public final class RMatrix extends EBIMatrix implements java.io.Serializable
Constructor and Description |
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RMatrix(BEMatrix reactantBE,
BEMatrix productBE,
AtomAtomMappingContainer mapping)
Class constructor.
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Modifier and Type | Method and Description |
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java.lang.Object |
clone()
data clone the EBIMatrix object.
|
int |
getAbsChanges() |
protected int |
getAtomCountWithoutHydrogens() |
protected int |
getMappedAtomCount() |
AtomAtomMappingContainer |
getMyMapping() |
org.openscience.cdk.interfaces.IAtom |
getProductAtom(int idx)
Returns the product atom in the idx-th position
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BEMatrix |
getProductBEMatrix() |
java.util.List<org.openscience.cdk.interfaces.IAtom> |
getProductsAtomArray()
Returns the ArrayList containing the product atoms of the RMatrix
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org.openscience.cdk.interfaces.IAtom |
getReactantAtom(int idx)
Returns the reactant atom in the idx-th position
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BEMatrix |
getReactantBEMatrix() |
java.util.List<org.openscience.cdk.interfaces.IAtom> |
getReactantsAtomArray()
Returns the ArrayList containing the reactant atoms of the RMatrix
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int |
getValueByProductAtoms(java.lang.String atomID1,
java.lang.String atomID2) |
int |
getValueByReactantAtoms(java.lang.String atomID1,
java.lang.String atomID2) |
void |
setMyMapping(AtomAtomMappingContainer myMapping) |
void |
setProductBEMatrix(BEMatrix productBEMatrix) |
void |
setReactantBEMatrix(BEMatrix reactantBEMatrix) |
java.lang.String |
toString()
Return a matrix as a String.
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arrayLeftDivide, arrayLeftDivideEquals, arrayRightDivide, arrayRightDivideEquals, arrayTimes, arrayTimesEquals, chol, cond, constructWithCopy, contraction, det, diagonalize, duplicate, eig, elimination, getArray, getArrayCopy, getColumnDimension, getColumnPackedCopy, getDiagonalElements, getMatrix, getMatrix, getMatrix, getMatrix, getRowDimension, getRowPackedCopy, getValue, identity, initMatrix, inverse, is_element_max_in_column, is_element_max_in_row, is_element_min_in_column, is_element_min_in_row, lu, minus, minusEquals, mul, mul, mul, norm1, norm2, normalize, normF, normInf, orthonormalize, pivot, plus, plusEquals, print, print, print, print, qr, random, rank, read, reSizeMatrix, set, setMatrix, setMatrix, setMatrix, setMatrix, setValue, similar, solve, solveTranspose, svd, swapColumns, swapRows, times, times, timesEquals, trace, transpose, uminus
public RMatrix(BEMatrix reactantBE, BEMatrix productBE, AtomAtomMappingContainer mapping) throws org.openscience.cdk.exception.CDKException
reactantBE
- Reactants BEMatrixproductBE
- Products BEMatrixmapping
- Atom-Atom mappings between reactant and products atomsorg.openscience.cdk.exception.CDKException
public org.openscience.cdk.interfaces.IAtom getProductAtom(int idx) throws org.openscience.cdk.exception.CDKException
idx
- the position for which the product atom is neededorg.openscience.cdk.exception.CDKException
public org.openscience.cdk.interfaces.IAtom getReactantAtom(int idx) throws org.openscience.cdk.exception.CDKException
idx
- the position for which the reactant atom is neededorg.openscience.cdk.exception.CDKException
public java.util.List<org.openscience.cdk.interfaces.IAtom> getReactantsAtomArray()
public java.util.List<org.openscience.cdk.interfaces.IAtom> getProductsAtomArray()
public int getValueByReactantAtoms(java.lang.String atomID1, java.lang.String atomID2) throws org.openscience.cdk.exception.CDKException
atomID1
- atomID2
- org.openscience.cdk.exception.CDKException
public int getValueByProductAtoms(java.lang.String atomID1, java.lang.String atomID2) throws org.openscience.cdk.exception.CDKException
atomID1
- atomID2
- org.openscience.cdk.exception.CDKException
public int getAbsChanges()
protected int getMappedAtomCount()
protected int getAtomCountWithoutHydrogens()
public BEMatrix getReactantBEMatrix()
public void setReactantBEMatrix(BEMatrix reactantBEMatrix)
reactantBEMatrix
- the reactantBEMatrix to setpublic BEMatrix getProductBEMatrix()
public void setProductBEMatrix(BEMatrix productBEMatrix)
productBEMatrix
- the productBEMatrix to setpublic AtomAtomMappingContainer getMyMapping()
public void setMyMapping(AtomAtomMappingContainer myMapping)
myMapping
- the myMapping to setpublic java.lang.String toString()
EBIMatrix