public void ToHMDB_metabolite(metabolite db_metabolite)
{
Hmdb_accession = db_metabolite.Hmdb_accession;
Hmdb_secondary_accessions = db_metabolite.Hmdb_secondary_accessions;
Name = db_metabolite.Name;
IsProblematic = db_metabolite.IsProblematic;
Synonym_names = db_metabolite.Synonym_names;
Description = db_metabolite.Description;
Description_chebi = db_metabolite.Description_chebi;
Quality = db_metabolite.Quality;
Comment = db_metabolite.Comment;
Charge = db_metabolite.Charge;
Formula = db_metabolite.Formula;
Formula_chebi = db_metabolite.Formula_chebi;
Average_molecular_weight = db_metabolite.Average_molecular_weight;
Monisotopic_molecular_weight = db_metabolite.Monisotopic_molecular_weight;
Mass = db_metabolite.Mass;
Monoisotopic_mass = db_metabolite.Monoisotopic_mass;
Iupac_name = db_metabolite.Iupac_name;
Traditional_iupac = db_metabolite.Traditional_iupac;
Cas_registry_number = db_metabolite.Cas_registry_number;
Cts_cas = db_metabolite.Cts_cas;
Smiles = db_metabolite.Smiles;
Inchi = db_metabolite.Inchi;
Inchi_chebi = db_metabolite.Inchi_chebi;
Inchikey = db_metabolite.Inchikey;
My_taxonomy = new taxonomy()
{
Direct_parent = db_metabolite.My_taxonomy.Direct_parent,
Kingdom = db_metabolite.My_taxonomy.Kingdom,
Super_class = db_metabolite.My_taxonomy.Super_class,
Tclass = db_metabolite.My_taxonomy.Tclass,
Substituents = db_metabolite.My_taxonomy.Substituents,
Other_descriptors = db_metabolite.My_taxonomy.Other_descriptors
};
My_onotology = new ontology()
{
Status = db_metabolite.My_onotology.Status,
Origins = db_metabolite.My_onotology.Origins,
Biofunctions = db_metabolite.My_onotology.Biofunctions,
Applications = db_metabolite.My_onotology.Applications,
Cellular_locations = db_metabolite.My_onotology.Cellular_locations
};
State = db_metabolite.State;
Biofluid_locations = db_metabolite.Biofluid_locations;
Tissue_locations = db_metabolite.Tissue_locations;
List_of_pathways = db_metabolite.List_of_pathways;
Drugbank_id = db_metabolite.Drugbank_id;
Drugbank_metabolite_id = db_metabolite.Drugbank_metabolite_id;
Chemspider_id = db_metabolite.Chemspider_id;
Kegg_id = db_metabolite.Kegg_id;
Cts_kegg = db_metabolite.Cts_kegg;
Metlin_id = db_metabolite.Metlin_id;
Pubchem_compound_id = db_metabolite.Pubchem_compound_id;
Chebi_id = db_metabolite.Chebi_id;
Cts_chebi = db_metabolite.Cts_chebi;
Synthesis_reference = db_metabolite.Synthesis_reference;
List_of_proteins = db_metabolite.List_of_proteins;
}
private void add_not_found_metabolite()
{
if (!string.IsNullOrEmpty(In_Hmdb_id) && !string.IsNullOrWhiteSpace(In_Hmdb_id))
{
outputToLog.WriteLine("no compounds detected with HMDB_ID=" + In_Hmdb_id + " (" + In_Name + ")");
}
else if (!string.IsNullOrEmpty(In_Cas_id) && !string.IsNullOrWhiteSpace(In_Cas_id))
{
outputToLog.WriteLine("no compounds detected with CAS_ID=" + In_Cas_id + " (" + In_Name + ")");
}
else if (!string.IsNullOrEmpty(In_Kegg_id) && !string.IsNullOrWhiteSpace(In_Kegg_id))
{
outputToLog.WriteLine("no compounds detected with KEGG_ID=" + In_Kegg_id + " (" + In_Name + ")");
}
else if (!string.IsNullOrEmpty(In_Chebi_id) && !string.IsNullOrWhiteSpace(In_Chebi_id))
{
outputToLog.WriteLine("no compounds detected with ChEBI_ID=" + In_Chebi_id + " (" + In_Name + ")");
}
else if (!string.IsNullOrEmpty(In_Pubchem_id) && !string.IsNullOrWhiteSpace(In_Pubchem_id))
{
outputToLog.WriteLine("no compounds detected with PubChem_ID=" + In_Pubchem_id + " (" + In_Name + ")");
}
else if (!string.IsNullOrEmpty(In_Chemspider_id) && !string.IsNullOrWhiteSpace(In_Chemspider_id))
{
outputToLog.WriteLine("no compounds detected with ChemSpider_ID=" + In_Chemspider_id + " (" + In_Name + ")");
}
else if (!string.IsNullOrEmpty(In_Lipidmaps_id) && !string.IsNullOrWhiteSpace(In_Lipidmaps_id))
{
outputToLog.WriteLine("no compounds detected with LipidMaps_ID=" + In_Lipidmaps_id + " (" + In_Name + ")");
}
else if (!string.IsNullOrEmpty(In_Metlin_id) && !string.IsNullOrWhiteSpace(In_Metlin_id))
{
outputToLog.WriteLine("no compounds detected with Metlin_ID=" + In_Metlin_id + " (" + In_Name + ")");
}
else
{
outputToLog.WriteLine("no compounds detected with Name=" + In_Name);
}
metabolite hmdb_metab = new metabolite();
hmdb_metab.metabolite_from_db(string.Format("{1}{0}{2}{0}{3}{0}{4}{0}{5}{0}{6}{0}{7}{0}{8}{0}{9}{0}{10}{0}{11}{0}{12}{0}{13}{0}{14}{0}{15}{0}{16}{0}{17}{0}{18}{0}{19}{0}{20}{0}{21}" +
"{0}{22}{0}{23}{0}{24}{0}{25}{0}{26}{0}{27}{0}{28}{0}{29}{0}{30}{0}{31}{0}{32}{0}{33}{0}{34}{0}{35}{0}{36}{0}{37}{0}{38}{0}{39}{0}{40}{0}{41}{0}{42}{0}{43}{0}{44}{0}{45}{0}{46}{0}{47}{0}{48}{0}{49}{0}{50}{0}{51}" +
"{0}{52}{0}{53}{0}{54}{0}{55}{0}{56}{0}{57}{0}{58}{0}{59}{0}{60}{0}{61}{0}{62}{0}{63}{0}{64}{0}{65}{0}{66}{0}{67}{0}{68}{0}{69}{0}{70}{0}{71}{0}{72}{0}{73}{0}{74}{0}{75}{0}{76}{0}{77}{0}{78}",
'\t', "", "", In_Name, "TRUE", "", "", "", "", "", "", In_Formula, "", "-1", "-1", In_Mass, "-1", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""));
ToHMDB_metabolite(hmdb_metab);
}
