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Add functionality to read CIF as unified before conversion #44

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Merged
Niolon merged 1 commit into from
Sep 26, 2025
Merged

Add functionality to read CIF as unified before conversion #44

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14 changes: 8 additions & 6 deletions qcrboxtools/cif/cif2cif/yaml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@
import yaml
from iotbx import cif

from ..entries import block_to_unified_keywords, entry_to_unified_keyword
from ..entries import block_to_unified_keywords, cif_to_unified_keywords, entry_to_unified_keyword
from ..merge import merge_cif_blocks
from ..read import cifdata_str_or_index, read_cif_safe
from ..trim import trim_cif_block
from ..uncertainties import split_su_block
from ..uncertainties import split_su_block, split_su_cif
from .base import cif_model_to_specific


Expand Down Expand Up @@ -543,13 +543,15 @@ def cif_text_to_specific_by_yml(input_cif_text: str, yml_path: Union[str, Path],

yml_input_settings = cif_input_entries_from_yml(yml_dict, command, parameter)

model = cif.reader(input_string=input_cif_text).model()
block, _ = cifdata_str_or_index(model, 0)
cif_model = cif.reader(input_string=input_cif_text).model()
cif_model = cif_to_unified_keywords(cif_model, yml_input_settings.custom_categories)
cif_model = split_su_cif(cif_model)
block, _ = cifdata_str_or_index(cif_model, 0)
block = block_to_unified_keywords(block, yml_input_settings.custom_categories)
block = split_su_block(block)

yml_input_settings = yml_entries_resolve_special(yml_input_settings, block)

cif_model = cif.reader(input_string=input_cif_text).model()

specific_cif_model = cif_model_to_specific(
cif_model,
yml_input_settings.required_entries,
Expand Down