Package csb :: Package bio :: Package hmm :: Class ProfileHMM |
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# Class ProfileHMM

source code

    object --+
             |
            ProfileHMM

Known Subclasses:
  - ProfileHMMSegment
  - , ProfileHMMRegion

Describes a protein profile Hidden Markov Model. Optional parameters:

Instance Methods
__init__(self, units=LogScales, scale=-1000.0, logbase=2) x.__init__(...) initializes x; see help(type(x)) for signature | source code
add_emission_pseudocounts(self, *a, **k) See csb.bio.hmm.pseudocounts.PseudocountBuilder | source code
add_transition_pseudocounts(self, *a, **k) See csb.bio.hmm.pseudocounts.PseudocountBuilder | source code
Chain |
chain(self, chain_id=None) Extract the structural information from the HMM. | source code
convert_scores(self, units=Probability, method=None) Convert emission and transition scores to the specified units. | source code
list |
emission_profile(self) Extract the emission scores of all match states in the profile. | source code
float |
emission_similarity(self, other) Compute the Log-sum-of-odds score between the emission tables of self and other (Soeding 2004). | source code
ProfileHMMSegment |
segment(self, start, end) Extract a sub-segment of the profile. | source code
serialize(self, file_name) Serialize this HMM to a file. | source code
Structure |
structure(self, chain_id=None, accession=None) Extract the structural information from the HMM. | source code
subregion(self, start, end) | source code
to_hmm(self, output_file=None, convert_scores=False) Dump the profile in HHM format. | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Static Methods
deserialize(file_name) De-serialize an HMM from a file. | source code

Properties
A3MAlignment | alignment Source multiple alignment
list of HMMLayer | all_layers A list of layers including start and start_insertion
AbstractSequence | consensus Consensus sequence
SecondaryStructure | dssp DSSP (calculated) secondary structure
str | dssp_solvent Solvent accessibility values
| effective_matches Number of effective matches (NEFF)
bool | emission_pseudocounts
State | end Final state (at the end layer)
EVDParameters | evd Extreme-value distribution parameters (EVD)
str | family Alternative entry ID (FAM)
bool | has_structure True if this profile contains structural data
str | id Profile entry ID (FILE)
HMMLayersCollection | layers List-like access to the HMM's layers
ProfileLength | length Profile length
float | logbase Base of the logarithm used for score scaling
str | name Profile name (NAME)
bool | pseudocounts
SecondaryStructure | psipred PSIPRED (predicted) secondary structure
collection of Residue | residues List of representative residues, attached to each layer
float | scale Score scaling factor
ScoreUnits member | score_units Current score units
State | start Start state (at the start layer)
State | start_insertion Insertion state at the start layer
bool | transition_pseudocounts
str | version Format version number (HHsearch)
Inherited from `object`: `__class__`

Method Details

### __init__(self, units=LogScales, scale=-1000.0, logbase=2) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `units` (ScoreUnits) - defines the units of the transition and emission scores `scale` (float) - the scaling factor used to convert emission/transition probabilities `logbase` (float) - the base of the logarithm used for scaling the emission and transition probabilities Overrides: object.__init__ (inherited documentation)

### chain(self, chain_id=None) | source code
Extract the structural information from the HMM. Parameters: `chain_id` (str) - defines explicitly the chain identifier Returns: Chain a shallow Chain wrapper around the residues in the HMM.

### convert_scores(self, units=Probability, method=None) | source code
  - Convert emission and transition scores to the specified units. Parameters: `units` (csb.core.EnumItem) - the target units for the conversion (a member of ScoreUnits). `method` (function, lambda) - if defined, implements the exact mathematical transformation that will be applied. It must be a function or lambda expression with the following signature:
             def (target_units, score, scale, logbase)
and it has to return the score converted to `target_units`. If method performs a conversion from probabilities to scaled logs, you should also update `hmm.scale` and `hmm.logbase`.

### deserialize(file_name) Static Method | source code
De-serialize an HMM from a file. Parameters: `file_name` (str) - source file name (pickle)

### emission_profile(self) | source code
Extract the emission scores of all match states in the profile. The metric of the emission scores returned depends on the current hmm.score_units setting - you may need to call hmm.convert_scores() to adjust the hmm to your particular needs. Returns: list a list of dictionaries; each dict key is a single amino acid

### emission_similarity(self, other) | source code
Compute the Log-sum-of-odds score between the emission tables of self and other (Soeding 2004). If no observable Match state is found at a given layer, the Insertion state is used instead. Parameters: `other` (ProfileHMM) - the subject HMM Returns: float emission log-sum-of-odds similarity between `self` and `other` Raises: `ValueError` - when self and other differ in their length, when the score_units are not Probability, or when no observable states are present Note: This is not a full implementation of the formula since only emission vectors are involved in the computation and any transition probabilities are ignored.

### segment(self, start, end) | source code
Extract a sub-segment of the profile. Parameters: `start` (int) - start layer of the segment (rank) `end` (int) - end layer of the segment (rank) Returns: ProfileHMMSegment a deepcopy of the extracted HMM segment

### serialize(self, file_name) | source code
Serialize this HMM to a file. Parameters: `file_name` (str) - target file name

### structure(self, chain_id=None, accession=None) | source code
Extract the structural information from the HMM. Parameters: `accession` (str) - defines the accession number of the structure `chain_id` (str) - defines explicitly the chain identifier Returns: Structure a shallow Structure wrapper around the residues in the HMM.

### to_hmm(self, output_file=None, convert_scores=False) | source code
Dump the profile in HHM format. Parameters: `output_file` (str) - the output file name `convert_scores` (bool) - if True, forces automatic convertion to ScoreUnits.LogScales, which is required by the output file format

Property Details

### alignment Source multiple alignment Get Method: unreachable.alignment(self) - Source multiple alignment Set Method: unreachable.alignment(self, value) Type: A3MAlignment

### all_layers A list of layers including start and start_insertion Get Method: unreachable.all_layers(self) - A list of layers including start and start_insertion Type: list of HMMLayer

### consensus Consensus sequence Get Method: unreachable.consensus(self) - Consensus sequence Set Method: unreachable.consensus(self, value) Type: AbstractSequence

### dssp DSSP (calculated) secondary structure Get Method: unreachable.dssp(self) - DSSP (calculated) secondary structure Set Method: unreachable.dssp(self, value) Type: SecondaryStructure

### dssp_solvent Solvent accessibility values Get Method: unreachable.dssp_solvent(self) - Solvent accessibility values Set Method: unreachable.dssp_solvent(self, value) Type: str

### effective_matches Number of effective matches (NEFF) Get Method: unreachable.effective_matches(self) - Number of effective matches (NEFF) Set Method: unreachable.effective_matches(self, value)

### emission_pseudocounts Get Method: unreachable.emission_pseudocounts(self) Set Method: unreachable.emission_pseudocounts(self, value) Type: bool

### end Final state (at the end layer) Get Method: unreachable.end(self) - Final state (at the end layer) Set Method: unreachable.end(self, value) Type: State

### evd Extreme-value distribution parameters (EVD) Get Method: unreachable.evd(self) - Extreme-value distribution parameters (EVD) Set Method: unreachable.evd(self, value) Type: EVDParameters

### family Alternative entry ID (FAM) Get Method: unreachable.family(self) - Alternative entry ID (FAM) Set Method: unreachable.family(self, value) Type: str

### has_structure True if this profile contains structural data Get Method: unreachable.has_structure(self) - True if this profile contains structural data Type: bool

### id Profile entry ID (FILE) Get Method: unreachable.id(self) - Profile entry ID (FILE) Set Method: unreachable.id(self, value) Type: str

### layers List-like access to the HMM's layers Get Method: unreachable.layers(self) - List-like access to the HMM's layers Type: HMMLayersCollection

### length Profile length Get Method: unreachable.length(self) - Profile length Set Method: unreachable.length(self, value) Type: ProfileLength

### logbase Base of the logarithm used for score scaling Get Method: unreachable.logbase(self) - Base of the logarithm used for score scaling Type: float

### name Profile name (NAME) Get Method: unreachable.name(self) - Profile name (NAME) Set Method: unreachable.name(self, value) Type: str

### pseudocounts Get Method: unreachable.pseudocounts(self) Set Method: unreachable.pseudocounts(self, value) Type: bool

### psipred PSIPRED (predicted) secondary structure Get Method: unreachable.psipred(self) - PSIPRED (predicted) secondary structure Set Method: unreachable.psipred(self, value) Type: SecondaryStructure

### residues List of representative residues, attached to each layer Get Method: unreachable.residues(self) - List of representative residues, attached to each layer Type: collection of Residue

### scale Score scaling factor Get Method: unreachable.scale(self) - Score scaling factor Type: float

### score_units Current score units Get Method: unreachable.score_units(self) - Current score units Type: ScoreUnits member

### start Start state (at the start layer) Get Method: unreachable.start(self) - Start state (at the start layer) Set Method: unreachable.start(self, value) Type: State

### start_insertion Insertion state at the start layer Get Method: unreachable.start_insertion(self) - Insertion state at the start layer Set Method: unreachable.start_insertion(self, value) Type: State

### transition_pseudocounts Get Method: unreachable.transition_pseudocounts(self) Set Method: unreachable.transition_pseudocounts(self, value) Type: bool

### version Format version number (HHsearch) Get Method: unreachable.version(self) - Format version number (HHsearch) Set Method: unreachable.version(self, value) Type: str