sys.path.append('../../affinityDB')
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",
import glob,os,sys,time
sys.path.append("../../affinityDB/")
import database
from ccdc import io
import ccdc
db_root = "/home/maksym/Projects/datasets/CSD1/"
pdb_folder = "pdbs"
afdb_file = "CSD1.db"
afdb = database.AffinityDB(os.path.join(db_root,afdb_file))
out_q,stop_event = afdb.open_table_with_queue(table_name="some_table",
col_names=["ccdc_id","filename","SMILES"],
col_types=[str,str,str])
# Creating a CSD entry reader
csd_entry_reader = io.EntryReader('CSD')
# Create a CSD entry reader including any updates
directory = ccdc.io.csd_directory()
csd_and_updates = glob.glob(os.path.join(directory, '*.inf'))
csd_and_updates_reader = io.EntryReader(csd_and_updates)
#for i in range(1000):
# out_q.put(["srandom text"])
exceptions = []
i = 0
for mol in csd_entry_reader.molecules():
start = time.time()
try:
import os, sys
import numpy as np
sys.path.append('../../')
from dataset_libs import VDS2
import database, sqlite3
import dataset_libs
flags = VDS2.FLAGS(os.path.join(os.getcwd(), 'data'))
afdb = database.AffinityDB(flags.db_path)
db_editor = database.DatabaseGardener(flags.db_path)
# def get_run_state(table_name):
# """
# get run_state from args table and insert into out table
# """
#
# db_editor.up_merge(table_name,table_name[:17]+'_arg_'+table_name[22:],["run_state"])
flags.download_init('main_pdb_target_list.txt')
"""
afdb.run_multithread(func='VDS2.download',
arg_types=[str],
arg_lists=[flags.pdb_list],
out_types=[str, str],
out_names = ['receptor','pdb_path'],
num_threads=1, commit_sec=1)
get_run_state('aug_17_2017_27_36_out_VDS2.download')
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"], {})
