Update __init__.py

[tomburnley]

Update ensemble_refinement to 2020 version. Added DEN restraints (now used by default). Fixed refinement flag manager. Added support for importing external TLS parameters from additional PDB.

[nwmoriarty]

Tom Can you tell me why DEN is default? Do you have any tests for these changes? Cheers Nigel

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--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty@LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

On Wed, Sep 16, 2020 at 9:09 AM Tom Burnley ***@***.***> wrote: @tomburnley <https://github.com/tomburnley> requested your review on: #528 <#528> Update *init*.py. — You are receiving this because your review was requested. Reply to this email directly, view it on GitHub <#528 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHYQPDIXHD5S4EZ74YCT3DSGDPLDANCNFSM4RPB7OWQ> .

[tomburnley]

Hi Nigel, DEN -> we found in testing that it makes the simulations more stable without negatively affecting sampling. W/out DEN on some occasions parts of the structure can unfold out of density. The attractive terms in Amber may alleviate this but for now w/ the repel potential it's better. The DEN pairs are regenerated multiple times during the simulation so sampling does not seem to be compromised. Testing -> yes... see separate email. Cheers, Tom On Wed, 16 Sep 2020 at 17:15, Nigel W. Moriarty <notifications@github.com> wrote:

…

Tom Can you tell me why DEN is default? Do you have any tests for these changes? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : ***@***.*** Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Sep 16, 2020 at 9:09 AM Tom Burnley ***@***.***> wrote: > @tomburnley <https://github.com/tomburnley> requested your review on: #528 > <#528> Update *init*.py. > > — > You are receiving this because your review was requested. > Reply to this email directly, view it on GitHub > <#528 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAHYQPDIXHD5S4EZ74YCT3DSGDPLDANCNFSM4RPB7OWQ > > . > — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#528 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACSF77V6VBGGQ2ZLVTQSFHLSGDQBXANCNFSM4RPB7OWQ> .

[olegsobolev]

Just a note, there are bunch of functions of the model class that deal with TLS:
get_header_tls_selections()
extract_tls_selections_from_input()
determine_tls_groups(self, selection_strings, generate_tlsos)

I see a lot of code to deal with TLS in this particular file, so maybe something more is going on, so I would not insist on using them in this particular case instead of things like

self.model.tls_groups.tlsos = fit_tlsos
fit_tlsos = [tls_tools.tlso(t=o.t, l=o.l, s=o.s, origin=o.origin) for o in tls_params.tls_params]

[olegsobolev]

please use iotbx.pdb.input() instead, preferably checking if the file exists.

[olegsobolev]

Still this, with the explanation in the previous message.

[bkpoon]

There are unused imports causing the Checks tests to fail.

In file __init__.py:
time imported at line 34
miller imported at line 19
geometry_restraints imported at line 17
cdl_utils imported at line 636
xray imported at line 21

An update will cause the CI to run again and the error for Full and Base should go away since I checked in some updates to the master branch.

[bkpoon]

Thanks! The Ci branch failures are fine. That pipeline does not run on the final, merged code with the updates to master.

[olegsobolev]

This requested change seems to be missed:

please use iotbx.pdb.input() instead of iotbx.pdb.hierarchy.input(), preferably checking if the file exists.

[tomburnley]

This requested change seems to be missed:

please use iotbx.pdb.input() instead of iotbx.pdb.hierarchy.input(), preferably checking if the file exists.

Can you explain the need for this and point to an example of use I can copy from please.

[olegsobolev]

@tomburnley , iotbx.pdb.hierarchy.input() seems to be a very thin wrapper that pretty much constructs hierarchy and keep input object:

cctbx_project/iotbx/pdb/hierarchy.py

Lines 2493 to 2536 in 1be58fd

	class input(input_hierarchy_pair):
	"""
	Class used for reading a PDB hierarchy from a file or string.
	Attributes
	----------
	input : iotbx.pdb.pdb_input_from_any
	hierarchy : iotbx.pdb.hierarchy.root
	Examples
	--------
	>>> import iotbx.pdb.hierarchy
	>>> pdb_in = iotbx.pdb.hierarchy.input(pdb_string='''
	... ATOM 1 N ASP A 37 10.710 14.456 9.568 1.00 15.78 N
	... ATOM 2 CA ASP A 37 9.318 14.587 9.999 1.00 18.38 C
	... ''')
	>>> print pdb_in.hierarchy.atoms_size()
	2
	"")
	"""
	def __init__(self, file_name=None,
	pdb_string=None, source_info=Auto, sort_atoms=True):
	"""
	Initializes an input from a file or string.
	Parameters
	----------
	file_name : str, optional
	pdb_string : str, optional
	source_info : str, optional
	Indicates where this PDB came from (i.e. "string")
	"""
	assert [file_name, pdb_string].count(None) == 1
	import iotbx.pdb
	if (file_name is not None):
	assert source_info is Auto
	pdb_inp = iotbx.pdb.input(file_name=file_name)
	else:
	if (source_info is Auto): source_info = "string"
	pdb_inp = iotbx.pdb.input(
	source_info=source_info, lines=flex.split_lines(pdb_string))
	super(input, self).__init__(input=pdb_inp, sort_atoms=sort_atoms)
	# END_MARKED_FOR_DELETION_OLEG

The original reason to create an extra layer for such a simple task is not clear to me in the first place. I could very well miss something, so clarifications from anyone are welcomed. As of now, I believe this whole layer better be removed, therefore advocate against using it anywhere.

In practical terms regarding this pull request I suggest to change this:

pdb_tls_inp = iotbx.pdb.hierarchy.input(file_name=pdb_import_tls)
tls_params = pdb_tls_inp.input.extract_tls_params(pdb_tls_inp.hierarchy)

to this:

pdb_tls_inp = iotbx.pdb.input(file_name=pdb_import_tls)
tls_params = pdb_tls_inp.extract_tls_params(pdb_tls_inp.construct_hierarchy())

Other examples of iotbx.pdb.input() usage can be found e.g. in iotbx/command_line/pdb_labels_comparison.py and many other files across the repository.