Class LigandPose

  • All Implemented Interfaces:
    Evaluable

    public class LigandPose
    extends java.lang.Object
    implements Evaluable
    • Field Detail

      • SEED

        public static long SEED
    • Method Detail

      • setMCSBondConstraints

        public void setMCSBondConstraints​(java.util.List<java.lang.Integer> constraints)
        for MCS docking:create array of bond indices that are allowed to be permuted
        Parameters:
        constraints -
      • getFGValue

        public double getFGValue​(double[] gradient)
        Fuhrmann J, Rurainski A, Lenhof HP, Neumann D. A new method for the gradient-based optimization of molecular complexes. J Comput Chem. 2009 Jul 15;30(9):1371-8. doi: 10.1002/jcc.21159. PMID: 19031415.
        Specified by:
        getFGValue in interface Evaluable
      • getContributions

        public java.util.Map<java.lang.String,​java.lang.Double> getContributions()
      • setInitialState

        public void setInitialState()
      • updateLigandCoordinates

        public void updateLigandCoordinates()
      • setState

        public void setState​(double[] state)
        Specified by:
        setState in interface Evaluable
      • getState

        public double[] getState​(double[] v)
      • getCartState

        public double[] getCartState()
      • getGyrationRadius

        public double getGyrationRadius()
      • getState

        public double[] getState()
        Specified by:
        getState in interface Evaluable
      • randomPerturbation

        public void randomPerturbation​(java.util.Random random)
      • addPositionalConstraints

        public void addPositionalConstraints​(double d)
      • removeConstraints

        public void removeConstraints()