public class SeqRes2AtomAligner
extends java.lang.Object
Constructor | Description |
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SeqRes2AtomAligner() |
Modifier and Type | Method | Description |
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void |
align(Structure s,
java.util.List<Chain> seqResList) |
|
java.lang.String |
getAlignmentString() |
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static java.lang.String |
getFullAtomSequence(java.util.List<Group> groups,
java.util.Map<java.lang.Integer,java.lang.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,
java.util.List<Chain> atomList) |
|
void |
mapSeqresRecords(Chain atomRes,
Chain seqRes) |
Map the seqRes groups to the atomRes chain.
|
static void |
storeUnAlignedSeqRes(Structure structure,
java.util.List<Chain> seqResChains,
boolean headerOnly) |
Storing unaligned SEQRES groups in a Structure.
|
public java.lang.String getAlignmentString()
public static Chain getMatchingAtomRes(Chain seqRes, java.util.List<Chain> atomList)
public void mapSeqresRecords(Chain atomRes, Chain seqRes)
atomRes
- the chain containing ATOM groups (in atomGroups slot). This chain
is modified to contain in its seqresGroups slot the mapped atom groupsseqRes
- the chain containing SEQRES groups (in atomGroups slot). This chain
is not modifiedpublic static java.lang.String getFullAtomSequence(java.util.List<Group> groups, java.util.Map<java.lang.Integer,java.lang.Integer> positionIndex, boolean isNucleotideChain)
groups
- the list of groups in a parentpositionIndex
- a Map to keep track of which group is at which sequence positionisNucleotideChain
- 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'