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java.lang.Object ProGAL.proteins.belta.SheetTopology
public class SheetTopology
Representation of the topology of a single sheet. Where the BetaTopology is represented
using a pairing matrix, the sheet topology uses a list of strand pairs that can be accessed
via the public strandPairs
field. The list of strand pairs is ordered such that
the pairs follow the order along the sheet, and the first strand from the N-terminal is in
the first half of the list.
getStrandOrder
and getStrandOrientation are alternative methods
to access the topology. The following example shows the relationship between the pairing-
matrix in the beta-topology and the order and orientation-arrays.
SecondaryStructure ss = new SecondaryStructure(" EE EE EE EE "); //Beta-topology with a single sheet BetaTopology bTop = new BetaTopology(ss); bTop.setPaired(1,0); bTop.setPaired(2,0); bTop.setPaired(2,3); SheetTopology sTop = new SheetTopology(bTop,0); System.out.println(sTop.getStrandOrderString()); //Prints "1 0 2 3" System.out.println(sTop.getStrandOrientationString()); //Prints "1110"
Nested Class Summary | |
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static class |
SheetTopology.StrandPair
A pair of strands specified by two strand-indices (i.e. |
Field Summary | |
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SecondaryStructure |
secondaryStructure
The secondary structure that the sheet-topology is related to |
java.util.List<SheetTopology.StrandPair> |
strandPairs
An ordered list of strand-pairs. |
java.util.List<java.lang.Integer> |
strands
A sorted list of strand-indices. |
Constructor Summary | |
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SheetTopology(BetaTopology bTop,
int strand)
Construct the sheet containing the specified strand. |
Method Summary | |
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boolean |
containsStrand(int strand)
Return true if the specified strand is in this sheet. |
int[] |
getNormalizedStrandOrder()
Return an array indicating the normalized strand order. |
int[] |
getStrandOrder()
Return an array indicating the strand order. |
java.lang.String |
getStrandOrderString()
String representation of strand order. |
int[] |
getStrandOrientation()
Return an array indicating orientation of strands. |
java.lang.String |
getStrandOrientationString()
String representation of strand orientation. |
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public final SecondaryStructure secondaryStructure
public final java.util.List<SheetTopology.StrandPair> strandPairs
public final java.util.List<java.lang.Integer> strands
secondaryStructure.getStrands()
-array.
Constructor Detail |
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public SheetTopology(BetaTopology bTop, int strand)
Method Detail |
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public boolean containsStrand(int strand)
strand
- A strand-index (i.e. an index in the
secondaryStructure.getStrands()
-array).public int[] getStrandOrder()
public int[] getNormalizedStrandOrder()
SheetTopology.this.strands
-array and
not to SheetTopology.this.secondaryStructure.getStrands()
as strand-
indices usually do.
public int[] getStrandOrientation()
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String getStrandOrderString()
public java.lang.String getStrandOrientationString()
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