/// <summary>
/// Author: Ryan Liang
/// </summary>
private TableRow CreateTableRow(Drug_Information drug, PDB_Interaction interaction, SNV_Mutation mutation)
{
TableRow tableRow = new TableRow();
tableRow.Cells.Add(new TableCell()
{
Text = drug.Drug_Common_Name
});
tableRow.Cells.Add(new TableCell()
{
Text = mutation.PDB_File_ID
});
tableRow.Cells.Add(new TableCell()
{
Text = mutation.Drug_PDB_ID
});
tableRow.Cells.Add(new TableCell()
{
Text = drug.PubChem_CID
});
tableRow.Cells.Add(new TableCell()
{
Text = drug.ChEMBL_ID
});
if (double.TryParse(interaction?.Interaction_Distance_Ratio, out double result))
{
tableRow.Cells.Add(new TableCell()
{
Text = result.ToString("0.0")
});
}
else
{
tableRow.Cells.Add(new TableCell()
{
Text = ""
});
}
string predictedEffiency = FindPredictedEffiency(mutation);
tableRow.Cells.Add(new TableCell()
{
Text = predictedEffiency
});
return(tableRow);
}
/// <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 static PDB_Interaction GetPDB_Interaction(string uniProt_ID, string drug_PDB_ID, string amino_acid_specification)
{
PDB_Interaction PDB_interaction = new PDB_Interaction();
using (DrugProNETEntities context = new DrugProNETEntities())
{
PDB_interaction = context.PDB_Interaction.Where(i =>
i.UniProt_ID.ToLower().Contains(uniProt_ID.ToLower()) &&
i.Drug_PDB_ID.ToLower().Contains(drug_PDB_ID.ToLower()) &&
(i.AA_Residue_Type + "-" + i.UniProt_Residue_Number).ToLower().Contains(amino_acid_specification.ToLower())
).FirstOrDefault();
}
return(PDB_interaction);
}
/// <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: Ryan Liang
/// </summary>
public static Dictionary <PDB_Distance, string> GetUniprotResidueNumberByDistance(List <PDB_Distance> distances)
{
Dictionary <PDB_Distance, string> DistanceAndUniprotResidueNumbers = new Dictionary <PDB_Distance, string>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
foreach (PDB_Distance distance in distances)
{
PDB_Interaction interaction = context.PDB_Interaction.Where(i =>
i.PDB_Entry.ToLower().Equals(distance.PDB_Entry) &&
i.AA_Residue_Type.Equals(distance.Protein_Residue) &&
distance.Protein_Residue_.Equals(i.PDB_Residue_Number)
).FirstOrDefault();
DistanceAndUniprotResidueNumbers.Add(distance, interaction.Uniprot_Residue_Number);
}
}
return(DistanceAndUniprotResidueNumbers);
}
/// <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);
}
}
