/// <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); }