def get_auth_asym_id_list(iciffile):
amino = [
'ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY', 'HIS', 'ILE', 'LYS', 'LEU',
'MET', 'ASN', 'PRO', 'GLN', 'ARG', 'SER', 'THR', 'VAL', 'TRP', 'TYR'
]
nuc = ['A', 'T', 'G', 'C', 'U', 'DA', 'DT', 'DG', 'DC', 'DU']
dat = {}
mmCIF.read_mmCIF_file(iciffile, dat, focus_category=['atom_site'])
property = {}
auth_asym_id_list = []
if ('atom_site' not in dat):
return (auth_asym_id_list, property)
S = dat['atom_site']
NATOM_auth_asym_id = {}
NHETATM_auth_asym_id = {}
NRES_auth_asym_id = {}
NBASE_auth_asym_id = {}
for i in range(len(S['id'])):
c = S['auth_asym_id'][i]
if (c not in property):
property[c] = {}
property[c]['NATOM'] = 0
property[c]['NHETATM'] = 0
property[c]['NRES'] = 0
property[c]['NBASE'] = 0
if (S['group_PDB'][i] == 'ATOM'):
property[c]['NATOM'] = property[c].get('NATOM', 0) + 1
if (S['group_PDB'][i]
== 'HETATM') and (S['label_comp_id'][i] != 'HOH'):
property[c]['NHETATM'] = property[c].get('NHETATM', 0) + 1
if (S['label_comp_id'][i] in amino) and (S['label_atom_id'][i]
== 'CA'):
property[c]['NRES'] = property[c].get('NRES', 0) + 1
if (S['label_comp_id'][i] in nuc) and (S['label_atom_id'][i] == 'P'):
property[c]['NBASE'] = property[c].get('NBASE', 0) + 1
auth_asym_id_list = sorted(property.keys(), lambda x, y: cmp(x, y))
for c in (auth_asym_id_list):
print "%s NATOM %d NHETATM %d NRES %d NBASE %d" % (
c, property[c]['NATOM'], property[c]['NHETATM'],
property[c]['NRES'], property[c]['NBASE'])
return (auth_asym_id_list, property)
def get_assembly_id_list(iciffile):
assembly_id_list = ['-']
dat = {}
mmCIF.read_mmCIF_file(iciffile,
dat,
focus_category=[
'atom_site', 'pdbx_struct_assembly',
'pdbx_struct_assembly_gen'
])
if ('atom_site' not in dat):
return ([])
if ('pdbx_struct_assembly' not in dat) or ('pdbx_struct_assembly_gen'
not in dat):
return (['-'])
S = dat['atom_site']
asym_id_dic = {}
for i in range(len(S['id'])):
asym_id_dic[S['label_asym_id'][i]] = 1
asym_id_list_asymmetric_unit = sorted(asym_id_dic.keys(),
lambda x, y: cmp(x, y))
A = dat['pdbx_struct_assembly']
G = dat['pdbx_struct_assembly_gen']
Nassembly = len(A['id'])
items = ('id', 'details', 'method_details', 'oligomeric_details',
'oligomeric_count')
for i in range(Nassembly):
assembly_id = A['id'][i]
for item in (items):
if (item in A.keys()):
sys.stdout.write(" %s" % (A[item][i]))
else:
sys.stdout.write("-")
sys.stdout.write(" %s" % (G['asym_id_list'][i]))
sys.stdout.write(" %s" % (G['oper_expression'][i]))
oper_expression_list = mmCIF.get_oper_expression_list(
G['oper_expression'][i])
asym_id_list = sorted(G['asym_id_list'][i].split(','),
lambda x, y: cmp(x, y))
## Check the assembly is equal to the asymmetric unit,or not
## (1) asym_id_list[] is identical asym_id_list_asymmetric_unit[]
## (2) Length of oper_expression_list[] is 1. (Single transformation)
if (asym_id_list
== asym_id_list_asymmetric_unit) and (len(oper_expression_list)
== 1):
sys.stdout.write("#assembly_id '%s' is the asymmetric_unit." %
(assembly_id))
else:
assembly_id_list.append(assembly_id)
sys.stdout.write("\n")
dat = {}
return (assembly_id_list)
#1ai1.cif.gz
#1ai2.cif.gz
field = file.split('.')
pdb_id = field[0]
pdb_id_list.append(pdb_id)
print "#len(pdb_id_list):%d" % (len(pdb_id_list))
### (3) do commands ###
MISS_PDB_ID = {}
for pdb_id in (pdb_id_list):
iciffile = OPT['icifdir'] + '/' + pdb_id[1:3] + '/' + pdb_id + '.cif.gz'
dat = {}
mmCIF.read_mmCIF_file(iciffile,
dat,
focus_category=['pdbx_struct_assembly'])
if ('pdbx_struct_assembly' in dat):
assembly_id_list = dat['pdbx_struct_assembly']['id']
else:
assembly_id_list = []
if (len(assembly_id_list) > 1):
ogmmdir = OPT['odir'] + '/' + pdb_id[1:3]
ogmmfile = ogmmdir + '/' + pdb_id + '-' + '1' + '.gmm'
if (os.path.isfile(ogmmfile) == 0):
assembly_id_list = get_assembly_id_list(iciffile)
print "#%s %s" % (pdb_id, assembly_id_list)
for assembly_id in (assembly_id_list):
pdbid_list = []
if (os.path.isdir(OPT['icifdir'])):
dirlist = os.listdir(OPT['icifdir'])
for subdir in (dirlist):
dir = OPT['icifdir'] + '/' + subdir
if (os.path.isfile(dir)):
pass
elif (os.path.isdir(dir)):
filelist = os.listdir(dir)
for file in (filelist):
filefull = OPT['icifdir'] + '/' + subdir + '/' + file
if (os.path.isfile(filefull)):
dat = {}
mmCIF.read_mmCIF_file(
filefull,
dat,
focus_category=['pdbx_struct_assembly_gen'])
findit = 0
if ('pdbx_struct_assembly_gen' in dat):
if ('oper_expression'
in dat['pdbx_struct_assembly_gen']):
for x in (dat['pdbx_struct_assembly_gen']
['oper_expression']):
if (x.find(')(')) > 0:
findit = 1
if (findit == 1):
print "COMBI_OPER '%s'" % (filefull)
field = file.split('.')
pdbid_list.append(field[0])
of = open(OPT['olist'], 'w')