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"], {})