/// <summary>
/// Author: Ryan Liang
/// </summary>
public static Protein_Information GetProtein(string query)
{
Protein_Information protein = null;
using (DrugProNETEntities context = new DrugProNETEntities())
{
DbSet <Protein_Information> dbSet = context.Protein_Information;
foreach (Protein_Information p in dbSet)
{
if (IsQueryInValues(query,
p.Protein_Short_Name,
p.Protein_Full_Name,
p.NCBI_Gene_ID,
p.PDB_Protein_Name,
p.Protein_Alias,
p.Uniprot_ID,
p.NCBI_RefSeq_NP_ID,
p.NCBI_Gene_Name,
p.PhosphoNET_Name))
{
protein = p;
}
}
}
return(protein);
}
/// <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: Andy Tang
/// </summary>
protected void Search_Textbox_Changed(object sender, EventArgs e)
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
List <Protein_Information> proteinList = new List <Protein_Information>();
const int minPrefixLength = 3;
if (search_textBox.Text.Length < minPrefixLength)
{
return;
}
Drug_Information drug = EF_Data.GetDrugsQuery(search_textBox.Text).FirstOrDefault();
if (drug != null)
{
List <PDB_Information> pdbInfoList = EF_Data.GetPDBInfoUsingDrug(drug.Drug_PDB_ID);
foreach (PDB_Information pdb in pdbInfoList)
{
Protein_Information protein = EF_Data.GetProteinByUniprotID(pdb.UniProt_ID);
if (protein != null)
{
proteinList.Add(protein);
}
}
}
if (proteinList.Count > 0)
{
List <string> valuesList = new List <string>();
foreach (Protein_Information protein in proteinList)
{
valuesList.Add(protein.UniProt_ID);
valuesList.Add(protein.Protein_Short_Name);
valuesList.Add(protein.Protein_Full_Name);
valuesList.Add(protein.Protein_Alias);
valuesList.Add(protein.NCBI_RefSeq_NP_ID);
valuesList.Add(protein.PhosphoNET_Name);
valuesList.Add(protein.PDB_Protein_Name);
}
valuesList = DataUtilities.FilterDropdownList(valuesList);
foreach (string value in valuesList)
{
search_drop_down.Items.Add(new ListItem(value, value, true));
}
}
else
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
/// <summary>
/// Author: Andy Tang
/// </summary>
protected void Search_Textbox_Changed(object sender, EventArgs e)
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
List <Drug_Information> drugList = new List <Drug_Information>();
const int minPrefixLength = 3;
if (search_textBox.Text.Length < minPrefixLength)
{
return;
}
Protein_Information protein = EF_Data.GetProteinsInfoQuery(search_textBox.Text).FirstOrDefault();
if (protein != null)
{
List <PDB_Information> pdbInfoList = EF_Data.GetPDBInfoUsingProtein(protein.UniProt_ID);
foreach (PDB_Information pdb in pdbInfoList)
{
Drug_Information drug = EF_Data.GetDrugByDrugPDBID(pdb.Drug_PDB_ID);
if (drug != null)
{
drugList.Add(drug);
}
}
}
if (drugList.Count > 0)
{
List <string> valuesList = new List <string>();
foreach (Drug_Information drug in drugList)
{
valuesList.Add(drug.Other_Drug_Name_Alias);
valuesList.Add(drug.Drug_Common_Name);
valuesList.Add(drug.Drug_Chemical_Name);
valuesList.Add(drug.Compound_CAS_ID);
valuesList.Add(drug.PubChem_CID);
valuesList.Add(drug.ChEMBL_ID);
}
valuesList = DataUtilities.FilterDropdownList(valuesList);
foreach (string value in valuesList)
{
search_drop_down.Items.Add(new ListItem(value, value, true));
}
}
else
{
search_drop_down.Items.Clear();
search_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
private void LoadTargetGeneID(Protein_Information protein, SNV_Mutation mutation)
{
ProcessRow(gene_name_row, gene_name, mutation.NCBI_Gene_Name);
ProcessRow(uniprot_id_row, uniprot_id, protein.UniProt_ID);
ProcessRow(ncbi_refseq_id_row, ncbi_refseq_id, protein.NCBI_RefSeq_NP_ID);
ProcessRow(chromosome_location_row, chromosome_location, protein.Human_Chromosome_Location);
gene_and_protein_info_url.Text = "Link to further gene and protein information";
gene_and_protein_info_url.NavigateUrl = "ProteinInfoResult.aspx?query_string=" + protein.UniProt_ID;
gene_and_protein_info_url.Target = "_blank";
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static Protein_Information GetProteinByUniprotID(string uniprotID)
{
Protein_Information protein = null;
using (DrugProNETEntities context = new DrugProNETEntities())
{
protein = context.Protein_Information.Where(p => p.Uniprot_ID.ToLower().Contains(uniprotID.ToLower())).FirstOrDefault();
}
return(protein);
}
protected void Search_Textbox_Changed(object sender, EventArgs e)
{
drug_specification_drop_down.Items.Clear();
drug_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
amino_acid_specification_drop_down.Items.Clear();
amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE);
const int minPrefixLength = 3;
if (search_textBox.Text.Length < minPrefixLength)
{
return;
}
Protein_Information protein = EF_Data.GetProteinsInfoQuery(search_textBox.Text).FirstOrDefault();
if (protein != null)
{
List <PDB_Information> pdbList = EF_Data.GetPDBInfoUsingProtein(protein.UniProt_ID);
List <Drug_Information> drugList = new List <Drug_Information>();
foreach (PDB_Information pdb in pdbList)
{
Drug_Information drug = EF_Data.GetDrugByDrugPDBID(pdb.Drug_PDB_ID);
if (drug != null)
{
drugList.Add(drug);
}
}
if (drugList.Count > 0)
{
List <string> dropdownValues = new List <string>();
foreach (Drug_Information drug in drugList)
{
dropdownValues.Add(drug.Drug_Name_for_Pull_Down_Menu);
}
dropdownValues = DataUtilities.FilterDropdownList(dropdownValues);
foreach (string dropdownValue in dropdownValues)
{
drug_specification_drop_down.Items.Add(dropdownValue);
}
}
else
{
drug_specification_drop_down.Items.Clear();
drug_specification_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE);
}
}
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
private void LoadData(Protein_Information protein)
{
ProcessRow(protein_short_name_row, protein_short_name, protein.Protein_Short_Name);
ProcessRow(protein_full_name_row, protein_full_name, protein.Protein_Full_Name);
ProcessRow(gene_name_row, gene_name, protein.NCBI_Gene_Name);
ProcessRow(alias_row, alias, protein.Protein_Alias);
ProcessRow(protein_type_row, protein_type, protein.Protein_Type_Specific);
ProcessRow(kinase_group_row, kinase_group, protein.Kinase_Group);
ProcessRow(kinase_family_row, kinase_family, protein.Kinase_Family);
ProcessRow(kinase_subfamily_row, kinase_subfamily, protein.Kinase_Subfamily);
ProcessRow(null, cell_component1, protein.GOCellComponent1, protein.GOCellComponent1URL);
ProcessRow(null, cell_component2, protein.GOCellComponent2, protein.GOCellComponent2URL);
ProcessRow(null, cell_component3, protein.GOCellComponent3, protein.GOCellComponent3URL);
ProcessControl(cell_component_row, protein.GOCellComponent1, protein.GOCellComponent2, protein.GOCellComponent3);
ProcessRow(null, mo1, protein.GOMolFunction1, protein.GOCellComponent1URL);
ProcessRow(null, mo2, protein.GOMolFunction2, protein.GOCellComponent2URL);
ProcessRow(null, mo3, protein.GOMolFunction3, protein.GOCellComponent3URL);
ProcessControl(molecular_function_row, protein.GOMolFunction1, protein.GOMolFunction2, protein.GOMolFunction3);
ProcessRow(null, bo1, protein.GOBioProcess1, protein.GOBioProcess1URL);
ProcessRow(null, bo2, protein.GOBioProcess2, protein.GOBioProcess2URL);
ProcessRow(null, bo3, protein.GOBioProcess3, protein.GOBioProcess3URL);
ProcessControl(biological_process_row, protein.GOBioProcess1, protein.GOBioProcess2, protein.GOBioProcess3);
ProcessControls(group_gene_ontology_terms, cell_component_row, molecular_function_row, biological_process_row);
ProcessRow(mass_da_row, mass_da, protein.Protein_Mass);
ProcessRow(number_aa_row, number_aa, protein.Protein_AA_Number);
ProcessRow(null, uniprot_id, protein.UniProt_ID, protein.UniProt_Entry_URL);
ProcessRow(null, uniprot_entry, protein.Entry_ID, protein.UniProt_Entry_URL);
ProcessControl(uniprot_row, protein.UniProt_ID, protein.Entry_ID);
ProcessRow(ncbi_refseq_id_row, ncbi_refseq_id, protein.NCBI_RefSeq_NP_ID, protein.NCBI_RefSeq_NP_ID_URL);
ProcessRow(int_protein_id_row, int_protein_id, protein.International_Prot_ID);
ProcessRow(phosphonet_id_row, phosphonet_id, protein.PhosphoNET_Name, protein.PhosphoNET_URL);
ProcessRow(phosphositeplus_row, phosphositeplus, protein.PhosphoSite_Plus_Entry, protein.PhosphoSite_Plus_Entry_URL);
ProcessRow(kinasenet_id_row, kinasenet_id, protein.UniProt_ID, protein.KinaseNET_URL);
kinasenet_id_row.Visible = !string.IsNullOrEmpty(protein.KinaseNET_URL?.Trim());
ProcessRow(onconet_id_row, onconet_id, protein.UniProt_ID, protein.OncoNET_URL);
onconet_id_row.Visible = !string.IsNullOrEmpty(protein.OncoNET_URL?.Trim());
ProcessRow(chromosome_no_row, chromosome_no, protein.Human_Chromosome_Number);
ProcessRow(chromosome_location_row, chromosome_location, protein.Human_Chromosome_Location);
ProcessRow(gene_location_row, gene_location, protein.Human_Gene_Location);
ProcessRow(ncbi_nucleotide_id_row, ncbi_nucleotide_id, protein.NCBI_Nucleotide_ID, protein.NCBI_Nucleotide_ID_URL);
ProcessRow(ncbi_gene_id_row, ncbi_gene_id, protein.NCBI_Gene_ID, protein.NCBI_Gene_URL);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public void LoadProtein(Protein_Information protein, PDB_Interaction interaction, SNV_Mutation mutation)
{
ProcessRow(gene_name_row, gene_name, mutation.NCBI_Gene_Name);
ProcessRow(uniprot_id_row, uniprot_id, mutation.UniProt_ID, protein.UniProt_Entry_URL);
ProcessRow(refseq_id_row, refseq_id, protein.NCBI_RefSeq_NP_ID, protein.NCBI_RefSeq_NP_ID_URL);
ProcessRow(nucleotide_id_row, nucleotide_id, protein.NCBI_Nucleotide_ID, protein.NCBI_Nucleotide_ID_URL);
ProcessRow(gene_id_row, gene_id, protein.NCBI_Gene_ID, protein.NCBI_Gene_URL);
ProcessRow(chromosome_location_row, chromosome_location, protein.Human_Chromosome_Location);
ProcessRow(gene_location_row, gene_location, protein.Human_Gene_Location);
ProcessRow(aa_residue_no_row, aa_residue_no, interaction.Uniprot_Residue_Number);
ProcessRow(atomic_interactions_row, atomic_interactions, interaction.Number_of_Atomic_Interactions);
ProcessRow(aa_residue_type_row, aa_residue_type, interaction.AA_Residue_Type);
ProcessRow(avg_atom_distance_row, avg_atom_distance, interaction.Average_Distance_Between_Atoms);
ProcessRow(interaction_distance_ratio_row, interaction_distance_ratio, interaction.Interaction_Distance_Ratio);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public void LoadProtein(Protein_Information protein)
{
ProcessRow(protein_name_row, protein_name, protein.Protein_Short_Name);
ProcessRow(protein_full_name_row, protein_full_name, protein.Protein_Full_Name);
ProcessRow(p_alias_row, p_alias, protein.Protein_Alias);
ProcessRow(uniprot_ID_row, uniprot_ID, protein.UniProt_ID);
ProcessRow(NCBI_ID_row, NCBI_ID, protein.NCBI_RefSeq_NP_ID);
ProcessRow(protein_type_row, protein_type, protein.Protein_Type_Specific);
ProcessRow(kinase_group_row, kinase_group, protein.Kinase_Group);
ProcessRow(kinase_family_row, kinase_family, protein.Kinase_Family);
ProcessRow(number_aa_row, number_aa, protein.Protein_AA_Number);
ProcessRow(protein_mass_da_row, protein_mass_da, protein.Protein_Mass);
ProcessRow(protein_information_result_url_row, protein_information_result_url, "Link to further protein information", "ProteinInfoResult.aspx?query_string=" + protein.UniProt_ID);
}
/// <summary>
/// Author: Andy Tang
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
string query = Request.QueryString["query_string"];
Protein_Information protein = EF_Data.GetProteinsInfoQuery(query).FirstOrDefault();
if (protein != null)
{
LoadData(protein);
}
else
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
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: Garth Nelson
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
SNV_ID_Key = Request.QueryString["query_string"];
try
{
string stringAfterPDot = SNV_ID_Key.Substring(SNV_ID_Key.IndexOf("p.") + 2);
string specifiedAAType = new string(stringAfterPDot.TakeWhile(c => char.IsLetter(c)).ToArray());
string specifiedAANumber = new string(stringAfterPDot.Substring(specifiedAAType.Length).TakeWhile(c => char.IsNumber(c)).ToArray());
string specifiedAA = specifiedAAType + "-" + specifiedAANumber;
mutations = EF_Data.GetMutationsBySNVIDKey(SNV_ID_Key);
proteinMutation = EF_Data.GetMutationBySNVIDKey(SNV_ID_Key);
protein = EF_Data.GetProteinByUniprotID(proteinMutation.UniProt_ID);
foreach (SNV_Mutation mutation in mutations)
{
Drug_Information drug = EF_Data.GetDrugByDrugPDBID(mutation.Drug_PDB_ID);
drugs.Add(drug);
PDB_Interaction interaction = EF_Data.GetPDB_Interaction(mutation.UniProt_ID, mutation.Drug_PDB_ID, specifiedAA);
interactions.Add(interaction);
}
Session["drugs"] = drugs;
Session["interactions"] = interactions;
Session["mutations"] = mutations;
Session["SNV_ID_Key"] = SNV_ID_Key;
LoadSNVID(SNV_ID_Key);
LoadTargetGeneID(protein, mutations[0]);
CreateIDofPDILinkedSNVTable(drugs, interactions, mutations);
}
catch (Exception)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
/// <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: Ryan Liang
/// </summary>
public static Protein_Information GetProtein(string query)
{
Protein_Information protein = null;
using (DrugProNETEntities context = new DrugProNETEntities())
{
protein = context.Protein_Information.Where(p =>
p.Protein_Short_Name.ToLower().Contains(query.ToLower()) ||
p.Protein_Full_Name.ToLower().Contains(query.ToLower()) ||
p.NCBI_Gene_ID.ToLower().Contains(query.ToLower()) ||
p.PDB_Protein_Name.ToLower().Contains(query.ToLower()) ||
p.Protein_Alias.ToLower().Contains(query.ToLower()) ||
p.UniProt_ID.ToLower().Contains(query.ToLower()) ||
p.NCBI_RefSeq_NP_ID.ToLower().Contains(query.ToLower()) ||
p.NCBI_Gene_Name.ToLower().Contains(query.ToLower()) ||
p.PhosphoNET_Name.ToLower().Contains(query.ToLower())
).FirstOrDefault();
}
return(protein);
}
/// <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: 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);
}
}
}
