//void SetMolDisplayFormatText()
//{
// MolDisplayFormatEdit.Text =
// QueryMolCtl.Molecule.PrimaryDisplayFormat == MoleculeRenderer.Helm ? "Biopolymer" : "Structure";
//}
/// <summary>
/// Get currently selected search type from form
/// </summary>
/// <returns></returns>
StructureSearchType GetSearchType()
{
StructureSearchType searchType = StructureSearchType.Unknown;
if (SubStruct.Checked)
{
searchType = StructureSearchType.Substructure;
}
else if (Full.Checked)
{
searchType = StructureSearchType.FullStructure;
}
else if (Similarity.Checked)
{
searchType = StructureSearchType.MolSim;
}
else if (SmallWorld.Checked)
{
searchType = StructureSearchType.SmallWorld;
}
return(searchType);
}
public static string StructureSearchTypeToExternalName(StructureSearchType sst)
{
if (sst == StructureSearchType.Unknown)
{
return("");
}
string txt = sst.ToString(); // default name
if (sst == StructureSearchType.Substructure)
{
txt = "Substructure";
}
else if (sst == StructureSearchType.MolSim)
{
txt = "Similar";
}
else if (sst == StructureSearchType.MatchedPairs)
{
txt = "Matched Pair";
}
return(txt);
}
/// <summary>
/// Get the list of related compounds
/// </summary>
/// <param name="mt"></param>
/// <param name="cid"></param>
/// <param name="str"></param>
public void StartSearchAndRetrievalOfRelatedStructures(
string mtName,
string cid,
MoleculeMx str,
StructureSearchType searchTypes)
{
RSC.RenderSearchResultsDelegate = RenderSearchResults; // set render callback
DisplayEmptySearchResults();
if (Lex.IsUndefined(str.PrimaryValue) || (!str.IsChemStructureFormat && str.IsBiopolymerFormat)) // reasonable structure?
{
return;
}
Cid = cid;
CidMtName = mtName;
QueryStruct = str;
SearchTypes = searchTypes;
Timer.Enabled = true;
Thread t = new Thread(new ParameterizedThreadStart(SearchAndRetrieveRelatedStructuresThreadMethod));
t.IsBackground = true;
t.SetApartmentState(ApartmentState.STA);
object[] parms = null;
t.Start(parms);
return;
}
/// <summary>
/// Get list of related structures using the supplied compound id for the query structure
/// </summary>
/// <param name="cid"></param>
/// <param name="type"></param>
/// <returns></returns>
public static string GetRelatedMatchCounts(
string cid,
string mtName,
string chime,
StructureSearchType searchTypes,
int searchId)
{
if (ServiceFacade.UseRemoteServices)
{
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusCompoundUtilService,
(int)Services.Native.ServiceOpCodes.MobiusCompoundUtilService.GetRelatedCompoundIds,
//new Services.Native.NativeMethodTransportObject(new object[] { cid, mtName, chime, (int)searchTypes, searchId }));
new Services.Native.NativeMethodTransportObject(new object[] { cid, mtName, chime, searchId }));
((System.ServiceModel.IClientChannel)nativeClient).Close();
string result = (resultObject != null) ? (string)resultObject.Value : null;
return(result);
}
else
{
return(QEL.MoleculeUtil.GetRelatedMatchCounts(cid, mtName, chime, searchTypes, searchId));
}
}
/// <summary>
/// Determine if match passes the current filter settings
/// </summary>
/// <param name="ssm"></param>
/// <param name="dbId"></param>
/// <param name="searchType"></param>
/// <param name="searchTypeCount"></param>
/// <param name="include"></param>
/// <returns></returns>
bool FilterMatch(
StructSearchMatch ssm,
int dbId,
StructureSearchType searchType,
CheckEdit searchTypeCtl,
ref int searchTypeCount,
ref bool include)
{
bool dbChecked = false;
if (dbId == CorpDbId)
{
dbChecked = CorpDB.Checked;
}
else if (dbId == ChemblDbId)
{
dbChecked = ChemblDB.Checked;
}
if (!dbChecked || ssm.SrcDbId != dbId || ssm.SearchType != searchType)
{
return(false);
}
if (searchTypeCtl.Checked)
{
include = true;
}
searchTypeCount++;
return(true);
}
/// <summary>
/// Get list of related structure compound Ids for a compound id
/// </summary>
/// <param name="cid"></param>
/// <param name="mtName"></param>
/// <param name="chime"></param>
/// <returns></returns>
public static string GetRelatedMatchCounts(
string cid,
string mtName,
string chime,
StructureSearchType searchTypes,
int searchId)
{
string result = RelatedStructureSearch.GetRelatedMatchCounts(cid, mtName, chime, searchTypes, searchId);
return(result);
}
/// <summary>
/// ShowModelSelectionMenu - static method
/// </summary>
/// <param name="location"></param>
/// <param name="molEditorCtl"></param>
/// <param name="qc"></param>
public static void ShowModelSelectionMenu(
Point location,
MoleculeControl molEditorCtl,
StructureSearchType searchType,
QueryColumn qc = null)
{
MoleculeSelectorControl i = new MoleculeSelectorControl();
i.MolEditorCtl = molEditorCtl;
i.Qc = qc;
i.StructureSearchType = searchType;
i.NewMoleculeMenu.Show(location);
return;
}
/// <summary>
/// AddToFavoritesList
/// </summary>
/// <param name="molEditorCtl"></param>
/// <param name="searchType"></param>
public static void AddToFavoritesList(
MoleculeControl molEditorCtl,
StructureSearchType searchType)
{
MoleculeListItem sli = null;
DialogResult dr;
MoleculeMx mol = molEditorCtl.Molecule;
if (MoleculeMx.IsUndefined(mol))
{
return;
}
mol = mol.Clone(); // make a copy for the list
sli = FindStructure(mol, GetFavoriteStructuresList());
if (sli != null)
{
dr = MessageBoxMx.Show("The current molecule already exists in Favorites list under the name: " + sli.Name + "\r\n" +
"Do you still want the add the current query molecule to the Favorites list?", "Molecule already in Favorites", MessageBoxButtons.YesNoCancel);
if (dr != DialogResult.Yes)
{
return;
}
}
string name = molEditorCtl.GetTemporaryStructureTag();
name = InputBoxMx.Show("Enter the name that you want to assign to the molecule", "Enter Name", name);
if (Lex.IsUndefined(name))
{
return;
}
sli = new MoleculeListItem();
sli.Name = name;
sli.Molecule = mol;
sli.UpdateDate = DateTime.Now;
sli.MoleculeType = StructureSearchTypeUtil.StructureSearchTypeToExternalName(searchType);
FavoritesList.ItemList.Insert(0, sli);
SaveStructureList(FavoritesList, FavoritesPreferencesParmName);
return;
}
public static string StructureSearchTypeToExternalName(StructureSearchType sst)
{
if (sst == StructureSearchType.Unknown) return "";
string txt = sst.ToString(); // default name
if (sst == StructureSearchType.Substructure)
txt = "Substructure";
else if (sst == StructureSearchType.MolSim)
txt = "Similar";
else if (sst == StructureSearchType.MatchedPairs)
txt = "Matched Pair";
return txt;
}
/// <summary>
/// AddToMruList
/// </summary>
/// <param name="molEditorCtl"></param>
/// <param name="searchType"></param>
public static void AddToMruList(
MoleculeControl molEditorCtl,
StructureSearchType searchType)
{
MoleculeListItem sli = null;
DialogResult dr;
MoleculeMx mol = molEditorCtl.Molecule;
if (Lex.IsUndefined(mol.PrimaryValue))
{
return;
}
mol = mol.Clone(); // make a copy of the mol
sli = FindStructure(mol, GetMruMoleculesList());
if (sli != null)
{
MruList.ItemList.Remove(sli);
}
sli = new MoleculeListItem();
sli.Name = molEditorCtl.GetTemporaryStructureTag(); // get any associated pre-edit mol name
sli.Molecule = mol;
sli.UpdateDate = DateTime.Now;
sli.MoleculeType = StructureSearchTypeUtil.StructureSearchTypeToExternalName(searchType);
MruList.ItemList.Insert(0, sli);
while (MruList.Count > MaxMruItems)
{
MruList.ItemList.RemoveAt(MaxMruItems - 1);
}
SaveStructureList(MruList, MruPreferencesParmName);
return;
}
object IInvokeServiceOps.InvokeServiceOperation(int opCode, object[] args)
{
MobiusCompoundUtilService op = (MobiusCompoundUtilService)opCode;
switch (op)
{
case MobiusCompoundUtilService.DoesCidExist:
{
string cid = (string)args[0];
string mtName = (string)args[1];
Mobius.Data.MetaTable mt = (mtName == null) ? null : Mobius.Data.MetaTableCollection.Get(mtName);
bool cidExists = Qel.CompoundIdUtil.Exists(cid, mt);
return(cidExists);
}
case MobiusCompoundUtilService.SelectMoleculeFromCid:
{
string cid = (string)args[0];
string mtName = (string)args[1];
Mobius.Data.MetaTable mt = (mtName == null) ? null : Mobius.Data.MetaTableCollection.Get(mtName);
Data.MoleculeMx nativeMolecule =
Qel.MoleculeUtil.SelectMoleculeForCid(cid, mt);
if (ClientState.MobiusClientVersionIsAtLeast(6, 0)) // Helm version or newer
{
byte[] ba = MobiusDataType.SerializeBinarySingle(nativeMolecule);
return(ba);
}
else
{
ChemicalStructure transferMolecule =
_transHelper.Convert <Mobius.Data.MoleculeMx, ChemicalStructure>(nativeMolecule);
return(transferMolecule);
}
}
case MobiusCompoundUtilService.SelectMoleculesForCidList:
{
List <string> cidList = (List <string>)args[0];
string mtName = (string)args[1];
Mobius.Data.MetaTable mt = (mtName == null) ? null : Mobius.Data.MetaTableCollection.Get(mtName);
Dictionary <string, Data.MoleculeMx> csDict =
Qel.MoleculeUtil.SelectMoleculesForCidList(cidList, mt);
return(csDict);
}
case MobiusCompoundUtilService.GetAllSaltForms:
{
string cid = (string)args[0];
string normalizedCid = Data.CompoundId.Normalize(cid);
List <string> cidList = new List <string>(new string[] { normalizedCid });
Dictionary <string, List <string> > cidDict = Qel.MoleculeUtil.GetAllSaltForms(cidList);
List <string> results = null;
if (cidDict.ContainsKey(cid))
{
results = cidDict[cid] as List <string>;
}
return(results);
}
case MobiusCompoundUtilService.GetAllSaltFormsForList:
{
List <string> cidList = (List <string>)args[0];
Dictionary <string, List <string> > allSaltIds = Qel.MoleculeUtil.GetAllSaltForms(cidList);
return(allSaltIds);
}
case MobiusCompoundUtilService.InsertSalts:
{
List <string> cidList = (List <string>)args[0];
List <string> result = Qel.MoleculeUtil.InsertSalts(cidList);
return(result);
}
case MobiusCompoundUtilService.GroupSalts:
{
List <string> cidList = (List <string>)args[0];
List <string> result = Qel.MoleculeUtil.GroupSalts(cidList);
return(result);
}
case MobiusCompoundUtilService.ValidateList:
{
string listText = (string)args[0];
string rootTableName = (string)args[1];
string result = Qel.CompoundIdUtil.ValidateList(listText, rootTableName);
return(result);
}
case MobiusCompoundUtilService.GetRelatedCompoundIds:
{
StructureSearchType searchTypes = // default for old client that doesn't supply this parm
StructureSearchType.FullStructure |
StructureSearchType.MolSim |
StructureSearchType.MatchedPairs |
StructureSearchType.SmallWorld;
int argIdx = 0;
string cid = (string)args[argIdx++];
string mtName = (string)args[argIdx++];
string chime = (string)args[argIdx++];
if (args.Length > 4)
{
searchTypes = (StructureSearchType)args[argIdx++];
}
int searchId = (int)args[argIdx++];
string result = Qel.MoleculeUtil.GetRelatedMatchCounts(cid, mtName, chime, searchTypes, searchId);
return(result);
}
case MobiusCompoundUtilService.GetRelatedStructures:
{
string cid = (string)args[0];
string mtName = (string)args[1];
string result = Qel.MoleculeUtil.GetRelatedMatchRowsSerialized(cid, mtName);
return(result);
}
case MobiusCompoundUtilService.ExecuteSmallWorldPreviewQuery:
{
string serializedQuery = (string)args[0];
object[] oa = Qel.MoleculeUtil.ExecuteSmallWorldPreviewQuerySerialized(serializedQuery);
return(oa);
}
}
return(null);
}
public static bool IsSSS(StructureSearchType searchTypes) => (searchTypes & StructureSearchType.Substructure) != 0;
public static bool IsSim(StructureSearchType searchTypes) => (searchTypes & StructureSearchType.MolSim) != 0;
public static bool IsSw(StructureSearchType searchTypes) => (searchTypes & StructureSearchType.SmallWorld) != 0;
public static bool IsMmp(StructureSearchType searchTypes) => (searchTypes & StructureSearchType.MatchedPairs) != 0;
public static bool IsFull(StructureSearchType searchTypes) => (searchTypes & StructureSearchType.FullStructure) != 0;
