def SelectionGproteinToggle(request):
"""Updates the selected g proteins arbitrary selections"""
g_protein_id = request.GET['g_protein_id']
preferred = request.GET['preferred']
all_gprots = ProteinGProtein.objects.all()
gprots = ProteinGProtein.objects.filter(pk=g_protein_id)
print("'{}'".format(ProteinGProtein.objects.get(pk=g_protein_id).name))
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# add the selected items to the selection
for gprot in gprots:
if preferred == 'true':
exists = selection.remove('pref_g_proteins', 'g_protein',
g_protein_id)
else:
exists = selection.remove('g_proteins', 'g_protein', g_protein_id)
if not exists:
selection_object = SelectionItem('g_protein', gprot)
if preferred == 'true':
selection.add('pref_g_proteins', 'g_protein', selection_object)
else:
selection.add('g_proteins', 'g_protein', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
if preferred == 'true':
context = selection.dict('pref_g_proteins')
else:
context = selection.dict('g_proteins')
context['gprots'] = ProteinGProtein.objects.all()
if preferred == 'true':
print(request.session['selection'])
return render(request,
'common/selection_filters_pref_gproteins_selector.html',
context)
else:
return render(request,
'common/selection_filters_gproteins_selector.html',
context)
def post(self, request, *args, **kwargs):
context = super(PDBClean, self).get_context_data(**kwargs)
self.posted = True
pref = True
water = False
hets = False
if 'pref_chain' not in request.POST.keys():
pref = False
if 'water' in request.POST.keys():
water = True
if 'hets' in request.POST.keys():
hets = True
# get simple selection from session
simple_selection = request.session.get('selection', False)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
out_stream = BytesIO()
io = PDBIO()
zipf = zipfile.ZipFile(out_stream, 'w', zipfile.ZIP_DEFLATED)
if selection.targets != []:
for selected_struct in [x for x in selection.targets if x.type == 'structure']:
struct_name = '{}_{}.pdb'.format(selected_struct.item.protein_conformation.protein.parent.entry_name, selected_struct.item.pdb_code.index)
if hets:
lig_names = [x.pdb_reference for x in StructureLigandInteraction.objects.filter(structure=selected_struct.item, annotated=True)]
else:
lig_names = None
gn_assigner = GenericNumbering(structure=PDBParser(QUIET=True).get_structure(struct_name, StringIO(selected_struct.item.get_cleaned_pdb(pref, water, lig_names)))[0])
tmp = StringIO()
io.set_structure(gn_assigner.assign_generic_numbers())
request.session['substructure_mapping'] = gn_assigner.get_substructure_mapping_dict()
io.save(tmp)
zipf.writestr(struct_name, tmp.getvalue())
del gn_assigner, tmp
for struct in selection.targets:
selection.remove('targets', 'structure', struct.item.id)
# export simple selection that can be serialized
simple_selection = selection.exporter()
request.session['selection'] = simple_selection
request.session['cleaned_structures'] = out_stream
attributes = inspect.getmembers(self, lambda a:not(inspect.isroutine(a)))
for a in attributes:
if not(a[0].startswith('__') and a[0].endswith('__')):
context[a[0]] = a[1]
return render(request, self.template_name, context)
def SelectionGproteinToggle(request):
"""Updates the selected g proteins arbitrary selections"""
g_protein_id = request.GET['g_protein_id']
preferred = request.GET['preferred']
all_gprots = ProteinGProtein.objects.all()
gprots = ProteinGProtein.objects.filter(pk=g_protein_id)
print("'{}'".format(ProteinGProtein.objects.get(pk=g_protein_id).name))
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# add the selected items to the selection
for gprot in gprots:
if preferred == 'true':
exists = selection.remove('pref_g_proteins', 'g_protein', g_protein_id)
else:
exists = selection.remove('g_proteins', 'g_protein', g_protein_id)
if not exists:
selection_object = SelectionItem('g_protein', gprot)
if preferred == 'true':
selection.add('pref_g_proteins', 'g_protein', selection_object)
else:
selection.add('g_proteins', 'g_protein', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
if preferred == 'true':
context = selection.dict('pref_g_proteins')
else:
context = selection.dict('g_proteins')
context['gprots'] = ProteinGProtein.objects.all()
if preferred == 'true':
print(request.session['selection'])
return render(request, 'common/selection_filters_pref_gproteins_selector.html', context)
else:
return render(request, 'common/selection_filters_gproteins_selector.html', context)
def SelectionSchemesToggle(request):
"""Updates the selected numbering schemes arbitrary selections"""
numbering_scheme_id = request.GET['numbering_scheme_id']
gns = ResidueNumberingScheme.objects.filter(pk=numbering_scheme_id)
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# add the selected items to the selection
for gn in gns:
exists = selection.remove('numbering_schemes', 'numbering_schemes', numbering_scheme_id)
if not exists:
selection_object = SelectionItem('numbering_schemes', gn)
selection.add('numbering_schemes', 'numbering_schemes', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('numbering_schemes')
context['gns'] = ResidueNumberingScheme.objects.exclude(slug=settings.DEFAULT_NUMBERING_SCHEME)
return render(request, 'common/selection_filters_numbering_schemes.html', context)
def SelectionSpeciesToggle(request):
"""Updates the selected species arbitrary selections"""
species_id = request.GET['species_id']
all_sps = Species.objects.all()
sps = Species.objects.filter(pk=species_id)
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# add the selected items to the selection
for sp in sps:
exists = selection.remove('species', 'species', species_id)
if not exists:
selection_object = SelectionItem('species', sp)
selection.add('species', 'species', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('species')
context['sps'] = Species.objects.all()
return render(request, 'common/selection_filters_species_selector.html', context)
def SelectionSchemesToggle(request):
"""Updates the selected numbering schemes arbitrary selections"""
numbering_scheme_id = request.GET['numbering_scheme_id']
gns = ResidueNumberingScheme.objects.filter(pk=numbering_scheme_id)
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# add the selected items to the selection
for gn in gns:
exists = selection.remove('numbering_schemes', 'numbering_schemes', numbering_scheme_id)
if not exists:
selection_object = SelectionItem('numbering_schemes', gn)
selection.add('numbering_schemes', 'numbering_schemes', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('numbering_schemes')
context['gns'] = ResidueNumberingScheme.objects.exclude(slug=settings.DEFAULT_NUMBERING_SCHEME)
return render(request, 'common/selection_filters_numbering_schemes.html', context)
def SelectionSpeciesToggle(request):
"""Updates the selected species arbitrary selections"""
species_id = request.GET['species_id']
all_sps = Species.objects.all()
sps = Species.objects.filter(pk=species_id)
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# add the selected items to the selection
for sp in sps:
exists = selection.remove('species', 'species', species_id)
if not exists:
selection_object = SelectionItem('species', sp)
selection.add('species', 'species', selection_object)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# add all species objects to context (for comparison to selected species)
context = selection.dict('species')
context['sps'] = Species.objects.all()
return render(request, 'common/selection_filters_species_selector.html', context)
def RemoveResidueGroup(request):
"""Receives a selection request, removes a residue group, and returns the updated selection"""
selection_type = request.GET['selection_type']
group_id = int(request.GET['group_id'])
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# find all positions in the group and delete them
for position in selection.segments:
if position.type == 'site_residue':
if position.properties['site_residue_group'] == group_id:
selection.remove(selection_type, position.type,
position.item.id)
else:
if position.properties['site_residue_group'] > group_id:
position.properties['site_residue_group'] -= 1
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# context
context = selection.dict(selection_type)
# amino acid groups
amino_acid_groups = {
'amino_acid_groups': definitions.AMINO_ACID_GROUPS,
'amino_acid_group_names': definitions.AMINO_ACID_GROUP_NAMES
}
context.update(amino_acid_groups)
# template to load
template = 'common/selection_lists_sitesearch.html'
return render(request, template, context)
def ConvertStructuresToProteins(request):
"For alignment from structure browser"
simple_selection = request.session.get('selection', False)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
if selection.targets != []:
for struct in selection.targets:
prot = struct.item.protein_conformation.protein.parent
selection.remove('targets', 'structure', struct.item.id)
selection.add('targets', 'protein', SelectionItem('protein', prot))
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
return HttpResponseRedirect('/alignment/segmentselection')
def RemoveResidueGroup(request):
"""Receives a selection request, removes a residue group, and returns the updated selection"""
selection_type = request.GET['selection_type']
group_id = int(request.GET['group_id'])
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# find all positions in the group and delete them
for position in selection.segments:
if position.type == 'site_residue':
if position.properties['site_residue_group'] == group_id:
selection.remove(selection_type, position.type, position.item.id)
else:
if position.properties['site_residue_group'] > group_id:
position.properties['site_residue_group'] -= 1
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# context
context = selection.dict(selection_type)
# amino acid groups
amino_acid_groups = {
'amino_acid_groups': definitions.AMINO_ACID_GROUPS,
'amino_acid_group_names': definitions.AMINO_ACID_GROUP_NAMES }
context.update(amino_acid_groups)
# template to load
template = 'common/selection_lists_sitesearch.html'
return render(request, template, context)
def RemoveFromSelection(request):
"""Removes one selected item from the session"""
selection_type = request.GET['selection_type']
selection_subtype = request.GET['selection_subtype']
selection_id = request.GET['selection_id']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# remove the selected item to the selection
selection.remove(selection_type, selection_subtype, selection_id)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# context
context = selection.dict(selection_type)
# template to load
if selection_subtype == 'site_residue':
template = 'common/selection_lists_sitesearch.html'
amino_acid_groups = {
'amino_acid_groups': definitions.AMINO_ACID_GROUPS,
'amino_acid_group_names': definitions.AMINO_ACID_GROUP_NAMES
}
context.update(amino_acid_groups)
else:
template = 'common/selection_lists.html'
return render(request, template, context)
def RemoveFromSelection(request):
"""Removes one selected item from the session"""
selection_type = request.GET['selection_type']
selection_subtype = request.GET['selection_subtype']
selection_id = request.GET['selection_id']
# get simple selection from session
simple_selection = request.session.get('selection', False)
# create full selection and import simple selection (if it exists)
selection = Selection()
if simple_selection:
selection.importer(simple_selection)
# remove the selected item to the selection
selection.remove(selection_type, selection_subtype, selection_id)
# export simple selection that can be serialized
simple_selection = selection.exporter()
# add simple selection to session
request.session['selection'] = simple_selection
# context
context = selection.dict(selection_type)
# template to load
if selection_subtype == 'site_residue':
template = 'common/selection_lists_sitesearch.html'
amino_acid_groups = {
'amino_acid_groups': definitions.AMINO_ACID_GROUPS,
'amino_acid_group_names': definitions.AMINO_ACID_GROUP_NAMES }
context.update(amino_acid_groups)
else:
template = 'common/selection_lists.html'
return render(request, template, context)
