public class SeqRes2AtomAligner
extends java.lang.Object
Constructor and Description |
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SeqRes2AtomAligner() |
Modifier and Type | Method and Description |
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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) |
public java.lang.String getAlignmentString()
public boolean isDEBUG()
public void setDEBUG(boolean debug)
public java.lang.String getFullAtomSequence(java.util.List<Group> groups)
groups
- the list of groups in a chainpublic boolean align(java.util.List<Group> seqRes, java.util.List<Group> atomRes) throws StructureException
seqRes
- atomRes
- StructureException
public static SubstitutionMatrix getSubstitutionMatrix(FiniteAlphabet alphabet) throws java.io.IOException, BioException
java.io.IOException
BioException