com.actelion.research.chem.phesa.pharmacophore.ChargedGroupDetector Maven / Gradle / Ivy

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package com.actelion.research.chem.phesa.pharmacophore;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;

import com.actelion.research.chem.RingCollection;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint;


/**
 * derives charged groups
 * @author wahljo1
 *
 */

public class ChargedGroupDetector {
	
	private StereoMolecule mol;
	private List> chargedGroups;
	private RingCollection ringCollection;
	
	public ChargedGroupDetector(StereoMolecule mol) {
		this.mol = mol;
		chargedGroups = new ArrayList>();
		ringCollection = mol.getRingSet();
	}
	
	public ArrayList detect() {
		ArrayList chargePoints = new ArrayList();
		//detect tetrazoles
		for(int r=0;r tetrazole = new ArrayList();
			int totCharge = 0;
			int[] ringAtoms = ringCollection.getRingAtoms(r);
			for(Integer atom : ringAtoms) {
				if(alreadyDetected(atom)) continue;
				if(mol.getAtomicNo(atom)==7 && mol.isAromaticAtom(atom) && mol.getConnAtoms(atom)<=2) {
					tetrazole.add(atom);
					totCharge += mol.getAtomCharge(atom);
				}
			}
			if(tetrazole.size()==4 && totCharge<0) {
				chargedGroups.add(tetrazole);
				ChargePoint cp = new ChargePoint(mol,tetrazole.get(0),Arrays.asList(tetrazole.get(1),
						tetrazole.get(2),tetrazole.get(3)),totCharge);
				chargePoints.add(cp);
			}
			
			
		}
		for(int a=0;a group = new ArrayList<>();
				group.add(cp.getChargeAtom());
				group.addAll(cp.getNeighbours());
				chargedGroups.add(group);
				}
			else if(mol.getAtomicNo(a)==7) {
				int carbonCenter = -1;
				int charge = 0;
				List neighbours = new ArrayList<>();
				if(!mol.isAromaticAtom(a) && mol.getConnAtoms(a)<=2) { //HNR2 or H2NR
					neighbours.add(a);
					charge+=mol.getAtomCharge(a);
					int nDBs = 0;
					for(int i=0;i1 && charge>0) {
						ChargePoint cp = new ChargePoint(mol,carbonCenter,neighbours,charge);
						chargePoints.add(cp);
						ArrayList group = new ArrayList<>();
						group.add(cp.getChargeAtom());
						group.addAll(cp.getNeighbours());
						chargedGroups.add(group);
						
				}
				
			}

		}
		if(alreadyDetected(a))continue;
		else {
			int charge = mol.getAtomCharge(a);
			if(charge!=0 && !hasCounterChargedNeighbour(a)) {
				charge = charge>0 ? 1 : -1;
				ChargePoint cp = new ChargePoint(mol,a,new ArrayList(),charge);
				chargePoints.add(cp);
				ArrayList group = new ArrayList<>();
				group.add(a);
				chargedGroups.add(group);
			}
			}
		}
		return chargePoints;
	}

	public List> getChargedGroups() {
		return chargedGroups;
	}

	private boolean hasCounterChargedNeighbour(int a) {
		for(int aa=0;aa neighbours = new ArrayList<>();
			neighbours.add(atom);
			int charge = 0;
			charge+=mol.getAtomCharge(atom);
			charge+=mol.getAtomCharge(connAtom);
			int nConnected2C = mol.getConnAtoms(connAtom);
			for (int i = 0; i < nConnected2C; i++) {
				int indexAtom = mol.getConnAtom(connAtom, i);
				
				if(indexAtom==atom){
					continue;
				}
				
				if(mol.getAtomicNo(indexAtom) != 8){
					continue;
				}
				
				charge+=mol.getAtomCharge(indexAtom);
				neighbours.add(indexAtom);
			}
			if(charge<0) {
				ChargePoint cp = new ChargePoint(mol,connAtom,neighbours,charge);
				return cp;
			
			}

		} else if (mol.getAtomicNo(connAtom) == 16) { // CSOOOH
			int nConnected2S = mol.getConnAtoms(connAtom);
			List neighbours = new ArrayList<>();
			neighbours.add(atom);
			int charge = 0;
			charge+=mol.getAtomCharge(atom);
			charge+=mol.getAtomCharge(connAtom);
			for (int i = 0; i < nConnected2S; i++) {
				int indexAtom = mol.getConnAtom(connAtom, i);
				
				if(indexAtom==atom)
					continue;

				if(mol.getAtomicNo(indexAtom) != 8)
					continue;
				charge+=mol.getAtomCharge(indexAtom);
				neighbours.add(indexAtom);
			}
			if(charge<0) {
				ChargePoint cp = new ChargePoint(mol,connAtom,neighbours,charge);
				return cp;
			}
			
		
		} else if(mol.getAtomicNo(connAtom)==15){ // CP=O(OH)(OH)
			int nConnected2P = mol.getConnAtoms(connAtom);
			List neighbours = new ArrayList<>();
			neighbours.add(atom);
			int charge = 0;
			charge+=mol.getAtomCharge(atom);
			charge+=mol.getAtomCharge(connAtom);
			for (int i = 0; i < nConnected2P; i++) {
				int indexAtom = mol.getConnAtom(connAtom, i);
				if(indexAtom==atom)
					continue;

				if(mol.getAtomicNo(indexAtom) != 8)
					continue;
				charge+=mol.getAtomCharge(indexAtom);
				neighbours.add(indexAtom);
			}
			if(charge<0) {
				ChargePoint cp = new ChargePoint(mol,connAtom,neighbours,charge);
				return cp;
			}
		}
		return null;

	}


}