com.actelion.research.chem.potentialenergy.EmpiricalLigandStrain Maven / Gradle / Ivy

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package com.actelion.research.chem.potentialenergy;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.AbstractMap.SimpleEntry;

import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.BondRotationHelper;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionPotential;
import com.actelion.research.chem.conf.torsionstrain.StatisticalTorsionTerm;
import com.actelion.research.chem.docking.scoring.idoscore.InteractionTerm;
import com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator;
import com.actelion.research.chem.interactionstatistics.InteractionDistanceStatistics;


public class EmpiricalLigandStrain implements PotentialEnergyTerm {
	
	private Conformer conf;
	private List strain;
	private BondRotationHelper torsionHelper;
	private List ligAtomPairs; 
	private int[] atomTypes;

	public EmpiricalLigandStrain(Conformer conf, int[] atomTypes, BondRotationHelper torsionHelper) {
		this.conf = conf;
		this.atomTypes = atomTypes;
		this.torsionHelper = torsionHelper;
		
		init();
	}
	
	private void init() {
		StereoMolecule mol = conf.getMolecule();
		strain = new ArrayList();
		ligAtomPairs = new ArrayList();
		List ligAtomTypesList = new ArrayList<>();
		for(int a=0;a> invalidPairs  = new HashSet>();
		StereoMolecule mol = conf.getMolecule();
		for(int a=0;a entry = a(a,aa) : new SimpleEntry<>(a,aa);
				invalidPairs.add(entry);
				for(int j=0;j(a,aaa) : new SimpleEntry<>(a,aaa);
					invalidPairs.add(entry);
					for(int k=0;k(a,aaaa) : new SimpleEntry<>(a,aaaa);
						invalidPairs.add(entry);
					}
				}
			}
		}
		for(int i=0;i entry =new SimpleEntry<>(i,j);
				if(invalidPairs.contains(entry))
					continue;
				else 
					ligAtomPairs.add(new int[] {i,j});
					
			}
		}
	}
	

	@Override
	public double getFGValue(double[] grad) {
		double energy = 0.0;
		for(PotentialEnergyTerm term : strain) {
			energy+=term.getFGValue(grad);
		}
		return energy;
	}


	
	

}