package com.hfg.bio;

import java.util.HashSet;
import java.util.Map;
import java.util.Set;

import com.hfg.chem.Charge;
import com.hfg.chem.Element;
import com.hfg.chem.IonizableGroup;
import com.hfg.chem.Molecule;
import com.hfg.xml.XMLNode;
import com.hfg.util.StringUtil;

//------------------------------------------------------------------------------
/**
 N-terminal protein group.
 <div>
  @author J. Alex Taylor, hairyfatguy.com
 </div>
 */
//------------------------------------------------------------------------------
// 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
// jataylor@hairyfatguy.com
//------------------------------------------------------------------------------

public class NTerminalGroup extends Molecule
{
   // This declaration has to come before the public constants below.
   private static Set<NTerminalGroup> sValues = new HashSet<>(15);

   //##########################################################################
   // PUBLIC FIELDS
   //##########################################################################

   public static final NTerminalGroup UNMODIFIED_N_TERMINUS  = new NTerminalGroup("Unmodified", "<");
   public static final NTerminalGroup BOC_T_BUTYLOXYCARBONYL = new NTerminalGroup("Boc (t-butyloxycarbonyl)-", "Boc-");
   public static final NTerminalGroup CBZ_BENZYLOXYCARBONLYL = new NTerminalGroup("CBZ (Benzyloxycarbonyl)-", "CBZ-");
   public static final NTerminalGroup N_ACETYL               = new NTerminalGroup("N-acetyl-", "N-acetyl-");
   public static final NTerminalGroup N_CARBAMYL             = new NTerminalGroup("N-carbamyl-", "N-carbamyl-");
   public static final NTerminalGroup N_FORMYL               = new NTerminalGroup("N-formyl-", "N-formyl-");
   public static final NTerminalGroup N_METHYL               = new NTerminalGroup("N-methyl-", "N-methyl-");
   public static final NTerminalGroup N_MYRISTOYL            = new NTerminalGroup("N-myristoyl-", "N-myristoyl-");
   public static final NTerminalGroup PYRO_GLU_N_TERM_GLU    = new NTerminalGroup("Pyro-glu (N-term E)", "pyroglu-");
   public static final NTerminalGroup PYRO_GLU_N_TERM_GLN    = new NTerminalGroup("Pyro-glu (N-term Q)", "pyroglu-");


   static
   {
      UNMODIFIED_N_TERMINUS
            .addAtoms(Element.HYDROGEN, 1)
            .addKa(new IonizableGroup(1.0E-8, Charge.POSITIVE))  // pKa 8.0
            .lock()
            .register();

      BOC_T_BUTYLOXYCARBONYL
            .addAtoms(Element.CARBON, 5)
            .addAtoms(Element.HYDROGEN, 9)
            .addAtoms(Element.OXYGEN, 2)
            .lock()
            .register();

      CBZ_BENZYLOXYCARBONLYL
            .addAtoms(Element.CARBON, 8)
            .addAtoms(Element.HYDROGEN, 7)
            .addAtoms(Element.OXYGEN, 2)
            .lock()
            .register();

      N_ACETYL
            .addAtoms(Element.CARBON, 2)
            .addAtoms(Element.HYDROGEN, 3)
            .addAtoms(Element.OXYGEN, 1)
            .lock()
            .register();

      N_CARBAMYL
            .addAtoms(Element.CARBON, 1)
            .addAtoms(Element.HYDROGEN, 2)
            .addAtoms(Element.NITROGEN, 1)
            .addAtoms(Element.OXYGEN, 1)
            .lock()
            .register();

      N_FORMYL
            .addAtoms(Element.CARBON, 1)
            .addAtoms(Element.HYDROGEN, 1)
            .addAtoms(Element.OXYGEN, 1)
            .lock()
            .register();

      N_METHYL
            .addAtoms(Element.CARBON, 1)
            .addAtoms(Element.HYDROGEN, 3)
            .lock()
            .register();

      N_MYRISTOYL
            .addAtoms(Element.CARBON, 14)
            .addAtoms(Element.HYDROGEN, 27)
            .addAtoms(Element.OXYGEN, 1)
            .lock()
            .register();

      PYRO_GLU_N_TERM_GLN
            .addAtoms(Element.HYDROGEN, -2)
            .addAtoms(Element.NITROGEN, -1)
            .lock()
            .register();

      PYRO_GLU_N_TERM_GLU
            .addAtoms(Element.HYDROGEN, -1)
            .addAtoms(Element.OXYGEN,   -1)
            .lock()
            .register();
   }

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

   private String                 mShortName;

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

   //--------------------------------------------------------------------------
   public NTerminalGroup(String inName)
   {
      super();
      setName(inName);
   }

   //--------------------------------------------------------------------------
   private NTerminalGroup(String inName, String inShortName)
   {
      this(inName);
      mShortName = inShortName;
   }

   //--------------------------------------------------------------------------
   public NTerminalGroup(String inName, Map inElementalComposition)
   {
      super(inName, inElementalComposition);
   }

   //--------------------------------------------------------------------------
   public NTerminalGroup(XMLNode inXML)
   {
      super(inXML);

      if (! inXML.getTagName().equals(HfgBioXML.NTERM_TAG))
      {
         throw new RuntimeException("Cannot construct an " + this.getClass().getSimpleName() + " from a " + inXML.getTagName() + " tag!");
      }

      XMLNode sidechainKasTag = inXML.getOptionalSubtagByName(HfgBioXML.SIDECHAIN_KAS_TAG);
      if (sidechainKasTag != null)
      {
         for (XMLNode subtag : sidechainKasTag.getXMLNodeSubtags())
         {
            addKa(new IonizableGroup(subtag));
         }
      }


      mShortName = inXML.getAttributeValue(HfgBioXML.SHORT_NAME_ATT);
   }

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

   //--------------------------------------------------------------------------
   public static NTerminalGroup[] values()
   {
      return sValues.toArray(new NTerminalGroup[sValues.size()]);
   }

   //--------------------------------------------------------------------------
   /**
    Returns the NTerminalGroup whose name matches the specified String.
    @param inString the name for the NTerminalGroup to retrieve
    @return the NTerminalGroup whose name matches the specified String
    */
   public static NTerminalGroup valueOf(String inString)
   {
      NTerminalGroup value = null;

      if (StringUtil.isSet(inString))
      {
         for (NTerminalGroup group : sValues)
         {
            if (group.name().equalsIgnoreCase(inString))
            {
               value = group;
               break;
            }
         }
      }

      return value;
   }

   //--------------------------------------------------------------------------
   /**
    Puts the NTerminalGroup into the Set of unique NTerminalGroups returned by NTerminalGroup.values().
    */
   public void register()
   {
      if (! isLocked())
      {
         throw new RuntimeException("Only locked NTerminalGroups can be added to the values list!");
      }

      sValues.add(this);
   }

   //--------------------------------------------------------------------------
   @Override
   public NTerminalGroup addAtoms(Element inElement, int inNum)
   {
      return (NTerminalGroup) super.addAtoms(inElement, inNum);
   }

   //--------------------------------------------------------------------------
   @Override
   public NTerminalGroup lock()
   {
      return (NTerminalGroup) super.lock();
   }


   //--------------------------------------------------------------------------
   @Override
   public NTerminalGroup addKa(IonizableGroup inValue)
   {
      return (NTerminalGroup) super.addKa(inValue);
   }

   //--------------------------------------------------------------------------
   public String getShortName()
   {
      return mShortName;
   }

   //--------------------------------------------------------------------------
   @Override
   public XMLNode toXMLNode()
   {
      XMLNode node = super.toXMLNode();
      node.setTagName(HfgBioXML.NTERM_TAG);

      if (StringUtil.isSet(mShortName)) node.setAttribute(HfgBioXML.SHORT_NAME_ATT, mShortName);

      return node;
   }


}