diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index 7f9e089ffe63b92f036fe35151593205b25ae6c9..4b1638f2ae3f561ecc1e5f42dd5f5994a319a164 100644
--- a/modules/bindings/pymod/msms.py
+++ b/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
diff --git a/modules/bindings/tests/test_msms.py b/modules/bindings/tests/test_msms.py
index 8cd56ee5a5b8577ba2c82a39e408bc01c60a4617..61810be5576058d45cbe6b929052eb9522ca1531 100755
--- a/modules/bindings/tests/test_msms.py
+++ b/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__":
diff --git a/modules/gui/pymod/init_context_menu.py b/modules/gui/pymod/init_context_menu.py
index 85e991a02fc9937b2d878b2d183ddf0b05e4e40d..b26e5d3d71d7c6e1f0e35697af3f8db1d339fb81 100644
--- a/modules/gui/pymod/init_context_menu.py
+++ b/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)