/// <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);
}
}
