def main(): try: opts, args = getopt.getopt(sys.argv[1:], 'a:b:h') except Exception, e: print "Error Options:[%s]"%e usage(sys.argv[0]) return -1
def main():
""" called when the file itself is executed"""
(options, values) = getopt.getopt(sys.argv[1:], "-d")
for option in options:
#print value
if option[0] == '-s':
try:
write_states('mongo')
except ValueError:
pass
def _value_after_option(self, option):
"""
内部函数，用来获取跟在选项后面的值
"""
"""
try:
# 获得选项位置
index = self.args.index(option)
# 下一位置即为选项值
return self.args[index + 1]
except (ValueError, IndexError):
print('Parameter Error')
exit()
"""
try:
# 把选项和参数装入数组
optlist, args = getopt.getopt(self.args, 'C:c:d:o:')
for i in range(len(optlist)):
if option in optlist[i]:
return optlist[i][1]
break
except getopt.GetoptError as err:
print(err)
exit()
def batch(self):
"""Automatic run of the tests"""
self.pre_run()
self.run()
def usage():
print """
./tester.py [-s|--simulate] <user> <conf1> <conf2>...
if no file are given in input it loads the configuration files configs/test_\d\w.ini
user is mandatory and will pick up the configuration from userconfs/*.ini
"""
sys.exit(0)
if __name__ == '__main__':
# TODO implementing a test cleaner
opts, args = getopt.getopt(sys.argv[1:],
'cvshdl', ['verbose', 'simulate', 'help', 'clean', 'debug', 'list'])
for o, a in opts:
if o in ('-h', '--help'):
usage()
if o in ('-d', '--debug'):
# Not functional programming
logging.getLogger().setLevel(logging.DEBUG)
if o in ('-v', '--verbose'):
logging.getLogger().setLevel(logging.INFO)
if o in ('-s', '--simulate'):
SIMULATE = True
if o in ('-l', '--list'):
def main():
global LISTEN_MODE
global CONNECT_MODE
global SCAN_MODE
mode = CONNECT_MODE
host = "localhost"
family = FAMILIES["inet"]
t = TYPES["tcp"]
ports = range(0, 300 + 1)
command = ""
sslkey = None
sslcert = None
systemArgs = sys.argv[1:] # ignore program name
optlist = []
args = []
try:
optlist, args = getopt.getopt(
systemArgs,
"",
[
"connect",
"listen",
"scan",
"family=",
"type=",
"port=",
"execute=",
"sslkey=",
"sslcert=",
"help"
]
)
except getopt.GetoptError:
usage()
if len(optlist) < 1 and len(args) < 1:
usage()
for option, value in optlist:
if option == "--help":
usage()
elif option == "--connect":
mode = CONNECT_MODE
elif option == "--family":
if value in FAMILIES:
family = FAMILIES[value]
else:
raise new TypeError("Family not valid")
elif option == "--type":
if value in TYPES:
t = TYPES[value]
else:
raise new TypeError("Type not valid")
elif option == "--port":
try:
ports = makerange(value)
except Exception, e:
usage()
elif option == "--listen":
mode = LISTEN_MODE
#!/usr/bin/python #coding:utf-8 """ @author:derek @contract:[email protected] @file: getopt_test.py @time: 2020-09-28 15:21 """ from getopt import getopt import sys opts, args = getopt.getopt(sys.argv[1:], "ho:", ["help", "output="]) print(opts) print(args)
def multidock(argv):
'''
自动多进程处理多个PDB晶体并完成自动对接 提取对接结果数据并保存为CSV文件
Parameters
----------
pdb_list: 包含多个pdb晶体ID的列表
'''
ligand_file = ''
try:
opts, argvs = getopt.getopt(argv, '-hr:l:')
except getopt.GetoptError:
print(
"usage: run py4schrodinger -r <receptors list file> -l <ligand file>\nUse run py4schrodinger.py -h for more information."
)
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print(
'usage: run py4schrodinger -r <receptors list file> [-l <ligand file>]'
)
print('''
Options
----------
-r 包含所有需要对接的受体PDB ID的列表文件(.txt)
-l 需要对接的外源配体文件(.pdb)
*当没有-l参数传入时，脚本仅执行受体列表内的晶体获取、处理与内源配体对接，而不会将任何外源配体对接到列表中的受体
''')
sys.exit(1)
elif opt == '-r':
list_file = arg
elif opt == '-l':
ligand_file = arg
try:
listname = list_file.split('.')[0]
with open(list_file, 'r') as f:
pdbs = f.readlines()
except FileNotFoundError:
print('Error: 未找到列表文件!')
sys.exit(2)
pdb_list = []
for i in pdbs:
j = i.strip().upper()
pdb_list.append(j)
print_title()
print('\nProcessing Input List...\n')
print('All Crystals to be Processed:',
''.join(str(x) + ' ' for x in pdb_list))
flag = input('\nContinue to Dock ? (Y/N)\n').strip().upper()
if flag == 'Y':
precision = input('请输入对接精度(HTVS|SP|XP):').strip().upper()
print('\nNumber of Total CPU:', multiprocessing.cpu_count(), end='\n')
cpus = int(input('请输入需要使用的CPU核心数量:'))
pool1 = multiprocessing.Pool(cpus)
pool2 = multiprocessing.Pool(cpus)
dic = {}
for pdb in pdb_list:
if not os.path.exists(pdb + '.pdb'): # 下载PDB文件
getpdb.get_pdb(pdb)
try:
os.makedirs(pdb)
except FileExistsError:
pass
dic[pdb] = get_ligname(pdb) # 如列表中有晶体存在多个配体 首先核对并确定唯一配体分子名
for pdb_code, ligand in dic.items(): # 采用进程池控制多线程运行
pool1.apply_async(autodock, (
pdb_code,
ligand,
precision,
))
time.sleep(1.5)
pool1.close() # 进程池关闭 不再提交新任务
pool1.join() # 阻塞进程 等待全部子进程结束
keys = dic.keys()
for k in keys: #异常晶体跳过
if not os.path.exists('./%s/%s_glide_dock_%s.maegz' %
(k, k, precision)):
del dic[k]
if ligand_file:
for pdb_code in pdb_list:
pool2.apply_async(dock_one_to_n, (
pdb_code,
ligand_file,
precision,
))
time.sleep(1.5)
pool2.close()
pool2.join()
prop = [
'PDB', 'Ligand', 'Docking_Score', 'rmsd', 'precision',
'ligand_efficiency', 'XP_Hbond', 'rotatable_bonds', 'ecoul',
'evdw', 'emodel', 'energy', 'einternal', 'lipo', 'hbond', 'metal',
'rewards', 'erotb', 'esite'
]
data = []
for pdb in pdb_list:
pro_ligand = dic[pdb]
prop_dic = extra_data(
'./%s/%s_glide_dock_%s.maegz' % (pdb, pdb, precision),
precision, pro_ligand)
data.append(prop_dic)
if ligand_file:
ligname = ligand_file.strip().split('.')[0]
ex_dic = extra_data(
'./%s/%s_glide_dock_on_%s_%s.maegz' %
(pdb, ligname, pdb, precision), precision, ligname)
data.append(ex_dic)
with open('%s_FINAL_RESULTS.csv' % listname,
'w',
encoding='UTF-8',
newline='') as f:
writer = csv.DictWriter(f, fieldnames=prop)
writer.writeheader()
writer.writerows(data)
print('\nAll Docking Jobs Done.\n')
else:
sys.exit(1)
