Package 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

Constructors

Constructor	Description
SeqRes2AtomAligner()

Method Summary

Modifier and Type	Method	Description
boolean	align(java.util.List<Group> seqRes, java.util.List<Group> atomRes)	aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain represents the groups obtained from the ATOM records (and containing the actual ATOM information).
void	align(Structure s, java.util.List<Chain> seqResList)
java.lang.String	getAlignmentString()
java.lang.String	getFullAtomSequence(java.util.List<Group> groups)	returns the full sequence of the Atom records of a chain with X instead of HETATMSs.
static SubstitutionMatrix	getSubstitutionMatrix(FiniteAlphabet alphabet)
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 java.lang.String getAlignmentString()

isDEBUG

public boolean isDEBUG()

setDEBUG

public void setDEBUG(boolean debug)

align

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

getFullAtomSequence

public java.lang.String getFullAtomSequence(java.util.List<Group> groups)

returns the full sequence of the Atom records of a chain 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 chain

Returns:

string representations

align

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

aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain 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

getSubstitutionMatrix

public static SubstitutionMatrix getSubstitutionMatrix(FiniteAlphabet alphabet)
                                                throws java.io.IOException,
                                                       BioException

Throws:

java.io.IOException

BioException