org.biojava.bio.structure.io
Class SeqRes2AtomAligner

java.lang.Object
  org.biojava.bio.structure.io.SeqRes2AtomAligner

public class SeqRes2AtomAligner
extends java.lang.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

SeqRes2AtomAligner()

Method Summary

boolean	align(java.util.List<Group> seqRes, java.util.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, java.util.List<Chain> seqResList)
boolean	alignNucleotideGroups(java.util.List<Group> seqRes, java.util.List<Group> atomRes)
java.lang.String	getAlignmentString()
static java.lang.String	getFullAtomSequence(java.util.List<Group> groups, java.util.Map<java.lang.Integer,java.lang.Integer> positionIndex) returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
Chain	getMatchingAtomRes(Chain seqRes, java.util.List<Chain> atomList)
boolean	isDEBUG()
void	mapSeqresRecords(Chain atomRes, Chain seqRes) map the seqres groups to the atomRes chain.
void	setDEBUG(boolean debug)
boolean	trySimpleMatch(java.util.List<Group> seqResGroups, java.util.List<Group> atmResGroups) a simple matching approach that tries to do a 1:1 mapping between SEQRES and ATOM records returns true if this simple matching approach worked fine

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 java.lang.String getAlignmentString()

isDEBUG

public boolean isDEBUG()

setDEBUG

public void setDEBUG(boolean debug)

getMatchingAtomRes

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

Throws:

StructureException

align

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

mapSeqresRecords

public void mapSeqresRecords(Chain atomRes,
                             Chain seqRes)
                      throws StructureException

map the seqres groups to the atomRes chain. updates the atomRes chain object with the mapped data seqRes chain shuold not be needed after this and atomRes should be continued to be used.

Parameters:

atomRes -

seqRes -

Throws:

StructureException

trySimpleMatch

public boolean trySimpleMatch(java.util.List<Group> seqResGroups,
                              java.util.List<Group> atmResGroups)

a simple matching approach that tries to do a 1:1 mapping between SEQRES and ATOM records returns true if this simple matching approach worked fine

Parameters:

seqRes -

atomList -

Returns:

getFullAtomSequence

public static java.lang.String getFullAtomSequence(java.util.List<Group> groups,
                                                   java.util.Map<java.lang.Integer,java.lang.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

alignNucleotideGroups

public boolean alignNucleotideGroups(java.util.List<Group> seqRes,
                                     java.util.List<Group> atomRes)
                              throws StructureException

Throws:

StructureException

align

public boolean align(java.util.List<Group> seqRes,
                     java.util.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