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\Amelaye\BioPHP\Domain\Parser\Service ParseExpasyEnzymeManager

Class ParseExpasyEnzymeManager ExPASy ENZYME entries describe an enzyme by its EC number, not a sequence - like ParsePdbManager and ParsePrositeManager, this class does not reuse the Sequence/Feature entities of ParseDbAbstractManager. Not to be confused with RestrictionEnzymeManager, which covers restriction endonucleases (a completely different Legacy/ExPASy database).

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getId
getDescription
getAlternateNames
getCatalyticActivities
getCofactors
getComments
getDiseases
getPrositeRefs
getSwissprotRefs
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
parseCatalyticActivities
accumulate
parseCofactors
parseDisease
parsePrositeRef
parseSwissprotRefs
id
description
alternateNames
catalyticActivities
aCaLines
cofactors
comments
diseases
prositeRefs
swissprotRefs
No private constants found

Properties

$id

$id : string

Type

string —

$description

$description : string

Type

string —

$alternateNames

$alternateNames : array

Type

array<string|int, mixed> —

$catalyticActivities

$catalyticActivities : array

One entry per reaction the enzyme catalyses : an enzyme acting on several substrates has as many, and the file numbers them "(1)", "(2)".

Type

array<string|int, mixed> —

$aCaLines

$aCaLines : array

Type

array<string|int, mixed> —

$cofactors

$cofactors : array

Type

array<string|int, mixed> —

$comments

$comments : string

Type

string —

$diseases

$diseases : \Amelaye\BioPHP\Domain\Parser\Interfaces\ExpasyDiseaseInterface[]

Type

array<string|int, ExpasyDiseaseInterface> —

$prositeRefs

$prositeRefs : array

Type

array<string|int, mixed> —

$swissprotRefs

$swissprotRefs : array

Type

array<string|int, mixed> —

Methods

__construct()

__construct() : mixed

Constructor.

Returns

mixed —

getFormat()

getFormat() : string

The name this format is known by in the collection records and in DatabaseParserFactory.

Returns

string —

isEntryStart()

isEntryStart(string  $sLine) : bool

Tells whether a line opens a new ExPASy ENZYME entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes a ExPASy ENZYME entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

getEntryId(array  $aFlines, string  $sLine) : string

Extracts the identifier uniquely naming a ExPASy ENZYME entry.

Parameters

array $aFlines

The whole file, buffered
string $sLine

The line opening the entry

Returns

string —

parseDataFile()

parseDataFile(array  $aFlines) : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

Parses an ExPASy ENZYME data file and populates this manager's fields.

Parameters

array $aFlines

The lines the script has to parse

Throws

\Exception

Returns

\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence —

$oSequence

getId()

getId() : string

Returns

string —

getDescription()

getDescription() : string

Returns

string —

getAlternateNames()

getAlternateNames() : array

Returns

array —

getCatalyticActivities()

getCatalyticActivities() : array

Returns

array —

getCofactors()

getCofactors() : array

Returns

array —

getComments()

getComments() : string

Returns

string —

getDiseases()

getDiseases() : \Amelaye\BioPHP\Domain\Parser\Interfaces\ExpasyDiseaseInterface[]

Returns

\Amelaye\BioPHP\Domain\Parser\Interfaces\ExpasyDiseaseInterface[] —

getPrositeRefs()

getPrositeRefs() : array

Returns

array —

getSwissprotRefs()

getSwissprotRefs() : array

Returns

array —

parseCatalyticActivities()

parseCatalyticActivities(array  $aLines) : array

Reads the CA field into one entry per reaction. An enzyme acting on several substrates has several, which the file numbers "(1)", "(2)"; an unnumbered line continues the reaction above it, a long reaction being wrapped rather than repeated.

Parameters

array $aLines

Returns

array —

accumulate()

accumulate(\ArrayIterator  $aLines, array  $aFlines, string  $sTag, string  $sJoiner) : string

Accumulates a multi-line field: the current line's data, plus every following line still tagged $sTag, joined with $sJoiner. Advances $aLines past what it reads.

Parameters

\ArrayIterator $aLines
array $aFlines
string $sTag
string $sJoiner

Returns

string —

parseCofactors()

parseCofactors(string  $sText) : array

Parses the CF field.

Format : CF Cofactor1; Cofactor2.

Parameters

string $sText

Returns

array —

parseDisease()

parseDisease(string  $sLine) : \Amelaye\BioPHP\Domain\Parser\Interfaces\ExpasyDiseaseInterface

Parses one DI line.

Format : DI Disease name; MIM: 123456.

Parameters

string $sLine

Returns

\Amelaye\BioPHP\Domain\Parser\Interfaces\ExpasyDiseaseInterface —

parsePrositeRef()

parsePrositeRef(string  $sLine) : string

Parses one PR line.

Format : PR PROSITE; PDOC00061;

Parameters

string $sLine

Returns

string —

parseSwissprotRefs()

parseSwissprotRefs(string  $sText) : array

Parses the DR field into an accession => entry name map.

Format : DR ACCESSION, ENTRY_NAME; ACCESSION, ENTRY_NAME; ...

Parameters

string $sText

Returns

array —