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;
}
// ## operation getType()
public String getType() {
// #[ operation getType()
return reactionTemplate.getName();
// #]
}