org.biojava.bio.structure.align.pairwise
Class FragmentJoiner
java.lang.Object
org.biojava.bio.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
Method Summary |
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)
|
static boolean |
reduceFragments(List 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 |
logger
public static Logger logger
FragmentJoiner
public FragmentJoiner()
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 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)
getRMS
public static double getRMS(Atom[] ca1,
Atom[] ca2,
JointFragments frag)
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[]