Class FatCat
- java.lang.Object
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- org.biojava.nbio.structure.align.fatcat.FatCat
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- Direct Known Subclasses:
FatCatFlexible
,FatCatRigid
public class FatCat extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
algorithmName
static java.lang.String
newline
static java.lang.String
VERSION
version history: 1.1 - Added more parameters to the command line 1.0 - Initial version
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Constructor Summary
Constructors Constructor Description FatCat()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected AFPChain
align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
AFPChain
alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)
AFPChain
alignRigid(Atom[] ca1, Atom[] ca2)
AFPChain
alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)
FatCatAligner
getFatCatAligner()
static void
main(java.lang.String[] argv)
See demo/FatCatDemo.java for an example how to run.java.lang.String
toString()
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Field Detail
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VERSION
public static final java.lang.String VERSION
version history: 1.1 - Added more parameters to the command line 1.0 - Initial version- See Also:
- Constant Field Values
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newline
public static java.lang.String newline
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algorithmName
public static final java.lang.String algorithmName
- See Also:
- Constant Field Values
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Method Detail
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main
public static void main(java.lang.String[] argv) throws ConfigurationException
See demo/FatCatDemo.java for an example how to run. Launch FatCat from command line. Parameters are:- Parameters:
argv
-- Throws:
ConfigurationException
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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alignRigid
public AFPChain alignRigid(Atom[] ca1, Atom[] ca2) throws StructureException
- Throws:
StructureException
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alignRigid
public AFPChain alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params) throws StructureException
- Throws:
StructureException
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alignFlexible
public AFPChain alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params) throws StructureException
- Throws:
StructureException
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align
protected AFPChain align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid) throws StructureException
- Throws:
StructureException
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getFatCatAligner
public FatCatAligner getFatCatAligner()
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