Package com.actelion.research.chem.conf

Class BondRotationHelper

java.lang.Object

com.actelion.research.chem.conf.BondRotationHelper

public class BondRotationHelper
extends java.lang.Object

Constructor Summary

Constructors

Constructor	Description
BondRotationHelper(StereoMolecule mol)

Method Summary

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 bond, double alpha, Conformer conf, boolean biggerSide)	rotate torsion angle of a conformer
void	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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BondRotationHelper

public BondRotationHelper(StereoMolecule mol)

Method Detail

initialize

public void initialize()

predictAtomSequence

public static void predictAtomSequence(StereoMolecule mol,
                                       int bond,
                                       int[] torsionAtoms,
                                       int[] rearAtoms)

isRotatableBond

public boolean isRotatableBond(int bond)

getRotatableBonds

public int[] getRotatableBonds()

rotateSmallerSide

public void rotateSmallerSide(int bond,
                              double alpha)

rotateAroundBond

public void rotateAroundBond(int bond,
                             double alpha,
                             Conformer conf,
                             boolean biggerSide)

rotate torsion angle of a conformer

Parameters:

bond -

alpha -

conf -

setRotatableBonds

public void setRotatableBonds(int[] rotatableBonds)

getSmallerSideAtomLists

public int[][] getSmallerSideAtomLists()

setSmallerSideAtomLists

public void setSmallerSideAtomLists(int[][] smallerSideAtomLists)

getTorsionAtoms

public int[][] getTorsionAtoms()

setTorsionAtoms

public void setTorsionAtoms(int[][] torsionAtoms)

getRearAtoms

public int[][] getRearAtoms()

setRearAtoms

public void setRearAtoms(int[][] rearAtoms)

getRotationCenters

public int[] getRotationCenters()

setRotationCenters

public void setRotationCenters(int[] rotationCenters)

getTorsionIDs

public java.lang.String[] getTorsionIDs()

setTorsionIDs

public void setTorsionIDs(java.lang.String[] torsionIDs)