de.bioforscher.singa.structure.parser.pdb.structures

Class StructureParser.MultiParser

java.lang.Object

de.bioforscher.singa.structure.parser.pdb.structures.StructureParser.MultiParser

All Implemented Interfaces:

Iterator<Structure>

Enclosing class:

StructureParser

public static class StructureParser.MultiParser
extends Object
implements Iterator<Structure>

The MultiParser performs parsing of multiple structures from a single source. Using the Iterator pattern the structures can be parsed and processed individually. Each specified structure will be parsed lazily so parsing until a certain condition is met can be done without parsing unused structures. Additionally some speedups are provided parsing multiple structures. Every ligand is only parsed once, the first time it is encountered, afterwards it is stored as a LeafSkeleton that is completed with the the concrete atom positions for each new occurrence.

Method Summary

Modifier and Type	Method and Description
String	getCurrentChainIdentifier() Returns the chain identifier of the next structure, if it can be accessed prior to parsing.
String	getCurrentPdbIdentifier() Returns the pdb identifier of the next structure, if it can be accessed prior to parsing.
int	getNumberOfQueuedStructures() Returns the number of structures totally queued.
int	getNumberOfRemainingStructures() Returns the number of structures remaining.
boolean	hasNext()
Structure	next()
List<Structure>	parse() Parses all structures that are queued for this StructureParser.MultiParser.
StructureParser.MultiParser	setOptions(StructureParserOptions options) Sets the StructureParserOptions for this parsing process.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Method Detail

getNumberOfQueuedStructures

public int getNumberOfQueuedStructures()

Returns the number of structures totally queued.

Returns:

The number of structures totally queued.

getNumberOfRemainingStructures

public int getNumberOfRemainingStructures()

Returns the number of structures remaining.

Returns:

The number of structures remaining.

getCurrentPdbIdentifier

public String getCurrentPdbIdentifier()

Returns the pdb identifier of the next structure, if it can be accessed prior to parsing.

Returns:

The pdb identifier of the next structure.

Throws:

IllegalStateException - if the structures identifier could not be accessed.

getCurrentChainIdentifier

public String getCurrentChainIdentifier()

Returns the chain identifier of the next structure, if it can be accessed prior to parsing.

Returns:

The chain identifier of the next structure.

Throws:

IllegalStateException - if the structures identifier could not be accessed.

setOptions

public StructureParser.MultiParser setOptions(StructureParserOptions options)

Sets the StructureParserOptions for this parsing process.

Parameters:

options - The options.

Returns:

The parser with the set options.

parse

public List<Structure> parse()

Parses all structures that are queued for this StructureParser.MultiParser.

Returns:

A list of structures.

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<Structure>

next

public Structure next()

Specified by:

next in interface Iterator<Structure>