Class GridCell
- java.lang.Object
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- org.biojava.nbio.structure.contact.GridCell
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public class GridCell extends java.lang.Object
A grid cell to be used in contact calculation via geometric hashing algorithm.- Author:
- duarte_j
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Constructor Summary
Constructors Constructor Description GridCell()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addIindex(int serial)
void
addJindex(int serial)
java.util.List<AtomContact>
getContactsToOtherCell(GridCell otherCell, Atom[] iAtoms, Atom[] jAtoms, double cutoff)
Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContactsjava.util.List<AtomContact>
getContactsWithinCell(Atom[] iAtoms, Atom[] jAtoms, double cutoff)
Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContactsint
getNumIindices()
int
getNumJindices()
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Method Detail
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addIindex
public void addIindex(int serial)
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addJindex
public void addJindex(int serial)
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getNumIindices
public int getNumIindices()
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getNumJindices
public int getNumJindices()
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getContactsWithinCell
public java.util.List<AtomContact> getContactsWithinCell(Atom[] iAtoms, Atom[] jAtoms, double cutoff)
Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContacts- Parameters:
iAtoms
- the first set of atoms to which the iIndices correspondjAtoms
- the second set of atoms to which the jIndices correspond, if null distances are within the iAtoms onlycutoff
-- Returns:
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getContactsToOtherCell
public java.util.List<AtomContact> getContactsToOtherCell(GridCell otherCell, Atom[] iAtoms, Atom[] jAtoms, double cutoff)
Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContacts- Parameters:
otherCell
-iAtoms
- the first set of atoms to which the iIndices correspondjAtoms
- the second set of atoms to which the jIndices correspond, if null distances are within the iAtoms onlycutoff
-- Returns:
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