/// <summary>
/// ShowFavoriteMoleculeMenu
/// </summary>
/// <param name="location"></param>
/// <param name="molEditorCtl"></param>
/// <param name="qc"></param>
public static void SelectFavoriteMolecule(
MoleculeControl molEditorCtl,
QueryColumn qc = null)
{
MoleculeSelectorControl i = new MoleculeSelectorControl();
i.MolEditorCtl = molEditorCtl;
i.Qc = qc;
i.SelectFavoriteMolecule();
}
public void SetupControl(
MoleculeMx molecule)
{
InSetup = true;
MoleculeControl.SetupAndRenderMolecule(molecule);
MolDisplayFormatEdit.Text =
molecule.PrimaryDisplayFormat == MoleculeRendererType.Helm ? "Biopolymer" : "Structure";
InSetup = false;
return;
}
/// <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>
/// Retrieve a saved molecule and store in Renditor
/// </summary>
/// <param name="ctl"></param>
public static void RetrieveSavedMolecule(MoleculeControl molCtl)
{
MoleculeMx cs;
string fileName = null;
if (!UIMisc.ReadMoleculeFileDialog(out cs, out fileName))
{
return;
}
molCtl.SetupAndRenderMolecule(cs);
molCtl.SetTemporaryMoleculeTag(Path.GetFileNameWithoutExtension(fileName)); // associate the file name in case saved as history/favorite
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;
}
/// <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>
/// ShowMruMoleculeMenu
/// </summary>
/// <param name="location"></param>
/// <param name="molEditorCtl"></param>
/// <param name="qc"></param>
public static void SelectMruMolecule(
MoleculeControl molEditorCtl,
QueryColumn qc = null)
{
MoleculeSelectorControl i = new MoleculeSelectorControl();
i.MolEditorCtl = molEditorCtl;
i.Qc = qc;
MoleculeList sl = GetMruMoleculesList();
i.Text = "Recent Query Structures";
//for (int i1 = 0; i1 < sl.Count; i1++) // rename to integers 1 to N
//{
// sl[i1].Name = (i1 + 1).ToString();
//}
i.StructureListControl.Setup(sl, i.ListItemSelectedCallback);
i.ShowDialog(SessionManager.ActiveForm);
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;
}
}
/// <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;
}
void Initialize2(
MRUEdit clc,
Form parentForm,
ContentsTreeControl contentsTree,
bool newPopup)
{
QuickSearchPopup qsp = this; // debug
//if (newPopup) // just created?
if (!Initialized)
{
Visible = false;
//Width = 236; // set proper size
//Height = 186;
Point p = clc.PointToScreen(new Point(0, clc.Bottom));
Point p2 = parentForm.PointToClient(p);
Left = p.X; // position below input control
Top = p.Y + clc.Height * 2;
BringToFront();
ContentsTree = contentsTree;
RelatedStructuresControl rsp = RelatedStructuresControl;
InitialStructurePanelWidth = StructurePanel.Width; //rsp.Width + 12; // initial StructurePanel width
InitialStructurePanelWidthWithoutRelatedStructureOptions = rsp.MoleculeControl.Right + 10;
//InitialStructurePanelWidth = 400; // debug
InitialStructurePanelHeight = rsp.Top + rsp.MoleculeControl.Height + 15; // initial StructurePanel height to just below structure box
StructurePanel.Dock = DockStyle.Fill;
OtherCidsList.Visible = false;
MoleculeControl strBox = RelatedStructuresControl.MoleculeControl; // make structure box wider to the left
int newBoxLeft = 4;
int dx = strBox.Left - newBoxLeft; // amount to widen structure box
int w2 = strBox.Width + dx;
int h2 = strBox.Height;
RSM = new RelatedStructureControlManager();
RelatedStructuresControl.RSM = RSM;
RSM.RSC = RelatedStructuresControl;
RSM.HideUndefinedStructureList = true; // don't show structure panel until after search complete
RelatedStructuresControl.RenderSearchResultsCompleteCallBack = RenderSearchResultsCompleteCallBack;
RelatedStructuresControl.SetupCheckmarks();
Initialized = true;
}
CommandLineControl = clc; // associated command line comtrol
clc.GotFocus += CommandLine_GotFocus;
clc.KeyDown += CommandLine_KeyDown; // add command line events for us
clc.KeyUp += CommandLine_KeyUp;
clc.PreviewKeyDown += CommandLine_PreviewKeyDown;
if (!Timer.Enabled)
{
Timer.Enabled = true;
PreviousInput = ""; // need to clear to get redisplay of structure
}
return;
}
/// <summary>
/// Add criteria to query to do a related structure search
/// </summary>
/// <param name="q"></param>
void ModifyQueryForRelatedStructureSearch(
Query q,
MoleculeControl queryMolCtl)
{
q.KeyCriteria = q.KeyCriteriaDisplay = ""; // always remove any existing key criteria
QueryTable sqt = AddStructureTableToQuery(q); // be sure we have a structure table in the query
QueryColumn sqc = sqt.FirstStructureQueryColumn;
sqc.Selected = true;
sqc.DisplayFormatString = "Highlight=true";
if (AlignMatches.Checked)
{
sqc.DisplayFormatString += ";Align=true";
}
QueryColumn qc = sqt.GetQueryColumnByName("molSrchType"); // include search type
if (qc != null)
{
qc.Selected = true;
}
qc = sqt.GetSimilarityScoreQueryColumn(); // and match score
if (qc != null)
{
qc.Selected = true;
}
ParsedStructureCriteria pssc = new ParsedStructureCriteria();
pssc.SearchType = StructureSearchType.Related;
//string mfText = sqt.KeyQueryColumn.ActiveLabel + ": " + queryCid; // (queryCid no longer be accurate)
//pssc.Structure = // just store a comment with the CID in the structure
// new ChemicalStructureMx(StructureFormat.MolFile, ChemicalStructureMx.GetTextMessageMolFile(mfText));
MoleculeMx m = QueryMolCtl.Molecule;
pssc.Molecule = new MoleculeMx(m.PrimaryFormat, m.PrimaryValue);
if (AltForms.Checked)
{
pssc.SearchTypeUnion |= StructureSearchType.FullStructure;
}
if (MatchedPairs.Checked)
{
pssc.SearchTypeUnion |= StructureSearchType.MatchedPairs;
}
if (SmallWorld.Checked)
{
pssc.SearchTypeUnion |= StructureSearchType.SmallWorld;
}
if (SimilarSearch.Checked)
{
pssc.SearchTypeUnion |= StructureSearchType.MolSim;
}
if (Substructure.Checked)
{
pssc.SearchTypeUnion |= StructureSearchType.Substructure;
}
pssc.MinimumSimilarity = .75;
pssc.MaxSimHits = 100;
pssc.Highlight = true;
pssc.Align = AlignMatches.Checked;
pssc.ConvertToQueryColumnCriteria(sqc);
if (ExcludeCurrentResultsCids.Checked && CurrentBaseQueryCidHitList != null) // add not in list criteria
{
string queryStrName = queryMolCtl.GetTemporaryStructureTag(); // see if we can get the cid
q.KeysToExclude = new HashSet <string>(CurrentBaseQueryCidHitList);
if (q.KeysToExclude.Contains(queryStrName)) // keep query id
{
q.KeysToExclude.Remove(queryStrName);
}
}
else
{
q.KeyCriteria = q.KeyCriteriaDisplay = ""; // no key criteria
}
return;
}