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java.lang.Object jgromacs.analysis.Superposition
public class Superposition
Collection of methods for superposing structures
Constructor Summary | |
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Superposition()
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Method Summary | |
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static PointList |
superposeTo(PointList toBeSuperposed,
PointList reference)
Calculates the superposition of a point list to another |
static Structure |
superposeTo(Structure toBeSuperposed,
IndexSet indices1,
Structure reference,
IndexSet indices2)
Calculates the superposition of a structure to another using a subset of atoms for fitting |
static Structure |
superposeTo(Structure toBeSuperposed,
Structure reference)
Calculates the superposition of a structure to another |
static Trajectory |
superposeTo(Trajectory t,
PointList reference)
Calculates the superposition of each frame of a trajectory to a common reference frame |
static Trajectory |
superposeTo(Trajectory t,
Structure reference)
Calculates the superposition of each frame of a trajectory to a common reference frame |
static Trajectory |
superposeTo(Trajectory t,
Structure reference,
IndexSet indices)
Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fitting |
static PointList |
weightedSuperposeTo(PointList toBeSuperposed,
PointList reference,
java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of a point list to another |
static Structure |
weightedSuperposeTo(Structure toBeSuperposed,
Structure reference,
java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of a structure to another |
static Trajectory |
weightedSuperposeTo(Trajectory t,
PointList reference,
java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of each frame of a trajectory to a common reference frame |
static Trajectory |
weightedSuperposeTo(Trajectory t,
Structure reference,
java.util.ArrayList<java.lang.Double> weights)
Calculates the weighted superposition of each frame of a trajectory to a common reference frame |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Superposition()
Method Detail |
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public static PointList superposeTo(PointList toBeSuperposed, PointList reference)
toBeSuperposed
- the point list to be superposedreference
- the reference point list
public static Structure superposeTo(Structure toBeSuperposed, Structure reference)
toBeSuperposed
- the structure to be superposedreference
- the reference structure
public static Structure superposeTo(Structure toBeSuperposed, IndexSet indices1, Structure reference, IndexSet indices2)
toBeSuperposed
- the structure to be superposedindices1
- first index setreference
- the reference structureindices2
- second index set
public static Trajectory superposeTo(Trajectory t, PointList reference)
t
- trajectory to be superposedreference
- reference point list
public static Trajectory superposeTo(Trajectory t, Structure reference)
t
- trajectory to be superposedreference
- reference structure
public static Trajectory superposeTo(Trajectory t, Structure reference, IndexSet indices)
t
- trajectory to be superposedreference
- reference structureindices
- index set
public static PointList weightedSuperposeTo(PointList toBeSuperposed, PointList reference, java.util.ArrayList<java.lang.Double> weights)
toBeSuperposed
- the point list to be superposedreference
- the reference point listweights
- vector of weights
public static Structure weightedSuperposeTo(Structure toBeSuperposed, Structure reference, java.util.ArrayList<java.lang.Double> weights)
toBeSuperposed
- the structure to be superposedreference
- the reference structureweights
- vector of weights
public static Trajectory weightedSuperposeTo(Trajectory t, PointList reference, java.util.ArrayList<java.lang.Double> weights)
t
- trajectory to be superposedreference
- reference point listweights
- vector of weights
public static Trajectory weightedSuperposeTo(Trajectory t, Structure reference, java.util.ArrayList<java.lang.Double> weights)
t
- trajectory to be superposedreference
- reference structureweights
- vector of weights
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