def handle_seqres_di(info_dict):
# Deal with SEQRES_COL
resides_col_li = DEFAULT_COLS['SEQRES_COL'][1:4]
mtoTool = Unit.MultiToOne()
for i in range(len(info_dict[resides_col_li[0]])):
for resides_col in resides_col_li:
info_dict[resides_col][i] = ''.join(
mtoTool.multi_letter_convert_to_one_letter(j)
for j in info_dict[resides_col][i])
pdbx_poly_key = DEFAULT_COLS['SEQRES_COL'][0]
coordinates_model_key = DEFAULT_COLS['SEQRES_COL'][8]
for i in range(len(info_dict[pdbx_poly_key])):
strand_id_index = [0]
li = info_dict[pdbx_poly_key][i]
save_id = li[0]
strand_id_li = [save_id]
for j in range(len(li)):
if li[j] != save_id:
save_id = li[j]
strand_id_index.append(j)
strand_id_li.append(save_id)
info_dict[pdbx_poly_key][i] = strand_id_li
for col in DEFAULT_COLS['SEQRES_COL'][1:4]:
info_dict[col][i] = [
MMCIF2Dfrm.get_index(strand_id_index, info_dict[col][i], j)
for j in range(len(strand_id_index))
]
for col in DEFAULT_COLS['SEQRES_COL'][4:8]:
info_dict[col][i] = [
';'.join(
MMCIF2Dfrm.get_index(strand_id_index,
info_dict[col][i], j))
for j in range(len(strand_id_index))
]
new_comodel_li = []
for ele in info_dict[coordinates_model_key][i]:
if ele not in new_comodel_li:
new_comodel_li.append(ele)
info_dict[coordinates_model_key][i] = new_comodel_li
def get_data_from_mmcif(self, path_list, outputPath=False):
'''
{
'_pdbx_audit_revision_history.revision_date': ['initial_version_time', 'newest_version_time'], # sometimes not a list
'_entity.pdbx_mutation': ['mutation_num', 'mutation_content'], # sometimes not a list
'_entity.id': ['entity_id_aidMuta'], # sometimes not a list
['_em_3d_reconstruction.resolution','_refine.ls_d_res_high']: ['resolution'], # not a lists
'_exptl.method': ['method'], # not a list
}
'''
info_dict = defaultdict(list)
for path in path_list:
if path[-3:] == 'cif':
print(path)
info_dict['pdb_id'].append(path[-8:-4])
MMCIF_unit.get_mmcif_info(
MMCIF_unit.CONFIG['COMMON_COL'] +
MMCIF_unit.CONFIG['BIOASS_COL'] +
MMCIF_unit.CONFIG['ENTITY_COL'] +
MMCIF_unit.CONFIG['TYPE_COL'] +
MMCIF_unit.CONFIG['SEQRES_COL'] +
MMCIF_unit.CONFIG['LIGAND_COL'],
MMCIF_unit.CONFIG['COMMON_COL'][1:], info_dict, path)
# Deal with Residues in SEQRES_COL
resides_col_li = MMCIF_unit.CONFIG['SEQRES_COL'][1:4]
mtoTool = Unit.MultiToOne()
for i in range(len(info_dict[resides_col_li[0]])):
for resides_col in resides_col_li:
info_dict[resides_col][i] = ''.join(
mtoTool.multi_letter_convert_to_one_letter(j)
for j in info_dict[resides_col][i])
def get_index(x, y, z):
return y[x[z]:x[z +
1]] if len(x) != 1 and z + 1 < len(x) else y[x[z]:]
# Deal with SEQRES_COL
pdbx_poly_key = MMCIF_unit.CONFIG['SEQRES_COL'][0]
for i in range(len(info_dict[pdbx_poly_key])):
strand_id_index = [0]
li = info_dict[pdbx_poly_key][i]
save_id = li[0]
strand_id_li = [save_id]
for j in range(len(li)):
if li[j] != save_id:
save_id = li[j]
strand_id_index.append(j)
strand_id_li.append(save_id)
info_dict[pdbx_poly_key][i] = strand_id_li
for col in MMCIF_unit.CONFIG['SEQRES_COL'][1:4]:
info_dict[col][i] = [
get_index(strand_id_index, info_dict[col][i], j)
for j in range(len(strand_id_index))
]
for col in MMCIF_unit.CONFIG['SEQRES_COL'][4:]:
info_dict[col][i] = [
';'.join(get_index(strand_id_index, info_dict[col][i], j))
for j in range(len(strand_id_index))
]
# Deal with LIGAND_COL
ligand_col_list = MMCIF_unit.CONFIG['LIGAND_COL']
metal_li = MMCIF_unit.CONFIG['LIGAND_LIST']
for i in range(len(info_dict[ligand_col_list[0]])):
if not info_dict[ligand_col_list[0]][i]:
info_dict[MMCIF_unit.CONFIG['METAL_LIGAND_COL'][0]].append(
np.nan)
info_dict[MMCIF_unit.CONFIG['METAL_LIGAND_COL'][1]].append(
np.nan)
continue
ligand_col_tp = tuple(info_dict[col][i] for col in ligand_col_list)
ligand_col_zip_li = list(zip(*ligand_col_tp))
aa_li = list(MMCIF_unit.SEQ_DICT.keys())[:21]
metal_ligand_info = list(
filter(lambda x: x[0] == 'metalc', ligand_col_zip_li))
# chain_id: _struct_conn.ptnr2_auth_asym_id [4]
sub_metal_ligand_info_1 = filter(
lambda x: x[1] in metal_li and x[2] in aa_li,
metal_ligand_info)
# chain_id: _struct_conn.ptnr1_auth_asym_id [3]
sub_metal_ligand_info_2 = filter(
lambda x: x[2] in metal_li and x[1] in aa_li,
metal_ligand_info)
new_metal_ligand_info = []
for tp in sub_metal_ligand_info_1:
new_metal_ligand_info.append(
(tp[4], tp[1], tp[5], tp[2], tp[6]))
for tp in sub_metal_ligand_info_2:
new_metal_ligand_info.append(
(tp[3], tp[2], tp[6], tp[1], tp[5]))
new_metal_ligand_info.sort(key=lambda x: x[0])
try:
save_id = new_metal_ligand_info[0][0]
# print(new_metal_ligand_info)
except IndexError:
info_dict[MMCIF_unit.CONFIG['METAL_LIGAND_COL'][0]].append(
np.nan)
info_dict[MMCIF_unit.CONFIG['METAL_LIGAND_COL'][1]].append(
np.nan)
continue
strand_id_li = [save_id]
strand_id_index = [0]
for j in range(len(new_metal_ligand_info)):
if new_metal_ligand_info[j][0] != save_id:
save_id = new_metal_ligand_info[j][0]
strand_id_index.append(j)
strand_id_li.append(save_id)
info_dict[MMCIF_unit.CONFIG['METAL_LIGAND_COL'][0]].append(
strand_id_li)
info_dict[MMCIF_unit.CONFIG['METAL_LIGAND_COL'][1]].append([
get_index(strand_id_index,
[ele[1:] for ele in new_metal_ligand_info], j)
for j in range(len(strand_id_index))
])
df = pd.DataFrame(info_dict)
# Deal with the date of structure
df['initial_version_time'] = df.apply(
lambda x: x[MMCIF_unit.CONFIG['COMMON_COL'][0]][0], axis=1)
df['newest_version_time'] = df.apply(
lambda x: x[MMCIF_unit.CONFIG['COMMON_COL'][0]][-1], axis=1)
# Deal with the mutations
def muta_count(x):
return x.count(',') + 1 if x != '?' else 0
df['mutation_num'] = df.apply(
lambda x: [muta_count(i) for i in x['_entity.pdbx_mutation']],
axis=1)
# Deal with the resolution
df['resolution'] = df.apply(
lambda x: x[MMCIF_unit.CONFIG['COMMON_COL'][3]], axis=1)
df['resolution'] = df.apply(
lambda x: x[MMCIF_unit.CONFIG['COMMON_COL'][2]]
if isinstance(x['resolution'], float) else x['resolution'],
axis=1)
# Deal with chain type
def get_chainType_fun(ele):
return MMCIF_unit.CONFIG['CHAIN_TYPE_DICT'].get(ele, 'other')
df['pdb_contain_chain_type'] = df.apply(lambda x: ','.join(
sorted(
set(
map(get_chainType_fun,
json.loads(x['_entity_poly.type'].replace('\'', '"'))))
)) if isinstance(x['_entity_poly.type'], str) else ','.join(
sorted(set(map(get_chainType_fun, x['_entity_poly.type'])))),
axis=1)
# Deal with UNK_ALL in chain
def get_unk_fun(ele):
return len(ele) == ele.count('!')
df['UNK_ALL_IN_CHAIN'] = df.apply(
lambda x: list(
map(
get_unk_fun,
json.loads(x['_pdbx_poly_seq_scheme.mon_id'].replace(
'\'', '"'))))
if isinstance(x['_entity_poly.type'], str) else list(
map(get_unk_fun, x['_pdbx_poly_seq_scheme.mon_id'])),
axis=1)
# Deal with UNK_ALL in chains of a pdb
df['contains_unk_in_chain_pdb'] = df.apply(
lambda x: len(set(x['UNK_ALL_IN_CHAIN'])) == 2, axis=1)
# Add Info about pdb_type
df['pdb_type_MMCIF'] = df.apply(lambda x: MMCIF_unit.checkEntityType(
x['_entity_poly.type'], x['_entity_poly.pdbx_strand_id']),
axis=1)
# Change the columns
df.rename(columns={MMCIF_unit.CONFIG['COMMON_COL'][1]: 'method'},
inplace=True)
'''df.drop(columns=[MMCIF_unit.CONFIG['COMMON_COL'][0], MMCIF_unit.CONFIG['COMMON_COL']
[2], MMCIF_unit.CONFIG['COMMON_COL'][3]], inplace=True)'''
if os.path.exists(outputPath):
self.file_o(outputPath, df, mode='a+', header=False)
else:
self.file_o(outputPath, df)
return df
