org.biojava.bio.structure.align
Class AFPTwister
java.lang.Object
org.biojava.bio.structure.align.AFPTwister
public class AFPTwister
- extends Object
Method Summary |
static int |
afp2Res(AFPChain afpChain,
int afpn,
int[] afpPositions,
int listStart)
Set the list of equivalent residues in the two proteins given a list of AFPs
WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain! |
static Group[] |
twistOptimized(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
superimposing according to the optimized alignment |
static Group[] |
twistPDB(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
calculate the total rmsd of the blocks
output a merged pdb file for both proteins
protein 1, in chain A
protein 2 is twisted according to the twists detected, in chain B |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AFPTwister
public AFPTwister()
twistPDB
public static Group[] twistPDB(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
throws StructureException
- calculate the total rmsd of the blocks
output a merged pdb file for both proteins
protein 1, in chain A
protein 2 is twisted according to the twists detected, in chain B
- Returns:
- twisted Groups
- Throws:
StructureException
twistOptimized
public static Group[] twistOptimized(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
throws StructureException
- superimposing according to the optimized alignment
- Parameters:
afpChain
- ca1
- ca2
-
- Returns:
- Group array twisted.
- Throws:
StructureException
afp2Res
public static int afp2Res(AFPChain afpChain,
int afpn,
int[] afpPositions,
int listStart)
- Set the list of equivalent residues in the two proteins given a list of AFPs
WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
- Parameters:
afpChain
- the AFPChain to store resutsafpn
- nr of afpafpPositions
- listStart
-
- Returns:
- nr of eq residues