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Updated docs
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‎package/MDAnalysis/fetch/fetchers.py‎

Lines changed: 69 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -144,7 +144,7 @@ class StaticFetcher(_BaseFetcher):
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Attributes
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----------
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cache_path : pathlib.Path or ``None``
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cache_path : pathlib.Path
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Path to the cache directory.
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hash : str
@@ -225,16 +225,20 @@ def fetch(
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Examples
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--------
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Download a single CIF file from the RCSB Protein Data Bank.
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>>> StaticFetcher().fetch(file_name="1AKE.cif",
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base_url="https://files.wwpdb.org/download/")
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'./MDAnalysis_pdbs/1AKE.cif'
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.. code-block:: pycon
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Download multiple CIF files from the RCSB Protein Data Bank.
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>>> StaticFetcher().fetch(file_name=["1AKE.cif", "4AKE.cif"],
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base_url="https://files.wwpdb.org/download/")
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['./MDAnalysis_pdbs/1AKE.cif', './MDAnalysis_pdbs/4AKE.cif']
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Download a single CIF file from the RCSB Protein Data Bank.
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>>> StaticFetcher().fetch(file_name="1AKE.cif",
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base_url="https://files.wwpdb.org/download/")
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'./MDAnalysis_pdbs/1AKE.cif'
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Download multiple CIF files from the RCSB Protein Data Bank.
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>>> StaticFetcher().fetch(file_name=["1AKE.cif", "4AKE.cif"],
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base_url="https://files.wwpdb.org/download/")
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['./MDAnalysis_pdbs/1AKE.cif', './MDAnalysis_pdbs/4AKE.cif']
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Notes
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-----
@@ -345,6 +349,10 @@ def append_registry(self, db_path, files, write_duplicate=False):
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files : iterable of str or path-like
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File names or paths for cached files to append to the registry. Relative
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paths are interpreted relative to :attr:`cache_path`.
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write_duplicate : bool
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If set to True, append_registry will write the file and its hash to the registry
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regardless of the existing presence of a entry in the registry. Default behavior is
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False.
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Returns
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-------
@@ -426,24 +434,25 @@ def check_registry(self, db_path, files=None, ignore=None):
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Example
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-------
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.. code-block:: python
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>>> files = {
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... "file1.txt": "Molecular \\n",
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... "file2.txt": "Dynamics. \\n",
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... "file3.txt": "Analysis. \\n"
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... }
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>>> for filename, content in files.items():
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... with open(filename, "w") as f:
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... f.write(content)
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...
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>>> fetcher = StaticFetcher()
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>>> fetcher.write_registry(
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... "file_1_2_and_3_hash.txt",
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... files=["file1.txt"],
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... )
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>>> fetcher.check_registry("file_1_2_and_3_hash.txt")
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[Path('./MDAnalysis_pdbs/file3.txt'), Path('./MDAnalysis_pdbs/file2.txt')]
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>>> fetcher.check_registry("file_1_2_and_3_hash.txt", ignore=["file2.txt"])
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[Path('./MDAnalysis_pdbs/file3.txt')]
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>>> files = {
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... "file1.txt": "Molecular \\n",
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... "file2.txt": "Dynamics. \\n",
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... "file3.txt": "Analysis. \\n"
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... }
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>>> for filename, content in files.items():
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... with open(filename, "w") as f:
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... f.write(content)
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...
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>>> fetcher = StaticFetcher()
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>>> fetcher.write_registry(
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... "file_1_2_and_3_hash.txt",
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... files=["file1.txt"],
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... )
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>>> fetcher.check_registry("file_1_2_and_3_hash.txt")
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[Path('./MDAnalysis_pdbs/file3.txt'), Path('./MDAnalysis_pdbs/file2.txt')]
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>>> fetcher.check_registry("file_1_2_and_3_hash.txt", ignore=["file2.txt"])
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[Path('./MDAnalysis_pdbs/file3.txt')]
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Notes
@@ -496,22 +505,22 @@ def read_registry(self, db_path):
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-------
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.. code-block:: python
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>>> files = {
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... "file1.txt": "Molecular \\n",
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... "file2.txt": "Dynamics. \\n",
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... }
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>>> for filename, content in files.items():
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... with open(filename, "w") as f:
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... f.write(content)
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...
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>>> fetcher = StaticFetcher()
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>>> fetcher.write_registry(
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... "file_1_and_2_hash.txt",
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... ["file1.txt", "file2.txt"],
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... )
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>>> fetcher.read_registry("file_1_and_2_hash.txt")
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{'file1.txt': 'sha256:2da169c5aae36a823c202da49fb11935b76277efcb5cd42a4cf238ddda2a9b20',
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'file2.txt': 'sha256:3a0dbd9e2abc4a7bbae6adfe92e2858218135926dacd4a7d3fb4ca2dbdbe457a'}
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>>> files = {
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... "file1.txt": "Molecular \\n",
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... "file2.txt": "Dynamics. \\n",
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... }
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>>> for filename, content in files.items():
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... with open(filename, "w") as f:
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... f.write(content)
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...
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>>> fetcher = StaticFetcher()
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>>> fetcher.write_registry(
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... "file_1_and_2_hash.txt",
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... ["file1.txt", "file2.txt"],
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... )
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>>> fetcher.read_registry("file_1_and_2_hash.txt")
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{'file1.txt': 'sha256:2da169c5aae36a823c202da49fb11935b76277efcb5cd42a4cf238ddda2a9b20',
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'file2.txt': 'sha256:3a0dbd9e2abc4a7bbae6adfe92e2858218135926dacd4a7d3fb4ca2dbdbe457a'}
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Notes
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-----
@@ -557,22 +566,23 @@ def write_registry(self, db_path, files, mode="w"):
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Example
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-------
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.. code-block:: python
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>>> files = {
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... "file1.txt": "Molecular \\n",
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... "file2.txt": "Dynamics. \\n",
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... }
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>>> for filename, content in files.items():
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... with open(filename, "w") as f:
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... f.write(content)
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...
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>>> fetcher = StaticFetcher()
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>>> fetcher.write_registry(
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... "file_1_and_2_hash.txt",
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... ["file1.txt", "file2.txt"],
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... )
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>>> Path("file_1_and_2_hash.txt").read_text()
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file1.txt sha256:2da169c5aae36a823c202da49fb11935b76277efcb5cd42a4cf238ddda2a9b20
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file2.txt sha256:3a0dbd9e2abc4a7bbae6adfe92e2858218135926dacd4a7d3fb4ca2dbdbe457a
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>>> files = {
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... "file1.txt": "Molecular \\n",
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... "file2.txt": "Dynamics. \\n",
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... }
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>>> for filename, content in files.items():
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... with open(filename, "w") as f:
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... f.write(content)
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...
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>>> fetcher = StaticFetcher()
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>>> fetcher.write_registry(
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... "file_1_and_2_hash.txt",
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... ["file1.txt", "file2.txt"],
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... )
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>>> Path("file_1_and_2_hash.txt").read_text()
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file1.txt sha256:2da169c5aae36a823c202da49fb11935b76277efcb5cd42a4cf238ddda2a9b20
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file2.txt sha256:3a0dbd9e2abc4a7bbae6adfe92e2858218135926dacd4a7d3fb4ca2dbdbe457a
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Notes
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-----

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