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Index: pymol/ChangeLog
===================================================================
--- pymol/ChangeLog (revision 4030)
+++ pymol/ChangeLog (revision 4031)
@@ -2,6 +2,16 @@
CHANGE LOG
=========================================================================
+2013-06-13 Blaine Bell <blaine.bell@schrodinger.com>
+
+ * fixed labels when use_shaders is 0 and show_frame_rate is on
+
+2013-06-12 Thomas Holder <thomas.holder@schrodinger.com>
+
+ * update APBS Tools plugin
+
+ * fix spectrumany when minimum/maximum are provided
+
2013-06-11 Blaine Bell <blaine.bell@schrodinger.com>
* Open Source PyMOL v1.6.0.0
Index: pymol/layer1/Character.c
===================================================================
--- pymol/layer1/Character.c (revision 4030)
+++ pymol/layer1/Character.c (revision 4031)
@@ -276,16 +276,16 @@
rec->extent[2], rec->extent[1],
rec->extent[2], rec->extent[3]
};
- glEnableClientState(GL_VERTEX_ARRAY);
- glEnableClientState(GL_TEXTURE_COORD_ARRAY);
-#ifdef OPENGL_ES_1
- glClientActiveTexture(GL_TEXTURE1);
-#endif
- glVertexPointer(3, GL_FLOAT, 0, vertexVals);
- glTexCoordPointer(2, GL_FLOAT, 0, texVals);
- glDrawArrays(GL_TRIANGLE_STRIP, 0, 4);
- glDisableClientState(GL_VERTEX_ARRAY);
- glDisableClientState(GL_TEXTURE_COORD_ARRAY);
+ glBegin(GL_QUADS);
+ glTexCoord2f(rec->extent[0], rec->extent[1]);
+ glVertex3f(v0[0], v0[1], v0[2]);
+ glTexCoord2f(rec->extent[0], rec->extent[3]);
+ glVertex3f(v0[0], v1[1], v0[2]);
+ glTexCoord2f(rec->extent[2], rec->extent[3]);
+ glVertex3f(v1[0], v1[1], v0[2]);
+ glTexCoord2f(rec->extent[2], rec->extent[1]);
+ glVertex3f(v1[0], v0[1], v0[2]);
+ glEnd();
}
}
}
Index: pymol/modules/pymol/__init__.py
===================================================================
--- pymol/modules/pymol/__init__.py (revision 4030)
+++ pymol/modules/pymol/__init__.py (revision 4031)
@@ -252,9 +252,11 @@
# auto-detect bundled FREEMOL (if present)
if not os.environ.has_key("FREEMOL"):
- test_path = os.path.join(os.environ['PYMOL_PATH'],"freemol")
- if os.path.isdir(test_path):
- os.environ['FREEMOL'] = test_path
+ for test_path in ['freemol', 'ext']:
+ test_path = os.path.join(os.environ['PYMOL_PATH'], test_path)
+ if os.path.isdir(test_path):
+ os.environ['FREEMOL'] = test_path
+ break
# include FREEMOL's libpy in sys.path (if present)
@@ -339,9 +341,6 @@
elif vendor.startswith('Parallels'):
if renderer[0:8]=='Parallel':
pass
- # this was critical for older Parallels
- # but actually slows down current versions
- # cmd.set('texture_fonts',1)
elif vendor.startswith('ATI'):
if renderer[0:17]=='FireGL2 / FireGL3': # obsolete ?
Index: pymol/modules/pymol/preset.py
===================================================================
--- pymol/modules/pymol/preset.py (revision 4030)
+++ pymol/modules/pymol/preset.py (revision 4031)
@@ -21,7 +21,7 @@
tmp_sele = "_p_tmp"
-prot_and_dna_sele = "(resn ALA+CYS+CYX+ASP+GLU+PHE+GLY+HIS+HID+HIE+HIP+HISE+HISD+HISP+ILE+LYS+LEU+MET+MSE+ASN+PRO+GLN+ARG+SER+THR+VAL+TRP+TYR+A+C+T+G+U)"
+prot_and_dna_sele = "(resn ALA+CYS+CYX+ASP+GLU+PHE+GLY+HIS+HID+HIE+HIP+HISE+HISD+HISP+ILE+LYS+LEU+MET+MSE+ASN+PRO+GLN+ARG+SER+THR+VAL+TRP+TYR+A+C+T+G+U+DA+DC+DT+DG+DU+DI)"
wat_sele = "(resn WAT,H2O,HOH,TIP)"
ion_sele = "(resn CA,HG,K,NA,ZN,MG,CL)"
solv_sele = "("+wat_sele+"|"+ion_sele+")"
Index: pymol/modules/pymol/cmd.py
===================================================================
--- pymol/modules/pymol/cmd.py (revision 4030)
+++ pymol/modules/pymol/cmd.py (revision 4031)
@@ -310,8 +310,7 @@
selection_sc = lambda sc=Shortcut,gn=get_names:sc(gn('public')+['all'])
object_sc = lambda sc=Shortcut,gn=get_names:sc(gn('objects'))
map_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:map'))
- contour_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(
- gnot('object:mesh')+gnot('object:surface'))
+ contour_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:mesh')+gnot('object:surface'))
group_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:group'))
# Table for argument autocompletion
Index: pymol/modules/pymol/viewing.py
===================================================================
--- pymol/modules/pymol/viewing.py (revision 4030)
+++ pymol/modules/pymol/viewing.py (revision 4031)
@@ -1393,9 +1393,9 @@
if action=='clear':
for key in pymol._scene_dict.keys():
# free selections
- list = pymol._scene_dict[key]
- if len(list)>3:
- colorection = list[3]
+ scene_list = pymol._scene_dict[key]
+ if len(scene_list)>3:
+ colorection = scene_list[3]
if colorection!=None:
_self.del_colorection(colorection,key)
name = "_scene_"+key+"_*"
@@ -1427,6 +1427,8 @@
print "Error: scene '%s' not found."%key
elif new_key==None:
print "Error: must provide the 'new_key' argument"
+ elif new_key == key:
+ print "scene: '%s' not changed" % key
else:
new_scene_order = []
for a in pymol._scene_order:
@@ -1443,9 +1445,9 @@
if name in valid_names:
new_name = "_scene_"+new_key+"_"+rep_name
_self.set_name(name,new_name)
- list = pymol._scene_dict[new_key]
- if len(list)>3:
- _self.set_colorection_name(list[3],key,new_key)
+ scene_list = pymol._scene_dict[new_key]
+ if len(scene_list)>3:
+ _self.set_colorection_name(scene_list[3],key,new_key)
print" scene: '%s' renamed to '%s'."%(key,new_key)
pymol._scene_dict_sc.rebuild( pymol._scene_dict.keys())
_self.set("session_changed",1,quiet=1)
@@ -1464,29 +1466,29 @@
_self.set("scenes_changed",1,quiet=1);
key = pymol._scene_dict_sc.auto_err(key,'scene')
_self.set('scene_current_name', key, quiet=1)
- list = pymol._scene_dict[key]
- ll = len(list)
+ scene_list = pymol._scene_dict[key]
+ ll = len(scene_list)
if (ll>1) and (active):
- if list[1]!=None:
+ if scene_list[1]!=None:
_self.disable()
_self.deselect()
- _self.set_vis(list[1])
+ _self.set_vis(scene_list[1])
if (ll>2) and (frame):
- if list[2]!=None:
+ if scene_list[2]!=None:
if not _self.get_movie_playing(): # don't set frame when movie is already playing
- if _self.get_frame()!=list[2]: # only set the frame when it isn't already correct
- _self.frame(list[2],scene=1) # let frame know that it is being set by a scene
+ if _self.get_frame()!=scene_list[2]: # only set the frame when it isn't already correct
+ _self.frame(scene_list[2],scene=1) # let frame know that it is being set by a scene
else:
_self.set_frame(1,10) # seek scene
if (ll>3) and (color):
- if list[3]!=None:
- _self.set_colorection(list[3],key)
+ if scene_list[3]!=None:
+ _self.set_colorection(scene_list[3],key)
if (ll>4) and (rep):
- if list[4]==None:
+ if scene_list[4]==None:
rep = 0
if (ll>5) and (message==None):
- if list[5]!=None:
- message=list[5]
+ if scene_list[5]!=None:
+ message=scene_list[5]
if rep!=0:
_self.hide("(all)")
valid_names = _self.get_names("all")
@@ -1521,8 +1523,8 @@
if replace_flag and not mess_flag:
_self.wizard()
if (ll>0) and (view):
- if list[0]!=None:
- _self.set_view(list[0],animate,quiet,hand)
+ if scene_list[0]!=None:
+ _self.set_view(scene_list[0],animate,quiet,hand)
if not quiet and _feedback(fb_module.scene,fb_mask.actions,_self): # redundant
print " scene: \"%s\" recalled."%key
elif (action=='store') or (action=='update'):
@@ -1535,11 +1537,11 @@
if not pymol._scene_dict.has_key(key):
pymol._scene_dict_sc.append(key)
else: # get rid of existing one (if exists)
- list = pymol._scene_dict[key]
- if (action=='update') and (message==None) and len(list)>5:
+ scene_list = pymol._scene_dict[key]
+ if (action=='update') and (message==None) and len(scene_list)>5:
message = pymol._scene_dict[key][5]
- if len(list)>3:
- colorection = list[3]
+ if len(scene_list)>3:
+ colorection = scene_list[3]
if colorection!=None:
_self.del_colorection(colorection,key) # important -- free RAM
name = "_scene_"+key+"_*"
@@ -1575,9 +1577,9 @@
key = setting.get("scene_current_name",_self=_self)
key = pymol._scene_dict_sc.auto_err(key,'scene')
if pymol._scene_dict.has_key(key):
- list = pymol._scene_dict[key]
- if len(list)>3:
- colorection = list[3]
+ scene_list = pymol._scene_dict[key]
+ if len(scene_list)>3:
+ colorection = scene_list[3]
if colorection!=None:
_self.del_colorection(colorection,key) # important -- free RAM
lst = _scene_validate_list(_self)
@@ -2573,7 +2575,7 @@
v = e_it.next()
if v is None:
return False
- v = (float(v) - minimum) / val_range * (n_colors - 1)
+ v = min(1.0, max(0.0, (float(v) - minimum) / val_range)) * (n_colors - 1)
i = min(int(v), n_colors - 2)
p = v - i
rgb = [int(255 * (col_tuples[i+1][j] * p + col_tuples[i][j] * (1.0 - p)))
Index: pymol/modules/pymol/checking.py
===================================================================
--- pymol/modules/pymol/checking.py (revision 4030)
+++ pymol/modules/pymol/checking.py (revision 4031)
@@ -1,6 +1,9 @@
import types
-import cmd
+try:
+ import cmd
+except:
+ cmd = None
def _raising(code=-1,_self=cmd):
# WARNING: internal routine, subject to change
Index: pymol/modules/pymol/shortcut.py
===================================================================
--- pymol/modules/pymol/shortcut.py (revision 4030)
+++ pymol/modules/pymol/shortcut.py (revision 4031)
@@ -15,7 +15,10 @@
if __name__=='pymol.shortcut' or __name__=='shortcut':
import copy
- from pymol.checking import is_string, is_list
+ try:
+ from pymol.checking import is_string, is_list
+ except:
+ from checking import is_string, is_list
def mkabbr(a, m=1):
b = a.split('_')
Index: pymol/modules/pymol/editing.py
===================================================================
--- pymol/modules/pymol/editing.py (revision 4030)
+++ pymol/modules/pymol/editing.py (revision 4031)
@@ -400,13 +400,15 @@
if _self._raising(r,_self): raise pymol.CmdException
return r
- def push_undo(selection, state=0, _self=cmd):
+ def push_undo(selection, just_coordinates=1, finish_undo=0, add_objects=0, delete_objects=0, state=0, _self=cmd):
'''
DESCRIPTION
"push_undo" stores the current conformations of objects in the
selection onto their individual undo rings.
+ Notice: This command is only partly implemented in open-source PyMOL.
+
USAGE
push_undo (all)
Index: pymol/modules/pmg_tk/skins/normal/__init__.py
===================================================================
--- pymol/modules/pmg_tk/skins/normal/__init__.py (revision 4030)
+++ pymol/modules/pmg_tk/skins/normal/__init__.py (revision 4031)
@@ -106,19 +106,6 @@
self.app.destroycomponent('commandframe')
def createMessageBar(self):
- # Create the message bar area for help and status messages.
-# frame = self.app.createcomponent('bottomtray', (), None,
-# Frame,(self.app._hull,), relief=SUNKEN)
-# self.__messageBar = self.app.createcomponent('messagebar',
-# (), None,
-# Pmw.MessageBar,
-# (frame,),
-# #entry_width = 40,
-# entry_relief=SUNKEN,
-# entry_bd=1,
-# labelpos=None)
-# self.__messageBar.pack(side=LEFT, expand=NO, fill=X)
-
self.messageBar = Pmw.MessageBar(self.commandFrame, entry_width = 25,
entry_relief='sunken', entry_borderwidth=1) #, labelpos = 'w')
@@ -139,7 +126,6 @@
self.balloon.configure(statuscommand = self.messageBar.helpmessage)
def destroyMessageBar(self):
-
self.messageBar.destroy()
def get_current_session_file(self):
@@ -465,27 +451,6 @@
self.entry.bind('<Home>',lambda e,s=self: s.cmd.do("cmd._special(106,0,0)"))
self.entry.bind('<End>',lambda e,s=self: s.cmd.do("cmd._special(107,0,0)"))
-# obviated by changes made to the X11 OpenGL Window
-# if sys.platform=='darwin':
-# if self.app.pymol.invocation.options.external_gui==3: # PyMOLX11Hybrid focus kludge
-# self.root.bind_all('<Leave>',lambda e,s=self: s.focus_out(e))
-# self.root.bind_all('<Enter>',lambda e,s=self: s.focus_in(e))
-
-# def focus_in(self,event): # PyMOLX11Hybrid focus kludge
-# if self.refocus_entry:
-# self.cmd.do("_ cmd.window('defocus')") # deactivate MacPyMOL OpenGL window
-# self.refocus_entry = 0
-# self.entry.focus_set()
-
-# def focus_out(self,event): # PyMOLX11Hybrid focus kludge
-# # necessary so that the OpenGL portion of
-# # PyMOLX11Hybrid can exhibit click-through behavior
-# if id(event.widget) == id(self.root):
-# if ((event.y>event.widget.winfo_height())):
-# self.root.focus_set() # (return cursor to entry window)
-# self.cmd.do("_ cmd.window('focus')") # activate MacPyMOL OpenGL window
-# self.refocus_entry = 1
-
def update_feedback(self):
if self.focus_entry:
self.focus_entry=0
@@ -981,18 +946,16 @@
self.cmd.save(sfile,quiet=0)
def file_save_mpeg(self):
- ok = 1
try:
from freemol import mpeg_encode
if not mpeg_encode.validate():
- ok = 0
print "produce-error: Unable to validate freemol.mpeg_encode"
+ raise
except:
- ok = 0
- pass
- if not ok:
tkMessageBox.showerror("Error",
"MPEG encoder missing.\nThe FreeMOL add-ons may not be installed.")
+ return
+
else:
sfile = asksaveasfilename(defaultextension = _def_ext(".mpg"),
initialdir = self.initialdir,
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