sys.path.append('../../affinityDB/db_libs')
import database, sqlite3
import imp
db_dir = os.path.join(os.path.abspath(os.getcwd()), 'database')
db_path = os.path.join(db_dir, 'database.db')
data_dir = os.path.join(db_dir, 'data')
if not os.path.exists(data_dir):
os.makedirs(data_dir)
afdb = database.AffinityDB(db_path)
database_master = database.DatabaseMaster(db_path)
"""
with open('../VDS1/data/main_pdb_target_list.txt') as f: pdb_list = f.readline().strip().split(', ')
pdb_list = pdb_list[:2]
pdb_list = [str(p) for p in pdb_list]
fp, path, descr = imp.find_module('download_pdb_op')
lib_mod = imp.load_module('download_pdb_op', fp, path, descr)
lib_mod.Download_pdb_init(db_path=data_dir, download_dir = 'download')
afdb.run_multithread("download_pdb",
arg_types=[str],
print "sum test took: ", time.time(
Test_multout_init()
afdb.run_multithread("test_multout",
arg_types=[int],
arg_lists=[arg_ones],
out_types=[int],
out_names=['remainder'],
num_threads=20,commit_sec=1)
print "multout test took: ", time.time() - start, "seconds"
my_db = database.DatabaseMaster(db_path)
start = time.time()
run_idx = my_db.retrieve("arg_001_test_multout",
["run_idx"],
{"run_state":"{}==1"})[0]
print "len run idx:", len(run_idx)
out_idx = my_db.retrieve("out_001_test_multout",
["run_idx"],
{"run_idx":"{}<100000"})[0]
print "eln out idx", len(out_idx)
idx,val,order = my_db.list_search(out_idx,run_idx)
print idx
import sys, os, sqlite3, time
from glob import glob
from rdkit import Chem
sys.path.append('../../affinityDB')
import database
sys.path.append('../../affinityDB/dataset_libs')
import NEW
base_dir = '/home/cosmynx/Documents/database'
db_path = os.path.join(base_dir, 'labeled_pdb.db')
if os.path.isfile(db_path):
os.system('rm ' + db_path)
afdb = database.AffinityDB(db_path)
db_editor = database.DatabaseMaster(db_path)
# out_db_path = os.path.join(base_dir, 'labeled_pdb_out.db')
# if os.path.isfile(out_db_path):
# os.system('rm ' + out_db_path)
# afdb = database.AffinityDB(out_db_path)
"""Convert all the PDB files into mol files and generate ligand conformers-------"""
start = time.time()
ligand_files = glob(os.path.join(base_dir, 'labeled_pdb/crystal_ligands' + '/**/', '*[_]*.pdb'))[:]
NEW.GenerateConformersInit(base_dir=base_dir, num_conformers=100)
afdb.run_multithread(func="NEW.generate_conformers",
arg_types=[str],
arg_lists=[ligand_files],
out_types=[str, str, int],
import os, sys, time
import numpy as np
sys.path.append('../../affinityDB')
sys.path.append('../../affinityDB/lib_multithread')
import database, sqlite3
#import VDS1
from download_pdb_op import Download_pdb_init, download_pdb
from split_pdb_op import Split_pdb_init, split_pdb
from generate_conformers_op import Generate_conformers_init, generate_conformers
from pdb2mol_op import Pdb2mol_init, pdb2mol
from search_decoys_op import Search_decoys_init, search_decoys
db_root = "/home/maksym/Desktop/vds1/"
#os.remove(db_path)
afdb = database.AffinityDB(db_root, "test")
database_master = database.DatabaseMaster(os.path.join(db_root, "test.db"))
with open("./data/main_pdb_target_list.txt") as f:
raw_pdb_list = f.readlines()
pdb_list = raw_pdb_list[0].split(", ")
print "number of pdbs to download:", len(pdb_list), "will download only 20"
pdb_id_set = [(unicode(pdb_name), ) for pdb_name in pdb_list[:20]]
# download 20 pdbs
Download_pdb_init(db_root=db_root, download_dir="download_pdbs1")
afdb.run_multithread("download_pdb", arg_sets=pdb_id_set)
# # split 20 PDBs
disk_pdbs = database_master.retrieve("out_000_download_pdb",
["pdb_id", "pdb_file"], {})