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 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 |
setDEBUG(boolean debug) |
public java.lang.String getAlignmentString()
public boolean isDEBUG()
public void setDEBUG(boolean debug)
public Chain getMatchingAtomRes(Chain seqRes, java.util.List<Chain> atomList) throws StructureException
StructureException
public static java.lang.String getFullAtomSequence(java.util.List<Group> groups, java.util.Map<java.lang.Integer,java.lang.Integer> positionIndex)
groups
- the list of groups in a parentpositionIndex
- a Map to keep track of which group is at which sequence positionpublic boolean alignNucleotideGroups(java.util.List<Group> seqRes, java.util.List<Group> atomRes) throws StructureException
StructureException
public boolean align(java.util.List<Group> seqRes, java.util.List<Group> atomRes) throws StructureException
seqRes
- atomRes
- StructureException