Class CeSymmResult
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.internal.CeSymmResult
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public class CeSymmResult extends Object
This Class stores all the relevant information of an internal symmetry result obtained with CeSymm. The purpose is to carry all the information packed during the calculations and return a single object.- Since:
- 4.2.0
- Author:
- Aleix Lafita
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Constructor Summary
Constructors Constructor Description CeSymmResult()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Atom[]
getAtoms()
SymmetryAxes
getAxes()
MultipleAlignment
getMultipleAlignment()
int
getNumRepeats()
Return the symmetry order determined by the order detector if the symmetry is significant.CESymmParameters
getParams()
String
getReason()
Return a String describing the reasons for the CE-Symm final decision in this particular result.List<StructureIdentifier>
getRepeatsID()
Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.AFPChain
getSelfAlignment()
StructureIdentifier
getStructureId()
String
getSymmGroup()
int
getSymmLevels()
boolean
isRefined()
boolean
isSignificant()
Conditions checked are: score above the threshold, number of repeats higher than 1 and refinement succeeded.void
setAtoms(Atom[] atoms)
void
setAxes(SymmetryAxes axes)
void
setMultipleAlignment(MultipleAlignment multipleAlignment)
void
setNumRepeats(int symmOrder)
void
setParams(CESymmParameters params)
void
setRefined(boolean refined)
void
setSelfAlignment(AFPChain selfAlignment)
void
setStructureId(StructureIdentifier structureId)
void
setSymmGroup(String symmGroup)
String
toString()
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Constructor Detail
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CeSymmResult
public CeSymmResult()
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Method Detail
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isSignificant
public boolean isSignificant()
Conditions checked are: score above the threshold, number of repeats higher than 1 and refinement succeeded.- Returns:
- true if significant, false otherwise
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getRepeatsID
public List<StructureIdentifier> getRepeatsID() throws StructureException
Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.- Returns:
- List of StructureIdentifiers or null if not defined
- Throws:
StructureException
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getMultipleAlignment
public MultipleAlignment getMultipleAlignment()
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setMultipleAlignment
public void setMultipleAlignment(MultipleAlignment multipleAlignment)
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getSelfAlignment
public AFPChain getSelfAlignment()
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setSelfAlignment
public void setSelfAlignment(AFPChain selfAlignment)
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getParams
public CESymmParameters getParams()
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setParams
public void setParams(CESymmParameters params)
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getAxes
public SymmetryAxes getAxes()
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setAxes
public void setAxes(SymmetryAxes axes)
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getNumRepeats
public int getNumRepeats()
Return the symmetry order determined by the order detector if the symmetry is significant. Return 1 otherwise.- Returns:
- the order of symmetry if the result is significant
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setNumRepeats
public void setNumRepeats(int symmOrder)
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isRefined
public boolean isRefined()
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setRefined
public void setRefined(boolean refined)
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getSymmGroup
public String getSymmGroup()
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setSymmGroup
public void setSymmGroup(String symmGroup)
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getSymmLevels
public int getSymmLevels()
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getStructureId
public StructureIdentifier getStructureId()
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setStructureId
public void setStructureId(StructureIdentifier structureId)
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