public async Task <ActionResult <FunctionalGroup> > GetFunctionalGroups(string smiles)
{
var fG = await _context.AppFunctionalgroup.ToListAsync();
ChemInfo.Molecule molecule = new ChemInfo.Molecule(smiles);
var retVal = new List <AppFunctionalgroupDTO>();
foreach (var group in fG)
{
string smarts = group.Smarts;
if (!string.IsNullOrEmpty(group.Smarts))
{
if (molecule.FindFunctionalGroup(group))
{
retVal.Add(new AppFunctionalgroupDTO()
{
Id = group.Id,
Name = group.Name,
Smarts = group.Smarts
}
);
}
}
}
return(Ok(retVal));
}
public async Task <ActionResult <IEnumerable <FunctionalGroupAPI> > > Smiles(string id)
{
var fgList = await _context.AppFunctionalgroup.ToListAsync();
List <FunctionalGroup> fgFound = new List <FunctionalGroup>();
ChemInfo.Molecule molecule = new ChemInfo.Molecule(id.Trim());
if (molecule == null)
{
return(NotFound());
}
if (molecule.Atoms.Length != 0)
{
foreach (var fg in fgList)
{
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));
}
}
List <FunctionalGroupAPI> retVal = new List <FunctionalGroupAPI>();
foreach (var fg in fgFound)
{
retVal.Add(new FunctionalGroupAPI
{
Id = fg.Id,
Name = fg.Name,
Smarts = fg.Smarts,
URL = fg.URL,
Image = fg.Image,
});
}
return(retVal);
}
private void testChemicalListToolStripMenuItem_Click(object sender, EventArgs e)
{
List <DSSToxChemicals> chemicals = new List <DSSToxChemicals>();
// Open the document for editing.
string fileName = documentPath + "\\DSSTox_ToxCastRelease_20151019.xlsx";
using (DocumentFormat.OpenXml.Packaging.SpreadsheetDocument document = DocumentFormat.OpenXml.Packaging.SpreadsheetDocument.Open(fileName, false))
{
DocumentFormat.OpenXml.Packaging.WorkbookPart wbPart = document.WorkbookPart;
DocumentFormat.OpenXml.Packaging.WorksheetPart wsPart = wbPart.WorksheetParts.First();
DocumentFormat.OpenXml.Spreadsheet.SheetData sheetData = wsPart.Worksheet.Elements <DocumentFormat.OpenXml.Spreadsheet.SheetData>().First();
string text = string.Empty;
bool first = true;
foreach (DocumentFormat.OpenXml.Spreadsheet.Row r in sheetData.Elements <DocumentFormat.OpenXml.Spreadsheet.Row>())
{
if (!first)
{
foreach (DocumentFormat.OpenXml.Spreadsheet.Cell c in r.Elements <DocumentFormat.OpenXml.Spreadsheet.Cell>())
{
text = text + this.GetExcelCellValue(c, wbPart) + '\t';
}
chemicals.Add(new DSSToxChemicals(text));
}
first = false;
text = string.Empty;
}
document.Close();
}
foreach (DSSToxChemicals chem in chemicals)
{
if (!string.IsNullOrEmpty(chem.Structure_SMILES))
{
ChemInfo.Molecule mol = new ChemInfo.Molecule(chem.Structure_SMILES);
if (mol != null)
{
foreach (ChemInfo.FunctionalGroup f in this.fGroups)
{
if ((f.Name != "ESTER-SULFIDE") || (f.Name != "KETENIMINE"))
{
mol.FindFunctionalGroup(f);
}
}
}
chem.AddFunctionalGroups(mol.FunctionalGroups);
}
}
fileName = documentPath + "\\chemicals.json";
System.IO.File.WriteAllText(fileName, Newtonsoft.Json.JsonConvert.SerializeObject(chemicals, Newtonsoft.Json.Formatting.Indented));
}
public async Task <ActionResult <AppFunctionalgroup> > GetMolecule(string smiles)
{
var fG = await _context.AppFunctionalgroup.ToListAsync();
ChemInfo.Molecule molecule = new ChemInfo.Molecule(smiles);
var retVal = new List <AppFunctionalgroupDTO>();
foreach (var group in fG)
{
string smarts = group.Smarts;
if (!string.IsNullOrEmpty(group.Smarts))
{
molecule.FindFunctionalGroup(group);
}
}
return(Ok(molecule));
}
// GET: FunctionalGroups
public async Task <IActionResult> Index(string nameSearchString, string smilesSearchString)
{
var retVal = new List <AppFunctionalgroup>();
var groups = from s in _context.AppFunctionalgroup
select s;
if (!String.IsNullOrEmpty(nameSearchString))
{
groups = groups.Where(s => s.Name.Contains(nameSearchString, StringComparison.OrdinalIgnoreCase));
}
if (!String.IsNullOrEmpty(smilesSearchString))
{
await Task.Run(() =>
{
ChemInfo.Molecule molecule = new ChemInfo.Molecule(smilesSearchString);
foreach (var fg in groups)
{
string smarts = fg.Smarts;
if (!string.IsNullOrEmpty(fg.Smarts))
{
if (molecule.FindFunctionalGroup(fg.Smarts))
{
retVal.Add(fg);
}
}
}
});
}
else
{
retVal.AddRange(groups.ToList());
}
return(View(retVal.ToAsyncEnumerable()));
}
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));
}