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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.CeCPMain
public class CeCPMain
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
Nested Class Summary | |
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protected static class |
CeCPMain.CPRange
Tiny wrapper for the disallowed regions of an alignment. |
Field Summary | |
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static String |
algorithmName
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static int |
DEFAULT_MIN_CP_LENGTH
|
static String |
version
version history: 1.3 - Short CPs are now discarded 1.2 - now supports check AlignmentTools.isSequentialAlignment. |
Fields inherited from class org.biojava.bio.structure.align.ce.CeMain |
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calculator, params |
Fields inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment |
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newline |
Constructor Summary | |
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CeCPMain()
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Method Summary | |
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AFPChain |
align(Atom[] ca1,
Atom[] ca2,
Object param)
Aligns ca1 and ca2 using a heuristic to check for CPs. |
protected static CeCPMain.CPRange |
calculateMinCP(int[] block,
int blockLen,
int ca2len,
int minCPlength)
Finds the alignment index of the residues minCPlength before and after the duplication. |
static AFPChain |
filterDuplicateAFPs(AFPChain afpChain,
CECalculator ceCalc,
Atom[] ca1,
Atom[] ca2duplicated)
Takes as input an AFPChain where ca2 has been artificially duplicated. |
static AFPChain |
filterDuplicateAFPs(AFPChain afpChain,
CECalculator ceCalc,
Atom[] ca1,
Atom[] ca2duplicated,
int minCPlength)
|
String |
getAlgorithmName()
Get the name of the Algorithm |
String |
getVersion()
Get the Version information for this Algorithm. |
static void |
main(String[] args)
|
static AFPChain |
postProcessAlignment(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2m,
CECalculator calculator)
Circular permutation specific code to be run after the standard CE alignment |
Methods inherited from class org.biojava.bio.structure.align.ce.CeMain |
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align, getCECalculator, getParameters, setParameters |
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 int DEFAULT_MIN_CP_LENGTH
public static final String version
Constructor Detail |
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public CeCPMain()
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 static void main(String[] args)
public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException
Aligns ca1 against a doubled ca2, then cleans up the alignment.
align
in interface StructureAlignment
align
in class CeMain
ca1
- ca2
- param
-
StructureException
public static AFPChain postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator) throws StructureException
afpChain
- The finished alignementca1
- CA atoms of the first proteinca2m
- A duplicated copy of the second proteincalculator
- The CECalculator used to create afpChain
StructureException
public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated) throws StructureException
The current version chooses a CP site such that the length of the alignment is maximized.
This method does not update scores to reflect the filtered alignment. It does update the RMSD and superposition.
afpChain
- The alignment between ca1 and ca2-ca2. Blindly assumes
that ca2 has been duplicated.
StructureException
public static AFPChain filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated, int minCPlength) throws StructureException
StructureException
protected static CeCPMain.CPRange calculateMinCP(int[] block, int blockLen, int ca2len, int minCPlength)
block
- The permuted block being considered, generally optAln[0][1]blockLen
- The length of the block (in case extra memory was allocated in block)ca2len
- The length, in residues, of the protein specified by blockminCPlength
- The minimum number of residues allowed for a CP
block
of the residue such that
minCPlength
residues remain to the end of ca2len
,
or -1 if no residue fits that criterium.ca2len
.minCPlength
-th residue after ca2len,
or ca2len*2 if no residue fits that criterium.
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