Package com.actelion.research.chem
Class AromaticityResolver
- java.lang.Object
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- com.actelion.research.chem.AromaticityResolver
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public class AromaticityResolver extends java.lang.Object
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Constructor Summary
Constructors Constructor Description AromaticityResolver(ExtendedMolecule mol)
Creates a new AromaticityResolver for molecule mol.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
locateDelocalizedDoubleBonds(boolean[] isAromaticBond)
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.boolean
locateDelocalizedDoubleBonds(boolean[] isAromaticBond, boolean mayChangeAtomCharges, boolean allHydrogensAreExplicit)
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds.
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Constructor Detail
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AromaticityResolver
public AromaticityResolver(ExtendedMolecule mol)
Creates a new AromaticityResolver for molecule mol.- Parameters:
mol
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Method Detail
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locateDelocalizedDoubleBonds
public boolean locateDelocalizedDoubleBonds(boolean[] isAromaticBond)
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds. The delocalized part of the molecule may be defined by passing an array to isAromaticBond that has all bonds flagged, which are part of a delocalized area. In this case these bonds are assumed to have bond type cBondTypeSingle. Alternatively, one may pass null and indicate affected bonds with bond type cBondTypeDelocalized. Non-cyclic atom chains defined to be delocalized are treated depending on whether we have a molecule or a query fragment. For fragments the respective bond types will be set to cBondTypeDelocalized; for molecules the chain will have alternating single and double bonds starting with double at a non-ring end.- Returns:
- true if all bonds of the delocalized area could be consistently converted.
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locateDelocalizedDoubleBonds
public boolean locateDelocalizedDoubleBonds(boolean[] isAromaticBond, boolean mayChangeAtomCharges, boolean allHydrogensAreExplicit)
This method promotes all necessary bonds of the defined delocalized part of the molecule from single to double bonds in order to create a valid delocalized system of conjugated single and double bonds. The delocalized part of the molecule may be defined by passing an array to isAromaticBond that has all bonds flagged, which are part of a delocalized area. In this case these bonds are assumed to have bond type cBondTypeSingle. Alternatively, one may pass null and indicate affected bonds with bond type cBondTypeDelocalized. Non-cyclic atom chains defined to be delocalized are treated depending on whether we have a molecule or a query fragment. For fragments the respective bond types will be set to cBondTypeDelocalized; for molecules the chain will have alternating single and double bonds starting with double at a non-ring end.- Parameters:
isAromaticBond
- if null, then bond type cBondTypeDelocalized is used to indicate delocalized bondsmayChangeAtomCharges
- true if input molecule doesn't carry atom charges and these may be added to achieve aromaticityallHydrogensAreExplicit
- true this method can rely on all hydrogens being explicitly present- Returns:
- true if all bonds of the delocalized area could be consistently converted.
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