""" python/ui/picture_definition_classes.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. """ import dataobj,os.path DataList = [] DataLookup = {} CrystalList = [] twoDList = [] InlineList = [] SelectionSchemeList = [] ColourSchemeList = [] global ERROR_MESSAGE ERROR_MESSAGE = [] def get_dataobj(name=''): rv = dataobj.get_dataobj(name='') if rv: return rv[0] else: return None def DataObj_isGZIPPED(name='',dataparams={},object_type='MolData'): import utils if not name: if dataparams.has_key('filename'): if dataparams['filename'][1]: fname = dataparams['filename'][1] elif dataparams['filename'][2]: fname = dataparams['filename'][2] name = os.path.split(os.path.splitext(fname)[0])[-1] ext = os.path.splitext(fname)[1][1:].lower() extgz = None if ext == 'gz': ext2 = os.path.splitext(os.path.splitext(fname)[0])[1] if ext2 != '': extgz = (ext2 + '.' + ext)[1:].lower() fname = utils.gunzipToNamedFile(fname) if not fname: return False if dataparams['filename'][1]: dataparams['filename'][1] = fname elif dataparams['filename'][2]: dataparams['filename'][2] = fname return True return False def DataObj_name(name='',dataparams={},object_type='MolData'): if not name: if dataparams.has_key('filename'): if dataparams['filename'][1]: name = os.path.split(os.path.splitext(dataparams['filename'][1])[0])[-1] elif dataparams['filename'][2]: name = os.path.split(os.path.splitext(dataparams['filename'][2])[0])[-1] else: name = object_type+str(len(DataList)+1) return name def DispObj_parent(parent='',name='',object_type='MolData'): import types parent_obj = None #print "DispObj_parent in",parent,DataLookup if parent: if isinstance(parent,types.StringType): if DataLookup.has_key(parent): parent_obj = DataLookup[parent] elif isinstance (parent,dataobj.DataObj): for shadow in DataList: if shadow.dataobj == parent: parent_obj = shadow break elif name: for obj in DataList: if obj.object_type == object_type and obj.objnames.count(name): parent_obj = obj if not parent_obj: if len(DataList)>0: for ii in range(len(DataList)-1,-1,-1): if DataList[ii].object_type == object_type: parent_obj = DataList[ii] break #print "parent_obj",parent_obj return parent_obj def DispObj_name(parent_obj=None,name='',object_type='MolDisp'): if name: exi = parent_obj.objnames.count(name) if not exi and hasattr(parent_obj,'dataobj'): exi = parent_obj.dataobj.objnames.count(name) if not exi: return name n = len(parent_obj.objnames) if hasattr(parent_obj,'dataobj'): n = n + len(parent_obj.dataobj.objnames) contu = 1 while contu: n = n + 1 nname = parent_obj.name+object_type+str(n) contu = parent_obj.objnames.count(nname) if not contu and hasattr(parent_obj,'dataobj'): contu = parent_obj.dataobj.objnames.count(nname) return nname def ReadFile(filename=""): try: f = open(filename) text = f.read() f.close() except: text="" return text #-------------------------------------------------------------------- class MolData(dataobj.DataObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',reference='',objnames=[],visible=1,display_objects=[],**dataparams): dataparams['visible']=visible isGZ = DataObj_isGZIPPED(name=name,dataparams=dataparams,object_type='MolData') name = DataObj_name(name=name,dataparams=dataparams,object_type='MolData') if name: #print "Setting name to",name dataparams["name"] = name # Beware the following lines are VERY necessary to prevent all dataobjects # containing all display objects objnames = [] for item in display_objects: objnames.append(item) objinsts = [] self.reference = reference dataobj.DataObjShadow.__init__(self,name=name,object_type='MolData',objnames=objnames,objinsts=objinsts,dataparams=dataparams) #dataobj.DataObjShadow.set(display_objects=display_objects,dataparams=dataparams) DataList.append(self) DataLookup[name]=self #print 'Loaded picture definition: MolData',name def get(self,mode=''): if not hasattr(self,'dataobj'): self.restore() if hasattr(self,'dataobj'): return self.dataobj.get(mode=mode) else: return [] #-------------------------------------------------------------------- class MolDisp(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='MolDisp',selection_parameters={},colour_parameters={},style_parameters={},visible=1,**keywords): global ERROR_MESSAGE parent_obj= DispObj_parent(parent=parent,name=name,object_type='MolData') if not parent_obj: ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='MolDisp') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,selparams=selection_parameters,colparams=colour_parameters,styleparams=style_parameters,visible=visible,params=keywords) if self.params.has_key('selection'): rv = self.convert_selection(self.params['selection']) if not rv[0]: self.params['selection'] = rv[1] else: print name + ' : ' + rv[1] if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print "parent_obj.objnames",parent_obj.name,parent_obj.objnames,parent_obj.objinsts #print 'Loaded picture definition: MolDisp',name,'in DataObj',parent_obj.name #-------------------------------------------------------------------- class HBonds(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='HBonds',selection_parameters={},colour_parameters={},style_parameters={},visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='MolData') if not parent_obj: global ERROR_MESSAGE ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='HBonds') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,selparams=selection_parameters,colparams=colour_parameters,styleparams=style_parameters,visible=visible,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print 'Loaded picture definition: Hbonds',name #-------------------------------------------------------------------- class Contacts(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='Contacts',selection_parameters={},colour_parameters={},style_parameters={},visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='MolData') if not parent_obj: global ERROR_MESSAGE ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='Contacts') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,selparams=selection_parameters,colparams=colour_parameters,styleparams=style_parameters,visible=visible,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print 'Loaded picture definition: Contacts',name #-------------------------------------------------------------------- class AnisoU(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='AnisoU',selection_parameters={},colour_parameters={},style_parameters={},visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='MolData') if not parent_obj: global ERROR_MESSAGE ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='AnisoU') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,selparams=selection_parameters,colparams=colour_parameters,styleparams=style_parameters,visible=visible,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print 'Loaded picture definition: AnisoU',name #-------------------------------------------------------------------- class Annotation(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='Annotation',selection_parameters={},colour_parameters={},style_parameters={},visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='MolData') if not parent_obj: global ERROR_MESSAGE ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='Annotation') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,selparams=selection_parameters,colparams=colour_parameters,styleparams=style_parameters,visible=visible,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print 'Loaded picture definition: Annotation',name #-------------------------------------------------------------------- class SurfaceDispobj(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='SurfaceDispobj',selection_parameters={},colour_parameters={},style_parameters={},visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='MolData') if not parent_obj: global ERROR_MESSAGE ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='SurfaceDispobj') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,visible=visible,selparams=selection_parameters,colparams=colour_parameters,styleparams=style_parameters,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print 'Loaded picture definition: SurfaceDispobj',name #-------------------------------------------------------------------- class CrystalData(dataobj.DataObjShadow): #-------------------------------------------------------------------- def __init__(self,name='CrystalData',display_objects=[],**dataparams): pass #dataobj.DataObjShadow.__init__(self,name=name,object_type='CrystalData',objnames=objnames,dataparams=dataparams) #DataList.append(self) #print 'Loaded picture definition: CrystalData',name #-------------------------------------------------------------------- class Crystal(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',object_type='Crystal',visible=1,**keywords): if not name: name = 'Crystal'+str(len(CrystalList)+1) dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,visible=visible,params=keywords) if name: CrystalList.append(self) #print 'Loaded picture definition: Crystal',name #---------------------------------------------------------------------------- class MapData(dataobj.DataObjShadow): #---------------------------------------------------------------------------- def __init__(self,name='MapData',display_objects=[],visible=1,**dataparams): dataparams['visible']=visible name = DataObj_name(name=name,dataparams=dataparams,object_type='MapData') objnames = [] for item in display_objects: objnames.append(item) objinsts = [] dataobj.DataObjShadow.__init__(self,name=name,object_type='MapData',objnames=display_objects,objinsts=objinsts,dataparams=dataparams) DataList.append(self) DataLookup[name]=self #print 'Loaded picture definition: MapData',name #---------------------------------------------------------------------------- class MapDisp(dataobj.DispObjShadow): #---------------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='MapDisp',visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='MapData') if not parent_obj: return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='MapDisp') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,visible=visible,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print "parent_obj.objnames",parent_obj.name,parent_obj.objnames,parent_obj.objinsts #print 'Loaded picture definition: MapDisp',name,'in DataObj',parent_obj.name #-------------------------------------------------------------------- class VectorsData(dataobj.DataObjShadow): #-------------------------------------------------------------------- def __init__(self,name='VectorsData',display_objects=[],visible=1,**dataparams): dataparams['visible']=visible name = DataObj_name(name=name,dataparams=dataparams,object_type='VectorsData') # Beware the following lines are VERY necessary to prevent all dataobjects # containing all display objects objnames = [] for item in display_objects: objnames.append(item) objinsts = [] dataobj.DataObjShadow.__init__(self,name=name,object_type='VectorsData',objnames=display_objects,objinsts=objinsts,dataparams=dataparams) DataList.append(self) DataLookup[name]=self #print 'Loaded picture definition: VectorsData',name #-------------------------------------------------------------------- class VectorsDispobj(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='VectorsDispobj',visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='VectorsData') if not parent_obj: global ERROR_MESSAGE ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='VectorsDispobj') dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,visible=visible,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print 'Loaded picture definition: VectorsDispobj',name #-------------------------------------------------------------------- class Legend(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',object_type='Legend',visible=1,**keywords): dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,visible=visible,params=keywords) twoDList.append(self) #print 'Loaded picture definition: Legend',name #-------------------------------------------------------------------- class Image(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',object_type='Image',visible=1,**keywords): dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,visible=visible,params=keywords) twoDList.append(self) #print 'Loaded picture definition: Image',name #-------------------------------------------------------------------- class FieldData(dataobj.DataObjShadow): #-------------------------------------------------------------------- def __init__(self,name='FieldData',display_objects=[],visible=1,**dataparams): dataparams['visible']=visible name = DataObj_name(name=name,dataparams=dataparams,object_type='FieldData') # Beware the following lines are VERY necessary to prevent all dataobjects # containing all display objects objnames = [] for item in display_objects: objnames.append(item) objinsts = [] dataobj.DataObjShadow.__init__(self,name=name,object_type='FieldData',objnames=display_objects,objinsts=objinsts,dataparams=dataparams) DataLookup[name] = self DataList.append(self) #print 'Loaded picture definition: FieldData',name #-------------------------------------------------------------------- class FieldDisp(dataobj.DispObjShadow): #-------------------------------------------------------------------- def __init__(self,name='',parent='',object_type='FieldDisp',visible=1,**keywords): parent_obj= DispObj_parent(parent=parent,name=name,object_type='FieldData') if not parent_obj: global ERROR_MESSAGE ERROR_MESSAGE.append('Can not find parent DataObj for '+object_type + ' ' + name) return name = DispObj_name(parent_obj=parent_obj,name=name,object_type='FieldDisp') if not name: name = parent_obj.name+'MolDisp'+str(len(parent_obj.objnames)+1) dataobj.DispObjShadow.__init__(self,name=name,object_type=object_type,visible=visible,params=keywords) if not parent_obj.objnames.count(name): parent_obj.objnames.append(name) parent_obj.objinsts.append(self) #print 'Loaded picture definition: FieldDisp',name #============================================================================ class ParamsManager: insts = [] def __init__(self,name = '', **keywords): self.name = name self.params = {} for key,value in keywords.items(): self.params[key] = value ParamsManager.insts.append(self) #print 'Loaded picture definition: ParamsManager',name #print "ParamsManager.insts",ParamsManager.insts class ColourSchemeManager: insts = [] def __init__(self,name = '', **keywords): self.name = name self.params = {} for key,value in keywords.items(): self.params[key] = value ColourSchemeManager.insts.append(self) #print 'Loaded picture definition: ColourSchemeManager',name #print "ColourSchemeManager.insts",ColourSchemeManager.insts class View: insts = [] def __init__(self,name='',**keywords): self.name = name self.params = {} for key,value in keywords.items(): self.params[key] = value View.insts.append(self) class Colours: insts = [] def __init__(self,colour_definitions={},**keywords): self.params = [] if colour_definitions: for key,value in colour_definitions.items(): self.params.append([key,value]) elif keywords: for key,value in keywords.items(): self.params.append ([key,value]) Colours.insts.append(self) class Wizard: def __init__(self,MolData1='',drawing_style='',**keywords): global ERROR_MESSAGE parent_obj = DispObj_parent(parent=MolData1,object_type='MolData') if not parent_obj: return if parent_obj.get_filename()[0] != "INLINE": parent_obj.restore() import string,global_definitions wizard = global_definitions.PICTUREWIZARD() folder,index = string.split(drawing_style,':',1) if index and folder: if os.path.exists(os.path.join(wizard.master_dir,folder)): theDir = os.path.join(wizard.master_dir,folder) else: theDir = os.path.join(utils.get_CCP4MG(),'data','picture_wizard_files',folder) mgpic_file = wizard.snapshot_file(index=index,mode='mgpic',dir=theDir) #print "mgpic_file",mgpic_file # Initialise the choices rv,choices = wizard.read_mgpic_file_choices(filename=mgpic_file) #print " rv,choices", rv,choices if rv<=0: for param in choices: if param.has_key('name'): if param.has_key('initial'): globals()[param['name']] = param['initial'] else: globals()[param['name']] = '' import global_definitions if len(global_definitions.get_dataobj(name=parent_obj.name))>0: globals()["MolData1"] = global_definitions.get_dataobj(name=parent_obj.name)[0] else: globals()["MolData1"] =parent_obj.name # Run the wizard script rv,script_text = wizard.read_mgpic_file_section(filename=mgpic_file,section='SCRIPT') #print "script_text",script_text if not rv: for key,value in keywords.items(): globals()[key] = value try: locs = {} exec(script_text,globals(),locs) except StandardError, e: #print "ERROR in Wizard",e ERROR_MESSAGE.append( 'ERROR handing Wizard '+e) else: #print "ERROR in Wizard reading script for "+drawing_style ERROR_MESSAGE.append("ERROR in Wizard reading script for "+drawing_style) class Inline: def __init__(self,name = '', data = ''): self.name = name self.data = data InlineList.append(self) #print "data",data def unpack (self,target=''): import utils if not target: target = utils.get_filename('INLINE',self.name) #print "unpack target",target rv = utils.saveFile(target,text=self.data) if rv: return [1,'Error saving inline data to file '+target] if os.path.splitext(self.name)[-1] == '.gz': import gzip try: i = gzip.open(target) o = open(target[0:-3],'wb') o.write(i.read()) except: return [1,'Error uncompressing '+target] return [0] class SelectionScheme: def __init__(self,name='',context='',selection='',selparams={},**keywords): self.name = name if context == 'generic': self.parent_obj='generic' else: self.parent_obj= DispObj_parent(parent=context,object_type='MolData') if not self.parent_obj: self.parent_obj = 'generic' self.selection = selection SelectionSchemeList.append(self) #print "SelectionScheme parent_obj",self.parent_obj class ColourScheme: def __init__(self,name='',context='',colours='',**keywords): self.name = name if context == 'generic': self.parent_obj='generic' else: self.parent_obj= DispObj_parent(parent=context,object_type='MolData') if not self.parent_obj: self.parent_obj = 'generic' self.colours = colours ColourSchemeList.append(self) #print "ColourScheme parent_obj",self.parent_obj