public void TestReactionSet2()
{
SpeciesDescription info1;
Species reactant1;
CreateSpeciesInfoAndSpecies("reactant1", 10, out info1, out reactant1);
SpeciesDescription info2;
Species reactant2;
CreateSpeciesInfoAndSpecies("reactant2", 40, out info2, out reactant2);
SpeciesDescription info3;
Species product1;
CreateSpeciesInfoAndSpecies("product1", 90, out info3, out product1);
SpeciesDescription info4;
Species reactant3;
CreateSpeciesInfoAndSpecies("reactant3", 1, out info4, out reactant3);
SpeciesDescription info5;
Species reactant4;
CreateSpeciesInfoAndSpecies("reactant4", 2, out info5, out reactant4);
SpeciesDescription info6;
Species product2;
CreateSpeciesInfoAndSpecies("product2", 3, out info6, out product2);
const double rate1 = 2.0;
const double rate2 = 3.0;
Reaction reaction1 = CreateReaction(info1, reactant1, info2, reactant2, info3, product1, rate1);
Reaction reaction2 = CreateReaction(info4, reactant3, info5, reactant4, info6, product2, rate2);
var reactions = new List <Reaction> {
reaction1, reaction2
};
var reactionSet = new ReactionSet(reactions);
double[] gamma = { 1.5, 2 };
Assert.AreEqual(9.0, reactionSet.UpdateRates(gamma));
Assert.AreEqual(3.0, reactionSet.CurrentRates[1]);
Assert.AreEqual(3.0, reactionSet.PredilectionRates[0]);
Assert.AreEqual(2, reactionSet.NumReactions);
reactionSet.FireReaction(0);
Assert.AreEqual(9, reactant1.Value);
Assert.AreEqual(39, reactant2.Value);
Assert.AreEqual(91, product1.Value);
reactionSet.FireReaction(1);
Assert.AreEqual(0, reactant3.Value);
Assert.AreEqual(1, reactant4.Value);
Assert.AreEqual(4, product2.Value);
int mu = reactionSet.SelectReaction(reactionSet.CurrentRates.Sum());
Assert.AreEqual(1, mu);
mu = reactionSet.SelectReaction(0.0);
Assert.AreEqual(0, mu);
}
/*!
* \brief Initialize the Medium
* \param reactionsSets The list of all the reactions sets
* \param moleculesSets The list of all the molecules sets
*/
public void Init(LinkedList <ReactionSet> reactionsSets, LinkedList <MoleculeSet> moleculesSets)
{
//Receive a linkedlist of Sets
_reactions = new LinkedList <IReaction>();
_numberGenerator = new NumberGenerator(NumberGenerator.normale, -10f, 10f, 0.01f);
//Try to find the good set in the LinkedList
ReactionSet reactSet = ReactionEngine.getReactionSetFromId(_reactionsSet, reactionsSets);
MoleculeSet molSet = ReactionEngine.getMoleculeSetFromId(_moleculesSet, moleculesSets);
//Put all the different molecules from the linkedList in an arrayList
ArrayList allMolecules = ReactionEngine.getAllMoleculesFromMoleculeSets(moleculesSets);
if (reactSet == null)
{
Logger.Log("Medium::Init Cannot find group of reactions named " + _reactionsSet, Logger.Level.WARN);
}
if (molSet == null)
{
Logger.Log("Medium::Init Cannot find group of molecules named" + _moleculesSet, Logger.Level.WARN);
}
initATPProduction();
initReactionsFromReactionSet(reactSet);
initMoleculesFromMoleculeSets(molSet, allMolecules);
initDegradationReactions(allMolecules);
foreach (IReaction r in _reactions)
{
r.enableSequential = _enableSequential;
}
}
public async Task addReactionToPost(int userId, int postId, int reactionId)
{
if (await this._db.reactions.AnyAsync(x => x.id == reactionId))
{
if (await this._db.posts.AnyAsync(x => x.id == postId))
{
if (await this._db.users.AnyAsync(x => x.id == userId))
{
ReactionSet reactionSet = new ReactionSet();
Reaction reaction = new Reaction();
reactionSet.postId = postId;
reactionSet.reactionId = reactionId;
reactionSet.userId = userId;
reactionSet.date = DateTime.Now;
if (!this._db.reactionSets.Any(x => ((x.postId == postId) && (x.userId == userId))))
{
reactionSet.reaction = await this._db.reactions.FirstOrDefaultAsync(x => x.id == reactionId);
this._db.Add(reactionSet);
}
}
}
}
}
public void SetUp()
{
string filename1 = "NCDK.Data.MDL.reaction-1.rxn";
var ins1 = ResourceLoader.GetAsStream(filename1);
MDLRXNReader reader1 = new MDLRXNReader(ins1);
ReactionSet set = (ReactionSet)reader1.Read(new ReactionSet());
reaction = set[0];
reader1.Close();
}
public void SetUp()
{
builder = ChemObjectBuilder.Instance;
string filename1 = "NCDK.Data.MDL.reaction-1.rxn";
var ins1 = ResourceLoader.GetAsStream(filename1);
MDLRXNReader reader1 = new MDLRXNReader(ins1);
set = (ReactionSet)reader1.Read(new ReactionSet());
reader1.Close();
}
/*!
* \brief Load reactions from a ReactionSet
* \param reactionsSet The set to load
*/
public void initReactionsFromReactionSet(ReactionSet reactionsSet)
{
if (reactionsSet == null)
{
return;
}
foreach (IReaction reaction in reactionsSet.reactions)
{
addReaction(IReaction.copyReaction(reaction));
}
// _reactions.AddLast(reaction);
}
public void TestRemoveAtomAndConnectedElectronContainers_IChemModel_IAtom()
{
IAtomContainer mol1 = new AtomContainer();
IAtom atom1 = new Atom("Cl");
mol1.Atoms.Add(atom1);
mol1.Atoms.Add(new Atom("Cl"));
IBond bond1 = new Bond(mol1.Atoms[0], mol1.Atoms[1]);
mol1.Bonds.Add(bond1);
IAtomContainer mol2 = new AtomContainer();
IAtom atom2 = new Atom("I");
mol2.Atoms.Add(atom2);
mol2.Atoms.Add(new Atom("I"));
IBond bond2 = new Bond(mol2.Atoms[0], mol2.Atoms[1]);
mol2.Bonds.Add(bond2);
var molSet = ChemObjectBuilder.Instance.NewAtomContainerSet();
molSet.Add(mol1);
IReaction r = new Reaction();
r.Products.Add(mol2);
IReactionSet rSet = new ReactionSet
{
r
};
var model = new ChemModel
{
MoleculeSet = molSet,
ReactionSet = rSet
};
IAtom otherAtom = new Atom("Cl");
Assert.AreEqual(2, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(4, ChemModelManipulator.GetAtomCount(model));
ChemModelManipulator.RemoveAtomAndConnectedElectronContainers(model, otherAtom);
Assert.AreEqual(2, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(4, ChemModelManipulator.GetAtomCount(model));
ChemModelManipulator.RemoveAtomAndConnectedElectronContainers(model, atom1);
Assert.AreEqual(1, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(3, ChemModelManipulator.GetAtomCount(model));
ChemModelManipulator.RemoveAtomAndConnectedElectronContainers(model, atom2);
Assert.AreEqual(0, ChemModelManipulator.GetBondCount(model));
Assert.AreEqual(2, ChemModelManipulator.GetAtomCount(model));
}
public void TestReactionSet_1()
{
IReaction reaction11 = builder.NewReaction();
IAtomContainer hydroxide = builder.NewAtomContainer();
hydroxide.Atoms.Add(builder.NewAtom("O"));
reaction11.Reactants.Add(hydroxide);
IAtomContainer proton = builder.NewAtomContainer();
proton.Atoms.Add(builder.NewAtom("H"));
reaction11.Reactants.Add(proton);
IAtomContainer water = builder.NewAtomContainer();
water.Atoms.Add(builder.NewAtom("O"));
reaction11.Products.Add(water);
IReactionSet reactionSet = new ReactionSet();
reactionSet.Add(reaction11);
// now serialize to MDL RXN
StringWriter writer = new StringWriter();
string file = "";
MDLRXNWriter mdlWriter = new MDLRXNWriter(writer);
mdlWriter.Write(reactionSet);
mdlWriter.Close();
file = writer.ToString();
Assert.IsTrue(file.Length > 0);
// now deserialize the MDL RXN output
IReaction reaction2 = builder.NewReaction();
MDLRXNReader reader = new MDLRXNReader(new StringReader(file));
reaction2 = (IReaction)reader.Read(reaction2);
reader.Close();
Assert.AreEqual(2, reaction2.Reactants.Count);
Assert.AreEqual(1, reaction2.Reactants[0].Atoms.Count);
Assert.AreEqual(1, reaction2.Reactants[1].Atoms.Count);
Assert.AreEqual(1, reaction2.Products.Count);
Assert.AreEqual(1, reaction2.Products[0].Atoms.Count);
}
public void TestReactionSet1()
{
SpeciesDescription info1;
Species reactant1;
CreateSpeciesInfoAndSpecies("reactant1", 10, out info1, out reactant1);
SpeciesDescription info2;
Species reactant2;
CreateSpeciesInfoAndSpecies("reactant2", 40, out info2, out reactant2);
SpeciesDescription info3;
Species product1;
CreateSpeciesInfoAndSpecies("product1", 90, out info3, out product1);
const double rate1 = 2.0;
Reaction reaction1 = CreateReaction(info1, reactant1, info2, reactant2, info3, product1, rate1);
Assert.AreEqual(reaction1.Reactants[0], reactant1);
Assert.AreEqual(reaction1.Reactants[1], reactant2);
Assert.AreEqual(reaction1.Products[0], product1);
var reactions = new List <Reaction> {
reaction1
};
var reactionSet1 = new ReactionSet(reactions);
Assert.AreEqual(reactionSet1.Reactions[0].Name, reactions[0].Name);
double[] gamma = { 2.0 };
Assert.AreEqual(4.0, reactionSet1.UpdateRates(gamma));
Assert.AreEqual(4.0, reactionSet1.PredilectionRates[0]);
Assert.AreEqual(2.0, reactionSet1.CurrentRates[0]);
Assert.AreEqual(1, reactionSet1.NumReactions);
reactionSet1.FireReaction(0);
Assert.AreEqual(9, reactant1.Value);
Assert.AreEqual(39, reactant2.Value);
Assert.AreEqual(91, product1.Value);
reactionSet1.FireReaction(0);
Assert.AreEqual(8, reactant1.Value);
Assert.AreEqual(38, reactant2.Value);
Assert.AreEqual(92, product1.Value);
}
public async Task <bool> deleteUserReactionsOnPost(int userId, int postId)
{
if (!await this._db.posts.AnyAsync(x => x.id == postId))
{
if (!await this._db.users.AnyAsync(x => x.id == userId))
{
return(false);
}
}
ReactionSet reactionSet = await _db.reactionSets.FirstOrDefaultAsync(x => ((x.userId == userId) && (x.postId == postId)));
if (reactionSet == null)
{
return(false);
}
_db.Remove(reactionSet);
return(true);
}
public async Task addReactionByNameToPost(int userId, int postId, string reactionName)
{
if (await this._db.reactions.AnyAsync(x => x.name == reactionName))
{
if (await this._db.posts.AnyAsync(x => x.id == postId))
{
if (await this._db.users.AnyAsync(x => x.id == userId))
{
ReactionSet reactionSet = new ReactionSet();
Reaction reaction = new Reaction();
Reaction reactionToGetId = await this._db.reactions.FirstOrDefaultAsync(x => x.name == reactionName);
reactionSet.postId = postId;
reactionSet.reactionId = reactionToGetId.id;
reactionSet.userId = userId;
reactionSet.date = DateTime.Now;
if (!this._db.reactionSets.Any(x => ((x.postId == postId) && (x.userId == userId) && (x.reaction.name == reactionName))))
{
reactionSet.reaction = await this._db.reactions.FirstOrDefaultAsync(x => x.id == reactionToGetId.id);
this._db.Add(reactionSet);
}
if (this._db.reactionSets.Any(x => ((x.postId == postId) && (x.userId == userId) && (x.reaction.name == reactionName))))
{
await this.deleteUserReactionsOnPost(userId, postId);
reactionSet.reaction = await this._db.reactions.FirstOrDefaultAsync(x => x.id == reactionToGetId.id);
}
else if (this._db.reactionSets.Any(x => ((x.postId == postId) && (x.userId == userId))))
{
await this.deleteUserReactionsOnPost(userId, postId);
reactionSet.reaction = await this._db.reactions.FirstOrDefaultAsync(x => x.id == reactionToGetId.id);
this._db.Add(reactionSet);
}
}
}
}
}
public async Task <Reaction> getUserReactionToPost(int userId, int postId)
{
if (!await this._db.users.AnyAsync(x => x.id == userId))
{
if (!await this._db.posts.AnyAsync(x => x.id == postId))
{
return(null);
}
}
ReactionSet reactionSet = new ReactionSet();
reactionSet = await this._db.reactionSets.Include(x => x.reaction).FirstOrDefaultAsync(x => ((x.postId == postId) && (x.userId == userId)));
Reaction reaction = new Reaction();
if (reactionSet == null)
{
return(null);
}
reaction = reactionSet.reaction;
return(reaction);
}
/*!
\brief Load reactions from a ReactionSet
\param reactionsSet The set to load
*/
public void initReactionsFromReactionSet(ReactionSet reactionsSet)
{
if (reactionsSet == null)
return;
foreach (IReaction reaction in reactionsSet.reactions)
addReaction(IReaction.copyReaction(reaction));
// _reactions.AddLast(reaction);
}
