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set uno_cutoff=15 in align for atom mapping #462

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Add optional argument uno_cutoff=15 as suggested in MolSSI/QCElemental#270

Unable to test locally due to unmet dependencies (Gaussian, KinBot:

$ nosetests mappingTest.py:TestMapping.test_map_two_species
E
======================================================================
ERROR: Failure: NameError (name 'ReactionGenerator' is not defined)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/fuller/miniconda3/envs/arc_env/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/home/fuller/miniconda3/envs/arc_env/lib/python3.7/site-packages/nose/loader.py", line 417, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/fuller/miniconda3/envs/arc_env/lib/python3.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/fuller/miniconda3/envs/arc_env/lib/python3.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/fuller/miniconda3/envs/arc_env/lib/python3.7/imp.py", line 244, in load_module
    return load_package(name, filename)
  File "/home/fuller/miniconda3/envs/arc_env/lib/python3.7/imp.py", line 216, in load_package
    return _load(spec)
  File "<frozen importlib._bootstrap>", line 696, in _load
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/fuller/Dropbox/Documents/Technion/Code/ARC/arc/__init__.py", line 2, in <module>
    import arc.main
  File "/home/fuller/Dropbox/Documents/Technion/Code/ARC/arc/main.py", line 39, in <module>
    from arc.job.ssh import SSHClient
  File "/home/fuller/Dropbox/Documents/Technion/Code/ARC/arc/job/__init__.py", line 2, in <module>
    import arc.job.adapters
  File "/home/fuller/Dropbox/Documents/Technion/Code/ARC/arc/job/adapters/__init__.py", line 7, in <module>
    import arc.job.adapters.ts
  File "/home/fuller/Dropbox/Documents/Technion/Code/ARC/arc/job/adapters/ts/__init__.py", line 3, in <module>
    import arc.job.adapters.ts.kinbot_ts
  File "/home/fuller/Dropbox/Documents/Technion/Code/ARC/arc/job/adapters/ts/kinbot_ts.py", line 387, in <module>
    ) -> ReactionGenerator:
NameError: name 'ReactionGenerator' is not defined

...

root: DEBUG: Did not find Gaussian on path, checking if it exists in a declared GAUSS_EXEDIR, g09root or g03root...
--------------------- >> end captured logging << ---------------------

----------------------------------------------------------------------
Ran 1 test in 0.001s

FAILED (errors=1)

@mefuller mefuller requested a review from alongd August 23, 2021 08:24
@mefuller mefuller closed this Jan 13, 2022
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