def run(self):
if checkfile(self.filepath)[0] and checkfile(self.filepath)[1] == 1:
self.singFile = True
if self.connect_to_server():
self.filefinder = FileFinder(self)
self.filefinder.recycle = False
self.filefinder.list_flie(self.filepath)
elif checkfile(self.filepath)[0] and checkfile(self.filepath)[1] == 0:
self.singFile = False
self.findfileOver = False
if self.connect_to_server():
print(dict('cd') + os.path.basename(self.filepath))
self.commandThread.send_command(
COMMANE_FILE_INFO + divider_arg +
os.path.basename(self.filepath) + divider_arg + '-1' +
divider_arg + str(msg_index))
while self.waitingCreateDir:
time.sleep(0.1)
self.waitingCreateDir = True
self.filefinder = FileFinder(self)
self.filefinder.recycle = False
self.filefinder.list_flie(self.filepath)
self.findfileOver = True
elif not checkfile(self.filepath)[0]:
print(dict('picf'))
def run(self):
if checkfile(self.filepath)[0] and checkfile(self.filepath)[1] == 1: # 文件
self.singFile = True
if self.connect_to_server():
self.filefinder = FileFinder(self)
self.filefinder.recycle = False
self.filefinder.list_flie(self.filepath)
elif checkfile(self.filepath)[0] and checkfile(self.filepath)[1] == 0: # 目录
self.singFile = False
self.findfileOver = False
if self.connect_to_server():
print('创建文件夹' + os.path.basename(self.filepath))
self.commandThread.send_command(COMMANE_FILE_INFO + divider_arg+
os.path.basename(self.filepath) + divider_arg +
'-1' +divider_arg
+ str(msg_index))
while self.waitingCreateDir: #等待服务端（接收端的目录创建完成）
time.sleep(0.1)
self.waitingCreateDir = True
self.filefinder = FileFinder(self)
self.filefinder.recycle = False
self.filefinder.list_flie(self.filepath) # 主体的循环，调用OnFindDir,OnFindFile
self.findfileOver = True # 结束传输
elif not checkfile(self.filepath)[0]:
print('请输入正确的文件路径')
def parse_PDB(pdb_file):
u.checkfile(pdb_file)
atom_names = []
res_names = []
res_ids = []
atom_coord = []
with open(pdb_file) as f:
for line in f:
# Read Atoms
if line[0:4] == 'ATOM' or line[0:6] == 'HETATM':
atom_names.append(line[12:15])
res_names.append(line[17:19])
try:
res_ids.append(int(line[22:25]))
except ValueError:
res_ids.append(None)
x = float(line[30:37])
y = float(line[38:45])
z = float(line[46:53])
atom_coord.append([x, y, z])
return atom_coord
def keyInSavePath():
while True:
filepath = input(dict('pidp'))
if checkfile(filepath)[0] and checkfile(filepath)[1] == 0:
return filepath, True
elif not checkfile(filepath)[0]:
warning(dict('pde'))
elif checkfile(filepath)[0] and checkfile(filepath)[1] == 1:
warning(dict('dpif'))
def keyInSavePath():
'''
输入存储的文件加路径
'''
while True:
filepath = input('请输入文件夹路径')
if checkfile(filepath)[0] and checkfile(filepath)[1] == 0:
return filepath, True
elif not checkfile(filepath)[0]:
warning('该路径下不存在任何文件')
elif checkfile(filepath)[0] and checkfile(filepath)[1] == 1:
warning('这个路径指向一个文件')
def keyInFilePath():
while True:
filepath = input('请输入文件或者文件夹的路径：')
if filepath.endswith(dir_divider()):
filepath2 = filepath[:len(filepath)-1]
else:
filepath2 = filepath
if checkfile(filepath2)[0]:
return filepath2, True
else:
print('该路径下不存在任何东西')
def keyInFilePath():
while True:
filepath = input(dict('pif'))
if filepath.endswith(dir_divider()):
filepath2 = filepath[:len(filepath) - 1]
else:
filepath2 = filepath
if checkfile(filepath2)[0]:
return filepath2, True
else:
print(dict('pde'))
def parse_MOL2(mol2_file):
u.checkfile(mol2_file)
atom_names = []
atom_types = []
res_names = []
res_ids = []
atom_coord = []
with open(mol2_file) as f:
while True:
line = f.readline()
if not line:
break
# Read initial lines
if line[0:17] == '@<TRIPOS>MOLECULE':
f.readline()
info = f.readline().split()
NAtoms = int(info[0])
try:
NRes = int(info[2])
except:
NRes = 1
# Read Atoms
elif line[0:13] == '@<TRIPOS>ATOM':
for i in range(NAtoms):
data = f.readline().split()
# save data for the old one
atom_names.append(data[1])
atom_types.append(data[5])
atom_coord.append(map(float, data[2:5]))
return atom_coord
filepath_ok = True
port_ok = True
host_ok = False
if args.port and args.port > 0 :
port = args.port
if port == default_command_socket_port:
warning('%s %d %s,%s' % ('端口',default_command_socket_port,'不可用','请输入其他的数字'))
port , port_ok = keyInPort()
elif args.port and args.port <=0:
warning('端口号必须为正整数')
port, port_ok = keyInPort()
filepath = args.filepath
if not filepath:
filepath , filepath_ok = keyInFilePath()
elif not checkfile(args.filepath)[0]:
warning('该路径下不存在任何文件')
filepath , filepath_ok = keyInFilePath()
host = args.host
if not host:
host , host_ok = keyInHost()
else:
host_ok = True
if port_ok and filepath_ok and host_ok:
findercallback = MyfinderCallback()
if not checkfile(filepath)[1]:
print('%s %s' % ('在此查找文件：',filepath))
FileFinder_Fast(findercallback).list_flie(filepath)
global sumsize
'--host',
required=False,
help=(dict('thtp')),
type=str)
args = parser.parse_args()
port = default_data_socket_port
port_ok = True
host_ok = False
save_path_ok = False
save_path = args.dir
if not save_path:
save_path = 'downloads'
if checkfile(save_path)[0] and checkfile(save_path)[1] == 0:
if not os.path.exists(save_path): os.makedirs(save_path)
save_path_ok = True
else:
if not checkfile(save_path)[0]:
warning(dict('pde'))
save_path, save_path_ok = keyInSavePath()
else:
save_path_ok = True
if args.host:
host = args.host
host_ok = True
else:
host = '0.0.0.0'
host_ok = True
def parse_input(infile):
'''Returns a Dictionary with dipole types,
and a list of tuples for points of application of the dipoles.
The keys of dipole types dictionary are the flags set ny the user in the input.
Each value is a tuple. The first element of the tuple is a list containing the
Dipolar Strength, the Excitation energy and the damping. The second element of
the tuple is a flag defining the type of polarizability to calculate (electric or
magnetic). The third element of the tuple if present only for magnetic polarizabilities
and it is the bj coefficient.
For application points, the data are tuples of 3 elements.
Each tuple contains, as first element, the center expressed in terms
of atom indexes and, as second element, the weight to be applied on the
first element of the list. As third element, we have a list of dipoles to be applied
in that point. The dipole is described through a list containing the dipole
type and its orientation, in terms of atomic indexes.'''
u.checkfile(infile)
type_counter = 0
center_counter = 0
dipole_types = {}
centers = []
with open(infile) as f:
while True:
line = f.readline()
if not line:
break
if line.strip():
if line.startswith('#'):
continue
# Create Dipole Types Dictionary
elif line.split()[0].lower() == 'type':
type_counter += 1
type_flag = line.split()[1]
# Try to read TYPE definition without optional keyword
try:
dipole = map(float, line.split()[2:])
pol_type = 'ele'
dipole_types[type_flag] = (map(float, line.split()[2:]), pol_type)
# Read TYPE definition with optional keyword
except ValueError:
pol_type = line.split()[-2]
bj = float(line.split()[-1])
dipole_types[type_flag] = (map(float, line.split()[2:-2]), pol_type, bj)
type_counter += 1
# Centers
elif line.split()[0].lower() == 'center':
center_counter += 1
weight = float(line.split()[1])
atom_idx = u.extend_compact_list(line.split()[2:])
# Adjust indices to Python's numeration
atom_idx = map(lambda x: x - 1, atom_idx)
data = f.readline().strip()
# Retrieve dipoles applied in this center
dipoles = []
while True:
if not data or data.split()[0].lower() != 'dipole':
break
data = data.split()
dip_type = [data[1]]
dip_ori = data[2:]
if len(dip_ori) == 2:
dip_ori = u.extend_compact_list(dip_ori)
elif len(dip_ori) > 2:
theta = float(dip_ori[-1])
dip_ori = u.extend_compact_list(dip_ori[:-1])
dip_ori = dip_ori + [theta]
dipole = dip_type + dip_ori
dipoles.append(dipole)
data = f.readline().strip()
centers.append((atom_idx, weight, dipoles))
# Dipoles
elif line.split()[0].lower() == 'dipole':
if center_counter == 0:
print(u.banner(text='ERROR', ch='#', length=80))
print
print(" You defined a DIPOLE before assigning it a CENTER in %s" % infile)
print
sys.exit()
# dipole_counter += 1
if type_counter == 0:
print(u.banner(text='ERROR', ch='#', length=80))
print
print(" No dipole TYPE has been defined in %s" % infile)
print
sys.exit()
return dipole_types, centers
def parse_XYZ(xyz_file):
u.checkfile(xyz_file)
struct = np.loadtxt(xyz_file, skiprows=2, usecols=[1, 2, 3])
return struct.tolist()
