def execute(self, args):
"""Remove specified elements."""
db = MessDB()
cur = db.cursor()
for row in args.inchikeys:
inchikey = row.split()[0].strip()
try:
inchikey_dir = get_inchikey_dir(inchikey)
shutil.rmtree(inchikey_dir)
self.log_all.info('%s dir removed', inchikey)
except OSError:
self.log_console.info('%s did not have a directory', inchikey)
try:
parent = os.path.relpath(os.path.join(inchikey_dir, '../'))
os.removedirs(parent)
except OSError:
pass
records = 0
query = 'DELETE from molecule WHERE inchikey=?'
cur.execute(query, (inchikey,))
records += cur.rowcount
query = 'DELETE from molecule_synonym WHERE inchikey=?'
cur.execute(query, (inchikey,))
records += cur.rowcount
query = 'DELETE from molecule_source WHERE inchikey=?'
cur.execute(query, (inchikey,))
records += cur.rowcount
query = ('DELETE from molecule_state_method_property '
'WHERE inchikey=?')
cur.execute(query, (inchikey,))
records += cur.rowcount
db.commit()
self.log_all.info('%i %s records removed from db',
records, inchikey)
def __init__(self):
"""Initialize db cursor.
Args:
db (obj): A MessDB object
"""
self.db = MessDB()
self.log = Log('all')
self.source_dir = None
self.id = None
self.name = None
self.dirname = None
self.url = None
self.url_template = None
self.last_update = None
def execute(self, args):
"""Run self checks."""
self.db = MessDB()
cur = self.db.execute('SELECT inchikey FROM molecule')
self.db_inchikeys = set()
# check that inchikeys are all valid
for result in cur:
if is_inchikey(result.inchikey, enforce_standard=True):
self.db_inchikeys.add(result.inchikey)
else:
self.log_console.warning(('%s is not a valid standard '
'InChiKey!'), result.inchikey)
self.check_dir_structure()
self.check_db_structure()
self.check_db_dir_inchikey_concordance()
self.summary()
def __init__(self):
"""Set up db, check for attributes, dependencies, and setup."""
self.db = MessDB()
self.path = MethodPath()
self.log_console = Log('console')
self.log_all = Log('all')
self.method_name = self.get_method_name()
try:
self.parameters
self.description
self.geop # flag indicates method results in new xyz coordinates
self.prog_name
self.prog_version
self.prog_url
except AttributeError as err:
print(''.join([str(err), '\n']), file=sys.stderr)
sys.exit(('Each method class needs to define description, geop, '
'prog_name, prog_version, prog_url, '
'parameters as attributes.'))
self.check_dependencies()
class Source(object):
"""This class provides methods for importing sources and maintaining source
information in mess.db and in the molecule directories.
Attributes:
db (obj): A MessDB object
log (obj): A Log('all') object
source_dir (str): A path to the source directory
id (int): The source_id in the mess.db source table
name (str): A name for the source
dirname (str): The name of the source subdirectory in the 'sources'
directory
url (str): Url where the source can be downloaded
url_template (str): A url template that can be used to go to the web
page for a particular molecule in a source catalog
last_update (str): Date when source was last downloaded
"""
def __init__(self):
"""Initialize db cursor.
Args:
db (obj): A MessDB object
"""
self.db = MessDB()
self.log = Log('all')
self.source_dir = None
self.id = None
self.name = None
self.dirname = None
self.url = None
self.url_template = None
self.last_update = None
@classmethod
def get_sources(cls):
"""Returns a dictionary of source basenames mapped to source paths."""
source_dir = os.path.join(os.path.dirname(__file__), '../sources/')
sources = {}
for root, _, filenames in os.walk(source_dir):
for filename in [f for f in filenames
if f.endswith('.ini')
and not (f.startswith('.') or f.startswith('~'))]:
ini_basename = os.path.splitext(filename)[0]
if ini_basename == os.path.basename(root):
sources[ini_basename] = os.path.abspath(root)
return sources
def files(self):
"""Returns a list of importable files in the source directory."""
return [f for f in os.listdir(self.source_dir)
if not (f.startswith('.')
or f.startswith('~')
or f.endswith('.txt'))
and f.split('.')[-1] in pybel.informats]
def setup(self, source):
"""Setup source in mess.db.
Args:
source: A path to a source directory or a source basename.
"""
source_basename = os.path.basename(source.rstrip(os.sep))
if source_basename.endswith('.ini'):
source_basename = os.path.splitext(source_basename)[0]
sources = self.get_sources()
if source_basename not in sources:
sys.exit(("All sources must reside in the 'sources' directory, "
'read sources/SOURCES_README.md for details.'))
self.source_dir = sources[source_basename]
source_ini = os.path.join(self.source_dir, '%s.ini' % source_basename)
source_attributes = self.parse_ini(source_ini)
# insert/update source in the database
total_changes = self.db.total_changes
insert_query = ('INSERT OR IGNORE INTO source '
'(name, dirname, url, url_template, '
'citation, last_update) '
'VALUES (?, ?, null, null, null, null)')
update_query = ('UPDATE source '
'SET url=?, url_template=?, citation=?, last_update=? '
'WHERE dirname=?;')
self.db.execute(insert_query, (source_attributes['name'],
source_basename))
self.db.execute(update_query, (source_attributes['url'],
source_attributes['url_template'],
source_attributes['citation'],
source_attributes['last_update'],
source_basename))
if self.db.total_changes - total_changes > 1:
self.log.info('%s added to sources in database', source_basename)
select_query = ('SELECT source_id, name, dirname, '
'url, url_template, last_update '
'FROM source WHERE dirname=?')
source_row = self.db.execute(select_query,
(source_basename,)).fetchone()
# set attributes
self.id = source_row.source_id
self.name = source_row.name
self.dirname = source_row.dirname
self.url = source_row.url
self.url_template = source_row.url_template
self.last_update = source_row.last_update
def parse_ini(self, ini):
"""Parse source ini and return attributes."""
source_attributes = {
'url': None,
'url_template': None,
'citation': None
}
config = cp.ConfigParser(dict_type=CaseInsensitiveDict)
config.read(ini)
for section in config.sections():
for option in config.options(section):
source_attributes[option] = unicode_replace(config.get(section,
option))
required_attributes = ('name', 'last_update')
if not all(att in source_attributes for att in required_attributes):
sys.exit('Source INI missing required attributes: %s.'
% ' and/or '.join(required_attributes))
return source_attributes
def update_molecule_source_query(self, inchikey, identifier):
"""Update the source in mess.db.
Args:
inchikey: A molecule InChIKey.
identifier: A source identifier (usually a catalog number).
"""
query = ('INSERT OR IGNORE INTO molecule_source '
'(inchikey, source_id, identifier) '
'VALUES (?, ?, ?)')
return (query, (inchikey, self.id, identifier))
def update_source_tsv(self, inchikey, identifier):
"""Update the sources.tsv file.
Args:
inchikey_dir: Dir to a molecule in the molecules dir.
identifier: A source identifier (usually a catalog number).
"""
inchikey_dir = get_inchikey_dir(inchikey)
name = self.name.encode('ascii', 'replace')
dirname = self.dirname.encode('ascii', 'replace')
identifier = identifier.encode('ascii', 'replace')
sources_tsv = os.path.join(inchikey_dir, '%s.sources.tsv' % inchikey)
with codecs.open(sources_tsv, 'r', 'ascii') as sources_in:
with codecs.open(sources_tsv, 'a', 'ascii') as sources_out:
sources_in = csv.reader(sources_in, delimiter=b'\t')
sources_out = csv.writer(sources_out, delimiter=b'\t')
# check if source has been recorded
source_present = False
for row in sources_in:
try:
if row[1] == dirname and row[2] == identifier:
source_present = True
except IndexError:
pass
if not source_present:
if self.url_template:
url_split = re.split(r"\[|\]", self.url_template)
(match, replace) = re.split(r",\s?", url_split[1])
url_identifier = re.sub(match, replace, identifier)
source_url = url_split[0] + url_identifier
if 2 < len(url_split):
source_url += url_split[2]
else:
source_url = ''
sources_out.writerow([name, dirname, identifier,
source_url.encode('ascii',
'replace')])
self.log.inchikey = inchikey
self.log.info('%s added to %s sources', name, inchikey)
self.log.inchikey = None
class Check(AbstractTool):
"""This tool verifies that data in the database and the molecules directory
is self-consistent.
"""
def __init__(self):
"""Set description of tool."""
self.description = 'Check integrity of db/mess.db and molecules dir'
self.epilog = ''
def subparse(self, subparser):
"""Set tool-specific argparse arguments."""
pass # no arguments
def execute(self, args):
"""Run self checks."""
self.db = MessDB()
cur = self.db.execute('SELECT inchikey FROM molecule')
self.db_inchikeys = set()
# check that inchikeys are all valid
for result in cur:
if is_inchikey(result.inchikey, enforce_standard=True):
self.db_inchikeys.add(result.inchikey)
else:
self.log_console.warning(('%s is not a valid standard '
'InChiKey!'), result.inchikey)
self.check_dir_structure()
self.check_db_structure()
self.check_db_dir_inchikey_concordance()
self.summary()
def check_db_dir_inchikey_concordance(self):
"""Check concordance between inchikey dirs and mess.db."""
# get list of inchikeys from molecules/ dir
dir_inchikeys = set()
inchis = glob.glob(os.path.join(os.path.dirname(__file__),
'../../molecules/*/*/*/', '*.inchi'))
for i in inchis:
s = i.split('/')[-1]
dir_inchikeys.add(s.split('.')[0])
# compare inchikeys from db vs dir
in_db_not_dir = self.db_inchikeys - dir_inchikeys
in_db_msg = '%d InChIKeys in mess.db that are not in molecules dir'
if len(in_db_not_dir) > 0:
self.log_console.warning(in_db_msg, len(in_db_not_dir))
print('\n'.join(i for i in in_db_not_dir), file=sys.stderr)
in_dir_not_db = dir_inchikeys - self.db_inchikeys
in_dir_msg = '%d InChIKeys in molecules dir that are not in mess.db'
if len(in_dir_not_db) > 0:
self.log_console.warning(in_dir_msg, len(in_db_not_dir))
print('\n'.join(i for i in in_dir_not_db), file=sys.stderr)
def check_dir_structure(self):
"""Check that the structure of the molecules dir is consistent."""
moldir = os.path.join(os.path.dirname(__file__), '../../molecules')
for l in os.listdir(moldir):
lp = os.path.join(moldir, l)
if not os.path.isdir(lp):
if 'README' not in l and not l.startswith('.'):
self.log_console.warning(('Unexpected file in '
'molecules dir: %s'), l)
continue
if not len(l) == 1:
self.log_console.warning(('Unexpected dir in '
'molecules dir: %s'), l)
continue
for ll in os.listdir(lp):
llp = os.path.join(moldir, l, ll)
if not os.path.isdir(llp):
self.log_console.warning(('Unexpected file '
'in molecules dir: '
'%s/%s'), l, ll)
continue
if not (len(ll) == 2 and ll.isalpha()):
self.log_console.warning(('Unexpected dir '
'in molecules dir: '
'%s/%s'), l, ll)
continue
for lll in os.listdir(llp):
lllp = os.path.join(moldir, l, ll, lll)
if not os.path.isdir(lllp):
self.log_console.warning(('Unexpected file '
'in molecules dir: '
'%s/%s/%s'), l, ll, lll)
continue
if not is_inchikey(l + ll + lll, enforce_standard=True):
self.log_console.warning(('Unexpected dir '
'in molecules dir: '
'%s/%s/%s'), l, ll, lll)
continue
self.check_molecule_dir(l + ll + lll, lllp)
def check_molecule_dir(self, inchikey, d):
"""Check that molecule directory has the proper file in it."""
l = os.listdir(d)
if not inchikey + '.inchi' in l:
self.log_console.warning('%s does not contain inchi',
inchikey)
if not inchikey + '.log' in l:
self.log_console.warning('%s does not contain log file',
inchikey)
if not inchikey + '.notes' in l:
self.log_console.warning('%s does not contain notes',
inchikey)
if not inchikey + '.png' in l:
self.log_console.warning('%s does not contain png',
inchikey)
if 'sources.tsv' not in l:
self.log_console.warning(('%s does not contain '
'sources.tsv file'), inchikey)
else:
self.check_sources_tsv(os.path.join(d, 'sources.tsv'))
for ll in l:
if os.path.isdir(ll):
self.check_method_dir(os.path.join(d, ll))
def check_sources_tsv(self, s):
"""Check that sources.tsv files are consistent with mess.db."""
pass
def check_method_dir(self, d):
"""Check that method dirs are consistent with mess.db."""
pass
def check_db_structure(self):
"""Check that DB structure/data is self-consistent."""
# check inchikey foreign keys
molecule_synonym_inchikeys = set()
q = 'SELECT DISTINCT inchikey FROM molecule_synonym'
for r in self.db.execute(q).fetchall():
molecule_synonym_inchikeys.add(r.inchikey)
molecule_source_inchikeys = set()
q = 'SELECT DISTINCT inchikey FROM molecule_source'
for r in self.db.execute(q).fetchall():
molecule_source_inchikeys.add(r.inchikey)
q = 'SELECT DISTINCT inchikey FROM molecule_method_property'
molecule_method_property_inchikeys = set()
for r in self.db.execute(q).fetchall():
molecule_method_property_inchikeys.add(r.inchikey)
loose_keys_mol_syn = molecule_synonym_inchikeys - self.db_inchikeys
loose_keys_mol_src = molecule_source_inchikeys - self.db_inchikeys
loose_keys_mol_met_prp = (molecule_method_property_inchikeys -
self.db_inchikeys)
if len(loose_keys_mol_syn) > 0:
self.log_console.warning(('%d loose InChIKeys in '
'molecule_synonym table'),
len(loose_keys_mol_syn))
print('\n'.join(i for i in loose_keys_mol_syn), file=sys.stderr)
if len(loose_keys_mol_src) > 0:
self.log_console.warning(('%d loose InChIKeys in '
'molecule_source table'),
len(loose_keys_mol_src))
print('\n'.join(i for i in loose_keys_mol_src), file=sys.stderr)
if len(loose_keys_mol_met_prp) > 0:
self.log_console.warning(('%d loose InChIKeys in '
'molecule_method_property table'),
len(loose_keys_mol_met_prp))
print('\n'.join(i for i in loose_keys_mol_met_prp),
file=sys.stderr)
# check that sources in db exist in sources dir
q = 'SELECT source_id, dirname FROM source'
source_ids = set()
source_path = os.path.join(os.path.dirname(__file__), '../../sources')
for r in self.db.execute(q).fetchall():
source_ids.add(r.source_id)
if not os.path.isdir(os.path.join(source_path, r.dirname)):
self.log_console.warning('%s not in sources directory',
r.dirname)
# check source foreign keys
molecule_source_ids = set()
q = 'SELECT DISTINCT source_id FROM molecule_source'
for r in self.db.execute(q).fetchall():
molecule_source_ids.add(r.source_id)
loose_source_ids = molecule_source_ids - source_ids
if len(loose_source_ids) > 0:
self.log_console.warning(('%d loose source_ids in '
'molecule_source table'),
len(loose_source_ids))
print('\n'.join(i for i in loose_source_ids), file=sys.stderr)
# check program foreign keys
program_ids = set()
q = 'SELECT program_id FROM program'
for r in self.db.execute(q).fetchall():
program_ids.add(r.program_id)
method_program_ids = set()
q = 'SELECT DISTINCT program_id FROM method'
for r in self.db.execute(q).fetchall():
method_program_ids.add(r.program_id)
loose_program_ids = method_program_ids - program_ids
if len(loose_program_ids) > 0:
self.log_console.warning(('%d loose program_ids in '
'method table'),
len(loose_program_ids))
print('\n'.join(i for i in loose_program_ids), file=sys.stderr)
# check parameter foreign keys
parameter_ids = set()
q = 'SELECT parameter_id FROM parameter'
for r in self.db.execute(q).fetchall():
parameter_ids.add(r.parameter_id)
method_parameter_ids = set()
q = 'SELECT DISTINCT parameter_id FROM method_parameter'
for r in self.db.execute(q).fetchall():
method_parameter_ids.add(r.parameter_id)
method_tag_parameter_ids = set()
q = 'SELECT DISTINCT parameter_id FROM method_tag'
for r in self.db.execute(q).fetchall():
method_tag_parameter_ids.add(r.parameter_id)
loose_m_pids = method_parameter_ids - parameter_ids
if len(loose_m_pids) > 0:
self.log_console.warning(('%d loose parameter_ids in '
'method_parameter table'),
len(loose_m_pids))
print('\n'.join(i for i in loose_m_pids), file=sys.stderr)
loose_mt_pids = method_tag_parameter_ids - parameter_ids
if len(loose_mt_pids) > 0:
self.log_console.warning(('%d loose parameter_ids in '
'method_tag table'),
len(loose_mt_pids))
print('\n'.join(i for i in loose_mt_pids), file=sys.stderr)
property_ids = set()
q = 'SELECT property_id FROM property'
for r in self.db.execute(q).fetchall():
property_ids.add(r.property_id)
mmp_property_ids = set()
q = 'SELECT DISTINCT property_id FROM molecule_method_property'
for r in self.db.execute(q).fetchall():
mmp_property_ids.add(r.property_id)
loose_mmp_property_ids = mmp_property_ids - property_ids
if len(loose_mmp_property_ids) > 0:
self.log_console.warning(('%d loose property_ids in '
'method_tag table'),
len(loose_mmp_property_ids))
print('\n'.join(i for i in loose_mmp_property_ids),
file=sys.stderr)
# check that methods in db exist in methods dir
method_ids = set()
q = 'SELECT method_id, name FROM method'
for r in self.db.execute(q).fetchall():
method_ids.add(r.method_id)
# check method foreign keys
method_parameter_mids = set()
q = 'SELECT DISTINCT method_id FROM method_parameter'
for r in self.db.execute(q).fetchall():
method_parameter_mids.add(r.method_id)
method_edge_mids = set()
q = ('SELECT DISTINCT parent_method_id, child_method_id '
'FROM method_edge')
for r in self.db.execute(q).fetchall():
method_edge_mids.add(r.parent_method_id)
method_edge_mids.add(r.child_method_id)
loose_method_parameter_mids = method_parameter_mids - method_ids
if len(loose_method_parameter_mids) > 0:
self.log_console.warning(('%d loose method_ids in '
'method_parameter table'),
len(loose_method_parameter_mids))
print('\n'.join(i for i in loose_method_parameter_mids),
file=sys.stderr)
loose_method_edge_mids = method_edge_mids - method_ids
if len(loose_method_edge_mids) > 0:
self.log_console.warning(('%d loose method_ids in '
'method_edge table'),
len(loose_method_edge_mids))
print('\n'.join(i for i in loose_method_edge_mids),
file=sys.stderr)
# check edge foreign keys
method_edge_ids = set()
q = 'SELECT method_edge_id FROM method_edge'
for r in self.db.execute(q).fetchall():
method_edge_ids.add(r.method_edge_id)
method_path_edge_ids = set()
q = 'SELECT DISTINCT method_edge_id FROM method_path_edge'
for r in self.db.execute(q).fetchall():
method_path_edge_ids.add(r.method_edge_id)
loose_method_path_edge_ids = method_path_edge_ids - method_edge_ids
if len(loose_method_path_edge_ids) > 0:
self.log_console.warning(('%d loose method_edge_ids in '
'method_path_edge table'),
len(loose_method_path_edge_ids))
print('\n'.join(i for i in loose_method_path_edge_ids),
file=sys.stderr)
# check path foreign keys
method_path_ids = set()
q = 'SELECT method_path_id FROM method_path'
for r in self.db.execute(q).fetchall():
method_path_ids.add(r.method_path_id)
method_path_edge_pids = set()
q = 'SELECT DISTINCT method_path_id FROM method_path_edge'
for r in self.db.execute(q).fetchall():
method_path_edge_pids.add(r.method_path_id)
loose_method_path_edge_pids = method_path_edge_pids - method_path_ids
if len(loose_method_path_edge_pids) > 0:
self.log_console.warning(('%d loose method_path_ids in '
'method_path_edge table'),
len(loose_method_path_edge_pids))
print('\n'.join(i for i in loose_method_path_edge_pids),
file=sys.stderr)
# check edge closure
# check path completeness, connectedness, and length concordance
def summary(self):
"""Print summary statistics about molecules in MESS.DB."""
self.log_console.info('%d molecules in MESS.DB',
len(self.db_inchikeys))
def execute(self, args):
"""Match molecules to SMARTS patterns."""
if args.inchikeys.name == '<stdin>' and args.inchikeys.isatty():
sys.exit('No input specified.')
# parse args
if not (args.smarts or args.fingerprint or args.spectrophore):
sys.exit('No operations were selected, nothing to match.')
if sum(bool(arg) for arg in (args.smarts,
args.fingerprint,
args.spectrophore)) > 1:
sys.exit(('One thing at a time, please. The arguments --smarts, '
'--fingerprint, and --spectrophore are mutually '
'exclusive.'))
if args.smarts and args.target:
self.log_console.warning(('--target ignored, proceeding with '
'SMARTS matching'))
if args.spectrophore:
if args.path is None:
sys.exit(('Spectrophore calculation requires 3D geometry. '
'You must specify a 3D geometry with --path.'))
else:
path = MethodPath()
path.set_path(args.path)
method_dir = path.get_path_directory()
sp_args = {'normalization': args.spectrophore_normalization,
'accuracy': args.spectrophore_accuracy,
'stereo': args.spectrophore_stereospecificity,
'resolution': args.spectrophore_resolution}
# load target and target fingerprints
target_mol = None
target_fp = None
target_sp = None
if args.target:
if os.path.exists(args.target):
target_mol = pybel.readfile(args.target.split('.')[-1],
args.target).next()
else:
target_mol = pybel.readstring('smi', args.target)
if target_mol is not None:
if args.fingerprint:
target_fp = self.calculate_fingerprint(target_mol,
args.fingerprint)
if args.spectrophore:
target_sp = self.calculate_spectrophore(target_mol, sp_args)
# match every input
db = MessDB()
inchi_query = 'SELECT inchi FROM molecule WHERE inchikey = ?'
fp_query = ('SELECT fingerprint FROM molecule_fingerprint '
'WHERE inchikey = ? AND name = ? '
'AND settings = ? AND method_path_id = ?')
writer = csv.writer(sys.stdout, delimiter=args.delimiter)
for row in args.inchikeys:
inchikey = row.split()[0].strip()
if args.smarts or args.fingerprint:
inchi = db.execute(inchi_query, (inchikey,)).fetchone()[0]
mol = pybel.readstring('inchi', 'InChI=%s' % inchi)
if args.smarts:
canonical = pybel.ob.OBOp.FindType(b"canonical")
canonical.Do(mol.OBMol)
for (smarts_obj,
smarts_str) in self.smarts_generator(args.smarts):
matches = [match for match in smarts_obj.findall(mol)]
if len(matches) > 0:
writer.writerow([inchikey, smarts_str] + matches)
if args.fingerprint:
try:
fp = db.execute(fp_query, (inchikey, args.fingerprint,
'', '')).fetchone()[0]
except TypeError:
fp = self.calculate_fingerprint(mol, args.fingerprint)
if target_fp is not None:
similarity = self.calculate_similarity(target_fp, fp,
'tanimoto')
if similarity > args.cutoff:
writer.writerow([inchikey, args.fingerprint,
args.target, similarity])
else:
writer.writerow([inchikey, args.fingerprint] + fp)
if args.spectrophore:
try:
sp = db.execute(fp_query, (inchikey, 'Spectrophore',
json.dumps(sp_args,
sort_keys=True),
args.path)).fetchone()[0]
except TypeError:
xyz_file = os.path.join(get_inchikey_dir(inchikey),
method_dir,
'%s.xyz' % inchikey)
mol = pybel.readfile('xyz', xyz_file).next()
sp = Match.calculate_spectrophore(mol, sp_args)
if target_sp is not None:
try:
similarity = self.calculate_similarity(target_sp, sp,
'cos')
except ValueError:
similarity = 0
if similarity > args.cutoff:
writer.writerow([inchikey, 'Spectrophore',
args.target, similarity])
else:
writer.writerow([inchikey, 'Spectrophore'] + sp)
class AbstractMethod(object):
"""All methods must inherit from this class.
Attributes:
db (obj): A MessDB object
method_name (str): The name of the method
description (str): Description of method
geop (bool): Whether the method generates a new geometry
prog_name (str): Program name
prog_version (str): Program version
prog_url (str): Program url
parameters (dict): Parameters that affect program execution
"""
parameters = dict()
shortdesc = None
method_citation = None
prog_citation = None
_inchikey = None
_path_id = None
_parent_path_id = None
_method_dir = None
_parent_method_dir = None
def __init__(self):
"""Set up db, check for attributes, dependencies, and setup."""
self.db = MessDB()
self.path = MethodPath()
self.log_console = Log('console')
self.log_all = Log('all')
self.method_name = self.get_method_name()
try:
self.parameters
self.description
self.geop # flag indicates method results in new xyz coordinates
self.prog_name
self.prog_version
self.prog_url
except AttributeError as err:
print(''.join([str(err), '\n']), file=sys.stderr)
sys.exit(('Each method class needs to define description, geop, '
'prog_name, prog_version, prog_url, '
'parameters as attributes.'))
self.check_dependencies()
def __hash__(self):
"""Hash based on method name and parameters.
Returns:
A hex string of the sha1 hash of self.method_name plus
JSON-serialized self.parameters. Keys are sorted.
"""
return hashlib.sha1(self.method_name +
json.dumps(dict((str(k).lower(),
str(v).lower())
for k, v
in self.parameters.iteritems()),
sort_keys=True)).hexdigest()
@property
def hash(self):
"""Get hash."""
return self.__hash__()
@property
def method_id(self):
"""Get the object's method_id attribute."""
query = ('SELECT method_id FROM method '
'WHERE hash = ?;')
row = self.db.execute(query, (self.hash,)).fetchone()
return row.method_id
@property
def path_id(self):
"""Get the path id of the method."""
if not self.path.get_method_id() == self.method_id:
self._setup_path()
return self._path_id
@property
def method_dir(self):
"""Get the directory name of the method."""
if not self.path.get_method_id() == self.method_id:
self._setup_path()
return self._method_dir
@property
def parent_method_dir(self):
"""Get the parent directory name of the method."""
if not self.path.get_method_id() == self.method_id:
self._setup_path()
return self._parent_method_dir
@property
def inchikey(self):
"""Get inchikey."""
return self._inchikey
@inchikey.setter
def inchikey(self, inchikey):
"""Set inchikey, and update inchikey of logger."""
if inchikey is not None and not is_inchikey(inchikey):
raise RuntimeError('invalid inchikey: %s' % inchikey)
self._inchikey = inchikey
self.log_all.inchikey = inchikey
@classmethod
def get_method_name(cls):
"""Return the name of the method, derived from the subclass name."""
return cls.__name__.replace('_', '').lower()
def _setup_path(self):
"""Setup path given current method id and parent path."""
self.path.setup_path(self.method_id, self._parent_path_id)
self._path_id = self.path.get_path_id()
self._method_dir = self.path.get_path_directory()
self._parent_method_dir = self.path.get_parent_path_directory()
def _insert_method(self):
"""Set insert program to db, set up hash, and insert method to db."""
total_changes = self.db.total_changes
query = ('INSERT OR IGNORE INTO method '
'(program_id, geop, name, shortdesc, citation, hash) '
'SELECT program.program_id, ?, ?, ?, ?, ? '
'FROM program '
'WHERE program.name=? AND program.version=?')
self.db.execute(query, (self.geop, self.method_name, self.shortdesc,
self.method_citation, self.hash,
self.prog_name, self.prog_version))
if self.db.total_changes - total_changes > 0:
self.log_all.info('new %s method added to MESS.DB',
self.method_name)
def _insert_program(self):
"""Adds row to program table in mess.db."""
total_changes = self.db.total_changes
query = ('INSERT OR IGNORE INTO program '
'(name, version, url, citation) '
'VALUES (?, ?, ?, ?)')
self.db.execute(query,
(self.prog_name, self.prog_version, self.prog_url,
self.prog_citation))
if self.db.total_changes - total_changes > 0:
self.log_all.info('program %s %s added to MESS.DB',
self.prog_name, self.prog_version)
def _insert_parameters(self):
"""Import paramaters dict to mess.db.
Args:
name: Name of parameter.
setting: The value the parameter is set to.
"""
added_parameters = 0
for name, setting in self.parameters.items():
query = ('INSERT OR IGNORE INTO parameter (name) VALUES (?)')
self.db.execute(query, (name, ))
total_changes = self.db.total_changes
query = ('INSERT OR IGNORE INTO method_parameter '
'(method_id, parameter_id, setting) '
'SELECT ?, parameter.parameter_id, ? '
'FROM program, parameter '
'WHERE parameter.name=?')
self.db.execute(query, (self.method_id, setting, name))
added_parameters += (self.db.total_changes - total_changes)
if added_parameters > 0:
self.log_all.info('%i method parameters added to MESS.DB',
added_parameters)
def get_insert_property_query(self, inchikey, name, description,
format_, value, units=''):
"""Returns query to insert property value to mess.db.
Args:
inchikey: The inchikey of a molecule in MESS.DB.
method_path_id: Path id for the calculations that generated the
property.
name: The property name.
description: A description of the property.
format_: A description of the format the property is in.
value: The calculated property.
units: Units for the property value.
"""
query = ('INSERT OR IGNORE INTO molecule_method_property_denorm '
'VALUES (?, ?, ?, ?, ?, ?, ?);')
return (query, (inchikey, self.path_id, name, description,
format_, units, value))
def get_insert_moldata_queries(self, inchikey, mol,
description='', units=''):
"""Returns queries to insert molecule data values to mess.db."""
for name, value in mol.data.iteritems():
yield self.get_insert_property_query(inchikey,
name,
description,
type(value).__name__,
value,
units)
def get_timing_query(self, inchikey, start):
"""Get a query to insert execution time property into db."""
return self.get_insert_property_query(inchikey, 'runtime',
'execution time',
type(start).__name__,
time.time() - start, 's')
def set_parent_path(self, parent_path):
"""Set the parent path (e.g., path to method containing input
geometry.)"""
if parent_path > 0:
self._parent_path_id = parent_path
def has_parent_path(self, inchikey):
"""Returns True if molecule has had entire parent path calculated,
False otherwise."""
query = ('SELECT inchikey FROM molecule_method_property WHERE '
'inchikey = ? AND method_path_id = ?')
try:
self.db.execute(query,
(inchikey, self._parent_path_id)).fetchone()[0]
return True
except TypeError:
return False
def check_dependencies(self):
"""If check_dependencies is not implemented, raise error."""
raise NotImplementedError(("every method needs a 'check_dependencies' "
'method'))
def check(self):
"""If check is not implemented, raise error."""
# the check method should be called before a calculation (so
# calculations are not repeated) and after (to verify success)
raise NotImplementedError("every method needs a 'check' method")
def map(self, inchikey, inchikey_dir):
"""Generally, maps molecule to calculation via method, emits
query/value pairs.
"""
raise NotImplementedError(("every method needs a 'map' method"))
def reduce(self, query, values):
"""Run queries/values on the db."""
total_changes = self.db.total_changes
if query or values[0]:
self.db.executemany(query, values)
self.log_all.info('%i properties added to MESS.DB',
self.db.total_changes - total_changes)
total_changes = self.db.total_changes
def setup(self):
"""Set up method."""
self._insert_program()
self._insert_method()
self._insert_parameters()
def execute(self, args):
"""Run select query, output table."""
if args.inchikeys.name == '<stdin>' and args.inchikeys.isatty():
filter_from = None
else:
try:
filter_from = set(row.split()[0].strip()
for row in args.inchikeys)
except IndexError:
filter_from = set([])
return
if args.query and (args.property_name
or args.property_operator
or args.property_value):
sys.exit(('Custom SQL queries are mutually exclusive with '
'property filtering.'))
if (args.part or args.of) and not (args.part and args.of):
sys.exit(('If you specify a --part n, you must also specify --of '
'N (e.g. something like --part 1 --of 5).'))
if args.part and args.of:
if args.part > args.of:
sys.exit('--part must be smaller than --of.')
if args.part < 1:
sys.exit('--part must be >=1.')
alpha = string.ascii_uppercase
alpha3 = [''.join([a, b, c]) for a in alpha
for b in alpha
for c in alpha] # AAA to ZZZ
if args.of > len(alpha3):
sys.exit(('MESS.DB does not support subsetting into more than '
'%i parts.' % len(alpha3)))
subsets = [alpha3[i::args.of] for i in xrange(args.of)]
subset = subsets[args.part - 1]
db = MessDB()
cur = db.cursor()
if args.query:
try:
cur.execute(codecs.open(args.query, encoding='utf-8').read())
except sqlite3.OperationalError:
sys.exit("'%s' does not contain valid sql." % args.query)
except IOError:
try:
cur.execute(args.query)
except sqlite3.OperationalError:
sys.exit(("'%s' is neither valid sql nor a path "
'to a file containing valid sql.') % args.query)
elif (args.property_name and args.property_operator and
args.property_value is not None):
query, values = self.property_query(args.property_name,
args.property_operator,
args.property_value,
args.path)
cur.execute(query, values)
else:
cur.execute('SELECT inchikey FROM molecule')
# check that sql returns inchikey in first column
if not cur.description[0][0].lower() == 'inchikey':
sys.exit('Query must return inchikey in first column.')
# print table
writer = csv.writer(sys.stdout, delimiter=args.delimiter)
if args.headers:
writer.writerow(list(h[0] for h in cur.description))
for result in cur:
if filter_from is not None and result[0] not in filter_from:
continue
if args.regex_subset and not re.match(args.regex_subset, result[0],
re.IGNORECASE):
continue
if args.part and args.of:
if not any(result[0].startswith(a) for a in subset):
continue
if args.smarts:
matches = 0
query = 'SELECT inchi FROM molecule WHERE inchikey = ?'
inchi = db.execute(query, (result[0],)).fetchone()[0]
mol = pybel.readstring('inchi', 'InChI=%s' % inchi)
for (smarts_obj,
smarts_str) in Match.smarts_generator(args.smarts):
matches += len(smarts_obj.findall(mol))
if not matches:
continue
writer.writerow(list(xstr(v).decode('utf-8') for v in result))
db.close() # must be closed manually to prevent db locking during pipe
def execute(self, args):
"""Match molecules to SMARTS patterns."""
if args.inchikeys.name == '<stdin>' and args.inchikeys.isatty():
sys.exit('No input specified.')
if not (args.cir or args.fingerprint or args.spectrophore):
sys.exit('You did not request any annotations.')
if args.spectrophore:
if args.path is None:
sys.exit(('Spectrophore calculation requires 3D geometry. '
'You must specify a 3D geometry with --path.'))
else:
path = MethodPath()
path.set_path(args.path)
method_dir = path.get_path_directory()
sp_args = {'normalization': args.spectrophore_normalization,
'accuracy': args.spectrophore_accuracy,
'stereo': args.spectrophore_stereospecificity,
'resolution': args.spectrophore_resolution}
self.db = MessDB()
inchi_select_query = 'SELECT inchi FROM molecule WHERE inchikey = ?'
fp_select_query = ('SELECT fingerprint FROM molecule_fingerprint '
'WHERE inchikey = ? '
'AND name = ? '
'AND settings = ? '
'AND method_path_id = ?')
fp_insert_query = ('INSERT INTO molecule_fingerprint '
'(inchikey, name, settings, '
'fingerprint, method_path_id) '
'VALUES (?, ?, ?, ?, ?)')
for row in args.inchikeys:
self.inchikey = row.split()[0].strip()
if args.cir:
self.update_iupac(self.inchikey)
self.update_synonyms(self.inchikey)
if args.fingerprint:
inchi = self.db.execute(inchi_select_query,
(self.inchikey,)).fetchone()[0]
mol = pybel.readstring('inchi', 'InChI=%s' % inchi)
canonical = pybel.ob.OBOp.FindType(b'canonical')
canonical.Do(mol.OBMol)
fp = Match.calculate_fingerprint(mol, args.fingerprint)
try:
db_fp = self.db.execute(fp_select_query,
(self.inchikey,
args.fingerprint,
'',
'')).fetchone()[0]
if not str(fp) == db_fp:
self.log_console.warning(('new %s fingerprint '
'for %s did not match '
'fingerprint in db, '
'db not updated'),
args.fingerprint,
self.inchikey)
except TypeError:
self.db.execute(fp_insert_query, (self.inchikey,
args.fingerprint,
'',
str(fp),
''))
self.log_all.info('%s fingerprint for %s added to db',
args.fingerprint, self.inchikey)
if args.spectrophore:
xyz_file = os.path.join(get_inchikey_dir(self.inchikey),
method_dir,
'%s.xyz' % self.inchikey)
mol = pybel.readfile('xyz', xyz_file).next()
sp = Match.calculate_spectrophore(mol, sp_args)
try:
db_sp = self.db.execute(fp_select_query,
(self.inchikey,
'Spectrophore',
json.dumps(sp_args,
sort_keys=True),
args.path)).fetchone()[0]
if not str(sp) == db_sp:
self.log_console.warning(('new Spectrophore '
'fingerprint for '
'%s did not match '
'fingerprint in db, '
'db not updated'),
self.inchikey)
except TypeError:
json_sp_args = json.dumps(sp_args, sort_keys=True)
self.db.execute(fp_insert_query, (self.inchikey,
'Spectrophore',
json_sp_args,
str(sp),
args.path))
self.log_all.info(('Spectrophore fingerprint for %s '
'with parameters %s and '
'geometry from path %i '
'added to db'),
self.inchikey, json_sp_args, args.path)
class Annotate(AbstractTool):
"""This tool annotates molecules with synonyms (common names, CAS, etc) and
various fingerprints.
"""
def __init__(self):
"""Set description of tool."""
self.description = 'Annotate molecules with synonyms and fingerprints'
self.epilog = ''
def subparse(self, subparser):
"""Set tool-specific argparse arguments."""
subparser.add_argument('inchikeys', nargs='?',
type=argparse.FileType('r'), default=sys.stdin,
help=('a list of inchikeys (default: STDIN)'))
subparser.add_argument('-c', '--cir', action='store_true',
help=('get IUPAC names and other synonyms from '
'the Chemical Information Resolver web '
'service'))
subparser.add_argument('-f', '--fingerprint', type=str,
choices=[b'FP2', b'FP3', b'FP4',
b'MACCS', b'MNA', b'MPD'],
help=('calculate fingerprint'))
subparser.add_argument('-s', '--spectrophore', action='store_true',
help=('calculate Spectrophore '
'descriptor/fingerprint; '
'requires 3D geometry (i.e., you must '
'set a path to a method that has '
'generated xyz coordinates)'))
subparser.add_argument('-p', '--path', type=int, default=None,
help=('specify a path id, only used for '
'Spectrophore'))
sp_group = subparser.add_argument_group(('Spectrophore optional '
'arguments'))
sp_group.add_argument('-sn', '--spectrophore-normalization', type=str,
default='No', choices=[b'No',
b'ZeroMean',
b'UnitStd',
b'ZeroMeanAndUnitStd'],
help=('perform normalization of Spectrophore'))
sp_group.add_argument('-sa', '--spectrophore-accuracy', type=int,
default=20, choices=[1, 2, 5, 10, 15,
20, 30, 36, 45, 60],
help=('Spectrophore accuracy expressed as '
'angular stepsize; lower is more accurate'
'but slower'))
sp_group.add_argument('-ss', '--spectrophore-stereospecificity',
type=str, default='No',
choices=[b'No', b'Unique', b'Mirror', b'All'],
help=('cage type in terms of the underlying '
'pointgroup: P1 or P-1'))
sp_group.add_argument('-sr', '--spectrophore-resolution', type=float,
metavar='FLOAT', default=3.0,
help=('required Spectrophore resolution in '
'Angstroms'))
def execute(self, args):
"""Match molecules to SMARTS patterns."""
if args.inchikeys.name == '<stdin>' and args.inchikeys.isatty():
sys.exit('No input specified.')
if not (args.cir or args.fingerprint or args.spectrophore):
sys.exit('You did not request any annotations.')
if args.spectrophore:
if args.path is None:
sys.exit(('Spectrophore calculation requires 3D geometry. '
'You must specify a 3D geometry with --path.'))
else:
path = MethodPath()
path.set_path(args.path)
method_dir = path.get_path_directory()
sp_args = {'normalization': args.spectrophore_normalization,
'accuracy': args.spectrophore_accuracy,
'stereo': args.spectrophore_stereospecificity,
'resolution': args.spectrophore_resolution}
self.db = MessDB()
inchi_select_query = 'SELECT inchi FROM molecule WHERE inchikey = ?'
fp_select_query = ('SELECT fingerprint FROM molecule_fingerprint '
'WHERE inchikey = ? '
'AND name = ? '
'AND settings = ? '
'AND method_path_id = ?')
fp_insert_query = ('INSERT INTO molecule_fingerprint '
'(inchikey, name, settings, '
'fingerprint, method_path_id) '
'VALUES (?, ?, ?, ?, ?)')
for row in args.inchikeys:
self.inchikey = row.split()[0].strip()
if args.cir:
self.update_iupac(self.inchikey)
self.update_synonyms(self.inchikey)
if args.fingerprint:
inchi = self.db.execute(inchi_select_query,
(self.inchikey,)).fetchone()[0]
mol = pybel.readstring('inchi', 'InChI=%s' % inchi)
canonical = pybel.ob.OBOp.FindType(b'canonical')
canonical.Do(mol.OBMol)
fp = Match.calculate_fingerprint(mol, args.fingerprint)
try:
db_fp = self.db.execute(fp_select_query,
(self.inchikey,
args.fingerprint,
'',
'')).fetchone()[0]
if not str(fp) == db_fp:
self.log_console.warning(('new %s fingerprint '
'for %s did not match '
'fingerprint in db, '
'db not updated'),
args.fingerprint,
self.inchikey)
except TypeError:
self.db.execute(fp_insert_query, (self.inchikey,
args.fingerprint,
'',
str(fp),
''))
self.log_all.info('%s fingerprint for %s added to db',
args.fingerprint, self.inchikey)
if args.spectrophore:
xyz_file = os.path.join(get_inchikey_dir(self.inchikey),
method_dir,
'%s.xyz' % self.inchikey)
mol = pybel.readfile('xyz', xyz_file).next()
sp = Match.calculate_spectrophore(mol, sp_args)
try:
db_sp = self.db.execute(fp_select_query,
(self.inchikey,
'Spectrophore',
json.dumps(sp_args,
sort_keys=True),
args.path)).fetchone()[0]
if not str(sp) == db_sp:
self.log_console.warning(('new Spectrophore '
'fingerprint for '
'%s did not match '
'fingerprint in db, '
'db not updated'),
self.inchikey)
except TypeError:
json_sp_args = json.dumps(sp_args, sort_keys=True)
self.db.execute(fp_insert_query, (self.inchikey,
'Spectrophore',
json_sp_args,
str(sp),
args.path))
self.log_all.info(('Spectrophore fingerprint for %s '
'with parameters %s and '
'geometry from path %i '
'added to db'),
self.inchikey, json_sp_args, args.path)
def update_synonyms(self, inchikey):
"""Get synonyms from CIR and load them into mess.db."""
new_synonyms = 0
synonyms = self.cir_request(inchikey, 'names')
if synonyms:
select_query = ('SELECT inchikey FROM molecule_synonym '
'WHERE inchikey = ? AND name = ?')
insert_query = ('INSERT INTO molecule_synonym (inchikey, name) '
'VALUES (?, ?)')
for synonym in synonyms.split('\n'):
if self.db.execute(select_query,
(inchikey, synonym)).fetchone() is None:
self.db.execute(insert_query, (inchikey, synonym))
new_synonyms += 1
if new_synonyms > 0:
if new_synonyms > 1:
plural = 's'
else:
plural = ''
self.log_all.info('%i new synonym%s for %s added',
new_synonyms, plural, inchikey)
def update_iupac(self, inchikey):
"""Get IUPAC name from CIR and load it into mess.db."""
iupacs = []
iupac = None
new_synonyms = 0
try:
iupacs = self.cir_request(inchikey,
'iupac_name').splitlines(True)
# if multiple iupacs, take the longest (most specific) one
iupac = max(iupacs, key=len).rstrip()
except AttributeError:
return
if iupac is not None:
iupac_select_query = ('SELECT iupac FROM molecule '
'WHERE inchikey = ?')
iupac_update_query = ('UPDATE molecule SET iupac = ? '
'WHERE inchikey = ?')
db_iupac = self.db.execute(iupac_select_query,
(inchikey, )).fetchone()[0]
if not db_iupac == iupac:
self.db.execute(iupac_update_query, (iupac, inchikey))
self.log_all.info('iupac name for %s updated', inchikey)
if len(iupacs) > 1: # if multiple, add others as synonym
select_query = ('SELECT inchikey FROM molecule_synonym '
'WHERE inchikey = ? AND name = ?')
insert_query = ('INSERT INTO molecule_synonym '
'(inchikey, name) VALUES (?, ?)')
for i in iupacs:
if i != max(iupacs, key=len): # ignore longest iupac
synonym = i.rstrip()
if self.db.execute(select_query,
(inchikey,
synonym)).fetchone() is None:
self.db.execute(insert_query, (inchikey,
synonym))
new_synonyms += 1
if new_synonyms > 0:
if new_synonyms > 1:
plural = 's'
else:
plural = ''
self.log_all.info('%i new synonym%s for %s added',
new_synonyms, plural, inchikey)
def cir_request(self, inchikey, representation):
"""Make request to CIR (Chemical Information Resolver).
Args:
inchikey: A valid InChIKey.
representation: The representation desired from CIR.
Returns:
CIR's response, or None if there isn't one.
"""
url = 'http://cactus.nci.nih.gov/chemical/structure/%s/%s' %\
(inchikey, representation)
headers = {'User-Agent': 'MESS.DB'}
request = urllib2.Request(url, None, headers)
try:
response = urllib2.urlopen(request)
if response.getcode() == 200:
time.sleep(0.2) # protect cactus from hammering
return response.read()
except urllib2.URLError as err:
if hasattr(err, 'reason'):
reason = err.reason.lower()
self.log_console.info('%s %s %s in cir',
inchikey, representation, reason)
return None
