TinkerAtom.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 Vishwesh Venkatraman <vishwesh.venkatraman@ntnu.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.integration.tinker;
 
public class TinkerAtom implements Cloneable
{
    /*
     * tinker assigned atom type
     */
    private int ffAtomType;
    
    /*
     * tinker assigned atom string
     */
    private String atomStr;
    
    /*
     * the original 3d coordinates from which the IC representation is calculated
     */
    private double[] xyz; 
    
    /*
     * position of the atom in the list
     */
    private int xyzIndex;
    
    /*
     * store for distance, bond angle and the dihedral or third angle
     */
    private double[] distAngles;
    
    
    /*
     * atom neighbours, the first 3 members are the neighbours, the 4 position 
     * is reserved for the chiral definition (0/1/-1)
     */
    private int[] atmNb;
    
    /*
     * the vertex id with which the IC fragment is associated with
     */
    private long vtxId;
 
//------------------------------------------------------------------------------
 
    public TinkerAtom()
    {
    }
 
//------------------------------------------------------------------------------
 
    public TinkerAtom(int xyzIndex, String atomStr, int ffAtomType,
                      double[] xyz, int[] atmNb, double[] distAngles)
    {
        this.atomStr = atomStr;
        this.ffAtomType = ffAtomType;
        this.xyzIndex = xyzIndex;
        this.atmNb = new int[4];
        this.distAngles = new double[3];
        this.xyz = new double[3];
        
        for (int i=0; i<3; i++)
        {
            this.xyz[i] = xyz[i];
            this.distAngles[i] = distAngles[i];
        }
        System.arraycopy(atmNb, 0, this.atmNb, 0, 4);
    }
    
    
//------------------------------------------------------------------------------
 
    public void setAtomNeighbours(int[] atmNb)
    {
        this.atmNb = atmNb;
    }
 
//------------------------------------------------------------------------------
 
    public int[] getAtomNeighbours()
    {
        return this.atmNb;
    }
 
//------------------------------------------------------------------------------
 
    public void setDistAngle(double[] distAngles)
    {
        this.distAngles = distAngles;
    }    
 
//------------------------------------------------------------------------------
 
    public double[] getDistAngle()
    {
        return this.distAngles;
    }
 
//------------------------------------------------------------------------------
 
     public void moveTo(double[] d)
     {
         xyz[0] = d[0];
         xyz[1] = d[1];
         xyz[2] = d[2];
     }
 
//------------------------------------------------------------------------------
 
    public void moveTo(double a, double b, double c)
    {
         xyz[0] = a;
         xyz[1] = b;
         xyz[2] = c;
     }
 
//------------------------------------------------------------------------------
 
    public void setXYZ(double[] xyz)
    {
         this.xyz = xyz;
    }
 
//------------------------------------------------------------------------------
 
    public double[] getXYZ()
    {
         return xyz;
    }
 
//------------------------------------------------------------------------------
 
     public void getXYZ(double[] x)
     {
         x[0] = xyz[0];
         x[1] = xyz[1];
         x[2] = xyz[2];
     }
 
//------------------------------------------------------------------------------
 
     public int getXYZIndex()
     {
        return xyzIndex;
     }
 
//------------------------------------------------------------------------------
 
     public void setXYZIndex(int xyzIndex)
     {
         this.xyzIndex = xyzIndex;
     }
 
 
//------------------------------------------------------------------------------
 
     public String getAtomString()
     {
         return this.atomStr;
     }
 
//------------------------------------------------------------------------------
 
     public void setAtomString(String atomStr)
     {
          this.atomStr = atomStr;
     }
 
//------------------------------------------------------------------------------
 
     public int getAtomType()
     {
         return this.ffAtomType;
     }
 
//------------------------------------------------------------------------------
     
     public void setAtomType(int ffAtomType)
     {
          this.ffAtomType = ffAtomType;
     }
 
//------------------------------------------------------------------------------
     
     public void setVertexId(long vidx)
     {
         this.vtxId = vidx;
     }     
     
//------------------------------------------------------------------------------     
     
     public long getVertexId()
     {
         return this.vtxId;
     }
 
 
//------------------------------------------------------------------------------
 
    public boolean usesProperTorsion()
    {
    if ((this.atmNb[0] != 0) && (this.atmNb[1] != 0) &&
              (this.atmNb[2] != 0) && (this.atmNb[3] == 0))
    {
        return true;
    }
 
    return false;
    }
 
//------------------------------------------------------------------------------
 
    @Override
    public String toString()
    {
    String s = "TinkerAtom (ff: " + ffAtomType +
                " str: "+ atomStr +
                " xyz: [" + xyz[0] + "; " + xyz[1] +
                "; " + xyz[2] + "] " +
                " id: " + xyzIndex +
                " distAng: [" + distAngles[0] +
                "; " + distAngles[1] + "; " + distAngles[2] +
                "] " +
                " nb: [" + atmNb[0] + "; " + atmNb[1] +
                "; " + atmNb[2] + "; " + atmNb[3] + "] " +
                " vtx: " +vtxId + ")";
    return s;
    }
     
//------------------------------------------------------------------------------          
 
}