content: /*
   * Copyright (c) 1997 - 2016
   * Actelion Pharmaceuticals Ltd.
   * Gewerbestrasse 16
   * CH-4123 Allschwil, Switzerland
   *
   * All rights reserved.
   *
   * Redistribution and use in source and binary forms, with or without
   * modification, are permitted provided that the following conditions are met:
   *
   * 1. Redistributions of source code must retain the above copyright notice, this
   *    list of conditions and the following disclaimer.
   * 2. Redistributions in binary form must reproduce the above copyright notice,
   *    this list of conditions and the following disclaimer in the documentation
   *    and/or other materials provided with the distribution.
   * 3. Neither the name of the the copyright holder nor the
   *    names of its contributors may be used to endorse or promote products
   *    derived from this software without specific prior written permission.
   *
   * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
   * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
   * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
   * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
   * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
   * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
   * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
   * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
   * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
   * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
   *
   * @author Modest v. Korff
   */
  
  package com.actelion.research.chem.io.pdb.parser;
  
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.Molecule3D;
  import com.actelion.research.chem.io.pdb.calc.AminoAcids;
  import com.actelion.research.chem.io.pdb.calc.BondOrderCalculator;
  import com.actelion.research.chem.io.pdb.calc.BondsCalculator;
  
  import java.util.*;
  
  /**
   * Residue handles a group of atoms, e.g. a Ligand Molecule or an AminoAcid residue
   *
   * Created by korffmo1 on 11.04.18.
   */
  public class Residue {
  	public static double BOND_CUTOFF_SQ = 3.24;
  	private boolean mIsTerminal;
  	private final boolean mIsProtein;
  	private final boolean mAddBonds,mIncludeAltLocs;
      private Molecule3D mMol;
  	private final int mResNum;
  	private final String mResName,mChainID,mInsertionCode;
  	private final String mFragmentName;
  	private Map<String,AtomRecord> mAtomRecordMap;
  	private ArrayList<AtomRecord> mAtomList;
  
  	/**
  	 * @param addBonds
  	 * @param includeAltLocations
  	 */
  	public Residue(boolean isProtein, boolean addBonds, boolean includeAltLocations, AtomRecord firstAtom) {
  		mIsProtein = isProtein;
  		mAddBonds = addBonds;
  		mIncludeAltLocs = includeAltLocations;
  
  		mResNum = firstAtom.getAuthSeqID();
  		mResName = firstAtom.getResName();
  		mChainID = firstAtom.getChainID();
  		mInsertionCode = firstAtom.getInsertionCode();
  
  		// We use '1' as Model-No.
  		mFragmentName = firstAtom.getResName()+"_1_"+firstAtom.getChainID()+"_"+firstAtom.getAuthSeqID();
  
  		if (mIsProtein)
  			mAtomRecordMap = new HashMap<>();
  		else
  			mAtomList = new ArrayList<>();
  
  		addAtom(firstAtom);
  	}
  
  	public void addAtom(AtomRecord atom) {
  		if (mIsProtein)
  			mAtomRecordMap.put(atom.getLabelAtomName(), atom);
  		else mAtomList.add(atom);
  
  		if(atom.isTerminalC())
  			mIsTerminal = true;
  	}
  
  	public void build() {
  		mMol = mIsProtein ? AminoAcids.createResidue(getResname(), mAtomRecordMap) : null;
  		if (mMol == null)
  			mMol = constructFragmentFromGeometry(mIsProtein ? mAtomRecordMap.values() : mAtomList);
  		mMol.ensureHelperArrays(Molecule.cHelperNeighbours);
  		mMol.setName(mFragmentName);
  	}
  
  	public boolean isTerminal() {
  		return mIsTerminal;
  	}
  
      private void constructFragment(List<AtomRecord> records) {
  		AtomRecord ar = records.get(0);
  		mMol = AminoAcids.createResidue(getResname(), records);
  		if (mMol == null)
  			mMol = constructFragmentFromGeometry(records);
  		mMol.ensureHelperArrays(Molecule.cHelperNeighbours);
  		// We use '1' as Model-No.
  		mMol.setName(ar.getResName()+"_1_"+ar.getChainID()+"_"+ar.getAuthSeqID());
      }
  
  	private Molecule3D constructFragmentFromGeometry(Collection<AtomRecord> records) {
  		Molecule3D fragment = new Molecule3D();
  		String altLoc = null;
  		for(AtomRecord record : records) {
  			if (!mIncludeAltLocs) {
  				if (altLoc == null)
  					altLoc = record.getLabelAltID();
  				else if (!altLoc.equals(record.getLabelAltID()))
  					continue;
  			}
  			int atomicNo = record.getAtomicNo();
  			int atom = fragment.addAtom(atomicNo);
  			fragment.setAtomName(atom, record.getLabelAtomName());
  			fragment.setAtomAmino(atom, record.getResName());
  			fragment.setAtomSequence(atom,record.getSerialId());
  			fragment.setResSequence(atom, record.getAuthSeqID());
  			fragment.setAtomAmino(atom, record.getResName());
  			fragment.setAtomChainId(atom, record.getChainID());
  			fragment.setAtomX(atom,record.getX());
  			fragment.setAtomY(atom,record.getY());
  			fragment.setAtomZ(atom,record.getZ());
  		}
  
  		if (mAddBonds) {
  			try {
  				BondsCalculator.createBonds(fragment, true,null);
  				new BondOrderCalculator(fragment).calculateBondOrders();
  			} catch (Exception e) {
  				e.printStackTrace();
  			}
  		}
  
  		return fragment;
  	}
  	
  	public int getResnum() {
  		return mResNum;
  	}
  	
  	public Molecule3D getMolecule() {
  		return mMol;
  	}
  	
  	public String getResname() {
  		return mResName;
  	}
  	
  	public String getChainID() {
  		return mChainID;
  	}
  	
  	public String getInsertionCode() {
  		return mInsertionCode;
  	}
  	
  	/*
  	 * check if two residues are connected by a peptide bond, this is the residue with the (supposedly) terminal nitrogen,
  	 * resC should contain the terminal carbon
  	 *
  	public boolean areBonded(Residue resN) { 
  		AtomRecord recordC = null; 
  		AtomRecord recordN = null;
  		boolean areBonded = false;
  		for(AtomRecord rec : this.mAtomRecordList) {
  			if (rec.getAtomName().equals("C")) {
  				recordN = rec;
  				break;
  			}
  		}
  		
  		for(AtomRecord rec : resN.mAtomRecordList) {
  			if (rec.getAtomName().equals("N")) {
  				recordC = rec;
  				break;
  			}
  		}
  		if(recordN!=null && recordC!=null) {
  			double dx = recordN.getX()-recordC.getX();
  			double dy = recordN.getY()-recordC.getY();
  			double dz = recordN.getZ()-recordC.getZ();
  			double distSq = dx*dx + dy*dy + dz*dz;
  			if(distSq<BOND_CUTOFF_SQ)
  				areBonded=true;
  		}
  		return areBonded;
  	}*/
  }
  