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process_hmdb.py
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process_hmdb.py
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#!/usr/bin/env python
'''
Update local HMDB database
Originally written by: Lars Ridder
Adapted by: Dries Verdegem
'''
import zlib
import sqlite3
import sys
import argparse
import urllib2
import zipfile
import StringIO
import base64
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Crippen
def version():
return '1.0'
def process_hmdb(args):
conn = sqlite3.connect(args.database_dir + '/HMDB_MAGMa.db')
c = conn.cursor()
try:
c.execute("""CREATE TABLE molecules (id TEXT PRIMARY KEY,
mim INTEGER NOT NULL,
charge INTEGER NOT NULL,
natoms INTEGER NOT NULL,
molblock TEXT,
inchikey TEXT,
molform TEXT,
name TEXT,
reference TEXT,
logp INT)""")
conn.commit()
print ("HMDB_MAGMa.db created")
except:
print ("HMDB_MAGMa.db already exists (or error creating it)")
exit()
if args.data_dir == None:
zf = urllib2.urlopen('http://www.hmdb.ca/system/downloads/current/structures.zip')
else:
zf = open(args.data_dir + 'structures.zip')
sdfile = zipfile.ZipFile(StringIO.StringIO(zf.read())).open('structures.sdf')
memstore = {}
line = '$$$$'
while line != "":
record = []
amap = {}
skip = False
ionized = 0
# read heading:
for x in range(4):
line = sdfile.readline()
record.append(line)
if line == "":
continue
natoms = int(record[-1][:3])
nbonds = int(record[-1][3:6])
bonds = 0
y = 0
for x in range(natoms):
line = sdfile.readline()
if line[31:33] == 'H ':
# skip hydrogens
continue
y += 1
amap[x + 1] = y
if line[31:33] not in ['C ', 'N ', 'O ', 'P ', 'S ', 'F ', 'Cl', 'Br', 'I ']:
# filter non-organic compounds
skip = True
elif line[50:51] != '0':
# this flag has something to do with polymeric structures
# and resulted in deviation between calculated and given inchikeys, skip
skip = True
elif line[38:39] == '4':
# radical, resulted in deviation between calculated and given inchikeys
skip = True
record.append(line[:42] + '\n')
for x in range(nbonds):
line = sdfile.readline()
a1 = int(line[:3])
a2 = int(line[3:6])
# skip bonds involving hydrogens
if a1 in amap and a2 in amap:
bonds += 1
# use bonds with stereoflags set to zero
record.append('%3i%3i%s 0\n' %
(amap[a1], amap[a2], line[6:9]))
while line != 'M END\n' and line != '':
line = sdfile.readline()
record.append(line)
if line[:6] == 'M ISO':
skip = True
print 'Skipped isotopically labeled:', record[0][:-1]
while line != "$$$$\n" and line != "":
line = sdfile.readline()
if line == "> <HMDB_ID>\n":
hmdb_id = str(sdfile.readline()[:-1])
elif line == "> <GENERIC_NAME>\n":
molname = str(sdfile.readline()[:-1])
elif line == "> <INCHI_KEY>\n":
inchi_key = sdfile.readline()[:-1]
if line != "" and skip == False:
record[3] = repr(y).rjust(3) + repr(bonds).rjust(3) + record[3][6:]
molblock = ''.join(record)
mol = Chem.MolFromMolBlock(molblock)
if mol == None or mol.GetNumAtoms() == 0:
continue
smiles = Chem.MolToSmiles(mol)
if len(Chem.GetMolFrags(mol)) > 1:
print 'complex:', hmdb_id, smiles
continue
molform = Chem.rdMolDescriptors.CalcMolFormula(mol)
mim = Chem.rdMolDescriptors.CalcExactMolWt(mol)
charge = 0
if '-' in molform:
if molform[-1] == '-':
charge = -1
else:
continue
elif '+' in molform:
if molform[-1] == '+':
charge = 1
else:
continue
natoms = mol.GetNumHeavyAtoms()
logp = Crippen.MolLogP(mol)
inchikey = AllChem.InchiToInchiKey(AllChem.MolToInchi(mol))[:14]
if inchikey != inchi_key[:14]:
print 'given inchikey does not match calculated inchikey, skipped:', hmdb_id, smiles
continue
c.execute('''INSERT INTO molecules (id, mim, charge, natoms, molblock, inchikey,
molform, name, reference, logp) VALUES (?,?,?,?,?,?,?,?,?,?)''', (
hmdb_id.decode('utf8'),
int(round(mim * 1e6)),
charge,
int(natoms),
sqlite3.Binary(zlib.compress(molblock)),
inchikey.decode('utf8'),
molform.decode('utf8'),
unicode(molname, 'utf-8', 'xmlcharrefreplace'),
hmdb_id.decode('utf8'),
int(round(logp * 10))))
conn.commit()
print "Creating index ..."
c.execute('PRAGMA temp_store = 2')
c.execute(
'CREATE INDEX idx_cover ON molecules (charge,mim,natoms,reference,molform,inchikey,name,molblock,logp)')
conn.commit()
# main
mainparser = argparse.ArgumentParser(description=__doc__)
mainparser.add_argument(
'-v', '--version', action='version', version='%(prog)s ' + version())
mainparser.add_argument(
'-d', '--data_dir', help="""Directory where HMDB structures.zip file is stored
(default: %(default)s, attempt to read directly from HMDB server)""", default=None, type=str)
mainparser.add_argument(
'-b', '--database_dir', help="Directory where HMDB database is stored (default: %(default)s)", default="./", type=str)
mainparser.set_defaults(func=process_hmdb)
args = mainparser.parse_args(sys.argv[1:])
args.func(args)