def find_maps(self):
if not self.bound_conf:
return ValueError(
'Bound conf not set! use RefinementObjectFiles().find_bound_file()'
)
self.mtz_path = db_functions.check_file_status('refine.mtz',
self.bound_conf)
self.two_fofc_path = db_functions.check_file_status(
'2fofc.map', self.bound_conf)
self.fofc_path = db_functions.check_file_status(
'fofc.map', self.bound_conf)
# if can't find bound state, just use the latest pdb file
bound_conf = obj.pdb_latest
else:
# no pdb = no proasis upload (same for mtz, two_fofc and fofc)
# TODO: Turn this into a function instead of repeating file check
fail_count += 1
print('FAILURE FOR: ' + str(obj.crystal_name.crystal_name))
print('no pdb = no proasis upload (same for mtz, two_fofc and fofc)')
continue
print(bound_conf)
if 'split.bound-state' in bound_conf:
mtz = db_functions.check_file_status('refine.mtz', obj.pdb_latest)
two_fofc = db_functions.check_file_status('2fofc.map', obj.pdb_latest)
fofc = db_functions.check_file_status('fofc.map', obj.pdb_latest)
else:
mtz = db_functions.check_file_status('refine.mtz', bound_conf)
two_fofc = db_functions.check_file_status('2fofc.map', bound_conf)
fofc = db_functions.check_file_status('fofc.map', bound_conf)
if not mtz[0] or not two_fofc[0] or not fofc[0]:
fail_count += 1
print('FAILURE FOR: ' + str(obj.crystal_name.crystal_name))
print('missing file')
print(bound_conf)
print(mtz)
print(two_fofc)
def get_crystal_info(request):
queryset = Target.objects.filter()
filter_fields = ('target_name', )
submission = request.GET.get('target_name')
crystals = Crystal.objects.filter(target__target_name=submission)
data = []
for crys in crystals:
refinements = Refinement.objects.filter(crystal_name=crys,
outcome__gte=4)
for ref in refinements:
out_dict = {
'crys': '',
'refinement_status': '✘',
'pandda_model': '✘',
'pdb_present': '✘',
'twofofc_present': '✘',
'fofc_present': '✘',
'mtz_present': '✘',
'in_proasis': '✘',
'proasis_strucids': '✘',
'files_out': '✘',
'out_directory': '✘',
'uploaded_to_verne': '✘',
}
out_dict['crys'] = str(crys.crystal_name)
out_dict['refinement_status'] = str(ref.outcome)
events = list(
set([
pr.pandda_run
for pr in PanddaEvent.objects.filter(crystal=crys)
]))
if events:
out_dict['pandda_model'] = '✓'
proasis = ProasisHits.objects.filter(crystal_name=crys).exclude(
strucid=None).exclude(strucid='')
pout = []
bound_conf = ''
# if there is a pdb file named in the bound_conf field, use it as the upload structure for proasis
if ref.bound_conf:
if os.path.isfile(ref.bound_conf):
bound_conf = ref.bound_conf
# otherwise, use the most recent pdb file (according to soakdb)
elif ref.pdb_latest:
if os.path.isfile(ref.pdb_latest):
# if this is from a refinement folder, find the bound-state pdb file, rather than the ensemble
if 'Refine' in ref.pdb_latest:
search_path = '/'.join(ref.pdb_latest.split('/')[:-1])
print(search_path)
files = glob.glob(
str(search_path + '/refine*split.bound*.pdb'))
print(files)
if len(files) == 1:
bound_conf = files[0]
else:
# if can't find bound state, just use the latest pdb file
bound_conf = ref.pdb_latest
if bound_conf:
out_dict['pdb_present'] = bound_conf.split('/')[-1]
if 'split.bound-state' in bound_conf:
mtz = check_file_status('refine.mtz', ref.pdb_latest)
two_fofc = check_file_status('2fofc.map', ref.pdb_latest)
fofc = check_file_status('fofc.map', ref.pdb_latest)
else:
mtz = check_file_status('refine.mtz', bound_conf)
two_fofc = check_file_status('2fofc.map', bound_conf)
fofc = check_file_status('fofc.map', bound_conf)
if mtz[0]:
out_dict['mtz_present'] = '✓'
if two_fofc[0]:
out_dict['twofofc_present'] = '✓'
if fofc[0]:
out_dict['fofc_present'] = '✓'
if proasis:
out_dict['in_proasis'] = '✓'
proasis_strucids = [p.strucid for p in proasis]
out_dict['proasis_strucids'] = ', '.join(proasis_strucids)
for p in proasis:
pout = ProasisOut.objects.filter(crystal=crys, proasis=p)
if pout:
out_dirs = list(
set([os.path.join(o.root, o.start) for o in pout]))
out_dict['files_out'] = '✓'
out_dict['out_directory'] = ', '.join(out_dirs)
out_root = list(
set([
os.path.join(o.root,
o.start.split('/')[0]) for o in pout
]))
if len(out_root) == 1:
if os.path.isfile(
os.path.join(out_root[0],
'verne.transferred')):
out_dict['uploaded_to_verne'] = '✓'
data.append(out_dict)
return JsonResponse(data, safe=False)
def run(self):
fail_count = 0
# select anything 'in refinement' (3) or above
refinement = Refinement.objects.filter(outcome__gte=3)
# set up info for each entry that matches the filter
for obj in refinement:
# set up blank fields for entries in proasis hits table
bound_conf = ''
files = []
mtz = ''
two_fofc = ''
fofc = ''
mod_date = ''
proasis_hit_entry = ''
entry = ''
confs = []
ligand_list = []
# if there is a pdb file named in the bound_conf field, use it as the upload structure for proasis
if obj.bound_conf:
if os.path.isfile(obj.bound_conf):
bound_conf = obj.bound_conf
# otherwise, use the most recent pdb file (according to soakdb)
elif obj.pdb_latest:
if os.path.isfile(obj.pdb_latest):
# if this is from a refinement folder, find the bound-state pdb file, rather than the ensemble
if 'Refine' in obj.pdb_latest:
search_path = '/'.join(obj.pdb_latest.split('/')[:-1])
files = glob.glob(
str(search_path + '/refine*bound*.pdb'))
if len(files) == 1:
bound_conf = files[0]
else:
# if can't find bound state, just use the latest pdb file
bound_conf = obj.pdb_latest
else:
# no pdb = no proasis upload (same for mtz, two_fofc and fofc)
# TODO: Turn this into a function instead of repeating file check
fail_count += 1
continue
mtz = db_functions.check_file_status('refine.mtz', bound_conf)
two_fofc = db_functions.check_file_status('2fofc.map', bound_conf)
fofc = db_functions.check_file_status('fofc.map', bound_conf)
if not mtz[0] or not two_fofc[0] or not fofc[0]:
fail_count += 1
continue
# if a suitable pdb file is found, then search for ligands
if bound_conf:
try:
pdb_file = open(bound_conf, 'r')
ligand_list = []
for line in pdb_file:
if "LIG" in line:
try:
# ligands identified by 'LIG', with preceeding '.' for alt conf letter
lig_string = re.search(r".LIG.......",
line).group()
# just use lig string instead of separating into list items (to handle altconfs)
# TODO: This has changed from a list of ['LIG','RES','ID'] to string. Check usage
ligand_list.append(lig_string)
except:
continue
# if no ligands are found in the pdb file, no upload to proasis (checked that no strucs. had alternative
# labels in them)
except:
ligand_list = None
if not ligand_list:
continue
# get a unique list of ligands
unique_ligands = list(set(ligand_list))
# remove the first letter (alt conf) from unique ligands
lig_no_conf = [l[1:] for l in unique_ligands]
for l in lig_no_conf:
# check whether there are more than 1 entries for any of the lig strings without alt conf
if lig_no_conf.count(l) > 1:
# this is an alt conf situation - add the alt confs to the conf list
confs.extend([lig for lig in unique_ligands if l in lig])
# get the date the pdb file was modified
mod_date = misc_functions.get_mod_date(bound_conf)
if mod_date:
# if there's already an entry for that structure
if ProasisHits.objects.filter(
refinement=obj,
crystal_name=obj.crystal_name).exists():
# if there are no alternate conformations
if not confs:
# get the relevant entry
entry = ProasisHits.objects.get(
refinement=obj, crystal_name=obj.crystal_name)
# if the pdb file is older than the current one, or it has not been uploaded to proasis
if entry.modification_date < mod_date or not entry.strucid:
# delete structure and remove files to remove from proasis is strucid exists
if entry.strucid:
proasis_api_funcs.delete_structure(
entry.strucid)
entry.strucid = None
entry.save()
if self.hit_directory in entry.pdb_file:
os.remove(entry.pdb_file)
if self.hit_directory in entry.mtz:
os.remove(entry.mtz)
if self.hit_directory in entry.two_fofc:
os.remove(entry.two_fofc)
if self.hit_directory in entry.fofc:
os.remove(entry.fofc)
# otherwise, just update the relevant fields
entry.pdb_file = bound_conf
entry.modification_date = mod_date
entry.mtz = mtz[1]
entry.two_fofc = two_fofc[1]
entry.fofc = fofc[1]
entry.ligand_list = unique_ligands
entry.save()
# if there ARE alternate conformations
else:
# for each conformation
for conf in confs:
# do the same as above, but setting the altconf field too
# TODO: functionalise to add altconfs and not repeat method
entry = ProasisHits.objects.get(
refinement=obj,
crystal_name=obj.crystal_name,
altconf=conf)
if entry.modification_date < mod_date or not entry.strucid:
if entry.strucid:
proasis_api_funcs.delete_structure(
entry.strucid)
entry.strucid = None
entry.save()
if self.hit_directory in entry.pdb_file:
os.remove(entry.pdb_file)
if self.hit_directory in entry.mtz:
os.remove(entry.mtz)
if self.hit_directory in entry.two_fofc:
os.remove(entry.two_fofc)
if self.hit_directory in entry.fofc:
os.remove(entry.fofc)
entry.pdb_file = bound_conf
entry.modification_date = mod_date
entry.mtz = mtz[1]
entry.two_fofc = two_fofc[1]
entry.fofc = fofc[1]
entry.ligand_list = unique_ligands
entry.altconf = conf
entry.save()
# if there's not already an entry for that structure
else:
# if no altconfs
if not confs:
# create entry without an altconf
proasis_hit_entry = ProasisHits.objects.get_or_create(
refinement=obj,
crystal_name=obj.crystal_name,
pdb_file=bound_conf,
modification_date=mod_date,
mtz=mtz[1],
two_fofc=two_fofc[1],
fofc=fofc[1],
ligand_list=unique_ligands)
# if altconfs
if confs:
for conf in confs:
# create an entry for each altconf
# TODO: The pdb file will need to be edited later to pull out other altconfs of the same lig
proasis_hit_entry = ProasisHits.objects.get_or_create(
refinement=obj,
crystal_name=obj.crystal_name,
pdb_file=bound_conf,
modification_date=mod_date,
mtz=mtz[1],
two_fofc=two_fofc[1],
fofc=fofc[1],
ligand_list=unique_ligands,
altconf=conf)
dimple = Dimple.objects.filter(crystal_name=obj.crystal_name)
if dimple.count() == 1:
if dimple[0].reference and dimple[
0].reference.reference_pdb:
if os.path.isfile(dimple[0].reference.reference_pdb):
proasis_lead_entry = ProasisLeads.objects.get_or_create(
reference_pdb=dimple[0].reference)
else:
if ProasisLeads.objects.filter(
reference_pdb=dimple[0].reference).exists(
):
print('removing...')
proasis_lead_entry = ProasisLeads.objects.get(
reference_pdb=dimple[0].reference)
proasis_lead_entry.delete()
print(fail_count)
with self.output().open('w') as f:
f.write('')