Package pl.poznan.put.rna

Class ChainReorderer

java.lang.Object

pl.poznan.put.rna.ChainReorderer

public final class ChainReorderer
extends Object

A set of methods to reorder chains in an RNA structure. The order is derived from base pairing information in two steps: (1) a graph of connection is traversed to find connected components which are processed together, and (2) all permutations of each component's order are analyzed to find one which minimizes the pseudoknot order.

Method Summary

Modifier and Type	Method	Description
static PdbModel	reorderAtoms(PdbModel model)	Finds canonical base pairs (see CanonicalStructureExtractor.basePairs(ResidueCollection)) and reorders chains to keep connected ones together while minimizing the overall pseudoknot order.
static PdbModel	reorderAtoms(PdbModel model, Collection<? extends ClassifiedBasePair> basePairs)	Reorders chains according to given canonical base pairs to keep connected chains together while minimizing the overall pseudoknot order.

Methods inherited from class java.lang.Object

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

Method Detail

reorderAtoms

public static PdbModel reorderAtoms(PdbModel model)

Finds canonical base pairs (see CanonicalStructureExtractor.basePairs(ResidueCollection)) and reorders chains to keep connected ones together while minimizing the overall pseudoknot order.

Parameters:

model - The input PDB model.

Returns:

The PDB model filtered to contain only RNA and with chains reordered.

reorderAtoms

public static PdbModel reorderAtoms(PdbModel model,
                                    Collection<? extends ClassifiedBasePair> basePairs)

Reorders chains according to given canonical base pairs to keep connected chains together while minimizing the overall pseudoknot order.

Parameters:

model - The input PDB model.

basePairs - The list of base pairs to take into account.

Returns:

The PDB model filtered to contain only RNA and with chains reordered.