public static ROMol Parse(string smarts)
{
if (smarts == null)
{
throw new ArgumentNullException(nameof(smarts));
}
var pattern = SmartsCache.GetOrAdd(smarts, a_smarts =>
{
ROMol query = Chem.MolFromSmarts(a_smarts);
if (query == null)
{
return(nullSmarts);
}
query.setProp("source", "SMARTS");
return(query);
});
if (object.ReferenceEquals(pattern, nullSmarts))
{
return(null);
}
return(pattern);
}
/// <summary>
/// Read test data from file
/// </summary>
static IEnumerable <TestData> ReadTestData(string resourceName)
{
using (var r = new StreamReader(NCDK.ResourceLoader.GetAsStream($"NCDKExcel.test_data.QED.{resourceName}")))
{
int lineNo = 1;
string line;
while ((line = r.ReadLine()) != null)
{
if (!(line.Length == 0 || line[0] == '#'))
{
var temp = line.Trim().Split(',');
var smiles = temp[0];
var expected = double.Parse(temp[1]);
var mol = Chem.MolFromSmiles(smiles);
if (mol == null)
{
throw new AssertFailedException($"molecule construction failed on line {lineNo}");
}
yield return(new TestData()
{
LineNo = lineNo,
Smiles = smiles,
Mol = mol,
Expected = expected,
});
}
lineNo++;
}
yield break;
}
}
public async Task <IActionResult> Edit(int id, [Bind("ChemID,ChemComp,ChemAbbrev,ColorID,WarehouseLocationID")] Chem chem)
{
if (id != chem.ChemID)
{
return(NotFound());
}
if (ModelState.IsValid)
{
try
{
_context.Update(chem);
await _context.SaveChangesAsync();
}
catch (DbUpdateConcurrencyException)
{
if (!ChemExists(chem.ChemID))
{
return(NotFound());
}
else
{
throw;
}
}
return(RedirectToAction(nameof(Index)));
}
return(View(chem));
}
public void ExamplesTest()
{
// Paroxetine 0.935
Assert.AreEqual(0.934, QED.Calculate(Chem.MolFromSmiles("c1cc2OCOc2cc1OCC1CNCCC1c1ccc(F)cc1")), 0.01);
// Leflunomide 0.929
Assert.AreEqual(0.911, QED.Calculate(Chem.MolFromSmiles("C1=NOC(C)=C1C(=O)Nc1ccc(cc1)C(F)(F)F")), 0.01);
// Clomipramine 0.779
Assert.AreEqual(0.818, QED.Calculate(Chem.MolFromSmiles("CN(C)CCCN1c2ccccc2CCc2ccc(Cl)cc21")), 0.01);
// Tegaserod 0.213
Assert.AreEqual(0.235, QED.Calculate(Chem.MolFromSmiles("CCCCCNC(=N)NN=CC1=CNc2ccc(CO)cc21")), 0.01);
}
static void Main(string[] args)
{
IAtomContainer mol1 = Chem.MolFromSmiles("[C:1]([C:5]1[CH:10]=[CH:9][C:8]([OH:11])=[CH:7][CH:6]=1)([CH3:4])([CH3:3])[CH3:2]");
IMolecularFormula form1 = MolecularFormulaManipulator.GetMolecularFormula(mol1);
Console.WriteLine(MolecularFormulaManipulator.GetString(form1));
IAtomContainer mol2 = Chem.MolFromFile("/Users/john/My Documents/1,3-diisopropenylbenzene.mol");
var form2 = MolecularFormulaManipulator.GetMolecularFormula(mol2);
Console.WriteLine(MolecularFormulaManipulator.GetString(form2));
}
public async Task <IActionResult> Create([Bind("ChemID,ChemComp,ChemAbbrev,ColorID,WarehouseLocationID")] Chem chem)
{
if (ModelState.IsValid)
{
_context.Add(chem);
await _context.SaveChangesAsync();
return(RedirectToAction(nameof(Index)));
}
return(View(chem));
}
public void KekulizeTest()
{
{
var mol = Chem.MolFromSmiles("c1ccccc1");
Chem.Kekulize(mol);
Assert.IsTrue(mol.getAtomWithIdx(0).getIsAromatic());
}
{
var mol = Chem.MolFromSmiles("c1ccccc1");
Chem.Kekulize(mol, clearAromaticFlags: true);
Assert.IsFalse(mol.getAtomWithIdx(0).getIsAromatic());
}
}
public async Task <IActionResult> OnGetAsync(int?id)
{
if (id == null)
{
return(NotFound());
}
Chemistry = await _context.Chemistry.FirstOrDefaultAsync(m => m.ChemID == id);
if (Chemistry == null)
{
return(NotFound());
}
return(Page());
}
public async Task <IActionResult> OnPostAsync(int?id)
{
if (id == null)
{
return(NotFound());
}
Chemistry = await _context.Chemistry.FindAsync(id);
if (Chemistry != null)
{
_context.Chemistry.Remove(Chemistry);
await _context.SaveChangesAsync();
}
return(RedirectToPage("./Index"));
}
public TempFile GenerateTemporary(string text, double width, double height)
{
var min = Math.Min(width, height);
if (min < Config.MinimumEdgePixels)
{
double scale = Config.MinimumEdgePixels / min;
width *= scale;
height *= scale;
}
RWMol mol = null;
mol = Chem.MolFromSmiles(text);
if (mol == null)
{
mol = Chem.MolFromSmarts(text);
}
if (mol == null)
{
return(null);
}
var tempFile = new TempFile("." + Config.ImageType);
var filename = tempFile.FileName;
MolToFile(mol, filename, new Tuple <int, int>((int)width, (int)height));
if (filename.EndsWith(".svg"))
{
string svg;
using (var r = new StreamReader(filename))
{
svg = r.ReadToEnd();
}
if (ImageBGIsTransparent())
{
using (var r = new StreamWriter(filename))
{
r.Write(re_rect_tag.Replace(svg, ""));
}
}
}
return(tempFile);
}
public void PropertiesTest()
{
var m = Chem.MolFromSmiles("N=C(CCSCc1csc(N=C(N)N)n1)NS(N)(=O)=O");
var p = QED.CreateProperties(m);
Assert.AreEqual(337.045, p[MW], 0.01);
Assert.AreEqual(-0.55833, p[ALOGP], 0.01);
Assert.AreEqual(6, p[HBA]);
Assert.AreEqual(5, p[HBD]);
Assert.AreEqual(173.33, p[PSA], 0.01);
Assert.AreEqual(7, p[ROTB]);
Assert.AreEqual(1, p[AROM]);
Assert.AreEqual(3, p[ALERTS]);
p = QED.CreateProperties(m.AddHs());
Assert.AreEqual(337.045, p[MW], 0.01);
Assert.AreEqual(-0.55833, p[ALOGP], 0.01);
Assert.AreEqual(6, p[HBA]);
Assert.AreEqual(5, p[HBD]);
Assert.AreEqual(173.33, p[PSA], 0.01);
Assert.AreEqual(7, p[ROTB]);
Assert.AreEqual(1, p[AROM]);
Assert.AreEqual(3, p[ALERTS]);
}
/// <summary>
/// Read molecules and their info from SD file.
/// </summary>
/// <param name="sdfName">File name of the SD File.</param>
private static void _LoadSDFToNewSheet(string sdfName, ref object newSheet, ref int row)
{
var keyIndex = new Dictionary <string, int>();
const int ColumnTitle = 1;
const int ColumnMolBlock = 2;
int endIndex = ColumnMolBlock + 1; // for Title:1
using (var suppl = Chem.SDMolSupplier(sdfName))
{
int numSuppliedMol = 0;
foreach (var mol in suppl)
{
if (mol == null)
{
continue;
}
if (newSheet == null)
{
newSheet = Globals.ThisAddIn.Application.Sheets.Add();
((dynamic)newSheet).Cells[1, ColumnTitle] = "Title";
((dynamic)newSheet).Cells[1, ColumnMolBlock] = "MOL Text";
}
using (var sr = new StringWriter())
{
Excel.Range cells = ((dynamic)newSheet).Cells;
try
{
using (var w = new MDLV2000Writer(sr))
{
w.WriteMolecule(mol);
}
cells[row, ColumnTitle] = mol.Title;
foreach (var prop in mol.GetProperties())
{
switch (prop.Key)
{
case string key:
if (key.Equals(CDKPropertyName.Title, StringComparison.Ordinal))
{
break;
}
if (!keyIndex.TryGetValue(key, out int index))
{
keyIndex[key] = (index = endIndex++);
cells[1, index] = key;
}
cells[row, index] = prop.Value.ToString();
break;
default:
break;
}
}
}
catch (CDKException exception)
{
cells[row, ColumnTitle] = exception.Message;
}
cells[row, ColumnMolBlock] = sr.ToString();
}
row++;
numSuppliedMol++;
if (EnableProgressBar)
{
ProgressDialog.Current.ReportWithCancellationCheck($"Reading: {numSuppliedMol}");
}
}
}
}
public static string RDKit_StripMol(string smiles)
{
var stripped = Chem.StaticSaltRemover.StripMol(RDKitMol.Parse(smiles));
return(Chem.MolToSmiles(stripped));
}
public static string RDKit_RunReactionSmiles(string rxnIdent, string reactantsIdent)
{
var key = new Tuple <string, string>(rxnIdent, reactantsIdent);
var result = RunReactionCache.GetOrAdd(key, tuple =>
{
var a_rxnIdent = tuple.Item1;
var a_reactantsIdent = tuple.Item2;
try
{
var rxn = RDKitChemicalReaction.Parse(a_rxnIdent);
var mols = new List <ROMol>();
foreach (var reactant_smiles in a_reactantsIdent.Split('.'))
{
var mol = RDKitMol.Parse(reactant_smiles);
if (mol == null)
{
return(null);
}
mol = mol.AddHs();
mols.Add(mol);
}
if (rxn.getNumReactantTemplates() != mols.Count)
{
return(null);
}
var reactants = new ROMol_Vect(mols);
var products_candidate_list = rxn.runReactants(reactants);
if (products_candidate_list.Count == 0)
{
return(null);
}
return(string.Join(".", products_candidate_list.First().Select(mol => Chem.MolToSmiles(Chem.RemoveHs(mol)))));
}
catch (Exception ex)
{
return(ex.Message);
}
});
return(result);
}
