Spaces:
Sleeping
Sleeping
Commit
·
26f6c21
1
Parent(s):
3c047f4
Update code/pdb_featureVector.py
Browse files
code/pdb_featureVector.py
CHANGED
@@ -226,12 +226,15 @@ def pdb(input_set, mode, impute):
|
|
226 |
existing_pdb = [str(i) for i in existing_pdb]
|
227 |
existing_pdb = [i.split('/')[-1].split('.')[0].lower() for i in existing_pdb]
|
228 |
cnt = 0
|
|
|
229 |
for search in pdbs:
|
230 |
st.write('PDBS', search)
|
231 |
|
232 |
try:
|
233 |
if search.lower() not in existing_pdb:
|
|
|
234 |
file = pdbl.retrieve_pdb_file(search, pdir=Path(path_to_output_files / 'pdb_structures'), file_format="pdb")
|
|
|
235 |
else:
|
236 |
print('PDB structure file exists..')
|
237 |
for filename in list(Path(path_to_output_files / 'pdb_structures').glob("*")):
|
@@ -250,6 +253,7 @@ def pdb(input_set, mode, impute):
|
|
250 |
resolution_method = parser.get_structure(search, file)
|
251 |
for record in SeqIO.parse(file, "pdb-seqres"):
|
252 |
if record.dbxrefs[0].split(':')[0] == 'UNP':
|
|
|
253 |
pdb_fasta.at[index, 'pdbID'] = record.id.split(':')[0]
|
254 |
pdb_fasta.at[index, 'chain'] = record.id.split(':')[1]
|
255 |
pdb_fasta.at[index, 'pdbSequence'] = str(record.seq)
|
@@ -259,6 +263,7 @@ def pdb(input_set, mode, impute):
|
|
259 |
pdb_info.at[index, 'resolution'] = resolution_method.header['resolution']
|
260 |
index += 1
|
261 |
except:
|
|
|
262 |
IndexError
|
263 |
pdb_info.at[index, 'uniprotID'] = 'nan'
|
264 |
pdb_info.at[index, 'pdbID'] = 'nan'
|
|
|
226 |
existing_pdb = [str(i) for i in existing_pdb]
|
227 |
existing_pdb = [i.split('/')[-1].split('.')[0].lower() for i in existing_pdb]
|
228 |
cnt = 0
|
229 |
+
st.write('existing_pdb', existing_pdb)
|
230 |
for search in pdbs:
|
231 |
st.write('PDBS', search)
|
232 |
|
233 |
try:
|
234 |
if search.lower() not in existing_pdb:
|
235 |
+
st.write(Path(path_to_output_files / 'pdb_structures'))
|
236 |
file = pdbl.retrieve_pdb_file(search, pdir=Path(path_to_output_files / 'pdb_structures'), file_format="pdb")
|
237 |
+
st.write(file)
|
238 |
else:
|
239 |
print('PDB structure file exists..')
|
240 |
for filename in list(Path(path_to_output_files / 'pdb_structures').glob("*")):
|
|
|
253 |
resolution_method = parser.get_structure(search, file)
|
254 |
for record in SeqIO.parse(file, "pdb-seqres"):
|
255 |
if record.dbxrefs[0].split(':')[0] == 'UNP':
|
256 |
+
st.write('RECORD', record)
|
257 |
pdb_fasta.at[index, 'pdbID'] = record.id.split(':')[0]
|
258 |
pdb_fasta.at[index, 'chain'] = record.id.split(':')[1]
|
259 |
pdb_fasta.at[index, 'pdbSequence'] = str(record.seq)
|
|
|
263 |
pdb_info.at[index, 'resolution'] = resolution_method.header['resolution']
|
264 |
index += 1
|
265 |
except:
|
266 |
+
st.write('ERROR INDEX')
|
267 |
IndexError
|
268 |
pdb_info.at[index, 'uniprotID'] = 'nan'
|
269 |
pdb_info.at[index, 'pdbID'] = 'nan'
|