Package org.biojava.bio.structure.io
Class SeqRes2AtomAligner
- java.lang.Object
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- org.biojava.bio.structure.io.SeqRes2AtomAligner
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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
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Constructor Summary
Constructors Constructor Description SeqRes2AtomAligner()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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)
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Method Detail
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getAlignmentString
public java.lang.String getAlignmentString()
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isDEBUG
public boolean isDEBUG()
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setDEBUG
public void setDEBUG(boolean debug)
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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
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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
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getSubstitutionMatrix
public static SubstitutionMatrix getSubstitutionMatrix(FiniteAlphabet alphabet) throws java.io.IOException, BioException
- Throws:
java.io.IOException
BioException
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