org.simtk.molecularstructure.nucleicacid
Class BasePair

java.lang.Object
  org.simtk.molecularstructure.SecondaryStructureClass
      org.simtk.molecularstructure.nucleicacid.BasePair

All Implemented Interfaces:

java.lang.Iterable<Residue>, SecondaryStructure

public class BasePair
extends SecondaryStructureClass
implements java.lang.Iterable<Residue>

Nested Class Summary

static class	BasePair.BondOrientation
static class	BasePair.EdgeType

Nested classes/interfaces inherited from class org.simtk.molecularstructure.SecondaryStructureClass

SecondaryStructureClass.SourceType

Field Summary

protected BasePair.BondOrientation	bond_orient
protected java.util.HashMap<Residue,BasePair.EdgeType>	edges
protected java.lang.String	strand_orient

Fields inherited from class org.simtk.molecularstructure.SecondaryStructureClass

parentMolecules, residues, resLimit, sourceType

Constructor Summary

BasePair(Residue r1, Residue r2)

Method Summary

void	addResidue(Residue r)
boolean	equals(java.lang.Object o)
static BasePair	getBasePair(Residue r1, Residue r2, java.lang.String source)
Plane3D	getBasePlane()
BasePair.BondOrientation	getBond_orient()
BasePair.EdgeType	getEdge(Residue res)
Vector3D	getHelixCenter() Estimate position at center of a double helix containing this base pair
Residue	getResidue1()
Residue	getResidue2()
java.lang.String	getStrand_orient()
int	hashCode()
java.lang.Boolean	isBetween(Residue r1, Residue r2)
java.util.Iterator<Residue>	iterator()
static BasePair	makeBasePair(Residue r1, Residue r2, java.lang.String source)
void	setBond_orient(BasePair.BondOrientation bond_orient)
void	setBond_orient(java.lang.String bond)
void	setEdge(Residue res, BasePair.EdgeType edgeT)
void	setEdge(Residue res, java.lang.String edge)
void	setStrand_orient(java.lang.String strand_orient)
java.lang.String	toString()

Methods inherited from class org.simtk.molecularstructure.SecondaryStructureClass

addMolecule, getMolecules, getResidueIterator, getSource, residues, setMolecule, setSource

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

edges

protected java.util.HashMap<Residue,BasePair.EdgeType> edges

bond_orient

protected BasePair.BondOrientation bond_orient

strand_orient

protected java.lang.String strand_orient

Constructor Detail

BasePair

public BasePair(Residue r1,
                Residue r2)

Method Detail

getBasePair

public static BasePair getBasePair(Residue r1,
                                   Residue r2,
                                   java.lang.String source)

makeBasePair

public static BasePair makeBasePair(Residue r1,
                                    Residue r2,
                                    java.lang.String source)

getBond_orient

public BasePair.BondOrientation getBond_orient()

setBond_orient

public void setBond_orient(BasePair.BondOrientation bond_orient)

setBond_orient

public void setBond_orient(java.lang.String bond)

getEdge

public BasePair.EdgeType getEdge(Residue res)

setEdge

public void setEdge(Residue res,
                    BasePair.EdgeType edgeT)

setEdge

public void setEdge(Residue res,
                    java.lang.String edge)

getStrand_orient

public java.lang.String getStrand_orient()

setStrand_orient

public void setStrand_orient(java.lang.String strand_orient)

addResidue

public void addResidue(Residue r)

Specified by:

addResidue in interface SecondaryStructure

Overrides:

addResidue in class SecondaryStructureClass

getResidue1

public Residue getResidue1()

getResidue2

public Residue getResidue2()

getBasePlane

public Plane3D getBasePlane()
                     throws InsufficientAtomsException

Throws:

InsufficientAtomsException

getHelixCenter

public Vector3D getHelixCenter()
                        throws InsufficientAtomsException

Estimate position at center of a double helix containing this base pair

Returns:

the point at the center of the helix in the plane of the base pair

Throws:

InsufficientAtomsException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

iterator

public java.util.Iterator<Residue> iterator()

Specified by:

iterator in interface java.lang.Iterable<Residue>

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

isBetween

public java.lang.Boolean isBetween(Residue r1,
                                   Residue r2)