Feature/dssp #4304

marinegor · 2023-09-29T14:07:08Z

Fixes #1612

Changes made in this Pull Request:

introduces MDAnalysis.analysis.dssp.DSSP class for secondary structure analysis, using code implemented in pydssp package available for secondary structure annotation
adds tests from pydssp package

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

Developers certificate of origin

I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

📚 Documentation preview 📚: https://mdanalysis--4304.org.readthedocs.build/en/4304/

pep8speaks · 2023-09-29T14:07:18Z

Hello @marinegor! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file package/MDAnalysis/analysis/dssp/dssp.py:

Line 2:80: E501 line too long (90 > 79 characters)
Line 14:80: E501 line too long (87 > 79 characters)
Line 16:80: E501 line too long (115 > 79 characters)
Line 27:80: E501 line too long (83 > 79 characters)
Line 48:80: E501 line too long (80 > 79 characters)
Line 64:80: E501 line too long (80 > 79 characters)
Line 73:80: E501 line too long (84 > 79 characters)
Line 80:80: E501 line too long (83 > 79 characters)
Line 82:80: E501 line too long (84 > 79 characters)
Line 84:80: E501 line too long (80 > 79 characters)
Line 190:80: E501 line too long (80 > 79 characters)
Line 217:80: E501 line too long (80 > 79 characters)
Line 221:80: E501 line too long (81 > 79 characters)
Line 223:80: E501 line too long (81 > 79 characters)
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Line 301:80: E501 line too long (89 > 79 characters)
Line 309:80: E501 line too long (91 > 79 characters)
Line 338:80: E501 line too long (81 > 79 characters)

In the file package/MDAnalysis/analysis/dssp/pydssp_numpy.py:

Line 68:80: E501 line too long (85 > 79 characters)
Line 157:80: E501 line too long (84 > 79 characters)
Line 179:80: E501 line too long (83 > 79 characters)
Line 206:80: E501 line too long (80 > 79 characters)
Line 207:80: E501 line too long (81 > 79 characters)

In the file testsuite/MDAnalysisTests/analysis/test_dssp.py:

Line 10:80: E501 line too long (81 > 79 characters)
Line 11:80: E501 line too long (85 > 79 characters)
Line 12:80: E501 line too long (82 > 79 characters)
Line 30:80: E501 line too long (80 > 79 characters)
Line 42:80: E501 line too long (80 > 79 characters)
Line 52:80: E501 line too long (80 > 79 characters)
Line 55:80: E501 line too long (82 > 79 characters)

Comment last updated at 2024-05-29 07:17:22 UTC

github-actions · 2023-09-29T14:09:33Z

Linter Bot Results:

Hi @marinegor! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/9281867626/job/25538692880

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

marinegor · 2023-09-29T23:55:10Z

There's a problem I don't know the workaround for yet: prolines.

In the original pydssp following happens:

atoms get parsed from pdb regardless of residue type
hydrogens get guilt automatically
based on that, secondary structure is assigned

However, in my implementation all prolines (and N-terminal residue) are assigned '-' (=unstructured loop).

This is likely less correct than original implementation, but I'm not sure how to fix that.
My suggestion would be to:

if guess_hydrogens=False, use positions of existing hydrogens and fill in fake proline hydrogens with pydssp
if guess_hydrogens=True, default to pydssp behaviour with fully automatic hydrogens

…cture in trajectory

marinegor · 2023-10-02T16:19:50Z

The prolines problem is now dealt with, exactly as I described above -- if guess_hydrogens=False, it would take hydrogens from atoms that have them, and otherwise (=prolines & N-term) guess their positions. Otherwise, would guess all the positions.

package/MDAnalysis/analysis/dssp.py

orbeckst

This looks already very promising.

For an initial quick review please see inline comments.

Additional requests

Fix the tests: AttributeError: module 'MDAnalysisTests.datafiles' has no attribute 'DSSP'
We also need a test with a trajectory.
Compress the PDF files with bz2 or gz.
Update CHANGELOG.
Add a .. versionadded:: 2.7.0 to the docs.
Fix PEP8 complaints.

Initially distinguishing H,E,- is good but eventually it would be good to distinguish other secondary structures, too, in particular 3₁₀ and π helices.

package/MDAnalysis/analysis/dssp.py

orbeckst · 2023-10-10T02:19:13Z

package/MDAnalysis/analysis/dssp.py

+CONST_Q1Q2 = 0.084
+CONST_F = 332
+DEFAULT_CUTOFF = -0.5
+DEFAULT_MARGIN = 1.0


Do these constants from from the original DSSP algorithm?

yes -- see "Hydrogen-Bonded Structure" part of the paper.

package/MDAnalysis/analysis/dssp.py

orbeckst · 2023-10-10T02:24:18Z

package/MDAnalysis/analysis/dssp.py

+    h3 = h3 * ~np.roll(helix4, -1, 1) * ~helix4  # helix4 is higher prioritized
+    h5 = h5 * ~np.roll(helix4, -1, 1) * ~helix4  # helix4 is higher prioritized


Can we get 3_10 and π helix, too?

I'm not certain, but seems like yes (used this paper's Fig 1):

from MDAnalysis.analysis.dssp import DSSP import MDAnalysis as mda u = mda.Universe('./1FUR.pdb') r = DSSP(u).run() r.results.resids[151:158] # array([155, 156, 157, 158, 159, 160, 161]) ''.join(r.results.dssp[0])[151:158] # 'HHHH-HH'

Yes, it can detect 3-10 and pi helixes indeed -- I generated idealized structures with mmtbx from here and ran DSSP on them:

dssp/o_beta_seq.pdb -------------------- dssp/o_helix310_seq.pdb -HHHHHHHHHHHHHHHHHH- dssp/o_helix_seq.pdb -HHHHHHHHHHHHHHHHHH- o_helix_pi_seq.pdb -HHHHHHHHHHHHHHHHHH-

package/MDAnalysis/analysis/dssp.py

testsuite/MDAnalysisTests/analysis/test_dssp.py

marinegor · 2024-04-08T16:35:06Z

Hi @yuxuanzhuang and @orbeckst , thanks for your review! Main changes:

now works with AtomGroup (and there's a test for that)
there are no more dssp-related errors when doing sphinx doctest
moved # pragma: no cover to the codepaths that actually are not tested.

Hope that works!

UPD: also again, CI/CD failures are codecov-related, as far as I can see.

yuxuanzhuang

I've corrected a missing reference bracket; everything else seems fine to me! It's a great addition to MDAnalysis!

yuxuanzhuang · 2024-04-09T13:10:57Z

package/MDAnalysis/analysis/dssp/dssp.py

+    '--EEEE----------HHHH'
+
+
+Functions


I think Oliver means moving the section of function (i.e. this block) in the documentation after Analysis classes

marinegor · 2024-04-09T14:02:32Z

@yuxuanzhuang I don't get which section you mean. If this one: https://mdanalysis--4304.org.readthedocs.build/en/4304/documentation_pages/analysis_modules.html
Then DSSP is already there, under "protein structure"

yuxuanzhuang · 2024-04-09T14:10:52Z

@yuxuanzhuang I don't get which section you mean. If this one: https://mdanalysis--4304.org.readthedocs.build/en/4304/documentation_pages/analysis_modules.html Then DSSP is already there, under "protein structure"

modified :)

marinegor · 2024-04-09T14:27:43Z

ah yeah I see now, my bad :) thanks a lot!

IAlibay

Thanks for all the work here @marinegor.

Please consider anything covered by [enh] as enhancements - i.e. nice to haves.

There are a few small blockers here that need addressing.

A note: this adds roughly ~ 1 MB of extra compressed data to the testsuite. I don't consider this a blocker, but something to keep in mind (currently we are at 56 MB compressed).

LICENSE

IAlibay · 2024-04-14T07:15:26Z

package/CHANGELOG

@@ -39,6 +39,7 @@ Fixes
 * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)

 Enhancements
+ * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)


I'm not going to block on this, but if you can wrap around at 79 chars here that would be grand.

IAlibay · 2024-04-14T07:22:45Z

package/MDAnalysis/analysis/dssp/dssp.py

+    mean_secondary_structure = translate(
+        long_run.results.dssp_ndarray.mean(axis=0)
+        )
+    print(''.join(mean_secondary_structure)[:20])


I'm re-opening this, I had the exact same question as @orbeckst reading through this. I'm not sure if the 20 residues clarification got removed later for other reasons, so I'm not going to block over this.

IAlibay · 2024-04-14T07:23:46Z

package/MDAnalysis/analysis/dssp/dssp.py

+
+Running this code produces ::
+
+   '-EEEEEE------HHHHHHH'


I think there are better ways of doing this, especially if we want doctest to run well over this.

Something like this:

mdanalysis/package/MDAnalysis/analysis/align.py

Lines 73 to 79 in 73acc9b

In the simplest case, we can simply calculate the C-alpha RMSD between

two structures, using :func:`rmsd`::

>>> ref = mda.Universe(PDB_small)

>>> mobile = mda.Universe(PSF, DCD)

>>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions)

28.20178579474479

my understanding was the opposite, and I recall that code-block:: python actually gives some errors in doctest. I'll rewrite if necessary.

I kind of dislike the >>> form for longer code examples, at least if I as a human have to read it.

@ljwoods2 can I pick your brain? I think you recently wrote doctests that did not use >>>. How did you do that?

I dislike >>> too, perhaps this was the reason for me thinking that code-block syntax was correct.

IAlibay · 2024-04-14T07:26:48Z

package/MDAnalysis/analysis/dssp/dssp.py

+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In this example, we will find residue groups that maintain their secondary structure
+along the simulation, and have some meaningful ('E' or 'H') secondary structure
+during more than set `threshold` share of frames. We will call these residues


Suggested change

during more than set `threshold` share of frames. We will call these residues

during more than set `threshold` fraction of the total frames. We will call these residues

Feel free to reject, it's just a nitpick - reading this I wasn't sure if the code below was going to expect a set number of frames or a fraction of the total number of frames.

Indeed, thanks.

package/MDAnalysis/analysis/dssp/dssp.py

testsuite/MDAnalysisTests/analysis/test_dssp.py

IAlibay · 2024-04-14T08:16:06Z

testsuite/pyproject.toml

@@ -72,6 +72,7 @@ include=[
    "MDAnalysisTests.data.gromacs",
    "MDAnalysisTests.data.lammps",
    "MDAnalysisTests.data.mol2",
+    "MDAnalysisTests.data.dssp",


This specific folder location is missing an __init__.py file - could you add one please?

marinegor

Added some comments, will fix the rest (selections, hydrogens, and documentation) later.

LICENSE

marinegor · 2024-04-17T15:51:18Z

package/CHANGELOG

@@ -39,6 +39,7 @@ Fixes
 * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)

 Enhancements
+ * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)


marinegor · 2024-04-17T15:55:32Z

package/MDAnalysis/analysis/dssp/dssp.py

+    mean_secondary_structure = translate(
+        long_run.results.dssp_ndarray.mean(axis=0)
+        )
+    print(''.join(mean_secondary_structure)[:20])


I've added a little comment about that in the code snippet.

My reasoning behind [:20] was that the full output is this:

--EEEE----------HHHHHHH----EE----HHHHH------HHHHHHHHHH------HHHHHHHHHHH---------EEEE-----HHHHHHHHH------EEEEEE--HHHHHH----EE--------EE---E----------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH----EEEEE------HHHHHHHHH--

which is kinda lengthy for the documentation🤷‍♂️

marinegor · 2024-04-17T16:02:25Z

package/MDAnalysis/analysis/dssp/dssp.py

+
+Running this code produces ::
+
+   '-EEEEEE------HHHHHHH'


my understanding was the opposite, and I recall that code-block:: python actually gives some errors in doctest. I'll rewrite if necessary.

package/MDAnalysis/analysis/dssp/dssp.py

marinegor · 2024-04-17T16:22:17Z

package/MDAnalysis/analysis/dssp/dssp.py

+        self._guess_hydrogens = guess_hydrogens
+
+        ag: AtomGroup = (
+            atoms.select_atoms("protein") if isinstance(atoms, Universe) else atoms


What happens here if you pick up a amino acid residue with more protons than is "normally" expected? E.g. ASH or GLUH

I have requested the files of this type on discord, but if you have any in mind, please let me know.

Given you end up doing a lot of protein residue selection below, would it make sense to just do it here once?

Perhaps, yes. I'll try refactoring it.

orbeckst

Thank you for addressing my last comments. I found minor things and added a whole bunch of code changes — please add those together with the ones from @IAlibay 's review. Thanks!

package/MDAnalysis/analysis/dssp/dssp.py

orbeckst · 2024-04-18T00:38:00Z

package/MDAnalysis/analysis/dssp/dssp.py

+    mean_secondary_structure = translate(
+        long_run.results.dssp_ndarray.mean(axis=0)
+        )
+    print(''.join(mean_secondary_structure)[:20])


Can we just show everything to make clearer what's happening, especially without explanation? Please remove the [:20] and add the full output. It's not too long.

orbeckst · 2024-04-18T00:42:29Z

package/MDAnalysis/analysis/dssp/dssp.py

+
+Running this code produces ::
+
+   '-EEEEEE------HHHHHHH'


I kind of dislike the >>> form for longer code examples, at least if I as a human have to read it.

@ljwoods2 can I pick your brain? I think you recently wrote doctests that did not use >>>. How did you do that?

orbeckst · 2024-04-18T00:43:01Z

package/MDAnalysis/analysis/dssp/dssp.py

+
+
+class DSSP(AnalysisBase):
+    """Assign secondary structure using DSSP algorithm.


include please

package/MDAnalysis/analysis/dssp/dssp.py

package/MDAnalysis/analysis/dssp/pydssp_numpy.py

testsuite/MDAnalysisTests/analysis/test_dssp.py

orbeckst

There are minor doc issues to fix, please see comments (incorrect reST syntax, missing print(), ...)

Please also address other reviews.

I am going to approve because in principle I am satisfied. Good work!

package/MDAnalysis/analysis/dssp/dssp.py

test_dssp.py

manual test a top level, should not be in source

testsuite/MDAnalysisTests/analysis/test_dssp.py

orbeckst · 2024-05-03T22:19:07Z

@IAlibay would you mind taking a quick final glance at the DSSP PR?

I think your comments were addressed but would prefer you confirm instead of me dismissing a totally valid review.

Would be great if we could finally get that one in.

marinegor · 2024-05-20T13:29:27Z

@IAlibay any comments on this one?

IAlibay

Apologies for the long review delay.

I just have the one docstring confusion, once addressed then it's good to go.

Tagging @orbeckst here - please do dismiss my review if this gets addressed and I don't get a chance to re-review.

IAlibay · 2024-05-28T19:16:31Z

package/MDAnalysis/analysis/dssp/dssp.py

+            for calpha, hydrogen in zip(
+                self._heavy_atoms["CA"][1:], self._hydrogens[1:]
+            ):
+                if not hydrogen and calpha.resname != "PRO":


Thanks for adding the warning, however I'm still a bit confused with this https://github.com/MDAnalysis/mdanalysis/pull/4304/files#diff-cad8095a75b51cba3d6ef256c3c05073b457f309406ae4a94f45ac53257f3e81R202

It claims we're checking for "H" but we only expect one "H" according to the warning? (sorry I'm probably misreading something).

marinegor · 2024-05-29T07:19:37Z

Hi @IAlibay -- couldn't follow your link, maybe you explain in more detail? I updated class's documentation slightly to match the description of the run method, but not sure if it solves your confusion

orbeckst

@marinegor and @IAlibay I think I understand the point of your discussion: As far as I can tell, I agree with @IAlibay that the current ValueError check does not exactly check that there's exactly one HN. If we could change the code then that would be safer, please see comments.

I think I also found a potential issue with how _heavy_atoms and _hydrogens are constructed. Please check.

orbeckst · 2024-05-31T01:13:23Z

package/MDAnalysis/analysis/dssp/dssp.py

+    .. Warning::
+        For the DSSP to work properly, your atoms (either as ``Universe``
+        or ``AtomGroup``) must have only one hydrogen atom "H" per residue,
+        that corresponds to N-bound hydrogen in a peptide bond (or zero hydrogen
+        atoms, if the residue is proline). It is selected using `hydrogen_atom`
+        parameter. It is designed to hande most of the modern syntaxes,
+        but if you encounter an error or unusual results
+        during your run, please report an issue on MDAnalysi
+        `github <https://github.com/MDAnalysis/mdanalysis/issues>`_.


Maybe the following is clearer?

Suggested change

.. Warning::

For the DSSP to work properly, your atoms (either as ``Universe``

or ``AtomGroup``) must have only one hydrogen atom "H" per residue,

that corresponds to N-bound hydrogen in a peptide bond (or zero hydrogen

atoms, if the residue is proline). It is selected using `hydrogen_atom`

parameter. It is designed to hande most of the modern syntaxes,

but if you encounter an error or unusual results

during your run, please report an issue on MDAnalysi

`github <https://github.com/MDAnalysis/mdanalysis/issues>`_.

.. Warning::

For DSSP to work properly, your atoms must represent a protein. The

hydrogen atom bound to the backbone nitrogen atom is matched by name

as given by the keyword argument `hydrogen_atom`. There may only be

a single backbone nitrogen hydrogen atom per residue; the one exception

is proline, for which there should not exist any such hydrogens.

The default value of `hydrogen_atom` should to handle the common naming

conventions in the PDB and in force fields but if you encounter an error

or unusual results during your run, try to figure out how to select the

correct hydrogen atoms and report an issue in the MDAnalysis

`issue tracker <https://github.com/MDAnalysis/mdanalysis/issues>`_.

orbeckst · 2024-05-31T01:15:36Z

package/MDAnalysis/analysis/dssp/dssp.py

+    .. Note::
+       To work with different hydrogen-naming conventions by default, the default
+       selection is broad but if hydrogens are incorrectly selected (e.g., a
+       :exc:`ValueError` is raised) you must customize ``hydrogen_name`` for your


reference kwargs by single backticks

Suggested change

:exc:`ValueError` is raised) you must customize ``hydrogen_name`` for your

:exc:`ValueError` is raised) you must customize `hydrogen_name` for your

orbeckst · 2024-05-31T01:36:19Z

package/MDAnalysis/analysis/dssp/dssp.py

+            for calpha, hydrogen in zip(
+                self._heavy_atoms["CA"][1:], self._hydrogens[1:]
+            ):
+                if not hydrogen and calpha.resname != "PRO":


The warning says that we expect exactly one H for non-PRO. Can you write the if with the following logic

if calpha.resname == "PRO": # special case PRO if hydrogen: raise ValueError(f"PRO {calpha.resid} has a hydrogen {hydrogen}") # else: # pass # expected: PRO has no hydrogen elif not hydrogen or len(hydrogen) > 1: # not a PRO and not exactly one HN: that's bad raise ValueError(f"{calpha.resname} {calpha.resid} has not exactly one HN, instead it has {hydrogen}")

At least that's my understanding what we should be seeing, @marinegor ?

(There's better code to be written than what I wrote but for following the logic I inserted a pass etc...)

orbeckst · 2024-05-31T01:42:21Z

package/MDAnalysis/analysis/dssp/dssp.py

+        self._heavy_atoms: dict[str, "AtomGroup"] = {
+            t: ag.atoms[
+                np.isin(
+                    ag.names, t.split()
+                )  # need split() since `np.isin` takes an iterable as second argument
+                # and "N".split() -> ["N"]
+            ]
+            for t in heavyatom_names
+        }
+        self._hydrogens: list["AtomGroup"] = [
+            res.atoms.select_atoms(f"name {hydrogen_name}") for res in ag.residues
+        ]


From the following code I see that there's the assumption that the order of atoms in _heavy_atoms["CA"] is the same as in _hydrogens.

However, that may not be true: _hydrogens is created from a select_atoms() which always sorts the atoms by index in increasing order whereas ag's in _heavy_atoms are created by look up and slicing. If the original input ag is NOT ORDERED then _hydrogens will be ORDERED whereas _heavy_atoms remain in the CUSTOM ORDER of the original ag. At least that's what it looks like to me.

It may be safer to just sort the original ag first.

marinegor added 5 commits September 29, 2023 13:14

Add DSSP test files

5065e2d

Add DSSP test files

1dfdb29

First implementation of DSSP class

f73fcda

Remove pydssp dependency

fe66c30

Add documentation

13bc86a

github-actions bot added the Component-Analysis label Sep 29, 2023

marinegor added 2 commits September 29, 2023 17:53

Fix hydrogen selection issue

cf79a89

Remove unnecessary print

7230845

Fix problem with prolines and add example with average secondary stru…

929d011

…cture in trajectory

marinegor added 4 commits October 2, 2023 18:24

Fix pep8 formatting issues

7c966d5

Fix pep8 formatting issues

a5a4891

Replace ndarray in results with list, and remove unnecessary code

c2a333c

Add documentation for translate

bd5ba75

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orbeckst linked an issue Oct 10, 2023 that may be closed by this pull request

Support for secondary structure identification #1612

Open

orbeckst added the hackathon part of a MDAnalysis coding event label Oct 10, 2023

Added a reference to Kabsch 983 DSSP paper

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Update documentation and formatting

8840d9b

Make numpy docstrings

c6fca72

Compress dssp pdb files

20e672f

Update documentation and add trajectory tests

47c4123

Fix pep8 in docstrings and add pydssp license info

c4cf7c9

Add versionadded

de2133d

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add reference

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move functions below classes

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Improve selection syntax and add configurable selection names

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		h3 = h3 * ~np.roll(helix4, -1, 1) * ~helix4 # helix4 is higher prioritized
		h5 = h5 * ~np.roll(helix4, -1, 1) * ~helix4 # helix4 is higher prioritized

	In the simplest case, we can simply calculate the C-alpha RMSD between
	two structures, using :func:`rmsd`::

	>>> ref = mda.Universe(PDB_small)
	>>> mobile = mda.Universe(PSF, DCD)
	>>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions)
	28.20178579474479

	during more than set `threshold` share of frames. We will call these residues
	during more than set `threshold` fraction of the total frames. We will call these residues



		class DSSP(AnalysisBase):
		"""Assign secondary structure using DSSP algorithm.

	:exc:`ValueError` is raised) you must customize ``hydrogen_name`` for your
	:exc:`ValueError` is raised) you must customize `hydrogen_name` for your

		'--EEEE----------HHHH'


		Functions

Feature/dssp #4304

Are you sure you want to change the base?

Feature/dssp #4304

Conversation

marinegor commented Sep 29, 2023 • edited by orbeckst

PR Checklist

Developers certificate of origin

pep8speaks commented Sep 29, 2023 • edited

Comment last updated at 2024-05-29 07:17:22 UTC

github-actions bot commented Sep 29, 2023 • edited

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marinegor commented Apr 8, 2024 • edited

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marinegor commented Apr 9, 2024

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orbeckst commented May 3, 2024

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marinegor commented May 29, 2024

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orbeckst May 31, 2024 • edited

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marinegor commented Sep 29, 2023 •

edited by orbeckst

pep8speaks commented Sep 29, 2023 •

edited

github-actions bot commented Sep 29, 2023 •

edited

marinegor commented Sep 29, 2023 •

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marinegor commented Apr 8, 2024 •

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orbeckst May 31, 2024 •

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