org.biojava.bio.structure

Class AtomPositionMap

java.lang.Object

org.biojava.bio.structure.AtomPositionMap

public class AtomPositionMap
extends java.lang.Object

A map from ResidueNumbers to ATOM record positions in a PDB file. To use: AtomPositionMap map = new AtomPositionMap(new AtomCache().getAtoms("1w0p")); ResidueNumber start = new ResidueNumber("A", 100, null); ResidueNumber end = map.getEnd("A"); int pos = map.getPosition(start); int length = map.calcLength(start, end);

Author:

dmyerstu

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	AtomPositionMap.GroupMatcher

Field Summary

Fields

Modifier and Type	Field and Description
static AtomPositionMap.GroupMatcher	AMINO_ACID_MATCHER
static java.util.Set<java.lang.String>	AMINO_ACID_NAMES
static AtomPositionMap.GroupMatcher	ANYTHING_MATCHER

Constructor Summary

Constructors

Constructor and Description
AtomPositionMap(Atom[] atoms) Creates a new AtomPositionMap containing only amino acids C-alpha atoms.
AtomPositionMap(Atom[] atoms, AtomPositionMap.GroupMatcher matcher) Creates a new AtomPositionMap containing only atoms matched by matcher.

Method Summary

Methods

Modifier and Type	Method and Description
int	calcLength(int positionA, int positionB, char startingChain) This is not the same as subtracting getPosition(ResidueNumber) for positionB from getPosition(ResidueNumber) for positionA.
int	calcLength(int positionA, int positionB, java.lang.String startingChain) This is not the same as subtracting getPosition(ResidueNumber) for positionB from getPosition(ResidueNumber) for positionA.
int	calcLength(ResidueNumber positionA, ResidueNumber positionB) Convenience method for calcLength(int, int, String).
int	calcLengthDirectional(int positionStart, int positionEnd, char startingChain) Calculates the distance between positionStart and positionEnd.
int	calcLengthDirectional(int positionStart, int positionEnd, java.lang.String startingChain) Calculates the distance between positionStart and positionEnd.
int	calcLengthDirectional(ResidueNumber start, ResidueNumber end) Calculates the distance between positionStart and positionEnd.
ResidueNumber	getFirst()
ResidueNumber	getFirst(java.lang.String chainId)
ResidueNumber	getLast()
ResidueNumber	getLast(java.lang.String chainId)
java.util.NavigableMap<ResidueNumber,java.lang.Integer>	getNavMap()
java.lang.Integer	getPosition(ResidueNumber residueNumber)

Methods inherited from class java.lang.Object

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

Field Detail

AMINO_ACID_NAMES

public static final java.util.Set<java.lang.String> AMINO_ACID_NAMES

AMINO_ACID_MATCHER

public static final AtomPositionMap.GroupMatcher AMINO_ACID_MATCHER

ANYTHING_MATCHER

public static final AtomPositionMap.GroupMatcher ANYTHING_MATCHER

Constructor Detail

AtomPositionMap

public AtomPositionMap(Atom[] atoms)

Creates a new AtomPositionMap containing only amino acids C-alpha atoms. C-alpha atoms are identified somewhat liberally.

Parameters:

atoms -

AtomPositionMap

public AtomPositionMap(Atom[] atoms,
               AtomPositionMap.GroupMatcher matcher)

Creates a new AtomPositionMap containing only atoms matched by matcher.

Parameters:

atoms -

Method Detail

calcLength

public int calcLength(int positionA,
             int positionB,
             char startingChain)

This is not the same as subtracting getPosition(ResidueNumber) for positionB from getPosition(ResidueNumber) for positionA. The latter considers only positions of ATOM entries in the PDB file and ignores chains. This method only includes ATOMs from the same chain.

Parameters:

positionA -

positionB -

startingChain -

Returns:

calcLength

public int calcLength(int positionA,
             int positionB,
             java.lang.String startingChain)

This is not the same as subtracting getPosition(ResidueNumber) for positionB from getPosition(ResidueNumber) for positionA. The latter considers only positions of ATOM entries in the PDB file and ignores chains. This method only includes ATOMs from the same chain.

Parameters:

positionA -

positionB -

startingChain -

Returns:

calcLengthDirectional

public int calcLengthDirectional(ResidueNumber start,
                        ResidueNumber end)

Calculates the distance between positionStart and positionEnd. Will return a negative value if the start is past the end.

Parameters:

start -

end -

Returns:

calcLengthDirectional

public int calcLengthDirectional(int positionStart,
                        int positionEnd,
                        char startingChain)

Calculates the distance between positionStart and positionEnd. Will return a negative value if the start is past the end.

Parameters:

positionStart -

positionEnd -

startingChain -

Returns:

calcLengthDirectional

public int calcLengthDirectional(int positionStart,
                        int positionEnd,
                        java.lang.String startingChain)

Calculates the distance between positionStart and positionEnd. Will return a negative value if the start is past the end.

Parameters:

positionStart -

positionEnd -

startingChain -

Returns:

calcLength

public int calcLength(ResidueNumber positionA,
             ResidueNumber positionB)

Convenience method for calcLength(int, int, String).

Parameters:

positionA -

positionB -

Returns:

See Also:

calcLength(int, int, char)

getNavMap

public java.util.NavigableMap<ResidueNumber,java.lang.Integer> getNavMap()

getPosition

public java.lang.Integer getPosition(ResidueNumber residueNumber)

Parameters:

residueNumber -

Returns:

The position of the ATOM record in the PDB file corresponding to the residueNumber

getFirst

public ResidueNumber getFirst(java.lang.String chainId)

Parameters:

chainId -

Returns:

The first ResidueNumber of the specified chain (the one highest down in the PDB file)

getLast

public ResidueNumber getLast(java.lang.String chainId)

Parameters:

chainId -

Returns:

The last ResidueNumber of the specified chain (the one farthest down in the PDB file)

getFirst

public ResidueNumber getFirst()

Parameters:

chainId -

Returns:

The first ResidueNumber of any chain (the one farthest down in the PDB file)

getLast

public ResidueNumber getLast()

Parameters:

chainId -

Returns:

The last ResidueNumber of any chain (the one farthest down in the PDB file)