Package chemaxon.util
Class MolAligner
- java.lang.Object
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- chemaxon.util.MolAligner
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@PublicAPI public class MolAligner extends Object
Tool for aligning a target molecule to a pattern molecule. Can be used for 2D and 3D alignment as well.
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Constructor Summary
Constructors Constructor Description MolAligner()
Creates a new MolAligner object.MolAligner(Molecule patternMolecule, Molecule targetMolecule)
Creates a new MolAligner object while setting the pattern and target molecules
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
align()
Execute best alignment based on hit map provided earliervoid
align(int[] hit)
Calculates and performs the best alignment possible specified by the hit map array.void
calculate(int[] hit)
Calculate best alignment based on the hit mapdouble
getError()
Get the error for the best alignmentvoid
setPatternMolecule(Molecule mol)
Sets pattern molecule and calculates its dimensionvoid
setTargetMolecule(Molecule mol)
Sets target molecule and calculates its dimension
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Method Detail
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setPatternMolecule
public void setPatternMolecule(Molecule mol)
Sets pattern molecule and calculates its dimension- Parameters:
mol
- pattern molecule
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setTargetMolecule
public void setTargetMolecule(Molecule mol)
Sets target molecule and calculates its dimension- Parameters:
mol
- molecule to align
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getError
public double getError()
Get the error for the best alignment- Returns:
- the root mean square deviation of the mapping atoms
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calculate
public void calculate(int[] hit)
Calculate best alignment based on the hit map- Parameters:
hit
- hit map array, use -1 for no matching atom index
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align
public void align()
Execute best alignment based on hit map provided earlier- See Also:
calculate(int[])
,align(int[])
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align
public void align(int[] hit)
Calculates and performs the best alignment possible specified by the hit map array.- Parameters:
hit
- hit map array, use -1 for no matching atom index- See Also:
calculate(int[])
,align()
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