public async Task <IActionResult> Create([Bind("Id,Name,Smarts,ImageFile,URL")] SustainableChemistryWeb.ViewModels.FunctionalGroupViewModel functionalGroupView)
{
if (ModelState.IsValid)
{
string name = System.IO.Path.GetFileName(functionalGroupView.ImageFile.FileName);
FunctionalGroup appFunctionalGroup = new FunctionalGroup()
{
Name = functionalGroupView.Name,
Smarts = functionalGroupView.Smarts,
Image = "Images/FunctionalGroups/" + name,
URL = functionalGroupView.URL
};
if (functionalGroupView.ImageFile.Length > 0)
{
using (var stream = new System.IO.FileStream(_hostingEnvironment.WebRootPath + "/Images/FunctionalGroups/" + name, System.IO.FileMode.Create))
{
await functionalGroupView.ImageFile.CopyToAsync(stream);
stream.Close();
}
}
_context.Add(appFunctionalGroup);
await _context.SaveChangesAsync();
return(RedirectToAction(nameof(Index)));
}
return(View(functionalGroupView));
}
public AtomOption(FunctionalGroup fg)
{
Element = fg;
Foreground = new SolidColorBrush(Colors.Black);
Content = new FunctionalGroupBlock {
ParentGroup = fg
};
}
public FunctionalGroupTextSource(FunctionalGroup parentGroup, bool isFlipped = false)
{
foreach (var term in parentGroup.ExpandIntoTerms(isFlipped))
{
foreach (var part in term.Parts)
{
Runs.Add(new LabelTextSourceRun
{
IsAnchor = term.IsAnchor,
IsEndParagraph = false,
IsSubscript = part.Type == FunctionalGroupPartType.Subscript,
IsSuperscript = part.Type == FunctionalGroupPartType.Superscript,
Text = part.Text
});
}
}
}
public async Task <IActionResult> Index(int?Id, int?funcGroupId, int?namedReactionId, string nameSearchString, string smilesSearchString)
{
if (!string.IsNullOrEmpty(smilesSearchString))
{
ViewData["SearchString"] = smilesSearchString.Trim();
}
var viewModel = new SustainableChemistryWeb.ViewModels.FunctionalGroupIndexData();
viewModel.FunctionalGroups = await _context.AppFunctionalgroup
.Include(i => i.AppNamedreaction)
.ThenInclude(i => i.AppReference)
.AsNoTracking()
.OrderBy(i => i.Name)
.ToListAsync();
List <FunctionalGroup> fgFound = new List <FunctionalGroup>();
ChemInfo.Molecule molecule = null;
string IUPacName = string.Empty;
string CASNo = string.Empty;
string DTXSID = string.Empty;
if (!String.IsNullOrEmpty(smilesSearchString))
{
if (TestCASNo(ref CASNo, ref smilesSearchString, ref IUPacName, ref DTXSID))
{
molecule = new ChemInfo.Molecule(smilesSearchString.Trim());
if (molecule.Atoms.Length != 0)
{
foreach (var fg in viewModel.FunctionalGroups)
{
string smarts = fg.Smarts;
if (!string.IsNullOrEmpty(fg.Smarts))
{
if (molecule.FindFunctionalGroup(fg))
{
fgFound.Add(fg);
}
}
}
if (molecule.Aromatic)
{
fgFound.Add(_context.AppFunctionalgroup
.FirstOrDefault(m => m.Id == 35));
}
if (molecule.Heterocyclic)
{
fgFound.Add(_context.AppFunctionalgroup
.FirstOrDefault(m => m.Id == 118));
}
if (molecule.HeterocyclicAromatic)
{
fgFound.Add(_context.AppFunctionalgroup
.FirstOrDefault(m => m.Id == 224));
}
}
}
else
{
return(RedirectToAction("Index", "Home", new { message = "Search String \"" + smilesSearchString + "\" was not found." }));
}
}
else if (!String.IsNullOrEmpty(nameSearchString))
{
ViewData["NameSearchString"] = nameSearchString.Trim();
fgFound.AddRange(viewModel.FunctionalGroups.Where(s => s.Name.Contains(nameSearchString, StringComparison.OrdinalIgnoreCase)));
ViewData["FunctionalGroupName"] = nameSearchString.Trim();
}
else if (funcGroupId != null)
{
ViewData["FunctionalGroupID"] = funcGroupId.Value;
FunctionalGroup group = viewModel.FunctionalGroups.Where(
i => i.Id == funcGroupId.Value).Single();
fgFound.Add(group);
}
if (funcGroupId != null)
{
ViewData["FunctionalGroupID"] = funcGroupId.Value;
FunctionalGroup group = viewModel.FunctionalGroups.Where(
i => i.Id == funcGroupId.Value).Single();
viewModel.NamedReactions = group.AppNamedreaction;
ViewData["FunctionalGroupName"] = group.Name;
}
if (namedReactionId != null)
{
ViewData["NamedReactionID"] = namedReactionId.Value;
NamedReaction rxn = viewModel.NamedReactions.Where(
i => i.Id == namedReactionId.Value).Single();
var referenceViewModels = new List <SustainableChemistryWeb.ViewModels.ReferenceViewModel>();
ViewData["NamedReactionName"] = rxn.Name;
foreach (var referecnce in rxn.AppReference)
{
referenceViewModels.Add(new SustainableChemistryWeb.ViewModels.ReferenceViewModel
{
Id = referecnce.Id,
FunctionalGroupId = referecnce.FunctionalGroupId,
FunctionalGroup = viewModel.FunctionalGroups.Where(
i => i.Id == referecnce.FunctionalGroupId).Single(),
ReactionId = referecnce.ReactionId,
Reaction = referecnce.Reaction,
Risdata = referecnce.Risdata
});
}
viewModel.References = referenceViewModels;
}
if (!string.IsNullOrEmpty(nameSearchString) || !string.IsNullOrEmpty(smilesSearchString) || funcGroupId != null)
{
viewModel.FunctionalGroups = fgFound.OrderBy(i => i.Name);
}
ViewData["SmilesString"] = smilesSearchString;
ViewData["CASNO"] = CASNo;
ViewData["IUPACName"] = IUPacName;
ViewData["DTXSID"] = DTXSID;
return(View(viewModel));
}
public void CreateFunctionalGroupCharacters(Atom atom, Options options)
{
FunctionalGroup fg = atom.Element as FunctionalGroup;
double baFromNorth = Vector.AngleBetween(BasicGeometry.ScreenNorth, atom.BalancingVector(true));
CompassPoints nesw = BasicGeometry.SnapTo2EW(baFromNorth);
bool reverse = nesw == CompassPoints.West;
#region Set Up Atom Colours
string atomColour = "000000";
if (options.ColouredAtoms)
{
if (!string.IsNullOrEmpty(fg.Colour))
{
atomColour = fg.Colour;
// Strip out # as OoXml does not use it
atomColour = atomColour.Replace("#", "");
}
}
#endregion Set Up Atom Colours
List <FunctionalGroupTerm> terms = fg.ExpandIntoTerms(reverse);
#region Step 1 - Generate the characters and measure Bounding Boxes
var cursorPosition = atom.Position;
List <AtomLabelCharacter> fgCharacters = new List <AtomLabelCharacter>();
TtfCharacter hydrogenCharacter = _TtfCharacterSet['H'];
Rect fgBoundingBox = Rect.Empty;
Rect anchorBoundingBox = Rect.Empty;
foreach (var term in terms)
{
foreach (var part in term.Parts)
{
foreach (char c in part.Text)
{
Rect bb = AddCharacter(c, part.Type);
fgBoundingBox.Union(bb);
if (term.IsAnchor)
{
anchorBoundingBox.Union(bb);
}
}
}
}
#endregion Step 1 - Generate the characters and measure Bounding Boxes
#region Step 2 - Move all characters such that the anchor term is centered on the atom position
double offsetX;
double offsetY;
if (reverse)
{
offsetX = fgBoundingBox.Width - anchorBoundingBox.Width / 2;
offsetY = anchorBoundingBox.Height / 2;
}
else
{
offsetX = anchorBoundingBox.Width / 2;
offsetY = anchorBoundingBox.Height / 2;
}
offsetY = offsetY + anchorBoundingBox.Top - atom.Position.Y;
foreach (var alc in fgCharacters)
{
alc.Position = new Point(alc.Position.X - offsetX, alc.Position.Y - offsetY);
}
#endregion Step 2 - Move all characters such that the anchor term is centered on the atom position
#region Step 3 - Transfer characters into main list
foreach (var alc in fgCharacters)
{
_AtomLabelCharacters.Add(alc);
}
#endregion Step 3 - Transfer characters into main list
#region Step 4 - Convex Hull
_convexhHulls.Add(atom.Path, ConvexHull(atom.Path));
#endregion Step 4 - Convex Hull
// Local Function
Rect AddCharacter(char c, FunctionalGroupPartType type)
{
TtfCharacter ttf = _TtfCharacterSet[c];
var thisCharacterPosition = GetCharacterPosition(cursorPosition, ttf);
var alc = new AtomLabelCharacter(thisCharacterPosition, ttf, atomColour, c, atom.Path, atom.Parent.Path);
alc.IsSubScript = type == FunctionalGroupPartType.Subscript;
alc.IsSuperScript = type == FunctionalGroupPartType.Superscript;
alc.IsSmaller = alc.IsSubScript || alc.IsSuperScript;
Rect thisBoundingBox;
if (alc.IsSmaller)
{
// Start by assuming it's SubScript
thisCharacterPosition.Offset(0, OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height * OoXmlHelper.SUBSCRIPT_DROP_FACTOR, _meanBondLength));
if (alc.IsSuperScript)
{
// Shift up by height of H to make it SuperScript
thisCharacterPosition.Offset(0, -OoXmlHelper.ScaleCsTtfToCml(hydrogenCharacter.Height, _meanBondLength));
}
// Reset the character's position
alc.Position = thisCharacterPosition;
thisBoundingBox = new Rect(alc.Position,
new Size(OoXmlHelper.ScaleCsTtfToCml(alc.Character.Width, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR,
OoXmlHelper.ScaleCsTtfToCml(alc.Character.Height, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR));
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(alc.Character.IncrementX, _meanBondLength) * OoXmlHelper.SUBSCRIPT_SCALE_FACTOR, 0);
}
else
{
thisBoundingBox = new Rect(alc.Position,
new Size(OoXmlHelper.ScaleCsTtfToCml(alc.Character.Width, _meanBondLength),
OoXmlHelper.ScaleCsTtfToCml(alc.Character.Height, _meanBondLength)));
cursorPosition.Offset(OoXmlHelper.ScaleCsTtfToCml(alc.Character.IncrementX, _meanBondLength), 0);
}
fgCharacters.Add(alc);
return(thisBoundingBox);
}
}
public FunctionalGroupVisual(FunctionalGroup fg)
{
ParentGroup = fg;
}
