def chooseColor(self, event=None):
top = Tkinter.Toplevel()
colorChooser = ColorChooser(top,
title='library color',
immediate=1,
commands=[self.setColor])
colorChooser.pack()
def changeColor(self, event=None):
#col = self.palette.display(callback=self.color_cb, modal=1)
#self.palette.pack(fill='both', expand=1)
# Create a ColorChooser.
if not hasattr(self, 'palette'):
self.palette = ColorChooser(commands=self.color_cb,
exitFunction=self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
else:
self.palette.master.deiconify()
def onAddCmdToViewer(self):
self.verts = []
if self.vf.hasGui:
self.initGeom()
#from DejaVu.Labels import Labels
self.showAll = Tkinter.IntVar()
self.showAll.set(1)
self.vf.loadModule('labelCommands', 'Pmv', log=0)
# Create a ColorChooser.
self.palette = ColorChooser(commands=self.color_cb,
exitFunction=self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
self.showAll = None
self.width = 100
self.height = 100
self.winfo_x = None
self.winfo_y = None
def changeColor(self, event=None):
#col = self.palette.display(callback=self.color_cb, modal=1)
#self.palette.pack(fill='both', expand=1)
# Create a ColorChooser.
if not hasattr(self, 'palette'):
self.palette = ColorChooser(commands=self.color_cb,
exitFunction = self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
else:
self.palette.master.deiconify()
def onAddCmdToViewer(self):
self.verts = []
if self.vf.hasGui:
self.initGeom()
#from DejaVu.Labels import Labels
self.showAll = Tkinter.IntVar()
self.showAll.set(1)
self.vf.loadModule('labelCommands', 'Pmv', log=0)
# Create a ColorChooser.
self.palette = ColorChooser(commands=self.color_cb,
exitFunction = self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
self.showAll = None
self.width = 100
self.height = 100
self.winfo_x = None
self.winfo_y = None
def chooseColor(self, event=None):
top = Tkinter.Toplevel()
colorChooser = ColorChooser(top, title='library color', immediate=1,
commands=[self.setColor])
colorChooser.pack()
class DisplayStruts(MVCommand):
"""
* Display and Return a vector of support posts for rapid prototyping models
* along the lines of George Phillips for Pymol except on actual molecular
* segments (biopolymers), not PDB chains (which may or may not be
* continuous). => work actually on chain
\nPackage : Pmv
\nModule : strutsCommands
\nClass : DisplayStruts
\nCommand : displayStruts
\nSynopsis:\n
None <--- displayStruts(node)
"""
def __init__(self, func=None):
MVCommand.__init__(self, func)
self.flag = self.flag | self.objArgOnly
def initGeom(self):
#initialize:
# self.geom
# self.hasGeom
pass
def onAddCmdToViewer(self):
self.verts = []
if self.vf.hasGui:
self.initGeom()
#from DejaVu.Labels import Labels
self.showAll = Tkinter.IntVar()
self.showAll.set(1)
self.vf.loadModule('labelCommands', 'Pmv', log=0)
# Create a ColorChooser.
self.palette = ColorChooser(commands=self.color_cb,
exitFunction=self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
self.showAll = None
self.width = 100
self.height = 100
self.winfo_x = None
self.winfo_y = None
def hidePalette_cb(self, event=None):
self.palette.hide()
def reset(self):
self.geom.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
self.hasGeom = 0
def update(self, event=None):
self.radii = self.radii_esw.get()
self.hasGeom = 0
self.showAllStruts()
def color_cb(self, colors):
from DejaVu import colorTool
self.geom.Set(materials=(colors[:3], ), tagModified=False)
self.vf.GUI.VIEWER.Redraw()
def changeColor(self, event=None):
#col = self.palette.display(callback=self.color_cb, modal=1)
#self.palette.pack(fill='both', expand=1)
# Create a ColorChooser.
if not hasattr(self, 'palette'):
self.palette = ColorChooser(commands=self.color_cb,
exitFunction=self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
else:
self.palette.master.deiconify()
def getIfd(self, atNames):
#base class
pass
def setUpWidgets(self, atNames):
if not hasattr(self, 'ifd'):
self.getIfd(atNames)
self.radii_esw = self.ifd.entryByName['radii']['widget']
self.lb = self.ifd.entryByName['atsLC']['widget'].lb
def doit(self, ats):
#DisplayStruts base class
self.reset()
hbats = AtomSet(ats.get(lambda x: hasattr(x, 'struts')))
if not hbats:
self.warningMsg('no struts bonds found, please compute them')
return 'ERROR'
self.hats = hbats
self.showAllHBonds()
def updateQuality(self, event=None):
# asSpheres
self.quality = self.quality_sl.get()
self.geom.Set(quality=quality, tagModified=False)
self.showAllHBonds()
def dismiss_cb(self, event=None, **kw):
# base class
self.reset()
try:
self.width = str(self.toplevel.winfo_width())
self.height = str(self.toplevel.winfo_height())
self.winfo_x = str(self.toplevel.winfo_x())
self.winfo_y = str(self.toplevel.winfo_y())
except:
pass
self.vf.GUI.VIEWER.Redraw()
if hasattr(self, 'ifd'):
delattr(self, 'ifd')
if hasattr(self, 'form2'):
self.form2.destroy()
delattr(self, 'form2')
if hasattr(self, 'form'):
self.form.destroy()
delattr(self, 'form')
if hasattr(self, 'palette'):
#self.palette.exit()
self.palette.hide()
def setupDisplay(self):
#draw geom between hAts OR donAts and accAts
self.geom.Set(vertices=self.verts,
radius=self.radius,
tagModified=False)
self.vf.GUI.VIEWER.Redraw()
def interpolate(self, pt1, pt2):
# self.spacing = .4
length = dist(pt1, pt2)
c1 = Numeric.array(pt1)
c2 = Numeric.array(pt2)
n = length / self.spacing
npts = int(math.floor(n))
# use floor of npts to set distance between > spacing
delta = (c2 - c1) / (1.0 * npts)
##spacing = length/floor(npts)
vertList = []
for i in range(npts):
vertList.append((c1 + i * delta).tolist())
vertList.append(pt2.tolist())
return vertList
def setDVerts(self, entries, event=None):
if not hasattr(self, 'ifd2'):
self.changeDVerts()
lb = self.ifd2.entryByName['datsLC']['widget'].lb
if lb.curselection() == (): return
atName = lb.get(lb.curselection())
ind = int(lb.curselection()[0])
for h in self.hats:
for b in h.hbonds:
ats = b.donAt.parent.atoms.get(
lambda x, atName=atName: x.name == atName)
if ats is None or len(ats) == 0:
if b.hAt is not None: at = b.hAt
else: at = b.donAt
else:
at = ats[0]
b.spVert1 = at
self.hasGeom = 0
self.showAllHBonds()
def setAVerts(self, entries, event=None):
if not hasattr(self, 'ifd2'):
self.changeDVerts()
lb = self.ifd2.entryByName['aatsLC']['widget'].lb
if lb.curselection() == (): return
atName = lb.get(lb.curselection())
ind = int(lb.curselection()[0])
for h in self.hats:
for b in h.hbonds:
ats = b.accAt.parent.atoms.get(
lambda x, atName=atName: x.name == atName)
if ats is None or len(ats) == 0:
at = b.accAt
else:
at = ats[0]
b.spVert2 = at
self.hasGeom = 0
self.showAllHBonds()
def changeDVerts(self, event=None):
#for all residues in hbonds, pick new donorAttachment
# and new acceptorAttachment
entries = []
ns = ['N', 'C', 'O', 'CA', 'reset']
for n in ns:
entries.append((n, None))
if hasattr(self, 'form2'):
self.form2.root.tkraise()
return
ifd2 = self.ifd2 = InputFormDescr(title='Set Anchor Atoms')
ifd2.append({
'name': 'datsLC',
'widgetType': ListChooser,
'wcfg': {
'entries': entries,
'mode': 'single',
'title': 'Donor Anchor',
'command': CallBackFunction(self.setDVerts, entries),
'lbwcfg': {
'height': 5,
'selectforeground': 'red',
'exportselection': 0,
#'lbpackcfg':{'fill':'both', 'expand':1},
'width': 30
},
},
'gridcfg': {
'sticky': 'wens',
'columnspan': 2
}
})
ifd2.append({
'name': 'aatsLC',
'widgetType': ListChooser,
'wcfg': {
'entries': entries,
'mode': 'single',
'title': 'Acceptor Anchor',
'command': CallBackFunction(self.setAVerts, entries),
'lbwcfg': {
'height': 5,
'selectforeground': 'red',
#'lbpackcfg':{'fill':'both', 'expand':1},
'exportselection': 0,
'width': 30
},
},
'gridcfg': {
'sticky': 'wens',
'columnspan': 2
}
})
ifd2.append({
'name': 'doneBut',
'widgetType': Tkinter.Button,
'wcfg': {
'text': 'Done',
'command': self.closeChangeDVertLC
},
'gridcfg': {
'sticky': 'wens'
}
})
self.form2 = self.vf.getUserInput(self.ifd2, modal=0, blocking=0)
self.form2.root.protocol('WM_DELETE_WINDOW', self.closeChangeDVertLC)
def closeChangeDVertLC(self, event=None):
if hasattr(self, 'ifd2'):
delattr(self, 'ifd2')
if hasattr(self, 'form2'):
self.form2.destroy()
delattr(self, 'form2')
def showAllHBonds(self, event=None):
pass
#self.geom.Set(vertices = self.verts, radii = self.radii,
# tagModified=False)
#self.vf.GUI.VIEWER.Redraw()
def guiCallback(self):
#showHbonds
if not len(self.vf.Mols):
self.warningMsg('no molecules in viewer')
return
sel = self.vf.getSelection()
#put a selector here
if len(sel):
ats = sel.findType(Atom)
apply(self.doitWrapper, (ats, ), {})
class DisplayStruts(MVCommand):
"""
* Display and Return a vector of support posts for rapid prototyping models
* along the lines of George Phillips for Pymol except on actual molecular
* segments (biopolymers), not PDB chains (which may or may not be
* continuous). => work actually on chain
\nPackage : Pmv
\nModule : strutsCommands
\nClass : DisplayStruts
\nCommand : displayStruts
\nSynopsis:\n
None <--- displayStruts(node)
"""
def __init__(self, func=None):
MVCommand.__init__(self, func)
self.flag = self.flag | self.objArgOnly
def initGeom(self):
#initialize:
# self.geom
# self.hasGeom
pass
def onAddCmdToViewer(self):
self.verts = []
if self.vf.hasGui:
self.initGeom()
#from DejaVu.Labels import Labels
self.showAll = Tkinter.IntVar()
self.showAll.set(1)
self.vf.loadModule('labelCommands', 'Pmv', log=0)
# Create a ColorChooser.
self.palette = ColorChooser(commands=self.color_cb,
exitFunction = self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
self.showAll = None
self.width = 100
self.height = 100
self.winfo_x = None
self.winfo_y = None
def hidePalette_cb(self, event=None):
self.palette.hide()
def reset(self):
self.geom.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
self.hasGeom = 0
def update(self, event=None):
self.radii = self.radii_esw.get()
self.hasGeom =0
self.showAllStruts()
def color_cb(self, colors):
from DejaVu import colorTool
self.geom.Set(materials = (colors[:3],), tagModified=False)
self.vf.GUI.VIEWER.Redraw()
def changeColor(self, event=None):
#col = self.palette.display(callback=self.color_cb, modal=1)
#self.palette.pack(fill='both', expand=1)
# Create a ColorChooser.
if not hasattr(self, 'palette'):
self.palette = ColorChooser(commands=self.color_cb,
exitFunction = self.hidePalette_cb)
# pack
self.palette.pack(fill='both', expand=1)
# hide it
self.palette.hide()
else:
self.palette.master.deiconify()
def getIfd(self, atNames):
#base class
pass
def setUpWidgets(self, atNames):
if not hasattr(self, 'ifd'):
self.getIfd(atNames)
self.radii_esw = self.ifd.entryByName['radii']['widget']
self.lb = self.ifd.entryByName['atsLC']['widget'].lb
def doit(self, ats):
#DisplayStruts base class
self.reset()
hbats = AtomSet(ats.get(lambda x: hasattr(x, 'struts')))
if not hbats:
self.warningMsg('no struts bonds found, please compute them')
return 'ERROR'
self.hats = hbats
self.showAllHBonds()
def updateQuality(self, event=None):
# asSpheres
self.quality = self.quality_sl.get()
self.geom.Set(quality=quality, tagModified=False)
self.showAllHBonds()
def dismiss_cb(self, event=None, **kw):
# base class
self.reset()
try:
self.width = str(self.toplevel.winfo_width())
self.height = str(self.toplevel.winfo_height())
self.winfo_x = str(self.toplevel.winfo_x())
self.winfo_y = str(self.toplevel.winfo_y())
except:
pass
self.vf.GUI.VIEWER.Redraw()
if hasattr(self, 'ifd'):
delattr(self, 'ifd')
if hasattr(self, 'form2'):
self.form2.destroy()
delattr(self, 'form2')
if hasattr(self, 'form'):
self.form.destroy()
delattr(self, 'form')
if hasattr(self, 'palette'):
#self.palette.exit()
self.palette.hide()
def setupDisplay(self):
#draw geom between hAts OR donAts and accAts
self.geom.Set(vertices = self.verts, radius = self.radius,
tagModified=False)
self.vf.GUI.VIEWER.Redraw()
def interpolate(self, pt1, pt2):
# self.spacing = .4
length = dist(pt1, pt2)
c1 = Numeric.array(pt1)
c2 = Numeric.array(pt2)
n = length/self.spacing
npts = int(math.floor(n))
# use floor of npts to set distance between > spacing
delta = (c2-c1)/(1.0*npts)
##spacing = length/floor(npts)
vertList = []
for i in range(npts):
vertList.append((c1+i*delta).tolist())
vertList.append(pt2.tolist())
return vertList
def setDVerts(self, entries, event=None):
if not hasattr(self, 'ifd2'):
self.changeDVerts()
lb = self.ifd2.entryByName['datsLC']['widget'].lb
if lb.curselection() == (): return
atName = lb.get(lb.curselection())
ind = int(lb.curselection()[0])
for h in self.hats:
for b in h.hbonds:
ats = b.donAt.parent.atoms.get(lambda x, atName=atName: x.name==atName)
if ats is None or len(ats) == 0:
if b.hAt is not None: at = b.hAt
else: at = b.donAt
else:
at = ats[0]
b.spVert1 = at
self.hasGeom = 0
self.showAllHBonds()
def setAVerts(self, entries, event=None):
if not hasattr(self, 'ifd2'):
self.changeDVerts()
lb = self.ifd2.entryByName['aatsLC']['widget'].lb
if lb.curselection() == (): return
atName = lb.get(lb.curselection())
ind = int(lb.curselection()[0])
for h in self.hats:
for b in h.hbonds:
ats = b.accAt.parent.atoms.get(lambda x, atName=atName: x.name==atName)
if ats is None or len(ats) == 0:
at = b.accAt
else:
at = ats[0]
b.spVert2 = at
self.hasGeom = 0
self.showAllHBonds()
def changeDVerts(self, event=None):
#for all residues in hbonds, pick new donorAttachment
# and new acceptorAttachment
entries = []
ns = ['N','C','O','CA','reset']
for n in ns:
entries.append((n, None))
if hasattr(self, 'form2'):
self.form2.root.tkraise()
return
ifd2 = self.ifd2=InputFormDescr(title = 'Set Anchor Atoms')
ifd2.append({'name': 'datsLC',
'widgetType':ListChooser,
'wcfg':{
'entries': entries,
'mode': 'single',
'title': 'Donor Anchor',
'command': CallBackFunction(self.setDVerts, entries),
'lbwcfg':{'height':5,
'selectforeground': 'red',
'exportselection': 0,
#'lbpackcfg':{'fill':'both', 'expand':1},
'width': 30},
},
'gridcfg':{'sticky':'wens', 'columnspan':2}})
ifd2.append({'name': 'aatsLC',
'widgetType':ListChooser,
'wcfg':{
'entries': entries,
'mode': 'single',
'title': 'Acceptor Anchor',
'command': CallBackFunction(self.setAVerts, entries),
'lbwcfg':{'height':5,
'selectforeground': 'red',
#'lbpackcfg':{'fill':'both', 'expand':1},
'exportselection': 0,
'width': 30},
},
'gridcfg':{'sticky':'wens', 'columnspan':2}})
ifd2.append({'name':'doneBut',
'widgetType':Tkinter.Button,
'wcfg': { 'text':'Done',
'command': self.closeChangeDVertLC},
'gridcfg':{'sticky':'wens'}})
self.form2 = self.vf.getUserInput(self.ifd2, modal=0, blocking=0)
self.form2.root.protocol('WM_DELETE_WINDOW',self.closeChangeDVertLC)
def closeChangeDVertLC(self, event=None):
if hasattr(self, 'ifd2'):
delattr(self, 'ifd2')
if hasattr(self, 'form2'):
self.form2.destroy()
delattr(self, 'form2')
def showAllHBonds(self, event=None):
pass
#self.geom.Set(vertices = self.verts, radii = self.radii,
# tagModified=False)
#self.vf.GUI.VIEWER.Redraw()
def guiCallback(self):
#showHbonds
if not len(self.vf.Mols):
self.warningMsg('no molecules in viewer')
return
sel = self.vf.getSelection()
#put a selector here
if len(sel):
ats = sel.findType(Atom)
apply(self.doitWrapper, (ats,), {})
