def main():
print(
'This program regenerates the `%s` database using the "Chemical Component '
% DBNAME)
print(
'Dictionary" and "Protonation Variants Dictionary" from http://www.wwpdb.org/data/ccd'
)
if len(sys.argv) > 1 and sys.argv[1] == '--download':
print('Downloading newest CCD files ...\n')
download_ccd()
else:
print(
'Using cached download (run with "--download" to download a new version)'
)
residues = read_ccd()
db = utils.CompressedJsonDbm(DBNAME, 'n')
db['__FIELDS__'] = {'ATOMFIELDS': ATOMFIELDS, 'RESFIELDS': RESFIELDS}
for resname, data in residues:
store_residue(resname, data, db)
print('\nCreated db "%s" (%d records)' % (DBNAME, len(db)))
db.close()
self.index = self.hostdb['__FIELDS__']['RESFIELDS'].index(keyname)
def __repr__(self):
return '<Chemical component dictionary: "%s" entries>' % self.keyname
def __getitem__(self, item):
return self.hostdb[item][self.index]
__contains__ = utils.Alias('hostdb.__contains__')
def keys(self):
for key in self.hostdb.keys():
if key == '__FIELDS__':
continue
yield key
def items(self):
for key in self:
yield key, self[key]
__iter__ = keys
# This is a very big dict, so we load it as a compressed database
_bondfilename = os.path.join(PACKAGEPATH, '_static_data', 'chemical_components')
CCD_DATABASE = utils.CompressedJsonDbm(_bondfilename, 'r', dbm=utils.ReadOnlyDumb)
RESIDUE_BONDS = _DatabaseEntry(CCD_DATABASE, 'bonds')
RESIDUE_ATOMS = _DatabaseEntry(CCD_DATABASE, 'atoms')
RESIDUE_CCD_NAMES = _DatabaseEntry(CCD_DATABASE, 'name')
RESIDUE_CCD_TYPES = _DatabaseEntry(CCD_DATABASE, 'type')
ASN="N",
PRO="P",
GLN="Q",
ARG="R",
SER="S",
THR="T",
VAL="V",
TRP="W",
XAA="X",
TYR="Y",
GLX="Z")
# This is a very big dict, so we load it as a compressed database
_bondfilename = os.path.join(PACKAGEPATH, '_static_data/residue_bonds')
RESIDUE_BONDS = utils.CompressedJsonDbm(_bondfilename,
'r',
dbm=utils.ReadOnlyDumb)
AMINO_NAMES = {
"ALA": "Alanine",
"ARG": "Arginine",
"ASN": "Asparagine",
"ASP": "Aspartic acid",
"ASX": "ASP/ASN ambiguous",
"CYS": "Cysteine",
"GLN": "Glutamine",
"GLU": "Glutamic acid",
"GLX": "GLU/GLN ambiguous",
"GLY": "Glycine",
"HIS": "Histidine",
"HIE": "Histidine epsilon tautomer",