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Clean repo for publication #2

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This commit is contained in:
Jérôme Tubiana
2022-05-25 15:27:58 +03:00
parent 7c13a16680
commit 4557849375
25 changed files with 30 additions and 174 deletions
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6
preprocessing/PDBio.py
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@@ -129,7 +129,7 @@ class myPDBList(Bio.PDB.PDBList):
url = (self.pdb_server + '/pub/pdb/data/biounit/PDB/divided/%s/%s' %
(code[1:3], archive_fn))
elif file_format == 'biounit_mmCif':
url = (self.pdb_server + '/pub/pdb/data/biounit/mmCIF/divided/%s/%s' %
url = (self.pdb_server + '/pub/pdb/data/assemblies/mmCIF/divided/%s/%s' %
(code[1:3], archive_fn))
else:
url = ('http://mmtf.rcsb.org/v1.0/full/%s' % code)
@@ -274,10 +274,10 @@ def getPDB(identifier_string,biounit=True,structures_folder=structures_folder,ve
pdb_downloader = myPDBList(verbose=verbose)
if biounit:
location = pdb_downloader.retrieve_pdb_file(
structure_id, pdir=structures_folder, file_format='biounit_mmCif')
structure_id, pdir=structures_folder, file_format='biounit')
if location is None:
location = pdb_downloader.retrieve_pdb_file(
structure_id, pdir=structures_folder, file_format='biounit')
structure_id, pdir=structures_folder, file_format='biounit_mmCif')
else:
location = pdb_downloader.retrieve_pdb_file(
structure_id, pdir=structures_folder, file_format='mmCif')