Package org.biojava.nbio.structure.align.seq

Class SmithWaterman3Daligner

java.lang.Object

org.biojava.nbio.structure.align.AbstractStructureAlignment

org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner

All Implemented Interfaces:

StructureAlignment

public class SmithWaterman3Daligner
extends AbstractStructureAlignment
implements StructureAlignment

Provides a 3D superimposition of two structures based on their sequence alignment.

This algorithm includes a final step to iteratively drop columns of the alignment until a maximum RMSD threshold of the superimposition, or the minimum alignment length theshold, are fulfilled, similar to what pymol align algorithm does.

Author:

Andreas Prlic, Aleix Lafita

Field Summary

Fields

Modifier and Type	Field	Description
static final String	algorithmName

Constructor Summary

Constructors

Constructor	Description
SmithWaterman3Daligner()

Method Summary

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 parameters)	run an alignment and also send a bean containing the parameters.
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 parameters)	Set the default parameters for this algorithm to use

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

algorithmName

public static final String algorithmName

See Also:

• Constant Field Values

Constructor Details

SmithWaterman3Daligner

public SmithWaterman3Daligner()

Method Details

main

public static void main(String[] args)
                 throws ConfigurationException

Throws:

ConfigurationException

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 interface StructureAlignment

Specified by:

align in class AbstractStructureAlignment

Parameters:

ca1 -

ca2 -

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

align

public AFPChain align(Atom[] ca1,
 Atom[] ca2,
 Object parameters)
               throws StructureException

Description copied from interface: StructureAlignment

run an alignment and also send a bean containing the parameters.

Specified by:

align in interface StructureAlignment

Specified by:

align in class AbstractStructureAlignment

Parameters:

ca1 -

ca2 -

parameters -

Returns:

the afpChain object that contains the alignment.

Throws:

StructureException

getAlgorithmName

public String getAlgorithmName()

Description copied from interface: StructureAlignment

Get the name of the Algorithm

Specified by:

getAlgorithmName in interface StructureAlignment

Specified by:

getAlgorithmName in class AbstractStructureAlignment

Returns:

the name of the algorithm

getParameters

public ConfigStrucAligParams getParameters()

Description copied from interface: StructureAlignment

Return the paramers for this algorithm.

Specified by:

getParameters in interface StructureAlignment

Specified by:

getParameters in class AbstractStructureAlignment

Returns:

The returned object will be a Java bean.

getVersion

public String getVersion()

Description copied from interface: StructureAlignment

Get the Version information for this Algorithm.

Specified by:

getVersion in interface StructureAlignment

Specified by:

getVersion in class AbstractStructureAlignment

Returns:

the version of the algorithm

setParameters

public void setParameters(ConfigStrucAligParams parameters)

Description copied from interface: StructureAlignment

Set the default parameters for this algorithm to use

Specified by:

setParameters in interface StructureAlignment

Specified by:

setParameters in class AbstractStructureAlignment

Parameters:

parameters -