modified MSMS surface calculation

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2648 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/bindings/pymod/msms.py

@@ -134,7 +134,8 @@ def _RunMSMS(command):
 # \param attach_esa    Attaches per atom SESA to specified FloatProp at atom level
 # \return              Touplet of lists for (SES, SAS)
 def CalculateSurfaceArea(entity, density=1.0, radius=1.5,  all_surf=False,
-                         no_hydrogens=False, selection="",
+                         no_hydrogens=False, no_hetatoms=False, no_waters=False,
+                         selection="",
                          msms_exe=None, msms_env=None, keep_files=False, 
                          attach_asa=None, attach_esa=None):
   import re 
@@ -144,10 +145,19 @@ def CalculateSurfaceArea(entity, density=1.0, radius=1.5,  all_surf=False,
 
   # parse selection
   if no_hydrogens:
-    if selection=="":
-      selection="ele!=H"
-    else:
-      selection+=" and ele!=H"
+    if selection!='':
+      selection+=" and "
+    selection="ele!=H"
+  
+  if no_hetatoms:
+    if selection!='':
+      selection+=" and "
+    selection="ishetatm=False"
+  
+  if no_waters:
+    if selection!='':
+      selection+=" and "
+    selection="rname!=HOH"
 
   # setup files for msms
   (msms_data_dir, msms_data_file)=_SetupFiles(entity, selection)
@@ -208,8 +218,10 @@ def CalculateSurfaceArea(entity, density=1.0, radius=1.5,  all_surf=False,
 # \param keep_files    Do not delete temporary files
 # \return list of OST SurfaceHandle objects
 def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
-                     no_hydrogens=False, selection="",
+                     no_hydrogens=False, no_hetatoms=False, no_waters=False,
+                     selection="",
                      msms_exe=None, msms_env=None, keep_files=False):
+  
   import os
   import re
 
@@ -218,10 +230,19 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
 
   # parse selection
   if no_hydrogens:
-    if selection=="":
-      selection="ele!=H"
-    else:
-      selection+=" and ele!=H"
+    if selection!='':
+      selection+=" and "
+    selection="ele!=H"
+      
+  if no_hetatoms:
+    if selection!='':
+      selection+=" and "
+    selection="ishetatm=False"
+      
+  if no_waters:
+    if selection!='':
+      selection+=" and "
+    selection="rname!=HOH"
 
   # setup files for msms
   

modules/bindings/tests/test_msms.py

@@ -16,13 +16,13 @@ class TestMSMSBindings(unittest.TestCase):
     surf=msms.CalculateSurface(self.protein, msms_env='MSMSSERVER')[0]
     assert self.num_vert==len(surf.GetVertexIDList()) \
        and self.num_tri==len(surf.GetTriIDList()), \
-       "Number of surface vertices or triangles do not match precalculated values"
+       "Number of surface vertices (%i) or triangles (%i) do not match precalculated values (%i/%i)"%(len(surf.GetVertexIDList()),len(surf.GetTriIDList()),self.num_vert,self.num_tri)
   
   def testCalculateSurfaceAres(self):
      (msms_ases, msms_asas)=msms.CalculateSurfaceArea(self.protein, \
                                                       msms_env='MSMSSERVER')
      assert self.ases==msms_ases[0] and self.asas==msms_asas[0], \
-     "SASA or SESA do not match precalculated values"
+     "SASA (%f) or SESA (%f) do not match precalculated values (%f/%f)"%(msms_asas[0],msms_ases[0],self.asas,self.ases)
 
 
 if __name__ == "__main__":

modules/gui/pymod/init_context_menu.py

@@ -163,7 +163,11 @@ class CalculateSurfaceSettingsDialog(QtGui.QDialog):
     vb.addWidget(selection_label, 4, 0)
     vb.addWidget(self.selection_field, 4, 1, 1, 2)
     self.noh_box=QtGui.QCheckBox("no hydrogens")
-    vb.addWidget(self.noh_box, 5, 0, 1, 2)
+    vb.addWidget(self.noh_box, 5, 0)
+    self.nohet_box=QtGui.QCheckBox("no hetatoms")
+    vb.addWidget(self.nohet_box, 5, 1)
+    self.nowat_box=QtGui.QCheckBox("no waters")
+    vb.addWidget(self.nowat_box, 5, 2)
     
     cancel_btn = QtGui.QPushButton("Cancel", self)
     ok_btn = QtGui.QPushButton("OK", self)
@@ -176,7 +180,8 @@ class CalculateSurfaceSettingsDialog(QtGui.QDialog):
     
   def GetPath(self):
     path=QtGui.QFileDialog().getOpenFileName(self, "Choose MSMS Executable")
-    self.msmsexe_field.setText(path)
+    if path!='':
+      self.msmsexe_field.setText(path)
 
 class SurfaceContextMenu(QtCore.QObject):
   def __init__(self, context_menu):
@@ -204,9 +209,12 @@ class SurfaceContextMenu(QtCore.QObject):
                               cssd.density_spinbox.value(),
                               cssd.probe_spinbox.value(),
                               str(cssd.selection_field.text()),
-                              cssd.noh_box.isChecked())
+                              cssd.noh_box.isChecked(),
+                              cssd.nohet_box.isChecked(),
+                              cssd.nowat_box.isChecked())
       
-  def __CalculateSurface(self,ent_list,name,msms_exe,density,radius,selection,noh):
+  def __CalculateSurface(self,ent_list,name,msms_exe,density,
+                         radius,selection,noh,nohet,nowat):
     for entity in ent_list:
       if isinstance(entity, gfx.Entity):
         try:
@@ -215,11 +223,16 @@ class SurfaceContextMenu(QtCore.QObject):
                                   density=density,
                                   radius=radius,
                                   selection=selection,
-                                  no_hydrogens=noh)[0]
+                                  no_hydrogens=noh,
+                                  no_hetatoms=nohet,
+                                  no_waters=nowat)[0]
           gfx.Scene().Add(gfx.Surface("%s_%s"%(entity.GetName(),name),s))
         except (RuntimeError, CalledProcessError):
           LogError("WARNING: Surface could not be calculated")
           return
+        except UserWarning:
+          LogError("WARNING: Entry with the same name already present in scene")
+          return
   
 
 class AlignmentContextMenu(QtCore.QObject):
@@ -299,4 +312,4 @@ class AlignmentContextMenu(QtCore.QObject):
 def _InitContextMenu(app):
   cm=app.scene_win.GetContextMenu()
   AlignmentContextMenu(cm)
-  SurfaceContextMenu(cm)
\ No newline at end of file
+  SurfaceContextMenu(cm)