Source code for GSASIIconstrGUI
# -*- coding: utf-8 -*-
#GSASIIconstrGUI - constraint GUI routines
########### SVN repository information ###################
# $Date: 2015-07-21 13:28:34 -0500 (Tue, 21 Jul 2015) $
# $Author: vondreele $
# $Revision: 1943 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIconstrGUI.py $
# $Id: GSASIIconstrGUI.py 1943 2015-07-21 18:28:34Z vondreele $
########### SVN repository information ###################
'''
*GSASIIconstrGUI: Constraint GUI routines*
------------------------------------------
Used to define constraints and rigid bodies.
'''
import sys
import wx
import wx.grid as wg
import wx.lib.scrolledpanel as wxscroll
import time
import random as ran
import numpy as np
import numpy.ma as ma
import os.path
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 1943 $")
import GSASIIElem as G2elem
import GSASIIElemGUI as G2elemGUI
import GSASIIstrIO as G2stIO
import GSASIImapvars as G2mv
import GSASIImath as G2mth
import GSASIIlattice as G2lat
import GSASIIgrid as G2gd
import GSASIIctrls as G2G
import GSASIIplot as G2plt
import GSASIIobj as G2obj
VERY_LIGHT_GREY = wx.Colour(235,235,235)
[docs]class MultiIntegerDialog(wx.Dialog):
'''Input a series of integers based on prompts
'''
def __init__(self,parent,title,prompts,values):
wx.Dialog.__init__(self,parent,-1,title,
pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
self.values = values
self.prompts = prompts
self.Draw()
def Draw(self):
def OnValItem(event):
Obj = event.GetEventObject()
ind = Indx[Obj.GetId()]
try:
val = int(Obj.GetValue())
if val <= 0:
raise ValueError
except ValueError:
val = self.values[ind]
self.values[ind] = val
Obj.SetValue('%d'%(val))
self.panel.Destroy()
self.panel = wx.Panel(self)
mainSizer = wx.BoxSizer(wx.VERTICAL)
Indx = {}
for ival,[prompt,value] in enumerate(zip(self.prompts,self.values)):
mainSizer.Add(wx.StaticText(self.panel,-1,prompt),0,wx.ALIGN_CENTER)
valItem = wx.TextCtrl(self.panel,-1,value='%d'%(value),style=wx.TE_PROCESS_ENTER)
mainSizer.Add(valItem,0,wx.ALIGN_CENTER)
Indx[valItem.GetId()] = ival
valItem.Bind(wx.EVT_TEXT_ENTER,OnValItem)
valItem.Bind(wx.EVT_KILL_FOCUS,OnValItem)
OkBtn = wx.Button(self.panel,-1,"Ok")
OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
CancelBtn = wx.Button(self.panel,-1,'Cancel')
CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add((20,20),1)
btnSizer.Add(OkBtn)
btnSizer.Add(CancelBtn)
btnSizer.Add((20,20),1)
mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
self.panel.SetSizer(mainSizer)
self.panel.Fit()
self.Fit()
def GetValues(self):
return self.values
def OnOk(self,event):
parent = self.GetParent()
parent.Raise()
self.EndModal(wx.ID_OK)
def OnCancel(self,event):
parent = self.GetParent()
parent.Raise()
self.EndModal(wx.ID_CANCEL)
[docs]class ConstraintDialog(wx.Dialog):
'''Window to edit Constraint values
'''
def __init__(self,parent,title,text,data,separator='*',varname="",varyflag=False):
wx.Dialog.__init__(self,parent,-1,'Edit '+title,
pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
self.data = data[:]
self.newvar = [varname,varyflag]
panel = wx.Panel(self)
mainSizer = wx.BoxSizer(wx.VERTICAL)
topLabl = wx.StaticText(panel,-1,text)
mainSizer.Add((10,10),1)
mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL|wx.LEFT,10)
mainSizer.Add((10,10),1)
dataGridSizer = wx.FlexGridSizer(cols=3,hgap=2,vgap=2)
self.OkBtn = wx.Button(panel,wx.ID_OK)
for id in range(len(self.data)):
lbl1 = lbl = str(self.data[id][1])
if lbl[-1] != '=': lbl1 = lbl + ' ' + separator + ' '
name = wx.StaticText(panel,wx.ID_ANY,lbl1,
style=wx.ALIGN_RIGHT)
scale = G2G.ValidatedTxtCtrl(panel,self.data[id],0,
typeHint=float,
OKcontrol=self.DisableOK)
dataGridSizer.Add(name,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL,5)
dataGridSizer.Add(scale,0,wx.RIGHT,3)
if ':' in lbl:
dataGridSizer.Add(
wx.StaticText(panel,-1,G2obj.fmtVarDescr(lbl)),
0,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL,3)
else:
dataGridSizer.Add((-1,-1))
if title == 'New Variable':
name = wx.StaticText(panel,wx.ID_ANY,"New variable's\nname (optional)",
style=wx.ALIGN_CENTER)
scale = G2G.ValidatedTxtCtrl(panel,self.newvar,0,
typeHint=str,notBlank=False)
dataGridSizer.Add(name,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL,5)
dataGridSizer.Add(scale,0,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL,3)
self.refine = wx.CheckBox(panel,label='Refine?')
self.refine.SetValue(self.newvar[1]==True)
self.refine.Bind(wx.EVT_CHECKBOX, self.OnCheckBox)
dataGridSizer.Add(self.refine,0,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL,3)
mainSizer.Add(dataGridSizer,0,wx.EXPAND)
self.OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
self.OkBtn.SetDefault()
cancelBtn = wx.Button(panel,wx.ID_CANCEL)
cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add((20,20),1)
btnSizer.Add(self.OkBtn)
btnSizer.Add((20,20),1)
btnSizer.Add(cancelBtn)
btnSizer.Add((20,20),1)
mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
panel.SetSizer(mainSizer)
panel.Fit()
self.Fit()
self.CenterOnParent()
def DisableOK(self,setting):
if setting:
self.OkBtn.Enable()
else:
self.OkBtn.Disable()
def OnCheckBox(self,event):
self.newvar[1] = self.refine.GetValue()
def OnOk(self,event):
parent = self.GetParent()
parent.Raise()
self.EndModal(wx.ID_OK)
def OnCancel(self,event):
parent = self.GetParent()
parent.Raise()
self.EndModal(wx.ID_CANCEL)
def GetData(self):
return self.data
################################################################################
##### Constraints
################################################################################
[docs]def UpdateConstraints(G2frame,data):
'''Called when Constraints tree item is selected.
Displays the constraints in the data window
'''
if not data:
data.update({'Hist':[],'HAP':[],'Phase':[],'Global':[]}) #empty dict - fill it
if 'Global' not in data: #patch
data['Global'] = []
# DEBUG code ########################################
#import GSASIIconstrGUI
#reload(GSASIIconstrGUI)
#reload(G2obj)
#reload(G2stIO)
#import GSASIIstrMain
#reload(GSASIIstrMain)
#reload(G2mv)
#reload(G2gd)
###################################################
Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
G2obj.IndexAllIds(Histograms,Phases)
##################################################################################
# patch: convert old-style (str) variables in constraints to G2VarObj objects
for key,value in data.items():
if key.startswith('_'): continue
j = 0
for cons in value:
#print cons # DEBUG
for i in range(len(cons[:-3])):
if type(cons[i][1]) is str:
cons[i][1] = G2obj.G2VarObj(cons[i][1])
j += 1
if j:
print str(key) + ': '+str(j)+' variable(s) as strings converted to objects'
##################################################################################
rigidbodyDict = G2frame.PatternTree.GetItemPyData(
G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
globalList = rbDict.keys()
globalList.sort()
try:
AtomDict = dict([Phases[phase]['pId'],Phases[phase]['Atoms']] for phase in Phases)
except KeyError:
G2frame.ErrorDialog('Constraint Error','You must run least squares at least once before setting constraints\n'+ \
'We suggest you refine scale factor first')
return
# create a list of the phase variables
Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable,maxSSwave = G2stIO.GetPhaseData(Phases,rbIds=rbIds,Print=False)
phaseList = []
for item in phaseDict:
if item.split(':')[2] not in ['Ax','Ay','Az','Amul','AI/A','Atype','SHorder']:
phaseList.append(item)
phaseList.sort()
phaseAtNames = {}
phaseAtTypes = {}
TypeList = []
for item in phaseList:
Split = item.split(':')
if Split[2][:2] in ['AU','Af','dA']:
Id = int(Split[0])
phaseAtNames[item] = AtomDict[Id][int(Split[3])][0]
phaseAtTypes[item] = AtomDict[Id][int(Split[3])][1]
if phaseAtTypes[item] not in TypeList:
TypeList.append(phaseAtTypes[item])
else:
phaseAtNames[item] = ''
phaseAtTypes[item] = ''
# create a list of the hist*phase variables; include wildcards here
hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,Print=False)
hapList = [i for i in hapDict.keys() if i.split(':')[2] not in ('Type',)]
hapList.sort()
wildList = [] # list of variables with "*" for histogram number
for i in hapList:
s = i.split(':')
if s[1] == "": continue
s[1] = '*'
sj = ':'.join(s)
if sj not in wildList: wildList.append(sj)
#wildList.sort() # unneeded
hapList += wildList
histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
histList = []
for item in histDict:
if item.split(':')[2] not in ['Omega','Type','Chi','Phi',
'Azimuth','Gonio. radius',
'Lam1','Lam2','Back','Temperature','Pressure',
'FreePrm1','FreePrm2','FreePrm3',
]:
histList.append(item)
histList.sort()
wildList = []
# for i in histList: # any reason to have this for hist constraints?
# s = i.split(':')
# if s[1] == "": continue
# s[1] = '*'
# sj = ':'.join(s)
# if sj not in wildList: wildList.append(sj)
# histList += wildList
Indx = {}
G2frame.Page = [0,'phs']
def FindEquivVarb(name,nameList):
'Creates a list of variables appropriate to constrain with name'
outList = []
#phlist = []
items = name.split(':')
namelist = [items[2],]
if 'dA' in name:
namelist = ['dAx','dAy','dAz']
elif 'AU' in name:
namelist = ['AUiso','AU11','AU22','AU33','AU12','AU13','AU23']
elif 'RB' in name:
rbfx = 'RB'+items[2][2]
if 'T' in name and 'Tr' not in name:
namelist = [rbfx+'T11',rbfx+'T22',rbfx+'T33',rbfx+'T12',rbfx+'T13',rbfx+'T23']
if 'L' in name:
namelist = [rbfx+'L11',rbfx+'L22',rbfx+'L33',rbfx+'L12',rbfx+'L13',rbfx+'L23']
if 'S' in name:
namelist = [rbfx+'S12',rbfx+'S13',rbfx+'S21',rbfx+'S23',rbfx+'S31',rbfx+'S32',rbfx+'SAA',rbfx+'SBB']
if 'U' in name:
namelist = [rbfx+'U',]
for item in nameList:
keys = item.split(':')
#if keys[0] not in phlist:
# phlist.append(keys[0])
if items[1] == '*' and keys[2] in namelist: # wildcard -- select only sequential options
keys[1] = '*'
mitem = ':'.join(keys)
if mitem == name: continue
if mitem not in outList: outList.append(mitem)
elif keys[2] in namelist and item != name:
outList.append(item)
return outList
def SelectVarbs(page,FrstVarb,varList,legend,constType):
'''Select variables used in constraints after one variable has
been selected. This routine determines the appropriate variables to be
used based on the one that has been selected and asks for more to be added.
It then creates the constraint and adds it to the constraints list.
Called from OnAddEquivalence, OnAddFunction & OnAddConstraint (all but
OnAddHold)
:param list page: defines calling page -- type of variables to be used
:parm GSASIIobj.G2VarObj FrstVarb: reference to first selected variable
:param list varList: list of other appropriate variables to select from
:param str legend: header for selection dialog
:param str constType: type of constraint to be generated
:returns: a constraint, as defined in
:ref:`GSASIIobj <Constraint_definitions_table>`
'''
choices = [[i]+list(G2obj.VarDescr(i)) for i in varList]
meaning = G2obj.getDescr(FrstVarb.name)
if not meaning:
meaning = "(no definition found!)"
l = str(FrstVarb).split(':')
# make lists of phases & histograms to iterate over
phaselist = [l[0]]
if l[0]:
phaselbl = ['phase #'+l[0]]
if len(Phases) > 1:
phaselist += ['all']
phaselbl += ['all phases']
else:
phaselbl = ['']
histlist = [l[1]]
if l[1] == '*':
pass
elif l[1]:
histlbl = ['histogram #'+l[1]]
if len(Histograms) > 1:
histlist += ['all']
histlbl += ['all histograms']
typ = Histograms[G2obj.LookupHistName(l[1])[0]]['Instrument Parameters'][0]['Type'][1]
i = 0
for hist in Histograms:
if Histograms[hist]['Instrument Parameters'][0]['Type'][1] == typ: i += 1
if i > 1:
histlist += ['all='+typ]
histlbl += ['all '+typ+' histograms']
else:
histlbl = ['']
# make a list of equivalent parameter names
nameList = [FrstVarb.name]
for var in varList:
nam = var.split(":")[2]
if nam not in nameList: nameList += [nam]
# add "wild-card" names to the list of variables
if l[1] == '*':
pass
elif page[1] == 'phs':
if 'RB' in FrstVarb.name:
pass
elif FrstVarb.atom is None:
for nam in nameList:
for ph,plbl in zip(phaselist,phaselbl):
if plbl: plbl = 'For ' + plbl
var = ph+"::"+nam
if var == str(FrstVarb) or var in varList: continue
varList += [var]
choices.append([var,plbl,meaning])
else:
for nam in nameList:
for ph,plbl in zip(phaselist,phaselbl):
if plbl: plbl = ' in ' + plbl
for atype in ['']+TypeList:
if atype:
albl = "For "+atype+" atoms"
akey = "all="+atype
else:
albl = "For all atoms"
akey = "all"
var = ph+"::"+nam+":"+akey
if var == str(FrstVarb) or var in varList: continue
varList += [var]
choices.append([var,albl+plbl,meaning])
elif page[1] == 'hap':
if FrstVarb.name == "Scale":
meaning = "Phase fraction"
for nam in nameList:
for ph,plbl in zip(phaselist,phaselbl):
if plbl: plbl = 'For ' + plbl
for hst,hlbl in zip(histlist,histlbl):
if hlbl:
if plbl:
hlbl = ' in ' + hlbl
else:
hlbl = 'For ' + hlbl
var = ph+":"+hst+":"+nam
if var == str(FrstVarb) or var in varList: continue
varList += [var]
choices.append([var,plbl+hlbl,meaning])
elif page[1] == 'hst':
if FrstVarb.name == "Scale":
meaning = "Scale factor"
for nam in nameList:
for hst,hlbl in zip(histlist,histlbl):
if hlbl:
hlbl = 'For ' + hlbl
var = ":"+hst+":"+nam
if var == str(FrstVarb) or var in varList: continue
varList += [var]
choices.append([var,hlbl,meaning])
elif page[1] == 'glb':
pass
else:
raise Exception, 'Unknown constraint page '+ page[1]
if len(choices):
l1 = l2 = 1
for i1,i2,i3 in choices:
l1 = max(l1,len(i1))
l2 = max(l2,len(i2))
fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
atchoice = [fmt.format(*i) for i in choices]
dlg = G2G.G2MultiChoiceDialog(
G2frame.dataFrame,legend,
'Constrain '+str(FrstVarb)+' with...',atchoice,
toggle=False,size=(625,400),monoFont=True)
dlg.CenterOnParent()
res = dlg.ShowModal()
Selections = dlg.GetSelections()[:]
dlg.Destroy()
if res != wx.ID_OK: return []
if len(Selections) == 0:
dlg = wx.MessageDialog(
G2frame.dataFrame,
'No variables were selected to include with '+str(FrstVarb),
'No variables')
dlg.CenterOnParent()
dlg.ShowModal()
dlg.Destroy()
return []
else:
dlg = wx.MessageDialog(
G2frame.dataFrame,
'There are no appropriate variables to include with '+str(FrstVarb),
'No variables')
dlg.CenterOnParent()
dlg.ShowModal()
dlg.Destroy()
return []
# now process the variables provided by the user
varbs = [str(FrstVarb),] # list of selected variables
for sel in Selections:
var = varList[sel]
# phase(s) included
l = var.split(':')
if l[0] == "all":
phlist = [str(Phases[phase]['pId']) for phase in Phases]
else:
phlist = [l[0]]
# histogram(s) included
if l[1] == "all":
hstlist = [str(Histograms[hist]['hId']) for hist in Histograms]
elif '=' in l[1]:
htyp = l[1].split('=')[1]
hstlist = [str(Histograms[hist]['hId']) for hist in Histograms if
Histograms[hist]['Instrument Parameters'][0]['Type'][1] == htyp]
else:
hstlist = [l[1]]
if len(l) == 3:
for ph in phlist:
for hst in hstlist:
var = ph + ":" + hst + ":" + l[2]
if var in varbs: continue
varbs.append(var)
else: # constraints with atoms or rigid bodies
if len(l) == 5: # rigid body parameter
var = ':'.join(l)
if var in varbs: continue
varbs.append(var)
elif l[3] == "all":
for ph in phlist:
key = G2obj.LookupPhaseName(l[0])[0]
for hst in hstlist: # should be blank
for iatm,at in enumerate(Phases[key]['Atoms']):
var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm)
if var in varbs: continue
varbs.append(var)
elif '=' in l[3]:
for ph in phlist:
key = G2obj.LookupPhaseName(l[0])[0]
cx,ct,cs,cia = Phases[key]['General']['AtomPtrs']
for hst in hstlist: # should be blank
atyp = l[3].split('=')[1]
for iatm,at in enumerate(Phases[key]['Atoms']):
if at[ct] != atyp: continue
var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm)
if var in varbs: continue
varbs.append(var)
else:
for ph in phlist:
key = G2obj.LookupPhaseName(l[0])[0]
for hst in hstlist: # should be blank
var = ph + ":" + hst + ":" + l[2] + ":" + l[3]
if var in varbs: continue
varbs.append(var)
if len(varbs) >= 1 or 'constraint' in constType:
constr = [[1.0,FrstVarb]]
for item in varbs[1:]:
constr += [[1.0,G2obj.G2VarObj(item)]]
if 'equivalence' in constType:
return [constr+[None,None,'e']]
elif 'function' in constType:
return [constr+[None,False,'f']]
elif 'constraint' in constType:
return [constr+[1.0,None,'c']]
else:
raise Exception,'Unknown constraint type: '+str(constType)
else:
dlg = wx.MessageDialog(
G2frame.dataFrame,
'There are no selected variables to include with '+str(FrstVarb),
'No variables')
dlg.CenterOnParent()
dlg.ShowModal()
dlg.Destroy()
return []
def CheckAddedConstraint(newcons):
'''Check a new constraint that has just been input.
If there is an error display a message and give the user a
choice to keep or discard the last entry (why keep? -- they
may want to delete something else or edit multipliers).
Since the varylist is not available, no warning messages
should be generated.
:returns: True if constraint should be added
'''
allcons = []
for key in data:
if key.startswith('_'): continue
allcons += data[key]
allcons += newcons
if not len(allcons): return True
G2mv.InitVars()
constDictList,fixedList,ignored = G2stIO.ProcessConstraints(allcons)
errmsg, warnmsg = G2mv.CheckConstraints('',constDictList,fixedList)
if errmsg:
res = G2frame.ErrorDialog('Constraint Error',
'Error with newly added constraint:\n'+errmsg+
'\n\nDiscard newly added constraint?',parent=G2frame.dataFrame,
wtype=wx.YES_NO)
return res != wx.ID_YES
elif warnmsg:
print 'Unexpected contraint warning:\n',warnmsg
return True
def CheckChangedConstraint():
'''Check all constraints after an edit has been made.
If there is an error display a message and give the user a
choice to keep or discard the last edit.
Since the varylist is not available, no warning messages
should be generated.
:returns: True if the edit should be retained
'''
allcons = []
for key in data:
if key.startswith('_'): continue
allcons += data[key]
if not len(allcons): return True
G2mv.InitVars()
constDictList,fixedList,ignored = G2stIO.ProcessConstraints(allcons)
errmsg, warnmsg = G2mv.CheckConstraints('',constDictList,fixedList)
if errmsg:
res = G2frame.ErrorDialog('Constraint Error',
'Error after editing constraint:\n'+errmsg+
'\n\nDiscard last constraint edit?',parent=G2frame.dataFrame,
wtype=wx.YES_NO)
return res != wx.ID_YES
elif warnmsg:
print 'Unexpected contraint warning:\n',warnmsg
return True
def PageSelection(page):
'Decode page reference'
if page[1] == "phs":
vartype = "phase"
varList = phaseList
constrDictEnt = 'Phase'
elif page[1] == "hap":
vartype = "Histogram*Phase"
varList = hapList
constrDictEnt = 'HAP'
elif page[1] == "hst":
vartype = "Histogram"
varList = histList
constrDictEnt = 'Hist'
elif page[1] == "glb":
vartype = "Global"
varList = globalList
constrDictEnt = 'Global'
else:
raise Exception,'Should not happen!'
return vartype,varList,constrDictEnt
def OnAddHold(event):
'''Create a new Hold constraint
Hold constraints allows the user to select one variable (the list of available
variables depends on which tab is currently active).
'''
page = G2frame.Page
vartype,varList,constrDictEnt = PageSelection(page)
title1 = "Hold "+vartype+" variable"
if not varList:
G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
parent=G2frame.dataFrame)
return
l2 = l1 = 1
for i in varList:
l1 = max(l1,len(i))
loc,desc = G2obj.VarDescr(i)
l2 = max(l2,len(loc))
fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList]
#varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList]
legend = "Select variables to hold (Will not be varied, even if vary flag is set)"
dlg = G2G.G2MultiChoiceDialog(
G2frame.dataFrame,
legend,title1,varListlbl,toggle=False,size=(625,400),monoFont=True)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
for sel in dlg.GetSelections():
Varb = varList[sel]
VarObj = G2obj.G2VarObj(Varb)
newcons = [[[0.0,VarObj],None,None,'h']]
if CheckAddedConstraint(newcons):
data[constrDictEnt] += newcons
dlg.Destroy()
OnPageChanged(None)
def OnAddEquivalence(event):
'''add an Equivalence constraint'''
page = G2frame.Page
vartype,varList,constrDictEnt = PageSelection(page)
title1 = "Setup equivalent "+vartype+" variables"
title2 = "Select additional "+vartype+" variable(s) to be equivalent with "
if not varList:
G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
parent=G2frame.dataFrame)
return
legend = "Select variables to make equivalent (only one of the variables will be varied when all are set to be varied)"
GetAddVars(page,title1,title2,varList,constrDictEnt,'equivalence')
def OnAddAtomEquiv(event):
''' Add equivalences between all parameters on atoms '''
page = G2frame.Page
vartype,varList,constrDictEnt = PageSelection(page)
title1 = "Setup equivalent atom variables"
title2 = "Select additional atoms(s) to be equivalent with "
if not varList:
G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
parent=G2frame.dataFrame)
return
legend = "Select atoms to make equivalent (only one of the atom variables will be varied when all are set to be varied)"
GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'equivalence')
def OnAddRiding(event):
''' Add riding equivalences between all parameters on atoms '''
page = G2frame.Page
vartype,varList,constrDictEnt = PageSelection(page)
title1 = "Setup riding atoms "
title2 = "Select additional atoms(s) to ride on "
if not varList:
G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
parent=G2frame.dataFrame)
return
legend = "Select atoms to ride (only one of the atom variables will be varied when all are set to be varied)"
GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'riding')
def OnAddFunction(event):
'''add a Function (new variable) constraint'''
page = G2frame.Page
vartype,varList,constrDictEnt = PageSelection(page)
title1 = "Setup new variable based on "+vartype+" variables"
title2 = "Include additional "+vartype+" variable(s) to be included with "
if not varList:
G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
parent=G2frame.dataFrame)
return
legend = "Select variables to include in a new variable (the new variable will be varied when all included variables are varied)"
GetAddVars(page,title1,title2,varList,constrDictEnt,'function')
def OnAddConstraint(event):
'''add a constraint equation to the constraints list'''
page = G2frame.Page
vartype,varList,constrDictEnt = PageSelection(page)
title1 = "Setup constraint on "+vartype+" variables"
title2 = "Select additional "+vartype+" variable(s) to include in constraint with "
if not varList:
G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
parent=G2frame.dataFrame)
return
legend = "Select variables to include in a constraint equation (the values will be constrainted to equal a specified constant)"
GetAddVars(page,title1,title2,varList,constrDictEnt,'constraint')
def GetAddVars(page,title1,title2,varList,constrDictEnt,constType):
'''Get the variables to be added for OnAddEquivalence, OnAddFunction,
and OnAddConstraint. Then create and check the constraint.
'''
#varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList]
l2 = l1 = 1
for i in varList:
l1 = max(l1,len(i))
loc,desc = G2obj.VarDescr(i)
l2 = max(l2,len(loc))
fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList]
dlg = G2G.G2SingleChoiceDialog(G2frame.dataFrame,'Select 1st variable:',
title1,varListlbl,
monoFont=True,size=(625,400))
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
FrstVarb = varList[sel]
VarObj = G2obj.G2VarObj(FrstVarb)
moreVarb = FindEquivVarb(FrstVarb,varList)
newcons = SelectVarbs(page,VarObj,moreVarb,title2+FrstVarb,constType)
if len(newcons) > 0:
if CheckAddedConstraint(newcons):
data[constrDictEnt] += newcons
dlg.Destroy()
OnPageChanged(None)
def FindNeighbors(phase,FrstName,AtNames):
General = phase['General']
cx,ct,cs,cia = General['AtomPtrs']
Atoms = phase['Atoms']
atNames = [atom[ct-1] for atom in Atoms]
Cell = General['Cell'][1:7]
Amat,Bmat = G2lat.cell2AB(Cell)
atTypes = General['AtomTypes']
Radii = np.array(General['BondRadii'])
AtInfo = dict(zip(atTypes,Radii)) #or General['BondRadii']
Orig = atNames.index(FrstName.split()[1])
OType = Atoms[Orig][ct]
XYZ = G2mth.getAtomXYZ(Atoms,cx)
Neigh = []
Dx = np.inner(Amat,XYZ-XYZ[Orig]).T
dist = np.sqrt(np.sum(Dx**2,axis=1))
sumR = AtInfo[OType]+0.5 #H-atoms only!
IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
for j in IndB[0]:
if j != Orig:
Neigh.append(AtNames[j])
return Neigh
def GetAddAtomVars(page,title1,title2,varList,constrDictEnt,constType):
'''Get the atom variables to be added for OnAddAtomEquiv. Then create and
check the constraints. Riding for H atoms only.
'''
Atoms = {G2obj.VarDescr(i)[0]:[] for i in varList if 'Atom' in G2obj.VarDescr(i)[0]}
for item in varList:
atName = G2obj.VarDescr(item)[0]
if atName in Atoms:
Atoms[atName].append(item)
AtNames = Atoms.keys()
AtNames.sort()
dlg = G2G.G2SingleChoiceDialog(G2frame.dataFrame,'Select 1st atom:',
title1,AtNames,
monoFont=True,size=(625,400))
dlg.CenterOnParent()
FrstAtom = ''
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
FrstAtom = AtNames[sel]
if 'riding' in constType:
phaseName = (FrstAtom.split(' in ')[1]).strip()
phase = Phases[phaseName]
AtNames = FindNeighbors(phase,FrstAtom,AtNames)
else:
AtNames.remove(FrstAtom)
dlg.Destroy()
if FrstAtom == '':
print 'no atom selected'
return
dlg = G2G.G2MultiChoiceDialog(
G2frame.dataFrame,title2+FrstAtom,
'Constrain '+str(FrstAtom)+' with...',AtNames,
toggle=False,size=(625,400),monoFont=True)
if dlg.ShowModal() == wx.ID_OK:
Selections = dlg.GetSelections()[:]
else:
print 'no target atom selected'
dlg.Destroy()
return
dlg.Destroy()
for name in Atoms[FrstAtom]:
newcons = []
constr = []
if 'riding' in constType:
if 'AUiso' in name:
constr = [[1.0,G2obj.G2VarObj(name)]]
elif 'AU11' in name:
pass
elif 'AU' not in name:
constr = [[1.0,G2obj.G2VarObj(name)]]
else:
constr = [[1.0,G2obj.G2VarObj(name)]]
pref = name.rsplit(':',1)[0]
for sel in Selections:
id = Atoms[AtNames[sel]][0].rsplit(':',1)[-1]
if 'riding' in constType:
if 'AUiso' in pref:
parts = pref.split('AUiso')
constr += [[1.2,G2obj.G2VarObj('%s:%s'%(parts[0]+'AUiso',id))]]
elif 'AU' not in pref:
constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]]
else:
constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]]
if not constr:
continue
if 'frac' in pref and 'riding' not in constType:
newcons = [constr+[1.0,None,'c']]
else:
newcons = [constr+[None,None,'e']]
if len(newcons) > 0:
if CheckAddedConstraint(newcons):
data[constrDictEnt] += newcons
OnPageChanged(None)
def MakeConstraintsSizer(name,pageDisplay):
'''Creates a sizer displaying all of the constraints entered of
the specified type.
:param str name: the type of constraints to be displayed ('HAP',
'Hist', 'Phase', or 'Global')
:param wx.Panel pageDisplay: parent panel for sizer
:returns: wx.Sizer created by method
'''
constSizer = wx.FlexGridSizer(0,6,0,0)
maxlen = 70 # characters before wrapping a constraint
for Id,item in enumerate(data[name]):
refineflag = False
helptext = ""
eqString = ['',]
if item[-1] == 'h': # Hold on variable
constSizer.Add((-1,-1),0) # blank space for edit button
typeString = 'FIXED'
var = str(item[0][1])
varMean = G2obj.fmtVarDescr(var)
eqString[-1] = var +' '
helptext = "Prevents variable:\n"+ var + " ("+ varMean + ")\nfrom being changed"
elif isinstance(item[-1],str): # not true on original-style (2011?) constraints
constEdit = wx.Button(pageDisplay,-1,'Edit',style=wx.BU_EXACTFIT)
constEdit.Bind(wx.EVT_BUTTON,OnConstEdit)
constSizer.Add(constEdit,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER,1) # edit button
Indx[constEdit.GetId()] = [Id,name]
if item[-1] == 'f':
helptext = "A new variable"
if item[-3]:
helptext += " named "+str(item[-3])
helptext += " is created from a linear combination of the following variables:\n"
for term in item[:-3]:
var = str(term[1])
if len(eqString[-1]) > maxlen:
eqString.append(' ')
m = term[0]
if eqString[-1] != '':
if m >= 0:
eqString[-1] += ' + '
else:
eqString[-1] += ' - '
m = abs(m)
eqString[-1] += '%.3f*%s '%(m,var)
varMean = G2obj.fmtVarDescr(var)
helptext += "\n" + var + " ("+ varMean + ")"
if '_Explain' in data:
if data['_Explain'].get(item[-3]):
helptext += '\n\n'
helptext += data['_Explain'][item[-3]]
# typeString = 'NEWVAR'
# if item[-3]:
# eqString[-1] += ' = '+item[-3]
# else:
# eqString[-1] += ' = New Variable'
if item[-3]:
typeString = item[-3] + ' = '
else:
typeString = 'New Variable = '
#print 'refine',item[-2]
refineflag = True
elif item[-1] == 'c':
helptext = "The following variables constrained to equal a constant:"
for term in item[:-3]:
var = str(term[1])
if len(eqString[-1]) > maxlen:
eqString.append(' ')
if eqString[-1] != '':
if term[0] > 0:
eqString[-1] += ' + '
else:
eqString[-1] += ' - '
eqString[-1] += '%.3f*%s '%(abs(term[0]),var)
varMean = G2obj.fmtVarDescr(var)
helptext += "\n" + var + " ("+ varMean + ")"
typeString = 'CONST'
eqString[-1] += ' = '+str(item[-3])
elif item[-1] == 'e':
helptext = "The following variables are set to be equivalent, noting multipliers:"
for term in item[:-3]:
var = str(term[1])
if term[0] == 0: term[0] = 1.0
if len(eqString[-1]) > maxlen:
eqString.append(' ')
if eqString[-1] == '':
eqString[-1] += var+' '
first = term[0]
else:
eqString[-1] += ' = %.3f*%s '%(first/term[0],var)
varMean = G2obj.fmtVarDescr(var)
helptext += "\n" + var + " ("+ varMean + ")"
typeString = 'EQUIV'
else:
print 'Unexpected constraint',item
else:
print 'Removing old-style constraints'
data[name] = []
return constSizer
constDel = wx.Button(pageDisplay,-1,'Delete',style=wx.BU_EXACTFIT)
constDel.Bind(wx.EVT_BUTTON,OnConstDel)
Indx[constDel.GetId()] = [Id,name]
constSizer.Add(constDel,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER,1) # delete button
if helptext:
ch = G2G.HelpButton(pageDisplay,helptext)
constSizer.Add(ch,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER,1)
else:
constSizer.Add((-1,-1))
if refineflag:
ch = G2G.G2CheckBox(pageDisplay,'',item,-2)
constSizer.Add(ch,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER,1)
else:
constSizer.Add((-1,-1))
constSizer.Add(wx.StaticText(pageDisplay,-1,typeString),
0,wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT,3)
if len(eqString) > 1:
Eq = wx.BoxSizer(wx.VERTICAL)
for s in eqString:
Eq.Add(wx.StaticText(pageDisplay,-1,s),0,wx.ALIGN_CENTER_VERTICAL)
else:
Eq = wx.StaticText(pageDisplay,-1,eqString[0])
constSizer.Add(Eq,1,wx.ALIGN_CENTER_VERTICAL)
return constSizer
def OnConstDel(event):
'Delete a constraint'
Obj = event.GetEventObject()
Id,name = Indx[Obj.GetId()]
del(data[name][Id])
OnPageChanged(None)
def OnConstEdit(event):
'''Called to edit an individual contraint in response to a
click on its Edit button
'''
Obj = event.GetEventObject()
Id,name = Indx[Obj.GetId()]
if data[name][Id][-1] == 'f':
items = data[name][Id][:-3]
constType = 'New Variable'
if data[name][Id][-3]:
varname = data[name][Id][-3]
else:
varname = ""
lbl = 'Enter value for each term in constraint; sum = new variable'
dlg = ConstraintDialog(G2frame.dataFrame,constType,lbl,items,
varname=varname,varyflag=data[name][Id][-2])
elif data[name][Id][-1] == 'c':
items = data[name][Id][:-3]+[
[data[name][Id][-3],'fixed value =']]
constType = 'Constraint'
lbl = 'Edit value for each term in constant constraint sum'
dlg = ConstraintDialog(G2frame.dataFrame,constType,lbl,items)
elif data[name][Id][-1] == 'e':
items = data[name][Id][:-3]
constType = 'Equivalence'
lbl = 'The following terms are set to be equal:'
dlg = ConstraintDialog(G2frame.dataFrame,constType,lbl,items,'/')
else:
return
try:
prev = data[name][Id][:]
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetData()
for i in range(len(data[name][Id][:-3])):
if type(data[name][Id][i]) is tuple: # fix non-mutable construct
data[name][Id][i] = list(data[name][Id][i])
data[name][Id][i][0] = result[i][0]
if data[name][Id][-1] == 'c':
data[name][Id][-3] = str(result[-1][0])
elif data[name][Id][-1] == 'f':
# process the variable name to put in global form (::var)
varname = str(dlg.newvar[0]).strip().replace(' ','_')
if varname.startswith('::'):
varname = varname[2:]
varname = varname.replace(':',';')
if varname:
data[name][Id][-3] = varname
else:
data[name][Id][-3] = ''
data[name][Id][-2] = dlg.newvar[1]
if not CheckChangedConstraint():
data[name][Id] = prev
except:
import traceback
print traceback.format_exc()
finally:
dlg.Destroy()
OnPageChanged(None)
def UpdateConstraintPanel(panel,typ):
'''Update the contents of the selected Constraint
notebook tab. Called in :func:`OnPageChanged`
'''
if panel.GetSizer(): panel.GetSizer().Clear(True) # N.B. don't use panel.DestroyChildren()
# because it deletes scrollbars on Mac
Siz = wx.BoxSizer(wx.VERTICAL)
Siz.Add((5,5),0)
Siz.Add(MakeConstraintsSizer(typ,panel))
panel.SetSizer(Siz,True)
Size = Siz.GetMinSize()
Size[0] += 40
Size[1] = max(Size[1],450) + 20
panel.SetSize(Size)
panel.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
Size[1] = min(500,Size[1])
G2frame.dataFrame.setSizePosLeft(Size)
# G2frame.dataFrame.SetSize((500,250)) # set frame size here
def OnPageChanged(event):
'''Called when a tab is pressed or when a "select tab" menu button is
used (see RaisePage), or to refresh the current tab contents (event=None)
'''
if event: #page change event!
page = event.GetSelection()
else: # called directly, get current page
page = G2frame.dataDisplay.GetSelection()
oldPage = G2frame.dataDisplay.ChangeSelection(page)
text = G2frame.dataDisplay.GetPageText(page)
G2frame.dataFrame.ConstraintEdit.Enable(G2gd.wxID_EQUIVALANCEATOMS,False)
# G2frame.dataFrame.ConstraintEdit.Enable(G2gd.wxID_ADDRIDING,False)
if text == 'Histogram/Phase constraints':
G2frame.Page = [page,'hap']
UpdateConstraintPanel(HAPConstr,'HAP')
elif text == 'Histogram constraints':
G2frame.Page = [page,'hst']
UpdateConstraintPanel(HistConstr,'Hist')
elif text == 'Phase constraints':
G2frame.Page = [page,'phs']
G2frame.dataFrame.ConstraintEdit.Enable(G2gd.wxID_EQUIVALANCEATOMS,True)
# G2frame.dataFrame.ConstraintEdit.Enable(G2gd.wxID_ADDRIDING,True)
UpdateConstraintPanel(PhaseConstr,'Phase')
elif text == 'Global constraints':
G2frame.Page = [page,'glb']
UpdateConstraintPanel(GlobalConstr,'Global')
def RaisePage(event):
'Respond to a "select tab" menu button'
try:
i = (G2gd.wxID_CONSPHASE,
G2gd.wxID_CONSHAP,
G2gd.wxID_CONSHIST,
G2gd.wxID_CONSGLOBAL).index(event.GetId())
G2frame.dataDisplay.SetSelection(i)
OnPageChanged(None)
except ValueError:
print('Unexpected event in RaisePage')
def SetStatusLine(text):
Status.SetStatusText(text)
if G2frame.dataDisplay:
G2frame.dataDisplay.Destroy()
G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.ConstraintMenu)
G2frame.dataFrame.SetLabel('Constraints')
if not G2frame.dataFrame.GetStatusBar():
Status = G2frame.dataFrame.CreateStatusBar()
SetStatusLine('')
G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.ConstraintMenu)
G2frame.dataFrame.Bind(wx.EVT_MENU, OnAddConstraint, id=G2gd.wxID_CONSTRAINTADD)
G2frame.dataFrame.Bind(wx.EVT_MENU, OnAddFunction, id=G2gd.wxID_FUNCTADD)
G2frame.dataFrame.Bind(wx.EVT_MENU, OnAddEquivalence, id=G2gd.wxID_EQUIVADD)
G2frame.dataFrame.Bind(wx.EVT_MENU, OnAddHold, id=G2gd.wxID_HOLDADD)
G2frame.dataFrame.Bind(wx.EVT_MENU, OnAddAtomEquiv, id=G2gd.wxID_EQUIVALANCEATOMS)
# G2frame.dataFrame.Bind(wx.EVT_MENU, OnAddRiding, id=G2gd.wxID_ADDRIDING)
# tab commands
for id in (G2gd.wxID_CONSPHASE,
G2gd.wxID_CONSHAP,
G2gd.wxID_CONSHIST,
G2gd.wxID_CONSGLOBAL):
G2frame.dataFrame.Bind(wx.EVT_MENU, RaisePage,id=id)
G2frame.dataDisplay = G2G.GSNoteBook(parent=G2frame.dataFrame)
# note that order of pages is hard-coded in RaisePage
PhaseConstr = wx.ScrolledWindow(G2frame.dataDisplay)
G2frame.dataDisplay.AddPage(PhaseConstr,'Phase constraints')
HAPConstr = wx.ScrolledWindow(G2frame.dataDisplay)
G2frame.dataDisplay.AddPage(HAPConstr,'Histogram/Phase constraints')
HistConstr = wx.ScrolledWindow(G2frame.dataDisplay)
G2frame.dataDisplay.AddPage(HistConstr,'Histogram constraints')
GlobalConstr = wx.ScrolledWindow(G2frame.dataDisplay)
G2frame.dataDisplay.AddPage(GlobalConstr,'Global constraints')
OnPageChanged(None) # show initial page
G2frame.dataDisplay.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
# validate all the constrants -- should not see any errors here normally
allcons = []
for key in data:
if key.startswith('_'): continue
allcons += data[key]
if not len(allcons): return
G2mv.InitVars()
constDictList,fixedList,ignored = G2stIO.ProcessConstraints(allcons)
errmsg, warnmsg = G2mv.CheckConstraints('',constDictList,fixedList)
if errmsg:
G2frame.ErrorDialog('Constraint Error','Error in constraints:\n'+errmsg,
parent=G2frame.dataFrame)
elif warnmsg:
print 'Unexpected contraint warning:\n',warnmsg
################################################################################
#### Rigid bodies
################################################################################
[docs]def UpdateRigidBodies(G2frame,data):
'''Called when Rigid bodies tree item is selected.
Displays the rigid bodies in the data window
'''
if not data.get('RBIds') or not data:
data.update({'Vector':{'AtInfo':{}},'Residue':{'AtInfo':{}},
'RBIds':{'Vector':[],'Residue':[]}}) #empty/bad dict - fill it
global resList
Indx = {}
resList = []
plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1],}
def OnPageChanged(event):
global resList
resList = []
if event: #page change event!
page = event.GetSelection()
else:
page = G2frame.dataDisplay.GetSelection()
oldPage = G2frame.dataDisplay.ChangeSelection(page)
text = G2frame.dataDisplay.GetPageText(page)
if text == 'Vector rigid bodies':
G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.VectorBodyMenu)
G2frame.dataFrame.Bind(wx.EVT_MENU, AddVectorRB, id=G2gd.wxID_VECTORBODYADD)
G2frame.Page = [page,'vrb']
UpdateVectorRB()
elif text == 'Residue rigid bodies':
G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.RigidBodyMenu)
G2frame.dataFrame.Bind(wx.EVT_MENU, AddResidueRB, id=G2gd.wxID_RIGIDBODYADD)
G2frame.dataFrame.Bind(wx.EVT_MENU, OnImportRigidBody, id=G2gd.wxID_RIGIDBODYIMPORT)
G2frame.dataFrame.Bind(wx.EVT_MENU, OnDefineTorsSeq, id=G2gd.wxID_RESIDUETORSSEQ)
G2frame.Page = [page,'rrb']
UpdateResidueRB()
def getMacroFile(macName):
defDir = os.path.join(os.path.split(__file__)[0],'GSASIImacros')
dlg = wx.FileDialog(G2frame,message='Choose '+macName+' rigid body macro file',
defaultDir=defDir,defaultFile="",wildcard="GSAS-II macro file (*.mac)|*.mac",
style=wx.OPEN | wx.CHANGE_DIR)
try:
if dlg.ShowModal() == wx.ID_OK:
macfile = dlg.GetPath()
macro = open(macfile,'Ur')
head = macro.readline()
if macName not in head:
print head
print '**** ERROR - wrong restraint macro file selected, try again ****'
macro = []
else: # cancel was pressed
macro = []
finally:
dlg.Destroy()
return macro #advanced past 1st line
def getTextFile():
defDir = os.path.join(os.path.split(__file__)[0],'GSASIImacros')
dlg = wx.FileDialog(G2frame,'Choose rigid body text file', '.', '',
"GSAS-II text file (*.txt)|*.txt|XYZ file (*.xyz)|*.xyz|"
"Sybyl mol2 file (*.mol2)|*.mol2|PDB file (*.pdb;*.ent)|*.pdb;*.ent",
wx.OPEN | wx.CHANGE_DIR)
try:
if dlg.ShowModal() == wx.ID_OK:
txtfile = dlg.GetPath()
ext = os.path.splitext(txtfile)[1]
text = open(txtfile,'Ur')
else: # cancel was pressed
ext = ''
text = []
finally:
dlg.Destroy()
if 'ent' in ext:
ext = '.pdb'
return text,ext.lower()
def OnImportRigidBody(event):
page = G2frame.dataDisplay.GetSelection()
if 'Vector' in G2frame.dataDisplay.GetPageText(page):
pass
elif 'Residue' in G2frame.dataDisplay.GetPageText(page):
ImportResidueRB()
def AddVectorRB(event):
AtInfo = data['Vector']['AtInfo']
dlg = MultiIntegerDialog(G2frame.dataDisplay,'New Rigid Body',['No. atoms','No. translations'],[1,1])
if dlg.ShowModal() == wx.ID_OK:
nAtoms,nTrans = dlg.GetValues()
vectorRB = data['Vector']
rbId = ran.randint(0,sys.maxint)
vecMag = [1.0 for i in range(nTrans)]
vecRef = [False for i in range(nTrans)]
vecVal = [np.zeros((nAtoms,3)) for j in range(nTrans)]
rbTypes = ['C' for i in range(nAtoms)]
Info = G2elem.GetAtomInfo('C')
AtInfo['C'] = [Info['Drad'],Info['Color']]
data['Vector'][rbId] = {'RBname':'UNKRB','VectMag':vecMag,'rbXYZ':np.zeros((nAtoms,3)),
'rbRef':[0,1,2,False],'VectRef':vecRef,'rbTypes':rbTypes,'rbVect':vecVal,'useCount':0}
data['RBIds']['Vector'].append(rbId)
dlg.Destroy()
UpdateVectorRB()
def AddResidueRB(event):
AtInfo = data['Residue']['AtInfo']
macro = getMacroFile('rigid body')
if not macro:
return
macStr = macro.readline()
while macStr:
items = macStr.split()
if 'I' == items[0]:
rbId = ran.randint(0,sys.maxint)
rbName = items[1]
rbTypes = []
rbXYZ = []
rbSeq = []
atNames = []
nAtms,nSeq,nOrig,mRef,nRef = [int(items[i]) for i in [2,3,4,5,6]]
for iAtm in range(nAtms):
macStr = macro.readline().split()
atName = macStr[0]
atType = macStr[1]
atNames.append(atName)
rbXYZ.append([float(macStr[i]) for i in [2,3,4]])
rbTypes.append(atType)
if atType not in AtInfo:
Info = G2elem.GetAtomInfo(atType)
AtInfo[atType] = [Info['Drad'],Info['Color']]
rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[nOrig-1])
for iSeq in range(nSeq):
macStr = macro.readline().split()
mSeq = int(macStr[0])
for jSeq in range(mSeq):
macStr = macro.readline().split()
iBeg = int(macStr[0])-1
iFin = int(macStr[1])-1
angle = 0.0
nMove = int(macStr[2])
iMove = [int(macStr[i])-1 for i in range(3,nMove+3)]
rbSeq.append([iBeg,iFin,angle,iMove])
data['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbTypes,
'atNames':atNames,'rbRef':[nOrig-1,mRef-1,nRef-1,True],'rbSeq':rbSeq,
'SelSeq':[0,0],'useCount':0}
data['RBIds']['Residue'].append(rbId)
print 'Rigid body '+rbName+' added'
macStr = macro.readline()
macro.close()
UpdateResidueRB()
def ImportResidueRB():
AtInfo = data['Residue']['AtInfo']
text,ext = getTextFile()
if not text:
return
rbId = ran.randint(0,sys.maxint)
rbTypes = []
rbXYZ = []
rbSeq = []
atNames = []
txtStr = text.readline()
if 'xyz' in ext:
txtStr = text.readline()
txtStr = text.readline()
elif 'mol2' in ext:
while 'ATOM' not in txtStr:
txtStr = text.readline()
txtStr = text.readline()
elif 'pdb' in ext:
while 'ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]:
txtStr = text.readline()
#print txtStr
items = txtStr.split()
while len(items):
if 'txt' in ext:
atName = items[0]
atType = items[1]
rbXYZ.append([float(items[i]) for i in [2,3,4]])
elif 'xyz' in ext:
atType = items[0]
rbXYZ.append([float(items[i]) for i in [1,2,3]])
atName = atType+str(len(rbXYZ))
elif 'mol2' in ext:
atType = items[1]
atName = items[1]+items[0]
rbXYZ.append([float(items[i]) for i in [2,3,4]])
elif 'pdb' in ext:
atType = items[-1]
atName = items[2]
xyz = txtStr[30:55].split()
rbXYZ.append([float(x) for x in xyz])
atNames.append(atName)
rbTypes.append(atType)
if atType not in AtInfo:
Info = G2elem.GetAtomInfo(atType)
AtInfo[atType] = [Info['Drad'],Info['Color']]
txtStr = text.readline()
if 'mol2' in ext and 'BOND' in txtStr:
break
if 'pdb' in ext and ('ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]):
break
items = txtStr.split()
rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[0])
data['Residue'][rbId] = {'RBname':'UNKRB','rbXYZ':rbXYZ,'rbTypes':rbTypes,
'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
data['RBIds']['Residue'].append(rbId)
print 'Rigid body UNKRB added'
text.close()
UpdateResidueRB()
def FindNeighbors(Orig,XYZ,atTypes,atNames,AtInfo):
Radii = []
for Atype in atTypes:
Radii.append(AtInfo[Atype][0])
Radii = np.array(Radii)
Neigh = []
Dx = XYZ-XYZ[Orig]
dist = np.sqrt(np.sum(Dx**2,axis=1))
sumR = Radii[Orig]+Radii
IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
for j in IndB[0]:
if j != Orig:
Neigh.append(atNames[j])
return Neigh
def FindAllNeighbors(XYZ,atTypes,atNames,AtInfo):
NeighDict = {}
for iat,xyz in enumerate(atNames):
NeighDict[atNames[iat]] = FindNeighbors(iat,XYZ,atTypes,atNames,AtInfo)
return NeighDict
def FindRiding(Orig,Pivot,NeighDict):
riding = [Orig,Pivot]
iAdd = 1
new = True
while new:
newAtms = NeighDict[riding[iAdd]]
for At in newAtms:
new = False
if At not in riding:
riding.append(At)
new = True
iAdd += 1
if iAdd < len(riding):
new = True
return riding[2:]
def OnDefineTorsSeq(event):
rbKeys = data['Residue'].keys()
rbKeys.remove('AtInfo')
rbNames = [data['Residue'][k]['RBname'] for k in rbKeys]
rbIds = dict(zip(rbNames,rbKeys))
rbNames.sort()
rbId = 0
if len(rbNames) > 1:
dlg = wx.SingleChoiceDialog(G2frame,'Select rigid body for torsion sequence','Torsion sequence',rbNames)
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
rbId = rbIds[rbNames[sel]]
rbData = data['Residue'][rbId]
dlg.Destroy()
else:
rbId = rbIds[rbNames[0]]
rbData = data['Residue'][rbId]
if not len(rbData):
return
atNames = rbData['atNames']
AtInfo = data['Residue']['AtInfo']
atTypes = rbData['rbTypes']
XYZ = rbData['rbXYZ']
neighDict = FindAllNeighbors(XYZ,atTypes,atNames,AtInfo)
TargList = []
dlg = wx.SingleChoiceDialog(G2frame,'Select origin atom for torsion sequence','Origin atom',rbData['atNames'])
if dlg.ShowModal() == wx.ID_OK:
Orig = dlg.GetSelection()
xyz = XYZ[Orig]
TargList = neighDict[atNames[Orig]]
dlg.Destroy()
if not len(TargList):
return
dlg = wx.SingleChoiceDialog(G2frame,'Select pivot atom for torsion sequence','Pivot atom',TargList)
if dlg.ShowModal() == wx.ID_OK:
Piv = atNames.index(TargList[dlg.GetSelection()])
riding = FindRiding(atNames[Orig],atNames[Piv],neighDict)
Riding = []
for atm in riding:
Riding.append(atNames.index(atm))
rbData['rbSeq'].append([Orig,Piv,0.0,Riding])
dlg.Destroy()
UpdateResidueRB()
def UpdateVectorRB(Scroll=0):
AtInfo = data['Vector']['AtInfo']
refChoice = {}
SetStatusLine(' You may use e.g. "c60" or "s60" for a vector entry')
def rbNameSizer(rbId,rbData):
def OnRBName(event):
Obj = event.GetEventObject()
rbId = Indx[Obj.GetId()]
rbData['RBname'] = Obj.GetValue()
def OnDelRB(event):
Obj = event.GetEventObject()
rbId = Indx[Obj.GetId()]
del data['Vector'][rbId]
data['RBIds']['Vector'].remove(rbId)
rbData['useCount'] -= 1
wx.CallAfter(UpdateVectorRB)
def OnPlotRB(event):
Obj = event.GetEventObject()
rbId = Indx[Obj.GetId()]
Obj.SetValue(False)
G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,rbData,plotDefaults)
nameSizer = wx.BoxSizer(wx.HORIZONTAL)
nameSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Rigid body name: '),
0,wx.ALIGN_CENTER_VERTICAL)
RBname = wx.TextCtrl(VectorRBDisplay,-1,rbData['RBname'])
Indx[RBname.GetId()] = rbId
RBname.Bind(wx.EVT_TEXT_ENTER,OnRBName)
RBname.Bind(wx.EVT_KILL_FOCUS,OnRBName)
nameSizer.Add(RBname,0,wx.ALIGN_CENTER_VERTICAL)
nameSizer.Add((5,0),)
plotRB = wx.CheckBox(VectorRBDisplay,-1,'Plot?')
Indx[plotRB.GetId()] = rbId
plotRB.Bind(wx.EVT_CHECKBOX,OnPlotRB)
nameSizer.Add(plotRB,0,wx.ALIGN_CENTER_VERTICAL)
nameSizer.Add((5,0),)
if not rbData['useCount']:
delRB = wx.CheckBox(VectorRBDisplay,-1,'Delete?')
Indx[delRB.GetId()] = rbId
delRB.Bind(wx.EVT_CHECKBOX,OnDelRB)
nameSizer.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
return nameSizer
def rbRefAtmSizer(rbId,rbData):
def OnRefSel(event):
Obj = event.GetEventObject()
iref = Indx[Obj.GetId()]
sel = Obj.GetValue()
rbData['rbRef'][iref] = atNames.index(sel)
FillRefChoice(rbId,rbData)
refAtmSizer = wx.BoxSizer(wx.HORIZONTAL)
atNames = [name+str(i) for i,name in enumerate(rbData['rbTypes'])]
rbRef = rbData.get('rbRef',[0,1,2,False])
rbData['rbRef'] = rbRef
if rbData['useCount']:
refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1,
'Orientation reference atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
atNames[rbRef[1]],atNames[rbRef[2]])),0)
else:
refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1,
'Orientation reference atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
for i in range(3):
choices = [atNames[j] for j in refChoice[rbId][i]]
refSel = wx.ComboBox(VectorRBDisplay,-1,value='',
choices=choices,style=wx.CB_READONLY|wx.CB_DROPDOWN)
refSel.SetValue(atNames[rbRef[i]])
refSel.Bind(wx.EVT_COMBOBOX, OnRefSel)
Indx[refSel.GetId()] = i
refAtmSizer.Add(refSel,0,wx.ALIGN_CENTER_VERTICAL)
return refAtmSizer
def rbVectMag(rbId,imag,rbData):
def OnRBVectorMag(event):
Obj = event.GetEventObject()
rbId,imag = Indx[Obj.GetId()]
try:
val = float(Obj.GetValue())
if val <= 0.:
raise ValueError
rbData['VectMag'][imag] = val
except ValueError:
pass
Obj.SetValue('%8.4f'%(val))
wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbId],plotDefaults)
def OnRBVectorRef(event):
Obj = event.GetEventObject()
rbId,imag = Indx[Obj.GetId()]
rbData['VectRef'][imag] = Obj.GetValue()
magSizer = wx.wx.BoxSizer(wx.HORIZONTAL)
magSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Translation magnitude: '),
0,wx.ALIGN_CENTER_VERTICAL)
magValue = wx.TextCtrl(VectorRBDisplay,-1,'%8.4f'%(rbData['VectMag'][imag]))
Indx[magValue.GetId()] = [rbId,imag]
magValue.Bind(wx.EVT_TEXT_ENTER,OnRBVectorMag)
magValue.Bind(wx.EVT_KILL_FOCUS,OnRBVectorMag)
magSizer.Add(magValue,0,wx.ALIGN_CENTER_VERTICAL)
magSizer.Add((5,0),)
magref = wx.CheckBox(VectorRBDisplay,-1,label=' Refine?')
magref.SetValue(rbData['VectRef'][imag])
magref.Bind(wx.EVT_CHECKBOX,OnRBVectorRef)
Indx[magref.GetId()] = [rbId,imag]
magSizer.Add(magref,0,wx.ALIGN_CENTER_VERTICAL)
return magSizer
def rbVectors(rbId,imag,mag,XYZ,rbData):
def TypeSelect(event):
Obj = event.GetEventObject()
AtInfo = data['Vector']['AtInfo']
r,c = event.GetRow(),event.GetCol()
if vecGrid.GetColLabelValue(c) == 'Type':
PE = G2elemGUI.PickElement(G2frame,oneOnly=True)
if PE.ShowModal() == wx.ID_OK:
if PE.Elem != 'None':
El = PE.Elem.strip().lower().capitalize()
if El not in AtInfo:
Info = G2elem.GetAtomInfo(El)
AtInfo[El] = [Info['Drad'],Info['Color']]
rbData['rbTypes'][r] = El
vecGrid.SetCellValue(r,c,El)
PE.Destroy()
wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
def ChangeCell(event):
Obj = event.GetEventObject()
r,c = event.GetRow(),event.GetCol()
if r >= 0 and (0 <= c < 3):
try:
val = float(vecGrid.GetCellValue(r,c))
rbData['rbVect'][imag][r][c] = val
except ValueError:
pass
G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbId],plotDefaults)
wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
vecSizer = wx.BoxSizer()
Types = 3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]
colLabels = ['Vector x','Vector y','Vector z','Type','Cart x','Cart y','Cart z']
table = []
rowLabels = []
for ivec,xyz in enumerate(rbData['rbVect'][imag]):
table.append(list(xyz)+[rbData['rbTypes'][ivec],]+list(XYZ[ivec]))
rowLabels.append(str(ivec))
vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
vecGrid = G2G.GSGrid(VectorRBDisplay)
vecGrid.SetTable(vecTable, True)
vecGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell)
if not imag:
vecGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect)
attr = wx.grid.GridCellAttr()
attr.SetEditor(G2G.GridFractionEditor(vecGrid))
for c in range(3):
vecGrid.SetColAttr(c, attr)
for row in range(vecTable.GetNumberRows()):
if imag:
vecGrid.SetCellStyle(row,3,VERY_LIGHT_GREY,True)
for col in [4,5,6]:
vecGrid.SetCellStyle(row,col,VERY_LIGHT_GREY,True)
vecGrid.SetMargins(0,0)
vecGrid.AutoSizeColumns(False)
vecSizer.Add(vecGrid)
return vecSizer
def FillRefChoice(rbId,rbData):
choiceIds = [i for i in range(len(rbData['rbTypes']))]
rbRef = rbData.get('rbRef',[-1,-1,-1,False])
for i in range(3):
choiceIds.remove(rbRef[i])
refChoice[rbId] = [choiceIds[:],choiceIds[:],choiceIds[:]]
for i in range(3):
refChoice[rbId][i].append(rbRef[i])
refChoice[rbId][i].sort()
#VectorRB.DestroyChildren() # bad, deletes scrollbars on Mac!
if VectorRB.GetSizer():
VectorRB.GetSizer().Clear(True)
VectorRBDisplay = wx.Panel(VectorRB)
VectorRBSizer = wx.BoxSizer(wx.VERTICAL)
for rbId in data['RBIds']['Vector']:
if rbId != 'AtInfo':
rbData = data['Vector'][rbId]
FillRefChoice(rbId,rbData)
VectorRBSizer.Add(rbNameSizer(rbId,rbData),0)
VectorRBSizer.Add(rbRefAtmSizer(rbId,rbData),0)
XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
for imag,mag in enumerate(rbData['VectMag']):
XYZ += mag*rbData['rbVect'][imag]
VectorRBSizer.Add(rbVectMag(rbId,imag,rbData),0)
VectorRBSizer.Add(rbVectors(rbId,imag,mag,XYZ,rbData),0)
VectorRBSizer.Add((5,5),0)
data['Vector'][rbId]['rbXYZ'] = XYZ
VectorRBSizer.Layout()
VectorRBDisplay.SetSizer(VectorRBSizer,True)
Size = VectorRBSizer.GetMinSize()
Size[0] += 40
Size[1] = max(Size[1],450) + 20
VectorRBDisplay.SetSize(Size)
VectorRB.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
VectorRB.Scroll(0,Scroll)
Size[1] = min(Size[1],450)
G2frame.dataFrame.setSizePosLeft(Size)
def UpdateResidueRB():
AtInfo = data['Residue']['AtInfo']
refChoice = {}
RefObjs = []
def rbNameSizer(rbId,rbData):
def OnRBName(event):
Obj = event.GetEventObject()
rbId = Indx[Obj.GetId()]
rbData['RBname'] = Obj.GetValue()
def OnDelRB(event):
Obj = event.GetEventObject()
rbId = Indx[Obj.GetId()]
del data['Residue'][rbId]
data['RBIds']['Residue'].remove(rbId)
wx.CallAfter(UpdateResidueRB)
def OnPlotRB(event):
Obj = event.GetEventObject()
rbId = Indx[Obj.GetId()]
Obj.SetValue(False)
G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
nameSizer = wx.BoxSizer(wx.HORIZONTAL)
nameSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Residue name: '),
0,wx.ALIGN_CENTER_VERTICAL)
RBname = wx.TextCtrl(ResidueRBDisplay,-1,rbData['RBname'])
Indx[RBname.GetId()] = rbId
RBname.Bind(wx.EVT_TEXT_ENTER,OnRBName)
RBname.Bind(wx.EVT_KILL_FOCUS,OnRBName)
nameSizer.Add(RBname,0,wx.ALIGN_CENTER_VERTICAL)
nameSizer.Add((5,0),)
plotRB = wx.CheckBox(ResidueRBDisplay,-1,'Plot?')
Indx[plotRB.GetId()] = rbId
plotRB.Bind(wx.EVT_CHECKBOX,OnPlotRB)
nameSizer.Add(plotRB,0,wx.ALIGN_CENTER_VERTICAL)
nameSizer.Add((5,0),)
if not rbData['useCount']:
delRB = wx.CheckBox(ResidueRBDisplay,-1,'Delete?')
Indx[delRB.GetId()] = rbId
delRB.Bind(wx.EVT_CHECKBOX,OnDelRB)
nameSizer.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
return nameSizer
def rbResidues(rbId,rbData):
def TypeSelect(event):
AtInfo = data['Residue']['AtInfo']
r,c = event.GetRow(),event.GetCol()
if vecGrid.GetColLabelValue(c) == 'Type':
PE = G2elemGUI.PickElement(G2frame,oneOnly=True)
if PE.ShowModal() == wx.ID_OK:
if PE.Elem != 'None':
El = PE.Elem.strip().lower().capitalize()
if El not in AtInfo:
Info = G2elem.GetAtomInfo(El)
AtInfo[El] = [Info['Drad']['Color']]
rbData['rbTypes'][r] = El
vecGrid.SetCellValue(r,c,El)
PE.Destroy()
def ChangeCell(event):
r,c = event.GetRow(),event.GetCol()
if r >= 0 and (0 <= c < 3):
try:
val = float(vecGrid.GetCellValue(r,c))
rbData['rbVect'][imag][r][c] = val
except ValueError:
pass
def RowSelect(event):
r,c = event.GetRow(),event.GetCol()
if c < 0: #only row clicks
for vecgrid in resList:
vecgrid.ClearSelection()
vecGrid.SelectRow(r,True)
def OnRefSel(event):
Obj = event.GetEventObject()
iref,res,jref = Indx[Obj.GetId()]
sel = Obj.GetValue()
ind = atNames.index(sel)
rbData['rbRef'][iref] = ind
FillRefChoice(rbId,rbData)
for i,ref in enumerate(RefObjs[jref]):
ref.SetItems([atNames[j] for j in refChoice[rbId][i]])
ref.SetValue(atNames[rbData['rbRef'][i]])
if not iref: #origin change
rbXYZ = rbData['rbXYZ']
rbXYZ -= rbXYZ[ind]
res.ClearSelection()
resTable = res.GetTable()
for r in range(res.GetNumberRows()):
row = resTable.GetRowValues(r)
row[2:4] = rbXYZ[r]
resTable.SetRowValues(r,row)
res.ForceRefresh()
G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
Types = 2*[wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]
colLabels = ['Name','Type','Cart x','Cart y','Cart z']
table = []
rowLabels = []
for ivec,xyz in enumerate(rbData['rbXYZ']):
table.append([rbData['atNames'][ivec],]+[rbData['rbTypes'][ivec],]+list(xyz))
rowLabels.append(str(ivec))
vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
vecGrid = G2G.GSGrid(ResidueRBDisplay)
Indx[vecGrid.GetId()] = rbId
resList.append(vecGrid)
vecGrid.SetTable(vecTable, True)
vecGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell)
vecGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect)
vecGrid.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
attr = wx.grid.GridCellAttr()
attr.SetEditor(G2G.GridFractionEditor(vecGrid))
for c in range(3):
vecGrid.SetColAttr(c, attr)
for row in range(vecTable.GetNumberRows()):
for col in range(5):
vecGrid.SetCellStyle(row,col,VERY_LIGHT_GREY,True)
vecGrid.SetMargins(0,0)
vecGrid.AutoSizeColumns(False)
vecSizer = wx.BoxSizer()
vecSizer.Add(vecGrid)
refAtmSizer = wx.BoxSizer(wx.HORIZONTAL)
atNames = rbData['atNames']
rbRef = rbData['rbRef']
if rbData['rbRef'][3] or rbData['useCount']:
refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
'Orientation reference atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
atNames[rbRef[1]],atNames[rbRef[2]])),0)
else:
refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
'Orientation reference atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
refObj = [0,0,0]
for i in range(3):
choices = [atNames[j] for j in refChoice[rbId][i]]
refSel = wx.ComboBox(ResidueRBDisplay,-1,value='',
choices=choices,style=wx.CB_READONLY|wx.CB_DROPDOWN)
refSel.SetValue(atNames[rbRef[i]])
refSel.Bind(wx.EVT_COMBOBOX, OnRefSel)
Indx[refSel.GetId()] = [i,vecGrid,len(RefObjs)]
refObj[i] = refSel
refAtmSizer.Add(refSel,0,wx.ALIGN_CENTER_VERTICAL)
RefObjs.append(refObj)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(refAtmSizer)
mainSizer.Add(vecSizer)
return mainSizer
def SeqSizer(angSlide,rbId,iSeq,Seq,atNames):
def ChangeAngle(event):
Obj = event.GetEventObject()
rbId,Seq = Indx[Obj.GetId()][:2]
val = Seq[2]
try:
val = float(Obj.GetValue())
Seq[2] = val
except ValueError:
pass
Obj.SetValue('%8.2f'%(val))
G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,data['Residue'][rbId],plotDefaults)
def OnRadBtn(event):
Obj = event.GetEventObject()
Seq,iSeq,angId = Indx[Obj.GetId()]
data['Residue'][rbId]['SelSeq'] = [iSeq,angId]
angSlide.SetValue(int(100*Seq[2]))
def OnDelBtn(event):
Obj = event.GetEventObject()
rbId,Seq = Indx[Obj.GetId()]
data['Residue'][rbId]['rbSeq'].remove(Seq)
wx.CallAfter(UpdateResidueRB)
seqSizer = wx.FlexGridSizer(0,5,2,2)
seqSizer.AddGrowableCol(3,0)
iBeg,iFin,angle,iMove = Seq
ang = wx.TextCtrl(ResidueRBDisplay,-1,'%8.2f'%(angle),size=(50,20))
if not iSeq:
radBt = wx.RadioButton(ResidueRBDisplay,-1,'',style=wx.RB_GROUP)
data['Residue'][rbId]['SelSeq'] = [iSeq,ang.GetId()]
else:
radBt = wx.RadioButton(ResidueRBDisplay,-1,'')
radBt.Bind(wx.EVT_RADIOBUTTON,OnRadBtn)
seqSizer.Add(radBt)
delBt = wx.RadioButton(ResidueRBDisplay,-1,'')
delBt.Bind(wx.EVT_RADIOBUTTON,OnDelBtn)
seqSizer.Add(delBt)
bond = wx.TextCtrl(ResidueRBDisplay,-1,'%s %s'%(atNames[iBeg],atNames[iFin]),size=(50,20))
seqSizer.Add(bond,0,wx.ALIGN_CENTER_VERTICAL)
Indx[radBt.GetId()] = [Seq,iSeq,ang.GetId()]
Indx[delBt.GetId()] = [rbId,Seq]
Indx[ang.GetId()] = [rbId,Seq,ang]
ang.Bind(wx.EVT_TEXT_ENTER,ChangeAngle)
ang.Bind(wx.EVT_KILL_FOCUS,ChangeAngle)
seqSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
atms = ''
for i in iMove:
atms += ' %s,'%(atNames[i])
moves = wx.TextCtrl(ResidueRBDisplay,-1,atms[:-1],size=(200,20))
seqSizer.Add(moves,1,wx.ALIGN_CENTER_VERTICAL|wx.EXPAND|wx.RIGHT)
return seqSizer
def SlideSizer():
def OnSlider(event):
Obj = event.GetEventObject()
rbData = Indx[Obj.GetId()]
iSeq,angId = rbData['SelSeq']
val = float(Obj.GetValue())/100.
rbData['rbSeq'][iSeq][2] = val
Indx[angId][2].SetValue('%8.2f'%(val))
G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
slideSizer = wx.BoxSizer(wx.HORIZONTAL)
slideSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Selected torsion angle:'),0)
iSeq,angId = rbData['SelSeq']
angSlide = wx.Slider(ResidueRBDisplay,-1,
int(100*rbData['rbSeq'][iSeq][2]),0,36000,size=(200,20),
style=wx.SL_HORIZONTAL)
angSlide.Bind(wx.EVT_SLIDER, OnSlider)
Indx[angSlide.GetId()] = rbData
slideSizer.Add(angSlide,0)
return slideSizer,angSlide
def FillRefChoice(rbId,rbData):
choiceIds = [i for i in range(len(rbData['atNames']))]
for seq in rbData['rbSeq']:
for i in seq[3]:
try:
choiceIds.remove(i)
except ValueError:
pass
rbRef = rbData['rbRef']
for i in range(3):
try:
choiceIds.remove(rbRef[i])
except ValueError:
pass
refChoice[rbId] = [choiceIds[:],choiceIds[:],choiceIds[:]]
for i in range(3):
refChoice[rbId][i].append(rbRef[i])
refChoice[rbId][i].sort()
#ResidueRB.DestroyChildren() # bad, deletes scrollbars on Mac!
if ResidueRB.GetSizer():
ResidueRB.GetSizer().Clear(True)
ResidueRBDisplay = wx.Panel(ResidueRB)
ResidueRBSizer = wx.BoxSizer(wx.VERTICAL)
for rbId in data['RBIds']['Residue']:
rbData = data['Residue'][rbId]
FillRefChoice(rbId,rbData)
ResidueRBSizer.Add(rbNameSizer(rbId,rbData),0)
ResidueRBSizer.Add(rbResidues(rbId,rbData),0)
ResidueRBSizer.Add((5,5),0)
if rbData['rbSeq']:
slideSizer,angSlide = SlideSizer()
if len(rbData['rbSeq']):
ResidueRBSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
'Sel Del Bond Angle Riding atoms'),
0,wx.ALIGN_CENTER_VERTICAL)
for iSeq,Seq in enumerate(rbData['rbSeq']):
ResidueRBSizer.Add(SeqSizer(angSlide,rbId,iSeq,Seq,rbData['atNames']))
if rbData['rbSeq']:
ResidueRBSizer.Add(slideSizer,)
ResidueRBSizer.Add(wx.StaticText(ResidueRBDisplay,-1,100*'-'))
ResidueRBSizer.Add((5,25),)
ResidueRBSizer.Layout()
ResidueRBDisplay.SetSizer(ResidueRBSizer,True)
Size = ResidueRBSizer.GetMinSize()
Size[0] += 40
Size[1] = max(Size[1],450) + 20
ResidueRBDisplay.SetSize(Size)
ResidueRB.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
Size[1] = min(600,Size[1])
G2frame.dataFrame.setSizePosLeft(Size)
def SetStatusLine(text):
Status.SetStatusText(text)
if G2frame.dataDisplay:
G2frame.dataDisplay.Destroy()
G2gd.SetDataMenuBar(G2frame,G2frame.dataFrame.RigidBodyMenu)
G2frame.dataFrame.SetLabel('Rigid bodies')
if not G2frame.dataFrame.GetStatusBar():
Status = G2frame.dataFrame.CreateStatusBar()
SetStatusLine('')
G2frame.dataDisplay = G2G.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
VectorRB = wx.ScrolledWindow(G2frame.dataDisplay)
G2frame.dataDisplay.AddPage(VectorRB,'Vector rigid bodies')
ResidueRB = wx.ScrolledWindow(G2frame.dataDisplay)
G2frame.dataDisplay.AddPage(ResidueRB,'Residue rigid bodies')
UpdateVectorRB()
G2frame.dataDisplay.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
OnPageChanged(None)
