RingClosingAttractor.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 Marco Foscato <marco.foscato@uib.no>
 * 
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU Affero General Public License as published
 *   by the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU Affero General Public License for more details.
 *
 *   You should have received a copy of the GNU Affero General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
package denoptim.graph.rings;
 
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
 
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
 
import denoptim.constants.DENOPTIMConstants;
import denoptim.graph.APClass;
import denoptim.graph.Edge.BondType;
import denoptim.graph.Ring;
import denoptim.utils.MoleculeUtils;
 
 
//TODO: consider making subclass of Vertex?
 
public class RingClosingAttractor
{
    final Map<String,Double> paramAR11 = new HashMap<String,Double>() {
        private static final long serialVersionUID = 1L;
 
        {
            put("ATP", 1.0);
            put("ATM", 1.0);
            put("ATN", 1.0);
        };
    };
 
    final Map<String,Double> paramBR11 = new HashMap<String,Double>() {
        private static final long serialVersionUID = 1L;
        {
            put("ATP", 1.0);
            put("ATM", 1.0);
            put("ATN", 1.0);
        };
    };
 
    final Map<String,Double> paramAR12 = new HashMap<String,Double>() {
        private static final long serialVersionUID = 1L;
        {
            put("ATP", 5.0);
            put("ATM", 5.0);
            put("ATN", 5.0);
        };
    };
 
    final Map<String,Double> paramBR12 = new HashMap<String,Double>() {
        private static final long serialVersionUID = 1L;
        {
            put("ATP", 7.0);
            put("ATM", 7.0);
            put("ATN", 7.0);
        };  
    };
 
    private Double attA11 = 0.0;
 
    private Double attB11 = 0.0;
 
    private Double attA12 = 0.0;
 
    private Double attB12 = 0.0;
 
    private String attType = "none";
 
    private IAtom atm;
 
    private IAtom src;
 
    private APClass apClass;
    
    private BondType bndTyp;
    
    private Ring ringUser;
 
    private boolean used = false;
 
    public static final HashMap<APClass,String> RCALABELPERAPCLASS = 
            new HashMap<APClass,String>(){
                private static final long serialVersionUID = 1L;
    
            {
                try {
                    put(APClass.RCACLASSPLUS, "ATP");
                    put(APClass.RCACLASSMINUS, "ATM");
                    put(APClass.RCACLASSNEUTRAL, "ATN");
                } catch (Throwable t)
                {
                    //Will not happen
                }
            }};
 
    public static final Set<APClass> RCAAPCLASSSET = 
            new HashSet<APClass>(){
                private static final long serialVersionUID = 1L;
    
                {
                    add(APClass.RCACLASSPLUS);
                    add(APClass.RCACLASSMINUS);
                    add(APClass.RCACLASSNEUTRAL);
                }};
 
    public static final Map<APClass,APClass> RCAAPCMAP =
            new HashMap<APClass,APClass>() 
    {
        private static final long serialVersionUID = 3L;
    
        {
            put(APClass.RCACLASSPLUS, APClass.RCACLASSMINUS);
            put(APClass.RCACLASSMINUS, APClass.RCACLASSPLUS);
            put(APClass.RCACLASSNEUTRAL, APClass.RCACLASSNEUTRAL);
        };
    };
 
    public static final Map<String,String> RCATYPEMAP =
            new HashMap<String,String>() 
    {
        private static final long serialVersionUID = 3L;
    
        {
            put(RCALABELPERAPCLASS.get(APClass.RCACLASSPLUS), 
                    RCALABELPERAPCLASS.get(APClass.RCACLASSMINUS));
            put(RCALABELPERAPCLASS.get(APClass.RCACLASSMINUS), 
                    RCALABELPERAPCLASS.get(APClass.RCACLASSPLUS));
            put(RCALABELPERAPCLASS.get(APClass.RCACLASSNEUTRAL), 
                    RCALABELPERAPCLASS.get(APClass.RCACLASSNEUTRAL));
        };
    };
 
 
//-----------------------------------------------------------------------------
 
    public RingClosingAttractor()
    {
        this.atm = null;
    }
 
//-----------------------------------------------------------------------------
 
    public RingClosingAttractor(IAtom atm, IAtomContainer mol)
    {
        this.atm = atm;
        for (String atyp : RingClosingAttractor.RCATYPEMAP.keySet())
        {
            if (MoleculeUtils.getSymbolOrLabel(atm).equals(atyp))
            {
                this.attType = atyp;
                this.attA11 = paramAR11.get(atyp);
                this.attA12 = paramAR12.get(atyp);
                this.attB11 = paramBR11.get(atyp);
                this.attB12 = paramBR12.get(atyp);
                break;
            }
        }
        // We can try to build RCAs from any atom, but only those atoms that
        // really are RCAs do have the information we are extracting here
        if (isAttractor())
        {
            //Well, any atom might have neighbors, but RCA only have 1. So
            // the assumption is valid for RCAs.
            this.src = mol.getConnectedAtomsList(atm).get(0);
            // But, there are properties that can be found only in relation to
            // actual RCAs (whether used to make a ring, or not)
            this.apClass = (APClass) atm.getProperty(
                    DENOPTIMConstants.RCAPROPAPCTORCA);
            this.bndTyp = (BondType) atm.getProperty(
                    DENOPTIMConstants.RCAPROPCHORDBNDTYP);
            this.ringUser = (Ring) atm.getProperty(
                    DENOPTIMConstants.RCAPROPRINGUSER);
        }
    }
 
//-----------------------------------------------------------------------------
 
    public boolean isAttractor()
    {
        return (this.attType.equals("none")) ? false : true;
    }
 
//-----------------------------------------------------------------------------
 
    public boolean isCompatible(RingClosingAttractor other)
    {
        return RingClosingAttractor.RCATYPEMAP.get(this.attType).equals(
                                other.attType);
    }
 
//-----------------------------------------------------------------------------
 
    public String getType()
    {
        return attType;
    }
 
//-----------------------------------------------------------------------------
 
    public IAtom getIAtom()
    {
        return atm;
    }
    
//-----------------------------------------------------------------------------
 
    public void setIAtom(IAtom atm)
    {
        this.atm = atm;
    }
 
//-----------------------------------------------------------------------------
 
    public IAtom getSrcAtom()
    {
        return src;
    }
 
//-----------------------------------------------------------------------------
 
    public APClass getApClass()
    {
        return apClass;
    }
    
 //-----------------------------------------------------------------------------
 
    public BondType getRCBondType()
    {
        return bndTyp;
    }
    
 //-----------------------------------------------------------------------------
 
    public Ring getRingUser()
    {
        return ringUser;
    }
 
//-----------------------------------------------------------------------------
 
    public void setUsed()
    {
        this.used = true;
    }
 
//-----------------------------------------------------------------------------
 
    public boolean isUsed()
    {
        return used;
    }
 
//-----------------------------------------------------------------------------
 
    public Double getParamA11()
    {
        return attA11;
    }
 
//-----------------------------------------------------------------------------
 
    public Double getParamB11()
    {
        return attB11;
    }
 
//-----------------------------------------------------------------------------
 
    public Double getParamA12()
    {
        return attA12;
    }
 
//-----------------------------------------------------------------------------
 
    public Double getParamB12()
    {
        return attB12;
    }
 
//-----------------------------------------------------------------------------
 
    @Override public String toString()
    {
        String s = "RingClosingAttractor (Type:" + this.attType + " "
                    + "APClass:" + this.apClass + " "
                    + "Used:" + this.used + " "
                    + "Atm: " + MoleculeUtils.getSymbolOrLabel(this.atm) 
                    + " SrcAtm: " + MoleculeUtils.getSymbolOrLabel(this.src)
                    + ")";
        return s;
    }
 
//-----------------------------------------------------------------------------
}