public class BEMatrix extends EBIMatrix implements java.io.Serializable
Constructor and Description |
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BEMatrix(boolean skipHydrogen,
org.openscience.cdk.interfaces.IAtomContainerSet molSet,
java.util.List<org.openscience.cdk.interfaces.IBond> bonds,
java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> mappings)
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.
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double |
convertBondOrder(org.openscience.cdk.interfaces.IBond bond) |
int |
convertBondStereo(org.openscience.cdk.interfaces.IBond bond) |
org.openscience.cdk.interfaces.IBond.Stereo |
convertStereo(int stereoValue) |
org.openscience.cdk.interfaces.IAtom |
getAtom(int pos)
Returns the atom at the position pos in [0,..].
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org.openscience.cdk.interfaces.IAtomContainer |
getAtomContainer(org.openscience.cdk.interfaces.IAtom at) |
java.util.List<org.openscience.cdk.interfaces.IAtom> |
getAtoms()
Returns the ArrayList containing the atoms of the BEMatrix
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org.openscience.cdk.interfaces.IBond |
getBond(org.openscience.cdk.interfaces.IAtom a,
org.openscience.cdk.interfaces.IAtom b) |
double |
getBondOrder(org.openscience.cdk.interfaces.IAtom a,
org.openscience.cdk.interfaces.IAtom b) |
java.util.List<org.openscience.cdk.interfaces.IBond> |
getBonds() |
int |
getBondStereo(org.openscience.cdk.interfaces.IAtom a,
org.openscience.cdk.interfaces.IAtom b) |
int |
getOrder(org.openscience.cdk.interfaces.IAtom a1,
org.openscience.cdk.interfaces.IAtom a2)
The methods returns the order of the bond that connects two given atoms.
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int[] |
orderAtomArray(java.util.List<org.openscience.cdk.interfaces.IAtom> orderedAtomArray)
This method performs the sorting of the atoms of the BEMatrix according
to the ArrayList passed as parameter.
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void |
pivot(int i1,
int i2)
Perform the pivoting of the BEMatrix switching also the atoms in position
i1th and i2th.
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void |
setAromaticBond() |
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, 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 BEMatrix(boolean skipHydrogen, org.openscience.cdk.interfaces.IAtomContainerSet molSet, java.util.List<org.openscience.cdk.interfaces.IBond> bonds, java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> mappings)
molSet
- The IAtomContainerSet for which the BEMatrix is requiredskipHydrogen
- bonds
- mappings
- AAMpublic int getOrder(org.openscience.cdk.interfaces.IAtom a1, org.openscience.cdk.interfaces.IAtom a2)
a1
- The first IAtom atoma2
- The second IAtom atompublic int[] orderAtomArray(java.util.List<org.openscience.cdk.interfaces.IAtom> orderedAtomArray) throws org.openscience.cdk.exception.CDKException
orderedAtomArray
- ArrayList containing the new order of atomsorg.openscience.cdk.exception.CDKException
public void pivot(int i1, int i2)
public double getBondOrder(org.openscience.cdk.interfaces.IAtom a, org.openscience.cdk.interfaces.IAtom b) throws org.openscience.cdk.exception.CDKException
a
- b
- org.openscience.cdk.exception.CDKException
public int getBondStereo(org.openscience.cdk.interfaces.IAtom a, org.openscience.cdk.interfaces.IAtom b) throws org.openscience.cdk.exception.CDKException
a
- b
- org.openscience.cdk.exception.CDKException
public void setAromaticBond() throws org.openscience.cdk.exception.CDKException, org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
public java.util.List<org.openscience.cdk.interfaces.IAtom> getAtoms()
public org.openscience.cdk.interfaces.IAtom getAtom(int pos) throws org.openscience.cdk.exception.CDKException
pos
- The position of the atom to be retrieved.org.openscience.cdk.exception.CDKException
public org.openscience.cdk.interfaces.IBond getBond(org.openscience.cdk.interfaces.IAtom a, org.openscience.cdk.interfaces.IAtom b)
a
- first atomb
- second atompublic org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(org.openscience.cdk.interfaces.IAtom at)
at
- public double convertBondOrder(org.openscience.cdk.interfaces.IBond bond)
bond
- public int convertBondStereo(org.openscience.cdk.interfaces.IBond bond)
bond
- public org.openscience.cdk.interfaces.IBond.Stereo convertStereo(int stereoValue)
stereoValue
- public java.util.List<org.openscience.cdk.interfaces.IBond> getBonds()
public java.lang.String toString()
EBIMatrix