def gen_simi_search_sql(self, smiles, min_simi):
'''
gen_simi_search_sql(smiles, min_simi) -- Returns a string.
args:
smiles: str, smiles that represents a molecule.
min_simi: float, the minimal similarity value (tanimoto coefficient)
tanimoto coefficient
A is number of ones in fps of mol1
B is number of ones in fps of mol2
C is number of ones in A & B
similarity = C/(A+B-C)
returns a partial sql string like ' ,tanimoto as similarity FROM ... WHERE ... '
where 'tanimoto' is the sql string for calculating tanimoto value and 'similarity'
is the simi_field from env['SIMI_FIELD']
'''
s = ''
s_c = ''
s_b = ''
ones_a = 0
stat = {}
fps = {}
min_simi = float(min_simi)
mol = mymol('smi', smiles)
mol.get_mol_stat(stat)
mol.get_fps(fps)
record_keys = [
"NUM_C", "NUM_O", "NUM_N", "NUM_P", "NUM_S", "NUM_F", "NUM_Cl",
"NUM_Br", "NUM_I"
]
for i in record_keys:
if stat.has_key(i) and self.recorded_fields_dict.has_key(i):
s += self.recorded_fields_dict[i] + " >= " + \
str(( lambda x: x == int(x) and int(x) or int(x) + 1 )(min_simi * stat[i])) + \
" AND " + self.recorded_fields_dict[i] + " <= " + str(int(1 / min_simi * stat[i])) + ' AND '
fps_keys = fps.keys()
fps_keys.remove(self.env['FP_BITS_KEY'])
fps_keys.sort()
for i in fps_keys:
if self.recorded_fields_dict.has_key(i):
s_b += 'BIT_COUNT(%s) + ' % (self.recorded_fields_dict[i], )
if fps[i] != 0:
s_c += 'BIT_COUNT(%s & %s) + ' % (
self.recorded_fields_dict[i], fps[i])
#ones_a += str(bin(fps[i])).count('1')
s_b = (lambda x: x and '( ' + x + ' )' or '')(s_b.rstrip('+ '))
s_c = (lambda x: x and '( ' + x + ' )' or '')(s_c.rstrip('+ '))
ones_a = fps[self.env['FP_BITS_KEY']]
tanimoto = '%s / ( %s + %s - %s )' % (s_c, str(ones_a), s_b, s_c)
join_part_sql = self.gen_join_part_sql(self.dbd.tables,
self.env['PRI_FIELD'])
return ', %s as %s FROM %s WHERE ( (%s) AND (%s > %s) )' % (
tanimoto, self.env['SIMI_FIELD'], join_part_sql, s.rstrip(' AND '),
tanimoto, str(min_simi))
def gen_adv_search_sql(
self,
query,
smiles_dic={},
abbr_dic={},
black_words=['select', 'insert', 'update', 'drop', 'source']):
'''
gen_adv_search_sql(query[, smiles_dic[, abbr_dic[, black_words]]]) -- Returns a string.
args:
query: str, the query string.
smiles_dic: dict, contains the molecules which may be used in the query.
abbr_dic: dict, the dict of the abbreviated key words.
black_words: list, the list of the dangerous words.
returns a partial sql string like ' FROM ... WHERE ... '
'''
stats = []
s = ''
sub_mols = []
sup_mols = []
def gen_re_string(string):
s = ''
for i in str(string):
s += '[' + i + i.upper() + ']'
return s
# check if query contains black words
for i in black_words:
if re.findall(gen_re_string(i), query):
raise Exception, 'contains illegal words!'
# upper case the sql keywords 'and', 'or'
query = re.sub(r'([aA][nN][dD])|([oO][rR])',
lambda g: g.group(0).upper(), query) + ' '
# add space before and after >, <, =, >=, etc.
query = re.sub(r' *[><!=]+ *', lambda g: ' ' + g.group(0) + ' ', query)
# unabbreviating
r0 = re.compile(r'\w+')
def repl0(g):
if abbr_dic.has_key(g.group(0)):
return abbr_dic[g.group(0)]
else:
return g.group(0)
query = r0.sub(repl0, query)
# RE for extracting the sub (substructure) part
re_sub = re.compile(r'[sS][uU][bB] *[!=]+ *[^ )(]*(?=[ )(]+)')
def repl_sub(g, gen_sql=self.gen_search_sql_tuple):
sep = ''
sql = ''
smi = ''
g = g.group(0)
g = g.replace(' ', '')
if re.findall(r'!=', g):
sep = '!='
type = '3'
elif re.findall(r'=', g):
sep = '='
type = '2'
mol_key = g.split(sep)[-1].strip(' ')
if sep and smiles_dic.has_key(mol_key):
smi = smiles_dic[mol_key]
sql = gen_sql(str(smi), str(type), 1)
stats.append(sql[0])
return sql[1]
# RE for extracting the sup (superstructure) part
re_sup = re.compile(r'[sS][uU][pP] *[!=]+ *[^ )(]*(?=[ )(]+)')
def repl_sup(g, gen_sql=self.gen_search_sql_tuple):
sep = ''
sql = ''
smi = ''
g = g.group(0)
g = g.replace(' ', '')
if re.findall(r'!=', g):
sep = '!='
type = '5'
elif re.findall(r'=', g):
sep = '='
type = '4'
mol_key = g.split(sep)[-1].strip(' ')
if sep and smiles_dic.has_key(mol_key):
smi = smiles_dic[mol_key]
sql = gen_sql(str(smi), str(type), 1)
stats.append(sql[0])
return sql[1]
# get the sub_mols
for m in re_sub.findall(query):
if re.findall(r'[^!]=', m):
mol_key = m.split('=')[-1].strip(' ')
if smiles_dic.has_key(mol_key) and smiles_dic.get(mol_key):
sub_mols.append(smiles_dic.get(mol_key))
# get the sup_mols
for m in re_sup.findall(query):
if re.findall(r'[^!]=', m):
mol_key = m.split('=')[-1].strip(' ')
if smiles_dic.has_key(mol_key) and smiles_dic.get(mol_key):
sup_mols.append(smiles_dic.get(mol_key))
# if the query has both sub_mols and sup_mols, then, the sub_mols must be
# the substructure of sup_mols
if sup_mols:
for m in sub_mols:
mymol_obj = mymol('smi', m)
for m0 in sup_mols:
if not mymol_obj.sub_match('smi', m0):
raise Exception, 'sub and sup not match'
result = re_sub.sub(repl_sub, query)
result = re_sup.sub(repl_sup, result)
tmp_dic_sub = {}
tmp_dic_sup = {}
stats = [j for j in stats if j]
if stats:
for i in stats:
if 'sub' in i.keys():
if not tmp_dic_sub:
tmp_dic_sub = i['sub']
continue
else:
for k, v in i['sub'].items():
if tmp_dic_sub.has_key(k):
if tmp_dic_sub[k] < v:
tmp_dic_sub[k] = v
else:
tmp_dic_sub[k] = v
elif 'sup' in i.keys():
if not tmp_dic_sup:
tmp_dic_sup = i['sup']
continue
else:
for k, v in i['sup'].items():
if tmp_dic_sup.has_key(k):
if tmp_dic_sup[k] < v:
tmp_dic_sup[k] = v
else:
tmp_dic_sup[k] = v
val_k = ''
for k, v in tmp_dic_sub.items():
for j in self.def_dict.values():
if j.has_key(k):
val_k = j[k][0]
break
if val_k:
if tmp_dic_sup.has_key(k):
if int(v) == int(tmp_dic_sup[k]):
s += '%s = %s AND ' % (str(val_k), str(v))
elif int(v) > int(tmp_dic_sup[k]):
raise Exception, 'mol stat range err'
else:
s += '%s >= %s AND %s <= %s AND ' % (
str(val_k), str(v), str(val_k),
str(tmp_dic_sup[k]))
else:
s += str(val_k) + ' >= ' + str(v) + ' AND '
for k, v in tmp_dic_sup.items():
if k in tmp_dic_sub.keys():
continue
else:
for j in self.def_dict.values():
if j.has_key(k):
val_k = j[k][0]
break
if val_k:
s += str(val_k) + ' <= ' + str(v) + ' AND '
result = '(%s) AND (%s)' % (s.rstrip(' AND '), result.strip(' '))
join_part_sql = self.gen_join_part_sql(self.dbd.tables,
self.env['PRI_FIELD'])
return ' FROM %s WHERE (%s)' % (join_part_sql, result)
def gen_search_sql_tuple(self, smiles, search_type="1", out_put_type=1):
'''
gen_search_sql_tuple(smiles[, search_type[, out_put_type]]) -- Returns a tuple
args:
smiles: str, smiles that represents a molecule.
search_type: str. values:
'1': full march,
'2': target structure contains substructure,
'3': target structure dosen't contains substructure
'4': target structure contains superstructure,
'5': target structure dosen't contains superstructure
out_put_type: int. values:
1 or not 2: without the mol_stat part.
2: contains the mol_stat part
generates the search sql string according to the smiles string.
returns a tuple contains two elements:
0: stat, some statistic of the mol such as number of C, number of rings and etc.
1: the sql part, sql not fully generated, only a part like this " FROM ... WHERE ... "
'''
fp_sql = ""
stat = {}
head_flag = '('
end_flag = ')'
stat_part = ''
md5_ob_can_smi_key = self.env['MD5_OPENBABEL_CAN_SMI_KEY']
fp_bits_key = self.env['FP_BITS_KEY']
sign_mol_stat = ' >= '
try:
num_H_key = self.env['NUM_H_KEY']
except:
num_H_key = 'NUM_H'
bool_op = " AND "
mol_fp = {}
mol = mymol('smi', smiles)
mol.get_fps(mol_fp)
if search_type == "1":
if md5_ob_can_smi_key in self.recorded_fields_dict.keys():
return ({}, self.recorded_fields_dict[md5_ob_can_smi_key] +
" = '" +
md5(mymol('smi', smiles).gen_openbabel_can_smiles()) +
"'")
else:
return ({}, '')
elif search_type in ("2", "4"):
mol_stat = {}
tmp_stat = {}
mol.get_mol_stat(mol_stat)
if mol_stat.has_key(num_H_key):
mol_stat.pop(num_H_key)
tmp_stat[str(fp_bits_key)] = mol_fp[fp_bits_key]
tmp_stat.update(mol_stat)
if search_type == '2':
sign_mol_stat = ' >= '
stat['sub'] = tmp_stat
elif search_type == '4':
sign_mol_stat = ' <= '
stat['sup'] = tmp_stat
bool_op = ' AND '
elif search_type in ("3", "5"):
bool_op = ' AND '
head_flag = ' NOT ('
fps_keys = mol_fp.items()
fps_keys.sort()
for i, j in fps_keys:
if self.recorded_fields_dict.has_key(
i) and i != fp_bits_key and j != 0:
if search_type in ('2', '3'):
fp_sql += self.recorded_fields_dict[i] + " & " + str(
j) + ' = ' + str(j) + bool_op
elif search_type in ('4', '5'):
field = self.recorded_fields_dict[i]
fp_sql += field + " & " + str(j) + ' = ' + field + bool_op
if out_put_type == 2 and search_type in ('2', '4'):
val_k = []
for k, v in tmp_stat.items():
for j in self.def_dict.values():
if j.has_key(k):
val_k = j[k][0]
break
if val_k:
stat_part += str(val_k) + sign_mol_stat + str(v) + ' AND '
if stat_part:
head_flag = '(' + stat_part.rstrip('AND ') + ') AND ('
if fp_sql.rstrip(bool_op):
return (stat, head_flag + fp_sql.rstrip(bool_op) + end_flag)
else:
return ({}, '1')
def gen_adv_search_sql(
self, query, smiles_dic={}, abbr_dic={}, black_words=["select", "insert", "update", "drop", "source"]
):
"""
gen_adv_search_sql(query[, smiles_dic[, abbr_dic[, black_words]]]) -- Returns a string.
args:
query: str, the query string.
smiles_dic: dict, contains the molecules which may be used in the query.
abbr_dic: dict, the dict of the abbreviated key words.
black_words: list, the list of the dangerous words.
returns a partial sql string like ' FROM ... WHERE ... '
"""
stats = []
s = ""
sub_mols = []
sup_mols = []
def gen_re_string(string):
s = ""
for i in str(string):
s += "[" + i + i.upper() + "]"
return s
# check if query contains black words
for i in black_words:
if re.findall(gen_re_string(i), query):
raise Exception, "contains illegal words!"
# upper case the sql keywords 'and', 'or'
query = re.sub(r"([aA][nN][dD])|([oO][rR])", lambda g: g.group(0).upper(), query) + " "
# add space before and after >, <, =, >=, etc.
query = re.sub(r" *[><!=]+ *", lambda g: " " + g.group(0) + " ", query)
# unabbreviating
r0 = re.compile(r"\w+")
def repl0(g):
if abbr_dic.has_key(g.group(0)):
return abbr_dic[g.group(0)]
else:
return g.group(0)
query = r0.sub(repl0, query)
# RE for extracting the sub (substructure) part
re_sub = re.compile(r"[sS][uU][bB] *[!=]+ *[^ )(]*(?=[ )(]+)")
def repl_sub(g, gen_sql=self.gen_search_sql_tuple):
sep = ""
sql = ""
smi = ""
g = g.group(0)
g = g.replace(" ", "")
if re.findall(r"!=", g):
sep = "!="
type = "3"
elif re.findall(r"=", g):
sep = "="
type = "2"
mol_key = g.split(sep)[-1].strip(" ")
if sep and smiles_dic.has_key(mol_key):
smi = smiles_dic[mol_key]
sql = gen_sql(str(smi), str(type), 1)
stats.append(sql[0])
return sql[1]
# RE for extracting the sup (superstructure) part
re_sup = re.compile(r"[sS][uU][pP] *[!=]+ *[^ )(]*(?=[ )(]+)")
def repl_sup(g, gen_sql=self.gen_search_sql_tuple):
sep = ""
sql = ""
smi = ""
g = g.group(0)
g = g.replace(" ", "")
if re.findall(r"!=", g):
sep = "!="
type = "5"
elif re.findall(r"=", g):
sep = "="
type = "4"
mol_key = g.split(sep)[-1].strip(" ")
if sep and smiles_dic.has_key(mol_key):
smi = smiles_dic[mol_key]
sql = gen_sql(str(smi), str(type), 1)
stats.append(sql[0])
return sql[1]
# get the sub_mols
for m in re_sub.findall(query):
if re.findall(r"[^!]=", m):
mol_key = m.split("=")[-1].strip(" ")
if smiles_dic.has_key(mol_key) and smiles_dic.get(mol_key):
sub_mols.append(smiles_dic.get(mol_key))
# get the sup_mols
for m in re_sup.findall(query):
if re.findall(r"[^!]=", m):
mol_key = m.split("=")[-1].strip(" ")
if smiles_dic.has_key(mol_key) and smiles_dic.get(mol_key):
sup_mols.append(smiles_dic.get(mol_key))
# if the query has both sub_mols and sup_mols, then, the sub_mols must be
# the substructure of sup_mols
if sup_mols:
for m in sub_mols:
mymol_obj = mymol("smi", m)
for m0 in sup_mols:
if not mymol_obj.sub_match("smi", m0):
raise Exception, "sub and sup not match"
result = re_sub.sub(repl_sub, query)
result = re_sup.sub(repl_sup, result)
tmp_dic_sub = {}
tmp_dic_sup = {}
stats = [j for j in stats if j]
if stats:
for i in stats:
if "sub" in i.keys():
if not tmp_dic_sub:
tmp_dic_sub = i["sub"]
continue
else:
for k, v in i["sub"].items():
if tmp_dic_sub.has_key(k):
if tmp_dic_sub[k] < v:
tmp_dic_sub[k] = v
else:
tmp_dic_sub[k] = v
elif "sup" in i.keys():
if not tmp_dic_sup:
tmp_dic_sup = i["sup"]
continue
else:
for k, v in i["sup"].items():
if tmp_dic_sup.has_key(k):
if tmp_dic_sup[k] < v:
tmp_dic_sup[k] = v
else:
tmp_dic_sup[k] = v
val_k = ""
for k, v in tmp_dic_sub.items():
for j in self.def_dict.values():
if j.has_key(k):
val_k = j[k][0]
break
if val_k:
if tmp_dic_sup.has_key(k):
if int(v) == int(tmp_dic_sup[k]):
s += "%s = %s AND " % (str(val_k), str(v))
elif int(v) > int(tmp_dic_sup[k]):
raise Exception, "mol stat range err"
else:
s += "%s >= %s AND %s <= %s AND " % (str(val_k), str(v), str(val_k), str(tmp_dic_sup[k]))
else:
s += str(val_k) + " >= " + str(v) + " AND "
for k, v in tmp_dic_sup.items():
if k in tmp_dic_sub.keys():
continue
else:
for j in self.def_dict.values():
if j.has_key(k):
val_k = j[k][0]
break
if val_k:
s += str(val_k) + " <= " + str(v) + " AND "
result = "(%s) AND (%s)" % (s.rstrip(" AND "), result.strip(" "))
join_part_sql = self.gen_join_part_sql(self.dbd.tables, self.env["PRI_FIELD"])
return " FROM %s WHERE (%s)" % (join_part_sql, result)
def gen_simi_search_sql(self, smiles, min_simi):
"""
gen_simi_search_sql(smiles, min_simi) -- Returns a string.
args:
smiles: str, smiles that represents a molecule.
min_simi: float, the minimal similarity value (tanimoto coefficient)
tanimoto coefficient
A is number of ones in fps of mol1
B is number of ones in fps of mol2
C is number of ones in A & B
similarity = C/(A+B-C)
returns a partial sql string like ' ,tanimoto as similarity FROM ... WHERE ... '
where 'tanimoto' is the sql string for calculating tanimoto value and 'similarity'
is the simi_field from env['SIMI_FIELD']
"""
s = ""
s_c = ""
s_b = ""
ones_a = 0
stat = {}
fps = {}
min_simi = float(min_simi)
mol = mymol("smi", smiles)
mol.get_mol_stat(stat)
mol.get_fps(fps)
record_keys = ["NUM_C", "NUM_O", "NUM_N", "NUM_P", "NUM_S", "NUM_F", "NUM_Cl", "NUM_Br", "NUM_I"]
for i in record_keys:
if stat.has_key(i) and self.recorded_fields_dict.has_key(i):
s += (
self.recorded_fields_dict[i]
+ " >= "
+ str((lambda x: x == int(x) and int(x) or int(x) + 1)(min_simi * stat[i]))
+ " AND "
+ self.recorded_fields_dict[i]
+ " <= "
+ str(int(1 / min_simi * stat[i]))
+ " AND "
)
fps_keys = fps.keys()
fps_keys.remove(self.env["FP_BITS_KEY"])
fps_keys.sort()
for i in fps_keys:
if self.recorded_fields_dict.has_key(i):
s_b += "BIT_COUNT(%s) + " % (self.recorded_fields_dict[i],)
if fps[i] != 0:
s_c += "BIT_COUNT(%s & %s) + " % (self.recorded_fields_dict[i], fps[i])
# ones_a += str(bin(fps[i])).count('1')
s_b = (lambda x: x and "( " + x + " )" or "")(s_b.rstrip("+ "))
s_c = (lambda x: x and "( " + x + " )" or "")(s_c.rstrip("+ "))
ones_a = fps[self.env["FP_BITS_KEY"]]
tanimoto = "%s / ( %s + %s - %s )" % (s_c, str(ones_a), s_b, s_c)
join_part_sql = self.gen_join_part_sql(self.dbd.tables, self.env["PRI_FIELD"])
return ", %s as %s FROM %s WHERE ( (%s) AND (%s > %s) )" % (
tanimoto,
self.env["SIMI_FIELD"],
join_part_sql,
s.rstrip(" AND "),
tanimoto,
str(min_simi),
)
def gen_search_sql_tuple(self, smiles, search_type="1", out_put_type=1):
"""
gen_search_sql_tuple(smiles[, search_type[, out_put_type]]) -- Returns a tuple
args:
smiles: str, smiles that represents a molecule.
search_type: str. values:
'1': full march,
'2': target structure contains substructure,
'3': target structure dosen't contains substructure
'4': target structure contains superstructure,
'5': target structure dosen't contains superstructure
out_put_type: int. values:
1 or not 2: without the mol_stat part.
2: contains the mol_stat part
generates the search sql string according to the smiles string.
returns a tuple contains two elements:
0: stat, some statistic of the mol such as number of C, number of rings and etc.
1: the sql part, sql not fully generated, only a part like this " FROM ... WHERE ... "
"""
fp_sql = ""
stat = {}
head_flag = "("
end_flag = ")"
stat_part = ""
md5_ob_can_smi_key = self.env["MD5_OPENBABEL_CAN_SMI_KEY"]
fp_bits_key = self.env["FP_BITS_KEY"]
sign_mol_stat = " >= "
try:
num_H_key = self.env["NUM_H_KEY"]
except:
num_H_key = "NUM_H"
bool_op = " AND "
mol_fp = {}
mol = mymol("smi", smiles)
mol.get_fps(mol_fp)
if search_type == "1":
if md5_ob_can_smi_key in self.recorded_fields_dict.keys():
return (
{},
self.recorded_fields_dict[md5_ob_can_smi_key]
+ " = '"
+ md5(mymol("smi", smiles).gen_openbabel_can_smiles())
+ "'",
)
else:
return ({}, "")
elif search_type in ("2", "4"):
mol_stat = {}
tmp_stat = {}
mol.get_mol_stat(mol_stat)
if mol_stat.has_key(num_H_key):
mol_stat.pop(num_H_key)
tmp_stat[str(fp_bits_key)] = mol_fp[fp_bits_key]
tmp_stat.update(mol_stat)
if search_type == "2":
sign_mol_stat = " >= "
stat["sub"] = tmp_stat
elif search_type == "4":
sign_mol_stat = " <= "
stat["sup"] = tmp_stat
bool_op = " AND "
elif search_type in ("3", "5"):
bool_op = " AND "
head_flag = " NOT ("
fps_keys = mol_fp.items()
fps_keys.sort()
for i, j in fps_keys:
if self.recorded_fields_dict.has_key(i) and i != fp_bits_key and j != 0:
if search_type in ("2", "3"):
fp_sql += self.recorded_fields_dict[i] + " & " + str(j) + " = " + str(j) + bool_op
elif search_type in ("4", "5"):
field = self.recorded_fields_dict[i]
fp_sql += field + " & " + str(j) + " = " + field + bool_op
if out_put_type == 2 and search_type in ("2", "4"):
val_k = []
for k, v in tmp_stat.items():
for j in self.def_dict.values():
if j.has_key(k):
val_k = j[k][0]
break
if val_k:
stat_part += str(val_k) + sign_mol_stat + str(v) + " AND "
if stat_part:
head_flag = "(" + stat_part.rstrip("AND ") + ") AND ("
if fp_sql.rstrip(bool_op):
return (stat, head_flag + fp_sql.rstrip(bool_op) + end_flag)
else:
return ({}, "1")
