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java.lang.Objectorg.biojava.bio.structure.align.StructurePairAligner
public class StructurePairAligner
Constructor Summary | |
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StructurePairAligner()
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Method Summary | |
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void |
align(Atom[] ca1,
Atom[] ca2,
StrucAligParameters params)
calculate the actual protein structure superimposition. |
void |
align(Structure s1,
Structure s2)
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void |
align(Structure s1,
Structure s2,
StrucAligParameters params)
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AlternativeAlignment[] |
getAlignments()
return the alternative alignments that can be found for the two structures |
Matrix |
getDistMat()
return the difference of distance matrix between the two structures |
FragmentPair[] |
getFragmentPairs()
get the results of step 1 - the FragmentPairs used for seeding the alignment |
StrucAligParameters |
getParams()
get the parameters. |
static void |
main(String[] args)
example usage of this class |
void |
setFragmentPairs(FragmentPair[] fragPairs)
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void |
setParams(StrucAligParameters params)
set the parameters to be used for the algorithm |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public StructurePairAligner()
Method Detail |
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public static void main(String[] args)
args
- public FragmentPair[] getFragmentPairs()
public void setFragmentPairs(FragmentPair[] fragPairs)
public AlternativeAlignment[] getAlignments()
public Matrix getDistMat()
public StrucAligParameters getParams()
public void setParams(StrucAligParameters params)
params
- the Parameter objectpublic void align(Structure s1, Structure s2) throws StructureException
StructureException
public void align(Structure s1, Structure s2, StrucAligParameters params) throws StructureException
StructureException
public void align(Atom[] ca1, Atom[] ca2, StrucAligParameters params) throws StructureException
ca1
- set of Atoms of structure 1ca2
- set of Atoms of structure 2params
- the parameters to use for the alignment
StructureException
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