Class DisplayAFP
- java.lang.Object
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- org.biojava.nbio.structure.align.gui.DisplayAFP
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public class DisplayAFP extends Object
A utility class for visualistion of structure alignments- Author:
- Andreas Prlic
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Constructor Summary
Constructors Constructor Description DisplayAFP()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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, List<Group> hetatms1, List<Group> hetatms2)
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.static Atom[]
getAtomArray(Atom[] ca, List<Group> hetatms)
Returns the first atom for each groupstatic Atom
getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious)
Return the atom at alignment position aligPos. at the present only works with block 0static List<Integer>
getEQRAlignmentPos(AFPChain afpChain)
static List<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, String result)
static void
showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)
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Constructor Detail
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DisplayAFP
public DisplayAFP()
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Method Detail
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getEQRAlignmentPos
public static final List<Integer> getEQRAlignmentPos(AFPChain afpChain)
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getPDBresnum
public static final List<String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca)
Return a list of pdb Strings corresponding to the aligned positions of the molecule. Only supports a pairwise alignment with the AFPChain DS.- Parameters:
aligPos
-afpChain
-ca
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getAtomForAligPos
public static final Atom getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious) throws StructureException
Return the atom at alignment position aligPos. at the present only works with block 0- Parameters:
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 atom- Returns:
- a CA atom that is at a particular position of the alignment
- Throws:
StructureException
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getAtomArray
public static final Atom[] getAtomArray(Atom[] ca, List<Group> hetatms) throws StructureException
Returns the first atom for each group- Parameters:
ca
-hetatms
-- Returns:
- Throws:
StructureException
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display
public static final StructureAlignmentJmol display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2) throws StructureException
Note: ca2, hetatoms2 and nucleotides2 should not be rotated. This will be done here...- Throws:
StructureException
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showAlignmentPanel
public static void showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) throws StructureException
- Throws:
StructureException
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showAlignmentImage
public static void showAlignmentImage(AFPChain afpChain, String result)
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createArtificalStructure
public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.- Parameters:
afpChain
- the container of the alignmentca1
- atoms for protein 1ca2
- atoms for protein 2- Returns:
- a protein structure with 2 models.
- Throws:
StructureException
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