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\Amelaye\BioPHP\Domain\Parser\Service ParsePdbstrManager

Class ParsePdbstrManager A PDBSTR entry describes one member of a structural family in a single MEMBER line, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Not to be confused with ParsePdbManager, which reads the atomic coordinate files themselves.

Summary

Methods
Properties
Constants
__construct
getFormat
isEntryStart
isEntryEnd
getEntryId
parseDataFile
getMemberId
getMolType
getLength
getEntryGroup
getCreateDate
getUpdDate
No public properties found
No public constants found
No protected methods found
No protected properties found
No protected constants found
No private methods found
entryId
molType
length
entryGroup
createDate
updDate
No private constants found

Properties

$entryId

$entryId : string

Type

string —

$molType

$molType : string

Type

string —

$length

$length : int

Type

int —

$entryGroup

$entryGroup : string

Type

string —

$createDate

$createDate : string

Type

string —

$updDate

$updDate : string

Type

string —

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 PDBSTR entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes a PDBSTR entry.

Parameters

string $sLine

The line to analyze

Returns

bool —

getEntryId()

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

Extracts the identifier uniquely naming a PDBSTR 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 a PDBSTR data file and populates this manager's fields.

All six data items of a MEMBER line are mandatory, as in the original BioPHP parser. Example: MEMBER 1YIC_01 108 PROTEIN 1YIC 97/02/18 97/07/23

Parameters

array $aFlines

The lines the script has to parse

Throws

\Exception

Returns

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

$oSequence

getMemberId()

getMemberId() : string

The identifier of the family member described by the MEMBER line.

Returns

string —

getMolType()

getMolType() : string

Returns

string —

getLength()

getLength() : int

Returns

int —

getEntryGroup()

getEntryGroup() : string

Returns

string —

getCreateDate()

getCreateDate() : string

Returns

string —

getUpdDate()

getUpdDate() : string

Returns

string —