def extra_info(self):
for state in self.state_list:
try:
state['lam'] = units.energy['nm'] / (state['exc_en'] / units.energy['eV'])
except ZeroDivisionError:
pass
if 'coor_file' in self.ioptions:
self.struc = lib_struc.structure()
self.struc.read_file(self.ioptions['coor_file'], self.ioptions['coor_format'])
elif 'mo_file' in self.ioptions:
self.struc = lib_struc.structure()
self.struc.read_file(self.ioptions['mo_file'], 'molden')
else:
self.struc = None
def extra_info(self):
for state in self.state_list:
try:
state['lam'] = units.energy['nm'] / (state['exc_en'] /
units.energy['eV'])
except ZeroDivisionError:
pass
if 'coor_file' in self.ioptions:
self.struc = lib_struc.structure()
self.struc.read_file(self.ioptions['coor_file'],
self.ioptions['coor_format'])
elif 'mo_file' in self.ioptions:
self.struc = lib_struc.structure()
self.struc.read_file(self.ioptions['mo_file'], 'molden')
else:
self.struc = None
def file_at_lists(self):
print("Automatic generation of at_lists partitioning ...")
self.coor_file()
struc = lib_struc.structure()
struc.read_file(file_path=self['coor_file'], file_type=self['coor_format'])
return struc.ret_partition()
def file_at_lists(self):
print("Automatic generation of at_lists partitioning ...")
self.coor_file()
struc = lib_struc.structure()
struc.read_file(file_path=self['coor_file'],
file_type=self['coor_format'])
return struc.ret_partition()
Syntax: babel.py <intype> <infile> <outtype> <outfile>
e.g. babel.py tmol coord xyz coord.xyz
""")
if len(sys.argv) < 4+1:
print(""" Supported file types:
col -- Columbus and Newton-X format
colr -- Columbus format, atoms reordered
txyz2 -- Tinker format with reading possibility (verify the atom types in the output)
vnx -- veloctiy (Newton-X format)
ntxyz -- velocity (Tinker format)
additionally all formats from openbabel are included
type 'babel -H' for a complete list""")
print('\nFour arguments required.')
sys.exit()
(intype,infile,outtype,outfile) = sys.argv[1:]
if intype in lib_struc.veloc_types: # special treatment of velocities
veloc = struc_linalg.veloc()
veloc.read_file(file_path=infile, file_type=intype)
veloc.write_veloc(file_path=outfile,file_type=outtype)
else:
struc = lib_struc.structure()
struc.read_file(file_path=infile, file_type=intype)
struc.make_coord_file(file_path=outfile,file_type=outtype)
print("Finished: file %s written."%outfile)
Syntax: babel.py <intype> <infile> <outtype> <outfile>
e.g. babel.py tmol coord xyz coord.xyz
""")
if len(sys.argv) < 4 + 1:
print(""" Supported file types:
col -- Columbus and Newton-X format
colr -- Columbus format, atoms reordered
txyz2 -- Tinker format with reading possibility (verify the atom types in the output)
vnx -- veloctiy (Newton-X format)
ntxyz -- velocity (Tinker format)
additionally all formats from openbabel are included
type 'babel -H' for a complete list""")
print('\nFour arguments required.')
sys.exit()
(intype, infile, outtype, outfile) = sys.argv[1:]
if intype in lib_struc.veloc_types: # special treatment of velocities
veloc = struc_linalg.veloc()
veloc.read_file(file_path=infile, file_type=intype)
veloc.write_veloc(file_path=outfile, file_type=outtype)
else:
struc = lib_struc.structure()
struc.read_file(file_path=infile, file_type=intype)
struc.make_coord_file(file_path=outfile, file_type=outtype)
print("Finished: file %s written." % outfile)