Class ProfileHMM

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)

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 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.

De-serialize an HMM from a file.

Parameters:

• file_name (str) - source file name (pickle)

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

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

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 this HMM to a file.

Parameters:

• file_name (str) - target file name

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.

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

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