[Cctbx-cvs] SF.net SVN: cctbx:[14985] trunk/wxtbx

[<nat...@us...>]

Revision: 14985
          http://cctbx.svn.sourceforge.net/cctbx/?rev=14985&view=rev
Author:   natechols
Date:     2012-03-01 20:30:48 +0000 (Thu, 01 Mar 2012)
Log Message:
-----------
new reports module for various list displays, including PDB BLAST and symmetry search results, with mixin for linking to PDB

Modified Paths:
--------------
    trunk/wxtbx/browser.py

Added Paths:
-----------
    trunk/wxtbx/reports/
    trunk/wxtbx/reports/__init__.py
    trunk/wxtbx/reports/blast.py
    trunk/wxtbx/reports/pdb_symmetry.py

Removed Paths:
-------------
    trunk/wxtbx/blast_report.py

Deleted: trunk/wxtbx/blast_report.py
===================================================================
--- trunk/wxtbx/blast_report.py	2012-03-01 20:29:38 UTC (rev 14984)
+++ trunk/wxtbx/blast_report.py	2012-03-01 20:30:48 UTC (rev 14985)
@@ -1,122 +0,0 @@
-
-import wx
-import sys
-
-class BlastFrame (wx.Frame) :
-  def __init__ (self, *args, **kwds) :
-    super(BlastFrame, self).__init__(*args, **kwds)
-    self.statusbar = self.CreateStatusBar()
-    szr = wx.BoxSizer(wx.VERTICAL)
-    self.SetSizer(szr)
-    panel = wx.Panel(self)
-    szr.Add(panel, 1, wx.EXPAND)
-    pszr = wx.BoxSizer(wx.VERTICAL)
-    panel.SetSizer(pszr)
-    box = wx.StaticBox(panel, label="BLAST results")
-    boxszr = wx.StaticBoxSizer(box, wx.VERTICAL)
-    pszr.Add(boxszr, 1, wx.ALL|wx.EXPAND, 5)
-    boxszr.Add(wx.StaticText(panel, -1, "Query sequence:"))
-    self.seq_ctrl = wx.TextCtrl(panel, style=wx.TE_READONLY|wx.TE_MULTILINE,
-      size=(600,100))
-    boxszr.Add(self.seq_ctrl, 0, wx.ALL, 5)
-    boxszr.Add(wx.StaticText(panel, -1, "BLAST hits in PDB:"))
-    self.hit_list = BlastList(panel, style=wx.LC_REPORT|wx.LC_SINGLE_SEL,
-      size=(600,240))
-    #self.hit_list.SetMinSize((600,240))
-    boxszr.Add(self.hit_list, 1, wx.ALL|wx.EXPAND, 5)
-    szr2 = wx.BoxSizer(wx.HORIZONTAL)
-    boxszr.Add(szr2)
-    btn1 = wx.Button(panel, -1, "Download selected structure")
-    szr2.Add(btn1, 0, wx.ALL, 5)
-    self.Bind(wx.EVT_BUTTON, self.OnDownload, btn1)
-    btn2 = wx.Button(panel, -1, "View PDB web page")
-    szr2.Add(btn2, 0, wx.ALL, 5)
-    self.Bind(wx.EVT_BUTTON, self.OnViewPDB, btn2)
-    szr.Fit(panel)
-    self.Layout()
-    self.Fit()
-    self.SetMinSize(self.GetSize())
-    self.web_frame = None
-
-  def SetResults (self, query, results) :
-    assert (len(results) > 0)
-    self.statusbar.SetStatusText("%d results shown (top match: %s_%s)" %
-      (len(results), results[0].pdb_id, results[0].chain_id))
-    self.seq_ctrl.SetValue(query)
-    self.hit_list.SetResults(results)
-
-  def OnDownload (self, event) :
-    pdb_id = self.hit_list.GetSelectedID()
-    if (pdb_id is not None) :
-      def download (args) :
-        import mmtbx.command_line.fetch_pdb
-        return mmtbx.command_line.fetch_pdb.run2(args=args)
-      from wxtbx.process_control import download_file_basic
-      download_file_basic(
-        window=self,
-        dl_func=download,
-        args=[pdb_id])
-
-  def OnViewPDB (self, event) :
-    pdb_id = self.hit_list.GetSelectedID()
-    if (pdb_id is not None) :
-      url = "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s" %pdb_id
-      if (sys.platform == "darwin") :
-        from wxtbx import browser
-        if (self.web_frame is None) :
-          self.web_frame = browser.webkit_frame(self, -1, "RCSB PDB")
-          self.web_frame.SetHomepage("http://www.rcsb.org")
-          self.Bind(wx.EVT_WINDOW_DESTROY, self.OnCloseWWW, self.web_frame)
-          self.web_frame.Show()
-        self.web_frame.Raise()
-        self.web_frame.Open(url)
-        self.web_frame.Refresh()
-      else :
-        from libtbx import easy_run
-        easy_run.call("env LD_LIBRARY_PATH='' firefox %s" % url)
-
-  def OnCloseWWW (self, event) :
-      self.web_frame = None
-
-class BlastList (wx.ListCtrl) :
-  def __init__ (self, *args, **kwds) :
-    super(BlastList, self).__init__(*args, **kwds)
-    cols = ["PDB ID", "Chain ID", "E-value", "Length", "% Identity",
-            "% Positives"]
-    widths = [100, 80, 100, 100, 100, 100]
-    r, l = wx.LIST_FORMAT_RIGHT, wx.LIST_FORMAT_LEFT
-    alignments = [l, l, r, r, r, r]
-    for i, col in enumerate(cols) :
-      self.InsertColumn(i, col, alignments[i])
-      self.SetColumnWidth(i, widths[i])
-
-  def SetResults (self, results) :
-    self.DeleteAllItems()
-    for result in results :
-      i = self.InsertStringItem(sys.maxsize, result.pdb_id)
-      self.SetStringItem(i, 1, result.chain_id)
-      self.SetStringItem(i, 2, "%g" % result.evalue)
-      self.SetStringItem(i, 3, "%d" % result.length)
-      self.SetStringItem(i, 4, "%.2f" % result.identity)
-      self.SetStringItem(i, 5, "%.2f" % result.positives)
-
-  def GetSelectedID (self) :
-    item = self.GetFirstSelected()
-    if (item >= 0) :
-      return self.GetItem(item, 0).GetText()
-    return None
-
-if (__name__ == "__main__") :
-  from iotbx.command_line import blast_pdb
-  from iotbx.file_reader import any_file
-  seq_file = any_file(sys.argv[1], force_type="seq")
-  seq_file.check_file_type("seq")
-  seq_objects = seq_file.file_object
-  assert (len(seq_objects) == 1)
-  sequence = seq_objects[0].sequence
-  results = blast_pdb.summarize_blast_output(blast_file=sys.argv[2])
-  app = wx.App(0)
-  frame = BlastFrame(None, -1, "BLAST results")
-  frame.SetResults(sequence, results)
-  frame.Show()
-  app.MainLoop()

Modified: trunk/wxtbx/browser.py
===================================================================
--- trunk/wxtbx/browser.py	2012-03-01 20:29:38 UTC (rev 14984)
+++ trunk/wxtbx/browser.py	2012-03-01 20:30:48 UTC (rev 14985)
@@ -37,7 +37,6 @@
     #self.Bind(wx.EVT_WINDOW_CREATE, self.OnShow)
 
   def SetHomepage (self, url) :
-    print "URL: ", url
     self.home_url = url
 
   def SetupToolbar (self) :
@@ -64,7 +63,6 @@
     self.toolbar.Realize()
 
   def LoadURL (self, url) :
-    print "url: ", url
     if (wx.Platform == '__WXMAC__') :
       self.viewer.LoadURL(url)
     elif (wx.Platform == '__WXMSW__') :

Added: trunk/wxtbx/reports/__init__.py
===================================================================
--- trunk/wxtbx/reports/__init__.py	                        (rev 0)
+++ trunk/wxtbx/reports/__init__.py	2012-03-01 20:30:48 UTC (rev 14985)
@@ -0,0 +1,54 @@
+
+import wx
+import sys
+
+class PDBLinkMixin (object) :
+  """
+  Subclass this along with wx.Frame, etc. to link to the PDB from a list of
+  results.  get_pdb_id_for_viewing() must be re-implemented in subclasses.
+  """
+  def create_pdb_buttons (self, panel, sizer) :
+    szr2 = wx.BoxSizer(wx.HORIZONTAL)
+    sizer.Add(szr2)
+    btn1 = wx.Button(panel, -1, "Download selected structure")
+    szr2.Add(btn1, 0, wx.ALL, 5)
+    self.Bind(wx.EVT_BUTTON, self.OnDownload, btn1)
+    btn2 = wx.Button(panel, -1, "View PDB web page")
+    szr2.Add(btn2, 0, wx.ALL, 5)
+    self.Bind(wx.EVT_BUTTON, self.OnViewPDB, btn2)
+
+  def get_pdb_id_for_viewing (self) :
+    raise NotImplementedError()
+
+  def OnViewPDB (self, event) :
+    pdb_id = self.get_pdb_id_for_viewing()
+    if (pdb_id is not None) :
+      url = "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s" %pdb_id
+      if (sys.platform == "darwin") :
+        from wxtbx import browser
+        if (getattr(self, "web_frame", None) is None) :
+          self.web_frame = browser.browser_frame(self, -1, "RCSB PDB")
+          self.web_frame.SetHomepage("http://www.rcsb.org")
+          self.Bind(wx.EVT_WINDOW_DESTROY, self.OnCloseWWW, self.web_frame)
+          self.web_frame.Show()
+        self.web_frame.Raise()
+        self.web_frame.Open(url)
+        self.web_frame.Refresh()
+      else :
+        from libtbx import easy_run
+        easy_run.call("env LD_LIBRARY_PATH='' firefox %s" % url)
+
+  def OnDownload (self, event) :
+    pdb_id = self.get_pdb_id_for_viewing()
+    if (pdb_id is not None) :
+      def download (args) :
+        import mmtbx.command_line.fetch_pdb
+        return mmtbx.command_line.fetch_pdb.run2(args=args)
+      from wxtbx.process_control import download_file_basic
+      download_file_basic(
+        window=self,
+        dl_func=download,
+        args=[pdb_id])
+
+  def OnCloseWWW (self, event) :
+    self.web_frame = None

Copied: trunk/wxtbx/reports/blast.py (from rev 14978, trunk/wxtbx/blast_report.py)
===================================================================
--- trunk/wxtbx/reports/blast.py	                        (rev 0)
+++ trunk/wxtbx/reports/blast.py	2012-03-01 20:30:48 UTC (rev 14985)
@@ -0,0 +1,86 @@
+
+from wxtbx import reports
+import wx
+import sys
+
+class BlastFrame (wx.Frame, reports.PDBLinkMixin) :
+  def __init__ (self, *args, **kwds) :
+    super(BlastFrame, self).__init__(*args, **kwds)
+    self.statusbar = self.CreateStatusBar()
+    szr = wx.BoxSizer(wx.VERTICAL)
+    self.SetSizer(szr)
+    panel = wx.Panel(self)
+    szr.Add(panel, 1, wx.EXPAND)
+    pszr = wx.BoxSizer(wx.VERTICAL)
+    panel.SetSizer(pszr)
+    box = wx.StaticBox(panel, label="BLAST results")
+    boxszr = wx.StaticBoxSizer(box, wx.VERTICAL)
+    pszr.Add(boxszr, 1, wx.ALL|wx.EXPAND, 5)
+    boxszr.Add(wx.StaticText(panel, -1, "Query sequence:"))
+    self.seq_ctrl = wx.TextCtrl(panel, style=wx.TE_READONLY|wx.TE_MULTILINE,
+      size=(600,100))
+    boxszr.Add(self.seq_ctrl, 0, wx.ALL, 5)
+    boxszr.Add(wx.StaticText(panel, -1, "BLAST hits in PDB:"))
+    self.hit_list = BlastList(panel, style=wx.LC_REPORT|wx.LC_SINGLE_SEL,
+      size=(600,240))
+    #self.hit_list.SetMinSize((600,240))
+    boxszr.Add(self.hit_list, 1, wx.ALL|wx.EXPAND, 5)
+    self.create_pdb_buttons(panel, boxszr)
+    szr.Fit(panel)
+    self.Layout()
+    self.Fit()
+    self.SetMinSize(self.GetSize())
+    self.web_frame = None
+
+  def SetResults (self, query, results) :
+    assert (len(results) > 0)
+    self.statusbar.SetStatusText("%d results shown (top match: %s_%s)" %
+      (len(results), results[0].pdb_id, results[0].chain_id))
+    self.seq_ctrl.SetValue(query)
+    self.hit_list.SetResults(results)
+
+  def get_pdb_id_for_viewing (self) :
+    return self.hit_list.GetSelectedID()
+
+class BlastList (wx.ListCtrl) :
+  def __init__ (self, *args, **kwds) :
+    super(BlastList, self).__init__(*args, **kwds)
+    cols = ["PDB ID", "Chain ID", "E-value", "Length", "% Identity",
+            "% Positives"]
+    widths = [100, 80, 100, 100, 100, 100]
+    r, l = wx.LIST_FORMAT_RIGHT, wx.LIST_FORMAT_LEFT
+    alignments = [l, l, r, r, r, r]
+    for i, col in enumerate(cols) :
+      self.InsertColumn(i, col, alignments[i])
+      self.SetColumnWidth(i, widths[i])
+
+  def SetResults (self, results) :
+    self.DeleteAllItems()
+    for result in results :
+      i = self.InsertStringItem(sys.maxsize, result.pdb_id)
+      self.SetStringItem(i, 1, result.chain_id)
+      self.SetStringItem(i, 2, "%g" % result.evalue)
+      self.SetStringItem(i, 3, "%d" % result.length)
+      self.SetStringItem(i, 4, "%.2f" % result.identity)
+      self.SetStringItem(i, 5, "%.2f" % result.positives)
+
+  def GetSelectedID (self) :
+    item = self.GetFirstSelected()
+    if (item >= 0) :
+      return self.GetItem(item, 0).GetText()
+    return None
+
+if (__name__ == "__main__") :
+  from iotbx.command_line import blast_pdb
+  from iotbx.file_reader import any_file
+  seq_file = any_file(sys.argv[1], force_type="seq")
+  seq_file.check_file_type("seq")
+  seq_objects = seq_file.file_object
+  assert (len(seq_objects) == 1)
+  sequence = seq_objects[0].sequence
+  results = blast_pdb.summarize_blast_output(blast_file=sys.argv[2])
+  app = wx.App(0)
+  frame = BlastFrame(None, -1, "BLAST results")
+  frame.SetResults(sequence, results)
+  frame.Show()
+  app.MainLoop()

Added: trunk/wxtbx/reports/pdb_symmetry.py
===================================================================
--- trunk/wxtbx/reports/pdb_symmetry.py	                        (rev 0)
+++ trunk/wxtbx/reports/pdb_symmetry.py	2012-03-01 20:30:48 UTC (rev 14985)
@@ -0,0 +1,85 @@
+
+from wxtbx import reports
+import wx
+import sys
+
+class SymmetryListFrame (wx.Frame, reports.PDBLinkMixin) :
+  def __init__ (self, *args, **kwds) :
+    super(SymmetryListFrame, self).__init__(*args, **kwds)
+    self.statusbar = self.CreateStatusBar()
+    szr = wx.BoxSizer(wx.VERTICAL)
+    self.SetSizer(szr)
+    panel = wx.Panel(self)
+    szr.Add(panel, 1, wx.EXPAND)
+    pszr = wx.BoxSizer(wx.VERTICAL)
+    panel.SetSizer(pszr)
+    box = wx.StaticBox(panel, label="Symmetry search results")
+    boxszr = wx.StaticBoxSizer(box, wx.VERTICAL)
+    pszr.Add(boxszr, 1, wx.ALL|wx.EXPAND, 5)
+    box2 = wx.BoxSizer(wx.HORIZONTAL)
+    boxszr.Add(box2)
+    box2.Add(wx.StaticText(panel, -1, "Input symmetry:"), 0, wx.ALL, 5)
+    self.symm_txt = wx.StaticText(panel, -1, "", size=(540,-1))
+    box2.Add(self.symm_txt, 0, wx.ALL, 5)
+    boxszr.Add(wx.StaticText(panel, -1, "Closest matching PDB entries:"), 0,
+      wx.ALL, 5)
+    self.symm_list = PDBSymmList(
+      parent=self,
+      style=wx.LC_REPORT|wx.LC_SINGLE_SEL,
+      size=(740,200))
+    boxszr.Add(self.symm_list, 1, wx.ALL|wx.EXPAND, 5)
+    self.create_pdb_buttons(panel, boxszr)
+    szr.Fit(panel)
+    self.Layout()
+    self.Fit()
+    self.SetMinSize(self.GetSize())
+    self.web_frame = None
+
+  def SetResults (self, symmetry, hits) :
+    sg_txt = str(symmetry.space_group_info())
+    uc_txt = "%g %g %g %g %g %g" % symmetry.unit_cell().parameters()
+    self.symm_txt.SetLabel("%s (%s)" % (sg_txt, uc_txt))
+    self.statusbar.SetStatusText("%d results shown" % len(hits))
+    self.symm_list.SetResults(hits)
+
+  def get_pdb_id_for_viewing (self) :
+    return self.symm_list.GetSelectedID()
+
+class PDBSymmList (wx.ListCtrl) :
+  def __init__ (self, *args, **kwds) :
+    super(PDBSymmList, self).__init__(*args, **kwds)
+    cols = ["PDB ID", "RMSD", "Volume ratio", "Space group", "Unit cell"]
+    widths = [100, 80, 120, 120, 300]
+    r, l = wx.LIST_FORMAT_RIGHT, wx.LIST_FORMAT_LEFT
+    alignments = [l, r, r, r, r]
+    for i, col in enumerate(cols) :
+      self.InsertColumn(i, col, alignments[i])
+      self.SetColumnWidth(i, widths[i])
+
+  def SetResults (self, results) :
+    self.DeleteAllItems()
+    for result in results :
+      i = self.InsertStringItem(sys.maxsize, result.pdb_id)
+      self.SetStringItem(i, 1, "%6.3f" % result.rmsd)
+      self.SetStringItem(i, 2, "%g" % result.volume_ratio)
+      self.SetStringItem(i, 3, str(result.pdb_symmetry.space_group_info()))
+      self.SetStringItem(i, 4, "%g %g %g %g %g %g" %
+        result.pdb_symmetry.unit_cell().parameters())
+
+  def GetSelectedID (self) :
+    item = self.GetFirstSelected()
+    if (item >= 0) :
+      return self.GetItem(item, 0).GetText()
+    return None
+
+def run (args) :
+  from mmtbx.command_line import search_pdb_symmetry
+  results = search_pdb_symmetry.run(args=args)
+  app = wx.App(0)
+  frame = SymmetryListFrame(None, -1, "PDB symmetry search")
+  frame.SetResults(results.crystal_symmetry, results.hits)
+  frame.Show()
+  app.MainLoop()
+
+if (__name__ == "__main__") :
+  run(sys.argv[1:])

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