예제 #1
0
        public static void GetSingleBondGeometry(BondLayout descriptor, double standoff)
        {
            var start = descriptor.Start;
            var end   = descriptor.End;

            var sg = new StreamGeometry();

            if (descriptor.StartAtomHull != null)
            {
                AdjustTerminus(ref start, end, descriptor.StartAtomHull, standoff);
            }

            if (descriptor.EndAtomHull != null)
            {
                AdjustTerminus(ref end, start, descriptor.EndAtomHull, standoff);
            }

            using (var sgc = sg.Open())
            {
                sgc.BeginFigure(start, false, false);
                sgc.LineTo(end, true, false);
                sgc.Close();
            }

            sg.Freeze();
            descriptor.DefiningGeometry = sg;
        }
예제 #2
0
        public static BondLayout GetBondDescriptor(AtomVisual startAtomVisual, AtomVisual endAtomVisual,
                                                   double modelXamlBondLength, Globals.BondStereo parentStereo,
                                                   Point startAtomPosition, Point endAtomPosition,
                                                   double?parentOrderValue, Globals.BondDirection parentPlacement,
                                                   Point?centroid, Point?secondaryCentroid)
        {
            if (parentStereo == Globals.BondStereo.Wedge || parentStereo == Globals.BondStereo.Hatch)
            {
                WedgeBondLayout wbd = new WedgeBondLayout()
                {
                    Start           = startAtomPosition,
                    End             = endAtomPosition,
                    StartAtomVisual = startAtomVisual,
                    EndAtomVisual   = endAtomVisual
                };

                var  endAtom    = endAtomVisual.ParentAtom;
                var  otherBonds = endAtom.Bonds.Except(new[] { startAtomVisual.ParentAtom.BondBetween(endAtom) }).ToList();
                Bond bond       = null;
                if (otherBonds.Any())
                {
                    bond = otherBonds.ToArray()[0];
                }

                bool chamferBond = (otherBonds.Any() &&
                                    (endAtom.Element as Element) == Globals.PeriodicTable.C &&
                                    endAtom.SymbolText == "" &&
                                    bond.Order == Globals.OrderSingle);
                if (!chamferBond)
                {
                    wbd.CappedOff = false;
                    BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength);
                }
                else
                {
                    var nonHPs = (from b in otherBonds
                                  select b.OtherAtom(endAtom).Position).ToList();
                    if (nonHPs.Any())
                    {
                        wbd.CappedOff = true;
                        BondGeometry.GetChamferedWedgeGeometry(wbd, modelXamlBondLength, nonHPs);
                    }
                    else
                    {
                        wbd.CappedOff = false;
                        BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength);
                    }
                }

                return(wbd);
            }

            //wavy bond
            if (parentStereo == Globals.BondStereo.Indeterminate && parentOrderValue == 1.0)
            {
                BondLayout sbd = new BondLayout
                {
                    Start           = startAtomPosition,
                    End             = endAtomPosition,
                    StartAtomVisual = startAtomVisual,
                    EndAtomVisual   = endAtomVisual
                };
                BondGeometry.GetWavyBondGeometry(sbd, modelXamlBondLength);
                return(sbd);
            }

            switch (parentOrderValue)
            {
            //indeterminate double
            case 2 when parentStereo == Globals.BondStereo.Indeterminate:
                DoubleBondLayout dbd = new DoubleBondLayout()
                {
                    StartAtomVisual = startAtomVisual,
                    EndAtomVisual   = endAtomVisual,
                    Start           = startAtomPosition,
                    End             = endAtomPosition
                };
                BondGeometry.GetCrossedDoubleGeometry(dbd, modelXamlBondLength);
                return(dbd);

            //partial or undefined bonds
            case 0:
            case 0.5:
            case 1.0:
                BondLayout sbd = new BondLayout
                {
                    Start           = startAtomPosition,
                    End             = endAtomPosition,
                    StartAtomVisual = startAtomVisual,
                    EndAtomVisual   = endAtomVisual
                };

                BondGeometry.GetSingleBondGeometry(sbd);
                return(sbd);

            //double bond & 1.5 bond
            case 1.5:
            case 2:
                DoubleBondLayout dbd2 = new DoubleBondLayout()
                {
                    StartAtomVisual   = startAtomVisual,
                    EndAtomVisual     = endAtomVisual,
                    Start             = startAtomPosition,
                    End               = endAtomPosition,
                    Placement         = parentPlacement,
                    PrimaryCentroid   = centroid,
                    SecondaryCentroid = secondaryCentroid
                };

                BondGeometry.GetDoubleBondGeometry(dbd2, modelXamlBondLength);
                return(dbd2);

            //triple and 2.5 bond
            case 2.5:
            case 3:
                TripleBondLayout tbd = new TripleBondLayout()
                {
                    StartAtomVisual   = startAtomVisual,
                    EndAtomVisual     = endAtomVisual,
                    Start             = startAtomPosition,
                    End               = endAtomPosition,
                    Placement         = parentPlacement,
                    PrimaryCentroid   = centroid,
                    SecondaryCentroid = secondaryCentroid
                };
                BondGeometry.GetTripleBondGeometry(tbd, modelXamlBondLength);
                return(tbd);

            default:
                return(null);
            }
        }
예제 #3
0
        /// <summary>
        /// Quite ghastly routine to draw a wiggly bond
        /// </summary>
        /// <param name="descriptor">BondDescriptor which is populated</param>
        /// <param name="standardBondLength">Standard bond length as defined by the model</param>
        /// <param name="standoff"></param>
        public static void GetWavyBondGeometry(BondLayout descriptor, double standardBondLength, double standoff)
        {
            var sg = new StreamGeometry();

            //first do the adjustment for any atom visuals
            if (descriptor.StartAtomHull != null)
            {
                AdjustTerminus(ref descriptor.Start, descriptor.End, descriptor.StartAtomHull, standoff);
            }

            if (descriptor.EndAtomHull != null)
            {
                AdjustTerminus(ref descriptor.End, descriptor.Start, descriptor.EndAtomHull, standoff);
            }

            //Work out the control points for a quadratic Bezier by sprouting alternately along the bond line
            Vector halfAWiggle;

            using (var sgc = sg.Open())
            {
                var bondVector = descriptor.PrincipleVector;
                //come up with a number of wiggles that looks aesthetically sensible
                var noOfWiggles = (int)Math.Ceiling(bondVector.Length / (standardBondLength * Globals.BondOffsetPercentage * 2));
                if (noOfWiggles < 3)
                {
                    noOfWiggles = 3;
                }
                //now calculate a wiggle vector that is 60 degrees from the bond angle
                var wiggleLength = bondVector.Length / noOfWiggles;

                halfAWiggle = bondVector;
                halfAWiggle.Normalize();
                halfAWiggle *= wiggleLength / 2;

                //work out left and right sprouting vectors
                var toLeft = new Matrix();
                toLeft.Rotate(-60);
                var toRight = new Matrix();
                toRight.Rotate(60);

                var leftVector  = halfAWiggle * toLeft;
                var rightVector = halfAWiggle * toRight;

                var allpoints = new List <Point>();
                //allpoints holds the control points for the bezier
                allpoints.Add(descriptor.Start);

                var lastPoint = descriptor.Start;
                //move along the bond vector, sprouting control points alternately
                for (var i = 0; i < noOfWiggles; i++)
                {
                    var leftPoint = lastPoint + leftVector;
                    allpoints.Add(leftPoint);
                    allpoints.Add(lastPoint + halfAWiggle);
                    var rightPoint = lastPoint + halfAWiggle + rightVector;
                    allpoints.Add(rightPoint);
                    lastPoint += halfAWiggle * 2;
                    allpoints.Add(lastPoint);
                }

                allpoints.Add(descriptor.End);
                BezierFromPoints(sgc, allpoints);
                sgc.Close();
            }

            //define the boundary
            descriptor.Boundary.Clear();
            descriptor.Boundary.AddRange(new[]
            {
                descriptor.Start - halfAWiggle.Perpendicular(),
                descriptor.End - halfAWiggle.Perpendicular(),
                descriptor.End + halfAWiggle.Perpendicular(),
                descriptor.Start + halfAWiggle.Perpendicular()
            });

            sg.Freeze();
            descriptor.DefiningGeometry = sg;

            //local function
            void BezierFromPoints(StreamGeometryContext sgc, List <Point> allpoints)
            {
                sgc.BeginFigure(allpoints[0], false, false);
                sgc.PolyQuadraticBezierTo(allpoints.Skip(1).ToArray(), true, true);
            }
        }
예제 #4
0
        public static BondLayout GetBondDescriptor(AtomVisual startAtomVisual, AtomVisual endAtomVisual,
                                                   double modelXamlBondLength, Globals.BondStereo parentStereo,
                                                   Point startAtomPosition, Point endAtomPosition,
                                                   double?parentOrderValue, Globals.BondDirection parentPlacement,
                                                   Point?centroid, Point?secondaryCentroid, double standoff)
        {
            List <Point> startAtomHull = new List <Point>();
            List <Point> endAtomHull   = new List <Point>();

            if (startAtomVisual.ParentAtom.SymbolText != "" || startAtomVisual.ShowAllCarbons)
            {
                startAtomHull = startAtomVisual.Hull;
            }
            if (endAtomVisual.ParentAtom.SymbolText != "" || endAtomVisual.ShowAllCarbons)
            {
                endAtomHull = endAtomVisual.Hull;
            }
            if ((parentStereo == Globals.BondStereo.Wedge || parentStereo == Globals.BondStereo.Hatch) &&
                parentOrderValue == 1)
            {
                WedgeBondLayout wbd = new WedgeBondLayout
                {
                    Start         = startAtomPosition,
                    End           = endAtomPosition,
                    StartAtomHull = startAtomHull,
                    EndAtomHull   = endAtomHull
                };

                var endAtom    = endAtomVisual.ParentAtom;
                var otherBonds = endAtom.Bonds.Except(new[] { startAtomVisual.ParentAtom.BondBetween(endAtom) }).ToList();

                Bond bond    = null;
                bool oblique = true;
                if (otherBonds.Any())
                {
                    bond = otherBonds.ToArray()[0];
                    Vector wedgevector = wbd.End - wbd.Start;
                    foreach (Bond b in otherBonds)
                    {
                        Atom   otherAtom = b.OtherAtom(endAtom);
                        Vector v         = wbd.End - otherAtom.Position;
                        double angle     = System.Math.Abs(Vector.AngleBetween(wedgevector, v));

                        if (angle < 109.5 || angle > 130.5)
                        {
                            oblique = false;
                            break;
                        }
                    }
                }

                bool chamferBond = otherBonds.Any() &&
                                   oblique &&
                                   (endAtom.Element as Element) == Globals.PeriodicTable.C &&
                                   endAtom.SymbolText == "" &&
                                   bond.Order == Globals.OrderSingle;
                if (!chamferBond)
                {
                    wbd.CappedOff = false;
                    BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength, standoff);
                }
                else
                {
                    var nonHPs = (from b in otherBonds
                                  select b.OtherAtom(endAtom).Position).ToList();
                    if (nonHPs.Any())
                    {
                        wbd.CappedOff = true;
                        BondGeometry.GetChamferedWedgeGeometry(wbd, modelXamlBondLength, nonHPs, standoff);
                    }
                    else
                    {
                        wbd.CappedOff = false;
                        BondGeometry.GetWedgeBondGeometry(wbd, modelXamlBondLength, standoff);
                    }
                }

                return(wbd);
            }

            //wavy bond
            if (parentStereo == Globals.BondStereo.Indeterminate && parentOrderValue == 1.0)
            {
                BondLayout sbd = new BondLayout
                {
                    Start         = startAtomPosition,
                    End           = endAtomPosition,
                    StartAtomHull = startAtomHull,
                    EndAtomHull   = endAtomHull
                };
                BondGeometry.GetWavyBondGeometry(sbd, modelXamlBondLength, standoff);
                return(sbd);
            }

            switch (parentOrderValue)
            {
            //indeterminate double
            case 2 when parentStereo == Globals.BondStereo.Indeterminate:
                DoubleBondLayout dbd = new DoubleBondLayout()
                {
                    StartAtomHull          = startAtomHull,
                    EndAtomHull            = endAtomHull,
                    Start                  = startAtomPosition,
                    End                    = endAtomPosition,
                    StartNeigbourPositions = (from Atom a in startAtomVisual.ParentAtom.NeighboursExcept(endAtomVisual.ParentAtom)
                                              select a.Position).ToList(),
                    EndNeighbourPositions = (from Atom a in endAtomVisual.ParentAtom.NeighboursExcept(startAtomVisual.ParentAtom)
                                             select a.Position).ToList()
                };
                BondGeometry.GetCrossedDoubleGeometry(dbd, modelXamlBondLength, standoff);
                return(dbd);

            //partial or undefined bonds
            case 0:
            case 0.5:
            case 1.0:
                BondLayout sbd = new BondLayout
                {
                    Start         = startAtomPosition,
                    End           = endAtomPosition,
                    StartAtomHull = startAtomHull,
                    EndAtomHull   = endAtomHull
                };

                BondGeometry.GetSingleBondGeometry(sbd, standoff);
                return(sbd);

            //double bond & 1.5 bond
            case 1.5:
            case 2:
                DoubleBondLayout dbd2 = new DoubleBondLayout()
                {
                    StartAtomHull          = startAtomHull,
                    EndAtomHull            = endAtomHull,
                    Start                  = startAtomPosition,
                    End                    = endAtomPosition,
                    Placement              = parentPlacement,
                    PrimaryCentroid        = centroid,
                    SecondaryCentroid      = secondaryCentroid,
                    StartNeigbourPositions = (from Atom a in startAtomVisual.ParentAtom.NeighboursExcept(endAtomVisual.ParentAtom)
                                              select a.Position).ToList(),
                    EndNeighbourPositions = (from Atom a in endAtomVisual.ParentAtom.NeighboursExcept(startAtomVisual.ParentAtom)
                                             select a.Position).ToList()
                };

                BondGeometry.GetDoubleBondGeometry(dbd2, modelXamlBondLength, standoff);
                return(dbd2);

            //triple and 2.5 bond
            case 2.5:
            case 3:
                TripleBondLayout tbd = new TripleBondLayout()
                {
                    StartAtomHull     = startAtomHull,
                    EndAtomHull       = endAtomHull,
                    Start             = startAtomPosition,
                    End               = endAtomPosition,
                    Placement         = parentPlacement,
                    PrimaryCentroid   = centroid,
                    SecondaryCentroid = secondaryCentroid
                };
                BondGeometry.GetTripleBondGeometry(tbd, modelXamlBondLength, standoff);
                return(tbd);

            default:
                return(null);
            }
        }