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Clean repo for publication

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This commit is contained in:
Jérôme Tubiana
2022-05-25 11:30:35 +03:00
parent 24d41192aa
commit 7c13a16680
69 changed files with 1627 additions and 10633 deletions
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25
preprocessing/PDBio.py
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@@ -136,7 +136,7 @@ class myPDBList(Bio.PDB.PDBList):
elif is_uniprot:
assert file_format in ['pdb','mmCif']
url = self.alphafold_server + '/files/AF-%s-F1-model_v1%s'%(code, '.pdb' if file_format == 'pdb' else '.cif')
url = self.alphafold_server + '/files/AF-%s-F1-model_v2%s'%(code, '.pdb' if file_format == 'pdb' else '.cif')
archive_fn = url.split('/')[-1]
else:
return
@@ -175,7 +175,8 @@ class myPDBList(Bio.PDB.PDBList):
urlcleanup()
urlretrieve(url, filename)
except IOError:
print("Desired structure doesn't exists")
if self._verbose:
print("Desired structure doesn't exists")
return
else:
if is_pdb:
@@ -255,15 +256,15 @@ def getPDB(identifier_string,biounit=True,structures_folder=structures_folder,ve
if is_pdb:
pdb_id = structure_id.lower()
if biounit:
location1 = structures_folder + 'pdb' + pdb_id + '.bioent'
location2 = structures_folder + pdb_id + '_bioentry.cif'
location2 = structures_folder + 'pdb' + pdb_id + '.bioent'
location1 = structures_folder + pdb_id + '_bioentry.cif'
else:
location1 = structures_folder + 'pdb' + pdb_id + '.ent'
location2 = structures_folder + pdb_id + '.cif' # New§ format
location2 = structures_folder + 'pdb' + pdb_id + '.ent'
location1 = structures_folder + pdb_id + '.cif' # New§ format
else:
uniprot_id = structure_id
location1 = structures_folder + 'AF_' + uniprot_id + '.pdb'
location2 = structures_folder + 'AF_' + uniprot_id + '.cif'
location2 = structures_folder + 'AF_' + uniprot_id + '.pdb'
location1 = structures_folder + 'AF_' + uniprot_id + '.cif'
if os.path.exists(location1):
location = location1
@@ -273,16 +274,16 @@ 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')
structure_id, pdir=structures_folder, file_format='biounit_mmCif')
if location is None:
location = pdb_downloader.retrieve_pdb_file(
structure_id, pdir=structures_folder, file_format='biounit_mmCif')
structure_id, pdir=structures_folder, file_format='biounit')
else:
location = pdb_downloader.retrieve_pdb_file(
structure_id, pdir=structures_folder, file_format='pdb')
structure_id, pdir=structures_folder, file_format='mmCif')
if location is None:
location = pdb_downloader.retrieve_pdb_file(
structure_id, pdir=structures_folder, file_format='mmCif')
structure_id, pdir=structures_folder, file_format='pdb')
return location,chain