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object --+
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ProfileHMM
Describes a protein profile Hidden Markov Model. Optional parameters:
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| Chain |
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| list |
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| float |
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| ProfileHMMSegment |
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| Structure |
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Inherited from |
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| Static Methods | |||
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| 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 |
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effective_matches Number of effective matches (NEFF) |
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| 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) |
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Inherited from |
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| Method Details |
x.__init__(...) initializes x; see help(type(x)) for signature
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Extract the structural information from the HMM. |
Convert emission and transition scores to the specified units.
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De-serialize an HMM from a file.
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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.
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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.
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. |
Extract a sub-segment of the profile.
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Serialize this HMM to a file.
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Extract the structural information from the HMM. |
Dump the profile in HHM format.
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| Property Details |
alignmentSource multiple alignment
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all_layersA list of layers including start and start_insertion
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consensusConsensus sequence
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dsspDSSP (calculated) secondary structure
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dssp_solventSolvent accessibility values
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effective_matchesNumber of effective matches (NEFF)
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emission_pseudocounts
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endFinal state (at the end layer)
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evdExtreme-value distribution parameters (EVD)
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familyAlternative entry ID (FAM)
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has_structureTrue if this profile contains structural data
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idProfile entry ID (FILE)
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layersList-like access to the HMM's layers
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lengthProfile length
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logbaseBase of the logarithm used for score scaling
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nameProfile name (NAME)
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pseudocounts
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psipredPSIPRED (predicted) secondary structure
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residuesList of representative residues, attached to each layer
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scaleScore scaling factor
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score_unitsCurrent score units
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startStart state (at the start layer)
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start_insertionInsertion state at the start layer
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transition_pseudocounts
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versionFormat version number (HHsearch)
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