Source code for GSASIIrestrGUI

# -*- coding: utf-8 -*-
#GSASIIrestr - restraint GUI routines
########### SVN repository information ###################
# $Date: 2021-06-21 16:32:01 +0000 (Mon, 21 Jun 2021) $
# $Author: toby $
# $Revision: 4965 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIrestrGUI.py $
# $Id: GSASIIrestrGUI.py 4965 2021-06-21 16:32:01Z toby $
########### SVN repository information ###################
'''
*GSASIIrestrGUI: Restraint GUI routines*
----------------------------------------

Used to define restraints.

'''
from __future__ import division, print_function
import wx
import wx.grid as wg
import numpy as np
import numpy.ma as ma
import os.path
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 4965 $")
import GSASIImath as G2mth
import GSASIIlattice as G2lat
import GSASIIspc as G2spc
import GSASIIdataGUI as G2gd
import GSASIIplot as G2plt
import GSASIIdata as G2data
import GSASIIctrlGUI as G2G
import GSASIIphsGUI as G2phsGUI
import GSASIIobj as G2obj
import GSASIIconstrGUI as G2cnstG
import GSASIIexprGUI as G2exG

try:
    wx.NewIdRef
    wx.NewId = wx.NewIdRef
except AttributeError:
    pass

WACV = wx.ALIGN_CENTER_VERTICAL
VERY_LIGHT_GREY = wx.Colour(235,235,235)
VERY_YELLOW = wx.Colour(255,255,0)
TabSelectionIdDict = {}

################################################################################
#####  Restraints
################################################################################           
[docs]def GetSelectedRows(widget,lbl='edit',G2frame=None): '''Returns a list of selected rows. Rows can be selected, blocks of cells or individual cells can be selected. The column for selected cells is ignored. ''' try: rows = widget.GetSelectedRows() if rows: return rows top = widget.GetSelectionBlockTopLeft() bot = widget.GetSelectionBlockBottomRight() if top and bot: rows = range(top[0][0],bot[0][0]+1) if rows: return rows rows = sorted(list(set([cell[0] for cell in widget.GetSelectedCells()]))) if rows: return rows choices = ["{}: {}".format(widget.GetRowLabelValue(i),widget.GetCellValue(i,0)) for i in range(widget.GetNumberRows())] try: dlg = G2G.G2MultiChoiceDialog(G2frame,'Restraints to '+lbl, 'Select restraints',choices) if dlg.ShowModal() != wx.ID_OK: return return dlg.GetSelections() finally: dlg.Destroy() except: return
[docs]def UpdateRestraints(G2frame,data,phaseName): '''Respond to selection of the Restraints item on the data tree ''' # global Pages def getMacroFile(macName): defDir = os.path.join(os.path.split(__file__)[0],'GSASIImacros') dlg = wx.FileDialog(G2frame,message='Choose '+macName+' restraint macro file', defaultDir=defDir,defaultFile="",wildcard="GSAS-II macro file (*.mac)|*.mac", style=wx.FD_OPEN | wx.FD_CHANGE_DIR) try: macro = '' if dlg.ShowModal() == wx.ID_OK: macfile = dlg.GetPath() macro = open(macfile,'r') head = macro.readline() if macName not in head: print (head) print ('**** ERROR - wrong restraint macro file selected, try again ****') macro = [] finally: dlg.Destroy() return macro #advanced past 1st line def getMOGULFile(): dlg = wx.FileDialog(G2frame,message='Choose MOGUL csv file', defaultDir='.',defaultFile="",wildcard="MOGUL csv file (*.csv)|*.csv", style=wx.FD_OPEN | wx.FD_CHANGE_DIR) try: mogul = '' if dlg.ShowModal() == wx.ID_OK: csvfile = dlg.GetPath() mogul = open(csvfile,'r') head = mogul.readline() if 'Type' not in head: print (head) print ('**** ERROR - not a MOGUL csv file selected, try again ****') mogul = [] finally: dlg.Destroy() return mogul #advanced past 1st line def OnPlotAARestraint(event): page = G2frame.restrBook.GetSelection() if 'Torsion' in G2frame.restrBook.GetPageText(page): torNames = [] torNames += list(restrData['Torsion']['Coeff'].keys()) dlg = wx.SingleChoiceDialog(G2frame,'Select','Torsion data',torNames) try: if dlg.ShowModal() == wx.ID_OK: torName = torNames[dlg.GetSelection()] torsion = G2data.torsionDist[torName] torCoeff = restrData['Torsion']['Coeff'][torName] torList = restrData['Torsion']['Torsions'] Names = [] Angles = [] for i,[indx,ops,cofName,esd] in enumerate(torList): if cofName == torName: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '('+atoms[2][1]+atoms[2][0].strip()+atoms[2][2]+')' for atom in atoms: name += ' '+atom[3] XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) angle = G2mth.getRestTorsion(XYZ,Amat) Angles.append(angle) Names.append(name) G2plt.PlotTorsion(G2frame,phaseName,torsion,torName,Names,np.array(Angles),torCoeff) finally: dlg.Destroy() elif 'Rama' in G2frame.restrBook.GetPageText(page): ramaNames = ['All',] ramaNames += list(restrData['Rama']['Coeff'].keys()) dlg = wx.SingleChoiceDialog(G2frame,'Select','Ramachandran data',ramaNames) try: if dlg.ShowModal() == wx.ID_OK: ramaName = ramaNames[dlg.GetSelection()] rama = G2data.ramachandranDist[ramaName] ramaCoeff = [] if ramaName != 'All': ramaCoeff = restrData['Rama']['Coeff'][ramaName] ramaList = restrData['Rama']['Ramas'] Names = [] PhiPsi = [] for i,[indx,ops,cofName,esd] in enumerate(ramaList): if cofName == ramaName or (ramaName == 'All' and '-1' in cofName): atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '('+atoms[3][1]+atoms[3][0].strip()+atoms[3][2]+')' for atom in atoms: name += ' '+atom[3] XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) phi,psi = G2mth.getRestRama(XYZ,Amat) PhiPsi.append([phi,psi]) Names.append(name) G2plt.PlotRama(G2frame,phaseName,rama,ramaName,Names,np.array(PhiPsi),ramaCoeff) finally: dlg.Destroy() def SetupParmDict(G2frame): '''Creates a parameter dict with variable names as keys and numerical values (only) ''' G2cnstG.CheckAllScalePhaseFractions(G2frame) try: parmDict,varyList = G2frame.MakeLSParmDict() except: print('Error retrieving parameters') return {} return {i:parmDict[i][0] for i in parmDict} def OnAddRestraint(event): '''Adds a restraint depending on which tab is currently displayed''' page = G2frame.restrBook.GetSelection() if 'Bond' in G2frame.restrBook.GetPageText(page): AddBondRestraint(restrData['Bond']) elif 'Angle' in G2frame.restrBook.GetPageText(page): AddAngleRestraint(restrData['Angle']) elif 'Plane' in G2frame.restrBook.GetPageText(page): AddPlaneRestraint(restrData['Plane']) elif 'Chem' in G2frame.restrBook.GetPageText(page): AddChemCompRestraint(restrData['ChemComp']) elif 'Texture' in G2frame.restrBook.GetPageText(page): AddTextureRestraint(restrData['Texture']) elif 'General' in G2frame.restrBook.GetPageText(page): parmDict = SetupParmDict(G2frame) dlg = G2exG.ExpressionDialog(G2frame,parmDict, header="Create a restraint expression", fit=False,wildCard=G2frame.testSeqRefineMode()) restobj = dlg.Show(True) if restobj: restrData['General']['General'].append([restobj,0.0,1.0]) wx.CallAfter(UpdateGeneralRestr,restrData['General']) def OnAddAARestraint(event): page = G2frame.restrBook.GetSelection() if 'Bond' in G2frame.restrBook.GetPageText(page): AddAABondRestraint(restrData['Bond']) elif 'Angle' in G2frame.restrBook.GetPageText(page): AddAAAngleRestraint(restrData['Angle']) elif 'Plane' in G2frame.restrBook.GetPageText(page): AddAAPlaneRestraint(restrData['Plane']) elif 'Chiral' in G2frame.restrBook.GetPageText(page): AddAAChiralRestraint(restrData['Chiral']) elif 'Torsion' in G2frame.restrBook.GetPageText(page): AddAATorsionRestraint(restrData['Torsion']) elif 'Rama' in G2frame.restrBook.GetPageText(page): AddAARamaRestraint(restrData['Rama']) def OnUseMogul(event): page = G2frame.restrBook.GetSelection() if 'Bond' in G2frame.restrBook.GetPageText(page): AddMogulBondRestraint(restrData['Bond']) elif 'Angle' in G2frame.restrBook.GetPageText(page): AddMogulAngleRestraint(restrData['Angle']) def makeChains(Names,Ids): Chains = {} atoms = zip(Names,Ids) for name,Id in atoms: items = name.split(' ',2) rnum,res = items[0].split(':') rnum = int(rnum) if items[1] not in Chains: Residues = {} Chains[items[1]] = Residues if rnum not in Residues: Residues[rnum] = [[],[]] if items[2][3] in [' ','A']: Residues[rnum][0].append([res,items[2],Id]) if items[2][3] in [' ','B']: Residues[rnum][1].append([res,items[2],Id]) return Chains def AddBondRestraint(bondRestData): Lists = {'origin':[],'target':[]} for listName in ['origin','target']: dlg = G2G.G2MultiChoiceDialog(G2frame,'Bond restraint '+listName+' for '+General['Name'], 'Select bond restraint '+listName+' atoms',Names) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() for x in sel: if 'all' in Names[x]: allType = Types[x] for name,Type,coords,Id in zip(Names,Types,Coords,Ids): if Type == allType and 'all' not in name: Lists[listName].append([Id,Type,coords]) else: Lists[listName].append([Ids[x],Types[x],Coords[x],]) else: break if len(Lists['origin']) and len(Lists['target']): bond = 1.54 dlg = G2G.SingleFloatDialog(G2frame,'Distance','Enter restraint distance for bond',bond,[0.01,4.],'%.4f') if dlg.ShowModal() == wx.ID_OK: bond = dlg.GetValue() dlg.Destroy() Factor = bondRestData['Range'] indices = (-2,-1,0,1,2) Units = np.array([[h,k,l] for h in indices for k in indices for l in indices]) origAtoms = Lists['origin'] targAtoms = Lists['target'] dlg = wx.ProgressDialog("Generating bond restraints","Processed origin atoms",len(origAtoms), style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME) try: Norig = 0 for Oid,Otype,Ocoord in origAtoms: Norig += 1 dlg.Update(Norig) for Tid,Ttype,Tcoord in targAtoms: if 'macro' in General['Type']: result = [[Tcoord,1,[0,0,0],[]],] else: result = G2spc.GenAtom(Tcoord,SGData,False,Move=False) for Txyz,Top,Tunit,Spn in result: Dx = (Txyz-np.array(Ocoord))+Units dx = np.inner(Amat,Dx) dist = ma.masked_less(np.sqrt(np.sum(dx**2,axis=0)),bond/Factor) IndB = ma.nonzero(ma.masked_greater(dist,bond*Factor)) if np.any(IndB): for indb in IndB: for i in range(len(indb)): unit = Units[indb][i]+Tunit if np.any(unit): Topstr = '%d+%d,%d,%d'%(Top,unit[0],unit[1],unit[2]) else: Topstr = str(Top) newBond = [[Oid,Tid],['1',Topstr],bond,0.01] if newBond not in bondRestData['Bonds']: bondRestData['Bonds'].append(newBond) finally: dlg.Destroy() UpdateBondRestr(bondRestData) def AddAABondRestraint(bondRestData): macro = getMacroFile('bond') if not macro: return macStr = macro.readline() atoms = zip(Names,Coords,Ids) Factor = bondRestData['Range'] while macStr: items = macStr.split() if 'F' in items[0]: restrData['Bond']['wtFactor'] = float(items[1]) elif 'S' in items[0]: oIds = [] oCoords = [] oDis = [] tIds = [] tCoords = [] tDis = [] res = items[1] dist = float(items[2]) esd = float(items[3]) oAtm,tAtm = items[4:6] for Name,coords,Id in atoms: names = Name.split(' ',2) if res == '*' or res in names[0]: if oAtm.ljust(3) == names[2][:3]: oIds.append(Id) oCoords.append(np.array(coords)) oDis.append(names[2][3]) if tAtm.ljust(3) == names[2][:3]: tIds.append(Id) tCoords.append(np.array(coords)) tDis.append(names[2][3]) for i,[oId,oCoord,odis] in enumerate(zip(oIds,oCoords,oDis)): for tId,tCoord,tdis in list(zip(tIds,tCoords,tDis))[i:]: if odis+tdis in ['AB','BA']: continue obsd = np.sqrt(np.sum(np.inner(Amat,tCoord-oCoord)**2)) if dist/Factor < obsd < dist*Factor: newBond = [[oId,tId],['1','1'],dist,esd] if newBond not in bondRestData['Bonds']: bondRestData['Bonds'].append(newBond) macStr = macro.readline() macro.close() print(' Found %d bond restraints'%len(bondRestData['Bonds'])) UpdateBondRestr(bondRestData) def AddMogulBondRestraint(bondRestData): mogul = getMOGULFile() for line in mogul: items = line.split(',') if 'bond' == items[0]: oName,tName = items[2].split() oInd = Names.index(oName) tInd = Names.index(tName) if items[3] != 'No hits': dist = float(items[6]) esd = float(items[7]) else: dist = float(items[5]) esd = 0.02 newBond = [[Ids[oInd],Ids[tInd]],['1','1'],dist,esd] if newBond not in bondRestData['Bonds']: bondRestData['Bonds'].append(newBond) UpdateBondRestr(bondRestData) def AddAngleRestraint(angleRestData): Radii = dict(zip(General['AtomTypes'],zip(General['BondRadii'],General['AngleRadii']))) Lists = {'A-atom':[],'B-atom':[],'C-atom':[]} for listName in ['A-atom','B-atom']: dlg = G2G.G2MultiChoiceDialog(G2frame,'Select '+listName+' for angle A-B-C for '+General['Name'] , 'Select angle restraint '+listName,Names) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() for x in sel: if 'all' in Names[x]: allType = Types[x] for name,Type,coords,Id in zip(Names,Types,Coords,Ids): if Type == allType and 'all' not in name: if 'A' in listName: Lists[listName].append(Type) else: Lists[listName].append([Id,Type,coords]) else: if 'A' in listName: Lists[listName].append(Types[x]) else: Lists[listName].append([Ids[x],Types[x],Coords[x],]) else: break targAtoms = [[Ids[x+iBeg],Types[x+iBeg],Coords[x+iBeg]] for x in range(len(Names[iBeg:]))] if len(Lists['B-atom']): value = 109.54 dlg = G2G.SingleFloatDialog(G2frame,'Angle','Enter restraint angle ',value,[30.,180.],'%.2f') if dlg.ShowModal() == wx.ID_OK: value = dlg.GetValue() dlg.Destroy() Factor = angleRestData['Range'] indices = (-2,-1,0,1,2) Units = np.array([[h,k,l] for h in indices for k in indices for l in indices]) VectA = [] for Oid,Otype,Ocoord in Lists['B-atom']: IndBlist = [] VectB = [] for Tid,Ttype,Tcoord in targAtoms: result = G2spc.GenAtom(Tcoord,SGData,False,Move=False) BsumR = (Radii[Otype][0]+Radii[Ttype][0])*Factor AsumR = (Radii[Otype][1]+Radii[Ttype][1])*Factor for Txyz,Top,Tunit,Spn in result: Dx = (Txyz-Ocoord)+Units dx = np.inner(Amat,Dx) dist = ma.masked_less(np.sqrt(np.sum(dx**2,axis=0)),0.5) IndB = ma.nonzero(ma.masked_greater(dist,BsumR)) if np.any(IndB): for indb in IndB: for i in range(len(indb)): if str(dx.T[indb][i]) not in IndBlist: IndBlist.append(str(dx.T[indb][i])) unit = Units[indb][i]+Tunit if np.any(unit): Topstr = '%d+%d,%d,%d'%(Top,unit[0],unit[1],unit[2]) else: Topstr = str(Top) Dist = ma.getdata(dist[indb])[i] if (Dist-AsumR) <= 0.: VectB.append([Oid,'1',Ocoord,Ttype,Tid,Topstr,Tcoord,Dist]) VectA.append(VectB) for Vects in VectA: for i,vecta in enumerate(Vects): for vectb in Vects[:i]: if vecta[3] in Lists['A-atom']: ids = [vecta[4],vecta[0],vectb[4]] ops = [vecta[5],vecta[1],vectb[5]] angle = [ids,ops,value,1.0] if angle not in angleRestData['Angles']: angleRestData['Angles'].append(angle) UpdateAngleRestr(angleRestData) def AddAAAngleRestraint(angleRestData): macro = getMacroFile('angle') if not macro: return Chains = makeChains(Names,Ids) macStr = macro.readline() while macStr: items = macStr.split() if 'F' in items[0]: restrData['Angle']['wtFactor'] = float(items[1]) elif 'S' in items[0]: Res = items[1] Value = float(items[2]) Esd = float(items[3]) Atms = items[4:7] pAtms = ['','',''] for i,atm in enumerate(Atms): if '+' in atm: pAtms[i] = atm.strip('+') ids = [0,0,0] chains = list(Chains.keys()) chains.sort() for chain in chains: residues = list(Chains[chain].keys()) residues.sort() for residue in residues: for ires in [0,1]: if Res != '*': #works with disordered res for res,name,Id in Chains[chain][residue][ires]: if Res == res: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue else: try: for res,name,Id in Chains[chain][residue][ires]: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue for res,name,Id in Chains[chain][residue+1][ires]: try: ipos = pAtms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue except KeyError: continue if all(ids): angle = [list(ids),['1','1','1'],Value,Esd] if angle not in angleRestData['Angles']: angleRestData['Angles'].append(angle) ids = [0,0,0] macStr = macro.readline() macro.close() print(' Found %d angle restraints'%len(angleRestData['Angles'])) UpdateAngleRestr(angleRestData) def AddMogulAngleRestraint(angleRestData): mogul = getMOGULFile() for line in mogul: items = line.split(',') if 'angle' == items[0]: aName,bName,cName = items[2].split() aInd = Names.index(aName) bInd = Names.index(bName) cInd = Names.index(cName) if items[3] != 'No hits': angle = float(items[6]) esd = float(items[7]) else: angle = float(items[5]) esd = 2.00 newAngle = [[Ids[aInd],Ids[bInd],Ids[cInd]],['1','1','1'],angle,esd] if newAngle not in angleRestData['Angles']: angleRestData['Angles'].append(newAngle) UpdateAngleRestr(angleRestData) def AddPlaneRestraint(restrData): ids = [] dlg = G2G.G2MultiChoiceDialog(G2frame,'Select 4 or more atoms for plane in '+General['Name'], 'Select 4+ atoms',Names[iBeg:]) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() if len(sel) > 3: for x in sel: ids.append(Ids[x+iBeg]) ops = ['1' for i in range(len(sel))] plane = [ids,ops,0.0,0.01] if plane not in restrData['Planes']: restrData['Planes'].append(plane) else: print ('**** ERROR - not enough atoms for a plane restraint - try again ****') UpdatePlaneRestr(restrData) def AddAAPlaneRestraint(planeRestData): macro = getMacroFile('plane') if not macro: return Chains = makeChains(Names,Ids) macStr = macro.readline() while macStr: items = macStr.split() if 'F' in items[0]: restrData['Plane']['wtFactor'] = float(items[1]) elif 'S' in items[0]: Res = items[1] Esd = float(items[2]) Atms = items[3:] pAtms = ['' for i in Atms] for i,atm in enumerate(Atms): if '+' in atm: pAtms[i] = atm.strip('+') ids = [0,]*len(Atms) ops = ['1' for i in range(len(Atms))] chains = list(Chains.keys()) chains.sort() for chain in chains: residues = list(Chains[chain].keys()) residues.sort() for residue in residues: for ires in [0,1]: if residue == residues[-1] and Res == '*': continue if Res != '*': #works with disordered res for res,name,Id in Chains[chain][residue][ires]: if Res == res: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue else: try: for res,name,Id in Chains[chain][residue][ires]: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue for res,name,Id in Chains[chain][residue+1][ires]: try: ipos = pAtms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue except KeyError: continue if all(ids): plane = [list(ids),ops,0.0,Esd] if plane not in planeRestData['Planes']: planeRestData['Planes'].append(plane) ids = [0,]*len(Atms) macStr = macro.readline() macro.close() print(' Found %d plane restraints'%len(planeRestData['Planes'])) UpdatePlaneRestr(planeRestData) def AddAAChiralRestraint(chiralRestData): macro = getMacroFile('chiral') if not macro: return Chains = makeChains(Names,Ids) macStr = macro.readline() while macStr: items = macStr.split() if 'F' in items[0]: restrData['Chiral']['wtFactor'] = float(items[1]) elif 'S' in items[0]: Res = items[1] Value = float(items[2]) Esd = float(items[3]) Atms = items[4:8] ids = [0,0,0,0] chains = list(Chains.keys()) chains.sort() for chain in chains: residues = list(Chains[chain].keys()) residues.sort() for residue in residues: for ires in [0,1]: if residue == residues[-1] and Res == '*': continue if Res != '*': #works with disordered res for res,name,Id in Chains[chain][residue][ires]: if Res == res: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue else: try: for res,name,Id in Chains[chain][residue][ires]: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue except KeyError: continue if all(ids): chiral = [list(ids),['1','1','1','1'],Value,Esd] if chiral not in chiralRestData['Volumes']: chiralRestData['Volumes'].append(chiral) ids = [0,0,0,0] macStr = macro.readline() macro.close() print(' Found %d chiral volumes restraints'%len(chiralRestData['Volumes'])) UpdateChiralRestr(chiralRestData) def AddAATorsionRestraint(torsionRestData): macro = getMacroFile('torsion') if not macro: return Chains = makeChains(Names,Ids) macStr = macro.readline()[:-1] while macStr: items = macStr.split() if 'F' in items[0]: restrData['Torsion']['wtFactor'] = float(items[1]) elif 'A' in items[0]: name = items[10] coeff = np.zeros(9) for i,item in enumerate(items[1:10]): coeff[i] = float(item) torsionRestData['Coeff'][name] = coeff elif 'S' in items[0]: Name = items[1] Res = items[2] Esd = float(items[3]) Atms = items[4:8] pAtms = ['','','',''] for i,atm in enumerate(Atms): if '+' in atm: pAtms[i] = atm.strip('+') ids = [0,0,0,0] chains = list(Chains.keys()) chains.sort() for chain in chains: residues = list(Chains[chain].keys()) residues.sort() for residue in residues: for ires in [0,1]: if residue == residues[-1] and Res == '*': continue if Res != '*': #works with disordered res for res,name,Id in Chains[chain][residue][ires]: if Res == res: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue else: try: for res,name,Id in Chains[chain][residue][ires]: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue for res,name,Id in Chains[chain][residue+1][ires]: try: ipos = pAtms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue except KeyError: continue if all(ids): torsion = [list(ids),['1','1','1','1'],Name,Esd] if torsion not in torsionRestData['Torsions']: torsionRestData['Torsions'].append(torsion) ids = [0,0,0,0] macStr = macro.readline() macro.close() print(' Found %d torsion restraints'%len(torsionRestData['Torsions'])) UpdateTorsionRestr(torsionRestData) def AddAARamaRestraint(ramaRestData): macro = getMacroFile('Ramachandran') if not macro: return Chains = makeChains(Names,Ids) macStr = macro.readline() while macStr: items = macStr.split() if 'F' in items[0]: restrData['Rama']['wtFactor'] = float(items[1]) elif 'A' in items[0]: nTerms = int(items[1]) name = items[2] coeff = np.zeros((nTerms,6)) for i in range(nTerms): macStr = macro.readline() items = macStr.split() for j,val in enumerate(items): coeff[i][j] = float(val) ramaRestData['Coeff'][name] = coeff elif 'S' in items[0]: Name = items[1] Res = items[2] Esd = float(items[3]) Atms = items[4:9] mAtms = ['','','','',''] pAtms = ['','','','',''] for i,atm in enumerate(Atms): if '+' in atm: pAtms[i] = atm.strip('+') elif '-' in atm: mAtms[i] = atm.strip('-') ids = [0,0,0,0,0] chains = list(Chains.keys()) chains.sort() for chain in chains: residues = list(Chains[chain].keys()) residues.sort() if not (any(mAtms) or any(pAtms)): for residue in residues: for ires in [0,1]: for res,name,Id in Chains[chain][residue][ires]: if Res == res: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue if all(ids): rama = [list(ids),['1','1','1','1','1'],Name,Esd] if rama not in ramaRestData['Ramas']: ramaRestData['Ramas'].append(rama) ids = [0,0,0,0,0] else: for ires,residue in enumerate(residues[1:-1]): for jres in [0,1]: try: for res,name,Id in Chains[chain][residue-1][jres]: try: ipos = mAtms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue for res,name,Id in Chains[chain][residue+1][jres]: try: ipos = pAtms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue for res,name,Id in Chains[chain][residue][jres]: if Res == res: try: ipos = Atms.index(name[:3].strip()) ids[ipos] = Id except ValueError: continue if all(ids): rama = [list(ids),['1','1','1','1','1'],Name,Esd] if rama not in ramaRestData['Ramas']: ramaRestData['Ramas'].append(rama) ids = [0,0,0,0,0] except KeyError: continue macStr = macro.readline() macro.close() print(' Found %d Ramachandran restraints'%len(ramaRestData['Ramas'])) UpdateRamaRestr(ramaRestData) def AddChemCompRestraint(chemcompRestData): ids = [] factors = [] dlg = G2G.G2MultiChoiceDialog(G2frame,'Select atoms for chemical restraint in '+General['Name'], 'Select atoms',Names) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() for x in sel: if 'all' in Names[x]: allType = Types[x] for name,Type,Id in zip(Names,Types,Ids): if Type == allType and 'all' not in name: ids.append(Id) factors.append(1.0) else: ids.append(Ids[x]) factors.append(1.0) dlg.Destroy() if len(ids) > 0: value = 1.0 dlg = G2G.SingleFloatDialog(G2frame,'Cell sum','Enter unit cell sum ',value,[-1.e6,1.e6],'%.2f') if dlg.ShowModal() == wx.ID_OK: value = dlg.GetValue() comp = [ids,factors,value,0.01] if comp not in chemcompRestData['Sites']: chemcompRestData['Sites'].append(comp) UpdateChemcompRestr(chemcompRestData) else: print ('**** ERROR - not enough atoms for a composition restraint - try again ****') def AddTextureRestraint(textureRestData): dlg = wx.TextEntryDialog(G2frame,'Enter h k l for pole figure restraint','Enter HKL','') if dlg.ShowModal() == wx.ID_OK: text = dlg.GetValue() vals = text.split() try: hkl = [int(vals[i]) for i in range(3)] texture = [hkl,24,0.01,False,1.0] if texture not in textureRestData['HKLs']: textureRestData['HKLs'].append(texture) UpdateTextureRestr(textureRestData) except (ValueError,IndexError): print ('**** ERROR - bad input of h k l - try again ****') dlg.Destroy() def WtBox(wind,restData): if 'Range' not in restData: restData['Range'] = 1.1 #patch def OnUseData(event): Obj = event.GetEventObject() restData['Use'] = Obj.GetValue() wtBox = wx.BoxSizer(wx.HORIZONTAL) wtBox.Add(wx.StaticText(wind,-1,'Phase '+phaseName+' Restraint weight factor: '),0,WACV) wtfactor = G2G.ValidatedTxtCtrl(wind,restData,'wtFactor',nDig=(10,2),typeHint=float) wtBox.Add(wtfactor,0,WACV) useData = wx.CheckBox(wind,-1,label=' Use?') useData.Bind(wx.EVT_CHECKBOX, OnUseData) useData.SetValue(restData['Use']) wtBox.Add(useData,0,WACV) if 'Bonds' in restData or 'Angles' in restData: wtBox.Add(wx.StaticText(wind,-1,' Search range: '),0,WACV) sRange = G2G.ValidatedTxtCtrl(wind,restData,'Range',nDig=(10,2),typeHint=float) wtBox.Add(sRange,0,WACV) wtBox.Add(wx.StaticText(wind,-1,' x sum(atom radii)'),0,WACV) return wtBox def OnRowSelect(event): r,c = event.GetRow(),event.GetCol() Obj = event.GetEventObject() if r < 0 and c < 0: if Obj.IsSelection(): Obj.ClearSelection() else: for row in range(Obj.GetNumberRows()): Obj.SelectRow(row,True) elif c < 0: #only row clicks if event.ControlDown(): if r in Obj.GetSelectedRows(): Obj.DeselectRow(r) else: Obj.SelectRow(r,True) elif event.ShiftDown(): indxs = Obj.GetSelectedRows() Obj.ClearSelection() ibeg = 0 if indxs: ibeg = indxs[-1] for row in range(ibeg,r+1): Obj.SelectRow(row,True) else: Obj.ClearSelection() Obj.SelectRow(r,True) def UpdateBondRestr(bondRestData): def OnCellChange(event): r,c = event.GetRow(),event.GetCol() try: new = float(bondTable.GetValue(r,c)) if new <= 0.: raise ValueError bondRestData['Bonds'][r][c] = new except ValueError: pass wx.CallAfter(UpdateBondRestr,bondRestData) def OnChangeValue(event): rows = GetSelectedRows(Bonds) if not rows: return Bonds.ClearSelection() val = bondList[rows[0]][2] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new value for bond',val,[0.,5.],'%.4f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: bondRestData['Bonds'][r][2] = parm dlg.Destroy() UpdateBondRestr(bondRestData) def OnChangeEsd(event): rows = GetSelectedRows(Bonds) if not rows: return Bonds.ClearSelection() val = bondList[rows[0]][3] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new esd for bond',val,[0.,1.],'%.4f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: bondRestData['Bonds'][r][3] = parm dlg.Destroy() UpdateBondRestr(bondRestData) def OnDeleteRestraint(event): rows = GetSelectedRows(Bonds,'delete',G2frame) G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return Bonds.ClearSelection() rows.sort() rows.reverse() for row in rows: bondList.remove(bondList[row]) UpdateBondRestr(bondRestData) try: if BondRestr.GetSizer(): BondRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(BondRestr,bondRestData),0) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) bondList = bondRestData['Bonds'] if len(bondList) and len(bondList[0]) == 6: #patch bondList = bondRestData['Bonds'] = [] if len(bondList): table = [] rowLabels = [] bad = [] chisq = 0. Types = [wg.GRID_VALUE_STRING,]+4*[wg.GRID_VALUE_FLOAT+':10,3',] if 'macro' in General['Type']: colLabels = ['(res) A - (res) B','calc','target','esd','delt/sig'] for i,[indx,ops,obs,esd] in enumerate(bondList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '' for atom in atoms: name += '('+atom[1]+atom[0].strip()+atom[2]+') '+atom[3]+' - ' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) calc = G2mth.getRestDist(XYZ,Amat) chisq += bondRestData['wtFactor']*((obs-calc)/esd)**2 table.append([name[:-3],calc,obs,esd,(obs-calc)/esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) else: colLabels = ['A+SymOp - B+SymOp','calc','target','esd','delt/sig'] for i,[indx,ops,obs,esd] in enumerate(bondList): try: names = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,ct-1) XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) calc = G2mth.getRestDist(XYZ,Amat) chisq += bondRestData['wtFactor']*((obs-calc)/esd)**2 table.append([names[0]+'+('+ops[0]+') - '+names[1]+'+('+ops[1]+')',calc,obs,esd,(obs-calc)/esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) if len(bad): bad.reverse() for ibad in bad: del bondList[ibad] if len(bondList): bondTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) Bonds = G2G.GSGrid(BondRestr) Bonds.SetTable(bondTable, True) Bonds.AutoSizeColumns(False) for c in [0,1,4]: # format read-only rows attr = wx.grid.GridCellAttr() attr.IncRef() attr.SetBackgroundColour(VERY_LIGHT_GREY) attr.SetReadOnly(True) Bonds.SetColAttr(c, attr) Bonds.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): Bonds.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: Bonds.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True) G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) G2frame.Bind(wx.EVT_MENU, OnChangeValue, id=G2G.wxID_RESRCHANGEVAL) G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD) mainSizer.Add(wx.StaticText(BondRestr,-1, 'Bond restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ %(chisq,chisq/len(bondList))),0) Bonds.SetScrollRate(10,10) Bonds.SetMinSize((-1,300)) mainSizer.Add(Bonds,1,wx.EXPAND,1) else: mainSizer.Add(wx.StaticText(BondRestr,-1,'No bond distance restraints for this phase'),0,) else: mainSizer.Add(wx.StaticText(BondRestr,-1,'No bond distance restraints for this phase'),0,) wx.CallAfter(G2phsGUI.SetPhaseWindow,BondRestr,mainSizer,Scroll=0) def UpdateAngleRestr(angleRestData): def OnCellChange(event): r,c = event.GetRow(),event.GetCol() try: new = float(angleTable.GetValue(r,c)) if new <= 0. or new > 180.: raise ValueError angleRestData['Angles'][r][c] = new except ValueError: pass wx.CallAfter(UpdateAngleRestr,angleRestData) def OnChangeValue(event): rows = GetSelectedRows(Angles) if not rows: return Angles.ClearSelection() val = angleList[rows[0]][2] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new value for angle',val,[0.,360.],'%.2f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: angleRestData['Angles'][r][2] = parm dlg.Destroy() UpdateAngleRestr(angleRestData) def OnChangeEsd(event): rows = GetSelectedRows(Angles) if not rows: return Angles.ClearSelection() val = angleList[rows[0]][3] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new esd for angle',val,[0.,5.],'%.2f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: angleRestData['Angles'][r][3] = parm dlg.Destroy() UpdateAngleRestr(angleRestData) def OnDeleteRestraint(event): rows = GetSelectedRows(Angles,'delete',G2frame) G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return rows.sort() rows.reverse() for row in rows: angleList.remove(angleList[row]) UpdateAngleRestr(angleRestData) try: if AngleRestr.GetSizer(): AngleRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(AngleRestr,angleRestData),0) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) angleList = angleRestData['Angles'] if len(angleList): table = [] rowLabels = [] bad = [] chisq = 0. Types = [wg.GRID_VALUE_STRING,]+4*[wg.GRID_VALUE_FLOAT+':10,2',] if 'macro' in General['Type']: colLabels = ['(res) A - (res) B - (res) C','calc','target','esd','delt/sig'] for i,[indx,ops,obs,esd] in enumerate(angleList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '' for atom in atoms: name += '('+atom[1]+atom[0].strip()+atom[2]+') '+atom[3]+' - ' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) calc = G2mth.getRestAngle(XYZ,Amat) chisq += angleRestData['wtFactor']*((obs-calc)/esd)**2 table.append([name[:-3],calc,obs,esd,(obs-calc)/esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) else: colLabels = ['A+SymOp - B+SymOp - C+SymOp','calc','target','esd','delt/sig'] for i,[indx,ops,obs,esd] in enumerate(angleList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,ct-1) name = atoms[0]+'+('+ops[0]+') - '+atoms[1]+'+('+ops[1]+') - '+atoms[2]+ \ '+('+ops[2]+')' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) calc = G2mth.getRestAngle(XYZ,Amat) chisq += angleRestData['wtFactor']*((obs-calc)/esd)**2 table.append([name,calc,obs,esd,(obs-calc)/esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) if len(bad): bad.reverse() for ibad in bad: del angleList[ibad] if len(angleList): angleTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) Angles = G2G.GSGrid(AngleRestr) Angles.SetTable(angleTable, True) Angles.AutoSizeColumns(False) for c in [0,1,4]: # format readonly columns attr = wx.grid.GridCellAttr() attr.IncRef() attr.SetBackgroundColour(VERY_LIGHT_GREY) attr.SetReadOnly(True) Angles.SetColAttr(c, attr) Angles.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): Angles.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: Angles.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True) G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) G2frame.Bind(wx.EVT_MENU, OnChangeValue, id=G2G.wxID_RESRCHANGEVAL) G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD) mainSizer.Add(wx.StaticText(AngleRestr,-1, 'Angle restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ %(chisq,chisq/len(angleList))),0) Angles.SetScrollRate(10,10) Angles.SetMinSize((-1,300)) mainSizer.Add(Angles,1,wx.EXPAND,1) else: mainSizer.Add(wx.StaticText(AngleRestr,-1,'No bond angle restraints for this phase'),0,) else: mainSizer.Add(wx.StaticText(AngleRestr,-1,'No bond angle restraints for this phase'),0,) wx.CallAfter(G2phsGUI.SetPhaseWindow,AngleRestr,mainSizer,Scroll=0) def UpdatePlaneRestr(planeRestData): items = G2frame.dataWindow.RestraintEdit.GetMenuItems() for item in items: if item.GetItemLabelText() in ['Change value']: item.Enable(False) def OnCellChange(event): r,c = event.GetRow(),event.GetCol() try: new = float(planeTable.GetValue(r,c)) if new <= 0.: raise ValueError planeRestData['Planes'][r][c] = new except ValueError: pass wx.CallAfter(UpdatePlaneRestr,planeRestData) def OnChangeEsd(event): rows = GetSelectedRows(Planes) if not rows: return Planes.ClearSelection() val = planeList[rows[0]][3] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new esd for plane',val,[0.,5.],'%.2f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: planeRestData['Planes'][r][3] = parm dlg.Destroy() UpdatePlaneRestr(planeRestData) def OnDeleteRestraint(event): rows = GetSelectedRows(Planes,'delete',G2frame) G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return rows.sort() rows.reverse() for row in rows: planeList.remove(planeList[row]) UpdatePlaneRestr(planeRestData) try: if PlaneRestr.GetSizer(): PlaneRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(PlaneRestr,planeRestData),0) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) planeList = planeRestData['Planes'] if len(planeList): table = [] rowLabels = [] bad = [] chisq = 0. Types = [wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,2',] if 'macro' in General['Type']: colLabels = ['(res) atom','calc','target','esd'] for i,[indx,ops,obs,esd] in enumerate(planeList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '' for a,atom in enumerate(atoms): name += '('+atom[1]+atom[0].strip()+atom[2]+') '+atom[3]+' - ' if (a+1)%3 == 0: name += '\n' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) calc = G2mth.getRestPlane(XYZ,Amat) chisq += planeRestData['wtFactor']*((calc)/esd)**2 table.append([name[:-3],calc,obs,esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) else: colLabels = ['atom+SymOp','calc','target','esd'] for i,[indx,ops,obs,esd] in enumerate(planeList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,ct-1) XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) calc = G2mth.getRestPlane(XYZ,Amat) chisq += planeRestData['wtFactor']*((calc)/esd)**2 name = '' for a,atom in enumerate(atoms): name += atom+'+ ('+ops[a]+'),' if (a+1)%3 == 0: name += '\n' table.append([name[:-1],calc,obs,esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) if len(bad): bad.reverse() for ibad in bad: del planeList[ibad] if len(planeList): planeTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) Planes = G2G.GSGrid(PlaneRestr) Planes.SetTable(planeTable, True) Planes.AutoSizeColumns(False) Planes.AutoSizeRows(False) for r in range(len(planeList)): for c in range(3): Planes.SetReadOnly(r,c,True) Planes.SetCellStyle(r,c,VERY_LIGHT_GREY,True) Planes.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): Planes.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: Planes.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True) G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD) mainSizer.Add(wx.StaticText(PlaneRestr,-1, 'Plane restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ %(chisq,chisq/len(planeList))),0) Planes.SetScrollRate(10,10) Planes.SetMinSize((-1,300)) mainSizer.Add(Planes,1,wx.EXPAND,1) else: mainSizer.Add(wx.StaticText(PlaneRestr,-1,'No plane restraints for this phase'),0,) else: mainSizer.Add(wx.StaticText(PlaneRestr,-1,'No plane restraints for this phase'),0,) G2phsGUI.SetPhaseWindow(PlaneRestr,mainSizer,Scroll=0) def UpdateChiralRestr(chiralRestData): def OnCellChange(event): r,c = event.GetRow(),event.GetCol() try: new = float(volumeTable.GetValue(r,c)) if new <= 0.: raise ValueError chiralRestData['Volumes'][r][c] = new except ValueError: pass wx.CallAfter(UpdateChiralRestr,chiralRestData) def OnDeleteRestraint(event): rows = GetSelectedRows(Volumes,'delete',G2frame) G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return rows.sort() rows.reverse() for row in rows: volumeList.remove(volumeList[row]) UpdateChiralRestr(chiralRestData) def OnChangeValue(event): rows = GetSelectedRows(Volumes) if not rows: return Volumes.ClearSelection() val = volumeList[rows[0]][2] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new value for chiral volume',val,[0.,360.],'%.2f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: chiralRestData['Volumes'][r][2] = parm dlg.Destroy() UpdateChiralRestr(chiralRestData) def OnChangeEsd(event): rows = GetSelectedRows(Volumes) if not rows: return Volumes.ClearSelection() val = volumeList[rows[0]][3] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new esd for chiral volume',val,[0.,5.],'%.2f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: chiralRestData['Volumes'][r][3] = parm dlg.Destroy() UpdateChiralRestr(chiralRestData) try: if ChiralRestr.GetSizer(): ChiralRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(ChiralRestr,chiralRestData),0) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) volumeList = chiralRestData['Volumes'] if len(volumeList): table = [] rowLabels = [] bad = [] chisq = 0. Types = [wg.GRID_VALUE_STRING,]+4*[wg.GRID_VALUE_FLOAT+':10,2',] if 'macro' in General['Type']: colLabels = ['(res) O (res) A (res) B (res) C','calc','target','esd','delt/sig'] for i,[indx,ops,obs,esd] in enumerate(volumeList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '' for atom in atoms: name += '('+atom[1]+atom[0].strip()+atom[2]+') '+atom[3]+' ' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) calc = G2mth.getRestChiral(XYZ,Amat) chisq += chiralRestData['wtFactor']*((obs-calc)/esd)**2 table.append([name,calc,obs,esd,(obs-calc)/esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) else: colLabels = ['O+SymOp A+SymOp B+SymOp C+SymOp)','calc','target','esd','delt/sig'] for i,[indx,ops,obs,esd] in enumerate(volumeList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,ct-1) name = atoms[0]+'+('+ops[0]+') '+atoms[1]+'+('+ops[1]+') '+atoms[2]+ \ '+('+ops[2]+') '+atoms[3]+'+('+ops[3]+')' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) calc = G2mth.getRestChiral(XYZ,Amat) chisq += chiralRestData['wtFactor']*((obs-calc)/esd)**2 table.append([name,calc,obs,esd,(obs-calc)/esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) if len(bad): bad.reverse() for ibad in bad: del volumeList[ibad] if len(volumeList): volumeTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) Volumes = G2G.GSGrid(ChiralRestr) Volumes.SetTable(volumeTable, True) Volumes.AutoSizeColumns(False) for r in range(len(volumeList)): for c in [0,1,4]: Volumes.SetReadOnly(r,c,True) Volumes.SetCellStyle(r,c,VERY_LIGHT_GREY,True) Volumes.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): Volumes.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: Volumes.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) for i in (G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True) G2frame.Bind(wx.EVT_MENU, OnChangeValue, id=G2G.wxID_RESRCHANGEVAL) G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD) mainSizer.Add(wx.StaticText(ChiralRestr,-1, 'Chiral volume restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ %(chisq,chisq/len(volumeList))),0) Volumes.SetScrollRate(10,10) Volumes.SetMinSize((-1,300)) mainSizer.Add(Volumes,1,wx.EXPAND,1) else: mainSizer.Add(wx.StaticText(ChiralRestr,-1,'No chiral volume restraints for this phase'),0,) else: mainSizer.Add(wx.StaticText(ChiralRestr,-1,'No chiral volume restraints for this phase'),0,) G2phsGUI.SetPhaseWindow(ChiralRestr,mainSizer,Scroll=0) def UpdateTorsionRestr(torsionRestData): def OnCellChange(event): r,c = event.GetRow(),event.GetCol() try: new = float(torsionTable.GetValue(r,c)) if new <= 0. or new > 5.: raise ValueError torsionRestData['Torsions'][r][3] = new #only esd is editable except ValueError: pass wx.CallAfter(UpdateTorsionRestr,torsionRestData) def OnDeleteRestraint(event): rows = GetSelectedRows(TorsionRestr.Torsions,'delete',G2frame) G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return rows.sort() rows.reverse() for row in rows: torsionList.remove(torsionList[row]) wx.CallAfter(UpdateTorsionRestr,torsionRestData) def OnChangeEsd(event): rows = GetSelectedRows(TorsionRestr.Torsions) if not rows: return TorsionRestr.Torsions.ClearSelection() val = torsionList[rows[0]][4] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new esd for torsion restraints',val,[0.,5.],'%.2f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: torsionRestData['Torsions'][r][4] = parm dlg.Destroy() wx.CallAfter(UpdateTorsionRestr,torsionRestData) def coeffSizer(): table = [] rowLabels = [] Types = 9*[wg.GRID_VALUE_FLOAT+':10,4',] colLabels = ['Mag A','Pos A','Width A','Mag B','Pos B','Width B','Mag C','Pos C','Width C'] for item in coeffDict: rowLabels.append(item) table.append(coeffDict[item]) coeffTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) Coeff = G2G.GSGrid(TorsionRestr) Coeff.SetScrollRate(0,10) Coeff.SetTable(coeffTable, True) Coeff.AutoSizeColumns(False) for r in range(len(coeffDict)): for c in range(9): Coeff.SetReadOnly(r,c,True) Coeff.SetCellStyle(r,c,VERY_LIGHT_GREY,True) Coeff.SetMaxSize((-1,200)) return Coeff try: if TorsionRestr.GetSizer(): TorsionRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(TorsionRestr,torsionRestData),0) coeffDict = torsionRestData['Coeff'] torsionList = torsionRestData['Torsions'] if len(coeffDict): mainSizer.Add((5,5)) mainSizer.Add(wx.StaticText(TorsionRestr,-1,'Torsion function coefficients:'),0) mainSizer.Add(coeffSizer(),1,wx.EXPAND,1) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) if len(torsionList): mainSizer.Add(wx.StaticText(TorsionRestr,-1,'Torsion restraints:'),0) table = [] rowLabels = [] bad = [] chisq = 0. Types = 2*[wg.GRID_VALUE_STRING,]+4*[wg.GRID_VALUE_FLOAT+':10,2',] if 'macro' in General['Type']: colLabels = ['(res) A B C D','coef name','torsion','obs E','restr','esd'] for i,[indx,ops,cofName,esd] in enumerate(torsionList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '('+atoms[2][1]+atoms[2][0].strip()+atoms[2][2]+')' for atom in atoms: name += ' '+atom[3] XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) tor = G2mth.getRestTorsion(XYZ,Amat) restr,calc = G2mth.calcTorsionEnergy(tor,coeffDict[cofName]) chisq += torsionRestData['wtFactor']*(restr/esd)**2 table.append([name,cofName,tor,calc,restr,esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) if len(bad): bad.reverse() for ibad in bad: del torsionList[ibad] torsionTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) TorsionRestr.Torsions = G2G.GSGrid(TorsionRestr) TorsionRestr.Torsions.SetTable(torsionTable, True) TorsionRestr.Torsions.AutoSizeColumns(False) for r in range(len(torsionList)): for c in range(5): TorsionRestr.Torsions.SetReadOnly(r,c,True) TorsionRestr.Torsions.SetCellStyle(r,c,VERY_LIGHT_GREY,True) TorsionRestr.Torsions.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): TorsionRestr.Torsions.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: TorsionRestr.Torsions.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True) G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD) mainSizer.Add(wx.StaticText(TorsionRestr,-1, 'Torsion restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ %(chisq,chisq/len(torsionList))),0) TorsionRestr.Torsions.SetScrollRate(10,10) TorsionRestr.Torsions.SetMinSize((-1,300)) mainSizer.Add(TorsionRestr.Torsions,1,wx.EXPAND,1) else: mainSizer.Add(wx.StaticText(TorsionRestr,-1,'No torsion restraints for this phase'),0,) G2phsGUI.SetPhaseWindow(TorsionRestr,mainSizer,Scroll=0) def UpdateRamaRestr(ramaRestData): def OnCellChange(event): r,c = event.GetRow(),event.GetCol() try: new = float(ramaTable.GetValue(r,c)) if new <= 0. or new > 5.: raise ValueError ramaRestData['Ramas'][r][4] = new #only esd is editable except ValueError: pass wx.CallAfter(UpdateRamaRestr,ramaRestData) def OnDeleteRestraint(event): rows = GetSelectedRows(RamaRestr.Ramas,'delete',G2frame) G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return rows.sort() rows.reverse() for row in rows: ramaList.remove(ramaList[row]) UpdateRamaRestr(ramaRestData) def OnChangeEsd(event): rows = GetSelectedRows(RamaRestr.Ramas) if not rows: return RamaRestr.Ramas.ClearSelection() val = ramaList[rows[0]][4] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new esd for energy',val,[0.,5.],'%.2f') if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in rows: ramaRestData['Ramas'][r][4] = parm dlg.Destroy() UpdateRamaRestr(ramaRestData) def coeffSizer(): table = [] rowLabels = [] Types = 6*[wg.GRID_VALUE_FLOAT+':10,4',] colLabels = ['Mag','Pos phi','Pos psi','sig(phi)','sig(psi)','sig(cov)'] for item in coeffDict: for i,term in enumerate(coeffDict[item]): rowLabels.append(item+' term:'+str(i)) table.append(term) coeffTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) Coeff = G2G.GSGrid(RamaRestr) Coeff.SetScrollRate(0,10) Coeff.SetTable(coeffTable, True) Coeff.AutoSizeColumns(False) for r in range(Coeff.GetNumberRows()): for c in range(6): Coeff.SetReadOnly(r,c,True) Coeff.SetCellStyle(r,c,VERY_LIGHT_GREY,True) Coeff.SetMaxSize((-1,200)) return Coeff try: if RamaRestr.GetSizer(): RamaRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(RamaRestr,ramaRestData),0) ramaList = ramaRestData['Ramas'] coeffDict = ramaRestData['Coeff'] if len(coeffDict): mainSizer.Add(wx.StaticText(RamaRestr,-1,'Ramachandran function coefficients:'),0) mainSizer.Add(coeffSizer(),1,wx.EXPAND,1) if len(ramaList): mainSizer.Add(wx.StaticText(RamaRestr,-1,'Ramachandran restraints:'),0) table = [] rowLabels = [] bad = [] chisq = 0. Types = 2*[wg.GRID_VALUE_STRING,]+5*[wg.GRID_VALUE_FLOAT+':10,2',] if 'macro' in General['Type']: colLabels = ['(res) A B C D E','coef name','phi','psi','obs E','restr','esd'] for i,[indx,ops,cofName,esd] in enumerate(ramaList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,0,4) name = '('+atoms[3][1]+atoms[3][0].strip()+atoms[3][2]+')' for atom in atoms: name += ' '+atom[3] XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cx,3)) phi,psi = G2mth.getRestRama(XYZ,Amat) restr,calc = G2mth.calcRamaEnergy(phi,psi,coeffDict[cofName]) chisq += ramaRestData['wtFactor']*(restr/esd)**2 table.append([name,cofName,phi,psi,calc,restr,esd]) rowLabels.append(str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) if len(bad): bad.reverse() for ibad in bad: del ramaList[ibad] for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) if len(ramaList): ramaTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) RamaRestr.Ramas = G2G.GSGrid(RamaRestr) RamaRestr.Ramas.SetTable(ramaTable, True) RamaRestr.Ramas.AutoSizeColumns(False) for r in range(len(ramaList)): for c in range(6): RamaRestr.Ramas.SetReadOnly(r,c,True) RamaRestr.Ramas.SetCellStyle(r,c,VERY_LIGHT_GREY,True) RamaRestr.Ramas.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): RamaRestr.Ramas.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: RamaRestr.Ramas.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=True) G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) G2frame.Bind(wx.EVT_MENU, OnChangeEsd, id=G2G.wxID_RESTCHANGEESD) mainSizer.Add(wx.StaticText(RamaRestr,-1, 'Ramachandran restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ %(chisq,chisq/len(ramaList))),0) RamaRestr.Ramas.SetScrollRate(10,10) RamaRestr.Ramas.SetMinSize((-1,300)) mainSizer.Add(RamaRestr.Ramas,1,wx.EXPAND,1) else: mainSizer.Add(wx.StaticText(RamaRestr,-1,'No Ramachandran restraints for this phase'),0,) G2phsGUI.SetPhaseWindow(RamaRestr,mainSizer,Scroll=0) def UpdateChemcompRestr(chemcompRestData): def OnCellChange(event): r,c = event.GetRow(),event.GetCol() rowLabl = ChemComps.GetRowLabelValue(r) row = int(rowLabl.split(':')[1]) if 'Restr' in rowLabl: try: new = float(chemcompTable.GetValue(r,c)) chemcompRestData['Sites'][row][c-2] = new #obsd or esd except ValueError: pass else: try: new = float(chemcompTable.GetValue(r,c)) id = int(rowLabl.split(':')[2]) chemcompRestData['Sites'][row][1][id] = new #only factor except ValueError: pass wx.CallAfter(UpdateChemcompRestr,chemcompRestData) def OnDeleteRestraint(event): rows = GetSelectedRows(ChemComps,'delete',G2frame) #rows = ChemComps.GetSelectedRows() G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return terms = [] restrs = [] for r in sorted(rows,reverse=True): rowLabl = ChemComps.GetRowLabelValue(r) if 'Restr' in rowLabl: restrs.append(int(rowLabl.split(':')[1])) else: terms.append([int(i) for i in rowLabl.split(':')[1:]]) # delete terms first in case someone deletes a term in a restraint to be deleted for row,term in terms: del chemcompList[row][0][term] del chemcompList[row][1][term] for row in restrs: del chemcompList[row] UpdateChemcompRestr(chemcompRestData) # def OnChangeValue(event): # rows = GetSelectedRows(ChemComps) # if not rows: # return # ChemComps.ClearSelection() # dlg = G2G.SingleFloatDialog(G2frame,'New value', # 'Enter new value for restraint multiplier',1.0,[-1.e6,1.e6],'%.2f') # if dlg.ShowModal() == wx.ID_OK: # parm = dlg.GetValue() # for r in rows: # rowLabl = ChemComps.GetRowLabelValue(r) # if 'term' in rowLabl: # items = rowLabl.split(':') # chemcompRestData['Sites'][int(items[1])][1][int(items[2])] = parm # dlg.Destroy() # UpdateChemcompRestr(chemcompRestData) try: if ChemCompRestr.GetSizer(): ChemCompRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(ChemCompRestr,chemcompRestData),0) mainSizer.Add(wx.StaticText(ChemCompRestr,-1, 'NB: The chemical restraint sum is over the unit cell contents'),0) mainSizer.Add((5,5),0) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) chemcompList = chemcompRestData['Sites'] if len(chemcompList): table = [] rowLabels = [] bad = [] chisq = 0. Types = [wg.GRID_VALUE_STRING,]+5*[wg.GRID_VALUE_FLOAT+':10,2',] colLabels = ['Atoms','mul*frac','factor','calc','target','esd'] for i,[indx,factors,obs,esd] in enumerate(chemcompList): try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,ct-1) mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cs+1)) frac = np.array(G2mth.GetAtomItemsById(Atoms,AtLookUp,indx,cs-1)) mulfrac = mul*frac calcs = mul*frac*factors chisq += chemcompRestData['wtFactor']*((obs-np.sum(calcs))/esd)**2 for iatm,[atom,mf,fr,clc] in enumerate(zip(atoms,mulfrac,factors,calcs)): table.append([atom,mf,fr,clc,'','']) rowLabels.append('term:'+str(i)+':'+str(iatm)) table.append(['(Sum)','','',np.sum(calcs),obs,esd]) rowLabels.append('Restr:'+str(i)) except KeyError: print ('**** WARNING - missing atom - restraint deleted ****') bad.append(i) if len(bad): bad.reverse() for ibad in bad: del chemcompList[ibad] if len(chemcompList): chemcompTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) ChemComps = G2G.GSGrid(ChemCompRestr) ChemComps.SetTable(chemcompTable, True) ChemComps.AutoSizeColumns(False) for r in range(chemcompTable.GetNumberRows()): for c in range(2): ChemComps.SetReadOnly(r,c,True) ChemComps.SetCellStyle(r,c,VERY_LIGHT_GREY,True) if 'Restr' in ChemComps.GetRowLabelValue(r): for c in range(4): ChemComps.SetReadOnly(r,c,True) ChemComps.SetCellStyle(r,c,VERY_YELLOW,True) ChemComps.SetCellTextColour(r,1,VERY_YELLOW) # make spurious #'s disappear ChemComps.SetCellTextColour(r,2,VERY_YELLOW) else: for c in [3,4,5]: ChemComps.SetReadOnly(r,c,True) ChemComps.SetCellStyle(r,c,VERY_LIGHT_GREY,True) for c in [4,5]: ChemComps.SetCellTextColour(r,c,VERY_LIGHT_GREY) ChemComps.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): ChemComps.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: ChemComps.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) G2frame.dataWindow.RestraintEdit.Enable(id=G2G.wxID_RESTDELETE,enable=True) G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) #G2frame.Bind(wx.EVT_MENU, OnChangeValue, id=G2G.wxID_RESRCHANGEVAL) mainSizer.Add(wx.StaticText(ChemCompRestr,-1, 'Chemical composition restraints: sum(wt*(delt/sig)^2) = %.2f, mean(wt*(delt/sig)^2) = %.2f' \ %(chisq,chisq/len(chemcompList)))) mainSizer.Add(ChemComps) else: mainSizer.Add(wx.StaticText(ChemCompRestr,-1,'No chemical composition restraints for this phase'),0,) else: mainSizer.Add(wx.StaticText(ChemCompRestr,-1,'No chemical composition restraints for this phase'),0,) G2phsGUI.SetPhaseWindow(ChemCompRestr,mainSizer,Scroll=0) def UpdateTextureRestr(textureRestData): def OnDeleteRestraint(event): rows = GetSelectedRows(Textures,'delete',G2frame) G2frame.GetStatusBar().SetStatusText('',1) if not rows: G2frame.GetStatusBar().SetStatusText('First select restraints to be deleted',1) return rows.sort() rows.reverse() for row in rows: textureList.remove(textureList[row]) wx.CallAfter(UpdateTextureRestr,textureRestData) def OnCellChange(event): r,c = event.GetRow(),event.GetCol() try: if c == 1: #grid size new = int(textureTable.GetValue(r,c)) if new < 6 or new > 24: raise ValueError elif c in [2,4]: #esds new = float(textureTable.GetValue(r,c)) if new < -1. or new > 2.: raise ValueError else: new = textureTable.GetValue(r,c) textureRestData['HKLs'][r][c] = new except ValueError: pass wx.CallAfter(UpdateTextureRestr,textureRestData) try: if TextureRestr.GetSizer(): TextureRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(WtBox(TextureRestr,textureRestData),0) mainSizer.Add(wx.StaticText(TextureRestr,-1, 'NB: The texture restraints suppress negative pole figure values for the selected HKLs\n' ' "unit esd" gives a bias toward a flatter polefigure'),0) mainSizer.Add((5,5),0) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) textureList = textureRestData['HKLs'] if len(textureList): table = [] rowLabels = [] Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_LONG,wg.GRID_VALUE_FLOAT+':10,2', wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,2'] colLabels = ['HKL','grid','neg esd','use unit?','unit esd'] for i,[hkl,grid,esd1,ifesd2,esd2] in enumerate(textureList): table.append(['%d %d %d'%(hkl[0],hkl[1],hkl[2]),grid,esd1,ifesd2,esd2]) rowLabels.append(str(i)) textureTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) Textures = G2G.GSGrid(TextureRestr) Textures.SetTable(textureTable, True) Textures.AutoSizeColumns(False) for r in range(len(textureList)): Textures.SetReadOnly(r,0,True) Textures.SetCellStyle(r,0,VERY_LIGHT_GREY,True) if not textureTable.GetValue(r,3): Textures.SetReadOnly(r,4,True) Textures.SetCellStyle(r,4,VERY_LIGHT_GREY,True) Textures.SetCellTextColour(r,4,VERY_LIGHT_GREY) Textures.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) if 'phoenix' in wx.version(): Textures.Bind(wg.EVT_GRID_CELL_CHANGED, OnCellChange) else: Textures.Bind(wg.EVT_GRID_CELL_CHANGE, OnCellChange) G2frame.dataWindow.RestraintEdit.Enable(id=G2G.wxID_RESTDELETE,enable=True) G2frame.Bind(wx.EVT_MENU, OnDeleteRestraint, id=G2G.wxID_RESTDELETE) mainSizer.Add(Textures,0,) else: mainSizer.Add(wx.StaticText(TextureRestr,-1,'No texture restraints for this phase'),0,) G2phsGUI.SetPhaseWindow(TextureRestr,mainSizer,Scroll=0) def UpdateGeneralRestr(generalRestData): '''Display any generalized restraint expressions''' def OnEditGenRestraint(event): '''Edit a restraint expression''' n = event.GetEventObject().index parmDict = SetupParmDict(G2frame) dlg = G2exG.ExpressionDialog(G2frame,parmDict, exprObj=generalRestData['General'][n][0], header="Edit a restraint expression", fit=False,wildCard=G2frame.testSeqRefineMode()) restobj = dlg.Show(True) if restobj: generalRestData['General'][n][0] = restobj wx.CallAfter(UpdateGeneralRestr,restrData['General']) def OnDelGenRestraint(event): #does this work?? '''Delete a restraint expression''' n = event.GetEventObject().index del restrData['General']['General'][n] wx.CallAfter(UpdateGeneralRestr,restrData['General']) try: if GeneralRestr.GetSizer(): GeneralRestr.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) hSizer = wx.BoxSizer(wx.HORIZONTAL) hSizer.Add(wx.StaticText(GeneralRestr,wx.ID_ANY,'Weight factor: ')) hSizer.Add(G2G.ValidatedTxtCtrl(GeneralRestr,generalRestData, 'wtFactor',nDig=(10,1),typeHint=float)) btn = G2G.G2CheckBox(GeneralRestr,'Use?',generalRestData,'Use') hSizer.Add(btn) hSizer.Add((5,5),0) btn = wx.Button(GeneralRestr, wx.ID_ANY,"Add restraint") btn.Bind(wx.EVT_BUTTON,OnAddRestraint) hSizer.Add(btn,0,wx.EXPAND|wx.ALL) mainSizer.Add(hSizer,0) mainSizer.Add((5,5),0) for i in (G2G.wxID_RESTDELETE,G2G.wxID_RESRCHANGEVAL,G2G.wxID_RESTCHANGEESD): G2frame.dataWindow.RestraintEdit.Enable(id=i,enable=False) if generalRestData['General']: parmDict = SetupParmDict(G2frame) GridSiz = wx.FlexGridSizer(0,9,10,2) GridSiz.Add((-1,-1)) GridSiz.Add( wx.StaticText(GeneralRestr,wx.ID_ANY,'Expression'), 0,wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL) GridSiz.Add((-1,-1)) # for lbl in ('expression',' ','target\nvalue','current\nvalue','esd'): for lbl in ('target\nvalue','current\nvalue','esd'): GridSiz.Add( wx.StaticText(GeneralRestr,wx.ID_ANY,lbl,style=wx.CENTER), 0,wx.ALIGN_CENTER) GridSiz.Add((-1,-1)) GridSiz.Add((-1,-1)) GridSiz.Add( wx.StaticText(GeneralRestr,wx.ID_ANY,'Variables',style=wx.CENTER), 0,wx.ALIGN_CENTER) for i,rest in enumerate(generalRestData['General']): eq = rest[0] txt = '{}: '.format(i+1) GridSiz.Add(wx.StaticText(GeneralRestr,wx.ID_ANY,txt)) txt = eq.expression if len(txt) > 50: txt = txt[:47]+'... ' txtC = wx.StaticText(GeneralRestr,wx.ID_ANY,txt) GridSiz.Add(txtC) GridSiz.Add(wx.StaticText(GeneralRestr,wx.ID_ANY,' = ')) GridSiz.Add( G2G.ValidatedTxtCtrl(GeneralRestr,rest,1,nDig=(10,3,'g'),typeHint=float) ) # evaluate the expression try: calcobj = G2obj.ExpressionCalcObj(rest[0]) calcobj.SetupCalc(parmDict) txt = ' {:f} '.format(calcobj.EvalExpression()) except: txt = ' (error) ' txtC.SetForegroundColour("red") GridSiz.Add(wx.StaticText(GeneralRestr,wx.ID_ANY,txt)) GridSiz.Add( G2G.ValidatedTxtCtrl(GeneralRestr,rest,2,nDig=(10,3,'g'),typeHint=float) ) btn = wx.Button(GeneralRestr, wx.ID_ANY,"Edit",size=(40,-1)) btn.index = i btn.Bind(wx.EVT_BUTTON,OnEditGenRestraint) GridSiz.Add(btn) btn = wx.Button(GeneralRestr, wx.ID_ANY,"Delete",size=(60,-1)) btn.index = i btn.Bind(wx.EVT_BUTTON,OnDelGenRestraint) GridSiz.Add(btn) txt = '' for i in eq.assgnVars: if txt: txt += '; ' txt += str(i) + '=' + str(eq.assgnVars[i]) if len(txt) > 50: txt = txt[:47]+'...' GridSiz.Add(wx.StaticText(GeneralRestr,wx.ID_ANY,txt)) mainSizer.Add(GridSiz) G2phsGUI.SetPhaseWindow(GeneralRestr,mainSizer,Scroll=0) def OnPageChanged(event): page = event.GetSelection() #G2frame.restrBook.SetSize(G2frame.dataWindow.GetClientSize()) #TODO -almost right text = G2frame.restrBook.GetPageText(page) G2frame.dataWindow.RestraintEdit.SetLabel(G2G.wxID_RESRCHANGEVAL,'Change value') G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_USEMOGUL,False) if text == 'Bond': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_USEMOGUL,True) bondRestData = restrData['Bond'] UpdateBondRestr(bondRestData) elif text == 'Angle': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_USEMOGUL,True) angleRestData = restrData['Angle'] UpdateAngleRestr(angleRestData) elif text == 'Plane': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,False) planeRestData = restrData['Plane'] UpdatePlaneRestr(planeRestData) elif text == 'Chiral': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,False) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,True) chiralRestData = restrData['Chiral'] UpdateChiralRestr(chiralRestData) elif text == 'Torsion': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,False) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,False) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_AARESTRAINTPLOT,True) torsionRestData = restrData['Torsion'] UpdateTorsionRestr(torsionRestData) elif text == 'Ramachandran': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,False) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,False) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_AARESTRAINTPLOT,True) ramaRestData = restrData['Rama'] UpdateRamaRestr(ramaRestData) wx.CallAfter(G2plt.PlotRama,G2frame,phaseName,rama,ramaName) elif text == 'Chem. comp.': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,True) G2frame.dataWindow.RestraintEdit.SetLabel(G2G.wxID_RESRCHANGEVAL,'Change factor') G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTCHANGEESD,False) chemcompRestData = restrData['ChemComp'] UpdateChemcompRestr(chemcompRestData) elif text == 'Texture': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,True) textureRestData = restrData['Texture'] UpdateTextureRestr(textureRestData) elif text == 'General': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,True) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESRCHANGEVAL,False) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_RESTCHANGEESD,False) UpdateGeneralRestr(restrData['General']) event.Skip() # def RaisePage(event): # 'Respond to a "select tab" menu button' # # class PseudoEvent(object): # # def __init__(self,page): self.page = page # # def Skip(self): pass # # def GetSelection(self): return self.page # try: # i = tabIndex.get(event.GetId()) # G2frame.restrBook.SetSelection(i) # #OnPageChanged(PseudoEvent(i)) # except ValueError: # print('Unexpected event in RaisePage') # def OnSelectPage(event): 'Called when an item is selected from the Select page menu' # lookup the menu item that called us and get its text tabname = TabSelectionIdDict.get(event.GetId()) if not tabname: print ('Warning: menu item not in dict! id= %d'%event.GetId()) return # find the matching tab for PageNum in range(G2frame.restrBook.GetPageCount()): if tabname == G2frame.restrBook.GetPageText(PageNum): G2frame.restrBook.SetSelection(PageNum) return else: print ("Warning: tab "+tabname+" was not found") #### UpdateRestraints execution starts here try: phasedata = G2frame.GetPhaseData()[phaseName] except KeyError: #delete unknown or previously deleted phases from Restraints rId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints') pId = G2gd.GetGPXtreeItemId(G2frame,rId,phaseName) G2frame.GPXtree.Delete(pId) print('Unknown phase '+phaseName+' is deleted from Restraints') return restrData = data[phaseName] if 'Bond' not in restrData: restrData['Bond'] = {'wtFactor':1.0,'Range':1.1,'Bonds':[],'Use':True} if 'Angle' not in restrData: restrData['Angle'] = {'wtFactor':1.0,'Range':0.85,'Angles':[],'Use':True} if 'Plane' not in restrData: restrData['Plane'] = {'wtFactor':1.0,'Planes':[],'Use':True} if 'Chiral' not in restrData: restrData['Chiral'] = {'wtFactor':1.0,'Volumes':[],'Use':True} if 'Torsion' not in restrData: restrData['Torsion'] = {'wtFactor':1.0,'Coeff':{},'Torsions':[],'Use':True} if 'Rama' not in restrData: restrData['Rama'] = {'wtFactor':1.0,'Coeff':{},'Ramas':[],'Use':True} if 'Texture' not in restrData: restrData['Texture'] = {'wtFactor':1.0,'HKLs':[],'Use':True} if 'ChemComp' not in restrData: restrData['ChemComp'] = {'wtFactor':1.0,'Sites':[],'Use':True} if 'General' not in restrData: restrData['General'] = {'wtFactor':1.0,'General':[], 'Use':True} General = phasedata['General'] Cell = General['Cell'][1:7] #skip flag & volume Amat,Bmat = G2lat.cell2AB(Cell) SGData = General['SGData'] cx,ct,cs,cia = General['AtomPtrs'] Atoms = phasedata['Atoms'] AtLookUp = G2mth.FillAtomLookUp(Atoms,cia+8) if 'macro' in General['Type']: Names = [atom[0]+':'+atom[1]+atom[2]+' '+atom[3].ljust(4) for atom in Atoms] Ids = [] Coords = [] Types = [] iBeg = 0 else: Names = ['all '+ name for name in General['AtomTypes']] iBeg = len(Names) Types = [name for name in General['AtomTypes']] Coords = [ [] for type in Types] Ids = [ 0 for type in Types] Names += [atom[ct-1] for atom in Atoms] Types += [atom[ct] for atom in Atoms] Coords += [atom[cx:cx+3] for atom in Atoms] Ids += [atom[cia+8] for atom in Atoms] rama = G2data.ramachandranDist['All'] ramaName = 'All' G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RestraintMenu) G2frame.Bind(wx.EVT_MENU, OnAddRestraint, id=G2G.wxID_RESTRAINTADD) G2frame.Bind(wx.EVT_MENU, OnUseMogul, id=G2G.wxID_USEMOGUL) G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_USEMOGUL,True) if 'macro' in phasedata['General']['Type']: G2frame.dataWindow.RestraintEdit.Enable(G2G.wxID_AARESTRAINTADD,True) G2frame.Bind(wx.EVT_MENU, OnAddAARestraint, id=G2G.wxID_AARESTRAINTADD) G2frame.Bind(wx.EVT_MENU, OnPlotAARestraint, id=G2G.wxID_AARESTRAINTPLOT) # GUI defined here G2frame.restrBook = G2G.GSNoteBook(parent=G2frame.dataWindow) G2frame.dataWindow.GetSizer().Add(G2frame.restrBook,1,wx.ALL|wx.EXPAND,1) # clear menu and menu pointers Pages = [] txt = 'Bond' BondRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(BondRestr,txt) Pages.append(txt) txt = 'Angle' AngleRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(AngleRestr,txt) Pages.append(txt) txt = 'Plane' PlaneRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(PlaneRestr,txt) Pages.append(txt) txt = 'Chiral' ChiralRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(ChiralRestr,txt) Pages.append(txt) if 'macro' in General['Type']: txt = 'Torsion' TorsionRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(TorsionRestr,txt) Pages.append(txt) txt = 'Ramachandran' RamaRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(RamaRestr,txt) Pages.append(txt) txt = 'Chem. comp.' ChemCompRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(ChemCompRestr,txt) Pages.append(txt) txt = 'General' GeneralRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(GeneralRestr,txt) Pages.append(txt) if General['SH Texture']['Order']: txt = 'Texture' TextureRestr = wx.ScrolledWindow(G2frame.restrBook) G2frame.restrBook.AddPage(TextureRestr,txt) Pages.append(txt) UpdateBondRestr(restrData['Bond']) G2frame.restrBook.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged) # fill page selection menu menu = G2frame.dataWindow.RestraintTab for page in Pages: if menu.FindItem(page) >= 0: continue # is tab already in menu? Id = wx.NewId() TabSelectionIdDict[Id] = page menu.Append(Id,page,'') G2frame.Bind(wx.EVT_MENU, OnSelectPage, id=Id)