from __future__ import division import olex import olex_fs import glob import olx import os import time import math import olex_core import sys import programSettings from subprocess import * import htmlTools import HttpTools global _is_online _is_online = False sys.path.append(r".\src") import History import ExternalPrgParameters SPD, RPD = ExternalPrgParameters.SPD, ExternalPrgParameters.RPD from olexFunctions import OlexFunctions OV = OlexFunctions() import variableFunctions import MakeMovie import OlexVFS import threads as olxth haveGUI = OV.HasGUI() if haveGUI: import olex_gui def txt(): try: import uuid # This creates a custom unique filename determined by the the currently loaded in url output_file_name = "%s.txt"%uuid.uuid3(uuid.NAMESPACE_OID, '%s'%str(OV.FileFull())) # This is passed to the altered version of text creating the custom log instead of output.txt # Change: #  $spy.MakeHoverButton(toolbar-text, 'Text') to #  $spy.MakeHoverButton(toolbar-text, 'spy.txt\()') # in gui/blocks/snum-info.txt to make it default olx.Text(output_file_name) except ImportError, err: print "Could not initialise spy.txt() function: %s" %err OV.registerFunction(txt) def expand(start, finish, increment=1): """ expand creates returns a list based on start, finish and increment So C1, C6 would produce: C1 C2 C3 C4 C5 C6 """ import string start_atom = str(start).translate(None, string.digits).lower() start_number = int(str(start).translate(None, string.ascii_letters)) finish_atom = str(finish).translate(None, string.digits).lower() finish_number = int(str(finish).translate(None, string.ascii_letters)) if (finish_atom != start_atom) or (start_number == finish_number): print "The start and end element types must be the same and the numbers different" return return_string = [] for x in range(start_number, finish_number+1, int(increment)): return_string.append('%s%d'%(start_atom,x)) return ' '.join(return_string) OV.registerFunction(expand) if __debug__: #gc.set_debug(gc.DEBUG_LEAK | gc.DEBUG_STATS) #gc.set_debug(gc.DEBUG_STATS) #gc.set_debug(gc.DEBUG_SAVEALL | gc.DEBUG_STATS) def dump(): #a = gc.get_threshold() dump_garbage() #a = gc.garbage #b = gc.collect() OV.registerFunction(dump) def collect(generation=None): print gc.get_count() if generation != None: a = gc.collect(generation) else: a = gc.collect() print "%s garbage items collected" %a OV.registerFunction(collect) def getObjectCount(): #a = gc.get_objects() a = get_all_objects() #a = [] print "Number of objects: %s" %len(a) #print a[0] #print a[50] #print a[-10] #print "\n\n" a = [] gc.collect() return '' OV.registerFunction(getObjectCount) def dump_garbage(): """ show us what's the garbage about """ # force collection print "\nGARBAGE:" a = gc.collect() print "%s objects collected" %a print "\nGARBAGE OBJECTS:" for x in gc.garbage: s = str(x) if len(s) > 80: s = s[:80] print type(x),"\n ", s if type(x).__name__ == 'function': print x.func_code #print x.func_name print 'Size of garbage is: ',len(gc.garbage) # Recursively expand slist's objects # into olist, using seen to track # already processed objects. def _getr(slist, olist, seen): for e in slist: if id(e) in seen: continue seen[id(e)] = None olist.append(e) tl = gc.get_referents(e) if tl: _getr(tl, olist, seen) # The public function. def get_all_objects(): """Return a list of all live Python objects, not including the list itself.""" gcl = gc.get_objects() olist = [] seen = {} # Just in case: seen[id(gcl)] = None seen[id(olist)] = None seen[id(seen)] = None # _getr does the real work. _getr(gcl, olist, seen) return olist # -*- Mode: Python; tab-width: 4 -*- import types def get_refcounts(): d = {} sys.modules # collect all classes for m in sys.modules.values(): for sym in dir(m): o = getattr (m, sym) if type(o) is types.ClassType: d[o] = sys.getrefcount (o) # sort by refcount pairs = map (lambda x: (x[1],x[0]), d.items()) pairs.sort() pairs.reverse() return pairs def print_top_100(): for n, c in get_refcounts()[:100]: print '%10d %s' % (n, c.__name__) OV.registerFunction(print_top_100) #if headless: #from olexexc import * #else: #from olexexh import * #GuiFunctions.registerFunctions() class SpyVar(object): MatchedFragments = {} MatchedRms = [] class OlexRefinementModel(object): restraint_types = { 'dfix':'bond', 'dang':'bond', 'flat':'planarity', 'chiv':'chirality', 'sadi':'bond_similarity', 'simu':'adp_similarity', 'delu':'rigid_bond', 'isor':'isotropic_adp', 'olex2.restraint.angle':'angle', 'olex2.restraint.dihedral':'dihedral', 'olex2.restraint.adp_u_eq':'fixed_u_eq_adp', 'olex2.restraint.adp_u_eq_similar':'adp_u_eq_similarity', 'olex2.restraint.adp_volume_similar':'adp_volume_similarity', } constraint_types = { 'eadp':'adp', 'exyz':'site', } def __init__(self): olex_refinement_model = OV.GetRefinementModel(True) self._atoms = [] self._fixed_variables = {} self.atom_ids = [] asu = olex_refinement_model['aunit'] for residue in asu['residues']: for atom in residue['atoms']: self._atoms.append(atom) element_type = atom['type'] self.atom_ids.append(atom['aunit_id']) vars = olex_refinement_model['variables']['variables'] if len(vars) > 0: for var in vars[0]['references']: self._fixed_variables.setdefault(var['id'], []) self._fixed_variables[var['id']].append(var) self._cell = olex_refinement_model['aunit']['cell'] self.exptl = olex_refinement_model['exptl'] self._afix = olex_refinement_model['afix'] self.model= olex_refinement_model def atoms(self): return self._atoms def disorder_parts(self): return [atom['part'] for atom in self._atoms] def iterator(self): for i, atom in enumerate(self._atoms): name = str(atom['label']) element_type = str(atom['type']) xyz = atom['crd'][0] occu = atom['occu'][0] adp = atom.get('adp') if adp is None: uiso = atom.get('uiso')[0] u = (uiso,) else: u = adp[0] uiso_owner = atom.get('uisoOwner') if name[:1] != "Q": yield name, xyz, occu, u, uiso_owner, element_type, self._fixed_variables.get(i) def afix_iterator(self): for afix in self._afix: mn = afix['afix'] m, n = divmod(mn, 10) pivot = afix['pivot'] dependent = afix['dependent'] pivot_neighbours = [ i for i in self._atoms[pivot]['neighbours'] if not i in dependent] if len(dependent) == 0: continue dependent_part = self._atoms[dependent[0]]['part'] #pivot_neighbours = None bond_length = afix['d'] uiso = afix['u'] yield m, n, pivot, dependent, pivot_neighbours, bond_length def restraints_iterator(self, pair_sym_table=None): from libtbx.utils import flat_list from cctbx import sgtbx for shelxl_restraint in (self.restraint_types): for restraint in self.model.get(shelxl_restraint, ()): restraint_type = self.restraint_types.get(shelxl_restraint) if restraint_type is None: continue i_seqs = [i[0] for i in restraint['atoms']] kwds = dict(i_seqs=i_seqs) if restraint_type not in ( 'adp_similarity', 'adp_u_eq_similarity', 'adp_volume_similarity', 'rigid_bond', 'isotropic_adp', 'fixed_u_eq_adp'): kwds['sym_ops'] = [ (sgtbx.rt_mx(flat_list(i[1][:-1]), i[1][-1]) if i[1] is not None else None) for i in restraint['atoms']] if restraint_type in ('angle', 'dihedral'): esd_val = restraint['esd1']*180/math.pi else: esd_val = restraint['esd1'] kwds['weight'] = 1/math.pow(esd_val,2) value = restraint['value'] if restraint_type in ('adp_similarity', 'adp_u_eq_similarity', 'adp_volume_similarity', 'isotropic_adp', 'fixed_u_eq_adp'): kwds['sigma'] = restraint['esd1'] if restraint_type in ('adp_similarity', 'isotropic_adp'): kwds['sigma_terminal'] = restraint['esd2'] if restraint['esd2'] != 0 else None elif restraint_type == 'rigid_bond': kwds['sigma_12'] = restraint['esd1'] kwds['sigma_13'] = restraint['esd2'] if restraint['esd2'] != 0 else None if restraint_type == 'bond': kwds['distance_ideal'] = value elif restraint_type in ('angle', 'dihedral'): kwds['angle_ideal'] = value elif restraint_type in ('fixed_u_eq_adp',): kwds['u_eq_ideal'] = value elif restraint_type in ('bond_similarity', 'planarity'): kwds['weights'] = [kwds['weight']]*len(i_seqs) if restraint_type == 'bond_similarity': sym_ops = kwds['sym_ops'] kwds['i_seqs'] = [[i_seq for i_seq in i_seqs[i*2:(i+1)*2]] for i in range(int(len(i_seqs)/2))] kwds['sym_ops'] = [[sym_op for sym_op in sym_ops[i*2:(i+1)*2]] for i in range(int(len(sym_ops)/2))] if restraint_type in ('adp_similarity', 'isotropic_adp', 'rigid_bond'): kwds['pair_sym_table'] = pair_sym_table if 'weights' in kwds: del kwds['weight'] if restraint_type in ('bond', ): for i in range(int(len(i_seqs)/2)): yield restraint_type, dict( weight=kwds['weight'], distance_ideal=kwds['distance_ideal'], i_seqs=kwds['i_seqs'][i*2:(i+1)*2], sym_ops=kwds['sym_ops'][i*2:(i+1)*2]) elif restraint_type in ('angle', ): for i in range(int(len(i_seqs)/3)): yield restraint_type, dict( weight=kwds['weight'], angle_ideal=kwds['angle_ideal'], i_seqs=kwds['i_seqs'][i*3:(i+1)*3], sym_ops=kwds['sym_ops'][i*3:(i+1)*3]) elif restraint_type in ('dihedral', ): for i in range(int(len(i_seqs)/4)): yield restraint_type, dict( weight=kwds['weight'], angle_ideal=kwds['angle_ideal'], i_seqs=kwds['i_seqs'][i*4:(i+1)*4], sym_ops=kwds['sym_ops'][i*4:(i+1)*4]) else: yield restraint_type, kwds def constraints_iterator(self): from libtbx.utils import flat_list from cctbx import sgtbx for shelxl_constraint in (self.constraint_types): for constraint in self.model[shelxl_constraint]: constraint_type = self.constraint_types.get(shelxl_constraint) if constraint_type is None: continue if constraint_type == "adp": i_seqs = [i[0] for i in constraint['atoms']] kwds = dict(i_seqs=i_seqs) else: kwds = {"i_seqs": constraint} yield constraint_type, kwds def getCell(self): return [self._cell[param][0] for param in ('a','b','c','alpha','beta','gamma')] def getCellErrors(self): return [self._cell[param][1] for param in ('a','b','c','alpha','beta','gamma')] def numberAtoms(self): return sum(atom['occu'][0] for atom in self.atoms()) def number_non_hydrogen_atoms(self): return sum(atom['occu'][0] for atom in self.atoms() if atom['type'] not in ('H','Q')) def currentFormula(self): curr_form = {} for atom in self.atoms(): atom_type = atom['type'] atom_occu = atom['occu'][0] curr_form.setdefault(atom_type, 0) curr_form[atom_type] += atom_occu return curr_form def getExpectedPeaks(self): cell_volume = float(olx.xf.au.GetVolume()) expected_atoms = cell_volume/15 present_atoms = self.number_non_hydrogen_atoms() expected_peaks = expected_atoms - present_atoms if expected_peaks < 5: expected_peaks = 5 return int(expected_peaks) def getExpectedPeaks_and_AtomsPresent(self): cell_volume = float(olx.xf.au.GetVolume()) expected_atoms = cell_volume/15 present_atoms = self.number_non_hydrogen_atoms() expected_peaks = expected_atoms - present_atoms if expected_peaks < 5: expected_peaks = 5 return int(expected_peaks), int(present_atoms) def get_refine_ls_hydrogen_treatment(): afixes_present = [] afixes = {0:'refall', 1:'noref', 2:'refxyz', 3:'constr', 4:'constr', 5:'constr', 7:'constr', 8:'constr', } for atom in OlexRefinementModel().atoms(): if atom['type'] == 'H': afix = atom['afix'] n = int(afix[-1]) if len(afix) > 1: m = int(afix[:-1]) else: m = 0 if not afixes[n] in afixes_present: afixes_present.append(afixes[n]) if len(afixes_present) == 0: return 'undef' elif len(afixes_present) == 1: return afixes_present[0] else: return 'mixed' OV.registerFunction(get_refine_ls_hydrogen_treatment) def GetAvailableRefinementProgs(): retStr = "cctbx LBFGS<-cctbx;" retStr += "ShelXL L.S.;" retStr += "ShelXL CGLS;" retStr += "ShelXH L.S.;" retStr += "ShelXH CGLS;" if OV.IsPluginInstalled('ODAC'): retStr+= "cctbx AutoChem<-cctbx AutoChem" return retStr OV.registerFunction(GetAvailableRefinementProgs) def GetAvailableSolutionProgs(): retStr = "cctbx;" a = olx.file.Which('XS.exe') if a == "": a = olx.file.Which('ShelXS.exe') if a: retStr += "ShelXS;" return retStr OV.registerFunction(GetAvailableSolutionProgs) def OnMatchStart(argStr): OV.write_to_olex('match.htm', "RMS (Å) Matched Fragments
") SpyVar.MatchedFragments = {} SpyVar.MatchedRms = [] return "" if haveGUI: OV.registerCallback('startmatch',OnMatchStart) def OnMatchFound(rms, fragA, fragB): fragA = "'%s'" %fragA.replace(",", " ") fragB = "'%s'" %fragB.replace(",", " ") fragL = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U'] if len(SpyVar.MatchedFragments) > 16: return if fragA not in SpyVar.MatchedFragments: idA = fragL[len(SpyVar.MatchedFragments)] SpyVar.MatchedFragments.setdefault(fragA, {'fragID':idA}) else: idA = SpyVar.MatchedFragments[fragA].get('fragID') if fragB not in SpyVar.MatchedFragments: idB = fragL[len(SpyVar.MatchedFragments)] SpyVar.MatchedFragments.setdefault(fragB, {'fragID':idB}) else: idB = SpyVar.MatchedFragments[fragB].get('fragID') rms = float(rms) SpyVar.MatchedRms.append(rms) outStr = "" try: outStr += olex.readImage('match.htm') except: pass outStr+='' if rms < 0.2: outStr += '%.4f ' %(rms) elif rms < 1: outStr += '%.4f ' %(rms) elif rms < 2: outStr += '%.4f ' %(rms) else: outStr += '%.4f ' %(rms) outStr+=' %s ' %(fragA, idA) outStr+='%s ' %(fragB, idB) outStr+="
" OV.write_to_olex('match.htm',outStr) if haveGUI: OV.registerCallback('onmatch',OnMatchFound) #def getScreenSize(): #retval = () #from win32api import GetSystemMetrics #width = GetSystemMetrics (0) #height = GetSystemMetrics (1) #retval = (width, height) #print retval #olx.SetVar("screen_width", width) #olx.SetVar("screen_height", height) #return "OK" #OV.registerFunction(getScreenSize) def SetFormulaFromInput(): formula = OV.GetValue('SET_FORMULA') if not formula: return f = formula.split() Z = float(olx.xf.au.GetZ()) argStr = "" for element in f: try: n = int(element[1:])*Z el = element[:1] except: n = int(element[2:])*Z el = element[:2] argStr += "%s:%i," %(el, n) argStr = argStr.strip(',') argStr = "'%s'" %argStr olx.xf.SetFormula(argStr) return "" if haveGUI: OV.registerFunction(SetFormulaFromInput) #def suvvd(): #from RunPrg import RunPrg #a = RunPrg() #a.save_user_parameters() #print "The current settings have been saved for this user" #return "" #OV.registerFunction(suvvd) def ChooseLabelContent(cmd): s = "" switches = cmd.split() for switch in switches: s += "-%s " %switch olx.Labels(s) return "" OV.registerFunction(ChooseLabelContent) def FindZOfHeaviestAtomInFormua(): from PeriodicTable import PeriodicTable retVal = 0 PT = PeriodicTable() pt = PT.PeriodicTable() f = olx.xf.GetFormula('list') if not f: return retVal f = f.split(',') largestZ = 0 for element in f: ele = element.split(":")[0] Z = int(pt[ele].get('Z')) if Z > largestZ: largestZ = Z retVal = largestZ return retVal OV.registerFunction(FindZOfHeaviestAtomInFormua) last_formula = None def ElementButtonStates(symbol): if OV.GetParam('olex2.full_mode') == 'name -t=%s' %symbol: olex.m('mode off') else: if olex.f('Sel()') == '': olex.m('mode name -t=%s' %symbol) else: olex.m('name sel %s' %symbol) olex.m('sel -u') if haveGUI: OV.registerFunction(ElementButtonStates) def MakeElementButtonsFromFormula(): global last_formula global last_elements_html current_formula = OlexRefinementModel().currentFormula() #if current_formula == last_formula: #return last_elements_html from PilTools import ButtonMaker icon_size = OV.GetParam('gui.skin.icon_size') totalcount = 0 btn_dict = {} f = olx.xf.GetFormula('list') if not f: return f = f.split(',') Z_prime = float(olx.xf.au.GetZprime()) Z = float(olx.xf.au.GetZ()) html = "" for element in f: symbol = element.split(':')[0] max = float(element.split(':')[1]) max = round(max, 2) present = round(current_formula.get(symbol,0),2) if symbol != "H": totalcount += max max = max*Z_prime c = "" if present < max: bgcolour = (250,250,250) c = 'b' elif present == max: bgcolour = (210,255,210) c = 'g' else: bgcolour = (255,210,210) c = 'r' if c: name = "btn-element%s_%s" %(symbol, c) else: name = "btn-element%s" %(symbol) command = "if strcmp(sel(),'') then 'mode name -t=%s' else 'name sel %s'>>sel -u" %(symbol, symbol) target = OV.TranslatePhrase('change_element-target') #command = "if strcmp(spy.GetParam(olex2.in_mode),'mode name -t=%s') then 'mode off' else %%22 if strcmp(sel(),'') then 'mode name -t=%s' else 'name sel %s'>>sel -u%%22" %(symbol, symbol, symbol) command = 'spy.ElementButtonStates(%s)' %symbol namelower = 'btn-element%s' %(symbol) d = {} d.setdefault('namelower', name) d.setdefault('symbol', symbol) d.setdefault('cmds', command) d.setdefault('target', target + symbol) d.setdefault('bgcolor', OV.GetParam('gui.html.table_firstcol_colour')) html += ''' ''' %d d['namelower'] = 'Table' html += ''' ''' %d if current_formula != last_formula: last_formula = current_formula OV.write_to_olex('element_buttons.htm', html, 0) im_name='IMG_BTN-ELEMENT%s' %symbol OV.SetImage(im_name, name) SetAtomicVolumeInSnumPhil(totalcount) if haveGUI: OV.registerFunction(MakeElementButtonsFromFormula) def SetAtomicVolumeInSnumPhil(totalcount): cell_volume = 0 Z = 1 Z_prime = float(olx.xf.au.GetZprime()) try: cell_volume = float(olx.xf.au.GetCellVolume()) except: pass try: Z = float(olx.xf.au.GetZ()) except: pass if cell_volume and totalcount: atomic_volume = (cell_volume)/(totalcount * Z) OV.SetParam('snum.solution.current_atomic_volume','%.1f' %atomic_volume) else: OV.SetParam('snum.solution.current_atomic_volume',None) def CheckBoxValue(var, def_val='false'): if '.' in var: value = OV.GetParam(var) else: value = OV.FindValue(var,def_val) # XXX this should be gotten rid of if value in (True, 'True', 'true'): retVal = 'checked' else: retVal = '' return str(retVal) if haveGUI: OV.registerFunction(CheckBoxValue) def GetHklFileList(): reflection_file_extensions = ["hkl", "hkp", "raw", 'hklf5', 'hkc'] g = OV.ListFiles(OV.FilePath(), ';'.join(reflection_file_extensions)) g.sort() try: a = OV.HKLSrc().replace('\\', '/') if a[0] == "'" or a[0] == '"': a = a[1:-1] except: a = "" if not os.path.isfile(a) and not g: print "There is no reflection file or the reflection file is not accessible" reflection_files = "" for item in g: reflection_files+="%s.%s<-%s;" %(OV.FileName(item), OV.FileExt(item), item) return '"%s"' %reflection_files if haveGUI: OV.registerFunction(GetHklFileList) def tbxs_(name): retVal = "" txt = r'''
<-zimg border="0" src="#image.png">
''' txt += r''' '''%(name, name) txt += r''' ''' wFilePath = r"setup-%s.htm" %name OV.write_to_olex(wFilePath, txt) olex.m("popup setup-box 'setup-%s.htm' -b=tc -t='%s' -w=400 -h=400 -x=100 -y=200" %(name, name)) return retVal #OV.registerFunction(tbxs) def GetRInfo(txt="",format='html'): use_history_for_R1_display = True if use_history_for_R1_display: if olx.IsFileType('cif') == "true": R1 = olx.Cif('_refine_ls_R_factor_gt') else: tree = History.tree if tree.active_node is not None: R1 = tree.active_node.R1 else: R1 = 'n/a' if OV.HasGUI(): font_size = OV.GetParam('gui.html.font_size_large') else: font_size = 14 if 'html' in format: try: R1 = float(R1) col = GetRcolour(R1) R1 = "%.2f" %(R1*100) if 'report' in format: t = r"R1 = %s%%" %(font_size, col, R1) else: t = r"R1 = %s%%" %(font_size, col, R1) except: t = "" %(font_size, R1) finally: return t elif format == 'float': try: t = float(R1) except: t = 0 finally: return t else: if txt: t = "" %txt else: try: look = olex.f('IsVar(snum_refinement_last_R1)') if look == "true": R1 = olex.f('GetVar(snum_refinement_last_R1)') else: if olx.IsFileType('cif') == "true": R1 = olx.Cif('_refine_ls_R_factor_gt') else: R1 = olex.f('Lst(R1)') except: R1 = 0 try: R1 = float(R1) col = GetRcolour(R1) R1 = "%.2f" %(R1*100) t = r"" %(col, R1) except: t = "" %R1 #wFile = open(r"%s/displayR.htm" %olx.StrDir(), 'w') #wFile.write(t) #wFile.close() return t OV.registerFunction(GetRInfo) def GetRcolour(R1): retVal = "" try: R1 = float(R1) if R1 > 0.20: if OV.HasGUI(): retVal=OV.GetParam('gui.red') else: retVal="#b40000" elif R1 >0.10: if OV.HasGUI(): retVal=OV.GetParam('gui.orange') else: retVal="#ff8f00" else: if OV.HasGUI(): retVal=OV.GetParam('gui.green') else: retVal = "#00b400" except: retVal='grey' return str(retVal) def setMainToolbarTabButtons(btn, state=""): isCif = OV.IsFileType('cif') if isCif and btn != 'report': state = 'inactive' btns = [("solve", "solution-settings"), ("refine", "refinement-settings"), ("report","report-settings")] for item in btns: if item[0] == btn: if not state: state = olx.html.GetItemState(item[1]) if state == '-1': state = "off" elif state == '0': state = "on" #OV.CopyVFSFile("cbtn-%s2%s.png" %(item[0],state),"cbtn-%s2.png" %item[0]) OV.SetImage("IMG_CBTN-%s2" %btn.upper(),"cbtn-%s2%s.png" %(item[0], state)) OV.SetImage("IMG_BTN-%s2" %btn.upper(),"btn-%s2%s.png" %(item[0], state)) OV.SetVar('gui_MainToolbarTabButtonActive',btn) elif state != 'inactive' and not isCif: OV.CopyVFSFile("cbtn-%s2off.png" %item[0],"cbtn-%s2.png" %item[0]) return "Done" if haveGUI: OV.registerFunction(setMainToolbarTabButtons) def setAllMainToolbarTabButtons(): isCif = OV.IsFileType('cif') btns = [("solve", "solution-settings"), ("refine", "refinement-settings"), ("report","report-settings")] for item in btns: btn = item[0] if isCif and btn != 'report': state = 'inactive' if olx.html.IsItem(item[1]) == 'true': olx.html.ItemState(item[1],'-1') else: state = '' #state = 'off' if not state: #if OV.IsControl(item[1]): if olx.html.IsItem(item[1]) == 'true': try: state = olx.html.GetItemState(item[1]) except RuntimeError: pass if state == '-1': state = "off" elif state == '0': state = "on" elif state == '1': state = "off" else: state = 'off' try: OV.CopyVFSFile("cbtn-%s%s.png" %(btn,state),"cbtn-%s.png" %btn) except: olex.m('skin default_new') if state == 'on': OV.SetVar('gui_MainToolbarTabButtonActive',btn) return "Done" if haveGUI: OV.registerFunction(setAllMainToolbarTabButtons) def onCrystalColourChange(): if variableFunctions.initialisingVariables: return lustre = OV.FindValue('snum_metacif_exptl_crystal_colour_lustre') modifier = OV.FindValue('snum_metacif_exptl_crystal_colour_modifier') primary = OV.FindValue('snum_metacif_exptl_crystal_colour_primary') colour = ' '.join(item for item in (lustre,modifier,primary) if item != '?') if colour: OV.SetVar('snum_metacif_exptl_crystal_colour', colour) OV.registerFunction(onCrystalColourChange) def onRefinementProgramChange(prg_name, method=None, scope='snum'): if prg_name == 'Auto': OV.SetParam('autochem.refinement.method','Auto') return prg = RPD.programs[prg_name] if method is None or not method: method = sortDefaultMethod(prg) if method == 'Least Squares' and olx.LSM() == 'CGLS': method = 'CGLS' # work-around for bug #26 OV.SetParam("%s.refinement.program" %scope, prg_name) OV.SetParam("%s.refinement.method" %scope, method) onRefinementMethodChange(prg_name, method) OV.registerFunction(OV.set_refinement_program) def onRefinementMethodChange(prg_name, method): if method in RPD.programs[prg_name].methods: programSettings.doProgramSettings(prg_name, method) else: print "Please choose a valid method for the refinement program %s" %prg_name OV.registerFunction(onRefinementMethodChange) def onSolutionProgramChange(prg_name, method=None, scope='snum'): if prg_name == "Auto": OV.SetParam('%s.solution.method' %scope, 'Auto') #olx.html.SetValue('SET_autochem_solution_METHOD', 'Auto') return if prg_name != 'Unknown': prg = SPD.programs[prg_name] if method is None or not method: method = sortDefaultMethod(prg) if method == 'Direct Methods' and olx.Ins('PATT') != 'n/a': method = 'Patterson Method' # work-around for bug #48 OV.SetParam("%s.solution.program" %scope, prg_name) OV.SetParam("%s.solution.method" %scope, method) onSolutionMethodChange(prg_name, method) OV.registerFunction(OV.set_solution_program) def onSolutionMethodChange(prg_name, method): if method in SPD.programs[prg_name].methods: programSettings.doProgramSettings(prg_name, method) else: print "Please choose a valid method for the solution program %s" %prg_name return OV.registerFunction(onSolutionMethodChange) def sortDefaultMethod(prg): methods = [] for method in prg: order = method.order methods.append((order, method)) methods.sort() default = methods[0][1].name return default def get_solution_programs(scope='snum'): global available_solution_programs if available_solution_programs is None: p = [] for prg in SPD: a = which_program(prg) if not a: continue p.append(prg.name) p.sort() available_solution_programs = p else: p = available_solution_programs retval = ';'.join(p) if scope != 'snum': retval = 'Auto;' + retval return retval OV.registerFunction(get_solution_programs) def get_solution_methods(prg, scope='snum'): retval = "" if prg == '?' or prg == 'Unknown': return retval if prg == 'Auto': OV.SetParam("%s.solution.method" %scope,'Auto') return 'Auto' p = [] for method in SPD.programs[prg]: p.append(method.name) p.sort() for item in p: retval += "%s;" %item if scope != 'snum': retval = 'Auto;' + retval return retval OV.registerFunction(get_solution_methods) def which_program(prg): if "olex2" in prg.name.lower(): return True if prg.name in SPD or prg.name in RPD: exec_l = prg.execs else: exec_l = ["%s.exe" %prg, "%s" %prg, "%s" %prg.lower()] for item in exec_l: a = olx.file.Which('%s' %item) if a: break if 'wingx' in a.lower(): print "%s seems to be part of a WinGX installation. These ShelX executable cannot be used with Olex" %item return False return a OV.registerFunction(which_program) def getmap(mapName): if not OV.IsFileType('cif') and mapName != 'report': return '#map_%s' %mapName else: return '' if haveGUI: OV.registerFunction(getmap) available_refinement_programs = None available_solution_programs = None def get_refinement_programs(scope='snum'): global available_refinement_programs if available_refinement_programs is None: p = [] for prg in RPD: a = which_program(prg) if not a: continue p.append(prg.name) p.sort() available_refinement_programs = p else: p = available_refinement_programs retval = ';'.join(p) if scope != 'snum': retval = 'Auto;' + retval return retval OV.registerFunction(get_refinement_programs) def get_refinement_methods(prg, scope='snum'): retval = "" if prg == '?' or prg == 'Unknown': return retval if prg == 'Auto': OV.SetParam("%s.refinement.method" %scope,'Auto') return 'Auto' p = [] for method in RPD.programs[prg]: p.append(method.name) p.sort() for item in p: retval += "%s;" %item if scope != 'snum': retval = 'Auto;' + retval return retval OV.registerFunction(get_refinement_methods) def QPeaksSlide(value): val = int(value) * 5 if val >= 0: val = 100 - val else: val = -100 - val return val OV.registerFunction(QPeaksSlide) def UisoSelectSlide(value): val = int(value) * 5 if val >= 0: val = 100 - val val = val * 0.001 val = "> %.3f" %val else: val = val * 0.001 * -1 val = "< %.3f" %val # print val return val OV.registerFunction(UisoSelectSlide) def createRMSDisplay(outStr): for rms in SpyVar.MatchedRms: if rms < 0.2: outStr += '%.4f ' %(rms) elif rms < 1: outStr += '%.4f ' %(rms) elif rms < 2: outStr += '%.4f ' %(rms) else: outStr += '%.4f ' %(rms) return outStr def haveSelection(): retVal = False res = OV.olex_function('sel()') if res == "": retVal = False else: retVal = True return retVal def install_plugin(plugin, args): user_alert_uninstall_plugin = OV.FindValue('user_alert_uninstall_plugin') if not plugin: return poke = olx.IsPluginInstalled("%s" %plugin) if poke == 'false': try: olex.m("installplugin %s" %plugin) pass except: print "The plugin %s does not exist" return if user_alert_uninstall_plugin[0] == 'R': delete = user_alert_uninstall_plugin[-1] elif user_alert_uninstall_plugin == 'Y': delete = OV.Alert('Olex2', "This will delete all files and folders of plugin '%s'. Are you sure you want to continue?" %plugin, 'YNIR', "(Don't show this warning again)") else: returnspy.install_plugin if 'Y' in delete: olex.m("installplugin %s" %plugin) pass if 'R' in delete: user_alert_uninstall_plugin = 'RY' self.setVariables('alert') variableFunctions.save_user_parameters('alert') OV.registerMacro(install_plugin, "") def runSadabs(): olx.User("'%s'" %OV.FilePath()) olx.Exec("sadabs") #olx.WaitFor('process') # uncomment me!http://dimas.dur.ac.uk/olex-distro-odac/1.0-alpha/Durham-OLEX2-Demo/AutoChem%20Installer.exe OV.registerFunction(runSadabs) def getKey(key_directory=None, specific_key = None): if sys.platform[:3] != 'win': return None keyPath = "%s/Olex2u/OD/%s" %(os.environ['ALLUSERSPROFILE'], OV.GetTag()) if not key_directory: key_directory = keyPath if specific_key: g = glob.glob(r"%s/%s.%s" %(key_directory, specific_key, "priv")) for item in g: return item.split("\\")[-1:][0] import glob g = glob.glob(r"%s/*.%s" %(key_directory, "priv")) for item in g: keyname = item.split("\\")[-1:][0] return keyname.split(".")[0] def getKeys(key_directory): kl = [] import glob g = glob.glob(r"%s/*.%s" %(key_directory, "priv")) for item in g: keyname = item.split("\\")[-1:][0] kl.append(keyname.split(".")[0]) return kl def check_for_recent_update(): retVal = False if OV.GetParam('olex2.has_recently_updated'): return True version = OV.GetSVNVersion() try: V = OV.FindValue('last_version','0') last_version = int(V) except Exception, err: print "Alert: Reset parameter 'last_version'" last_version = 0 OV.SetVar('last_version','0') # print "Last Version: %i"%last_version if version > last_version: OV.SetParam('olex2.has_recently_updated',True) retVal = True # print "Olex2 has recently been updated" else: OV.SetParam('olex2.has_recently_updated',False) retVal = False # print "Olex2 has not been updated" OV.SetVar('last_version',str(version)) OV.StoreParameter('last_version') return retVal def register_new_odac(username=None, pwd=None): OV.Cursor("Please wait while AutoChem will be installed") mac_address = OV.GetMacAddress()[0] computer_name = os.getenv('COMPUTERNAME') url = "http://www.olex2.org/odac/register_new" olex2_tag = OV.GetTag() if not username: print("Please provide a username and password") OV.Cursor() return if not pwd: print("Please provide a username and password") OV.Cursor() return values = {'__ac_password':pwd, '__ac_name':username, 'olex2Tag':olex2_tag, 'computerName':computer_name, 'username':username, 'context':"None", 'macAddress':mac_address, } try: f = HttpTools.make_url_call(url, values) except Exception, err: print "You may have exceeded the number of AutoChem installs." print "Please contact contact xrdapplications@agilent.com for further information." return f = f.read() if not f: print "Please provide a valid username and password, and make sure your computer is online." print "You may also have used up the number of allowable installs." return elif not f.endswith(".exe"): print "Please provide valid username and password. If this problem persitsts, please" print "contact xrdapplications@agilent.com for further information." return p = "%s/Olex2u/OD/%s" %(os.environ['ALLUSERSPROFILE'], olex2_tag) p = os.path.abspath(p) if not os.path.exists(p): os.makedirs(p) else: try: import shutil shutil.rmtree(p) os.makedirs(p) except Exception, err: print "The installer could not delete this folder: %s" %p print "Please remove all files in this folder manually and run the installer again." olex.m('exec -o explorer "%s"' %p) return cont = GetHttpFile(f, force=True, fullURL = True) if cont: name = "AutoChem Installer.exe" wFile = open("%s/%s" %(p, name),'wb') wFile.write(cont) wFile.close() else: print "Could not get %s" %f return ins = "%s/AutoChem Installer.exe" %p cmd = r"%s /S" %ins # print cmd olx.Shell(ins) # Popen(cmd, shell=True, stdout=PIPE).stdout for i in xrange(10): try: os.remove(ins) break except: time.sleep(5) print "AutoChem is now installed on your computer." print "Please restart Olex2 now." OV.Cursor() OV.registerFunction(register_new_odac) def settings_tree(): l = [] added = [] handlers = [olx.phil_handler, olx.gui_phil_handler] for handler in handlers: raw_l = handler.get_root_scope_names() for item in raw_l: s = handler.get_scope_by_name(item) if item not in added: l.append("%s (%s)\n%s\n" %(item, s.short_caption, item)) added.append(item) for tem in s.objects: if tem.is_scope: l.append("\t%s (%s)\n%s.%s\n" %(tem.name, tem.short_caption, item, tem.name)) for em in tem.objects: if em.is_scope: l.append("\t\t%s (%s)\n%s.%s.%s\n" %(em.name, em.short_caption, item, tem.name, em.name)) for m in em.objects: if m.is_scope: l.append("\t\t\t%s (%s)\n%s.%s.%s.%s\n" %(m.name, m.short_caption, item, tem.name, em.name, m.name)) for m1 in m.objects: if m1.is_scope: l.append("\t\t\t\t%s (%s)\n%s.%s.%s.%s.%s\n" %(m1.name, m1.short_caption, item, tem.name, em.name, m.name, m1.name)) OV.write_to_olex('settings_tree.ind', ''.join(l)) OV.registerFunction(settings_tree) def GetOptionalHyphenString(txt): txt = txt.replace ("/", "/" + u"\u200B") txt = txt.replace ("\\", "\\" + u"\u200B") txt = txt.replace ("\\", "\\" + " ") return txt OV.registerFunction(GetOptionalHyphenString) def GetTwinLaw(html=False): olex_refinement_model = OV.GetRefinementModel(False) if olex_refinement_model.has_key('twin'): c = olex_refinement_model['twin']['matrix'] curr_law = [] for row in c: for el in row: curr_law.append(el) curr_law = tuple(curr_law) else: return txt = repr(curr_law) if html: txt = "" %(OV.GetParam('gui.red').hexadecimal, repr(curr_law)) return txt OV.registerFunction(GetTwinLaw) def HklStatsAnalysis(): import olex_core stats = olex_core.GetHklStat() OV.registerFunction(HklStatsAnalysis) def InstalledPlugins(): import olex_core l = olex_core.GetPluginList() return l def AvailablePlugins(): plugins = {'ODSkin': {'display':'Oxford Diffraction Skin', 'blurb':'A custom-made visual design for Oxford Diffraction'}, } plugins = { } s = "
" green = OV.GetParam('gui.green') red = OV.GetParam('gui.red') for plugin in plugins: display = plugins[plugin].get('display', plugin) blurb = plugins[plugin].get('blurb', plugin) if olx.IsPluginInstalled("%s" %plugin) == 'true': s += "%sUninstall
%s

" %(display, plugin, green, blurb) else: s += "%sInstall
%s

" %(display, plugin, red, blurb) return s OV.registerFunction(AvailablePlugins) def AvailableSkins(): skins = {'OD':{'display':'Oxford Diffraction Skin'}, 'HP':{'display':'Grey'}, 'default':{'display':'Default'}} s = "
" for skin in skins: if OV.FindValue('gui_skin_name') == skin: s += "%s
" %(skin, skins[skin].get('display', skin)) else: s += "%s
" %(skin, skins[skin].get('display', skin)) return s if haveGUI: OV.registerFunction(AvailableSkins) def AvailableExternalPrograms(prgType): if prgType == 'refinement': dict = RPD elif prgType == 'solution': dict = SPD p = {} for prg in dict: a = which_program(prg) if not a: continue p.setdefault(prg.name,a) return p def AvailableExternalProgramsHtml(): d = {} d.setdefault('refinement', AvailableExternalPrograms('refinement')) d.setdefault('solution', AvailableExternalPrograms('solution')) def makeSpecialCifCharacter(txt): txt = txt.replace(r"\a", r"α") txt = txt.replace(r"\A", r"Α") txt = txt.replace(r"\b", r"β") txt = txt.replace(r"\B", r"Β") txt = txt.replace(r"\c", r"χ") txt = txt.replace(r"\C", r"Χ") txt = txt.replace(r"\d", r"Δ") txt = txt.replace(r"\D", r"δ") txt = txt.replace(r"\e", r"ε") txt = txt.replace(r"\E", r"Ε") txt = txt.replace(r"\f", r"φ") txt = txt.replace(r"\F", r"Φ") txt = txt.replace(r"\g", r"γ") txt = txt.replace(r"\G", r"Γ") txt = txt.replace(r"\h", r"η") txt = txt.replace(r"\H", r"Η") txt = txt.replace(r"\k", r"κ") txt = txt.replace(r"\K", r"Κ") txt = txt.replace(r"\l", r"λ") txt = txt.replace(r"\L", r"Λ") txt = txt.replace(r"\m", r"ν") txt = txt.replace(r"\M", r"Μ") txt = txt.replace(r"\n", r"ν") txt = txt.replace(r"\N", r"Ν") txt = txt.replace(r"\o", r"ο") txt = txt.replace(r"\O", r"Ο") txt = txt.replace(r"\p", r"φ") txt = txt.replace(r"\P", r"Φ") txt = txt.replace(r"\q", r"θ") txt = txt.replace(r"\Q", r"Θ") txt = txt.replace(r"\r", r"ρ") txt = txt.replace(r"\R", r"Ρ") txt = txt.replace(r"\s", r"σ") txt = txt.replace(r"\S", r"Σ") txt = txt.replace(r"\t", r"τ") txt = txt.replace(r"\T", r"Τ") txt = txt.replace(r"\u", r"υ") txt = txt.replace(r"\U", r"Υ") txt = txt.replace(r"\w", r"ω") txt = txt.replace(r"\W", r"Ω") txt = txt.replace(r"\x", r"χ") txt = txt.replace(r"\X", r"Χ") txt = txt.replace(r"\y", r"ψ") txt = txt.replace(r"\Y", r"Ψ") txt = txt.replace(r"\z", r"ζ") txt = txt.replace(r"\Z", r"Ζ") return txt OV.registerFunction(makeSpecialCifCharacter) def getReportTitleSrc(): import PIL import Image import ImageDraw import PngImagePlugin import StringIO import base64 import EpsImagePlugin from ImageTools import ImageTools IT = ImageTools() width = OV.GetParam('gui.report.width') height = OV.GetParam('gui.report.title.height') colour = OV.GetParam('gui.report.title.colour').rgb font_name = OV.GetParam('gui.report.title.font_name') font_size = OV.GetParam('gui.report.title.font_size') font_colour = OV.GetParam('gui.report.title.font_colour') sNum = OV.GetParam('snum.report.title') IM = Image.new('RGBA', (width, height), colour) draw = ImageDraw.Draw(IM) IT.write_text_to_draw(draw, sNum, align='right', max_width=width, font_name=font_name, font_size=font_size, font_colour=font_colour) ## This bits would insert a logo into the header, but it doesn't look good. #imagePath = OV.GetParam('snum.report.image') #imagePath = "%s/etc/CIF/styles/logo.png" %OV.BaseDir() #im = Image.open(imagePath) #imHeight = height #oSize = im.size #nWidth = int(oSize[0]*(imHeight/oSize[1])) #im = im.resize((nWidth, imHeight), Image.BICUBIC) #IM.paste(im, (0,0), im) p = "%s/report_tmp.png" %OV.DataDir() IM.save(p, "PNG") rFile = open(p, 'rb').read() data = base64.b64encode(rFile) rFile.close() retVal ='data:image/png;base64,' + data return retVal OV.registerFunction(getReportTitleSrc) def dealWithReportImage(): from ImageTools import ImageTools IT = ImageTools() image_name = OV.GetParam('snum.report.image') if image_name == "No Image": # OV.SetParam('snum.report.image',None) return elif image_name == "SCREENSHOT": olex.m('showq a false') olex.m('showq b false') olex.m('pict -pq screenshot.png 1') filefull = "%s/screenshot.png" %OV.FilePath() IT.trim_image(im=filefull, padding=2, border=0.2, border_col = "#ababab") OV.SetParam('snum.report.image',"screenshot.png") OV.registerFunction(dealWithReportImage) def dealWithReportName(): report_name = OV.GetParam('snum.report.name') if not report_name: OV.SetParam('snum.report.name',OV.FileName()) return OV.registerFunction(dealWithReportName) def getReportImageSrc(): imagePath = OV.GetParam('snum.report.image') if OV.FilePath(imagePath) == OV.FilePath(): return olx.file.GetName(imagePath) else: return 'file:///%s' %imagePath OV.registerFunction(getReportImageSrc) def getReportExtraCIFItems(name_td_class, value_td_class, type='html'): cf_name = OV.file_ChangeExt(OV.FileFull(), 'cif') rv = '' if not os.path.exists(cf_name): return rv try: import iotbx fo = file(cf_name, "rUb") reader = iotbx.cif.reader(file_object=fo) fo.close() models = [] for k, v in reader.model().iteritems(): if k.lower() != 'global': models.append(v) if len(models) > 1: return rv flack = models[0]["_refine_ls_abs_structure_Flack"] if flack: if type == 'html': rv = ""\ %(name_td_class,value_td_class,flack) else: rv = r"Flack parameter & %s\\" % flack.replace('-', '@@-@@') except Exception, err: print err pass return rv OV.registerFunction(getReportExtraCIFItems) def get_text_from_vfs(item): return OV.get_txt_from_vfs(item) OV.registerFunction(get_text_from_vfs) def getReportPhilItem(philItem=None): item = OV.GetParam(philItem) if not item: philItemU = philItem.replace('snum', 'user') item = OV.GetParam(philItemU) if item: OV.SetParam(philItem, item) return item OV.registerFunction(getReportPhilItem) def getReportImageData(size='w400', imageName=None): import PIL import Image import PngImagePlugin import StringIO import base64 import ImageDraw import EpsImagePlugin make_border = False size_type = size[:1] size = int(size[1:]) if imageName is None: imageName = 'snum.report.image' make_border = OV.GetParam('snum.report.image_border') if not OV.HasGUI(): return "No Image available in Headless Mode! " if "snum.report" in imageName: imagePath = OV.GetParam(imageName) if not imagePath: imageNameU = imageName.replace('snum', 'user') imagePath = OV.GetParam(imageNameU) if imagePath: OV.SetParam(imageName, imagePath) if imagePath == "No Image" or imagePath is None: return "" if type(imagePath) == unicode: imagePaths = [] imagePaths.append(imagePath) else: imagePaths = imagePath html = "" i = 0 for imagePath in imagePaths: i += 1 if imagePath.startswith(r'BaseDir()'): imagePath = "%s/%s" %(OV.BaseDir(), imagePath.lstrip('BaseDir()')) if not os.path.exists(imagePath): OV.SetParam(imageName, None) # print "The previously made screenshot has been removed. Please select 'screenshot' to make a new one" return # else: # imagePath = r"%s/etc/CIF/styles/%s.png" %(OV.BaseDir(),imageName) imageLocalSrc = imagePath.split("/")[-1:][0] imageLocalSrc = imageLocalSrc.split("\\")[-1:][0] IM = Image.open(imagePath) oSize = IM.size if size_type == "w": if oSize[1] != size: nHeight = int(oSize[1]*(size/oSize[0])) nWidth = size IM = IM.resize((nWidth, nHeight), Image.BICUBIC) elif size_type == "h": if oSize[0] != size: nHeight = size nWidth = int(oSize[0]*(size/oSize[1])) IM = IM.resize((nWidth, nHeight), Image.BICUBIC) if make_border: from ImageTools import ImageTools IT = ImageTools() draw = ImageDraw.Draw(IM) fill = '#ababab' width, height = IM.size for i in xrange(make_border): draw.line((i,i,width-1-i,i), fill = fill) draw.line((i,height -1-i,width-1-i,height -1-i), fill = fill) draw.line((i,i,i,height - 1-i), fill = fill) draw.line((width -1-i,i,width-1-i,height -1-i), fill = fill) # weight = make_border # draw.line((0, int(weight/2)) + (IM.size[0], int(weight/2)), fill=fill, width=weight) # draw.line((0, 0) + (0, IM.size[1]), fill=fill, width=weight) # draw.line((IM.size[0] - weight, 0) + (IM.size[0] - weight, IM.size[1] - weight), fill=fill, width=weight) # draw.line((0, IM.size[1] - weight ) + (IM.size[0] - weight, IM.size[1] - weight) , fill=fill, width=weight) # del draw p = "%s/report_tmp_%i.png" %(OV.DataDir(), i) IM.save(p, "PNG") rFile = open(p, 'rb') img = rFile.read() data = base64.b64encode(img) d ='data:image/png;base64,' + data html += ''' '''%(int(size/2), imageLocalSrc, int(size/2), data) return html OV.registerFunction(getReportImageData) def getFileContents(p): if "snum.report" in p: p = OV.GetParam(p) if not p: return if not os.path.exists(p): return "%s does not exist" %p return open(p, 'rb').read() OV.registerFunction(getFileContents) def stopDebugging(): try: import wingdbstub wingdbstub.debugger.ProgramQuit() except: pass return OV.registerFunction(stopDebugging) def StoreSingleParameter(var, args): if var: OV.StoreParameter(var) OV.registerMacro(StoreSingleParameter, "") def reset_file_in_OFS(fileName,txt=" ",copyToDisk = False): OV.reset_file_in_OFS(fileName=fileName, txt=txt, copyToDisk=copyToDisk) OV.registerFunction(reset_file_in_OFS) def GetCurrentSelection(): return OV.GetCurrentSelection() OV.registerFunction(GetCurrentSelection) def getAllHelpBoxes(): import glob import re boxes = [] for htmfile in OV.ListFiles("%s/etc/gui/*.htm" %OV.BaseDir()): rFile = open(htmfile,'r') f = rFile.read() rFile.close() ## find all occurances of strings between help_ext=..; . These should be comma separated things to highlight. regex = re.compile(r"help_ext= (.*?) ;", re.X) l = regex.findall(f) if l: for item in l: boxes.append(item) return boxes def test_help_boxes(): import htmlTools boxes = getAllHelpBoxes() for box in boxes: htmlTools.make_help_box({'name':box}) OV.registerFunction(test_help_boxes) def olex_fs_copy(src_file, dst_file): txt = olex_fs.ReadFile(src_file) olex_fs.NewFile(dst_file,txt) OV.registerFunction(olex_fs_copy) def isPro(): p = "%s/pro.txt" %OV.BaseDir() if os.path.exists(p): OV.SetParam('olex2.hover_buttons',True) return True else: return False OV.registerFunction(isPro) def switch_tab_for_tutorials(tabname): olex.m("html.ItemState index* 0") olex.m("html.ItemState logo 0") olex.m("html.ItemState index-%s 1" %tabname) olex.m("html.ItemState info-title 1") if tabname.lower() == "work": olex.m("html.ItemState solve-settings 2") olex.m("html.ItemState refine-settings 2") olex.m("html.ItemState report-settings 2") olex.m("html.ItemState %s-toolbox 1" %tabname) olex.m("html.ItemState tab* 2") OV.registerFunction(switch_tab_for_tutorials) def revert_to_original(): extensions = ['res','ins','cif'] for extension in extensions: path = "%s/.olex/originals/%s.%s" %(OV.FilePath(), OV.FileName(), extension) if os.path.exists(path): rFile = open(path,'rb') txt = rFile.read() rFile.close() outpath = OV.file_ChangeExt(OV.FileFull(),'ins') wFile = open(outpath,'wb') wFile.write(txt) wFile.close() OV.AtReap(outpath) print("Reverted to the original file %s" %path) if OV.HasGUI(): olx.html.Update() return print("Could not revert to any original file!") OV.registerFunction(revert_to_original) def fade_in(speed=0): speed = OV.GetParam('user.use_fader') if speed == 0: return olex.m("fade 1 0 -%s" %speed) olex.m('waitfor fade') olex.m("ceiling off") OV.registerFunction(fade_in) def fade_out(speed=0): speed = OV.GetParam('user.use_fader') if speed == 0: return olex.m("fader.InitFG()") olex.m("fader.visible(true)") olex.m("fade 0 1 %s" %speed) olex.m("waitfor fade") OV.registerFunction(fade_out) def GetImageFilename(image_type): filename = OV.GetParam('snum.image.%s.name' %image_type.lower()) if image_type == "PS": fileext = "eps" elif image_type == "PR": fileext = "pov" else: fileext = OV.GetParam('snum.image.%s.type' %image_type.lower()) if not filename: try: filename = OV.GetValue('IMAGE_%s_NAME' % image_type) except: filename = None if not filename: import gui filename = gui.FileSave("Choose Filename", "*.%s" %fileext, OV.FilePath()) if not filename: return None, None, None if_exists = OV.GetParam('snum.image.if_file_exists') if os.path.exists("%s.%s" %(filename, fileext)): if if_exists == 'increment': fp = olx.FilePath() fn = filename inc = 1 while True: tf = os.path.normpath('%s/%s%d.%s' %(fp, fn, inc, fileext)) if not os.path.exists(tf): filename = '%s%d' %(fn, inc) filefull = "'%s.%s'" %(filename, fileext) break inc += 1 elif if_exists == 'ask': import gui filename = gui.FileSave("Choose Filename", "*.%s" %fileext, OV.FilePath(), default_name=filename) if not filename: return None, None, None if filename.endswith(".%s" %fileext): filefull = "'%s'" %filename else: filefull = "'%s.%s'" %(filename, fileext) OV.SetParam('snum.image.%s.name' %image_type.lower(),None) return filefull, filename, fileext def StringsAreEqual(str1, str2): return str1 == str2 OV.registerFunction(StringsAreEqual) def StringsAreNotEqual(str1, str2): if str1 == str2: return False else: return True OV.registerFunction(StringsAreNotEqual) def GetBitmapImageInstructions(): from ImageTools import ImageTools IT = ImageTools() filefull, filename, fileext = GetImageFilename(image_type = "BITMAP") if not filefull: return filesize = OV.GetValue('IMAGE_BITMAP_SIZE') if olx.html.GetData('BITMAP_NO_BG'): nbg = "-nbg" else: nbg = "" if fileext == "png/s": filefull = "%s.png" %filename filesize = 1 pict = "a " else: pict = " -pq" OV.Cursor('busy','Please Wait. Making image %s.%s. This may take some time' %(filename, fileext)) olex.m('pict%s %s %s %s' %(pict, nbg, filefull, filesize)) if olx.html.GetData('TRIM_IMAGE'): padding = float(olx.html.GetValue('TRIM_PADDING')) border = float(olx.html.GetValue('TRIM_BORDER')) colour = olx.html.GetValue('TRIM_BORDER_COLOUR') IT.trim_image(im=filefull, padding=padding, border=border, border_col = colour ) #import Image OV.Cursor() OV.registerFunction(GetBitmapImageInstructions) def GetPRImageInstructions(): filefull, filename, fileext = GetImageFilename(image_type = "PR") if not filefull: return OV.Cursor('busy','Please Wait. Making image %s.%s. This may take some time' %(filename, fileext)) olex.m('pictPR %s' %filefull) print 'Image %s created' %filefull OV.Cursor() OV.registerFunction(GetPRImageInstructions) def GetPSImageInstructions(): filefull, filename, fileext = GetImageFilename(image_type = "PS") if not filefull: return OV.Cursor('busy','Please Wait. Making image %s.%s. This may take some time' %(filename, fileext)) colour_line = OV.GetParam('snum.image.ps.colour_line') colour_bond = OV.GetParam('snum.image.ps.colour_bond') colour_fill = OV.GetParam('snum.image.ps.colour_fill') image_perspective = OV.GetParam('snum.image.ps.perspective') lw_ellipse = str(OV.GetParam('snum.image.ps.outline_width')) lw_octant = str(OV.GetParam('snum.image.ps.octant_width')) lw_pie = str(OV.GetParam('snum.image.ps.pie_width')) lw_font = str(OV.GetParam('snum.image.ps.font_weight')) div_pie = str(OV.GetParam('snum.image.ps.octant_count')) scale_hb = str(OV.GetParam('snum.image.ps.h_bond_width')) octant_atoms = str(OV.GetValue('IMAGE_PS_OCTANTS_ATOMS')) olex.m("pictps" + \ " " + filefull + \ " " + colour_line + \ " " + colour_bond + \ " " + colour_fill + \ " " + "-lw_ellipse=" + lw_ellipse + \ " " + "-lw_octant=" + lw_octant + \ " " + "-lw_pie=" + lw_pie + \ " " + "-lw_font=" + lw_font + \ " " + "-div_pie=" + div_pie + \ " " + "-octants=" + octant_atoms + \ " " + "-scale_hb=" + scale_hb) print 'Image %s created' %filefull OV.Cursor() OV.registerFunction(GetPSImageInstructions) def check_for_selection(need_selection=True): res = haveSelection() if not res and need_selection: print "\n++ This action requires a selection of atoms!" return False else: return True OV.registerFunction(check_for_selection) def round_to_n_digits(f, n=2): n = int(n) if len(f) < n: return f try: f = float(f) return "%.*f" %(n,f) except: return f OV.registerFunction(round_to_n_digits) def standardise_path(path): return OV.standardizePath(path) OV.registerFunction(standardise_path) def play_crystal_images(): import time l = OV.GetParam('snum.metacif.list_crystal_images_files')[0].split(';') for image in l: if os.path.exists(image): OV.SetParam('snum.report.crystal_image',OV.standardizePath(image)) olx.html.SetImage('CRYSTAL_IMAGE',image) OV.Refresh() OV.registerFunction(play_crystal_images) def advance_crystal_image(direction='forward'): l = OV.GetParam('snum.metacif.list_crystal_images_files')[0].split(';') i = 0 for image in l: i += 1 if image == OV.GetParam('snum.report.crystal_image'): if direction == 'forward': if i != len(l): p = l[i] OV.SetParam('snum.report.crystal_image',p) olx.html.SetImage('CRYSTAL_IMAGE',p) return else: print "Last image of the series!" return else: if i != 1: p = l[i-2] OV.SetParam('snum.report.crystal_image',p) olx.html.SetImage('CRYSTAL_IMAGE',p) return else: print "First image of the series!" return else: continue #p = OV.GetParam('snum.report.crystal_image') #n = int(p.split('\\')[-1].split(OV.FileName())[1].split('.')[0]) #if direction == 'forward': #n += 1 #else: #n -= 1 #base = ("\\").join(p.split('\\')[:-1]) #p = r"%s\%s%i%s" %(base, OV.FileName(), n, ".jpg") #if os.path.exists(p): #OV.SetParam('snum.report.crystal_image',p) #olx.html.SetImage('CRYSTAL_IMAGE',p) OV.registerFunction(advance_crystal_image) def getCellHTML(): crystal_systems = { 'Triclinic':('a', 'b', 'c', 'α', 'β', 'γ'), 'Monoclinic':('a', 'b', 'c', 'β'), 'Orthorhombic':('a', 'b', 'c'), 'Tetragonal':('a', 'c',), 'Hexagonal':('a', 'c'), 'Trigonal':('a', 'c'), 'Cubic':('a',), } cell_param_value_pairs = dict(zip( ('a', 'b', 'c', 'α', 'β', 'γ'), ('_cell_length_a','_cell_length_b','_cell_length_c','_cell_angle_alpha','_cell_angle_beta','_cell_angle_gamma'))) cell = {} for param, value in cell_param_value_pairs.items(): if param in ('a','b','c'): cell[param] = dict( value = '%%%s%%' %value, unit = ' Å' ) else: cell[param] = dict( value = '%%%s%%' %value, unit = '°' ) cell_html = dict((param, '%s = %s%s, ' %(param,cell[param]['value'],cell[param]['unit'])) for param in cell.keys()) crystal_system = OV.olex_function('sg(%s)') html = ''.join(cell_html[param] for param in crystal_systems[crystal_system]) return html OV.registerFunction(getCellHTML) def formatted_date_from_timestamp(dte): if not dte: return "No Date" if "." in dte: dte = OV.GetParam(dte) from datetime import date if not dte: return None try: dte = float(dte) except: return "Not A Date" dte = date.fromtimestamp(dte) return dte.strftime(OV.GetParam('snum.report.date_format')) OV.registerFunction(formatted_date_from_timestamp) if not haveGUI: def tbxs(name): print "This is not available in Headless Olex" return "" #OV.registerFunction(tbxs) OV.registerFunction(OV.IsPluginInstalled) OV.registerFunction(OV.GetTag) # def GetHttpFile(f, force=False, fullURL = False): URL = "http://dimas.dur.ac.uk/" global _is_online retVal = None go_online = _is_online verbose = OV.FindValue("ac_verbose", "False") if go_online or force: try: if not fullURL: url = "%s/%s" %(URL, f.replace(" ",r"%20")) else: url = f if verbose: print "--> Getting %s" %url, response = HttpTools.make_url_call(url,"") content = response.read() if verbose: print "OK" retVal = content except Exception, err: _is_online = False retVal = None print "Olex2 can not reach the update server: %s" %err print url else: retVal = None return retVal
%%setup-title-%s%%
%%setup-txt-%s%%
Swap the position of the GUI panel
Skin HP
Skin OD
%s%s%s%%%s
TWIN LAW %s
Flack parameter%s