Package chemaxon.marvin.alignment
Class MolAligner
java.lang.Object
chemaxon.marvin.alignment.MolAligner
- Direct Known Subclasses:
MolAligner
Tool for aligning a target molecule to a pattern molecule. Can be used for 2D
and 3D alignment as well.
-
Constructor Summary
ConstructorsConstructorDescriptionCreates 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()
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
Sets pattern molecule and calculates its dimensionvoid
Sets target molecule and calculates its dimension
-
Constructor Details
-
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 moleculetargetMolecule
-
-
-
Method Details
-
setPatternMolecule
Sets pattern molecule and calculates its dimension- Parameters:
mol
- pattern molecule
-
setTargetMolecule
Sets target molecule and calculates its dimension- Parameters:
mol
- molecule to align
-
getError
public double getError()Get the error for the best alignment- Returns:
- the root mean square deviation of the mapping atoms
-
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
-
align
public void align()Execute best alignment based on hit map provided earlier- See Also:
-
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:
-