public class FragmentJoiner
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.util.logging.Logger |
logger |
Constructor and Description |
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FragmentJoiner() |
Modifier and Type | Method and Description |
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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.
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static double |
getRMS(Atom[] ca1,
Atom[] ca2,
JointFragments frag)
get the RMS of the JointFragments pair frag
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static boolean |
reduceFragments(java.util.List<FragmentPair> fragments,
FragmentPair f,
Matrix rmsmat)
In helices often many similar fragments can be found.
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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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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 positionspublic 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