Package chemaxon.marvin.alignment
Class MolAligner
java.lang.Object
chemaxon.marvin.alignment.MolAligner
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
ConstructorDescriptionCreates a new MolAligner object.MolAligner
(Molecule patternMolecule, Molecule targetMolecule) Creates a new MolAligner object while setting the pattern and target molecules -
Method Summary
Modifier and TypeMethodDescriptionvoid
align()
Executes the best alignment based on hit map provided earliervoid
align
(int[] hit) Calculates and performs the best alignment possible specified by the hit map array.static void
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.static void
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.void
calculate
(int[] hit) Calculate best alignment based on the hit mapdouble
getError()
Get the error for the best alignmentvoid
Sets pattern molecule and calculates its dimensionvoid
Sets target molecule and calculates its dimension
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Constructor Details
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MolAligner
public MolAligner()Creates a new MolAligner object. -
MolAligner
Creates a new MolAligner object while setting the pattern and target molecules- Parameters:
patternMolecule
- the pattern molecule
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Method Details
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setPatternMolecule
Sets pattern molecule and calculates its dimension- Parameters:
mol
- pattern molecule
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setTargetMolecule
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()Executes the best alignment based on hit map provided earlier- See Also:
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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:
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align
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping. Possibly in the same position or optimally close to it.- Parameters:
pattern
- the pattern molecule for alignmenttarget
- the target molecule that should be aligned to the patternhit
- mapping of the atom IDs of the pattern molecule to the atom IDs of the target molecule, returned by a search. Its size must be equal to the atom count of the pattern molecule, and for each ID i, {@link hit[i]} must be the mapped target atom ID or -1 if the atom is not mapped
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align
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping. Possibly in the same position or optimally close to it.- Parameters:
pattern
- the pattern molecule for alignmenttarget
- the target molecule that should be aligned to the patterngroupHit
- mapping of the atom IDs of the pattern molecule to the atom IDs of the target molecule, returned by a search. Its size must be equal to the atom count of the pattern molecule, and for each ID i, {@link groupHit[i]} must be the array of mapped target atom IDs (usually exactly one)
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