org.biojava.nbio.structure.io

Class SeqRes2AtomAligner

java.lang.Object

org.biojava.nbio.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, Jose Duarte

Constructor Summary

Constructors

Constructor and Description
SeqRes2AtomAligner()

Method Summary

Modifier and Type	Method and Description
void	align(Structure s, List<Chain> seqResList)
String	getAlignmentString()
static String	getFullAtomSequence(List<Group> groups, Map<Integer,Integer> positionIndex, boolean isNucleotideChain) Returns the full sequence of the Atom records of a parent with X instead of HETATMSs.
static Chain	getMatchingAtomRes(Chain seqRes, List<Chain> atomList, boolean useChainId)
void	mapSeqresRecords(Chain atomRes, Chain seqRes) Map the seqRes groups to the atomRes chain.
static void	storeUnAlignedSeqRes(Structure structure, List<Chain> seqResChains, boolean headerOnly) Storing unaligned SEQRES groups in a Structure.

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()

getMatchingAtomRes

public static Chain getMatchingAtomRes(Chain seqRes,
                                       List<Chain> atomList,
                                       boolean useChainId)

Parameters:

seqRes -

atomList -

useChainId - if true chainId (Chain.getId) is used for matching, if false chainName (Chain.getName) is used

Returns:

align

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

mapSeqresRecords

public void mapSeqresRecords(Chain atomRes,
                             Chain seqRes)

Map the seqRes groups to the atomRes chain. Updates the atomRes chain object with the mapped data The seqRes chain should not be needed after this and atomRes should be further used.

Parameters:

atomRes - the chain containing ATOM groups (in atomGroups slot). This chain is modified to contain in its seqresGroups slot the mapped atom groups

seqRes - the chain containing SEQRES groups (in atomGroups slot). This chain is not modified

getFullAtomSequence

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

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

isNucleotideChain - whether the atom groups are predominantly nucleotides (the groups represent a nucleotide chain), if true non-standard nucleotides will be represented with ambiguous letter 'N' instead of 'X', if false all non-standard residues will be 'X'

Returns:

string representations

storeUnAlignedSeqRes

public static void storeUnAlignedSeqRes(Structure structure,
                                        List<Chain> seqResChains,
                                        boolean headerOnly)

Storing unaligned SEQRES groups in a Structure.

Parameters:

structure -

seqResChains -