public class DisplayAFP
extends java.lang.Object
Constructor | Description |
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DisplayAFP() |
Modifier and Type | Method | Description |
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static Structure |
createArtificalStructure(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
|
static StructureAlignmentJmol |
display(AFPChain afpChain,
Group[] twistedGroups,
Atom[] ca1,
Atom[] ca2,
java.util.List<Group> hetatms1,
java.util.List<Group> hetatms2) |
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
|
static Structure |
getAlignedStructure(Atom[] ca1,
Atom[] ca2) |
Get an artifical Structure containing both chains.
|
static Atom[] |
getAtomArray(Atom[] ca,
java.util.List<Group> hetatms) |
Returns the first atom for each group
|
static Atom |
getAtomForAligPos(AFPChain afpChain,
int chainNr,
int aligPos,
Atom[] ca,
boolean getPrevious) |
return the atom at alignment position aligPos.
|
static int |
getBlockNrForAlignPos(AFPChain afpChain,
int aligPos) |
Deprecated.
use AFPAlignmentDisplay.getBlockNrForAlignPos instead...
|
static java.util.List<java.lang.Integer> |
getEQRAlignmentPos(AFPChain afpChain) |
|
static java.util.List<java.lang.String> |
getPDBresnum(int aligPos,
AFPChain afpChain,
Atom[] ca) |
Return a list of pdb Strings corresponding to the aligned positions of the molecule.
|
static void |
showAlignmentImage(AFPChain afpChain,
java.lang.String result) |
|
static void |
showAlignmentPanel(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
AbstractAlignmentJmol jmol) |
public static final java.util.List<java.lang.Integer> getEQRAlignmentPos(AFPChain afpChain)
public static final java.util.List<java.lang.String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca)
aligPos
- afpChain
- ca
- @Deprecated public static int getBlockNrForAlignPos(AFPChain afpChain, int aligPos)
afpChain
- aligPos
- public static final Atom getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious) throws StructureException
chainNr
- the number of the aligned pair. 0... first chain, 1... second chain.afpChain
- an afpChain objectaligPos
- position on the alignmentgetPrevious
- gives the previous position if false, gives the next posible atomStructureException
public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) throws StructureException
ca1
- ca2
- StructureException
public static final Atom[] getAtomArray(Atom[] ca, java.util.List<Group> hetatms) throws StructureException
ca
- hetatms
- StructureException
public static final StructureAlignmentJmol display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, java.util.List<Group> hetatms1, java.util.List<Group> hetatms2) throws StructureException
StructureException
public static void showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) throws StructureException
StructureException
public static void showAlignmentImage(AFPChain afpChain, java.lang.String result)
public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
afpChain
- the container of the alignmentca1
- atoms for protein 1ca2
- atoms for protein 2StructureException