Class CeMain
- 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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- All Implemented Interfaces:
StructureAlignment
- Direct Known Subclasses:
CeCPMain
,CeSideChainMain
,OptimalCECPMain
public class CeMain extends AbstractStructureAlignment implements StructureAlignment
The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I. Shindyalov and P.Bourne (1998). The original CE paper is available from here: http://peds.oxfordjournals.org/cgi/content/short/11/9/739 For a demo of how to use this algorithm, visit the BioJava web site: CE usage example. The BioJava CE version is based on CE version 2.3 (2003 or 2004).- Author:
- Andreas Prlic.
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Field Summary
Fields Modifier and Type Field Description static String
algorithmName
protected CECalculator
calculator
protected CeParameters
params
static String
version
version history: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code-
Fields inherited from class org.biojava.nbio.structure.align.AbstractStructureAlignment
newline
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Constructor Summary
Constructors Constructor Description CeMain()
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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)
Run an alignment while specifying the atoms to be aligned.AFPChain
align(Atom[] ca1, Atom[] ca2, Object param)
Align ca2 onto ca1.String
getAlgorithmName()
Get the name of the AlgorithmCECalculator
getCECalculator()
ConfigStrucAligParams
getParameters()
Return the paramers for this algorithm.String
getVersion()
Get the Version information for this Algorithm.static void
main(String[] args)
Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cnavoid
setParameters(ConfigStrucAligParams params)
Set the default parameters for this algorithm to use
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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: 1.2 - Added more parameters to the command line, including -maxOptRMSD 1.1 - Additional parameters 1.0 - Initial port from C code- See Also:
- Constant Field Values
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params
protected CeParameters params
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calculator
protected CECalculator calculator
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Constructor Detail
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CeMain
public CeMain()
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Method Detail
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main
public static void main(String[] args) throws Exception
Example Parameters: -pdbFilePath /tmp -autoFetch -printCE -pdb1 1cnv -pdb2 3cna- Throws:
Exception
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align
public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException
Align ca2 onto ca1.- Specified by:
align
in interfaceStructureAlignment
- Specified by:
align
in classAbstractStructureAlignment
- Returns:
- the afpChain object that contains the alignment.
- Throws:
StructureException
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align
public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException
Description copied from interface:StructureAlignment
Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.- Specified by:
align
in interfaceStructureAlignment
- Specified by:
align
in classAbstractStructureAlignment
- Returns:
- the afpChain object that contains the alignment.
- Throws:
StructureException
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getAlgorithmName
public String getAlgorithmName()
Description copied from interface:StructureAlignment
Get the name of the Algorithm- Specified by:
getAlgorithmName
in interfaceStructureAlignment
- Specified by:
getAlgorithmName
in classAbstractStructureAlignment
- Returns:
- the name 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
- Specified by:
getParameters
in classAbstractStructureAlignment
- Returns:
- The returned object will be a Java bean.
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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
- Specified by:
setParameters
in classAbstractStructureAlignment
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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
- Specified by:
getVersion
in classAbstractStructureAlignment
- Returns:
- the version of the algorithm
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getCECalculator
public CECalculator getCECalculator()
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