org.biojava.nbio.structure

Class AtomPositionMap

java.lang.Object

org.biojava.nbio.structure.AtomPositionMap

public class AtomPositionMap
extends Object

A map from ResidueNumbers to ATOM record positions in a PDB file.

To use:

 Atom[] atoms = new AtomCache().getAtoms("1w0p");
 AtomPositionMap map = new AtomPositionMap(atoms);
 ResidueNumber start = new ResidueNumber("A", 100, null);
 ResidueNumber end = map.getEnd("A");
 int pos = map.getPosition(start);
 int length = map.calcLength(start, end);
 

Note: The getLength() methods were introduced in BioJava 4.0.0 to replace the calcLength methods. The new method returns the number of residues between two residues, inclusive, whereas the previous method returned 1 less than that.

Author:

Douglas Myers-Turnbull

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	AtomPositionMap.GroupMatcher Used as a Predicate to indicate whether a particular Atom should be mapped

Field Summary

Fields

Modifier and Type	Field and Description
static AtomPositionMap.GroupMatcher	AMINO_ACID_MATCHER Matches CA atoms of protein groups
static AtomPositionMap.GroupMatcher	ANYTHING_MATCHER Matches all atoms

Constructor Summary

Constructors

Constructor and Description
AtomPositionMap(Atom[] atoms) Creates a new AtomPositionMap containing peptide alpha-carbon atoms
AtomPositionMap(Atom[] atoms, AtomPositionMap.GroupMatcher matcher) Creates a new AtomPositionMap containing only atoms matched by matcher.
AtomPositionMap(Structure s) Creates a new AtomPositionMap containing representative atoms from a structure.

Method Summary

Modifier and Type	Method and Description
ResidueNumber	getFirst()
ResidueNumber	getFirst(String chainId)
ResidueNumber	getLast()
ResidueNumber	getLast(String chainId)
int	getLength(int positionA, int positionB, String startingChain) Calculates the number of residues of the specified chain in a given range, inclusive.
int	getLength(ResidueNumber start, ResidueNumber end) Calculates the number of atoms between two ResidueNumbers, inclusive.
int	getLengthDirectional(int positionStart, int positionEnd, String startingChain) Calculates the number of residues of the specified chain in a given range.
int	getLengthDirectional(ResidueNumber start, ResidueNumber end) Calculates the number of atoms between two ResidueNumbers, inclusive.
NavigableMap<ResidueNumber,Integer>	getNavMap()
Integer	getPosition(ResidueNumber residueNumber) Gets the 0-based index of residueNumber to the matched atoms
List<ResidueRangeAndLength>	getRanges() Returns a list of ResidueRanges corresponding to this entire AtomPositionMap.
ResidueRangeAndLength	trimToValidResidues(ResidueRange rr) Trims a residue range so that both endpoints are contained in this map.

Methods inherited from class java.lang.Object

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

Field Detail

AMINO_ACID_MATCHER

public static final AtomPositionMap.GroupMatcher AMINO_ACID_MATCHER

Matches CA atoms of protein groups

ANYTHING_MATCHER

public static final AtomPositionMap.GroupMatcher ANYTHING_MATCHER

Matches all atoms

Constructor Detail

AtomPositionMap

public AtomPositionMap(Atom[] atoms)

Creates a new AtomPositionMap containing peptide alpha-carbon atoms

Parameters:

atoms -

AtomPositionMap

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

Creates a new AtomPositionMap containing only atoms matched by matcher. If multiple atoms are present from a group, the first atom encountered will be used.

Parameters:

atoms -

AtomPositionMap

public AtomPositionMap(Structure s)

Creates a new AtomPositionMap containing representative atoms from a structure.

Parameters:

s -

Method Detail

getLength

public int getLength(int positionA,
                     int positionB,
                     String startingChain)

Calculates the number of residues of the specified chain in a given range, inclusive.

Parameters:

positionA - index of the first atom to count

positionB - index of the last atom to count

startingChain - Case-sensitive chain

Returns:

The number of atoms between A and B inclusive belonging to the given chain

getLengthDirectional

public int getLengthDirectional(int positionStart,
                                int positionEnd,
                                String startingChain)

Calculates the number of residues of the specified chain in a given range. Will return a negative value if the start is past the end.

Parameters:

positionStart - index of the first atom to count

positionEnd - index of the last atom to count

startingChain - Case-sensitive chain

Returns:

The number of atoms from A to B inclusive belonging to the given chain

getLength

public int getLength(ResidueNumber start,
                     ResidueNumber end)

Calculates the number of atoms between two ResidueNumbers, inclusive. Both residues must belong to the same chain.

Parameters:

start - First residue

end - Last residue

Returns:

The number of atoms from A to B inclusive

Throws:

IllegalArgumentException - if start and end are on different chains, or if either of the residues doesn't exist

getLengthDirectional

public int getLengthDirectional(ResidueNumber start,
                                ResidueNumber end)

Calculates the number of atoms between two ResidueNumbers, inclusive. Both residues must belong to the same chain. Will return a negative value if the start is past the end.

Parameters:

start - First residue

end - Last residue

Returns:

The number of atoms from A to B inclusive

Throws:

IllegalArgumentException - if start and end are on different chains, or if either of the residues doesn't exist

getNavMap

public NavigableMap<ResidueNumber,Integer> getNavMap()

getPosition

public Integer getPosition(ResidueNumber residueNumber)

Gets the 0-based index of residueNumber to the matched atoms

Parameters:

residueNumber -

Returns:

The position of the ATOM record in the PDB file corresponding to the residueNumber, or null if the residueNumber was not found

getFirst

public ResidueNumber getFirst(String chainId)

Parameters:

chainId -

Returns:

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

getLast

public ResidueNumber getLast(String chainId)

Parameters:

chainId -

Returns:

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

getFirst

public ResidueNumber getFirst()

Returns:

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

getLast

public ResidueNumber getLast()

Returns:

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

getRanges

public List<ResidueRangeAndLength> getRanges()

Returns a list of ResidueRanges corresponding to this entire AtomPositionMap.

trimToValidResidues

public ResidueRangeAndLength trimToValidResidues(ResidueRange rr)

Trims a residue range so that both endpoints are contained in this map.

Parameters:

rr - residue range

Returns:

residue range and length