public class AFPAlignmentDisplay
extends java.lang.Object
Constructor | Description |
---|---|
AFPAlignmentDisplay() |
Modifier and Type | Method | Description |
---|---|---|
static int |
aaScore(char a,
char b) |
|
static java.util.Map<java.lang.String,java.lang.Double> |
calcIdSimilarity(char[] seq1,
char[] seq2,
int alnLength) |
|
static Structure |
createArtificalStructure(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
|
static void |
getAlign(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
Extract the alignment output
|
static void |
getAlign(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
boolean showSeq) |
|
static Atom[] |
getAlignedAtoms1(AFPChain afpChain,
Atom[] ca1) |
|
static Atom[] |
getAlignedAtoms2(AFPChain afpChain,
Atom[] ca2) |
|
static int |
getBlockNrForAlignPos(AFPChain afpChain,
int aligPos) |
get the block number for an aligned position
|
static Matrix |
getRotMax(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
|
static Atom |
getTranslation(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
public static Matrix getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
StructureException
public static Atom getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
StructureException
public static void getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
eg
STWNTWACTWHLKQP--WSTILILA 111111111111 22222222 SQNNTYACSWKLKSWNNNSTILILGThose position pairs labeled by 1 and 2 are equivalent positions, belongs to two blocks 1 and 2. The residues between labeled residues are non-equivalent, with '-' filling in their resulting gaps.
The three lines can be accessed using
AFPChain.getAlnseq1()
, AFPChain.getAlnsymb()
,
and AFPChain.getAlnseq2()
.
public static void getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq)
Expects the following properties to be previously computed:
AFPChain.getOptAln()
and lengths
afpChain
- Alignment between ca1 and ca2ca1
- CA atoms of the first proteinca2
- CA atoms of the second proteinshowSeq
- Use symbols reflecting sequence similarity: '|' for identical,
':' for similar, '.' for dissimilar. Otherwise, use the block number
to show aligned residues.public static int aaScore(char a, char b)
public static java.util.Map<java.lang.String,java.lang.Double> calcIdSimilarity(char[] seq1, char[] seq2, int alnLength)
public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws java.lang.ClassNotFoundException, java.lang.NoSuchMethodException, java.lang.reflect.InvocationTargetException, java.lang.IllegalAccessException
afpChain
- ca1
- ca2
- java.lang.ClassNotFoundException
- If an error occurs when invoking jmoljava.lang.NoSuchMethodException
- If an error occurs when invoking jmoljava.lang.reflect.InvocationTargetException
- If an error occurs when invoking jmoljava.lang.IllegalAccessException
- If an error occurs when invoking jmolpublic static int getBlockNrForAlignPos(AFPChain afpChain, int aligPos)
afpChain
- aligPos
-