Package chemaxon.marvin.alignment

Class AlignRigidEasy

  • All Implemented Interfaces:
    chemaxon.license.Licensable
    @PublicAPI
public class AlignRigidEasy
extends Object
implements chemaxon.license.Licensable
    Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact. Example usage 
               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();
    Since:
    Marvin 5.4.2

    • Constructor Detail

      • AlignRigidEasy

        public AlignRigidEasy()

    • Method Detail

      • isLicensed

        public boolean isLicensed()
        Specified by:
        isLicensed in interface chemaxon.license.Licensable

      • setLicenseEnvironment

        public void setLicenseEnvironment​(String env)
        Specified by:
        setLicenseEnvironment in interface chemaxon.license.Licensable

      • setReference

        public void setReference​(Molecule m)
        sets the reference molecule which remains intact
        Parameters:
        m -

      • setRotatable

        public void setRotatable​(Molecule m)
        sets the molecule to translate and rotate during the alignment
        Parameters:
        m - molecule to translate and rotate

      • convert

        public static double[] convert​(double[][] c)

      • setReference

        public void setReference​(double[][] c)
        sets the coordinates of the reference molecule directly If this used the getReferenceAndRotatedFused() cannot be applied
        Parameters:
        c - double[number of atoms][3:x,y,z] format

      • setRotatable

        public void setRotatable​(double[][] c)
        sets the coordinates of the rotatable molecule directly If this used the getReferenceAndRotatedFused() and getRotatedMolecule() cannot be applied
        Parameters:
        c - double[number of atoms][3:x,y,z] format

      • getRotatedCoordinates

        public double[][] getRotatedCoordinates()
        before getRotatedCoordinates the align() method must be called
        Returns:
        the rotated coordinates in double[number of atoms][3:x,y,z] format

      • getRotatedMolecule

        public Molecule getRotatedMolecule()
        before getRotatedMolecule the align() method must be called
        Returns:
        the rotated molecule

      • getReferenceAndRotatedFused

        public Molecule getReferenceAndRotatedFused()
        before getRotatedMolecule the align() method must be called
        Returns:
        the rotated molecule

      • rmsd

        public double rmsd()
        calculates the rmsd value
        Returns:
        the rmsd value

      • align

        public void align()
        does a simple one-to-one atom mappin and aligns. The molecules must have the same atom count.
        Throws:
        chemaxon.license.LicenseException - if no valid LicenseGlobals.ALIGNMENT license was found.

      • align

        public void align​(int[][] index)
        Rigid alignment on the user defined atom index
        Parameters:
        index - in format int[number of pairs][reference atom index, atom to rotate index]
        Throws:
        chemaxon.license.LicenseException - if no valid LicenseGlobals.ALIGNMENT license was found.