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java.lang.Objectorg.biojava.bio.structure.align.AbstractStructureAlignment
org.biojava.bio.structure.align.ce.CeMain
public class CeMain
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).
Field Summary | |
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static String |
algorithmName
|
protected CECalculator |
calculator
|
protected CeParameters |
params
|
static String |
version
|
Fields inherited from class org.biojava.bio.structure.align.AbstractStructureAlignment |
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newline |
Constructor Summary | |
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CeMain()
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Method Summary | |
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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 Algorithm |
CECalculator |
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 3cna |
void |
setParameters(ConfigStrucAligParams params)
Set the default parameters for this algorithm to use |
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 CeParameters params
protected CECalculator calculator
Constructor Detail |
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public CeMain()
Method Detail |
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public static void main(String[] args)
public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException
align
in interface StructureAlignment
align
in class AbstractStructureAlignment
StructureException
public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException
StructureAlignment
align
in interface StructureAlignment
align
in class AbstractStructureAlignment
StructureException
public String getAlgorithmName()
StructureAlignment
getAlgorithmName
in interface StructureAlignment
getAlgorithmName
in class AbstractStructureAlignment
public ConfigStrucAligParams getParameters()
StructureAlignment
getParameters
in interface StructureAlignment
getParameters
in class AbstractStructureAlignment
public void setParameters(ConfigStrucAligParams params)
StructureAlignment
setParameters
in interface StructureAlignment
setParameters
in class AbstractStructureAlignment
public String getVersion()
StructureAlignment
getVersion
in interface StructureAlignment
getVersion
in class AbstractStructureAlignment
public CECalculator getCECalculator()
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