ParsePdbstrManager
in package
implements
ParseDatabaseInterface
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.
Tags
Table of Contents
Interfaces
- ParseDatabaseInterface
- Interface ParseDatabaseInterface
Properties
- $createDate : string
- $entryGroup : string
- $entryId : string
- $length : int
- $molType : string
- $updDate : string
Methods
- __construct() : mixed
- Constructor.
- getCreateDate() : string
- getEntryGroup() : string
- getEntryId() : string
- Extracts the identifier uniquely naming a PDBSTR entry.
- getFormat() : string
- The name this format is known by in the collection records and in DatabaseParserFactory.
- getLength() : int
- getMemberId() : string
- The identifier of the family member described by the MEMBER line.
- getMolType() : string
- getUpdDate() : string
- isEntryEnd() : bool
- Tells whether a line closes a PDBSTR entry.
- isEntryStart() : bool
- Tells whether a line opens a new PDBSTR entry.
- parseDataFile() : Sequence
- Parses a PDBSTR data file and populates this manager's fields.
Properties
$createDate
private
string
$createDate
= ""
$entryGroup
private
string
$entryGroup
= ""
$entryId
private
string
$entryId
= ""
$length
private
int
$length
= 0
$molType
private
string
$molType
= ""
$updDate
private
string
$updDate
= ""
Methods
__construct()
Constructor.
public
__construct() : mixed
getCreateDate()
public
getCreateDate() : string
Return values
stringgetEntryGroup()
public
getEntryGroup() : string
Return values
stringgetEntryId()
Extracts the identifier uniquely naming a PDBSTR entry.
public
static getEntryId(array<string|int, mixed> $aFlines, string $sLine) : string
Parameters
- $aFlines : array<string|int, mixed>
-
The whole file, buffered
- $sLine : string
-
The line opening the entry
Return values
stringgetFormat()
The name this format is known by in the collection records and in DatabaseParserFactory.
public
static getFormat() : string
Return values
stringgetLength()
public
getLength() : int
Return values
intgetMemberId()
The identifier of the family member described by the MEMBER line.
public
getMemberId() : string
Return values
stringgetMolType()
public
getMolType() : string
Return values
stringgetUpdDate()
public
getUpdDate() : string
Return values
stringisEntryEnd()
Tells whether a line closes a PDBSTR entry.
public
static isEntryEnd(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolisEntryStart()
Tells whether a line opens a new PDBSTR entry.
public
static isEntryStart(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolparseDataFile()
Parses a PDBSTR data file and populates this manager's fields.
public
parseDataFile(array<string|int, mixed> $aFlines) : Sequence
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
- $aFlines : array<string|int, mixed>
-
The lines the script has to parse
Tags
Return values
Sequence —$oSequence