/// <summary>
/// New update the list of related compounds
/// </summary>
/// <param name="mt"></param>
/// <param name="cid"></param>
/// <param name="queryStruct"></param>
private void UpdateRelatedCidsDisplay(
MetaTable mt,
string cid,
MoleculeMx queryStruct,
int renderId)
{
bool useNew = ServicesIniFile.ReadBool("UseNewRelatedCompoundsPopup", true); // use new or old related compounds display
if (!useNew)
{
UpdateRelatedCidsDisplayOld(mt, cid, queryStruct);
return;
}
//if (!SS.I.AllowGroupingBySalts || // need this?
// Lex.Ne(MetaTable.DefaultRootTable, mt.Name))
//{
// this.Height = RelatedStructuresPanel.Top;
// return;
//}
if (SS.I.FindRelatedCpdsInQuickSearch)
{
RSM.StartSearchAndRetrievalOfRelatedStructures(mt.Name, cid, queryStruct, RelatedStructureBrowser.StructureSearchTypes);
}
return;
}
/// <summary>
/// Calculate Tanimoto similarity between two compounds
/// </summary>
/// <param name="fp1"></param>
/// <param name="rp2"></param>
/// <returns></returns>
double CalculateSimilarity(
CompoundStructureActivityData cd1,
CompoundStructureActivityData cd2)
{
int l1 = -1, l2 = -1;
if (cd1.BitsetFingerprint == null || cd2.BitsetFingerprint == null)
return 0;
if (Debug)
{
if ((cd1.Cid == "111" && cd2.Cid == "222") ||
(cd2.Cid == "222" && cd1.Cid == "111"))
{
DebugLog.Message("Before: " + cd1.Cid + ": " + String.Join(", ", CdkMolUtil.GetBitSet(cd1.BitsetFingerprint)));
DebugLog.Message("Before: " + cd2.Cid + ": " + String.Join(", ", CdkMolUtil.GetBitSet(cd2.BitsetFingerprint)));
}
}
double sim = MoleculeMx.CalculateBitSetFingerprintSimilarity(cd1.BitsetFingerprint, cd2.BitsetFingerprint);
if (Debug)
{
if ((cd1.Cid == "111" && cd2.Cid == "222") ||
(cd2.Cid == "222" && cd1.Cid == "111"))
{
DebugLog.Message(cd1.Cid + ": " + String.Join(", ", CdkMolUtil.GetBitSet(cd1.BitsetFingerprint)));
DebugLog.Message(cd2.Cid + ": " + String.Join(", ", CdkMolUtil.GetBitSet(cd2.BitsetFingerprint)));
DebugLog.Message(cd1.Cid + ", " + cd2.Cid + " Similarity: " + sim);
}
}
return sim;
}
/// <summary>
/// SetStereoChemistryComments in structure object
/// </summary>
/// <param name="cs"></param>
/// <param name="comments"></param>
/// <param name="cid"></param>
public static void SetStereochemistryComments(
MoleculeMx cs,
string comments,
string cid)
{
if (Lex.IsUndefined(comments) || !ShowStereoComments)
{
return;
}
if (!ClientState.IsNativeSession)
{
return; // don't include if not native session (i.e regular Mobius Client)
}
cs.SetMolComments("CorpId=" + cid); // indicate this is an CorpId
if (cs.PrimaryFormat == MoleculeFormat.Unknown)
{ // be sure defined
cs.SetPrimaryTypeAndValue(MoleculeFormat.Chime, "");
}
try { cs.CreateStructureCaption(comments); }
catch (Exception ex)
{ DebugLog.Message("CreateStructureCaption exception for compound: " + cid); } // issue #216
return;
}
/// <summary>
/// Display the structure and other basic data for the supplied cid
/// </summary>
/// <param name="cidArg"></param>
void DisplayCidData(string cidArg)
{
MoleculeMx str = null;
string mwTxt = "", mfTxt = "", haTxt = "", tok;
string intCid = CompoundId.Normalize(cidArg, RootTable);
string extCid = CompoundId.Format(intCid, RootTable);
CidCtl.Text = extCid;
if (RootTable == null || RootTable.KeyMetaColumn.DataType == MetaColumnType.CompoundId)
{
str = MoleculeUtil.SelectMoleculeForCid(intCid, RootTable);
}
if (Lex.IsDefined(str?.PrimaryValue)) // have a structure with at least one atom
{
if (str.PrimaryDisplayFormat == MoleculeRendererType.Chemistry)
{
int ha = str.HeavyAtomCount;
if (ha > 0)
{
haTxt = ha.ToString();
}
double mw = str.MolWeight;
if (mw >= 0)
{
mwTxt = String.Format("{0:f3}", mw);
}
HeavyAtoms.Text = "";
Weight.Text = mwTxt;
string mf = str.MolFormula;
HeavyAtoms.Text = "";
Formula.Text = mf;
}
else
{
} // biopolymer, don't calc structure props (too slow for now)
HeavyAtoms.Text = haTxt;
Weight.Text = mwTxt;
Formula.Text = mfTxt;
MolCtl.Molecule = str;
return;
}
else // no structure
{
HeavyAtoms.Text = "";
Weight.Text = "";
Formula.Text = "";
MolCtl.ClearMolecule();
return;
}
}
/// <summary>
/// Format structure for output to SDFile
/// </summary>
/// <param name="molid"></param>
void FormatSdfileStructure(
MoleculeMx cs)
{
string molFile, cid;
if (SS.I.RemoveLeadingZerosFromCids) // normal formatting
{
cid = CompoundId.Format(CurrentKey);
}
else
{
cid = CurrentKey; // just use internal formatting
}
cs = cs.Convert(Rf.StructureFlags | MoleculeTransformationFlags.RemoveStructureCaption, cid);
molFile = cs.GetMolfileString();
if (molFile.IndexOf("\r") < 0) // add carriage returns to molfile if it doesn't contain them
{
molFile = molFile.Replace("\n", "\r\n");
}
SdfLine = molFile;
return;
}
/// <summary>
/// Update the list of related compounds
/// </summary>
/// <param name="mt"></param>
/// <param name="cid"></param>
/// <param name="str"></param>
private void UpdateRelatedCidsDisplayOld(
MetaTable mt,
string cid,
MoleculeMx str)
{
if (SS.I.AllowGroupingBySalts) // build list of salts & send
{
List <string> salts = MoleculeUtil.GetAllSaltForms(Cid);
if (salts == null || salts.Count == 0) // nothing related
{
OtherCidsList.Visible = false; // hide list
}
else
{
OtherCidsList.Properties.Items.Clear();
foreach (string s in salts)
{
string extCid = CompoundId.Format(s);
OtherCidsList.Properties.Items.Add(extCid);
}
string listHeader = salts.Count.ToString() + " Other Match";
if (salts.Count > 1)
{
listHeader += "es"; // use proper grammar
}
OtherCidsList.Text = listHeader; // select first item
OtherCidsList.Visible = true;
}
}
else
{
OtherCidsList.Visible = false; // hide list
}
}
/// <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;
}
public void Setup(ColumnInfo colInfo)
{
bool check;
InSetup = true;
ColInfo = colInfo; // save ref to colInfo
ParsedSingleCriteria psc = MqlUtil.ParseSingleCriteria(ColInfo.Qc.SecondaryCriteria); // parse criteria
if (psc == null)
{
StructureRenditor.MolfileString = "";
}
else
{
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Chime, psc.Value);
MoleculeMx.SetRendererStructure(StructureRenditor, cs);
}
Timer.Enabled = true;
StructureChanged = false;
InSetup = false;
return;
}
private void Timer1_Tick(object sender, EventArgs e)
{
if (ServiceFacade.ServiceFacade.InServiceCall)
{
return; // avoid multiplexing service calls that could cause problems
}
if (InTimer_Tick)
{
return;
}
InTimer_Tick = true;
string currentCid = CidCtl.Text;
if (currentCid == PreviousCid)
{
InTimer_Tick = false;
return;
}
PreviousCid = currentCid;
string cid = CompoundId.Normalize(currentCid, MetaTable);
MetaTable mt = CompoundId.GetRootMetaTableFromCid(cid, MetaTable);
MoleculeMx mol = MoleculeUtil.SelectMoleculeForCid(cid, mt);
QuickStructure.SetupAndRenderMolecule(mol);
InTimer_Tick = false;
return;
}
/// <summary>
/// Get substituent for a decomposition rgroup & map position & store in list
/// </summary>
/// <param name="rSub">Substituent structure</param>
/// <param name="rSubs">List of substituents so far</param>
/// <returns>Index of the substituent in rSubs</returns>
public static int Get(
MoleculeMx rSub,
List <RgroupSubstituent> rSubs)
{
double mw = rSub.MolWeight;
int si;
for (si = 0; si < rSubs.Count; si++)
{ // see if we've seen this substituent
if (mw != rSubs[si].Mw)
{
continue; // quick compare on mol weight first
}
if (matcher == null)
{
matcher = new StructureMatcher();
}
if (matcher.Equal(rSub, rSubs[si].Struct))
{
break;
}
}
if (si >= rSubs.Count)
{ // add new item
RgroupSubstituent rgs = new RgroupSubstituent();
rgs.Mw = mw;
rgs.Struct = rSub;
rSubs.Add(rgs);
}
return(si);
}
private void Timer_Tick(object sender, EventArgs e)
{
if (!StructureChanged)
{
return;
}
QueryColumn qc = ColInfo.Qc;
if (String.IsNullOrEmpty(StructureRenditor.MolfileString))
{
qc.SecondaryCriteria = qc.SecondaryCriteriaDisplay = "";
}
else
{
// Chime: CYAAFQwAncwQGj8h7GZ^yjgsajoFd0PQ1OYrnIdaPTl0lGnQYLHH2prJeJi$BhUHcMsE1TyQisJflsW2r293v92iC1^wVm$8wwLM7^krIFa8A1X6Jvu8VIYgCgJ8$y1RuqgCc5ifKbMAflB
string chimeString = MoleculeMx.MolfileStringToChimeString(StructureRenditor.MolfileString);
qc.SecondaryCriteria = "SSS ( " + qc.MetaColumn.Name + ", " + Lex.AddSingleQuotes(chimeString) + ") = 1";
qc.SecondaryCriteriaDisplay = qc.ActiveLabel + " contains substructure";
}
qc.SecondaryFilterType = FilterType.StructureSearch;
QueryManager.QueryResultsControl.UpdateFiltering(ColInfo);
FilterBasicCriteriaControl.SyncBaseQuerySecondaryCriteria(qc); // sync any base query
StructureChanged = false;
return;
}
public List <StructSearchMatch> ExecuteSearch(
MoleculeMx queryMolMx)
{
CdkMol m2 = (CdkMol)queryMolMx.CdkMol;
IAtomContainer queryMol = m2.NativeMol;
return(ExecuteSearch(queryMol));
}
/// <summary>
/// Select a MoleculeMx object for a compound id
/// </summary>
/// <param name="cid"></param>
/// <param name="mt"></param>
/// <returns></returns>
public static MoleculeMx SelectMoleculeForCid(
string cid,
MetaTable mt = null)
{
MoleculeMx mol = null;
Stopwatch sw = Stopwatch.StartNew();
mol = MoleculeCache.Get(cid); // see if molecule in cache
if (mol != null)
{
return(mol);
}
if (ServiceFacade.UseRemoteServices)
{
string mtName = mt?.Name;
Mobius.Services.Native.INativeSession nativeClient = ServiceFacade.CreateNativeSessionProxy();
Services.Native.NativeMethodTransportObject resultObject =
ServiceFacade.InvokeNativeMethod(nativeClient,
(int)Services.Native.ServiceCodes.MobiusCompoundUtilService,
(int)Services.Native.ServiceOpCodes.MobiusCompoundUtilService.SelectMoleculeFromCid,
new Services.Native.NativeMethodTransportObject(new object[] { cid, mtName })); // , setStereoChemistryComments
((System.ServiceModel.IClientChannel)nativeClient).Close();
if (resultObject == null)
{
return(null);
}
byte[] ba = resultObject.Value as byte[];
if (ba != null && ba.Length > 0)
{
MobiusDataType mdt = MobiusDataType.DeserializeBinarySingle(ba);
mol = mdt as MoleculeMx;
}
}
else
{
mol = QEL.MoleculeUtil.SelectMoleculeForCid(cid, mt);
}
if (MoleculeMx.IsDefined(mol))
{
bool isUcdb = (mt != null && mt.Root.IsUserDatabaseStructureTable); // user compound database
if (!isUcdb)
{
MoleculeCache.AddMolecule(cid, mol); // add to cache
}
}
long ms = sw.ElapsedMilliseconds;
return(mol);
}
// public static string CTabToCharExpression = // expression to convert a ctab into a Oracle char type. Returns 'Large Structure' if too big & handle at retrieve time
// "case when length(chime(ctab)) <= 4000 then to_char(chime(ctab)) else 'Large Structure' end";
// public static string LargeStructureString = "Large Structure"; // string that indicates that chime for structure is > 4000 chars
// Examples: 3203030, 3020939, 3020943, 3046095, 2240877, 2312187, 2836746
/// <summary>
/// Convert an objectinto a ChemicalStructure object
/// </summary>
/// <param name="fieldValue"></param>
/// <returns></returns>
public static MoleculeMx ConvertObjectToChemicalStructure(
object fieldValue)
{
MoleculeMx cs;
MoleculeFormat structureFormat;
string txt;
if (fieldValue == null)
{
cs = null;
}
else if (fieldValue is MoleculeMx)
{
cs = (MoleculeMx)fieldValue;
}
else if (fieldValue is string || fieldValue is CompoundId || fieldValue is QualifiedNumber)
{
if (fieldValue is string)
{
txt = (string)fieldValue;
}
else if (fieldValue is CompoundId)
{
txt = ((CompoundId)fieldValue).Value;
}
else
{
txt = ((QualifiedNumber)fieldValue).TextValue;
}
structureFormat = MoleculeMx.GetMoleculeFormatType(txt);
if (structureFormat != MoleculeFormat.Unknown) // just convert is known format
{
cs = MoleculeMx.MolStringToMoleculeMx(txt);
}
else // see if unqualified compound id
{
cs = MoleculeUtil.SelectMoleculeForCid(txt);
}
}
else
{
throw new Exception("Object is not a recognized structure format");
}
return(cs);
}
/// <summary>
/// Insert molecule into Excel table cell
/// </summary>
/// <param name="cs"></param>
/// <param name="row"></param>
/// <param name="col"></param>
public static void SetCellMolecule(
int row,
int col,
MoleculeMx cs)
{
if (IsInsightForExcelAvailable)
{
SetInsightForExcelMolecule(row, col, cs);
}
return;
}
public void SetupControl(
MoleculeMx molecule)
{
InSetup = true;
MoleculeControl.SetupAndRenderMolecule(molecule);
MolDisplayFormatEdit.Text =
molecule.PrimaryDisplayFormat == MoleculeRendererType.Helm ? "Biopolymer" : "Structure";
InSetup = false;
return;
}
/// <summary>
/// Fix HCl etc groups for proper left side H display
/// </summary>
/// <param name="skid"></param>
/// <returns></returns>
public static int FixSingleAtomHydrogens(
MoleculeMx cs)
{
int atmcnt, ai, oldmode, fixcnt, atype, i1, i2, i3;
string fontname;
int size, emphasis;
double x = 0, y = 0, z = 0;
int aid, na, nb, sgrp;
long t1, t2;
string lp;
return(0);
}
/// <summary>
/// Do generic display of a structure
/// </summary>
/// <param name="title"></param>
/// <param name="cidLabel"></param>
/// <param name="structLabel"></param>
/// <param name="structure"></param>
public static void DisplayStructure(
string title,
string cidLabel,
string structLabel,
MoleculeMx structure,
MoleculeGridPanel gridPanel,
bool embedDataInQuery)
{
List <MoleculeMx> structures = new List <MoleculeMx>();
structures.Add(structure);
DisplayStructures(title, cidLabel, structLabel, structures, gridPanel, embedDataInQuery);
return;
}
// # Get list of bits where at least one must be in result fp. Use least popular bits if possible.
// if db.mfp_counts:
// reqbits = [count['_id'] for count in db.mfp_counts.find({'_id': {'$in': qfp
// }
//}).sort('count', 1).limit(ncommon)]
// else:
// reqbits = qfp[:ncommon]
// results = []
// for fp in db.molecules.find({'mfp.bits': {'$in': reqbits}, 'mfp.count': {'$gte': qmin, '$lte': qmax}}):
// intersection = len(set(qfp) & set(fp['mfp']['bits']))
// pn = fp['mfp']['count']
// tanimoto = float(intersection) / (pn + qn - intersection)
// if tanimoto >= threshold:
// results.append((tanimoto, fp['chembl_id'], fp['smiles']))
// return results
/// <summary>
/// Test to calculate similarity between pairs of structures (Alt syntax: Call SimSearchMx.Test [cid1] [cid2]
/// Tautomers:
/// Isotopes:
/// Neg Counterion, (Cl-) with 2 quatternary N+ with H attached in main frag:
/// Neg Counterion, (I-) with quatternary N+ (no attached H) in main frag:
/// Pos Counterion (Li+) with O- in main frag:
/// Benzene, cyclohexane:
/// StereoIsomers:
/// StereoIsomers:
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
public static string Test(string args)
{
string[] sa = args.Split(' ');
string cid1 = CompoundId.Normalize(sa[0]);
string cid2 = CompoundId.Normalize(sa[1]);
int smiLen = 40;
MoleculeMx s1 = MoleculeMx.SelectMoleculeForCid(cid1);
IAtomContainer mol = CdkMol.MolfileToAtomContainer(s1.GetMolfileString());
UniChemData ucd1 = UniChemUtil.BuildUniChemData(mol);
List <FingerprintMx> fps1 = UniChemDataToFingerprintMxList(ucd1);
MoleculeMx s2 = MoleculeMx.SelectMoleculeForCid(cid2);
IAtomContainer mol2 = CdkMol.MolfileToAtomContainer(s2.GetMolfileString());
UniChemData ucd2 = UniChemUtil.BuildUniChemData(mol2);
List <FingerprintMx> fps2 = UniChemDataToFingerprintMxList(ucd2);
string fps2Smiles = (sa[0] + " / " + sa[1]).PadRight(smiLen);
string scores = "";
for (int i1 = 0; i1 < fps1.Count; i1++)
{
FingerprintMx fp1 = fps1[i1];
for (int i2 = 0; i2 < fps2.Count; i2++)
{
FingerprintMx fp2 = fps2[i2];
if (i1 == 0) // build smiles headers of cid2 frags if first cid1 frag
{
fps2Smiles += "\t" + fp2.CanonSmiles.PadRight(smiLen);
}
if (i2 == 0)
{
scores += "\r\n" + fp1.CanonSmiles.PadRight(smiLen); // include smiles at start of each line
}
float simScore = CalculateFingerprintPairSimilarityScore(fp1, fp2);
scores += "\t" + string.Format("{0:0.00}", simScore).PadRight(smiLen);
}
}
scores = fps2Smiles + scores;
FileUtil.WriteAndOpenTextDocument("SimilarityScores", scores);
return("");
}
/// <summary>
/// DisplayStructureInPopupGrid
/// </summary>
/// <param name="title"></param>
/// <param name="cidLabel"></param>
/// <param name="structLabel"></param>
/// <param name="structure"></param>
public static void DisplayStructureInPopupGrid(
string title,
string cidLabel,
string structLabel,
MoleculeMx structure)
{
List <MoleculeMx> structures = new List <MoleculeMx>();
structures.Add(structure);
PopupGrid pg = new PopupGrid();
bool embedDataInQuery = false;
DisplayStructures(title, cidLabel, structLabel, structures, pg.MoleculeGridPanel, embedDataInQuery);
return;
}
/// <summary>
/// Modal edit of molecule
/// </summary>
public static MoleculeMx Edit(
MoleculeMx mol,
MoleculeRendererType editorType = MoleculeRendererType.Unknown,
string title = "")
{
MoleculeMx mol2 = null;
try
{
if (editorType == MoleculeRendererType.Unknown) // need to assign editor type?
{
if (mol.IsChemStructureFormat)
{
editorType = MoleculeRendererType.Chemistry;
}
else if (mol.IsBiopolymerFormat)
{
editorType = MoleculeRendererType.Helm;
}
else
{
editorType = MoleculeRendererType.Chemistry; // final default
}
}
bool useChemEditor = (editorType != MoleculeRendererType.Helm);
if (useChemEditor)
{
mol2 = mol.ConvertTo(MoleculeFormat.Molfile);
return(EditCdkMolMolecule(mol2, title));
}
else // use Helm editor
{
return(EditHelmMolecule(mol, title));
}
}
catch (Exception ex)
{
XtraMessageBox.Show(ex.Message, "Error editing molecule");
return(null);
}
}
/// <summary>
/// Copy the structure associated with the specified compound id to the clipboard
/// </summary>
/// <param name="cn"></param>
/// <param name="mt"></param>
/// <returns></returns>
public static bool CopyCompoundIdStructureToClipBoard(
string cn,
MetaTable mt)
{
MoleculeMx mol = MoleculeUtil.SelectMoleculeForCid(cn, mt);
if (mol != null)
{
MoleculeControl.CopyMoleculeToClipboard(mol);
return(true);
}
else
{
MessageBoxMx.Show("Unable to retrieve structure");
return(false);
}
}
/// <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;
}
private void ViewMoleculeInNewWindowMenuItem_Click(object sender, EventArgs e)
{
int gri = MoleculeGrid.LastMouseDownRowIdx;
if (gri < 0 || gri >= StructureList.Count)
{
return;
}
MoleculeListItem sli = StructureList[gri];
if (!MoleculeMx.IsDefined(sli.Molecule))
{
return;
}
MoleculeViewer.ShowMolecule(sli.Molecule);
return;
}
void ListItemSelectedCallback(MoleculeListItem sli)
{
if (MolEditorCtl == null)
{
return;
}
if (sli == null)
{
DialogResult = DialogResult.Cancel;
return;
}
MoleculeMx mol = sli.Molecule;
MolEditorCtl.SetPrimaryTypeAndValue(mol.PrimaryFormat, mol.PrimaryValue);
MolEditorCtl.TagString = sli.Name + "\t" + sli.Molecule.PrimaryValue; // store name to use if molecule is unchanged
DialogResult = DialogResult.OK;
}
/// <summary>
/// EditHelmMolecule
/// </summary>
/// <param name="title"></param>
/// <param name="mol"></param>
/// <returns></returns>
public static MoleculeMx EditHelmMolecule(
MoleculeMx mol,
string title = "")
{
MoleculeMx mol2 = mol.ConvertTo(MoleculeFormat.Helm);
string helm = mol2.HelmString;
HelmEditorDialog editor = new HelmEditorDialog();
string newHelm = editor.Edit(helm);
if (newHelm == null)
{
return(null);
}
mol2.SetPrimaryTypeAndValue(MoleculeFormat.Helm, newHelm);
return(mol2);
}
/// <summary>
/// Edit Molecule
/// </summary>
/// <param name="title"></param>
/// <param name="mol"></param>
/// <returns></returns>
public static MoleculeMx EditCdkMolMolecule(
MoleculeMx mol,
string title = "")
{
MoleculeMx mol2 = null;
MoleculeFormat molFormat;
string molString;
try
{
Instance.MoleculeCtl.Molecule = mol;
INativeMolControl molCtl = (INativeMolControl)Instance.MoleculeCtl.KekuleControl;
molCtl.EditorReturnedHandler = new MolEditorReturnedHandler(Instance.MolLibEditorReturned);
Instance.Text = title;
//molCtl.RenditorName = title; // shows as tooltip on editor Done button
Instance.MoleculeCtl.InSetup = true;
MoleculeMx.SetRendererStructure(molCtl, mol);
Instance.MoleculeCtl.InSetup = false;
Instance.MoleculeChanged = false;
DialogResult dr = // Show the form. The shown event invokes Draw & the dialog is ended when drawing is done
Instance.ShowDialog(SessionManager.ActiveForm);
if (dr != DialogResult.OK)
{
return(null);
}
molCtl.GetMolecule(out molFormat, out molString);
mol2 = new MoleculeMx(molFormat, molString);
return(mol2);
}
catch (Exception ex)
{
XtraMessageBox.Show(ex.Message, "Error editing structure");
Instance.MoleculeCtl.InSetup = false;
return(null);
}
}
/// <summary>
/// Do Generic display of a list of structures
/// </summary>
/// <param name="title"></param>
/// <param name="cidLabel"></param>
/// <param name="structLabel"></param>
/// <param name="structures"></param>
public static void DisplayStructures(
string title,
string cidLabel,
string structLabel,
List <MoleculeMx> structures,
MoleculeGridPanel gridPanel,
bool embedDataInQuery)
{
QueryManager qm = null;
MetaTable mt = MetaTableCollection.GetWithException("Generic_Structure_Table");
mt.MetaBrokerType = MetaBrokerType.NoSql;
Query q = ToolHelper.InitEmbeddedDataToolQuery(mt);
QueryTable qt = q.Tables[0];
qt.Label = title;
qt.GetQueryColumnByName("CompoundId").Label = cidLabel;
qt.GetQueryColumnByName("Structure").Label = structLabel;
DataTableMx dt = q.ResultsDataTable as DataTableMx;
for (int mi = 0; mi < structures.Count; mi++)
{
MoleculeMx cs = structures[mi];
DataRowMx dr = dt.NewRow();
string cid = cs.Id;
if (Lex.IsUndefined(cid))
{
cid = (mi + 1).ToString();
}
dr[qt.Alias + ".CompoundId"] = new CompoundId(cid);
dr[qt.Alias + ".Structure"] = cs;
dt.Rows.Add(dr);
}
DisplayData(q, dt, gridPanel, embedDataInQuery);
return;
}
private void DelayedEditMolecule(object arg)
{
try
{
int ci = (int)arg;
string txt = Criteria.Text.Substring(ci + 16); // pick up structure name
int i1 = txt.IndexOf("]");
if (i1 < 0)
{
return;
}
string sid = txt.Substring(0, i1).Trim().ToUpper();
string chime = "";
if (LabeledCriteria.Structures.ContainsKey(sid))
{
chime = LabeledCriteria.Structures[sid];
}
MoleculeMx mol = new MoleculeMx(MoleculeFormat.Chime, chime);
MoleculeMx mol2 = MoleculeEditor.Edit(mol, MoleculeRendererType.Unknown, "Edit Structure");
if (mol2 == null)
{
return;
}
if (mol2.IsChemStructureFormat) // store chime for chem structure
{
mol2.ConvertTo(MoleculeFormat.Chime);
}
LabeledCriteria.Structures[sid] = mol2.GetPrimaryTypeAndValueString();
return;
}
catch (Exception ex)
{
return;
}
}
/// <summary>
/// Retrieve an existing molecule and store in MoleculeControl
/// </summary>
/// <param name="molCtl"></param>
/// <param name="mc"></param>
public static void RetrieveDatabaseStructure(
MoleculeControl molCtl,
MetaColumn mc)
{
MetaTable mt = null;
string cid = "", txt;
txt = "compound id";
if (mc != null)
{
mt = mc.MetaTable;
txt += " (" + mt.KeyMetaColumn.Label + ", etc.)";
}
txt = "Enter the " + txt + " that you want to use as a model.";
while (true)
{
cid = InputCompoundId.Show(txt, "Retrieve Molecule from Database", cid, mt);
if (String.IsNullOrEmpty(cid))
{
return;
}
string molString = InputCompoundId.Molecule.PrimaryValue;
if (String.IsNullOrEmpty(molString))
{
MessageBoxMx.ShowError("Compound number is not in the database, try again.");
continue;
}
MoleculeMx cs = InputCompoundId.Molecule;
cs.RemoveStructureCaption(); // remove any caption
molCtl.SetPrimaryTypeAndValue(cs.PrimaryFormat, cs.PrimaryValue); // set mol
molCtl.SetTemporaryMoleculeTag(cid); // associate the cid in case saved as history/favorite
break;
}
}
