Class FragmentJoiner
- java.lang.Object
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- org.biojava.bio.structure.align.pairwise.FragmentJoiner
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public class FragmentJoiner extends java.lang.Object
Joins the initial Fragments together to larger Fragments- Since:
- 1.5
- Version:
- %I% %G%
- Author:
- Andreas Prlic, Peter Lackner
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Field Summary
Fields Modifier and Type Field Description static java.util.logging.Logger
logger
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Constructor Summary
Constructors Constructor Description FragmentJoiner()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description JointFragments[]
approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, 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 fragstatic boolean
reduceFragments(java.util.List<FragmentPair> fragments, FragmentPair f, Matrix rmsmat)
In helices often many similar fragments can be found.static java.lang.Object
resizeArray(java.lang.Object oldArray, int newSize)
Reallocates an array with a new size, and copies the contents of the old array to the new array.
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Method Detail
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resizeArray
public static java.lang.Object resizeArray(java.lang.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.
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reduceFragments
public static boolean reduceFragments(java.util.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.
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approach_ap3
public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
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getRMS
public static double getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)
get the RMS of the JointFragments pair frag- Parameters:
ca1
- the array of all atoms of structure1ca2
- the array of all atoms of structure1frag
- the JointFragments object that contains the list of identical positions- Returns:
- the rms
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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[] arrayangleDiff
- angle cutofffragCompatDist
- distance cutoffmaxRefine
- max number of solutions to keep- Returns:
- JointFragments[]
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