def geometry(geom, name="default"):
"""Function to create a molecule object of name *name* from the
geometry in string *geom*. Permitted for user use but deprecated
in driver in favor of explicit molecule-passing. Comments within
the string are filtered.
"""
core.efp_init()
geom = pubchemre.sub(process_pubchem_command, geom)
geom = filter_comments(geom)
molecule = core.Molecule.create_molecule_from_string(geom)
molecule.set_name(name)
activate(molecule)
return molecule
def geometry(geom, name="default"):
"""Function to create a molecule object of name *name* from the
geometry in string *geom*. Permitted for user use but deprecated
in driver in favor of explicit molecule-passing. Comments within
the string are filtered.
"""
core.efp_init()
geom = pubchemre.sub(process_pubchem_command, geom)
geom = filter_comments(geom)
molecule = core.Molecule.create_molecule_from_string(geom)
molecule.set_name(name)
# Attempt to go ahead and construct the molecule
try:
molecule.update_geometry()
except:
core.print_out("Molecule: geometry: Molecule is not complete, please use 'update_geometry'\n"
" once all variables are set.\n")
activate(molecule)
return molecule
def geometry(geom, name="default"):
"""Function to create a molecule object of name *name* from the
geometry in string *geom*. Permitted for user use but deprecated
in driver in favor of explicit molecule-passing. Comments within
the string are filtered.
"""
core.efp_init()
geom = pubchemre.sub(process_pubchem_command, geom)
geom = filter_comments(geom)
molecule = core.Molecule.create_molecule_from_string(geom)
molecule.set_name(name)
# Attempt to go ahead and construct the molecule
try:
molecule.update_geometry()
except:
core.print_out("Molecule: geometry: Molecule is not complete, please use 'update_geometry'\n"
" once all variables are set.\n")
activate(molecule)
return molecule