private void enterSMILEToolStripMenuItem_Click(object sender, EventArgs e)
{
smilesInput smiles = new smilesInput();
smiles.ShowDialog();
if (string.IsNullOrEmpty(smiles.SMILES))
{
return;
}
this.molecule = new ChemInfo.Molecule(smiles.SMILES);
this.dataGridView1.Rows.Clear();
if (molecule == null)
{
return;
}
this.moleculeViewer1.Molecule = this.molecule;
this.propertyGrid1.SelectedObject = this.molecule;
foreach (System.Data.DataRow dr in app_functionalgroup.Rows)
{
string smarts = dr["Smarts"].ToString();
if (!string.IsNullOrEmpty(smarts))
{
this.molecule.FindFunctionalGroup(dr);
}
}
this.textBox1.Text = Newtonsoft.Json.JsonConvert.SerializeObject(this.molecule, Newtonsoft.Json.Formatting.Indented);
foreach (string group in this.molecule.FunctionalGroups)
{
this.functionalGroupComboBox.Items.Add(group);
}
}
public Form1()
{
InitializeComponent();
dataPath = System.Environment.GetFolderPath(System.Environment.SpecialFolder.CommonApplicationData) + "\\SustainableChemistry\\Data";
if (!System.IO.Directory.Exists(dataPath))
{
dataPath = "..\\..\\..\\..\\SustainableChemistryData\\SustainableChemistryData";
}
imagePath = System.Environment.GetFolderPath(System.Environment.SpecialFolder.CommonApplicationData) + "\\SustainableChemistry\\Data";
if (!System.IO.Directory.Exists(imagePath))
{
imagePath = "..\\..\\..\\..\\SustainableChemistryData\\SustainableChemistryData\\static\\media\\";
}
m_dbConnection = new System.Data.SQLite.SQLiteConnection("Data Source=" + dataPath + "\\SustainableChemistry.sqlite3;Version=3;");
app_catalyst = GetDataTable("app_catalyst");
app_compound = GetDataTable("app_compound");
app_functionalgroup = GetDataTable("app_functionalgroup");
app_namedreaction = GetDataTable("app_namedreaction");
app_reference = GetDataTable("app_reference");
app_namedreaction_ByProd = GetDataTable("app_namedreaction_ByProducts");
app_namedreaction_ByProd.Rows.Clear();
app_namedreaction_Reactants = GetDataTable("app_namedreaction_Reactants");
app_namedreaction_Reactants.Rows.Clear();
app_reactant = GetDataTable("app_reactant");
app_solvent = GetDataTable("app_solvent");
//app_compound = GetDataTable("app_compound");
molecule = new ChemInfo.Molecule();
this.trackBar1.Value = (int)(this.moleculeViewer1.Zoom * 100);
documentPath = Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments) + "\\USEPA\\SustainableChemistry";
currentReferences = new List <Reference>();
}
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 Form1()
{
InitializeComponent();
//System.Data.SQLite.SQLiteConnection.CreateFile("MyDatabase.sqlite");
m_dbConnection = new System.Data.SQLite.SQLiteConnection("Data Source=..\\..\\Data\\SustainableChemistry.sqlite;Version=3;");
m_dbConnection.Open();
FunctionalGroups = new DataTable();
NamedReactions = new DataTable();
molecule = new ChemInfo.Molecule();
fGroups = new ChemInfo.FunctionalGroupCollection();
reactions = new ChemInfo.NamedReactionCollection();
this.trackBar1.Value = (int)(this.moleculeViewer1.Zoom * 100);
documentPath = Environment.GetFolderPath(Environment.SpecialFolder.MyDocuments) + "\\USEPA\\SustainableChemistry";
this.OpenFunctionGroupExcelResource();
System.IO.FileStream fs = new System.IO.FileStream("..\\..\\Data\\references.dat", System.IO.FileMode.Open);
// Construct a BinaryFormatter and use it to serialize the data to the stream.
System.Runtime.Serialization.Formatters.Binary.BinaryFormatter formatter = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
try
{
m_References = (ChemInfo.References)formatter.Deserialize(fs);
}
catch (System.Runtime.Serialization.SerializationException e)
{
Console.WriteLine("Failed to deserialize. Reason: " + e.Message);
throw;
}
finally
{
fs.Close();
}
//Reads in functional groups from JSON file. This should be used after Excel file is completed.
//var json = new System.Web.Script.Serialization.JavaScriptSerializer();
//functionalGroups = (List<ChemInfo.FunctionalGroup>)json.Deserialize(ChemInfo.Functionalities.AvailableFunctionalGroups(), typeof(List<ChemInfo.FunctionalGroup>)); // string text = ChemInfo.Functionalities.FunctionalGroups("P(c1ccccc1)(c1ccccc1)(N)=O", "json");
// Test code for generating a results file from a functional group name.
//Results res = new Results("phosphoramidite", m_References);
//string results = json.Serialize(res);
// Initial code to load references from text RIS resource files. Can be deleted when done.
//m_References = new ChemInfo.References();
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Diisoproprylethyamine Solvent", enc8.GetString(Properties.Resources.S0040403900813763)));
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Diisoproprylethyamine Solvent", enc8.GetString(Properties.Resources.S0040403900942163)));
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Diisoproprylethyamine Solvent", enc8.GetString(Properties.Resources.S0040403901904617)));
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Diisoproprylethyamine Solvent", enc8.GetString(Properties.Resources.achs_jacsat105_661)));
//m_References.Add(new ChemInfo.Reference("phosphate", "No Name", enc8.GetString(Properties.Resources.S1001841712003142)));
//m_References.Add(new ChemInfo.Reference("phosphate", "Catalyst", Properties.Resources._10_1002_2Fchin_199605199));
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Catalyst Solvent", enc8.GetString(Properties.Resources.europepmc)));
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Catalyst Solvent", enc8.GetString(Properties.Resources.europepmc1)));
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Catalyst Solvent", enc8.GetString(Properties.Resources.achs_oprdfk4_175)));
//m_References.Add(new ChemInfo.Reference("phosphoramidite", "Catalyst Solvent", enc8.GetString(Properties.Resources.BIB)));
}
public ReactionEditor(System.Data.DataTable fGroups)
{
InitializeComponent();
molecule = null;
this.m_FunctionalGroups = fGroups;
//this.productComboBox.Items.AddRange(m_FunctionalGroups.FunctionalGroups);
//reactantAComboBox.Items.AddRange(ChemInfo.Reactants.ReactantList);
//reactantBComboBox.Items.AddRange(ChemInfo.Reactants.ReactantList);
this.linkLabel1.Text = string.Empty;
}
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));
}
private string[] GetFunctionalGroups(string smiles)
{
List <string> retVal = new List <string>();
ChemInfo.Molecule m = new ChemInfo.Molecule(smiles);
foreach (System.Data.DataRow dr in app_functionalgroup.Rows)
{
string smarts = dr["Smarts"].ToString();
if (this.molecule.FindFunctionalGroup(dr))
{
retVal.Add(dr["Name"].ToString());
}
}
return(retVal.ToArray <string>());
}
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));
}
private void enterSMILEToolStripMenuItem_Click(object sender, EventArgs e)
{
smilesInput smiles = new smilesInput();
smiles.ShowDialog();
if (string.IsNullOrEmpty(smiles.SMILES))
{
return;
}
this.molecule = new ChemInfo.Molecule(smiles.SMILES);
this.listBox1.Items.Clear();
if (molecule == null)
{
return;
}
this.moleculeViewer1.Molecule = this.molecule;
this.propertyGrid1.SelectedObject = this.molecule;
foreach (ChemInfo.FunctionalGroup f in this.fGroups)
{
if ((f.Name != "ESTER-SULFIDE") || (f.Name != "KETENIMINE"))
{
this.molecule.FindFunctionalGroup(f);
}
}
this.textBox1.Text = Newtonsoft.Json.JsonConvert.SerializeObject(this.molecule, Newtonsoft.Json.Formatting.Indented);
foreach (ChemInfo.FunctionalGroup group in this.molecule.FunctionalGroups)
{
this.functionalGroupComboBox.Items.Add(group.Name);
}
//if (this.molecule.FunctionalGroups.Length > 0)
// if (this.molecule.FunctionalGroups[0].NamedReactions.Count > 0)
// {
// this.pictureBox1.Image = this.molecule.FunctionalGroups[0].NamedReactions[0].ReactionImage[0];
// foreach (ChemInfo.Reference r in this.molecule.FunctionalGroups[0].NamedReactions[0].References)
// {
// this.listBox1.Items.Add(r.ToString());
// }
// }
}
private void comboBox1_SelectedIndexChanged(object sender, EventArgs e)
{
System.Data.DataRow row = null;
foreach (System.Data.DataRow dr in fGroups.Rows)
{
if (string.Equals(dr["Name"].ToString(), this.comboBox1.Text))
{
row = dr;
break;
}
}
this.textBox2.Text = row["Smarts"].ToString();
molecule = new ChemInfo.Molecule(this.textBox2.Text);
this.moleculeViewer1.Molecule = molecule;
string filename = m_ImagePath + row["Image"].ToString().Replace("/", "\\");;
if (System.IO.File.Exists(filename))
{
this.pictureBox1.Image = System.Drawing.Image.FromFile(filename);
}
}
void PopulateForm(System.Data.DataRow group)
{
if (group == null)
{
this.pictureBox1.Image = null;
//this.textBox1.Text = string.Empty;
this.textBox2.Text = string.Empty;
this.moleculeViewer1 = null;
molecule = null;
return;
}
//this.pictureBox1.Image = group.Image;
//this.textBox1.Text = group["Name"].ToString();
this.textBox2.Text = group["Smart"].ToString();
if (!String.IsNullOrEmpty(this.textBox2.Text))
{
molecule = new ChemInfo.Molecule(this.textBox2.Text);
// molecule.FindRings();
//molecule.FindAllPaths();
this.moleculeViewer1.Molecule = molecule;
}
}
void PopulateForm(ChemInfo.FunctionalGroup group)
{
if (group == null)
{
this.pictureBox1.Image = null;
this.textBox1.Text = string.Empty;
this.textBox2.Text = string.Empty;
this.moleculeViewer1 = null;
molecule = null;
return;
}
this.pictureBox1.Image = group.Image;
this.textBox1.Text = group.Name;
this.textBox2.Text = group.Smart;
if (!String.IsNullOrEmpty(group.Smart))
{
molecule = new ChemInfo.Molecule(group.Smart);
// molecule.FindRings();
//molecule.FindAllPaths();
this.moleculeViewer1.Molecule = molecule;
}
}
private void importFormTESTToolStripMenuItem_Click(object sender, EventArgs e)
{
TestResults test = null;
try
{
test = new TestResults();
}
catch (Exception)
{
return;
}
test.ShowDialog();
string filepath = test.FilePath;
if (string.IsNullOrEmpty(filepath))
{
return;
}
molecule = ChemInfo.MoleFileReader.ReadMoleFile(test.FilePath);
this.dataGridView1.Rows.Clear();
this.moleculeViewer1.Molecule = molecule;
this.propertyGrid1.SelectedObject = this.molecule;
foreach (System.Data.DataRow dr in app_functionalgroup.Rows)
{
string smarts = dr["Smarts"].ToString();
if (!string.IsNullOrEmpty(smarts))
{
this.molecule.FindFunctionalGroup(dr);
}
}
this.textBox1.Text = Newtonsoft.Json.JsonConvert.SerializeObject(this.molecule, Newtonsoft.Json.Formatting.Indented);
foreach (string group in this.molecule.FunctionalGroups)
{
this.functionalGroupComboBox.Items.Add(group);
}
}
private void importFormTESTToolStripMenuItem_Click(object sender, EventArgs e)
{
TestResults test = null;
try
{
test = new TestResults();
}
catch (Exception)
{
return;
}
test.ShowDialog();
string filepath = test.FilePath;
if (string.IsNullOrEmpty(filepath))
{
return;
}
molecule = ChemInfo.MoleFileReader.ReadMoleFile(test.FilePath);
this.listBox1.Items.Clear();
this.moleculeViewer1.Molecule = molecule;
}
private void button2_Click(object sender, EventArgs e)
{
checkedListBox1.Items.Clear();
List <DSSToxChemicals> .Enumerator enumerator = (List <DSSToxChemicals> .Enumerator)tabPage4.Tag;
enumerator.MoveNext();
this.dataGridView1.Rows.Clear();
if (string.IsNullOrEmpty(enumerator.Current.Structure_SMILES))
{
return;
}
molecule = new ChemInfo.Molecule(enumerator.Current.Structure_SMILES);
if (molecule == null)
{
return;
}
// molecule.FindAllPaths();
this.moleculeViewer1.Molecule = molecule;
this.propertyGrid1.SelectedObject = molecule;
this.textBox1.Text = Newtonsoft.Json.JsonConvert.SerializeObject(this.molecule, Newtonsoft.Json.Formatting.Indented);
pictureBox2.Image = PUGGetCompoundImage(enumerator.Current.Structure_SMILES, enumerator.Current.Substance_CASRN);
checkedListBox1.Items.Add("Other");
if (molecule.Aromatic)
{
checkedListBox1.Items.Add("AROMATIC");
}
if (molecule.Heterocyclic)
{
checkedListBox1.Items.Add("HETEROCYCLIC");
}
if (molecule.HeterocyclicAromatic)
{
checkedListBox1.Items.Add("HETEROCYCLICAROMATIC");
}
checkedListBox1.Items.AddRange(enumerator.Current.FunctionalGroups);
tabPage4.Tag = enumerator;
}
// 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));
}
public Results(string smiles, System.Data.DataTable fGroups, System.Data.DataTable namedReactions, System.Data.DataTable reactants, System.Data.DataTable rxnReactants, System.Data.DataTable catalysts, System.Data.DataTable solvents, System.Data.DataTable byProducts, System.Data.DataTable references)
{
Molecule = new ChemInfo.Molecule(smiles);
groups = new List <FunctionalGroup>();
this.AddFunctionalGroups(smiles, fGroups, namedReactions, reactants, rxnReactants, catalysts, solvents, byProducts, references);
}
