Added in all option for MR and bug fixes

[hlasimpk]

• Eugene requested that an option to run MR on all comparable space groups in addition to the current option to run MR on enantimophic space groups. I've added in a functions to do this in both MOLREP and PHASER, but I've changed the bool -enant argument to sgalternative where all and enant are options. I need to check this doesn't break Jens' i2 code.

• Note, there is an SG ALL option in Molrep which I had hoped would allow me to run against all alternative space groups, however I was unable to get this to work correctly in testing.

• I've added in a PDB standardize function to remove hydrogens and hetatms from pdb files downloaded from the PDB. If a ligand isn't recognised in the refmac5 ligand dictionary, refmac5 will exit without refining the molecule. There might be a more elegant way to handle this, currently using tempfiles.

• I encountered a bug when running testing SIMBAD on MTZ files with only intensities. Previously the miller arrays were handled as follows: find intensity miller array >> convert intensity miller array to amplitude miller array >> add amplitude array to mtz >> add intensity array to mtz Unfortunately the intensity miller array was being overwritten. I've modified this so that this no longer happens.

[fsimkovic]

Test cases do not run anymore. Please fix @hlasimpk

======================================================================
FAIL: test_get_labels_1 (util.tests.test_mtz_util.Test)
Test case for mtz_util.get_labels
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/felix/develop/SIMBAD-rig/simbad/util/tests/test_mtz_util.py", line 55, in test_get_labels_1
    self.assertEqual(data, reference_data)
AssertionError: Tuples differ: ('FTOXD3', 'SIGFTOXD3', 'I', '... != ('F', 'SIGF', 'I', 'SIGI', Non...

First differing element 0:
FTOXD3
F

- ('FTOXD3', 'SIGFTOXD3', 'I', 'SIGI', None, None, 'FreeR_flag')
?    -----        -----

+ ('F', 'SIGF', 'I', 'SIGI', None, None, 'FreeR_flag')

======================================================================
FAIL: test_get_labels_2 (util.tests.test_mtz_util.Test)
Test case for mtz_util.get_labels
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/felix/develop/SIMBAD-rig/simbad/util/tests/test_mtz_util.py", line 69, in test_get_labels_2
    self.assertEqual(data, reference_data)
AssertionError: Tuples differ: ('FHG2', 'SIGFHG2', 'I', 'SIGI... != ('F', 'SIGF', 'I', 'SIGI', 'DA...

First differing element 0:
FHG2
F

- ('FHG2', 'SIGFHG2', 'I', 'SIGI', 'DANOFHG2', 'SIGDANOFHG2', 'FreeR_flag')
?    ---        ---                      ---            ---

+ ('F', 'SIGF', 'I', 'SIGI', 'DANOF', 'SIGDANOF', 'FreeR_flag')