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

source code

    object --+
             |
            HHpredHit

Represents a single HHsearch hit.

Instance Methods
__init__(self, rank, id, start, end, qstart, qend, probability, qlength) x.__init__(...) initializes x; see help(type(x)) for signature | source code
__lt__(self, other) | source code
__repr__(self) repr(x) | source code
__str__(self) str(x) | source code
add_alignment(self, query, subject) Add query/subject alignment to the hit. | source code
bool |
equals(self, other) Return True if `self` is completely identical to `other` (same id, same start and end positions). | source code
bool |
includes(self, other, tolerance=1) Return True if `other` overlaps with `self`, that means `other` is fully or partially included in `self` when aligned over the query. | source code
bool |
surpasses(self, other) Return True if `self` is a superior to `other` in terms of length and probability. | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__setattr__`, `__sizeof__`, `__subclasshook__`

Properties
| alignment
| end
| evalue
| id
| identity
| length
| prob_sum
| probability
| pvalue
| qend
| qlength
| qstart
| rank
| score
| similarity
| slength
| ss_score
| start
Inherited from `object`: `__class__`

Method Details

### __init__(self, rank, id, start, end, qstart, qend, probability, qlength) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `rank` (int) - rank of the hit `id` (str) - id of the hit `start` (int) - subject start `end` (int) - subject end `qstart` (int) - query start `qend` (int) - query end `probability` (float) - probability of the hit `qlength` (int) - length of the query Overrides: object.__init__ (inherited documentation)

### __repr__(self) (Representation operator) | source code
repr(x) Overrides: object.__repr__ (inherited documentation)

### __str__(self) (Informal representation operator) | source code
str(x) Overrides: object.__str__ (inherited documentation)

### add_alignment(self, query, subject) | source code
Add query/subject alignment to the hit. Parameters: `query` (str) - the query sequence within the alignment region, with gaps `subject` (str) - the subject sequence within the alignment region, with gaps

### equals(self, other) | source code
Return True if `self` is completely identical to `other` (same id, same start and end positions). Parameters: `other` (HHpredHit) - right-hand-term Returns: bool

### includes(self, other, tolerance=1) | source code
Return True if `other` overlaps with `self`, that means `other` is fully or partially included in `self` when aligned over the query. Parameters: `other` (HHpredHit) - right-hand-term `tolerance` (int) - allow partial overlaps for that number of residues at either end Returns: bool

### surpasses(self, other) | source code
Return True if `self` is a superior to `other` in terms of length and probability. These criteria are applied in the following order: Length (the longer hit is better) Probability (if they have the same length, the one with the higher probability is better) Address (if they have the same length and probability, the one with higher memory ID wins; for purely practical reasons) Parameters: `other` (HHpredHit) - right-hand-term Returns: bool

Property Details

### alignment Get Method: unreachable.alignment(self)

### end Get Method: unreachable.end(self) Set Method: unreachable.end(self, value)

### evalue Get Method: unreachable.evalue(self) Set Method: unreachable.evalue(self, value)

### id Get Method: unreachable.id(self) Set Method: unreachable.id(self, value)

### identity Get Method: unreachable.identity(self) Set Method: unreachable.identity(self, value)

### length Get Method: unreachable.length(self)

### prob_sum Get Method: unreachable.prob_sum(self) Set Method: unreachable.prob_sum(self, value)

### probability Get Method: unreachable.probability(self) Set Method: unreachable.probability(self, value)

### pvalue Get Method: unreachable.pvalue(self) Set Method: unreachable.pvalue(self, value)

### qend Get Method: unreachable.qend(self) Set Method: unreachable.qend(self, value)

### qlength Get Method: unreachable.qlength(self) Set Method: unreachable.qlength(self, value)

### qstart Get Method: unreachable.qstart(self) Set Method: unreachable.qstart(self, value)

### rank Get Method: unreachable.rank(self) Set Method: unreachable.rank(self, value)

### score Get Method: unreachable.score(self) Set Method: unreachable.score(self, value)

### similarity Get Method: unreachable.similarity(self) Set Method: unreachable.similarity(self, value)

### slength Get Method: unreachable.slength(self) Set Method: unreachable.slength(self, value)

### ss_score Get Method: unreachable.ss_score(self) Set Method: unreachable.ss_score(self, value)

### start Get Method: unreachable.start(self) Set Method: unreachable.start(self, value)