java.io.Serializable
, java.lang.Cloneable
public class BiologicalAssemblyTransformation
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable
CrystalTransform
,
Serialized FormConstructor | Description |
---|---|
BiologicalAssemblyTransformation() |
Default Constructor
|
BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src) |
Copy Constructor
|
Modifier and Type | Method | Description |
---|---|---|
static BiologicalAssemblyTransformation |
combine(BiologicalAssemblyTransformation matrix1,
BiologicalAssemblyTransformation matrix2) |
Returns the combination (product) of two biological assembly transformations.
|
static java.util.List<BiologicalAssemblyTransformation> |
fromMultiXML(java.lang.String xml) |
|
static BiologicalAssemblyTransformation |
fromXML(java.lang.String xml) |
|
java.lang.String |
getChainId() |
Returns the chain identifier this transformation should be applied to.
|
java.lang.String |
getId() |
Returns the identifier for this biological assembly transformation.
|
javax.vecmath.Matrix4d |
getTransformationMatrix() |
Return the transformation (both rotational and translational component) as a 4x4 transformation matrix.
|
static java.lang.String |
rotMatrixToString(javax.vecmath.Matrix4d m) |
|
void |
setChainId(java.lang.String chainId) |
Sets the chain identified this transformation should be applied to.
|
void |
setId(java.lang.String id) |
Sets the identifier for this biological assembly transformation.
|
void |
setRotationMatrix(double[][] m) |
|
void |
setTransformationMatrix(javax.vecmath.Matrix4d transformation) |
Sets the transformation using a 4x4 transformation matrix
|
void |
setTranslation(double[] t) |
|
java.lang.String |
toString() |
|
java.lang.String |
toXML() |
|
void |
toXML(PrettyXMLWriter xml) |
|
void |
transformPoint(double[] point) |
Applies the transformation to given point.
|
static java.lang.String |
translVecToString(javax.vecmath.Matrix4d m) |
public BiologicalAssemblyTransformation()
public BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)
src
- public void setId(java.lang.String id)
id
- public java.lang.String getId()
public void setChainId(java.lang.String chainId)
chainId
- public java.lang.String getChainId()
public void setTransformationMatrix(javax.vecmath.Matrix4d transformation)
transformation
- public javax.vecmath.Matrix4d getTransformationMatrix()
CrystalCell.transfToCrystal(Matrix4d)
Note that this is a reference to the variable, thus it remains linked to this object's transformation field.
The user must deep copy it if need changing it.public void setRotationMatrix(double[][] m)
public void setTranslation(double[] t)
public void transformPoint(double[] point)
public static BiologicalAssemblyTransformation combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2)
matrix1
- matrix2
- public java.lang.String toXML() throws java.io.IOException
java.io.IOException
public void toXML(PrettyXMLWriter xml) throws java.io.IOException
java.io.IOException
public static BiologicalAssemblyTransformation fromXML(java.lang.String xml) throws org.xml.sax.SAXException, java.io.IOException, javax.xml.parsers.ParserConfigurationException
org.xml.sax.SAXException
java.io.IOException
javax.xml.parsers.ParserConfigurationException
public static java.util.List<BiologicalAssemblyTransformation> fromMultiXML(java.lang.String xml) throws javax.xml.parsers.ParserConfigurationException, org.xml.sax.SAXException, java.io.IOException
javax.xml.parsers.ParserConfigurationException
org.xml.sax.SAXException
java.io.IOException
public java.lang.String toString()
toString
in class java.lang.Object
public static java.lang.String rotMatrixToString(javax.vecmath.Matrix4d m)
public static java.lang.String translVecToString(javax.vecmath.Matrix4d m)