def get_compounds_from_database( database_file=None, **kw):
"""easy to use interface to the SQL - keyword arguments are converted to
corresponding SQL commands.
Examples:
get_compounds_from_database( smiles='C1CCCCC1')
get_compounds_from_database( inchi='1/C4H10/c1-3-4-2/h3-4H2,1-2H3')
"""
for fname in (database_file, Config.database_file):
if fname and os.path.exists(fname):
break
else:
raise oasa_exceptions.oasa_error("Structure database not found. Try running 'python structure_database.py structures.txt.gz' in oasa directory to create the database file from default source.")
if 'inchi' in kw:
if not 'inchikey' in kw:
import inchi_key
kw['inchikey'] = inchi_key.key_from_inchi( kw['inchi'])
del kw['inchi']
search = ["%s=?" % k for k in kw.keys()]
values = kw.values()
tables = "structures"
if "synonym" in kw:
tables = "structures, synonyms"
search.append( "structures.id=synonyms.id")
if search:
sql = "SELECT structures.* FROM %s WHERE %s" % (tables, " AND ".join( search))
else:
sql = "SELECT structures.* FROM %s" % (tables)
connection = sqlite.connect( Config.database_file)
c = connection.cursor()
try:
c.execute( sql, values)
except sqlite.OperationalError, e:
raise oasa_exceptions.oasa_error( "Error reading from structure database: '%s'" % e)
def database_string_to_compound(line):
a, name = line.split("###")
inchi, cid = a.split()
inchikey = inchi_key.key_from_inchi(inchi)
return {
'inchikey': inchikey.strip(),
'cid': cid.strip(),
'name': name.strip()
}
def generate_inchi_and_inchikey(m,
program=None,
fixed_hs=True,
ignore_key_error=False):
"""ignore the case when InChIKey cannot be generated for some reason
(no mhash library and old InChI program)"""
if not program:
import config
program = config.Config.inchi_binary_path
mf = molfile.mol_to_text(m)
if os.name == 'nt':
options = "/AUXNONE /STDIO /Key" + (fixed_hs and " /FixedH" or "")
else:
options = "-AUXNONE -STDIO -Key" + (fixed_hs and " -FixedH" or "")
#print options
command = [os.path.abspath(program)] + options.split()
text = _run_command(command, mf)
inchi = ""
key = ""
warnings = []
for line in text.splitlines():
if line.startswith("Warning"):
warnings.append(line.strip() + "\n")
elif line.startswith("End of file detected"):
pass
elif line.startswith("InChIKey="):
key = line.strip()[9:]
break
elif line.startswith("InChI="):
inchi = inchi + line.strip()
elif line.startswith("Error"):
break
if not inchi:
raise oasa_inchi_error("InChI program did not create any output InChI")
if not key:
# probably old version of the InChI software
try:
import inchi_key
except ImportError:
if ignore_key_error:
key = None
else:
raise oasa_inchi_error(
"InChIKey could not be generated - inchi_key module failed to load properly."
)
else:
key = inchi_key.key_from_inchi(inchi)
return inchi, key, warnings
def generate_inchi_and_inchikey( m, program=None, fixed_hs=True, ignore_key_error=False):
"""ignore the case when InChIKey cannot be generated for some reason
(no mhash library and old InChI program)"""
if not program:
import config
program = config.Config.inchi_binary_path
mf = molfile.mol_to_text( m)
if os.name == 'nt':
options = "/AUXNONE /STDIO /Key" + (fixed_hs and " /FixedH" or "")
else:
options = "-AUXNONE -STDIO -Key" + (fixed_hs and " -FixedH" or "")
#print options
command = [os.path.abspath( program)] + options.split()
text = _run_command( command, mf)
inchi = ""
key = ""
warnings = []
for line in text.splitlines():
if line.startswith( "Warning"):
warnings.append(line.strip() + "\n")
elif line.startswith( "End of file detected"):
pass
elif line.startswith( "InChIKey="):
key = line.strip()[9:]
break
elif line.startswith( "InChI="):
inchi = inchi + line.strip()
elif line.startswith( "Error"):
break
if not inchi:
raise oasa_inchi_error( "InChI program did not create any output InChI")
if not key:
# probably old version of the InChI software
try:
import inchi_key
except ImportError:
if ignore_key_error:
key = None
else:
raise oasa_inchi_error( "InChIKey could not be generated - inchi_key module failed to load properly.")
else:
key = inchi_key.key_from_inchi( inchi)
return inchi, key, warnings
def compound_to_database_string(c):
c['inchi'] = normalize_inchi(c['inchi'])
c['inchikey'] = inchi_key.key_from_inchi(c['inchi'])
return "%(inchikey)s %(cid)s ### %(name)s\n" % c
def database_string_to_compound( line):
a,name = line.split( "###")
inchi, cid = a.split()
inchikey = inchi_key.key_from_inchi( inchi)
return {'inchikey':inchikey.strip(), 'cid':cid.strip(), 'name':name.strip()}
def compound_to_database_string( c):
c['inchi'] = normalize_inchi( c['inchi'])
c['inchikey'] = inchi_key.key_from_inchi( c['inchi'])
return "%(inchikey)s %(cid)s ### %(name)s\n" % c
