Ejemplo n.º 1
0
        public object Visit(ASTGroup node, object data)
        {
            IAtomContainer fullQuery = (IAtomContainer)data;

            if (fullQuery == null)
            {
                fullQuery = new QueryAtomContainer(builder);
            }

            // keeps track of component grouping
            var components = fullQuery.GetProperty <int[]>("COMPONENT.GROUPING", Array.Empty <int>());
            int maxId      = 0;

            if (components.Length > 0)
            {
                foreach (int id in components)
                {
                    if (id > maxId)
                    {
                        maxId = id;
                    }
                }
            }

            for (int i = 0; i < node.JjtGetNumChildren(); i++)
            {
                ASTSmarts smarts = (ASTSmarts)node.JjtGetChild(i);
                ringAtoms = new RingIdentifierAtom[10];
                query     = new QueryAtomContainer(builder);

                smarts.JjtAccept(this, null);

                // update component info
                if (components.Length > 0 || smarts.ComponentId > 0)
                {
                    components = Arrays.CopyOf(components, 1 + fullQuery.Atoms.Count + query.Atoms.Count);
                    int id = smarts.ComponentId;
                    Arrays.Fill(components, fullQuery.Atoms.Count, components.Length, id);
                    if (id > maxId)
                    {
                        maxId = id;
                    }
                }

                fullQuery.Add(query);
            }

            // only store if there was a component grouping
            if (maxId > 0)
            {
                components[components.Length - 1] = maxId; // we left space to store how many groups there were
                fullQuery.SetProperty("COMPONENT.GROUPING", components);
            }

            // create tetrahedral elements
            foreach (var atom in neighbors.Keys)
            {
                IList <IAtom> localNeighbors = neighbors[atom];
                if (localNeighbors.Count == 4)
                {
                    fullQuery.StereoElements.Add(new TetrahedralChirality(atom, localNeighbors.ToArray(),
                                                                          TetrahedralStereo.Clockwise)); // <- to be modified later
                }
                else if (localNeighbors.Count == 5)
                {
                    localNeighbors.Remove(atom);                                                         // remove central atom (which represented implicit part)
                    fullQuery.StereoElements.Add(new TetrahedralChirality(atom, localNeighbors.ToArray(),
                                                                          TetrahedralStereo.Clockwise)); // <- to be modified later
                }
            }

            // for each double bond, find the stereo bonds. Currently doesn't
            // handle logical bonds i.e. C/C-,=C/C
            foreach (var bond in doubleBonds)
            {
                IAtom      left      = bond.Begin;
                IAtom      right     = bond.End;
                StereoBond leftBond  = FindStereoBond(left);
                StereoBond rightBond = FindStereoBond(right);
                if (leftBond == null || rightBond == null)
                {
                    continue;
                }
                DoubleBondConformation conformation = leftBond.GetDirection(left) == rightBond.GetDirection(right) ? DoubleBondConformation.Together
                       : DoubleBondConformation.Opposite;
                fullQuery.StereoElements.Add(new DoubleBondStereochemistry(bond, new IBond[] { leftBond, rightBond },
                                                                           conformation));
            }

            return(fullQuery);
        }
Ejemplo n.º 2
0
 public object Visit(ASTGroup node, object data)
 {
     return(node.JjtGetChild(0).JjtAccept(this, data));
 }