adding H5MD-format writer #2869

edisj · 2020-07-24T22:09:20Z

Changes made in this Pull Request:

adds class H5MDWriter to H5MD.py

This is a continuation from #2787

Some info:
H5MD documentation - the writer is following these file format guidelines
pyh5md github - A lot of the code is borrowed (with credit attributed to the author) from this library

PR Checklist

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

pep8speaks · 2020-07-24T22:09:23Z

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

In the file maintainer/update_json_stubs_sitemap.py:

Line 118:80: E501 line too long (87 > 79 characters)
Line 119:80: E501 line too long (92 > 79 characters)

In the file package/MDAnalysis/__init__.py:

Line 205:1: E402 module level import not at top of file

In the file package/MDAnalysis/analysis/data/filenames.py:

Line 79:29: E261 at least two spaces before inline comment
Line 79:80: E501 line too long (81 > 79 characters)

In the file package/MDAnalysis/analysis/encore/similarity.py:

Line 807:80: E501 line too long (81 > 79 characters)

In the file package/MDAnalysis/analysis/hole2/hole.py:

Line 203:80: E501 line too long (102 > 79 characters)
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Line 785:80: E501 line too long (83 > 79 characters)

In the file package/MDAnalysis/coordinates/H5MD.py:

Line 628:80: E501 line too long (108 > 79 characters)
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Line 979:50: E231 missing whitespace after ','
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Line 1007:1: E305 expected 2 blank lines after class or function definition, found 1
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Line 1009:5: E113 unexpected indentation
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In the file package/MDAnalysis/coordinates/PDB.py:

Line 1087:80: E501 line too long (91 > 79 characters)

In the file package/MDAnalysis/coordinates/RDKit.py:

Line 27:80: E501 line too long (105 > 79 characters)
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Line 309:45: E128 continuation line under-indented for visual indent
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Line 628:1: W293 blank line contains whitespace
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Line 766:80: E501 line too long (88 > 79 characters)
Line 771:80: E501 line too long (86 > 79 characters)

In the file package/MDAnalysis/core/groups.py:

Line 412:80: E501 line too long (80 > 79 characters)

In the file package/MDAnalysis/core/selection.py:

Line 577:10: E225 missing whitespace around operator

In the file package/MDAnalysis/core/topologyattrs.py:

Line 528:80: E501 line too long (83 > 79 characters)
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In the file package/setup.py:

Line 268:80: E501 line too long (81 > 79 characters)
Line 271:80: E501 line too long (81 > 79 characters)

In the file testsuite/MDAnalysisTests/coordinates/test_pdb.py:

Line 45:80: E501 line too long (82 > 79 characters)
Line 235:80: E501 line too long (81 > 79 characters)

In the file testsuite/MDAnalysisTests/coordinates/test_rdkit.py:

Line 417:72: W291 trailing whitespace
Line 419:60: W291 trailing whitespace

In the file testsuite/MDAnalysisTests/core/test_accumulate.py:

Line 121:80: E501 line too long (81 > 79 characters)
Line 143:80: E501 line too long (81 > 79 characters)

In the file testsuite/MDAnalysisTests/core/test_atomgroup.py:

Line 1024:31: E201 whitespace after '['
Line 1027:31: E201 whitespace after '['
Line 1067:80: E501 line too long (84 > 79 characters)
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Line 1071:80: E501 line too long (127 > 79 characters)
Line 1303:39: E127 continuation line over-indented for visual indent
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Line 1344:39: E127 continuation line over-indented for visual indent
Line 1358:39: E127 continuation line over-indented for visual indent

In the file testsuite/MDAnalysisTests/core/test_atomselections.py:

Line 78:80: E501 line too long (100 > 79 characters)

In the file testsuite/MDAnalysisTests/core/test_segmentgroup.py:

Line 93:80: E501 line too long (84 > 79 characters)
Line 93:81: E231 missing whitespace after ','

In the file testsuite/MDAnalysisTests/formats/test_libdcd.py:

Line 357:21: E127 continuation line over-indented for visual indent

In the file testsuite/MDAnalysisTests/utils/test_meta.py:

Line 47:80: E501 line too long (87 > 79 characters)

Comment last updated at 2021-03-16 01:33:57 UTC

edisj · 2020-07-24T22:15:39Z

The first commit is a preliminary commit just so I get the pull request up and familiarize again with github branching. I'll remove the draft tag when a working version is pushed.

TODO:

add pyh5md licensing information into the LICENCE file
push commits with borrowed code with proper credit attributed

…alysis into issue-2866-h5mdwriter

tylerjereddy · 2020-07-29T02:51:41Z

package/MDAnalysis/coordinates/H5MD.py

+                ts = ag.trajectory.ts
+            except AttributeError:
+                errmsg = "Input obj is neither an AtomGroup or Universe"
+                raise TypeError(errmsg) from None


For this block I'm also reminded of cases in the code base that look something like this:

if isinstance(arg, Universe): # action 1 elif isinstance(arg, AtomGroup): # action 2 else: raise ValueError("arg is not a Universe or AtomGroup")

I don't know if it is formally cleaner than the try/except, maybe it is just the nesting that made me think an alternative might be desired.

Maybe

try: ts = ag.universe.trajectory.ts except AttributeError: ...

?

I think there's a performance difference to try/except vs if/else, where try/except is faster unless the exception is raised.

Edit: that being said, the if/else is probably cleaner because it's more restrictive in the allowed types.

Python Zen says "It's easier to ask for forgiveness than to ask for permission." (which supposedly means that idiomatic Python uses try/except instead of if when possible). The try/except also allows duck-typing (if so desired).

For the performance question: could be tested.

I think it is just the nesting that caught my attention really--if the approach from @lilyminium is equivalent that may be nicer.

If you're really keen on avoiding the conditionals, looks like there are some opportunities in the code base.

I doubt it is worth much energy though.

richardjgowers · 2020-07-30T07:13:36Z

Iirc for performance the try branch is much faster than the except. An if is more 50/50.

…

On Wed, Jul 29, 2020 at 19:31, Oliver Beckstein ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In package/MDAnalysis/coordinates/H5MD.py <#2869 (comment)> : > + ---------- + ag : AtomGroup or Universe + + .. versionadded:: 2.0.0 + + """ + try: + # Atomgroup? + ts = ag.ts + except AttributeError: + try: + # Universe? + ts = ag.trajectory.ts + except AttributeError: + errmsg = "Input obj is neither an AtomGroup or Universe" + raise TypeError(errmsg) from None Python Zen says "It's easier to ask for forgiveness than to ask for permission." (which supposedly means that idiomatic Python uses try/except instead of if when possible). The try/except also allows duck-typing (if so desired). For the performance question: could be tested. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2869 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACGSGB6LY7NF5CXSWLPWBPTR6BTIRANCNFSM4PHDQDOQ> .

* Overview of work done in PR This PR adds the `RDKitConverter` class which converts MDAnalysis `Universe`/`Atomgroup` objects to `RDKit rdchem.Mol` objects. * Limitations - Bonds and elements must be present (the former will be inferred if not present). - This converter mainly aims at supporting cases where explicit hydrogens are present. * Extra implementation details - Bond order and formal charges are inferred via atomic valencies & the number of unpaired electrons (see `_infer_bo_and_charges`). - In part due to the influence of atom read order on inferring, bond conjugation and functional groups are standardized using SMARTS reactions (see `_standardize_patterns`). * Other changes Also includes some PEP8 changes and some cleaning up of the tests for the `RDKITReader`. * References For more information on the development process for this PR, see: 1) https://cbouy.github.io/blog/2020/07/01/rdkit-converter 2) https://cbouy.github.io/blog/2020/07/22/rdkit-converter-part2

…ter (Issue MDAnalysis#2468) Towards MDAnalysis#2468 (RDKit interoperability GSOC project) PR MDAnalysis#2916 -> Originally PR MDAnalysis#2775 ##Overview of work done in PR This PR adds the RDKitConverter class which converts MDAnalysis Universe/Atomgroup objects to RDKit rdchem.Mol objects. ##Limitations - Bonds and elements must be present (the former will be inferred if not present). - This converter mainly aims at supporting cases where explicit hydrogens are present. ##Extra implementation details - Bond order and formal charges are inferred via atomic valencies & the number of unpaired electrons (see _infer_bo_and_charges). - In part due to the influence of atom read order on inferring, bond conjugation and functional groups are standardized using SMARTS reactions (see _standardize_patterns). ##Other changes Also includes some PEP8 changes and some cleaning up of the tests for the RDKITReader. ##References For more information on the development process for this PR, see: https://cbouy.github.io/blog/2020/07/01/rdkit-converter https://cbouy.github.io/blog/2020/07/22/rdkit-converter-part2

@jbarnoud

* modified AtomNames topologyattr to include lookup table index * cheeky little optimisation * rework atom name selection to use lookup tables * Update topologyattrs.py * fixed test supplying integer as atom name really topologyattrs need to be statically typed and protective about this * Update test_topologyattrs.py * use dict-lookup string attrs EVERYWHERERE * removed some code duplication made protein selection faster, 48ms -> 0.5ms on GRO testfile * improved nucleic/backbone selections * Added explicit tests for Resnames topologyattr tests now provide str types for resnames/icodes * use fnmatchcase to be case sensitive * Update package/MDAnalysis/core/selection.py @jbarnoud's fix * apply suggestions from code review Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * added test for setting multiple segids at once Co-authored-by: Oliver Beckstein <orbeckst@gmail.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

- Removes `as_Universe` from MDAnalysis.core.universe - LeafletFinder no longer accepts paths to files as Universes

Update function signatures in core.Universe

Towards MDAnalysis#2468 ## Work done in this PR Adds a new SMARTS based selection which uses the RDKit converter.

* Fixes MDAnalysis#2860 * refactor transformations from closure into class (necessary so that a Universe with transformations can be pickled). * change universe pickling to `__reduce__` (instead of `__setstate__`/`__getstate__`, which did not work with transformations) * add test for pickling a Universe with transformations * update docs for transformations - examples (written as class) - deprecate transformations as closures (still works but cannot be pickled due to limitations in Python's pickle module) * update changelog

Fixes issue MDAnalysis#2939 ## Work done in this PR - Adds missing file types of testsuite/setup.py (*top, *in, *sdf, and the contents of data/gromacs/gromos54a7_edited.ff/*).

fix MDAnalysis#2943

* fix hip with reaction

- fix MDAnalysis#2934 - use unistd.h in ENCORE's spe.c when not WIN32 (e.g. __unix__ or __APPLE__ but to be consistent with other uses in the code base we do not specifically test for __unix__ || __APPLE__) - update CHANGELOG

…apple ensure that unistd.h is included on recent clang

Towards MDAnalysis#2739 ## Work done in this PR Removes the old helanal code in favour of helix_analysis

Fixes issue MDAnalysis#2951 ## Work done in this PR - Restores the parmed intersphinx link.

Fixes MDAnalysis#2979 ## Work done in this PR The file test_bat_IO.npy was created in one test and used in another one. This leads to the second test possibly failing when the tests are run in parallel. This commit moves creating the file into a fixture that the two tests depends. The new fixture also uses the tmpdir fixture to avoid the file created during the tests to remain in the test directory.

Not an issue targetted fix. ## Overview mamba is a dropin replacement for the conda CLI but faster ## Work done in this PR Enabled the `MAMBA` environment variable keyword for the CI helper.

* Fixes MDAnalysis#2990 * Update indexing in Charges and Masses get_residues: Avoid indexing a numpy array with a list of arrays, use a tuple of array instead. Multidimensional indexing of arrays with a non-tuple argument is deprecated. * Turn warnings into errors to avoid regression over MDAnalysis#2990 * Update CHANGELOG

… with (MDAnalysis#2992) unwrapping (closes MDAnalysis#2984).

* TST, CI: add ARM64 Graviton 2 to CI * start testing MDAnalysis on ARM64 using new AWS Graviton 2 architecture available in Travis CI * testing on my fork shows only two failures in the MDAnalysis test suite using a fairly minimal set of dependencies; we can probably either fix those or skip them and open an issue * the test failures are: `test_written_remarks_property` `TestEncoreClustering.test_clustering_three_ensembles_two_identical` * run time for this CI entry is about 23 minutes, which is solid for ARM; we save a lot of time using experimental upstream wheels in some cases and excluding (source builds of) dependencies where possible until the ARM64 binary wheel ecosystem matures a bit more * MAINT: ARM64 shims * adjust `CAffinityPropagation()` C-level function to use `double` instead of `float` in some strategic locations that allow the `test_clustering_three_ensembles_two_identical()` test to pass on gcc115 ARM64 machine * mark `test_written_remarks_property()` as a known failure on ARM64; it fails in Travis CI on that platform, but not on gcc115 ARM64 machine; that said, this test is already known to be flaky on Windows 32-bit (may depend on character settings on machine?) * MAINT: MR 2956 revisions * reduce optimization level of MDAnalysis builds on ARM64 to avoid problems with `ap.c` causing test failures on that architecture * revert any source changes to `ap.c`

Fixes issue MDAnalysis#1989, completes PR MDAnalysis#2956 ## Work done in this PR * Switches CI to using recently released SciPy `1.5.3` with "official" Linux ARM64 wheels over the weekend, instead of the previous "special"/unreleased wheels * Add a `CHANGELOG` entry to reflect preliminary MDAnalysis support for the Linux ARM64 platform (minimal dependencies)

Fixes MDAnalysis#2993 Redirect URLs in stable/sitemap.xml and dev/sitemap.xml to correct locations

* Add a reindex argument to the PDBWritter * Tests for PDB reindex * Remove extra print * Test PDB CONECT with reindex=False * Update CHANGELOG * More precise version change for PDB reindex * Fix long lines * Increase test coverage for MDAnalysis#2886 Also silence some warnings for the tests in the PR. * Remove useless branch in PDB.py There was a test in PDBWriter._write_pdb_bonds about writing the bonds for an atomgroup that does not have AG.ids but asking to not reindex. The test was silencing the problem and would lead to the bonds not being written. However, that part of the code would never be reached because writing the atoms would have raised an exception before that method is called. This commit removes this test. Now, if that part of the code is called (which should not happen), an exception is raised when the method tries to access AG.ids.

orbeckst · 2021-03-16T00:52:48Z

@edisj you might want to rebase against latest develop (or at least merge and clean up conflicts) — a lot has changed since last year.

edisj · 2021-03-16T01:34:18Z

@orbeckst rebase is complete and everything is up to date now (I hope)

edit: I feel like I didn't do it correctly... are all of the new commits since then supposed to appear in this pull request?

orbeckst · 2021-03-16T07:44:08Z

They are not supposed to be here. The history should look as if you just branched of the latest develop. Maybe your own develop was not up-to-date?

edisj · 2021-03-16T07:52:20Z

My develop seems to be up to date... I'm going to save the code and try to do a hard reset in the morning

orbeckst · 2021-03-16T09:28:27Z

If you make a branch "backup" right here in your local repo, then switch back to your issue-2866-h5mdwriter branch, then you can always come back to this state by checking out backup. git keeps stuff around.

Btw, does your local history show all these other commits?

edisj · 2021-03-24T23:41:01Z

I'm moving this pull request to #3189 to avoid all the issues caused by rebasing.

edisj added 2 commits July 24, 2020 15:03

preliminary commit, copying commits from h5mdreader PR

8c28301

removed pyh5md code

7944b0d

edisj added 4 commits July 28, 2020 00:45

pulled from upstream and fixing merge conflict

5be9916

Merge branch 'issue-2866-h5mdwriter' of https://github.com/edisj/mdan…

6a03f37

…alysis into issue-2866-h5mdwriter

added pyh5md LICENSE info, other small adjustments

ed054c9

adding cobrotoxin file

22324f3

tylerjereddy reviewed Jul 29, 2020

View reviewed changes

orbeckst mentioned this pull request Jul 29, 2020

add h5md format #2787

Merged

4 tasks

updated cobrotoxin

877d0fd

orbeckst added the NSF REU NSF Research Experience for Undergraduates project label Aug 7, 2020

orbeckst self-assigned this Aug 7, 2020

Cédric Bouysset and others added 16 commits August 21, 2020 17:15

updated function signatures

84d2275

Remove as_Universe (Issue MDAnalysis#2920) (MDAnalysis#2922)

3e6b38c

- Removes `as_Universe` from MDAnalysis.core.universe - LeafletFinder no longer accepts paths to files as Universes

Merge pull request MDAnalysis#2923 from lilyminium/fix-2921

a8227f0

Update function signatures in core.Universe

Add SMARTS selection (MDAnalysis#2883)

b2b7bcb

Towards MDAnalysis#2468 ## Work done in this PR Adds a new SMARTS based selection which uses the RDKit converter.

Add test files (MDAnalysis#2940)

3148207

Fixes issue MDAnalysis#2939 ## Work done in this PR - Adds missing file types of testsuite/setup.py (*top, *in, *sdf, and the contents of data/gromacs/gromos54a7_edited.ff/*).

oops

f0899e4

add docs for analysis.align.AverageStructure

ddb354e

fix MDAnalysis#2943

RDKitConverter bugfix on HIP residue (MDAnalysis#2941)

c4478d3

* fix hip with reaction

ensure that unistd.h is included for spe.c with recent clang

56c5ea9

- fix MDAnalysis#2934 - use unistd.h in ENCORE's spe.c when not WIN32 (e.g. __unix__ or __APPLE__ but to be consistent with other uses in the code base we do not specifically test for __unix__ || __APPLE__) - update CHANGELOG

Merge pull request MDAnalysis#2949 from MDAnalysis/issue-2934-unistd-…

a321fa7

…apple ensure that unistd.h is included on recent clang

Remove helanal (MDAnalysis#2929)

3df4581

Towards MDAnalysis#2739 ## Work done in this PR Removes the old helanal code in favour of helix_analysis

comment out parmed intersphinx

2687c40

lilyminium and others added 10 commits October 10, 2020 17:50

restores parmed intersphinx (MDAnalysis#2978, Issue MDAnalysis#2951)

a9543ba

Fixes issue MDAnalysis#2951 ## Work done in this PR - Restores the parmed intersphinx link.

Have CI use mamba (MDAnalysis#2983)

2ee4e9d

Not an issue targetted fix. ## Overview mamba is a dropin replacement for the conda CLI but faster ## Work done in this PR Enabled the `MAMBA` environment variable keyword for the CI helper.

Fixed AtomGroup.center's behavior when using compounds in conjugation…

beb5232

… with (MDAnalysis#2992) unwrapping (closes MDAnalysis#2984).

Re-write URLs in sitemap.xml (MDAnalysis#2994)

6b0cbd6

Fixes MDAnalysis#2993 Redirect URLs in stable/sitemap.xml and dev/sitemap.xml to correct locations

H5MDWriter working version - does not write observables group yet

2912678

edisj mentioned this pull request Mar 16, 2021

Adding H5MDWriter to H5MD.py #2866

Closed

edisj marked this pull request as ready for review March 16, 2021 00:44

edisj and others added 6 commits March 15, 2021 18:09

preliminary commit, copying commits from h5mdreader PR

29e7ef1

removed pyh5md code

23c7e7a

added pyh5md LICENSE info, other small adjustments

dcf09c9

H5MDWriter working version - does not write observables group yet

9727bdd

updated working h5mdwriter

3a92a22

fixing azure-piplines conflict

93b52d6

deleted duplicated code

a6e793b

edisj added 2 commits March 17, 2021 01:52

shape tuple

b55bffe

need to fix condition if file doesn't contain vel or forces

0097591

edisj mentioned this pull request Mar 24, 2021

adding H5MDWriter to H5MD.py #3189

Merged

4 tasks

edisj closed this Mar 24, 2021

edisj deleted the issue-2866-h5mdwriter branch April 7, 2024 07:28

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adding H5MD-format writer #2869

adding H5MD-format writer #2869

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adding H5MD-format writer #2869

adding H5MD-format writer #2869

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