) - cluster number
  • ref (model) - reference structure
  • avg (float OR [float]) - return the average rmsd (1) OR a list with all rmsds (0) (default: 1)

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