Package com.actelion.research.chem.conf
Class BondRotationHelper
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- com.actelion.research.chem.conf.BondRotationHelper
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public class BondRotationHelper extends java.lang.Object
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Constructor Summary
Constructors Constructor Description BondRotationHelper(StereoMolecule mol)
BondRotationHelper(StereoMolecule mol, boolean includeTerminalPolarH)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int[][]
getRearAtoms()
int[]
getRotatableBonds()
int[]
getRotationCenters()
int[][]
getSmallerSideAtomLists()
int[][]
getTorsionAtoms()
java.lang.String[]
getTorsionIDs()
void
initialize()
boolean
isRotatableBond(int bond)
static void
predictAtomSequence(StereoMolecule mol, int bond, int[] torsionAtoms, int[] rearAtoms)
void
rotateAroundBond(int bondIndex, double alpha, Conformer conf, boolean biggerSide)
rotate torsion angle of a conformervoid
rotateSmallerSide(int bond, double alpha)
void
setRearAtoms(int[][] rearAtoms)
void
setRotatableBonds(int[] rotatableBonds)
void
setRotationCenters(int[] rotationCenters)
void
setSmallerSideAtomLists(int[][] smallerSideAtomLists)
void
setTorsionAtoms(int[][] torsionAtoms)
void
setTorsionIDs(java.lang.String[] torsionIDs)
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Constructor Detail
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BondRotationHelper
public BondRotationHelper(StereoMolecule mol)
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BondRotationHelper
public BondRotationHelper(StereoMolecule mol, boolean includeTerminalPolarH)
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Method Detail
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initialize
public void initialize()
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predictAtomSequence
public static void predictAtomSequence(StereoMolecule mol, int bond, int[] torsionAtoms, int[] rearAtoms)
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isRotatableBond
public boolean isRotatableBond(int bond)
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getRotatableBonds
public int[] getRotatableBonds()
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rotateSmallerSide
public void rotateSmallerSide(int bond, double alpha)
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rotateAroundBond
public void rotateAroundBond(int bondIndex, double alpha, Conformer conf, boolean biggerSide)
rotate torsion angle of a conformer- Parameters:
bond
-alpha
-conf
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setRotatableBonds
public void setRotatableBonds(int[] rotatableBonds)
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getSmallerSideAtomLists
public int[][] getSmallerSideAtomLists()
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setSmallerSideAtomLists
public void setSmallerSideAtomLists(int[][] smallerSideAtomLists)
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getTorsionAtoms
public int[][] getTorsionAtoms()
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setTorsionAtoms
public void setTorsionAtoms(int[][] torsionAtoms)
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getRearAtoms
public int[][] getRearAtoms()
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setRearAtoms
public void setRearAtoms(int[][] rearAtoms)
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getRotationCenters
public int[] getRotationCenters()
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setRotationCenters
public void setRotationCenters(int[] rotationCenters)
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getTorsionIDs
public java.lang.String[] getTorsionIDs()
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setTorsionIDs
public void setTorsionIDs(java.lang.String[] torsionIDs)
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