Bug fix when displaying X-H hydrogens

Added a selector for selector hydrogen linked to sulphur atoms

MDANSE/Framework/Selectors/CarboHydrogen.py

@@ -38,17 +38,29 @@ class CarboHydrogen(ISelector):
     
     section = "hydrogens"
 
-    def select(self, *args):
+    def __init__(self, universe):
+        
+        ISelector.__init__(self,universe)
 
-        sel = set()
-            
         for obj in self._universe.objectList():
                                         
             carbons = [at for at in obj.atomList() if at.type.name.strip().lower() == 'carbon']
             
             for car in carbons:
                 neighbours = car.bondedTo()
-                hydrogens = [neigh for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
-                sel.update(hydrogens)
-                    
-        return sel
\ No newline at end of file
+                hydrogens = [neigh.fullName().strip().lower() for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
+                self._choices.extend(sorted(hydrogens))
+                
+    def select(self, names):
+    
+        sel = set()
+
+        if '*' in names:
+            names = self._choices[1:]
+            
+        vals = set([v.lower() for v in names])
+        sel.update([at for at in self._universe.atomList() if at.fullName().strip().lower() in vals])
+        
+        return sel
+    
+    
\ No newline at end of file

MDANSE/Framework/Selectors/HeteroHydrogen.py

@@ -38,17 +38,27 @@ class HeteroHydrogenBound(ISelector):
     
     section = "hydrogens"
 
-    def select(self, *args):
+    def __init__(self, universe):
+        
+        ISelector.__init__(self,universe)
 
-        sel = set()
-            
         for obj in self._universe.objectList():
                                         
             heteroatoms = [at for at in obj.atomList() if at.type.name.strip().lower() not in ['carbon','hydrogen']]
             
             for het in heteroatoms:
                 neighbours = het.bondedTo()
-                hydrogens = [neigh for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
-                sel.update(hydrogens)
-                    
+                hydrogens = [neigh.fullName().strip().lower() for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
+                self._choices.extend(sorted(hydrogens))
+
+    def select(self, names):
+    
+        sel = set()
+
+        if '*' in names:
+            names = self._choices[1:]
+            
+        vals = set([v.lower() for v in names])
+        sel.update([at for at in self._universe.atomList() if at.fullName().strip().lower() in vals])
+        
         return sel

MDANSE/Framework/Selectors/NitroHydrogen.py

@@ -38,17 +38,28 @@ class NitroHydrogen(ISelector):
     
     section = "hydrogens"
 
-    def select(self, *args):
+    def __init__(self, universe):
+        
+        ISelector.__init__(self,universe)
 
-        sel = set()
-            
         for obj in self._universe.objectList():
                                         
             nitrogens = [at for at in obj.atomList() if at.type.name.strip().lower() == 'nitrogen']
             
-            for nit in nitrogens:
-                neighbours = nit.bondedTo()
-                hydrogens = [neigh for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
-                sel.update(hydrogens)
-                    
+            for nitro in nitrogens:
+                neighbours = nitro.bondedTo()
+                hydrogens = [neigh.fullName().strip().lower() for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
+                self._choices.extend(sorted(hydrogens))
+                
+    def select(self, names):
+    
+        sel = set()
+
+        if '*' in names:
+            names = self._choices[1:]
+            
+        vals = set([v.lower() for v in names])
+        sel.update([at for at in self._universe.atomList() if at.fullName().strip().lower() in vals])
+        
         return sel
+    

MDANSE/Framework/Selectors/OxyHydrogen.py

@@ -38,17 +38,28 @@ class OxyHydrogen(ISelector):
     
     section = "hydrogens"
 
-    def select(self, *args):
+    def __init__(self, universe):
+        
+        ISelector.__init__(self,universe)
 
-        sel = set()
-            
         for obj in self._universe.objectList():
                                         
             oxygens = [at for at in obj.atomList() if at.type.name.strip().lower() == 'oxygen']
             
             for oxy in oxygens:
                 neighbours = oxy.bondedTo()
-                hydrogens = [neigh for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
-                sel.update(hydrogens)
-                    
-        return sel
\ No newline at end of file
+                hydrogens = [neigh.fullName().strip().lower() for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
+                self._choices.extend(sorted(hydrogens))
+                
+    def select(self, names):
+    
+        sel = set()
+
+        if '*' in names:
+            names = self._choices[1:]
+            
+        vals = set([v.lower() for v in names])
+        sel.update([at for at in self._universe.atomList() if at.fullName().strip().lower() in vals])
+        
+        return sel
+    

MDANSE/Framework/Selectors/SulphurHydrogen.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Mar 27, 2015
+
+:author: Eric C. Pellegrini
+'''
+
+from MDANSE.Framework.Selectors.ISelector import ISelector
+
+class OxyHydrogen(ISelector):
+    
+    type = "sulphur_hydrogen"
+    
+    section = "hydrogens"
+
+    def __init__(self, universe):
+        
+        ISelector.__init__(self,universe)
+
+        for obj in self._universe.objectList():
+                                        
+            sulphurs = [at for at in obj.atomList() if at.type.name.strip().lower() in ['sulphur', 'sulfur']]
+            
+            for sul in sulphurs:
+                neighbours = sul.bondedTo()
+                hydrogens = [neigh.fullName().strip().lower() for neigh in neighbours if neigh.type.name.strip().lower() == 'hydrogen']
+                self._choices.extend(sorted(hydrogens))
+                
+    def select(self, names):
+    
+        sel = set()
+
+        if '*' in names:
+            names = self._choices[1:]
+            
+        vals = set([v.lower() for v in names])
+        sel.update([at for at in self._universe.atomList() if at.fullName().strip().lower() in vals])
+        
+        return sel
+