Пример #1
0
  public static TemplateReaction makeTemplateReaction(
      Structure p_structureSp,
      Kinetics[] p_kinetics,
      ReactionTemplate p_template,
      Structure p_structure) {
    double PT = System.currentTimeMillis();
    // Look for pre-existing reaction in Template's reactionDictionaryByStructure.
    TemplateReaction reaction = p_template.getReactionFromStructure(p_structureSp);
    Global.getReacFromStruc =
        Global.getReacFromStruc + (System.currentTimeMillis() - PT) / 1000 / 60;

    if (reaction == null) {
      // Create a new reaction.
      reaction = new TemplateReaction(p_structureSp, p_kinetics, p_template);
      if (reaction.isBackward()) {
        Logger.info(
            "Created new reverse " + p_template.getName() + " reaction: " + reaction.toString());
        TemplateReaction reverse =
            reaction.generateReverseForBackwardReaction(p_structure, p_structureSp);
        if (reverse == null) return null;
        reaction.setReverseReaction(reverse);
      } else {
        Logger.info(
            "Created new forwards " + p_template.getName() + " reaction: " + reaction.toString());
        ReactionTemplate fRT = reaction.getReactionTemplate();
        ReactionTemplate rRT = null;
        if (fRT.isNeutral()) rRT = fRT;
        else rRT = fRT.getReverseReactionTemplate();
        if (rRT != null) {
          TemplateReaction reverse =
              new TemplateReaction(p_structureSp.generateReverseStructure(), p_kinetics, rRT);
          reaction.setReverseReaction(reverse);
          reverse.setReverseReaction(reaction);
          rRT.addReaction(reverse);
        }
      }
      if (!reaction.repOk()) {
        throw new InvalidTemplateReactionException();
      }

      p_template.addReaction(reaction);
    }
    Global.makeTR += (System.currentTimeMillis() - PT) / 1000 / 60;

    if (!reaction.repOk()) {
      throw new InvalidTemplateReactionException();
    }
    return reaction;
  }
Пример #2
0
 // ## operation getType()
 public String getType() {
   // #[ operation getType()
   return reactionTemplate.getName();
   // #]
 }