No .cif files.

[tdaff]

Original report by Sean Collins (Bitbucket: scollins3, ).

---

Running this portion of code.

hydro = subprocess.Popen(['fapswitch', mof, '-o', 'fapswitch_custom_strings=[]'], stdout=subprocess.PIPE) while not os.path.exists('%sfunc.cif' % mof): time.sleep(1)

And get's stuck on the while not os.path.exists('%sfunc.cif' % mof). Eventually it gives an error.

Traceback (most recent call last): File "/home3/scollins/bin/fapswitch", line 1026, in main() File "/home3/scollins/bin/fapswitch", line 964, in main input_structure.gen_babel_uff_properties() File "/home3/scollins/bin/fapswitch", line 217, in gen_babel_uff_properties pybel_mol = pybel.readstring('fract', pybel_string) File "/home2/tdaff/Software/lib/python2.7/site-packages/pybel.py", line 117, in readstring success = obconversion.ReadString(obmol, string)

Seems only to happen with MOF-74. Will send you the file.

[tdaff]

Original comment by Tom Daff (Bitbucket: tdaff, GitHub: tdaff).

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Works in most recent version

#!txt

~/Compile/fapswitch/function_switch.py MOF-74 -o fapswitch_custom_strings=\[\] -v -o initial_structure_format=cif
-- No site options found; using defaults
-- No job options found; using defaults
-- an attribute: job_name
>> Initialising a new structure. This may take some time.
-- a custom -o option: initial_structure_format
>> Reading positions from cif file: MOF-74.cif
-- Found 162 unique atoms in 162
-- Calculating neighbour list.
-- Neighbour list already calculated
>> Structure attachment sites: ['H10']
** Assuming periodic openbabel; not generating supercell
>> Dumping cache of structure connectivity.
-- Reading groups from functional_groups.lib
-- Groups in library: ['Br', 'CN', 'COOH', 'Cl', 'Et', 'F', 'H', 'HCO',
   'I', 'Me', 'NH2', 'NO2', 'OEt', 'OH', 'OMe', 'OPr', 'Ph', 'Pr']
-- a default: daemon
-- a custom -o option: fapswitch_custom_strings
-- Random option strings: []
-- Site replacement options strings: ['']
-- []
>> Generated (0): []
-- a default: fapswitch_replace_only
-- a default: fapswitch_replace_groups
-- a default: fapswitch_replace_all_sites
-- a default: fapswitch_random_structure_count