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java.lang.Objectorg.biojava.bio.structure.align.pairwise.FragmentJoiner
public class FragmentJoiner
Joins the initial Fragments together to larger Fragments
Field Summary | |
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static java.util.logging.Logger |
logger
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Constructor Summary | |
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FragmentJoiner()
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Method Summary | |
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JointFragments[] |
approach_ap3(Atom[] ca1,
Atom[] ca2,
FragmentPair[] fraglst,
StrucAligParameters params)
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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(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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static java.util.logging.Logger logger
Constructor Detail |
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public FragmentJoiner()
Method Detail |
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public static java.lang.Object resizeArray(java.lang.Object oldArray, int newSize)
oldArray
- the old array, to be reallocated.newSize
- the new array size.
public static boolean reduceFragments(java.util.List<FragmentPair> fragments, FragmentPair f, Matrix rmsmat)
fragments
- f
- rmsmat
-
public JointFragments[] approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
public static double getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)
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
public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst, int angleDiff, float fragCompatDist, int maxRefine)
fraglst
- FragmentPair[] arrayangleDiff
- angle cutofffragCompatDist
- distance cutoffmaxRefine
- max number of solutions to keep
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