private void InsertScriptButton_Click(object sender, EventArgs e)
{
string fileName = @"<MiscConfigDir>\MobiusSpotfireApi.IronPythonScript.txt";
string script = new ServerFile().ReadAll(fileName);
string args = "";
Api.ConfigureAnalysisForMobiusUse(args);
Clipboard.SetText(script); // put script on clipboard
string msg =
@"The necessary Document Properties have been created.
You must manually create a script named MobiusSpotfireApi, insert the
text currently on the clipboard into the script and save it.
Then, associate this script with the MobiusSpotfireApiCall so that the script
is called whenever the the property is changed.
Finally, save the analysis to the Spotfire Libary. You can then add this Spotfire
analysis to any Mobius query from the Query Results page using the
Add View > Select Spotfire analysis from library command.";
MessageBoxMx.Show(msg);
return;
}
private bool GetPersonalMoeExecutableLocation(string mxp)
{
string moeArgs, newCl = "";
while (true) // loop til we get a valid executable name or cancelled
{
if (mxp != null)
{
string msg =
"Unable to find MOE executable:\r\n\r\n" +
" " + mxp + "\r\n\r\n" +
"Would you like to define a new location for the MOE executable?";
DialogResult dr = MessageBoxMx.Show(msg, "Can't Find MOE", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Exclamation);
if (dr != System.Windows.Forms.DialogResult.Yes)
{
return(false);
}
}
string cl = Preferences.Get("MoeCommandLine"); // get any personal preference first
string txt =
"Enter your preferred \"non-standard\" personal location for MOE executable file.\r\n" +
"For example, the Target field from the MOE Desktop shortcut.\r\n" +
"To use the system default executable set the value to blank.";
newCl = InputBoxMx.Show(txt, "Set location of MOE executable file", cl);
if (newCl == null)
{
return(false); // cancelled
}
else if (newCl.Trim() == "")
{
break; // use system default
}
else
{
ParseMoeCommandLine(newCl, out mxp, out moeArgs);
if (File.Exists(mxp))
{
break;
}
}
}
Preferences.Set("MoeCommandLine", newCl);
return(true);
}
private void OKButton_Click(object sender, EventArgs e)
{
if (ExportToFile.Checked)
{
if (ExportSingle.Checked)
{
string fileName = FileName.Text;
if (Directory.Exists(fileName))
{
MessageBoxMx.Show("\"" + fileName + "\" appears to be a folder name rather than a file name", "Mobius",
MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
FileName.Focus();
return;
}
string fullFileName = UIMisc.CheckFileName(2, FileName, _lastValidatedFileName, ClientDirs.DefaultMobiusUserDocumentsFolder, ".pdb");
if (fullFileName == "")
{
return;
}
FileName.Text = fullFileName;
}
else
{
string folder = FileName.Text;
if (String.IsNullOrEmpty(folder))
{
folder = ClientDirs.DefaultMobiusUserDocumentsFolder;
}
folder = Path.GetDirectoryName(folder);
if (!Directory.Exists(folder))
{
MessageBoxMx.Show("Folder does not exist: " + folder, "Mobius",
MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
FileName.Focus();
return;
}
}
}
DialogResult = DialogResult.OK;
//UIMisc.BringActiveFormToFront(); // after showdialog be sure active form is on top
}
/// <summary>
/// If the user selected a field from a non-summarized table, give them the option to replace it with the field from the
/// summarized table (if available). Performance is better. This will also avoid extra rows as well as a cartesian product.
/// </summary>
private void CheckForSummarizedVersionOfMetaColumn()
{
return;
#if false // disabled for now
if (SelectedColumn == null || SelectedColumn.QueryColumn == null)
{
return;
}
QueryColumn qc = SelectedColumn.QueryColumn;
MetaColumn mc = qc.MetaColumn;
MetaTable mt = mc.MetaTable;
QueryTable qt = new QueryTable(mt);
bool unsummarrizedVersionSelected = (!mt.UseSummarizedData && mt.SummarizedExists);
if (!unsummarrizedVersionSelected)
{
return;
}
QueryTable summarizedQt = qt.AdjustSummarizationLevel(useSummarized: true);
QueryColumn summarizedQc = summarizedQt.GetQueryColumnByName(qc.ActiveLabel);
if (summarizedQc == null)
{
return;
}
string msg =
"You have selected the un-summarized version of " + qc.ActiveLabel + ".\n" +
"Using the summarized version will result in better performance and avoid unwanted extra rows.\n" +
"It is recommended that the summarized version be used for calculated fields.\n\n" +
"Would you like to use the summarized version instead?\n";
DialogResult dialogResult = MessageBoxMx.Show(msg, "Summarized Data Available!", MessageBoxButtons.YesNo, MessageBoxIcon.Question);
if (dialogResult == DialogResult.Yes)
{
SelectedColumn = null //summarizedQc.MetaColumn;
return;
}
#endif
}
/// <summary>
/// OK clicked - Update the query in the query builder and run if a new query
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void OK_Click(object sender, EventArgs e)
{
string title = "";
KeyQc = KeyCriteriaCtl.QueryColumn;
if (Lex.IsUndefined(KeyQc?.Criteria))
{
MessageBoxMx.Show("You must supply one or more compound ids.", UmlautMobius.String);
KeyCriteriaCtl.Cids.Focus();
return;
}
//TargetSummaryOptions tso = Tso; // copy to force update of Query fields
//if (!KeyCriteriaCtl.GetFormValues(tso)) return;
//Tso = tso;
//TargetSummaryOptionsControl.SavePreferences(Tso);
BuildQuery("");
if (!QueryRendered)
{
QueryCount++;
Query.UserObject.Name = "Summarized Target Results Analysis " + QueryCount;
QbUtil.AddQueryAndRender(Query, false); // add query if necessary
QueryRendered = true;
}
else
{
//QbUtil.NewQuery(Query.UserObject.Name); // show in query builder
//QbUtil.SetCurrentQueryInstance(Query);
QueryTable qt = GetUnpivotedSummaryTable(Query);
QbUtil.RenderQuery(qt);
}
DialogResult = DialogResult.OK;
return;
}
/// <summary>
/// Search button clicked, process input
/// </summary>
/// <returns></returns>
DialogResult ProcessInput()
{
CidList cidList = null;
StreamReader structureFileReader = null;
string qid; // query identifier, compoundId, file name or sdFile key value
QueryManager qm;
DataTableMx dt;
DataColumn dc;
DataRowMx dr;
//object[] dr; // if using Qe
DialogResult dlgRslt = DialogResult.OK;
Query q = null;
QueryTable qt = null;
QueryColumn simScoreQc, structQc; // query column containing latest query settings
MetaTable mt = null;
MetaColumn keyMc = null, structMc = null, dbSetMc = null, simScoreMc = null, mc;
MetaColumnType storageType;
string txt, tok;
if (DatabasesToSearch.Text == "")
{
MessageBoxMx.ShowError("Databases to search must be defined.");
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
// Get list of databases
string[] dba = DatabasesToSearch.Text.Split(',');
List <MetaTable> tables = new List <MetaTable>();
foreach (string dbLabel0 in dba)
{
string dbLabel = dbLabel0.Trim();
RootTable dbInfo = RootTable.GetFromTableLabel(dbLabel);
if (dbInfo == null)
{
MessageBoxMx.ShowError("Can't find database " + DatabasesToSearch.Text);
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
mt = MetaTableCollection.Get(dbInfo.MetaTableName);
if (mt == null)
{
MessageBoxMx.ShowError("Unable to locate parent structure table for database: " + DatabasesToSearch.Text);
DatabasesToSearch.Focus();
return(DialogResult.Cancel);
}
if (dbSetMc == null)
{
dbSetMc = mt.DatabaseListMetaColumn;
}
tables.Add(mt);
}
if (dbSetMc == null)
{
throw new Exception("\"Databases\" metacolumn not found for any of the databases to search");
}
// Validate other form values
RetrieveStructures = RetrieveMatchingStructures.Checked;
bool fromList = FromList.Checked;
int listCidsRead = 0;
int inputQueryCount = -1;
if (fromList) // using list, validate list name
{
if (SavedListUo == null)
{
MessageBoxMx.ShowError("Compound list must be defined.");
ListName.Focus();
return(DialogResult.Cancel);
}
cidList = CidListCommand.Read(SavedListUo);
if (cidList == null)
{
MessageBoxMx.ShowError("Error reading list.");
ListName.Focus();
return(DialogResult.Cancel);
}
inputQueryCount = cidList.Count;
}
else // Using SdFile, validate SdFile name
{
StructureFile = FileName.Text;
if (StructureFile == "")
{
MessageBoxMx.ShowError("File must be defined.");
FileName.Focus();
return(DialogResult.Cancel);
}
try { structureFileReader = new StreamReader(StructureFile); structureFileReader.Close(); }
catch (Exception ex)
{
MessageBoxMx.ShowError("Can't read file: " + Lex.Dq(StructureFile));
FileName.Focus();
return(DialogResult.Cancel);
}
keyField = KeyField.Text; // get key, blank to use name in 1st line
inputQueryCount = -1; // don't know how many queries unless we read the file (todo?)
}
tok = ResultsName.Text.Trim(); // name to store results under
if (tok == "")
{
MessageBoxMx.ShowError("A name for the results must be provided.");
ResultsName.Focus();
return(DialogResult.Cancel);
}
if (SubStruct.Checked)
{
Psc.SearchType = StructureSearchType.Substructure;
}
else if (Full.Checked)
{
Psc.SearchType = StructureSearchType.FullStructure;
}
else if (Similarity.Checked)
{
Psc.SearchType = StructureSearchType.MolSim;
}
else
{
throw new Exception("Unrecognized search type");
}
// Write initial log entries
SearchCount++;
string logFileName = ClientDirs.DefaultMobiusUserDocumentsFolder + @"\Multistructure Search " + SearchCount + ".txt";
if (!UIMisc.CanWriteFileToDefaultDir(logFileName))
{
return(DialogResult.Cancel);
}
LogStream = new StreamWriter(logFileName);
if (ResultsUo == null)
{
ResultsUo = new UserObject(UserObjectType.Annotation);
}
ResultsUo.Name = tok;
UserObjectTree.GetValidUserObjectTypeFolder(ResultsUo);
DateTime startTime = DateTime.Now;
WriteToLog("Multiple " + Psc.SearchType + " Search");
WriteToLog("Databases: " + DatabasesToSearch.Text);
WriteToLog("Date: " + startTime);
if (fromList)
{
WriteToLog("Input List: " + SavedListUo.Name);
}
else
{
WriteToLog("Input Structure File: " + StructureFile);
}
WriteToLog("Output List: " + ResultsUo.Name);
WriteToLog("Log File: " + logFileName);
WriteToLog("");
WriteToLog("Query, Match, Score");
int queryCount = 0;
int matchAtLeastOneCount = 0;
MoleculeMx queryStructure = null; // current structure being searched
CidList matchList = new CidList();
List <MatchData> matchData = new List <MatchData>();
if (FromFile.Checked) // open SdFile as required
{
structureFileReader = new StreamReader(StructureFile);
}
// Search of structures one at a time
while (true)
{
if (fromList) // get next structure from list
{
if (listCidsRead >= cidList.Count)
{
break;
}
qid = cidList[listCidsRead].Cid;
listCidsRead++;
if (qid.Trim() == "")
{
continue;
}
if (qid.ToLower().IndexOf(".mol") > 0 || qid.ToLower().IndexOf(".skc") > 0)
{ // file reference
if (!File.Exists(qid))
{
continue;
}
if (qid.ToLower().IndexOf(".mol") > 0)
{
queryStructure = MoleculeMx.ReadMolfile(qid);
}
else
{
queryStructure = MoleculeMx.ReadSketchFile(qid);
}
}
else
{
queryStructure = MoleculeUtil.SelectMoleculeForCid(qid);
}
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue; // oops
}
}
else // get next structure from input file
{
qid = null;
if (StructureFile.ToLower().EndsWith(".sdf"))
{
List <SdFileField> fList = SdFileDao.Read(structureFileReader);
if (fList == null) // end of sdFile
{
structureFileReader.Close();
break;
}
if (fList.Count == 0)
{
continue;
}
queryStructure = new MoleculeMx(MoleculeFormat.Molfile, fList[0].Data);
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue;
}
if (keyField != "") // key field specified?
{
qid = SdFileDao.GetDataField(fList, keyField);
}
else // get name from 1st line of molfile
{
string molFile = fList[0].Data;
int i1 = molFile.IndexOf("\n");
if (i1 == 0)
{
qid = "";
}
else
{
qid = molFile.Substring(0, i1).Trim();
}
}
if (string.IsNullOrEmpty(qid))
{
qid = SdFileDao.GetDataField(fList, "compound_id");
}
}
else // assume smiles file
{
string smiles = structureFileReader.ReadLine();
if (smiles == null) // end of sdFile
{
structureFileReader.Close();
break;
}
smiles = smiles.Trim();
if (smiles.Length == 0)
{
continue;
}
int i1 = smiles.IndexOf(","); // get any preceeding queryId
if (i1 < 0)
{
i1 = smiles.IndexOf("\t");
}
if (i1 >= 0)
{
qid = smiles.Substring(0, i1).Trim();
smiles = smiles.Substring(i1 + 1).Trim();
}
queryStructure = new MoleculeMx(MoleculeFormat.Smiles, smiles);
if (queryStructure == null || queryStructure.AtomCount == 0)
{
continue;
}
}
if (qid == null || qid.Trim() == "")
{
qid = (queryCount + 1).ToString(); // be sure we have a query id
}
}
queryCount++; // count the query
if (queryStructure == null || queryStructure.AtomCount == 0)
{
WriteToLog("Error converting specific structure " + queryCount.ToString() + ", " + qid);
continue;
}
queryStructure.RemoveStructureCaption(); // remove any Mobius-added caption
Psc.Molecule = queryStructure;
string msg =
"Searching Structure: " + queryCount.ToString();
if (inputQueryCount > 0)
{
msg += " of " + inputQueryCount.ToString();
}
msg += "\n" +
"Structures with one or more matches: " + matchAtLeastOneCount.ToString() + "\n" +
"Total Matches: " + matchList.Count.ToString();
Progress.Show(msg);
// Do the search over the list of databases
for (int ti = 0; ti < tables.Count; ti++)
{
mt = tables[ti];
q = new Query(); // build basic query
//q.SingleStepExecution = true; // do in single step (doesn't currently return sim score)
q.ShowStereoComments = false;
qt = new QueryTable(mt);
q.AddQueryTable(qt);
qt.SelectKeyOnly(); // start selecting desired cols
keyMc = mt.KeyMetaColumn;
structMc = mt.FirstStructureMetaColumn;
structQc = qt.GetQueryColumnByName(structMc.Name);
structQc.Selected = RetrieveStructures;
dbSetMc = mt.DatabaseListMetaColumn;
if (dbSetMc == null)
{
throw new Exception("\"Databases\" metacolumn not found for table: " + mt.Label);
}
QueryColumn dbSetQc = qt.GetQueryColumnByName(dbSetMc.Name);
dbSetQc.Selected = true; // select the database name
RootTable root = RootTable.GetFromTableName(mt.Name);
txt = " in (" + root.Label + ")";
dbSetQc.Criteria = dbSetMc.Name + txt;
dbSetQc.CriteriaDisplay = txt;
simScoreMc = mt.SimilarityScoreMetaColumn;
simScoreQc = null;
if (simScoreMc != null) // get sim score if it exists
{
simScoreQc = qt.GetQueryColumnByName(simScoreMc.Name);
simScoreQc.Selected = true; // return sim score
}
Psc.QueryColumn = structQc;
ParsedStructureCriteria psc2 = AdjustSearchForSmallWorldAsNeeded(Psc);
psc2.ConvertToQueryColumnCriteria(structQc); // format the QC for the structure search
DateTime t0 = DateTime.Now;
//QueryEngine qe = new QueryEngine();
//qe.NextRowsMin = 1000; // minimum number of rows to prefetch
//qe.NextRowsMax = -1; // maximum number of rows to prefetch
//qe.NextRowsMaxTime = 10000; // max time in milliseconds for next fetch
//qe.ExecuteQuery(q);
qm = new QueryManager();
try { dlgRslt = qm.ExecuteQuery(ref q); }
catch (Exception ex)
{
WriteToLog("Error searching structure: " + ex.Message + ", " + queryCount.ToString() + ", " + qid);
continue;
}
if (dlgRslt != DialogResult.OK)
{
return(dlgRslt);
}
double executeTime = TimeOfDay.Delta(ref t0);
int offset = qm.DataTableManager.KeyValueVoPos + 1;
//int offset = 0; // for QE
int keyPos = offset++;
int strPos = RetrieveStructures ? offset++ : -1;
int dbPos = offset++;
int simPos = offset++;
int fetchCnt = 0;
while (true)
{
dr = qm.NextRow();
//dr = qe.NextRow(); // for Qe
if (dr == null)
{
break;
}
fetchCnt++;
if (fetchCnt == 1)
{
matchAtLeastOneCount++; // number of queries that have at least one match
}
MatchData md = new MatchData();
md.Qno = queryCount;
md.Qid = qid;
if (RetrieveStructures)
{
md.Qstr = "Chime=" + queryStructure.GetChimeString();
}
CompoundId cid = CompoundId.ConvertTo(dr[keyPos]);
md.Mid = cid.Value;
if (RetrieveStructures)
{
MoleculeMx ms = MoleculeMx.ConvertTo(dr[strPos]);
if (!NullValue.IsNull(ms))
{
md.Mstr = "Chime=" + ms.GetChimeString();
}
}
StringMx db = StringMx.ConvertTo(dr[dbPos]);
if (!NullValue.IsNull(db))
{
md.Db = db.Value;
}
if (Psc.SearchType == StructureSearchType.MolSim)
{
NumberMx nex = NumberMx.ConvertTo(dr[simPos]);
if (!NullValue.IsNull(nex))
{
md.Score = nex.Value;
}
}
if (matchList.Contains(cid.Value)) // already have compound id as match for other query?
{
if (Psc.SearchType != StructureSearchType.MolSim)
{
continue; // if similarity search see if more similar
}
CidListElement le = matchList.Get(cid.Value); // reference current score
if (le.Tag > md.Score)
{
continue; // only replace if more similar
}
matchList.Remove(le.Cid); // remove from list
for (int mi = 0; mi < matchData.Count; mi++) // remove from data
{
if (matchData[mi].Mid == md.Mid)
{
matchData.RemoveAt(mi);
break;
}
}
}
matchList.Add(md.Mid);
matchList.Get(md.Mid).Tag = md.Score; // keep score in list
matchData.Add(md); // add to results
txt = md.Qid + ", " + md.Mid + ", " + md.Score.ToString();
WriteToLog(txt);
} // Fetch result loop
double fetchTime = TimeOfDay.Delta(ref t0);
} // DB loop
if (Progress.CancelRequested)
{
Progress.Hide();
MessageBoxMx.ShowError("Search cancelled.");
try { LogStream.Close(); } catch { }
return(DialogResult.Cancel);
}
} // key loop
CidListCommand.WriteCurrentList(matchList); // write the list of numbers
UsageDao.LogEvent("MultipleStructSearch");
txt =
"=== Multiple structure search complete ===\r\n\r\n" +
"Structures Searched: " + queryCount.ToString() + "\r\n";
txt +=
"Structures with one or more matches: " + matchAtLeastOneCount.ToString() + "\r\n" +
"Total Matches: " + matchList.Count.ToString() + "\r\n";
TimeSpan ts = DateTime.Now.Subtract(startTime);
ts = new TimeSpan(ts.Hours, ts.Minutes, ts.Seconds);
txt += "Total Time: " + ts + "\r\n\r\n";
WriteToLog("\r\n" + txt);
try { LogStream.Close(); } catch { }
if (matchList.Count == 0)
{
Progress.Hide();
MessageBoxMx.ShowError("No matches have been found.");
return(DialogResult.Cancel);
}
tok = "Matching compound ids";
if (Psc.SearchType == StructureSearchType.MolSim)
{
tok = "Similar compound ids";
}
txt += tok + " have been written to the current list: " + ResultsUo.Name + "\n" +
"Log file written to: " + logFileName + "\n\n" +
"Do you want to view the match results?";
DialogResult dRslt = MessageBoxMx.Show(txt, "Multiple Structure Search", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dRslt == DialogResult.Cancel)
{
return(DialogResult.Cancel);
}
else if (dRslt == DialogResult.No) // show log
{
SystemUtil.StartProcess(logFileName);
return(DialogResult.Cancel);
}
// Display results
Progress.Show("Formatting results...");
mt = new MetaTable();
mt.Name = "MULTSTRUCTSEARCH_" + SearchCount;
mt.Label = "Multiple Structure Search " + SearchCount;
mt.TableMap = "Mobius.Tools.MultStructSearch"; // plugin id
mt.MetaBrokerType = MetaBrokerType.NoSql;
ColumnSelectionEnum structureColumnSelection = RetrieveStructures ? ColumnSelectionEnum.Selected : ColumnSelectionEnum.Unselected;
keyMc = keyMc.Clone();
keyMc.Name = "MatchingCid";
keyMc.Label = "Matching Compound Id";
mt.AddMetaColumn(keyMc);
structMc = structMc.Clone();
structMc.Name = "MatchingStructure";
structMc.Label = "Matching Structure";
structMc.InitialSelection = structureColumnSelection;
mt.AddMetaColumn(structMc);
dbSetMc = dbSetMc.Clone();
dbSetMc.Name = "Database";
mt.AddMetaColumn(dbSetMc);
//if (DatabasesToSearch.Text.Contains(","))
dbSetMc.InitialSelection = ColumnSelectionEnum.Selected;
mc = mt.AddMetaColumn("Molsimilarity", "Similarity Search Score", MetaColumnType.Number, ColumnSelectionEnum.Unselected, 10);
if (Psc.SearchType == StructureSearchType.MolSim)
{
mc.InitialSelection = ColumnSelectionEnum.Selected;
}
mc = mt.AddMetaColumn("QueryNo", "Query Number", MetaColumnType.Integer);
//mc = mt.AddMetaColumn("QueryMatchNo", "Query Match Number", MetaColumnType.Integer);
mc = mt.AddMetaColumn("QueryId", "Query Id", MetaColumnType.String);
mc = mt.AddMetaColumn("QueryStructure", "Query Structure", MetaColumnType.Structure);
mc.InitialSelection = structureColumnSelection;
q = ToolHelper.InitEmbeddedDataToolQuery(mt);
dt = q.ResultsDataTable as DataTableMx;
for (int mi = 0; mi < matchData.Count; mi++)
{
MatchData md = matchData[mi];
dr = dt.NewRow();
dr[qt.Alias + ".MatchingCid"] = new CompoundId(md.Mid);
if (RetrieveStructures)
{
dr[qt.Alias + ".MatchingStructure"] = new MoleculeMx(MoleculeFormat.Chime, md.Mstr);
}
dr[qt.Alias + ".Database"] = new StringMx(md.Db);
if (Psc.SearchType == StructureSearchType.MolSim)
{
dr[qt.Alias + ".Molsimilarity"] = new NumberMx(md.Score);
}
dr[qt.Alias + ".QueryNo"] = new NumberMx(md.Qno);
dr[qt.Alias + ".QueryId"] = new StringMx(md.Qid);
if (RetrieveStructures)
{
dr[qt.Alias + ".QueryStructure"] = new MoleculeMx(MoleculeFormat.Chime, md.Qstr);
}
dt.Rows.Add(dr);
}
ToolHelper.DisplayData(q, dt, true);
Progress.Hide();
return(DialogResult.OK);
}
/// <summary>
/// Handle a click on a link to a 3D structure & open in Vida
/// If clicked from an XtraGrid give the user a range of options for the data
/// to be exported. If clicked from a HTML page give limited options.
/// </summary>
/// <param name="mtName"></param>
/// <param name="mcName"></param>
/// <param name="url"></param>
public void ClickFunction(
string mtName,
string mcName,
string url)
{
ResultsFormatter fmtr = null;
ResultsField rfld = null;
//DataRowMx dr;
StringMx sx;
StreamWriter sw;
int markedCount = 0;
string densityMapUrl = null;
string target = null;
_currentMetaTable = mtName;
_currentPdbColumnName = mcName;
IncludeElectronDensityPyMol.Checked = false;
MetaTable mt = MetaTableCollection.Get(mtName);
if (mt == null)
{
return;
}
MetaColumn mc = mt.GetMetaColumnByName(mcName);
if (mc == null)
{
return;
}
_xRay2Request = Lex.Contains(mtName, "XRay2"); // newer XRay2 database table?
_urlFileName = Path.GetFileName(url); // extract file name from url
QueryManager qm = ClickFunctions.CurrentClickQueryManager;
if (qm != null)
{
Query q = qm.Query;
ResultsFormat rf = qm.ResultsFormat;
fmtr = qm.ResultsFormatter;
rfld = rf.GetResultsField(mc);
if (rfld == null)
{
return;
}
QueryTable qt = q.GetQueryTableByNameWithException(mtName);
_qcProtein = qt.GetQueryColumnByNameWithException(mcName);
if (_xRay2Request) // newer XRay2 database
{
string mapUrl = "";
if (mcName == "ALIGNED_SPLIT_COMPLEX_URL")
{
mapUrl = "ALIGNED_SPLIT_MAP_URL";
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL")
{
mapUrl = "ALIGNED_FULL_MAP_URL";
}
else if (mcName == "ORIGINAL_PDB_URL")
{
mapUrl = "ORIGINAL_MAP_URL";
} //{ mapUrl = "ORIGINAL_MAP_URL"; }
_qcDensity = qt.GetQueryColumnByName(mapUrl); //("ALIGNED_SPLIT_MAP_URL");
if (_qcDensity != null && !_qcDensity.Selected)
{
_qcDensity = null;
}
_qcTarget = qt.GetQueryColumnByName("primary_gene_name_alias");
if (_qcTarget != null && !_qcTarget.Selected)
{
_qcTarget = null;
}
}
if (_qcDensity != null)
{
// if there is a density map url located in the density column, enable the PyMol CheckEdit
DataRowMx dr = qm.DataTable.Rows[qm.MoleculeGrid.LastMouseDownCellInfo.DataRowIndex];
densityMapUrl = Lex.ToString(dr[_qcDensity.VoPosition]);
}
else
{
// user did not select the map column, try to retrieve the XRay1 or Xray2 density map url fromt he metatable
densityMapUrl = _xRay2Request ? GetXray2DensityMapUrl(url, qt.MetaTable.Name, mcName) : GetXray1DensityMapUrl(url, qt.MetaTable.Name);
}
// default checkbox to false so user does not load electron density maps everytime, since these take
// extra time to load.
IncludeElectronDensityPyMol.Checked = false;
IncludeElectronDensityPyMol.Enabled = !string.IsNullOrEmpty(densityMapUrl);
if (_qcProtein == null && _qcDensity == null)
{
throw new Exception("Neither the PDB nor the MAP column is selected in the query");
}
markedCount = fmtr.MarkedRowCount;
int unmarkedCount = fmtr.UnmarkedRowCount;
if (markedCount == 0 || unmarkedCount == 0) // if no specific selection assume user wants single structure
{
ExportSingle.Checked = true;
FileName.Text = _urlFileName;
}
else
{
ExportMarked.Checked = true; // assume wants marked structures
}
ExportMarked.Enabled = true;
}
else // simple setup for click from HTML display
{
ExportSingle.Checked = true;
ExportMarked.Enabled = false;
FileName.Text = _urlFileName;
densityMapUrl = GetXray2DensityMapUrl(url, _currentMetaTable, mcName);
target = GetTarget(url, _currentMetaTable, mcName);
////IncludeProtein.Enabled = IncludeElectronDensityEnabled = false;
////if (Lex.Eq(mcName, "bsl_xray_cmplx_url"))
//// IncludeProtein.Checked = true;
////else if (Lex.Eq(mcName, "bsl_xray_edensity_url"))
//// IncludeElectronDensityChecked = true;
}
if (mcName == "ALIGNED_SPLIT_MAP_URL" || mcName == "ALIGNED_FULL_MAP_URL" || mcName == "ORIGINAL_MAP_URL") // not viewable fileds
{
DisablePymol();
DisableMoe();
ExportToFile.Enabled = ExportToFile.Checked = true;
}
else if (mcName == "ALIGNED_FULL_COMPLEX_URL" || mcName == "ORIGINAL_PDB_URL" || mcName == "ALIGNED_SPLIT_COMPLEX_URL") // viewable by PyMol
{
EnableMoe();
EnablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
else //everything else should be viewable by MOE
{
EnableMoe();
DisablePymol();
ExportToFile.Enabled = true;
ExportToFile.Checked = false;
}
DialogResult dlgRslt = ShowDialog(SessionManager.ActiveForm);
if (dlgRslt == DialogResult.Cancel)
{
return;
}
bool exportSingle = ExportSingle.Checked;
bool exportMarked = !exportSingle;
if (!IncludeElectronDensityPyMol.Checked)
{
densityMapUrl = null;
}
if (exportMarked) // see if reasonable count if exporting marked rows
{
string msg;
if (markedCount == 0)
{
msg = "No rows have been marked for export";
MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
if (markedCount > 10)
{
msg =
markedCount + " structures have been selected out export.\n" +
"Are you sure these are the structures you want to export?";
dlgRslt = MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.YesNoCancel, MessageBoxIcon.Question);
if (dlgRslt != DialogResult.Yes)
{
return;
}
}
}
// Export to PyMol (Schrodinger) - Collab with Paul Sprengeler and Ken Schwinn
// Relavant Files:
// 1. Plugin: CorpView.py (in Mobius config dir)
// 2. Script: CorpView.pml - Runs the plugin and then passes in the .csv file (in Mobius config dir)
// Expected content (note: <csv-file-name> gets replaced):
// import pymol
// pluginLocation = 'C:\Progra~1\PyMOL\PyMOL\modules\pmg_tk\startup\CorpView.py'
// cmd.do('run ' + pluginLocation)
// cmd.do('lv_create_environment')
// cmd.do('lv_import_mobius <csv-file-name>')
// cmd.do('lv_destroy_environment')
// 3. Csv file: PyMolBatchLoad.csv - Csv file in format expected by plugin (in Mobius temp dir)
if (ExportToPyMol.Checked)
{
ExportToPyMolMethod(url, densityMapUrl, target, qm);
}
else if (ExportToMOE.Checked) // Export to MOE
{
ExportToMOEMethod(url, qm, fmtr, rfld);
}
else
{
ExportToFilesMethod(url, qm, fmtr, rfld);
}
}
/// <summary>
/// Startup Vida with supplied arguments
/// </summary>
/// <param name="args"></param>
public void StartVida(
string args)
{
RegistryKey key = null;
string rootKeyName = null, version = null, installPath = null, msg;
string[] sa = args.Split('\t');
string[] vidaPaths = sa[0].Split(';'); // array of paths to try
string startArgs = sa[1]; // args to pass to Vida
for (int pi = 0; pi < vidaPaths.Length; pi++)
{
string path = vidaPaths[pi].Trim();
if (path == "")
{
continue;
}
else if (!String.IsNullOrEmpty(Path.GetDirectoryName(path))) // directory name
{
if (Directory.Exists(path))
{
installPath = path;
//DebugLog.Message("StartVida installPath: " + installPath);
break;
}
}
else // registry key
{
string keyName = path;
key = Registry.CurrentUser.OpenSubKey(keyName);
if (key != null)
{
rootKeyName = keyName;
version = (string)key.GetValue("version");
if (!String.IsNullOrEmpty(version))
{
key = Registry.CurrentUser.OpenSubKey(rootKeyName + @"\" + version);
if (key != null)
{
installPath = (string)key.GetValue("InstallPath");
//DebugLog.Message("StartVida key: " + rootKeyName + @"\" + version + ", installPath: " + installPath);
break;
}
}
break;
}
}
}
if (String.IsNullOrEmpty(installPath))
{
msg = "Mobius is unable to locate a VIDA installation on this machine.";
MessageBoxMx.Show(msg, "Mobius", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
string startFile = installPath + @"\vida.bat";
try
{
//DebugLog.Message("startFile: " + startFile);
//DebugLog.Message("startArgs: " + startArgs);
Process p = Process.Start(startFile, startArgs);
}
catch (Exception ex)
{
MessageBoxMx.Show("Failed to start VIDA: " + startFile + " " + startArgs + "\n" + ex.Message, "Mobius");
return;
}
return;
}
