moved oneUnbonded function to make_Atom_and_bondpoints method

author: Bruce Smith <bruce@nanorex.com> 2009-01-12 23:43:33 +0000
committer: Bruce Smith <bruce@nanorex.com> 2009-01-12 23:43:33 +0000
commit: eedffc4ad72c0bf596cbeee66ee0c633b208517c (patch)
tree: 54fe8dcb1a5bb876e2bf5045b86e36dabf1a745c
parent: c0e1948c73472001c41d4b60e0919c50f15f1cca (diff)
download: nanoengineer-eedffc4ad72c0bf596cbeee66ee0c633b208517c.tar.gz
nanoengineer-eedffc4ad72c0bf596cbeee66ee0c633b208517c.zip
6 files changed, 64 insertions, 62 deletions
diff --git a/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py b/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py
index ae29c8194..049d9eb20 100755
--- a/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py
+++ b/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py
@@ -1,4 +1,4 @@
-# Copyright 2004-2008 Nanorex, Inc.  See LICENSE file for details. 
+# Copyright 2004-2009 Nanorex, Inc.  See LICENSE file for details. 
 """
 BuildAtoms_GraphicsMode.py 
 
@@ -13,7 +13,7 @@ For example:
 
                         
 @version: $Id$
-@copyright: 2004-2008 Nanorex, Inc.  See LICENSE file for details.
+@copyright: 2004-2009 Nanorex, Inc.  See LICENSE file for details.
 
 TODO: [as of 2008-01-04]
 - Items mentioned in Select_GraphicsMode.py 
@@ -63,7 +63,6 @@ from platform_dependent.PlatformDependent import fix_plurals
 
 from model.chunk import Chunk
 from model.chem import Atom
-from model.chem import oneUnbonded
 from model.elements import Singlet
 from geometry.VQT import Q, A, norm, twistor
 
@@ -1061,10 +1060,10 @@ class BuildAtoms_basicGraphicsMode(SelectAtoms_basicGraphicsMode):
 
         else: # Deposit atom at the cursor position and prep it for dragging
             cursorPos = atom_or_pos
-            a = self.o.selatom = oneUnbonded(atype.element, 
-                                             self.o.assy, 
-                                             cursorPos, 
-                                             atomtype = atype)
+            a = self.o.assy.make_Atom_and_bondpoints(atype.element, 
+                                                     cursorPos, 
+                                                     atomtype = atype )
+            self.o.selatom = a
             self.objectSetup(a)
             self.baggage, self.nonbaggage = a.baggage_and_other_neighbors()
             if self.pickit(): 
@@ -1074,7 +1073,6 @@ class BuildAtoms_basicGraphicsMode(SelectAtoms_basicGraphicsMode):
             chunk = self.o.selatom.molecule #bruce 041207
         
         return chunk, status
-    
         
     def ensure_visible(self, stuff, status):
         """
diff --git a/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py b/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py
index d27a4ba1f..24500b50b 100755
--- a/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py
+++ b/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py
@@ -1,4 +1,4 @@
-# Copyright 2006-2008 Nanorex, Inc.  See LICENSE file for details. 
+# Copyright 2006-2009 Nanorex, Inc.  See LICENSE file for details. 
 """
 CoNTubGenerator.py
 
@@ -6,7 +6,7 @@ Generator functions which use cad/plugins/CoNTub.
 
 @author: Bruce
 @version: $Id$
-@copyright: 2006-2008 Nanorex, Inc.  See LICENSE file for details.
+@copyright: 2006-2009 Nanorex, Inc.  See LICENSE file for details.
 
 Also intended as a prototype of code which could constitute the nE-1 side
 of a "generator plugin API". Accordingly, the CoNTub-specific code should
@@ -619,7 +619,7 @@ class PluginlikeGenerator:
         n = max(params[0],1)
         for x in range(n):
           for y in range(2):
-            ## build methane, from oneUnbonded
+            ## build methane, much like make_Atom_and_bondpoints method does it
             pos = V(x,y,0)
             atm = Atom('C', pos, mol)
             atm.make_bondpoints_when_no_bonds() # notices atomtype
diff --git a/cad/src/graphics/widgets/ThumbView.py b/cad/src/graphics/widgets/ThumbView.py
index 8b00a73d6..20262c5fb 100755
--- a/cad/src/graphics/widgets/ThumbView.py
+++ b/cad/src/graphics/widgets/ThumbView.py
@@ -1,4 +1,4 @@
-# Copyright 2004-2008 Nanorex, Inc.  See LICENSE file for details. 
+# Copyright 2004-2009 Nanorex, Inc.  See LICENSE file for details. 
 """
 ThumbView.py - a simpler OpenGL widget, similar to GLPane
 (which unfortunately has a lot of duplicated but partly modified
@@ -6,7 +6,7 @@ code copied from GLPane)
 
 @author: Huaicai
 @version: $Id$
-@copyright: 2004-2008 Nanorex, Inc.  See LICENSE file for details. 
+@copyright: 2004-2009 Nanorex, Inc.  See LICENSE file for details. 
 """
 
 from Numeric import dot
@@ -734,7 +734,7 @@ class ElementView(ThumbView):
     
     def constructModel(self, elm, pos, dispMode):
         """
-        This is to try to repeat what 'oneUnbonded()' function does,
+        This is to try to repeat what 'make_Atom_and_bondpoints()' method does,
         but hope to remove some stuff not needed here.
         The main purpose is to build the geometry model for element display.
         
@@ -872,7 +872,7 @@ class MMKitView(ThumbView):
             
     def constructModel(self, elm, pos, dispMode):
         """
-        This is to try to repeat what 'oneUnbonded()' function does,
+        This is to try to repeat what 'make_Atom_and_bondpoints()' method does,
         but hope to remove some stuff not needed here.
         The main purpose is to build the geometry model for element display. 
 
diff --git a/cad/src/model/chem.py b/cad/src/model/chem.py
index 11537efbc..4c0d565e7 100755
--- a/cad/src/model/chem.py
+++ b/cad/src/model/chem.py
@@ -100,7 +100,6 @@ from utilities.constants import atKey
     # read from an mmp file), so we now require this in the future even if the
     # key type is changed. [Note: this comment appears in two files.]
 
-from utilities.constants import gensym
 from utilities.constants import intRound
 
 from utilities.constants import diDEFAULT
@@ -4770,43 +4769,6 @@ register_class_changedicts( Atom, _Atom_global_dicts )
 
 # ==
 
-def oneUnbonded(elem, assy, pos, atomtype = None, Chunk_class = None):
-    """
-    Create one unbonded atom, of element elem
-    and (if supplied) the given atomtype
-    (otherwise the default atomtype for elem),
-    at position pos, in its own new chunk,
-    with enough bondpoints to have no valence error.
-
-    @param Chunk_class: constructor for the returned atom's new chunk
-                        (assy.Chunk by default)
-
-    @return: one newly created Atom object, already placed into a new
-             chunk which has been added to the model using addnode
-    """
-    #bruce 041215 moved this from chunk.py to chem.py, and split part of it
-    # into the new atom method make_bondpoints_when_no_bonds, to help fix bug 131.
-    #bruce 050510 added atomtype option
-    #bruce 080520 added Chunk_class option
-    #todo: refile into operations, maybe as an assy or part method
-    if Chunk_class is None:
-        Chunk_class = assy.Chunk
-    chunk = Chunk_class(assy, 'bug') # name is reset below!
-    atom = Atom(elem.symbol, pos, chunk)
-    # bruce 041124 revised name of new chunk, was gensym('Chunk.');
-    # no need for gensym since atom key makes the name unique, e.g. C1.
-    atom.set_atomtype_but_dont_revise_singlets(atomtype) 
-        # ok to pass None, type name, or type object; this verifies no change in elem
-        # note, atomtype might well already be the value we're setting; 
-        # if it is, this should do nothing
-    ## chunk.name = "Chunk-%s" % str(atom)
-    chunk.name = gensym("Chunk", assy) #bruce 080407 per Mark NFR desire
-    atom.make_bondpoints_when_no_bonds() # notices atomtype
-    assy.addnode(chunk)
-    return atom
-
-# ==
-
 def move_atoms_and_normalize_bondpoints(alist, newPositions): 
     """
     Move the atoms in alist to the new positions in the given array or sequence
diff --git a/cad/src/model/virtual_site_indicators.py b/cad/src/model/virtual_site_indicators.py
index 07f179f34..09e743150 100644
--- a/cad/src/model/virtual_site_indicators.py
+++ b/cad/src/model/virtual_site_indicators.py
@@ -1,4 +1,4 @@
-# Copyright 2008 Nanorex, Inc.  See LICENSE file for details.
+# Copyright 2008-2009 Nanorex, Inc.  See LICENSE file for details.
 """
 virtual_site_indicators.py - graphical indicators related to virtual sites
 (as used in the current GROMACS implementation of the PAM5 force field);
@@ -7,7 +7,7 @@ not as part of their implementation for minimize.
 
 @author: Bruce
 @version: $Id$
-@copyright: 2008 Nanorex, Inc.  See LICENSE file for details.
+@copyright: 2008-2009 Nanorex, Inc.  See LICENSE file for details.
 """
 
 from model.jigs import Jig
@@ -405,9 +405,8 @@ def make_virtual_site( assy, parent_atoms, site_params, MT_name = None):
     """
     @return: ( object to assign to site_atom_id, list of nodes to add to MT )
     """
-    from model.chem import oneUnbonded
     from model.elements import Vs0
-    site_atom = oneUnbonded(Vs0, assy, V(0,0,0), Chunk_class = VirtualSiteChunk)
+    site_atom = assy.make_Atom_and_bondpoints(Vs0, V(0,0,0), Chunk_class = VirtualSiteChunk)
     jig = VirtualSiteJig(assy, parent_atoms + [site_atom])
     jig.setProps(site_params) # so it knows how to compute site_position
     jig._update_site_atom_position()
@@ -432,7 +431,7 @@ def add_virtual_site(assy, parent_atoms, site_params, MT_name = None):
     site_atom, nodes = make_virtual_site( assy, parent_atoms, site_params, MT_name = MT_name)
     for node in nodes:
         assy.addnode(node) # todo: add them in a better place?
-            # review: redundant with oneUnbonded?
+            # review: redundant with make_Atom_and_bondpoints?
     return site_atom
 
 # ==
diff --git a/cad/src/operations/ops_atoms.py b/cad/src/operations/ops_atoms.py
index 0c8e922ec..5fd30a739 100755
--- a/cad/src/operations/ops_atoms.py
+++ b/cad/src/operations/ops_atoms.py
@@ -1,11 +1,11 @@
-# Copyright 2004-2008 Nanorex, Inc.  See LICENSE file for details. 
+# Copyright 2004-2009 Nanorex, Inc.  See LICENSE file for details. 
 """
 ops_atoms.py -- operations on the atoms and/or bonds inside a Part.
 These operations generally create or destroy atoms, bondpoints, or real bonds.
 Operations specific to single modes (Build, Crystal, Extrude) are not included here.
 
 @version: $Id$
-@copyright: 2004-2008 Nanorex, Inc.  See LICENSE file for details.
+@copyright: 2004-2009 Nanorex, Inc.  See LICENSE file for details.
 
 History:
 
@@ -16,9 +16,13 @@ from existing modules, from class Part and class basicMode.
 from utilities.Log import greenmsg, redmsg
 
 from utilities.constants import SELWHAT_CHUNKS, SELWHAT_ATOMS
+from utilities.constants import gensym
 
 from platform_dependent.PlatformDependent import fix_plurals
+
 from model.elements import Singlet
+from model.chem import Atom
+
 import foundation.env as env
 
 class ops_atoms_Mixin:
@@ -26,7 +30,47 @@ class ops_atoms_Mixin:
     Mixin class for providing these methods to class Part
     """
     
-    def modifyTransmute(self, elem, force = False, atomType=None): 
+    def make_Atom_and_bondpoints(self, 
+                                 elem, 
+                                 pos, 
+                                 atomtype = None, 
+                                 Chunk_class = None ):
+        """
+        Create one unbonded atom, of element elem
+        and (if supplied) the given atomtype
+        (otherwise the default atomtype for elem),
+        at position pos, in its own new chunk,
+        with enough bondpoints to have no valence error.
+    
+        @param Chunk_class: constructor for the returned atom's new chunk
+                            (self.assy.Chunk by default)
+                            
+        @return: one newly created Atom object, already placed into a new
+                 chunk which has been added to the model using addnode
+        """
+        #bruce 041215 moved this from chunk.py to chem.py, and split part of it
+        # into the new atom method make_bondpoints_when_no_bonds, to help fix bug 131.
+        #bruce 050510 added atomtype option
+        #bruce 080520 added Chunk_class option
+        #bruce 090112 renamed oneUnbonded function and turned it into this method
+        assy = self.assy
+        if Chunk_class is None:
+            Chunk_class = assy.Chunk
+        chunk = Chunk_class(assy, 'bug') # name is reset below!
+        atom = Atom(elem.symbol, pos, chunk)
+        # bruce 041124 revised name of new chunk, was gensym('Chunk.');
+        # no need for gensym since atom key makes the name unique, e.g. C1.
+        atom.set_atomtype_but_dont_revise_singlets(atomtype) 
+            # ok to pass None, type name, or type object; this verifies no change in elem
+            # note, atomtype might well already be the value we're setting; 
+            # if it is, this should do nothing
+        ## chunk.name = "Chunk-%s" % str(atom)
+        chunk.name = gensym("Chunk", assy) #bruce 080407 per Mark NFR desire
+        atom.make_bondpoints_when_no_bonds() # notices atomtype
+        assy.addnode(chunk) # REVIEW: same as self.addnode?
+        return atom
+        
+    def modifyTransmute(self, elem, force = False, atomType = None): 
         """
         This method was originally a method of class mode and selectMode.
         Transmute selected atoms into <elem> and with an optional <atomType>. 
@@ -61,7 +105,6 @@ class ops_atoms_Mixin:
         
         return
     
-    
     def modifyDeleteBonds(self):
         """
         Delete all bonds between selected and unselected atoms or chunks
author	Bruce Smith <bruce@nanorex.com>	2009-01-12 23:43:33 +0000
committer	Bruce Smith <bruce@nanorex.com>	2009-01-12 23:43:33 +0000
commit	eedffc4ad72c0bf596cbeee66ee0c633b208517c (patch)
tree	54fe8dcb1a5bb876e2bf5045b86e36dabf1a745c
parent	c0e1948c73472001c41d4b60e0919c50f15f1cca (diff)
download	nanoengineer-eedffc4ad72c0bf596cbeee66ee0c633b208517c.tar.gz nanoengineer-eedffc4ad72c0bf596cbeee66ee0c633b208517c.zip