com.hfg.chem.IonizableGroup Maven / Gradle / Ivy

Show more of this group Show more artifacts with this name
Show all versions of com_hfg Show documentation
com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.chem;

import com.hfg.util.CompareUtil;
import com.hfg.xml.XMLNode;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 Ionizable chemical group.
 
  @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------

public class IonizableGroup implements Comparable
{

   public static final String IONIZABLE_GROUP_TAG = "IonizableGrp";
   public static final String PROTONATED_FORM_ATT = "protonatedForm";
   public static final String KA_ATT              = "ka";

   //##########################################################################
   // PRIVATE FIELDS
   //##########################################################################

   private Charge  mProtonatedForm;
   private double  mKa;

   //##########################################################################
   // CONSTRUCTORS
   //##########################################################################

   //--------------------------------------------------------------------------
   public IonizableGroup(double inKa, Charge inProtonatedForm)
   {
      if (inKa > 1
          || inKa < 0)
      {
         throw new RuntimeException("Illegal Ka value: " + inKa + "! The Ka cannot be > 1 or < 0! (Be sure the value entered is not the pKa.)");
      }

      mKa = inKa;

      if (null == inProtonatedForm)
      {
         throw new RuntimeException("The protonated form cannot be null!");
      }
      else if (inProtonatedForm == Charge.NEGATIVE)
      {
         throw new RuntimeException("The protonated form cannot be negative!");
      }

      mProtonatedForm = inProtonatedForm;
   }


   //--------------------------------------------------------------------------
   public IonizableGroup(XMLNode inXML)
   {
      if (! inXML.getTagName().equals(IONIZABLE_GROUP_TAG))
      {
         throw new RuntimeException("Cannot construct an " + this.getClass().getSimpleName() + " from a " + inXML.getTagName() + " tag!");
      }

      mKa = Double.parseDouble(inXML.getAttributeValue(KA_ATT));
      mProtonatedForm = Charge.valueOf(inXML.getAttributeValue(PROTONATED_FORM_ATT));
   }

   //##########################################################################
   // PUBLIC METHODS
   //##########################################################################

   //--------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      return Float.valueOf((float) getKa()).hashCode() + 31 * getProtonatedForm().hashCode();
   }

   //--------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      boolean result = false;

      if (inObj2 != null
            && inObj2 instanceof IonizableGroup)
      {
         result = (0 == compareTo((IonizableGroup) inObj2));
      }

      return result;
   }

   //--------------------------------------------------------------------------
   @Override
   public int compareTo(IonizableGroup inObj2)
   {
      int result = -1;

      if (inObj2 != null)
      {
         result = 0;

         if (this != inObj2)
         {
            result = CompareUtil.compare(getKa(), inObj2.getKa());

            if (0 == result)
            {
               result = CompareUtil.compare(getProtonatedForm(), inObj2.getProtonatedForm());
            }
         }
      }

      return result;
   }

   //--------------------------------------------------------------------------
   public Charge getProtonatedForm()
   {
      return mProtonatedForm;
   }

   //--------------------------------------------------------------------------
   public float getpKa()
   {
      return (float) - Math.log10(mKa);
   }

   //--------------------------------------------------------------------------
   public double getKa()
   {
      return mKa;
   }

   //--------------------------------------------------------------------------
   public double getCharge(int inCount, double inConcOfHIons)
   {
      double value = 0;

      if (inCount > 0)
      {
         if (getProtonatedForm() == Charge.POSITIVE)
         {
            value = inCount * ((inConcOfHIons / (inConcOfHIons + getKa())));
         }
         else if (getProtonatedForm() == Charge.NEUTRAL)
         {
            value = -1 * inCount * (1 - (inConcOfHIons / (inConcOfHIons + getKa())));
         }
      }

      return value;
   }

   //--------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return String.format("%.2E (%s)", mKa, mProtonatedForm.toString());
   }

   //--------------------------------------------------------------------------
   public XMLNode toXMLNode()
   {
      XMLNode node = new XMLTag(IONIZABLE_GROUP_TAG);
      node.setAttribute(KA_ATT, mKa + "");
      node.setAttribute(PROTONATED_FORM_ATT, mProtonatedForm.toString());

      return node;
   }
}