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update af2 versions to latest #121

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merged 6 commits into from
Apr 10, 2023
Merged

update af2 versions to latest #121

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d9e92ff
update af2 versions to latest
a-r-j Apr 4, 2023
25c2dd1
Merge branch 'main' into main
a-r-j Apr 4, 2023
039a6a0
change tests to deal with af2 version deprecation
a-r-j Apr 6, 2023
20b8254
add new test files
a-r-j Apr 6, 2023
bf61511
Merge branch 'main' of https://www.github.com/a-r-j/biopandas into main
a-r-j Apr 6, 2023
e042fbb
test fixes
a-r-j Apr 6, 2023
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16 changes: 6 additions & 10 deletions biopandas/mmcif/pandas_mmcif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ def fetch_mmcif(self, pdb_code: Optional[str] = None, uniprot_id: Optional[str]

source : str
The source to retrieve the structure from
(`"pdb"`, `"alphafold2-v1"`, `"alphafold2-v2"` or `"alphafold2-v3"`). Defaults to `"pdb"`.
(`"pdb"`, `"alphafold2-v3"` or `"alphafold2-v4"`). Defaults to `"pdb"`.

Returns
---------
Expand All @@ -95,7 +95,7 @@ def fetch_mmcif(self, pdb_code: Optional[str] = None, uniprot_id: Optional[str]
invalid_input_identifier_2 = pdb_code is not None and uniprot_id is not None
invalid_input_combination_1 = uniprot_id is not None and source == "pdb"
invalid_input_combination_2 = pdb_code is not None and source in {
"alphafold2-v1", "alphafold2-v2", "alphafold2-v3"}
"alphafold2-v3", "alphafold2-v4"}

if invalid_input_identifier_1 or invalid_input_identifier_2:
raise ValueError(
Expand All @@ -110,19 +110,15 @@ def fetch_mmcif(self, pdb_code: Optional[str] = None, uniprot_id: Optional[str]

if source == "pdb":
self.mmcif_path, self.mmcif_text = self._fetch_mmcif(pdb_code)
elif source == "alphafold2-v1":
af2_version = 1
self.mmcif_path, self.mmcif_text = self._fetch_af2(
uniprot_id, af2_version)
elif source == "alphafold2-v2":
af2_version = 2
self.mmcif_path, self.mmcif_text = self._fetch_af2(uniprot_id, af2_version)
elif source == "alphafold2-v3":
af2_version = 3
self.mmcif_path, self.mmcif_text = self._fetch_af2(uniprot_id, af2_version)
elif source == "alphafold2-v4":
af2_version = 4
self.mmcif_path, self.mmcif_text = self._fetch_af2(uniprot_id, af2_version)
else:
raise ValueError(f"Invalid source: {source}."
" Please use one of 'pdb', 'alphafold2-v1', 'alphafold2-v2' or 'alphafold2-v3.")
" Please use one of 'pdb', 'alphafold2-v3' or 'alphafold2-v4'.")

self._df = self._construct_df(text=self.mmcif_text)
return self
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