@PublicAPI public class AlignRigidEasy extends java.lang.Object implements chemaxon.license.Licensable
AlignRigidEasy easy = new AlignRigidEasy(); easy.setReference(m1); easy.setRotatable(m2); int[][] easyMap = new int[number of pairs][2]; for (int i = 0; i < easyMap.length; i++) { easyMap[i][0] = atom index from m1; easyMap[i][1] = atom index from m2; } easy.align(easyMap); double rmsd = easy.rmsd();
Constructor and Description |
---|
AlignRigidEasy() |
Modifier and Type | Method and Description |
---|---|
void |
align()
does a simple one-to-one atom mappin and aligns.
|
void |
align(int[][] index)
Rigid alignment on the user defined atom index
|
static double[] |
convert(double[][] c) |
Molecule |
getReferenceAndRotatedFused()
before getRotatedMolecule the
align() method must be called |
double[][] |
getRotatedCoordinates()
before getRotatedCoordinates the
align() method must be called |
Molecule |
getRotatedMolecule()
before getRotatedMolecule the
align() method must be called |
boolean |
isLicensed() |
double |
rmsd()
calculates the rmsd value
|
void |
setLicenseEnvironment(java.lang.String env) |
void |
setReference(double[][] c)
sets the coordinates of the reference molecule directly If this used the
getReferenceAndRotatedFused() cannot be applied |
void |
setReference(Molecule m)
sets the reference molecule which remains intact
|
void |
setRotatable(double[][] c)
sets the coordinates of the rotatable molecule directly If this used the
getReferenceAndRotatedFused() and getRotatedMolecule()
cannot be applied |
void |
setRotatable(Molecule m)
sets the molecule to translate and rotate during the alignment
|
public boolean isLicensed()
isLicensed
in interface chemaxon.license.Licensable
public void setLicenseEnvironment(java.lang.String env)
setLicenseEnvironment
in interface chemaxon.license.Licensable
public void setReference(Molecule m)
m
- public void setRotatable(Molecule m)
m
- molecule to translate and rotatepublic static double[] convert(double[][] c)
public void setReference(double[][] c)
getReferenceAndRotatedFused()
cannot be appliedc
- double[number of atoms][3:x,y,z] formatpublic void setRotatable(double[][] c)
getReferenceAndRotatedFused()
and getRotatedMolecule()
cannot be appliedc
- double[number of atoms][3:x,y,z] formatpublic double[][] getRotatedCoordinates()
align()
method must be calledpublic Molecule getRotatedMolecule()
align()
method must be calledpublic Molecule getReferenceAndRotatedFused()
align()
method must be calledpublic double rmsd()
public void align()
chemaxon.license.LicenseException
- if no valid LicenseGlobals.ALIGNMENT
license was
found.public void align(int[][] index)
index
- in format int[number of pairs][reference atom index, atom to
rotate index]chemaxon.license.LicenseException
- if no valid LicenseGlobals.ALIGNMENT
license was
found.