Class OptimalCECPMain
- java.lang.Object
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- org.biojava.nbio.structure.align.AbstractStructureAlignment
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- org.biojava.nbio.structure.align.ce.CeMain
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- org.biojava.nbio.structure.align.ce.OptimalCECPMain
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- All Implemented Interfaces:
StructureAlignment
public class OptimalCECPMain extends CeMain
A wrapper forCeMain
which sets default parameters to be appropriate for finding circular permutations.A circular permutation consists of a single cleavage point and rearrangement between two structures, for example:
ABCDEFG DEFGABC
- Author:
- Spencer Bliven.
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Field Summary
Fields Modifier and Type Field Description static String
algorithmName
protected OptimalCECPParameters
params
static String
version
version history: 1.0 - Initial version-
Fields inherited from class org.biojava.nbio.structure.align.ce.CeMain
calculator
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Fields inherited from class org.biojava.nbio.structure.align.AbstractStructureAlignment
newline
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Constructor Summary
Constructors Constructor Description OptimalCECPMain()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description AFPChain
align(Atom[] ca1, Atom[] ca2, Object param)
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).AFPChain
alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments)
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).AFPChain
alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp)
Aligns ca1 with ca2 permuted by cp residues.String
getAlgorithmName()
Get the name of the AlgorithmConfigStrucAligParams
getParameters()
Return the paramers for this algorithm.String
getVersion()
Get the Version information for this Algorithm.static void
main(String[] args)
void
setParameters(ConfigStrucAligParams params)
Set the default parameters for this algorithm to use-
Methods inherited from class org.biojava.nbio.structure.align.ce.CeMain
align, getCECalculator
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Field Detail
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algorithmName
public static final String algorithmName
- See Also:
- Constant Field Values
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version
public static final String version
version history: 1.0 - Initial version- See Also:
- Constant Field Values
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params
protected OptimalCECPParameters params
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Constructor Detail
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OptimalCECPMain
public OptimalCECPMain()
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Method Detail
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getAlgorithmName
public String getAlgorithmName()
Description copied from interface:StructureAlignment
Get the name of the Algorithm- Specified by:
getAlgorithmName
in interfaceStructureAlignment
- Overrides:
getAlgorithmName
in classCeMain
- Returns:
- the name of the algorithm
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getVersion
public String getVersion()
Description copied from interface:StructureAlignment
Get the Version information for this Algorithm.- Specified by:
getVersion
in interfaceStructureAlignment
- Overrides:
getVersion
in classCeMain
- Returns:
- the version of the algorithm
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getParameters
public ConfigStrucAligParams getParameters()
Description copied from interface:StructureAlignment
Return the paramers for this algorithm.- Specified by:
getParameters
in interfaceStructureAlignment
- Overrides:
getParameters
in classCeMain
- Returns:
- an
OptimalCECPParameters
object
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setParameters
public void setParameters(ConfigStrucAligParams params)
Description copied from interface:StructureAlignment
Set the default parameters for this algorithm to use- Specified by:
setParameters
in interfaceStructureAlignment
- Overrides:
setParameters
in classCeMain
- Parameters:
params
- Should be anOptimalCECPParameters
object specifying alignment options
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alignPermuted
public AFPChain alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) throws StructureException
Aligns ca1 with ca2 permuted by cp residues.WARNING: Modifies ca2 during the permutation. Be sure to make a copy before calling this method.
- Parameters:
ca1
-ca2
-param
-cp
-- Returns:
- Throws:
StructureException
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align
public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException
Finds the optimal alignment between two proteins allowing for a circular permutation (CP). The precise algorithm is controlled by theparameters
. If the parametertryAllCPs
is true, all possible CP sites are tried and the optimal site is returned. Otherwise, thecpPoint
parameter is used to determine the CP point, greatly reducing the computation required.- Specified by:
align
in interfaceStructureAlignment
- Overrides:
align
in classCeMain
- Parameters:
ca1
- CA atoms of the first proteinca2
- CA atoms of the second proteinparam
-CeParameters
object- Returns:
- The best-scoring alignment
- Throws:
StructureException
- See Also:
alignOptimal(Atom[], Atom[], Object, AFPChain[])
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alignOptimal
public AFPChain alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) throws StructureException
Finds the optimal alignment between two proteins allowing for a circular permutation (CP). This algorithm performs a CE alignment for each possible CP site. This is quite slow. Use#alignHeuristic(Atom[], Atom[], Object)
for a faster algorithm.- Parameters:
ca1
- CA atoms of the first proteinca2
- CA atoms of the second proteinparam
-CeParameters
objectalignments
- If not null, should be an empty array of the same length as ca2. This will be filled with the alignments from permuting ca2 by 0 to n-1 residues.- Returns:
- The best-scoring alignment
- Throws:
StructureException
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