content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program is free software: you can redistribute it and/or modify  *
  *  it under the terms of the GNU 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 General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package com.act.biointerpretation.metadata;
  
  import java.util.List;
  import java.util.Map;
  
  public class ProteinMetadata {
      //These are strict requirements that these be ok
      Long reactionId;
      List<Long> sequences;
      Map<Host, Integer> cloned;
      Double kcatkm;
      Double specificActivity;
  
      //These things should be downranked but not dealbreakers, they are fixable
      Map<Host, Localization> localization;
      Boolean heteroSubunits;
      Boolean modifications;
  
      public void setReactionId(Long reactionId) {
          this.reactionId = reactionId;
      }
  
      public boolean isValid(Host host) {
          if (sequences.isEmpty()) {
              return false;
          }
          //Don't bother if it's a really bad enzyme
          if(kcatkm != null && kcatkm < 1.0) {
              //Not in the top 80% of proteins, and anecdotally the bare minimum activity limit
              return false;
          }
  
          //Don't bother if it's a really bad enzyme
          if(specificActivity != null && specificActivity < 0.3) {
              //Not in the top 80% of proteins
              return false;
          }
  
          //Don't bother if there is a negaative observation about the protein working in the host
          Integer clonedval = cloned.get(host);
          if(clonedval != null && clonedval < 0) {
              return false;
          }
  
          return true;
      }
  }
  