org.biojava.bio.structure.io

Class SeqRes2AtomAligner

java.lang.Object

org.biojava.bio.structure.io.SeqRes2AtomAligner

public class SeqRes2AtomAligner
extends Object

Aligns the SEQRES residues to the ATOM residues. The AminoAcids that can be matched between the two of them will be set in the SEQRES chains

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
SeqRes2AtomAligner()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	align(List<Group> seqRes, List<Group> atomRes) aligns two chains of groups, where the first parent is representing the list of amino acids as obtained from the SEQRES records, and the second parent represents the groups obtained from the ATOM records (and containing the actual ATOM information).
void	align(Structure s, List<Chain> seqResList)
String	getAlignmentString()
static String	getFullAtomSequence(List<Group> groups, Map<Integer,Integer> positionIndex) returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
Chain	getMatchingAtomRes(Chain seqRes, List<Chain> atomList)
boolean	isDEBUG()
void	setDEBUG(boolean debug)

Methods inherited from class java.lang.Object

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

Constructor Detail

SeqRes2AtomAligner

public SeqRes2AtomAligner()

Method Detail

getAlignmentString

public String getAlignmentString()

isDEBUG

public boolean isDEBUG()

setDEBUG

public void setDEBUG(boolean debug)

getMatchingAtomRes

public Chain getMatchingAtomRes(Chain seqRes,
                       List<Chain> atomList)
                         throws StructureException

Throws:

StructureException

align

public void align(Structure s,
         List<Chain> seqResList)

getFullAtomSequence

public static String getFullAtomSequence(List<Group> groups,
                         Map<Integer,Integer> positionIndex)

returns the full sequence of the Atom records of a parent with X instead of HETATMSs. The advantage of this is that it allows us to also align HETATM groups back to the SEQRES.

Parameters:

groups - the list of groups in a parent

positionIndex - a Map to keep track of which group is at which sequence position

Returns:

string representations

align

public boolean align(List<Group> seqRes,
            List<Group> atomRes)
              throws StructureException

aligns two chains of groups, where the first parent is representing the list of amino acids as obtained from the SEQRES records, and the second parent represents the groups obtained from the ATOM records (and containing the actual ATOM information). This does the actual alignment and if a group can be mapped to a position in the SEQRES then the corresponding position is repplaced with the group that contains the atoms.

Parameters:

seqRes -

atomRes -

Returns:

true if no match has bee found

Throws:

StructureException