Package org.biojava.nbio.structure

Class ResidueRange

java.lang.Object

org.biojava.nbio.structure.ResidueRange

Direct Known Subclasses:

ResidueRangeAndLength

public class ResidueRange
extends Object

A chainName, a start residue, and an end residue. The chainName is matched to Chain.getName(), so for mmCIF files it indicates the authorId rather than the asymId. Chain may be null when referencing a single-chainName structure; for multi-chainName structures omitting the chainName is an error. Start and/or end may also be null, which is interpreted as the first and last residues in the chainName, respectively.

Author:

dmyerstu

See Also:

ResidueNumber, ResidueRangeAndLength

Field Summary

Fields

Modifier and Type	Field	Description
static Pattern	CHAIN_REGEX
static Pattern	RANGE_REGEX

Constructor Summary

Constructors

Constructor	Description
ResidueRange(String chainName, String start, String end)
ResidueRange(String chainName, ResidueNumber start, ResidueNumber end)

Method Summary

Modifier and Type	Method	Description
boolean	contains(ResidueNumber residueNumber, AtomPositionMap map)
boolean	equals(Object obj)
String	getChainName()
ResidueNumber	getEnd()
ResidueNumber	getResidue(int positionInRange, AtomPositionMap map)	Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
ResidueNumber	getStart()
int	hashCode()
Iterator<ResidueNumber>	iterator(AtomPositionMap map)	Returns a new Iterator over every ResidueNumber in this ResidueRange.
static Iterator<ResidueNumber>	multiIterator(AtomPositionMap map, List<? extends ResidueRange> rrs)	Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
static Iterator<ResidueNumber>	multiIterator(AtomPositionMap map, ResidueRange... rrs)	Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
static ResidueRange	parse(String s)	Parse the residue range from a string.
static List<ResidueRange>	parseMultiple(String s)
static List<ResidueRange>	parseMultiple(List<String> ranges)
String	toString()
static String	toString(List<? extends ResidueRange> ranges)
static List<String>	toStrings(List<? extends ResidueRange> ranges)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

RANGE_REGEX

public static final Pattern RANGE_REGEX

CHAIN_REGEX

public static final Pattern CHAIN_REGEX

Constructor Detail

ResidueRange

public ResidueRange(String chainName,
                    String start,
                    String end)

ResidueRange

public ResidueRange(String chainName,
                    ResidueNumber start,
                    ResidueNumber end)

Method Detail

parse

public static ResidueRange parse(String s)

Parse the residue range from a string. Several formats are accepted:

• chainName.start-end
• chainName.residue
• chain_start-end (for better filename compatibility)

Residues can be positive or negative and may include insertion codes. See ResidueNumber.fromString(String).

Examples:

• A:5-100
• A_5-100
• A_-5
• A:-12I-+12I
• A:^-$

Parameters:

s - residue string to parse

Returns:

The unique ResidueRange corresponding to s

parseMultiple

public static List<ResidueRange> parseMultiple(String s)

Parameters:

s - A string of the form chain_start-end,chain_start-end, ... For example: A.5-100,R_110-190,Z_200-250.

Returns:

The unique ResidueRange corresponding to s.

See Also:

parse(String)

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getChainName

public String getChainName()

getEnd

public ResidueNumber getEnd()

getStart

public ResidueNumber getStart()

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

getResidue

public ResidueNumber getResidue(int positionInRange,
                                AtomPositionMap map)

Returns the ResidueNumber that is at position positionInRange in this ResidueRange.

Returns:

The ResidueNumber, or false if it does not exist or is not within this ResidueRange

contains

public boolean contains(ResidueNumber residueNumber,
                        AtomPositionMap map)

Returns:

True if and only if residueNumber is within this ResidueRange

iterator

public Iterator<ResidueNumber> iterator(AtomPositionMap map)

Returns a new Iterator over every ResidueNumber in this ResidueRange. Stores the contents of map until the iterator is finished, so calling code should set the iterator to null if it did not finish.

multiIterator

public static Iterator<ResidueNumber> multiIterator(AtomPositionMap map,
                                                    ResidueRange... rrs)

Returns a new Iterator over every ResidueNumber in the list of ResidueRanges. Stores the contents of map until the iterator is finished, so calling code should set the iterator to null if it did not finish.

multiIterator

public static Iterator<ResidueNumber> multiIterator(AtomPositionMap map,
                                                    List<? extends ResidueRange> rrs)

Returns a new Iterator over every ResidueNumber in the list of ResidueRanges. Stores the contents of map until the iterator is finished, so calling code should set the iterator to null if it did not finish.

parseMultiple

public static List<ResidueRange> parseMultiple(List<String> ranges)

toStrings

public static List<String> toStrings(List<? extends ResidueRange> ranges)

toString

public static String toString(List<? extends ResidueRange> ranges)