/// <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);
}
public static Dictionary <PDB_Distance, string> GetDistanceAndUniprotResidueNumbers(string pdb_File_ID, double interaction_distance)
{
var DistanceAndUniprotResidueNumbers = new Dictionary <PDB_Distance, string>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
DistanceAndUniprotResidueNumbers = context.PDB_Distance.Where(distance =>
distance.PDB_File_ID == pdb_File_ID &&
distance.Distance <= interaction_distance)
.Join(context.PDB_Interaction,
distance => new
{
PDB_File_ID = distance.PDB_File_ID.ToLower(),
Protein_Residue = distance.Protein_Residue,
Protein_Residue_Number = distance.Protein_Residue_Number,
},
interaction => new
{
PDB_File_ID = interaction.PDB_File_ID.ToLower(),
Protein_Residue = interaction.AA_Residue_Type,
Protein_Residue_Number = interaction.PDB_Residue_Number,
},
(distance, interaction) => new
{
distance,
interaction,
}
).OrderBy(a => a.distance.Distance)
.ToDictionary(a => a.distance, a => a.interaction.PDB_Residue_Number);
}
return(DistanceAndUniprotResidueNumbers);
}
/// <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: Ryan Liang
/// </summary>
public static SNV_Mutation GetMutationBySNVKey(string SNV_Key)
{
SNV_Mutation SNV_mutation = new SNV_Mutation();
using (DrugProNETEntities context = new DrugProNETEntities())
{
SNV_mutation = context.SNV_Mutation.Where(m => m.SNV_Key.Equals(SNV_Key, StringComparison.OrdinalIgnoreCase)).SingleOrDefault();
}
return(SNV_mutation);
}
/// <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);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static Drug_Information GetDrugByDrugPDBID(string query)
{
Drug_Information drug = null;
using (DrugProNETEntities context = new DrugProNETEntities())
{
drug = context.Drug_Information.Where(d =>
d.Drug_PDB_ID.ToLower().Contains(query.ToLower())).FirstOrDefault();
}
return(drug);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static List <PDB_Information> GetPDBInfoUsingDrug(string drug_pdb_id)
{
List <PDB_Information> PDB_information = new List <PDB_Information>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
PDB_information = context.PDB_Information.Where(p =>
p.Drug_PDB_ID.ToLower().Contains(drug_pdb_id.ToLower())).ToList();
}
return(PDB_information);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static List <PDB_Information> GetPDBInfoUsingProtein(string uniprot_ID)
{
List <PDB_Information> list = new List <PDB_Information>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
list = context.PDB_Information.Where(pdb =>
pdb.Uniprot_ID.ToLower().Contains(uniprot_ID.ToLower())).ToList();
}
return(list);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static Drug_Information GetDrugUsingDropDownName(string query)
{
Drug_Information drug = null;
using (DrugProNETEntities context = new DrugProNETEntities())
{
drug = context.Drug_Information.Where(d =>
d.Drug_Name_for_Pull_Down_Menu.ToLower().Contains(query.ToLower())).FirstOrDefault();
}
return(drug);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static List <SNV_Mutation> GetMutations(string uniprot_ID, string drug_PDB_ID, string PDB_File_ID)
{
List <SNV_Mutation> SNV_Mutation = new List <SNV_Mutation>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
SNV_Mutation = context.SNV_Mutation.Where(m =>
m.UniProt_ID.Equals(uniprot_ID, StringComparison.OrdinalIgnoreCase) &&
m.Drug_PDB_ID.Equals(drug_PDB_ID, StringComparison.OrdinalIgnoreCase) &&
m.PDB_File_No.Equals(PDB_File_ID, StringComparison.OrdinalIgnoreCase)).ToList();
}
return(SNV_Mutation);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static List <PDB_Interaction> GetPDB_Interaction(string uniprot_ID, string drug_pdb_id)
{
List <PDB_Interaction> interactions = new List <PDB_Interaction>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
interactions = context.PDB_Interaction.Where(i =>
i.UniProt_ID.ToLower().Contains(uniprot_ID.ToLower()) &&
i.Drug_PDB_ID.ToLower().Contains(drug_pdb_id.ToLower())
).ToList();
}
return(interactions.OrderByDescending(i => double.Parse(i.Interaction_Distance_Ratio)).ToList());
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static List <PDB_Interaction> GetPDB_Interaction(string uniprot_ID)
{
List <PDB_Interaction> interactions = new List <PDB_Interaction>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
foreach (PDB_Interaction interaction in context.PDB_Interaction.Where(i => i.UniProt_ID == uniprot_ID))
{
interactions.Add(interaction);
}
}
return(interactions.OrderByDescending(i => double.Parse(i.Interaction_Distance_Ratio)).ToList());
}
/// <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: Ryan Liang
/// </summary>
public static List <Drug_Information> GetDrugsQuery(string query)
{
List <Drug_Information> drugs = new List <Drug_Information>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
drugs = context.Drug_Information.Where(d =>
d.Other_Drug_Name_Alias.ToLower().Contains(query.ToLower()) ||
d.Drug_Common_Name.ToLower().Contains(query.ToLower()) ||
d.Drug_Chemical_Name.ToLower().Contains(query.ToLower()) ||
d.Compound_CAS_ID.ToLower().Contains(query.ToLower()) ||
d.PubChem_CID.ToLower().Contains(query.ToLower()) ||
d.ChEMBL_ID.ToLower().Contains(query.ToLower())
).ToList();
}
return(drugs);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static List <PDB_Distance> GetPDB_Distance(string pdb_entry, double interaction_distance)
{
List <PDB_Distance> distances = new List <PDB_Distance>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
List <PDB_Distance> temp = context.PDB_Distance.Where(d => d.PDB_Entry.ToLower().Contains(pdb_entry.ToLower())).ToList();
foreach (PDB_Distance distance in temp)
{
if (double.Parse(distance.Distance) < interaction_distance)
{
distances.Add(distance);
}
}
}
return(distances.OrderBy(d => double.Parse(d.Distance)).ToList());
}
/// <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 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: Ryan Liang
/// </summary>
public static List <Protein_Information> GetProteinsInfoQuery(string query)
{
List <Protein_Information> proteins = new List <Protein_Information>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
proteins = 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())
).ToList();
}
return(proteins);
}
/// <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: Ryan Liang
/// </summary>
public static List <SNV_Mutation> GetMutationsBySNVIDKeyContains(string snv_ID_Key)
{
List <SNV_Mutation> SNV_Mutation = new List <SNV_Mutation>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
SNV_Mutation = context.SNV_Mutation.Where(m =>
m.SNV_P1W_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P2W_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P3W_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P1M1_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P1M2_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P1M3_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P2M1_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P2M2_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P2M3_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P3M1_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P3M2_ID.ToLower().Contains(snv_ID_Key.ToLower()) ||
m.SNV_P3M3_ID.ToLower().Contains(snv_ID_Key.ToLower())
).ToList();
}
return(SNV_Mutation);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static List <SNV_Mutation> GetMutationsBySNVIDKey(string snv_ID_Key)
{
List <SNV_Mutation> SNV_Mutation = new List <SNV_Mutation>();
using (DrugProNETEntities context = new DrugProNETEntities())
{
SNV_Mutation = context.SNV_Mutation.Where(m =>
m.SNV_P1W_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P2W_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P3W_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P1M1_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P1M2_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P1M3_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P2M1_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P2M2_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P2M3_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P3M1_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P3M2_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase) ||
m.SNV_P3M3_ID.Equals(snv_ID_Key, StringComparison.OrdinalIgnoreCase)
).ToList();
}
return(SNV_Mutation);
}