org.biojava.nbio.structure.align.pairwise

Class FragmentJoiner

java.lang.Object

org.biojava.nbio.structure.align.pairwise.FragmentJoiner

public class FragmentJoiner
extends Object

Joins the initial Fragments together to larger Fragments

Since:

1.5

Version:

%I% %G%

Author:

Andreas Prlic, Peter Lackner

Field Summary

Fields

Modifier and Type	Field and Description
static Logger	logger

Constructor Summary

Constructors

Constructor and Description
FragmentJoiner()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	angleCheckOk(FragmentPair a, FragmentPair b, float distcutoff)
JointFragments[]	approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
void	extendFragments(Atom[] ca1, Atom[] ca2, JointFragments[] fragments, StrucAligParameters params)
void	extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, StrucAligParameters params)
JointFragments[]	frag_pairwise_compat(FragmentPair[] fraglst, int angleDiff, float fragCompatDist, int maxRefine) Calculate the pairwise compatibility of fpairs.
static double	getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag) get the RMS of the JointFragments pair frag
static boolean	reduceFragments(List<FragmentPair> fragments, FragmentPair f, Matrix rmsmat) In helices often many similar fragments can be found.
static Object	resizeArray(Object oldArray, int newSize) Reallocates an array with a new size, and copies the contents of the old array to the new array.

Methods inherited from class java.lang.Object

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

Field Detail

logger

public static Logger logger

Constructor Detail

FragmentJoiner

public FragmentJoiner()

Method Detail

resizeArray

public static Object resizeArray(Object oldArray,
                 int newSize)

Reallocates an array with a new size, and copies the contents of the old array to the new array.

Parameters:

oldArray - the old array, to be reallocated.

newSize - the new array size.

Returns:

A new array with the same contents.

reduceFragments

public static boolean reduceFragments(List<FragmentPair> fragments,
                      FragmentPair f,
                      Matrix rmsmat)

In helices often many similar fragments can be found. To reduce these to a few representative ones this check can be used. It does a distance check between all known Fragments and a new one. If this one is on a similar diagonal and it has a lower rms, this one is a better representation. Note: shifts of one are not allowed.

Parameters:

fragments -

f -

rmsmat -

Returns:

true - if this is a better representant for a group of locala fragments.

approach_ap3

public JointFragments[] approach_ap3(Atom[] ca1,
                            Atom[] ca2,
                            FragmentPair[] fraglst,
                            StrucAligParameters params)
                              throws StructureException

Throws:

StructureException

getRMS

public static double getRMS(Atom[] ca1,
            Atom[] ca2,
            JointFragments frag)
                     throws StructureException

get the RMS of the JointFragments pair frag

Parameters:

ca1 - the array of all atoms of structure1

ca2 - the array of all atoms of structure1

frag - the JointFragments object that contains the list of identical positions

Returns:

the rms

Throws:

StructureException

angleCheckOk

public boolean angleCheckOk(FragmentPair a,
                   FragmentPair b,
                   float distcutoff)

frag_pairwise_compat

public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst,
                                    int angleDiff,
                                    float fragCompatDist,
                                    int maxRefine)

Calculate the pairwise compatibility of fpairs. Iterates through a list of fpairs and joins them if they have compatible rotation and translation parameters.

Parameters:

fraglst - FragmentPair[] array

angleDiff - angle cutoff

fragCompatDist - distance cutoff

maxRefine - max number of solutions to keep

Returns:

JointFragments[]

extendFragments

public void extendFragments(Atom[] ca1,
                   Atom[] ca2,
                   JointFragments[] fragments,
                   StrucAligParameters params)
                     throws StructureException

Throws:

StructureException

extendFragments

public void extendFragments(Atom[] ca1,
                   Atom[] ca2,
                   JointFragments fragments,
                   StrucAligParameters params)
                     throws StructureException

Throws:

StructureException