Class BondsCalculator
- java.lang.Object
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- com.actelion.research.chem.io.pdb.converter.BondsCalculator
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public class BondsCalculator extends java.lang.Object
BondsCalculator is used to recreate the bonds and / or calculate the bonds orders based on the 3D coordinates of the atoms
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Constructor Summary
Constructors Constructor Description BondsCalculator()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static boolean
aromatize(StereoMolecule mol, java.util.ArrayList<java.lang.Integer>[] atomToRings, RingCollection ringSet, java.util.Set<java.lang.Integer> aromaticAtoms, java.util.Set<java.lang.Integer> aromaticBonds)
static boolean
aromatize(StereoMolecule mol, java.util.Set<java.lang.Integer> aromaticAtoms, java.util.Set<java.lang.Integer> aromaticBonds)
static void
calculateBondOrders(StereoMolecule mol, boolean lenient)
Calculate the bond orders of the molecule (without knowing the hydrogens).static int
connected(StereoMolecule mol, int a, int atomicNo, int bondOrder)
static void
createBonds(StereoMolecule mol, boolean lenient, java.util.Map<java.lang.Integer,java.lang.String> atomToGroup)
Calculates the bonds of a molecule by checking the distance between all atoms.
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Method Detail
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createBonds
public static void createBonds(StereoMolecule mol, boolean lenient, java.util.Map<java.lang.Integer,java.lang.String> atomToGroup) throws java.lang.Exception
Calculates the bonds of a molecule by checking the distance between all atoms. The bond order is not set with this function. Complexity O(nAtoms) Memory O(nAtoms)- Parameters:
mol
-lenient
-atomToGroup
-- Throws:
java.lang.Exception
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calculateBondOrders
public static void calculateBondOrders(StereoMolecule mol, boolean lenient) throws java.lang.Exception
Calculate the bond orders of the molecule (without knowing the hydrogens). The calculation is based on the bond distance between each atoms. http://www.ccp14.ac.uk/ccp/web-mirrors/i_d_brown/valence.txt s = exp((Ro - R)/B)- Parameters:
mol
-- Throws:
java.lang.Exception
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aromatize
public static boolean aromatize(StereoMolecule mol, java.util.Set<java.lang.Integer> aromaticAtoms, java.util.Set<java.lang.Integer> aromaticBonds)
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aromatize
public static boolean aromatize(StereoMolecule mol, java.util.ArrayList<java.lang.Integer>[] atomToRings, RingCollection ringSet, java.util.Set<java.lang.Integer> aromaticAtoms, java.util.Set<java.lang.Integer> aromaticBonds)
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connected
public static int connected(StereoMolecule mol, int a, int atomicNo, int bondOrder)
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