org.simtk.molecularstructure
Class SequenceAlignment

java.lang.Object
  org.simtk.molecularstructure.SequenceAlignment

public class SequenceAlignment
extends java.lang.Object

Constructor Summary

SequenceAlignment(Biopolymer m1, Biopolymer m2)

Method Summary

void	alignNaively() Creates an alignment where the first residue of the first molecule is aligned with the first residue of the second molecule, the second residue is aligned with the second residue, and so on.
HomogeneousTransform	getSuperposition() Generates rigid-body transformation that when applied to the first molecule's residues, minimizes the least squared deviation from the second molecule's residues.
java.util.Iterator	iterator()

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceAlignment

public SequenceAlignment(Biopolymer m1,
                         Biopolymer m2)

Method Detail

alignNaively

public void alignNaively()

Creates an alignment where the first residue of the first molecule is aligned with the first residue of the second molecule, the second residue is aligned with the second residue, and so on. This method is only appropriate when the two molecular sequences are identical, or in other cases where there is a complete ordered one-to-one mapping of the residues between the two molecules.

iterator

public java.util.Iterator iterator()

getSuperposition

public HomogeneousTransform getSuperposition()

Generates rigid-body transformation that when applied to the first molecule's residues, minimizes the least squared deviation from the second molecule's residues. Only works for residues that have atomic structures.