def retrieve_cif_list():
server = PDBList(server='ftp://ftp.wwpdb.org', pdb='input_files', obsolete_pdb=None ,verbose=True)
pdb_list = open('input_files/protlist.txt','r')
content = pdb_list.read().split()
pdb_list.close()
server.download_pdb_files(content,pdir="input_files/cif",file_format='mmCif', overwrite=True,obsolete= False)
def build_xtalstable(dbpathstr, sourcedbpathstrs, pdbformat='cif'):
dbpath = Path(dbpathstr)
today = datetime.date.today()
todaystr = f'{today.year}-{today.month:02d}-{today.day:02d}'
conn = seqdbutils.gracefuldbopen(dbpath)
xtaldirpath = Path(dbpath).parent / 'Xtals'
if not xtaldirpath.exists():
os.mkdir(xtaldirpath)
c = conn.cursor()
c.execute(
'''CREATE TABLE IF NOT EXISTS XTALS (pdbid text, acc text, srcdb text,dldate text,
relpath text, pdbformat text, dlsuccess int, obsolete int)''')
pdbl = PDBList()
cxRE = re.compile('([A-Za-z0-9]{4})\[')
#by default folder containing xtals is named 'xtals' and in same directory as xtalsdb
for srcdbpathstr in sourcedbpathstrs:
srcdbpath = Path(srcdbpathstr)
srcdbstr = srcdbpath.name
src_conn = seqdbutils.gracefuldbopen(srcdbpath)
seqdbutils.check_tables_exist(src_conn, ['CAZYSEQDATA'])
src_c = src_conn.cursor()
src_c.execute(
'SELECT acc,pdbids FROM CAZYSEQDATA WHERE pdbids NOT NULL')
pdbrows = src_c.fetchall()
dbpdbs = []
dbaccs = []
for pdbrow in pdbrows:
pdbentry = pdbrow['pdbids']
accentry = pdbrow['acc']
pdbs = cxRE.findall(pdbentry)
dbaccs.extend([accentry for _ in range(len(pdbs))])
dbpdbs.extend(pdbs)
#dbpdbs=['4IM4']
pdbl.download_pdb_files(dbpdbs, pdir=xtaldirpath) #,obsolete=True)
for acc, pdb in zip(dbaccs, dbpdbs):
rel_pdbpath = xtaldirpath / f'{pdb}.cif'
download_success = os.path.exists(rel_pdbpath)
str_relpath = str(rel_pdbpath)
c.execute(
'''SELECT COUNT(*) FROM XTALS WHERE pdbid=(?) AND dlsuccess=(?)''',
(pdb, 1))
already_downloaded = c.fetchone()[0]
if already_downloaded:
continue
c.execute(
'''SELECT COUNT(*) FROM XTALS WHERE pdbid=(?) AND dlsuccess=(?)''',
(pdb, 0))
previously_failed = c.fetchone()[0]
if previously_failed:
if download_success:
print(f'new download of previously failed {pdb}')
c.execute(
'''UPDATE XTALS SET dldate = (?), dlsuccess = (?) WHERE pdbid=(?)''',
(todaystr, 1, pdb))
continue
c.execute('''INSERT INTO XTALS VALUES (?,?,?,?,?,?,?,?)''',\
(pdb,acc,srcdbstr,todaystr,str_relpath,pdbformat,download_success,None))
conn.commit()
src_conn.close()
conn.close()
def download_pdb(pdb_id, pdbs_path):
"""Downloads a pdb file
Parameters
----------
pdb_id : str
pdb id
pdbs_path: str, optional
path of folder containing the pdbs (default is "pdbs")
"""
pdbl = PDBList(obsolete_pdb=True)
pdbl.download_pdb_files(pdb_id, file_format="pdb", pdir=pdbs_path)
def download_pdb_files(FASTA_FILE, PDB_OUTPUT):
"""Downloads all pdb files from a given fasta file with pdb ids
Parameters
----------
FASTA_FILE : str
The file location of the .fasta
PDB_OUTPUT : str
The directory for pdb outputs
"""
# get protein ids
records = list(SeqIO.parse(FASTA_FILE, "fasta"))
protein_ids = set([x.id[:-1] for x in records])
# download pdbs
pdbl = PDBList()
pdbl.download_pdb_files(protein_ids, pdir=PDB_OUTPUT)
def obtain_pdb(dataset):
# download the pdb set
pdb_set = list(set(dataset['pdb']))
if not os.path.exists('./PDB'):
os.mkdir('./PDB')
PDB_dl_handle = PDBList(verbose=False)
PDB_dl_handle.download_pdb_files(pdb_codes=pdb_set,
file_format='pdb',
pdir='./PDB')
# download the fasta set
if not os.path.exists('./FASTA'):
os.mkdir('./FASTA')
for item in pdb_set:
if not os.path.exists("./FASTA/{}.fasta".format(item)):
os.system(
"""wget -q -O - "https://www.rcsb.org/pdb/download/viewFastaFiles.do?structureIdList={}&compressionType=uncompressed" > ./FASTA/{}.fasta"""
.format(item, item))
time.sleep(0.1)
assert (os.stat("./FASTA/{}.fasta".format(item)).st_size !=
0), 'Download Failed, Empty File generated.'
if i != ',':
outputlist.append(pdbID + str(i))
#string functions together and generate output in folders organized by taxID
for taxID in taxidlist:
os.mkdir(str(taxID))
os.chdir(str(taxID))
outfilename = str(taxID) + '.txt'
pdbids = []
query(taxID)
initial_num_entries = len(pdbids)
pdbl = PDBList()
cwd = os.getcwd()
pdbl.download_pdb_files(pdbids,
obsolete=False,
pdir=cwd,
file_format='mmCif')
for pdbID in pdbids:
try:
filter_bad_strc(pdbID)
except:
print "No pdb entries for protein: " + str(pdbID)
mainlist = []
for pdbID in pdbids:
fetch(pdbID)
filteredpdbIDs = []
filter_redundant_strc(mainlist)
outputlist = []
for pdbID in filteredpdbIDs:
try:
get_chains(pdbID)
pdbs_path = os.path.join(current_path, 'pdb')
if pdbs_path not in glob(os.path.join(current_path, '*')):
os.mkdir(pdbs_path)
with open(os.path.join(current_path, 'pdbs.txt'), 'r') as f:
pdbs = [pdb[:-1] for pdb in f]
if len(pdbs) == 1:
pdb_id = pdbs[0]
else:
pdb_id = current_path.rsplit('/', 1)[1]
pdbl = PDBList(obsolete_pdb=True)
if not glob(os.path.join(pdbs_path, '*')):
pdbl.download_pdb_files(pdbs, file_format='pdb', pdir=pdbs_path)
#initialize databases to report
database_1 = []
database_2 = []
pdbs = glob(os.path.join(pdbs_path, '*'))
for pdb in pdbs:
mol = bg.Pmolecule(pdb)
net = mol.network()
# take only selected positions:
if selected_positions:
for node in list(net.nodes):
pos = int(node[1::])
def retrieve_pdb_files(pdb_codes: List[str], pdb_data_dir: Union[Path, str], file_format: str = "mmCif"):
pdbl = PDBList(server="ftp://ftp.wwpdb.org", pdb=pdb_data_dir)
filenames = pdbl.download_pdb_files(pdb_codes, file_format=file_format)
return filenames
from Bio.PDB import PDBList
##this script may download pdb files for a list of pdb codes.
if len(sys.argv) < 3:
print 'python DownloadPDBs.py pdbcodeListFile format [ResDir]'
print '\tpdbcodeListFile: a file of PDB IDs, in upper or lower case'
print '\tformat: pdb or mmCif. This option specifies which PDB file format needed'
exit(1)
listFile = sys.argv[1]
with open(listFile, 'r') as fh:
content = [line.strip() for line in list(fh)]
pdbcodes = []
for c in content:
pdbcodes.extend(c.split())
format = sys.argv[2]
ResDir = os.getcwd()
if len(sys.argv) > 3:
ResDir = sys.argv[3]
if not os.path.isdir(ResDir):
os.mkdir(ResDir)
pdblist = PDBList()
pdblist.download_pdb_files(pdbcodes, file_format=format, pdir=ResDir)
#!/Applications/Anaconda/anaconda/bin/python3
from Bio.PDB import PDBList
pdbl = PDBList()
#pdbl.retrieve_pdb_file('1FAT',file_format='pdb')
##download_pdb_files(self, pdb_codes, obsolete=False, pdir=None, file_format='pdb', overwrite=False)
mylist = [
'6eqd', '6ane', '5yfe', '5xjh', '5xg0', '5xfy', '5xfz', '5xh3', '5yns'
]
pdbl.download_pdb_files(
mylist,
obsolete=False,
pdir="/Users/astuart/Ramapo/Research/PlasticDegradingEnzymes/Structures/",
file_format='pdb')
'CudaPrecision': 'mixed',
'CudaDeviceIndex': (CUDA_DEV_IDX if CUDA_DEV_IDX else 0)}
""" Helper function to choose mutant residues """
RESIDUES = ['ACE', 'ALA', 'ALAD', 'ARG', 'ARGN', 'ASF', 'ASH', 'ASN', 'ASN1', 'ASP', 'ASPH', 'CALA', 'CARG', 'CASF', 'CASN', 'CASP', 'CCYS', 'CCYX', 'CGLN', 'CGLU', 'CGLY', 'CHID', 'CHIE', 'CHIP', 'CILE', 'CLEU', 'CLYS', 'CME', 'CMET', 'CPHE', 'CPRO', 'CSER', 'CTHR', 'CTRP', 'CTYR', 'CVAL', 'CYM', 'CYS', 'CYS1', 'CYS2', 'CYSH', 'CYX', 'DAB', 'GLH', 'GLN', 'GLU', 'GLUH', 'GLY', 'HID', 'HIE', 'HIP', 'HIS', 'HIS1', 'HIS2', 'HISA', 'HISB', 'HISD', 'HISE', 'HISH', 'HSD', 'HSE', 'HSP', 'HYP', 'ILE', 'LEU', 'LYN', 'LYS', 'LYSH', 'MET', 'MSE', 'NALA', 'NARG', 'NASN', 'NASP', 'NCYS', 'NCYX', 'NGLN', 'NGLU', 'NGLY', 'NHID', 'NHIE', 'NHIP', 'NILE', 'NLEU', 'NLYS', 'NME', 'NMET', 'NPHE', 'NPRO', 'NSER', 'NTHR', 'NTRP', 'NTYR', 'NVAL', 'ORN', 'PGLU', 'PHE', 'PRO', 'QLN', 'SER', 'THR', 'TRP', 'TYR', 'VAL']
STANDARDS = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS','ILE', 'LEU', 'LYN', 'LYS', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL']
def randres(standard=False):
pool = STANDARDS if standard else RESIDUES
return pool[rd.randint(0,len(pool)-1)]
###
# Seed
###
""" Download seed scFv (RCSB PDB ID: 1MFA) """
pdbl = PDBList(obsolete_pdb='/dev/null')
pdbl.download_pdb_files([SEED_PDB], pdir=PDB_DIR, file_format='pdb')
""" Extract 1MFA components """
uni_1MFA = mda.Universe(f'{PDB_DIR}/pdb{SEED_PDB}.ent')
assert hasattr(uni_1MFA, 'trajectory')
lig_1MFA = uni_1MFA.select_atoms('not protein and not resname HOH')
lig_1MFA.write(f'{PDB_DIR}/{SEED_PDB}.lig.pdb')
fab_1MFA = uni_1MFA.select_atoms('protein')
fab_1MFA.write(f'{PDB_DIR}/{SEED_PDB}.fab.pdb')
# light_1MFA = uni_1MFA.select_atoms('segid L')
# heavy_1MFA = uni_1MFA.select_atoms('segid H')
""" Fix/clean the FAb apo protein and save it """
fixer = PDBFixer(PDB_DIR + '/' + SEED_PDB + '.fab.pdb')
