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java.lang.Objectorg.biojava.bio.structure.align.AbstractStructureAlignment
org.biojava.bio.structure.align.ce.CeMain
org.biojava.bio.structure.align.ce.OptimalCECPMain
public class OptimalCECPMain
A wrapper for CeMain
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
Field Summary | |
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static String |
algorithmName
|
protected OptimalCECPParameters |
params
|
static String |
version
|
Fields inherited from class org.biojava.bio.structure.align.ce.CeMain |
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calculator |
Fields inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment |
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newline |
Constructor Summary | |
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OptimalCECPMain()
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Method Summary | |
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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 Algorithm |
ConfigStrucAligParams |
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.bio.structure.align.ce.CeMain |
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align, getCECalculator |
Methods inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment |
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printHelp |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.bio.structure.align.StructureAlignment |
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printHelp |
Field Detail |
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public static final String algorithmName
public static final String version
protected OptimalCECPParameters params
Constructor Detail |
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public OptimalCECPMain()
Method Detail |
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public String getAlgorithmName()
StructureAlignment
getAlgorithmName
in interface StructureAlignment
getAlgorithmName
in class CeMain
public String getVersion()
StructureAlignment
getVersion
in interface StructureAlignment
getVersion
in class CeMain
public ConfigStrucAligParams getParameters()
StructureAlignment
getParameters
in interface StructureAlignment
getParameters
in class CeMain
OptimalCECPParameters
objectpublic void setParameters(ConfigStrucAligParams params)
StructureAlignment
setParameters
in interface StructureAlignment
setParameters
in class CeMain
params
- Should be an OptimalCECPParameters
object specifying alignment optionspublic AFPChain alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) throws StructureException
WARNING: Modifies ca2 during the permutation. Be sure to make a copy before calling this method.
ca1
- ca2
- param
- cp
-
StructureException
public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException
parameters
. If the parameter
tryAllCPs
is true, all possible
CP sites are tried and the optimal site is returned. Otherwise, the
cpPoint
parameter is used to
determine the CP point, greatly reducing the computation required.
align
in interface StructureAlignment
align
in class CeMain
ca1
- CA atoms of the first proteinca2
- CA atoms of the second proteinparam
- CeParameters
object
StructureException
alignOptimal(Atom[], Atom[], Object, AFPChain[])
public AFPChain alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) throws StructureException
#alignHeuristic(Atom[], Atom[], Object)
for a
faster algorithm.
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.
StructureException
public static void main(String[] args)
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