def upgrade_chemcomps_and_create_entities_where_needed(
entry: pynmrstar.Entry, schema: pynmrstar.Schema) -> None:
""" Generates an entity saveframe for each chem comp saveframe. """
# Store a mapping of chem_comp name to new entity name
chem_comp_entity_map = {}
need_linking = []
linked_items = set(entry.get_tag('_Entity_assembly.Entity_label'))
for linked_item in linked_items:
# Remove the '$' from the beginning of the tag
linked_saveframe = entry.get_saveframe_by_name(linked_item[1:])
if linked_saveframe.category == 'chem_comp':
need_linking.append(linked_saveframe)
need_linking = _sort_saveframes(list(need_linking))
# Create the entity for the chem_comps that need linking
for saveframe in need_linking:
if 'PDB_code' in saveframe and saveframe['PDB_code'][
0] not in pynmrstar.definitions.NULL_VALUES:
try:
chemcomp_entry = pynmrstar.Entry.from_database(
'chemcomp_' + saveframe['PDB_code'][0].upper())
except IOError:
saveframe['Note_to_annotator'] = 'Attempted to automatically look up the chem_comp and entity' \
' from the PDB_code, but it isn\'t valid. Please rectify.'
chem_comp_entity_map[
saveframe.name] = create_entity_for_saveframe_and_attach(
entry, saveframe, schema)
continue
chemcomp_saveframe = chemcomp_entry.get_saveframes_by_category(
'chem_comp')[0]
chemcomp_saveframe['Paramagnetic'] = saveframe['Paramagnetic'][0]
chemcomp_saveframe['Aromatic'] = saveframe['Aromatic'][0]
if 'details' in saveframe:
chemcomp_saveframe['Details'] = saveframe['Details'][0]
new_entity = chemcomp_entry.get_saveframes_by_category('entity')[0]
new_entity['Paramagnetic'] = saveframe['Paramagnetic'][0]
# Replace the existing saveframes with the new ones (first rename, to preserve the links)
entry.rename_saveframe(saveframe.name, chemcomp_saveframe.name)
entry[chemcomp_saveframe.name] = chemcomp_saveframe
entry.add_saveframe(new_entity)
chem_comp_entity_map[saveframe.name] = new_entity.name
else:
chem_comp_entity_map[
saveframe.name] = create_entity_for_saveframe_and_attach(
entry, saveframe, schema)
# Update the entity_assembly loop in each assembly to point to the entity rather than the chem_comp
for each_entity_assembly in entry.get_loops_by_category(
'_Entity_assembly'):
entity_label_col = each_entity_assembly.tag_index('Entity_label')
for row in each_entity_assembly.data:
if row[entity_label_col][1:] in chem_comp_entity_map:
row[entity_label_col] = f"${chem_comp_entity_map[row[entity_label_col][1:]]}"
def create_entity_for_saveframe_and_attach(parent_entry: pynmrstar.Entry,
saveframe: pynmrstar.Saveframe,
schema: pynmrstar.Schema) -> str:
""" For a chem_comp, create an entity for it and attach it to the entry. Return the new entry name. """
next_entity: int = max([
int(x.name.split('_')[-1])
for x in parent_entry.get_saveframes_by_category('entity')
]) + 1
new_entity = pynmrstar.Saveframe.from_template(
'entity',
name='entity_%s' % next_entity,
schema=schema,
all_tags=False,
entry_id=parent_entry.entry_id)
new_entity.loops = []
new_entity['Name'] = saveframe['Name'][0]
new_entity['Paramagnetic'] = saveframe['Paramagnetic'][0]
new_entity['Type'] = 'non-polymer'
new_entity['Ambiguous_conformational_states'] = 'no'
new_entity['Nstd_chirality'] = 'no'
new_entity['Nstd_linkage'] = 'no'
new_entity['Thiol_state'] = 'not available'
new_entity.add_missing_tags(schema=schema)
comp_index_loop: pynmrstar.Loop = pynmrstar.Loop.from_scratch(
'_Entity_comp_index')
comp_index_loop.add_tag(['ID', 'Comp_ID', 'Comp_label', 'Entry_ID'])
comp_index_loop.add_data([
1, saveframe['ID'][0], '$' + saveframe['Sf_framecode'][0],
parent_entry.entry_id
])
comp_index_loop.add_missing_tags(schema=schema)
if '_Entity_comp_index' in new_entity:
del new_entity['_Entity_comp_index']
new_entity.add_loop(comp_index_loop)
parent_entry.add_saveframe(new_entity)
return new_entity.name
def merge_entries(template_entry: pynmrstar.Entry,
existing_entry: pynmrstar.Entry,
new_schema: pynmrstar.Schema,
preserve_entry_information: bool = False):
""" By default it does not copy over the entry information - but it should for cloned entries, so the
preserve_entry_information boolean is available."""
existing_entry.normalize()
# Rename the saveframes in the uploaded entry before merging them
for category in existing_entry.category_list:
for x, saveframe in enumerate(
_sort_saveframes(
existing_entry.get_saveframes_by_category(category))):
# Set the "Name" tag if it isn't already set
if (saveframe.tag_prefix + '.name').lower() in new_schema.schema:
try:
saveframe.add_tag('Name',
saveframe['sf_framecode'][0].replace(
"_", " "),
update=False)
except ValueError:
pass
new_name = "%s_%s" % (saveframe.category, x + 1)
if saveframe.name != new_name:
existing_entry.rename_saveframe(saveframe.name, new_name)
for category in existing_entry.category_list:
delete_saveframes = template_entry.get_saveframes_by_category(category)
for saveframe in delete_saveframes:
if saveframe.category == "entry_interview":
continue
del template_entry[saveframe]
for saveframe in existing_entry.get_saveframes_by_category(category):
# Don't copy over the entry interview at all
if saveframe.category == "entry_interview":
continue
# If the saveframe isn't in the dictionary, or has some other issue, better to skip it
# than to crash
try:
new_saveframe = pynmrstar.Saveframe.from_template(
category,
name=saveframe.name,
entry_id=template_entry.entry_id,
default_values=True,
schema=new_schema,
all_tags=True)
except ValueError:
continue
frame_prefix_lower = saveframe.tag_prefix.lower()
# Don't copy the tags from entry_information
if saveframe.category != "entry_information" or preserve_entry_information:
for tag in saveframe.tags:
lower_tag = tag[0].lower()
if lower_tag not in [
'sf_category', 'sf_framecode', 'id', 'entry_id',
'nmr_star_version', 'original_nmr_star_version',
'atomic_coordinate_file_name',
'atomic_coordinate_file_syntax',
'constraint_file_name'
]:
fqtn = frame_prefix_lower + '.' + lower_tag
if fqtn in new_schema.schema or lower_tag == '_deleted':
new_saveframe.add_tag(tag[0], tag[1], update=True)
for loop in saveframe.loops:
# Don't copy the experimental data loops
if loop.category == "_Upload_data":
continue
lower_tags = [_.lower() for _ in loop.tags]
try:
tags_to_pull = [
_ for _ in new_saveframe[loop.category].tags
if _.lower() in lower_tags
]
# Skip loops that don't exist in the schema used
except KeyError:
continue
filtered_original_loop = loop.filter(tags_to_pull)
filtered_original_loop.add_missing_tags(schema=new_schema,
all_tags=True)
new_saveframe[
filtered_original_loop.category] = filtered_original_loop
template_entry.add_saveframe(new_saveframe)
# Strip off any loop Entry_ID tags from the original entry
for saveframe in template_entry.frame_list:
for loop in saveframe:
for tag in loop.tags:
fqtn = (loop.category + "." + tag).lower()
try:
tag_schema = new_schema.schema[fqtn]
if tag_schema['Natural foreign key'] == '_Entry.ID':
loop[tag] = [None] * len(loop[tag])
except KeyError:
pass