/// <summary>
/// Author: Andy Tang
/// </summary>
public static PDB_Information GetPDBInfo(Protein_Information protein, Drug_Information drug)
{
PDB_Information PDBInfo = null;
if (protein == null || drug == null)
{
return(PDBInfo);
}
string uniprot_ID = protein.Uniprot_ID;
string drug_PDB_ID = drug.Drug_PDB_ID;
using (DrugProNETEntities context = new DrugProNETEntities())
{
DbSet <PDB_Information> dbSet = context.PDB_Information;
foreach (PDB_Information pdb in dbSet)
{
if (string.Equals(pdb.Uniprot_ID, uniprot_ID, StringComparison.OrdinalIgnoreCase) &&
string.Equals(pdb.Drug_PDB_ID, drug_PDB_ID, StringComparison.OrdinalIgnoreCase))
{
PDBInfo = pdb;
}
}
}
return(PDBInfo);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public void LoadPDB_Info(PDB_Information PDB_Info)
{
ProcessRow(PDB_File_ID_row, PDB_File_ID, PDB_Info.PDB_File_ID, "https://www.rcsb.org/structure/" + PDB_Info.PDB_File_ID);
ProcessRow(release_date_row, release_date, PDB_Info.PDB_Released);
ProcessRow(resolution_row, resolution, PDB_Info.Resolution);
ProcessRow(title_row, title, PDB_Info.PDB_Entry_Title);
ProcessRow(authors_row, authors, PDB_Info.Authors);
ProcessRow(reference_row, reference, PDB_Info.Journal_Reference);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public void LoadDrug(Drug_Information drug, PDB_Information PDB_Info)
{
ProcessRow(PDB_drug_ID_row, PDB_drug_ID, drug.Drug_PDB_ID);
ProcessRow(drug_name_row, drug_name, drug.Drug_Common_Name);
ProcessRow(drug_chemical_name, drug_chemical_name, drug.Drug_Chemical_Name);
ProcessRow(drug_alias_row, drug_alias, drug.Other_Drug_Name_Alias);
ProcessRow(drug_formula_row, drug_formula, drug.Drug_Formula);
ProcessRow(drug_mass_da_row, drug_mass_da, drug.Molecular_Mass);
ProcessRow(potency_row, potency, "IC50 (nM):" + PDB_Info.IC50_nM_
+ " (BINDINGDB); Ki (nM): " + PDB_Info.Ki_nM_
+ " (BINDINGDB); Kd(nM): " + PDB_Info.Kd_nM_
+ " (BINDINGDB)");
ProcessRow(drug_information_result_url_row, drug_information_result_url, "Link to further drug information", "DrugInfoResult.aspx?query_string=" + drug.Drug_Name_for_Pull_Down_Menu);
}
protected void LoadAminoAcidDropDown(object sender, EventArgs e)
{
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
try
{
if (drug_specification_drop_down.SelectedItem.Value != DROP_DOWN_PROMPT_MESSAGE)
{
Protein_Information protein = EF_Data.GetProtein(search_textBox.Text);
Drug_Information drug = EF_Data.GetDrugUsingDropDownName(drug_specification_drop_down.SelectedItem.Value);
PDB_Information PDB = EF_Data.GetPDBInfo(protein, drug);
List <SNV_Mutation> mutations = EF_Data.GetMutations(protein.UniProt_ID, drug.Drug_PDB_ID, PDB.PDB_File_ID);
if (mutations.Count > 0)
{
List <string> dropdownValues = new List <string>();
foreach (SNV_Mutation mutation in mutations)
{
dropdownValues.Add(mutation.SNV_Key);
}
dropdownValues = DataUtilities.FilterDropdownList(dropdownValues);
foreach (string dropdownValue in dropdownValues)
{
amino_acid_specification_drop_down.Items.Add(dropdownValue);
}
}
else
{
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
}
catch (Exception)
{
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
}
}
/// <summary>
/// Author: Andy Tang
/// </summary>
public static PDB_Information GetPDBInfo(Protein_Information protein, Drug_Information drug)
{
PDB_Information PDBInfo = null;
if (protein == null || drug == null)
{
return(PDBInfo);
}
using (DrugProNETEntities context = new DrugProNETEntities())
{
PDBInfo = context.PDB_Information.Where(pdb =>
pdb.UniProt_ID.Equals(protein.UniProt_ID, StringComparison.OrdinalIgnoreCase) &&
pdb.Drug_PDB_ID.Equals(drug.Drug_PDB_ID, StringComparison.OrdinalIgnoreCase)
).FirstOrDefault();
}
return(PDBInfo);
}
/// <summary>
/// Author: Garth Nelson
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
try
{
string protein_specification = Request.QueryString["query_string"];
string drug_specification = Request.QueryString["drug_specification"];
string SNV_Key = Request.QueryString["snv_id_key"];
Session["SNV_Key"] = SNV_Key;
Protein_Information protein = EF_Data.GetProtein(protein_specification);
Drug_Information drug = EF_Data.GetDrugUsingDropDownName(drug_specification);
PDB_Information PDB = EF_Data.GetPDBInfo(protein, drug);
string[] SNV_KEYsplit = SNV_Key.Split('-');
// Retrieve second and third elements
string amino_acid_specification = SNV_KEYsplit[1] + "-" + SNV_KEYsplit[2];
PDB_Interaction interaction = EF_Data.GetPDB_Interaction(protein.Uniprot_ID, drug.Drug_PDB_ID, amino_acid_specification);
mutation = EF_Data.GetMutationBySNVKey(SNV_Key);
Session["mutation"] = mutation;
LoadProtein(protein, interaction, mutation);
LoadDrug(drug, mutation);
LoadPDB_Info(PDB);
CreateSNVIdentificationTable(mutation);
}
catch (Exception)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public void LoadPDB_Info(PDB_Information PDB_Info)
{
ProcessRow(PDB_entry_row, PDB_entry, PDB_Info.PDB_File_ID, "https://www.rcsb.org/structure/" + PDB_Info.PDB_File_ID);
}
/// <summary>
/// Author: Andy Tang, Ryan Liang
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
if (!IsPostBack)
{
string fromPage = null;
string query_string = null;
try
{
query_string = Request.QueryString["query_string"];
drug_specification = Request.QueryString["drug_specification"];
protein_specification = Request.QueryString["protein_specification"];
if (!string.IsNullOrEmpty(drug_specification))
{
protein_specification = query_string;
fromPage = "protein";
}
else if (!string.IsNullOrEmpty(protein_specification))
{
drug_specification = query_string;
fromPage = "drug";
}
drug = EF_Data.GetDrugsQuery(drug_specification).FirstOrDefault();
protein = EF_Data.GetProteinsInfoQuery(protein_specification).FirstOrDefault();
PDB = EF_Data.GetPDBInfo(protein, drug);
Session["PDB_File_ID"] = PDB.PDB_File_ID;
interaction_distance = double.Parse(Request.QueryString["interaction_distance"]);
protein_chain = bool.Parse(Request.QueryString["protein_chain"]);
protein_atoms = bool.Parse(Request.QueryString["protein_atoms"]);
protein_residues = bool.Parse(Request.QueryString["protein_residues"]);
protein_residue_numbers = bool.Parse(Request.QueryString["protein_residue_numbers"]);
drug_atoms = bool.Parse(Request.QueryString["drug_atoms"]);
Session["interaction_distance"] = interaction_distance;
}
catch (Exception)
{
throw;
}
if (drug == null || protein == null || PDB == null)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
if (fromPage != null)
{
ExceptionUtilities.DisplayAlert(this, fromPage.Equals("drug") ? DRUG_QUERY_PAGE : PROTEIN_QUERY_PAGE);
}
else
{
ExceptionUtilities.DisplayAlert(this, DEFAULT_REDIRECT_PAGE);
}
}
else
{
Session["interaction_distance"] = interaction_distance;
Session["protein_chain"] = protein_chain;
Session["protein_atoms"] = protein_atoms;
Session["protein_residues"] = protein_residues;
Session["protein_residue_numbers"] = protein_residue_numbers;
Session["drug_atoms"] = drug_atoms;
LoadProtein(protein);
LoadDrug(drug, PDB);
LoadPDB_Info(PDB);
GetDrugAtomNumberingImage(drug);
CreateInteractionList(PDB, interaction_distance, protein_chain, protein_atoms, protein_residues, protein_residue_numbers, drug_atoms);
CreateInteractionSummary();
ScriptManager.RegisterStartupScript(Page, GetType(), "D_3DViewer", "javascript:loadDrugLigand('" + drug.Drug_PDB_ID + "');", true);
ScriptManager.RegisterStartupScript(Page, GetType(), "PDB_3DViewer", "javascript:loadStage('" + drug.PDB_File_ID + "', '" + drug.Drug_PDB_ID + "');", true);
}
}
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
private void CreateInteractionList(PDB_Information PDB, double interaction_distance, bool protein_chain, bool protein_atoms, bool protein_residues, bool protein_residue_numbers, bool drug_atoms)
{
TableHeaderRow tableHeaderRow = new TableHeaderRow {
TableSection = TableRowSection.TableHeader
};
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Distance (Å)"
});
if (protein_chain)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Protein Chain"
});
}
if (protein_residue_numbers)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Protein Residue Number"
});
}
if (protein_residues)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Amino Acid Residue Type"
});
}
if (protein_atoms)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Amino Acid Residue Atom"
});
}
if (drug_atoms)
{
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Drug Atom"
});
}
interaction_list.Rows.Add(tableHeaderRow);
var DistanceAndUniprotResidueNumbers = EF_Data.GetDistanceAndUniprotResidueNumbers(PDB.PDB_File_ID, interaction_distance);
Session["DistanceAndUniprotResidueNumbers"] = DistanceAndUniprotResidueNumbers;
foreach (KeyValuePair <PDB_Distance, string> kvp in DistanceAndUniprotResidueNumbers)
{
TableRow tableRow = new TableRow();
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Distance.ToString("0.00")
});
if (protein_chain)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Protein_Chain
});
}
if (protein_residue_numbers)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Value
});
}
if (protein_residues)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Protein_Residue
});
}
if (protein_atoms)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Protein_Atom
});
}
if (drug_atoms)
{
tableRow.Cells.Add(new TableCell {
Text = kvp.Key.Compound_Atom
});
}
interaction_list.Rows.Add(tableRow);
}
}
