""" python/ui/picture_definition.py: CCP4MG Molecular Graphics Program Copyright (C) 2001-2008 University of York, CCLRC Copyright (C) 2009-2010 University of York Copyright (C) 2012 STFC This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ from global_definitions import * from picture_definition_classes import ParamsManager import utils import version reqRunAfterModelLoad = [] class picture_definition: insts = '' preferences = {} preferences['content'] = { 'create_DispObj' : 1, 'keep_current' : 0 } preferences['order'] = ['keep_current','create_DispObj'] preferences['export'] = 1 def __init__(self): picture_definition.insts = self self.colour_export_objects = {'COLOUR' : 1 } self.pm_all = 0 self.save_visible = 0 #--------------------------------------------------------------------------- def save_picture_definition(self,filename='',DIR_filename='', limited_save=1,save_visible = '', save_list=['view','colours','display','params'], style='method',**keywords): #--------------------------------------------------------------------------- if filename: import pprint,sys,dataobj,time import services filename = utils.get_filename(DIR_filename,filename) active_colour_schemes = [] header = '''# CCP4mg picture definition file # See http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/picture_definition.html # or your local copy of CCP4mg documentation. # CCP4mg version '''+ version.ccp4mg_version +''' # Created ''' + str(time.asctime(time.localtime())) + '\n\n\n' choices_stream = 'CHOICES = [\n' stream = '' pretty_print = pprint.PrettyPrinter() all = not int(limited_save) if save_visible: self.save_visible = int(save_visible) #if picture_definition.preferences['export']: # stream = stream + utils.picture_defn_item('preferences',picture_definition.preferences['content'],pretty_print,indent=0,dict_order=picture_definition.preferences['order']) for item in save_list: if item == 'view': style = 'method' indent = 5 # Save the view view_params = MAINWINDOW().getViewParams() stream = 'view = View (' stream = stream+utils.picture_defn_item('orientation',view_params['quat'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('centre_xyz',view_params['pos'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('scale',view_params['scale'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('fog_enabled',view_params['fog_enabled'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('fog_near',view_params['fog_near'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('fog_far',view_params['fog_far'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('slab_enabled',view_params['slab_enabled'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('slab_width',view_params['slab_width'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('slab_offset',view_params['slab_offset'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('clip_cap',view_params['clip_cap'],pretty_print,style=style,indent=indent) stream = stream+utils.picture_defn_item('customClipPlanes',view_params['customClipPlanes'],pretty_print,style=style,indent=indent) stream = stream + ' )\n\n' elif item == 'colours': #Save colours if self.colour_export_objects.has_key('COLOUR'): stream = stream + MGCOLOUR().save_picture_definition(pretty_print=pretty_print,all=self.pm_all) elif item == 'display': label_num = ['second','third','fourth'] choices_stream = '#SECTION CHOICES\n\nCHOICES = [\n' ntype = {} # Save any generic user selection/colour schemes that are currently used generic_schemes = [] for obj in get_dataobj(object_type='MolData'): scms = obj.get_open_schemes() for item in scms: if not generic_schemes.count(item): generic_schemes.append(item) #print "picture_definition generic_schemes",generic_schemes if generic_schemes: stream = stream + MODELINFO().save_picture_definition(pretty_print=pretty_print,set='generic',info='user_selection',keys=generic_schemes) generic_schemes = [] for obj in get_dataobj(object_type='MolData'): scms = obj.get_open_schemes(info="user_colour_schemes") for item in scms: if not generic_schemes.count(item): generic_schemes.append(item) if generic_schemes: stream = stream + MODELINFO().save_picture_definition(pretty_print=pretty_print,set='generic',info='user_colour_schemes',keys=generic_schemes) for object_type in dataobj.DATAOBJ_TYPES: for obj in dataobj.get_dataobj(object_type=object_type): if (not self.save_visible) or obj.visible: shadowobj = dataobj.DataObjShadow() rv = shadowobj.save(obj,all=all) if rv: del shadowobj else: stream = stream + shadowobj.save_picture_definition(pretty_print=pretty_print,style=style) # Add .ccp4mg file info for MolData objects if object_type == 'MolData': stream = stream + MODELINFO().save_picture_definition(pretty_print=pretty_print,set=obj.name_label,info='user_selection') stream = stream + MODELINFO().save_picture_definition(pretty_print=pretty_print,set=obj.name_label,info='user_colour_schemes') # Add an element to the CHOICES list label = '' if ntype.has_key(object_type): ntype[object_type] = ntype[object_type]+1 if ntype<=4: label=label_num[ntype-1] else: ntype[object_type] = 1 if object_type != 'MolData': label = label + object_type[0:-4] else: label = label + 'model' name = object_type+str(ntype[object_type]) choices_stream = choices_stream + \ " { 'name' : '"+name+"', " + \ "'type' : '"+object_type+"', " + \ "'label' : 'Select "+label+"', " + \ "'multi' : 0 },\n" if style != 'mgpic': name='' for disp in shadowobj.objinsts: if (not self.save_visible) or disp.visible: if not style == 'mgpic' or not ['Crystal','Legend','Image'].count(disp.object_type): stream = stream + disp.save_picture_definition(pretty_print=pretty_print,style='method',parent=name) if hasattr(disp,'colparams'): if services.ColourSchemeManager.colour_pref_alias.count(disp.colparams.get('colour_mode','')): active_colour_schemes.append(disp.colparams.get('colour_mode','')) choices_stream = choices_stream[0:-2]+ '\n ]\n\n' elif item == 'params': # Save ParamsManagers etc for pm in PM('all'): if pm.picture_definition>0: stream = stream + pm.save_picture_definition(pretty_print=pretty_print,all=self.pm_all) #print "active_colour_schemes",active_colour_schemes for pm in active_colour_schemes: obj = PM(name=pm) if obj: stream = stream + obj.save_picture_definition(pretty_print=pretty_print,all=self.pm_all) stream = stream + 'ParamsManager(\n' stream = stream + " name = 'gui_params',\n" stream = stream + " show_axes = " + str(MAINWINDOW().glWidget.getAxes()) + ",\n" stream = stream + " background_colour = " + str(MAINWINDOW().glWidget.getBackground()) + "\n" stream = stream + ')\n' lights = MAINWINDOW().glWidget.getLights() import opengl ls = {} nlights = 0 for i,light in zip(range(len(lights)),lights): l = {} if light and light.has_key("depth") and light.has_key("pos"): l['position'] = [light["pos"].x(),light["pos"].y(),light["depth"]] l['ambient'] = light['params'][opengl.GL_AMBIENT] l['specular'] = light['params'][opengl.GL_SPECULAR] l['diffuse'] = light['params'][opengl.GL_DIFFUSE] l['on'] = 1 ls[str(i)] = l nlights = nlights + 1 stream = stream + '\nParamsManager(\n' stream = stream + " name = 'light_params',\n" stream = stream + utils.picture_defn_item('lights',ls,pretty_print,style='method',indent=indent) stream = stream + '\n nLights = ' + str(nlights) + '\n' stream = stream + ')\n' for object_type in dataobj.PLUGIN_DATAOBJ_TYPES: for obj in dataobj.get_dataobj(object_type=object_type): stream = stream + obj.save_picture_definition(pretty_print=pretty_print,style=style) for plug in MAINWINDOW().plugins: if hasattr(plug,"save_picture_definition") and callable(plug.save_picture_definition): try: stream = stream + plug.save_picture_definition(pretty_print=pretty_print,style=style) except: print "call of",plug,"save_picture_definition failed" pass if style == 'mgpic': stream = header + "#SECTION TITLE\n\n#SECTION NOTES\n\n" + choices_stream + "#SECTION SCRIPT\n\n\nglobal ERROR_MESSAGE\n\n" + stream else: stream = header + stream utils.saveFile(filename,text=stream) #print stream return 0 def loadShadowPlugins(self): import os, glob pluginpaths=os.path.join(os.environ["CCP4MG"],os.path.join('qtgui','plugins')) plugins = glob.glob(os.path.join(pluginpaths,'*')) modules = [] modules.extend(glob.glob(os.path.normpath(os.path.join(pluginpaths,'*_Shadow.py')))) for pluginpath in plugins: modules.extend(glob.glob(os.path.normpath(os.path.join(pluginpath,'*_Shadow.py')))) return modules #--------------------------------------------------------------------------- def read_picture_definition(self,filename='',trap_errors=-1,default_dir=''): #--------------------------------------------------------------------------- import re import os,exceptions,pprint if trap_errors<0: trap_errors = 1-DEVELOPER() message = '' globs = {} #print "Setting globs['default_dir']",default_dir globs['default_dir'] = default_dir locs = {} try: execfile(os.path.join(os.environ["CCP4MG"],'python','ui','picture_definition_classes.py'),globs) plugs = self.loadShadowPlugins() for plug in plugs: execfile(plug,globs) except StandardError, e: message = message + 'Error loading picture_definition_classes.py' print e.args if trap_errors: try: execfile(filename,globs,locs) except StandardError, e: message = message + 'Error reading '+filename if isinstance(e,exceptions.SyntaxError) and e.offset: spaces='' for i in range(0,e.offset): spaces = spaces+' ' message = message + 'Invalid syntax in line '+ str(e.lineno)+ \ ':\n\n'+ re.sub('\n','',e.text) +'\n' + \ spaces + '*\n\n' + \ '(Hint: also check preceeding line)\n' else: pp = pprint.PrettyPrinter() message = message + pp.pformat(e.args) # Keep this diagnostic to go to log file print "Error reading ",filename,e.args else: # Let it crash execfile(filename,globs,locs) #print 'locs',locs return [message,globs,locs] #--------------------------------------------------------------------------- def restore_picture_definition(self,filename='',DIR_filename='',trap_errors=-1,test=0,keep_current=0,override_visible=1,restore_list=['view','colours','display','params'],delay_delete=0,default_dir='',**keywords): #--------------------------------------------------------------------------- if trap_errors<0: trap_errors = 1-DEVELOPER() if not filename: return [1,''] import dataobj,os,exceptions,re,pprint,picture_definition_classes #Delete existing loaded data? delete_list = [] if not keep_current: for obj in dataobj.DataObj.dataobj_insts: delete_list.append(obj) if not delay_delete: for obj in delete_list: obj.delete() else: # NEED TO ENSURE OBJECTS REDRAW NOT TRIGGERED BY CHANGED PARAMETERS pass if default_dir == '': default_dir = os.path.dirname(filename) filename = utils.get_filename(DIR_filename,filename) if not os.path.exists(filename): return [1,''] ccp4mg_version_str = version.ccp4mg_version print "restore_picture_definition",filename try: f = open(filename) lines = f.readlines() for l in lines: if l.startswith("# CCP4mg version "): ccp4mg_version_str = l[len('# CCP4mg version '):].rstrip() break f.close() except: ccp4mg_version_str = version.ccp4mg_version old_colours=False MGCOLOUR().usingOldColours = False ccp4mg_version = utils.parseVersion(ccp4mg_version_str) print 'Reading status file from version',ccp4mg_version if ccp4mg_version[0] >= 2 and ccp4mg_version[1] <= 5 and ccp4mg_version[2] < 3: #print "Need to use old colours" old_colours=True if old_colours: MGCOLOUR().rgbreps = [] MGCOLOUR().n_standard_rgbreps = 0 MGCOLOUR().RGBReps.clear() MGCOLOUR().usingOldColours = True MGCOLOUR().load_old_default() else: MGCOLOUR().rgbreps = [] MGCOLOUR().n_standard_rgbreps = 0 MGCOLOUR().RGBReps.clear() MGCOLOUR().load_default() MGCOLOUR().initialiseRGBReps() message,globs,locs = self.read_picture_definition(filename,trap_errors,default_dir=default_dir) #Everything OK? if message: MGGUI().WarningMessage(message,help='picture_definition',target='errors') return [1,message] elif globs['ERROR_MESSAGE']: message = 'Error interpreting '+filename +'\n\n' for line in globs['ERROR_MESSAGE']: message = message + line + '\n' MGGUI().WarningMessage(message,help='picture_definition',target='errors') return [1,message] if restore_list.count('colours') and globs['Colours'].insts: #print "Setting (picdef)",globs['Colours'].insts[0].params for key,value in globs['Colours'].insts[0].params: indx = MGCOLOUR().index(key,safe=0) if indx>=0: MGCOLOUR().reset(name=key,newrgb=value) else: MGCOLOUR().new(newname=key,newrgb=value) #Sort out preferences preferences = { 'create_DispObj' : 1 } if locs.has_key('preferences'): preferences.update(locs['preferences']) for key in preferences.keys(): if keywords.has_key(key): preferences[key] = int(keywords[key]) if restore_list.count('display'): if globs['CrystalList']: xtl=dataobj.DataObjShadow(name='CrystalData',object_type='CrystalData',objinsts=globs['CrystalList']) if globs['twoDList']: twoD=dataobj.DataObjShadow(name='GL2dScreen',object_type='GL2dScreen',objinsts=globs['twoDList']) #Everything OK? if message: MGGUI().WarningMessage(message,help='picture_definition',target='errors') return [1,message] if test: return [0,''] # Try restoring ParamsManagers first PM_remaining = [] pm = None if restore_list.count('params'): import picture_definition_classes for obj in globs['ParamsManager'].insts: pm = PM(obj.name) if pm: pm.restore_picture_definition(params=obj.params) else: import services if obj.name.startswith('HBond_drawing_style'): import HBonds pm = HBonds.createDrawingStylePM(name=obj.name) pm.setparams(obj.params) PM_remaining.append(obj) globs['ParamsManager'].insts = [] #print "PM_remaining",PM_remaining # Load any colour scheme managers for obj in globs['ColourSchemeManager'].insts: pm = PM(obj.name) if pm: pm.restore_picture_definition(params=obj.params) globs['ColourSchemeManager'].insts = [] override_visible=int(override_visible) if restore_list.count('display'): #Unpack any inline data for obj in globs['InlineList']: rv = obj.unpack() if rv[0]: message = message + rv[1] + '\n' del globs['InlineList'] #Restore any generic SelectionSchemes import model_selection SelParser = None for scheme in globs['SelectionSchemeList']: if scheme.parent_obj == 'generic': #print "restoring generic SelectionScheme",scheme.name if not SelParser: SelParser=model_selection.SelectionParser() stat,sel =SelParser .command_to_list(scheme.selection) if stat: message = message+"Can not interpret SelectionScheme "+scheme.name+'\n' else: rv = MODELINFO().add_info(set='generic',info='user_selection', key=utils.oneWord(scheme.name),value=sel) for scheme in globs['ColourSchemeList']: if scheme.parent_obj == 'generic': #print "restoring generic ColourScheme",scheme.name com2list = [] for col,sel in scheme.colours: if not SelParser: SelParser=model_selection.SelectionParser() stat,listsel = SelParser.command_to_list(sel) if not stat: com2list.append([col,listsel,{}]) #print "restoring ColourScheme",scheme.name,com2list if not com2list: message = message+"Can not interpret ColourScheme "+scheme.name+'\n' else: #print "user_colour_schemes",scheme.name,com2list stat = MODELINFO().add_info( \ set='generic',info='user_colour_schemes', key=utils.oneWord(scheme.name),value=com2list) data_old_colours = False for obj in globs['DataList']: if hasattr(obj,"dataparams"): if not obj.dataparams.has_key("ccp4mg_creator_version"): obj.dataparams["ccp4mg_creator_version"] = ccp4mg_version_str ccp4mg_creator_version = utils.parseVersion(obj.dataparams["ccp4mg_creator_version"]) if ccp4mg_creator_version[0] >= 2 and ccp4mg_creator_version[1] <= 5 and ccp4mg_creator_version[2] < 3: #print "Need to use old colours because object needs them." data_old_colours = True print ccp4mg_creator_version if data_old_colours and not old_colours: MGCOLOUR().rgbreps = [] MGCOLOUR().n_standard_rgbreps = 0 MGCOLOUR().RGBReps.clear() MGCOLOUR().usingOldColours = True MGCOLOUR().load_old_default() MGCOLOUR().initialiseRGBReps() old_colours = True if restore_list.count('colours') and globs['Colours'].insts: #print "Setting (picdef)",globs['Colours'].insts[0].params for key,value in globs['Colours'].insts[0].params: indx = MGCOLOUR().index(key,safe=0) if indx>=0: MGCOLOUR().reset(name=key,newrgb=value) else: MGCOLOUR().new(newname=key,newrgb=value) print "restoring from",filename rv = obj.restore(default_dir=default_dir) if rv[1]: message = message+rv[1]+'\n' if not rv[0]: for scheme in globs['SelectionSchemeList']: if scheme.parent_obj == obj: stat,sel = obj.dataobj.command_to_list(scheme.selection) #print "saving SelectionScheme",scheme.name,obj.dataobj.name if stat: message = message+"Can not interpret SelectionScheme "+scheme.name+'\n' else: stat = MODELINFO().add_info( \ set=obj.dataobj.name,info='user_selection', key=utils.oneWord(scheme.name),value=sel) for scheme in globs['ColourSchemeList']: if scheme.parent_obj == obj: com2list = [] for col,sel in scheme.colours: stat,listsel = obj.dataobj.command_to_list(sel) if not stat: com2list.append([col,listsel,{}]) #print "restoring ColourScheme",scheme.name,obj.dataobj.name,com2list if not com2list: message = message+"Can not interpret ColourScheme "+scheme.name+'\n' else: #print "user_colour_schemes",scheme.name,com2list stat = MODELINFO().add_info( \ set=obj.dataobj.name,info='user_colour_schemes', key=utils.oneWord(scheme.name),value=com2list) rv = obj.restore_display_objects(override_visible=override_visible) if rv[1]: message = message+rv[1]+'\n' if globs['twoDList']: if not keep_current or not get_dataobj('Legends&Images'): rv = twoD.restore() if rv[1]: message = message+rv[1]+'\n' else: twoD.set_dataobj(get_dataobj('Legends&Images')[0]) rv = twoD.restore_display_objects(override_visible=override_visible) if rv[1]: message = message+rv[1]+'\n' if globs['CrystalList']: if not keep_current or not get_dataobj('CrystalData'): rv = xtl.restore() if rv[1]: message = message+rv[1]+'\n' else: xtl.set_dataobj(get_dataobj('CrystalData')[0]) rv = xtl.restore_display_objects(override_visible=override_visible) if rv[1]: message = message+rv[1]+'\n' # Try restoring any remaining PMs - they may have been # associated with a DataObj or DispObj for obj in PM_remaining: if obj.name == "gui_params": MAINWINDOW().setParams(params=obj.params) elif obj.name == "light_params": import copy ps = copy.deepcopy(obj.params) if hasattr(ps,'has_key') and ps.has_key('lights') and ps.has_key('nLights'): ps2 = ps['lights'] # Fudge to deal with the fact that keys may be # strings rather than ints in pic def file. ps3 = copy.deepcopy(ps2) for key in ps2: ps3[int(key)] = ps3[key] ps3['nLights'] = ps['nLights'] MAINWINDOW().setLightParams(ps3) else: pm = PM(obj.name) if pm: pm.setparams(obj.params) #pm.restore_picture_definition(params=obj.params) else: message = message + "Can not restore the ParamsManager: "+obj.name+'\n' del PM_remaining if restore_list.count('view') and globs['View'].insts: MAINWINDOW().setViewParams(params= globs['View'].insts[0].params) for p in reqRunAfterModelLoad: if hasattr(p,"runAfterModelLoad") and callable(p.runAfterModelLoad): p.runAfterModelLoad() if delay_delete: import rebuild,time rebuild.UpdateDisplay() time.sleep(1.0) for item in delete_list: item.delete() del delete_list print message if message: MGGUI().WarningMessage(message,help='picture_definition',target='errors') return [1,message] del locs,globs return [0,''] #---------------------------------------------------------------------- def loadInlinePDB(self,filename,mode='mman',name=''): #---------------------------------------------------------------------- message,globs,locs=self.read_picture_definition(filename) #print 'picture_definition.loadInlinePDB',message if message: return [1,'Error extracting data from file\n'+filename] #Unpack any inline data to a pdb file if not globs['InlineList']: return [1,'No inline data in file\n'+filename] import os pdbfile = os.path.splitext(filename)[0]+'.pdb' #print 'picture_definition.loadInlinePDB',pdbfile rv = globs['InlineList'][0].unpack(pdbfile) if rv[0]: return [1,'No extracting inline data from file\n'+filename] if mode == 'MolData': import model m = model.MolData (filename=pdbfile,name=name) rv = m.loaddata(warnings=1) if rv[0]==1: m.delete() return [1,'Error loading file: '+filename+'\n'+rv[1]] return [0,m] else: import mmut import mmdb2 as mmdb if mode == 'mman': molHnd = mmut.CMMANManager(RESOURCES().SRS,RESOURCES().CMolBondParams) else: # Make MMDBManager of the PDB molHnd = mmdb.Manager() molHnd.SetFlag(mmdb.MMDBF_IgnoreRemarks) molHnd.SetFlag(mmdb.MMDBF_IgnoreBlankLines) molHnd.SetFlag(mmdb.MMDBF_IgnoreHash) #molHnd.SetFlag(mmdb.MMDBF_EnforceUniqueChainID) #molHnd.ReadCoorFile(pdbfile) utils.ReadCoorFile(molHnd,pdbfile) return [0,molHnd]