Package csb :: Package bio :: Package fragments :: Module isites :: Class Cluster

Class Cluster

object --+
         |
        Cluster

Object representation of an I-Sites library peptide fragment.

Instance Methods

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

source code

__lt__(self, other)

source code

attach_structure(self, pdb_file)
Parse the paradigm's pdb_file and attach structural data to cluster.representative (source and structure attributes). source code

float

city_block(self, profile, start=0)
Compute the similarity score of profile matching self's profile using the exponential city block metric (see Baker 1995). source code

float

cross_entropy(self, profile, start=0)
Compute the similarity score of profile matching self's profile using the cross entropy method. source code

function

fragment_comparer(self, mode=Bystroff)
Return a callable fragment comparer that implements the specified comparison mode.

source code

float

profile_similarity(self, profile, start=0)
Compute the similarity score of profile matching self's profile (see Bystroff 2001, 2008). source code

float

sequence_similarity(self, sequence, start=0)
Compute the log-odds score of sequence matching self's profile. source code

serialize(self, file)
Serialize the cluster to a file.

source code

list

slide_over(self, target, mode=Bystroff)
Find profile and structural matches by sliding the fragment over a specified target chain. source code

list

slide_over_fast(self, target, mode=Bystroff)
Find profile matches only (do not compute RMSD) by sliding the fragment over a specified target chain. source code

float

sum_of_odds(self, profile, start=0)
Compute the similarity score of profile matching self's profile using the log-sum-of-odds method (Soeding). source code

hmm.ProfileHMM

to_hmm(self)
Convert this fragment into a profile HMM segment.

source code

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

Static Methods

Cluster

deserialize(file)
Load a cluster from a serialized object.

source code

Cluster

from_hmm(source, id, start=None, end=None, rep_accession=None, rep_chain=None, alpha=0.2)
Build a fragment from a Profile HMM.

source code

Properties
	has_structure
	isite
	length
Inherited from `object`: `__class__`

Method Details

init(self)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

attach_structure(self, pdb_file)

source code

Parse the paradigm's pdb_file and attach structural data to cluster.representative (source and structure attributes).

Parameters:

pdb_file (str) - source PDB file containing the structure of the paradigm

Raises:

InternalISitesError - on parse and/or structure assignment errors
InvalidParadigmError - when the torsion angles in the cluster do not match the angles computed from the PDB file

city_block(self, profile, start=0)

source code

Compute the similarity score of profile matching self's profile using the exponential city block metric (see Baker 1995).

Parameters:

profile (ProteinProfile) - subject profile
start (int) - do the comparison starting with this offset in the subject

Returns: float

the city block similarity between the profiles

cross_entropy(self, profile, start=0)

source code

Compute the similarity score of profile matching self's profile using the cross entropy method.

Parameters:

profile (ProteinProfile) - subject profile
start (int) - do the comparison starting with this offset in the subject

Returns: float

the cross entropy between the profiles

deserialize(file)
Static Method

source code

Load a cluster from a serialized object.

Parameters:

file (str) - source file name

Returns: Cluster

deserialized fragment object

fragment_comparer(self, mode=Bystroff)

source code

Return a callable fragment comparer that implements the specified comparison mode.

Parameters:

mode (csb.core.EnumItem) - specifies the desired comparison method to be implemented by the callable - a member of the FragmentMatching enum

Returns: function

the proper comparison function which implements fragment comparison with the mode method

Raises:

ValueError - on invalid mode specified

from_hmm(source, id, start=None, end=None, rep_accession=None, rep_chain=None, alpha=0.2)
Static Method

source code

Build a fragment from a Profile HMM.

Parameters:

source (hmm.ProfileHMM, hmm.ProfileHMMSegment) - the HMM to convert
id (int) - ID of the new fragment
start (int) - start position (optional)
end (int) - end position (optional)
rep_accession (str) - accession number for cluster.representative
rep_chain (str) - chain ID for cluster.representative
alpha (float) - alpha pseudocount for cluster.profile.pssm

Returns: Cluster

an I-Sites cluster wrapper

Raises:

TypeError - when the HMM's structural data is missing or interrupted

profile_similarity(self, profile, start=0)

source code

Compute the similarity score of profile matching self's profile (see Bystroff 2001, 2008).

Parameters:

profile (ProteinProfile) - subject profile, built with alpha=0.5
start (int) - do the comparison starting with this offset in the subject

Returns: float

similarity score calculated with Bystroff's metric

Raises:

ValueError - on mismatch in the amino acid content at a given column in both profiles; or when the subject has not been created with alpha=0.5

sequence_similarity(self, sequence, start=0)

source code

Compute the log-odds score of sequence matching self's profile.

Parameters:

sequence (str) - subject sequence
start (int) - do the comparison starting with this offset in the sequence

Returns: float

log-odds score

serialize(self, file)

source code

Serialize the cluster to a file.

Parameters:

file (str) - output file name

slide_over(self, target, mode=Bystroff)

source code

Find profile and structural matches by sliding the fragment over a specified target chain.

Parameters:

target (structure.Chain) - subject chain to be scanned to fragment instances
mode (csb.core.EnumItem) - fragment instance searching mode - a FragmentMatching member

Returns: list

a list of ProfileMatches

slide_over_fast(self, target, mode=Bystroff)

source code

Find profile matches only (do not compute RMSD) by sliding the fragment over a specified target chain.

Parameters:

target (structure.Chain) - subject chain to be scanned to fragment instances
mode (csb.core.EnumItem) - fragment instance searching mode - a FragmentMatching member

Returns: list

a list of ProfileMatches

sum_of_odds(self, profile, start=0)

source code

Compute the similarity score of profile matching self's profile using the log-sum-of-odds method (Soeding).

Parameters:

profile (ProteinProfile) - subject profile
start (int) - do the comparison starting with this offset in the subject

Returns: float

the log-sum-of-odds similarity between the profiles

to_hmm(self)

source code

Convert this fragment into a profile HMM segment. Each column in the fragment's profile becomes a Match state with equivalent emissions. However, all Match states are connected with a fixed transition probability of 100%.

Returns: hmm.ProfileHMM: an HMM wrapper around the cluster's profile

Property Details

has_structure

Get Method:: unreachable.has_structure(self)

isite

Get Method:: unreachable.isite(self)

length

Get Method:: unreachable.length(self)

Class Cluster

__init__(self) (Constructor)

attach_structure(self, pdb_file)

city_block(self, profile, start=0)

cross_entropy(self, profile, start=0)

deserialize(file) Static Method

fragment_comparer(self, mode=Bystroff)

from_hmm(source, id, start=None, end=None, rep_accession=None, rep_chain=None, alpha=0.2) Static Method

profile_similarity(self, profile, start=0)

sequence_similarity(self, sequence, start=0)

serialize(self, file)

slide_over(self, target, mode=Bystroff)

slide_over_fast(self, target, mode=Bystroff)

sum_of_odds(self, profile, start=0)

to_hmm(self)

has_structure

isite

length

init(self)
(Constructor)

deserialize(file)
Static Method

from_hmm(source, id, start=None, end=None, rep_accession=None, rep_chain=None, alpha=0.2)
Static Method