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Simplify CIF helper functions in pdb_deposition.py #86

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Merged
tdudgeon merged 1 commit into from
Jun 10, 2026
Merged

Simplify CIF helper functions in pdb_deposition.py #86

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181 changes: 43 additions & 138 deletions src/pdbdepo/pdb_deposition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,24 +305,24 @@ def process_input(
structure_cif_doc.write_file(str(xtal_out_path / 'original.cif'))

# find and delete the _exptl loop as mmcifgen handles this
delete_pair_item(structure_cif_doc, '_exptl')
delete_cif_items(structure_cif_doc, '_exptl', pairs=True)

merge_entity(xtal_name, structure_cif_block0, mmcif_gen_entity_tags, mmcif_gen_entity_values)

# do some cleaning
delete_pair_item(structure_cif_doc, '_struct')
delete_pair_item(structure_cif_doc, '_struct_keywords')
delete_pair_item(structure_cif_doc, '_pdbx_database_status')
delete_loop_item(structure_cif_doc, '_exptl')
delete_loop_item(structure_cif_doc, '_reflns')
delete_cif_items(structure_cif_doc, '_struct', pairs=True)
delete_cif_items(structure_cif_doc, '_struct_keywords', pairs=True)
delete_cif_items(structure_cif_doc, '_pdbx_database_status', pairs=True)
delete_cif_items(structure_cif_doc, '_exptl', loops=True)
delete_cif_items(structure_cif_doc, '_reflns', loops=True)

refine_item = find_loop_item(structure_cif_block0, '_refine')
if refine_item:
# probably a loop if generated from refmac pdb file
model_refine_tags = list(refine_item.loop.tags)
model_refine_values = list(refine_item.loop.values)
refine_item.erase()
append_loop_items(
build_loop(
structure_cif_block0,
model_refine_tags,
model_refine_values,
Expand All @@ -333,11 +333,10 @@ def process_input(
# might be pairs if generated by buster
d = read_pairs(structure_cif_block0, '_refine', True)
if d:
model_refine_tags, model_refine_values = dict_to_tags_values(d)
append_loop_items(
build_loop(
structure_cif_block0,
model_refine_tags,
model_refine_values,
list(d.keys()),
list(d.values()),
mmcifgen_refine_tags,
mmcifgen_refine_values,
)
Expand Down Expand Up @@ -432,8 +431,18 @@ def process_input(
collection_info_diffrn_item = item
continue
structure_cif_block0.add_item(item)
combine_diffrn_loops(
collection_info_diffrn_item, mmcifgen_diffrn_tags, mmcifgen_diffrn_values, structure_cif_block0
collection_diffrn_tags = (
list(collection_info_diffrn_item.loop.tags) if collection_info_diffrn_item else None
)
collection_diffrn_values = (
list(collection_info_diffrn_item.loop.values) if collection_info_diffrn_item else None
)
build_loop(
structure_cif_block0,
collection_diffrn_tags,
collection_diffrn_values,
mmcifgen_diffrn_tags,
mmcifgen_diffrn_values,
)

# add in the _software section
Expand Down Expand Up @@ -600,20 +609,6 @@ def scrape_aimless_version(aimless_p):
return None


def dict_to_tags_values(d: dict):
"""
Convert a dict to lists of tags and values suitable for a loop
:param d:
:return:
"""
tags = []
values = []
for t, v in d.items():
tags.append(t)
values.append(v)
return tags, values


def read_mmcifgen_entity_data_and_erase(mmcifgen_block):
mmcifgen_entity_item = find_loop_item(mmcifgen_block, '_entity')

Expand Down Expand Up @@ -676,38 +671,26 @@ def collect_entity_values(tags, values, exclude_pairs=[]):
d = None
for i, value in enumerate(values):
if i % len(tags) == 0:
if d:
add_row_if_not_excluded(d, rows, exclude_pairs)
if d and not any(d.get(k) == v for k, v in exclude_pairs):
rows.append(d)
d = {}
tag = tags[i % len(tags)]
d[tag] = value
add_row_if_not_excluded(d, rows, exclude_pairs)
if d and not any(d.get(k) == v for k, v in exclude_pairs):
rows.append(d)
return rows


def add_row_if_not_excluded(d, rows, exclude_pairs):
is_excluded = False
for exclude in exclude_pairs:
if d.get(exclude[0]) == exclude[1]:
is_excluded = True
if not is_excluded:
rows.append(d)


def delete_pair_item(doc, prefix):
def delete_cif_items(doc, prefix, *, pairs: bool = False, loops: bool = False):
for block in doc:
for item in block:
if item.pair is not None:
if item.pair[0].startswith(prefix + '.'):
if pairs:
for item in block:
if item.pair is not None and item.pair[0].startswith(prefix + '.'):
item.erase()


def delete_loop_item(doc, prefix):
for block in doc:
item = find_loop_item(block, prefix)
if item:
# print('erasing', item)
item.erase()
if loops:
loop_item = find_loop_item(block, prefix)
if loop_item:
loop_item.erase()


def find_loop_item(block, prefix):
Expand Down Expand Up @@ -737,94 +720,16 @@ def read_pairs(block, prefix, erase: bool):
return d


def append_loop_items(block_to_add_to: cif.Block, tags1, values1, tags2, values2):
"""Simplistic approach that merges two 1-row loops, add the data from item2 into item1
def build_loop(block: cif.Block, tags1, values1, tags2, values2):
"""Create a single-row loop in block by concatenating two tag/value lists.

:param block_to_add_to: the block the loop needs to be added to
:param tags1: the first tags to append
:param values1: the first values to append
:param tags1: the second tags to append
:param values1: the second values to append
:return:
# gemmi does not allow appending to an existing loop's tags/values in place
Either argument pair may be None (treated as empty).
"""

# its seems that you can't just append to the existing loop's tags and value, you have to create a new loop
combined_tags = []
combined_values = []
combined_tags.extend(tags1)
combined_tags.extend(tags2)
combined_values.extend(values1)
combined_values.extend(values2)

loop = block_to_add_to.init_loop('', combined_tags)

loop.add_row(combined_values)


def append_data_to_values(tags1, values1, tags2, values2, ordinal_col):
"""
Append the data is tags/values2 to that in tags/values1, ensuring the order is correct
If no value is found then ? is written
:param tags1:
:param values1:
:param tags2:
:param values2:
:return: A list of lists of the values
"""

if ordinal_col:
ordinal_idx = tags1.index(ordinal_col)
else:
ordinal_idx = None

combined_values = []
combined_values.append(values1)
n = len(tags2)
dicts = []
d = None
ordinal_count = len(combined_values)
for i, val in enumerate(values2):
ordinal_count += 1
if i % n == 0:
d = {}
dicts.append(d)
if i % n == ordinal_idx:
d[tags2[i % n]] = str(ordinal_count)
else:
d[tags2[i % n]] = val

for d in dicts:
l = []
combined_values.append(l)
for tag1 in tags1:
if tag1 in d:
l.append(d[tag1])
else:
l.append('?')

return tags1, combined_values


def combine_diffrn_loops(collection_info_item: cif.Item, tags_list: list, values_list: list, into: cif.Block):
tags = []
if collection_info_item:
tags.extend(collection_info_item.loop.tags)
if tags_list:
tags.extend(tags_list)
values = []
if collection_info_item:
values.extend(collection_info_item.loop.values)
if values_list:
values.extend(values_list)
if tags:
new_loop = into.init_loop('', tags)
new_loop.add_row(values)


def prune_loop(loop, retain):
for tag in loop.tags:
if not tag.startswith(retain):
loop.remove_column(tag)
combined_tags = list(tags1 or []) + list(tags2 or [])
combined_values = list(values1 or []) + list(values2 or [])
if combined_tags:
block.init_loop('', combined_tags).add_row(combined_values)


def validate_structure_cif_doc(doc: cif.Document, xtal_name: str = '') -> list[str]:
Expand All @@ -851,7 +756,7 @@ def validate_structure_cif_doc(doc: cif.Document, xtal_name: str = '') -> list[s
if not found:
issues.append(prefix + f'required pair category {cat} not found')

# 2. Duplicate tags in any loop (catches naive concatenation bugs in append_loop_items)
# 2. Duplicate tags in any loop (catches naive concatenation bugs in build_loop)
for item in block:
if item.loop is not None:
tags = item.loop.tags
Expand Down
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