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Implement Mdtraj-hdf5 format #108

Merged
merged 33 commits into from
Jul 21, 2023
Merged

Implement Mdtraj-hdf5 format #108

merged 33 commits into from
Jul 21, 2023

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agrossfield
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name: Pull request
about: support hdf5 format
title: ''
labels: ''
assignees: ''

Changes proposed in this pull request

- Add new classes MDTraj and MDTrajTraj to read MDTraj hdf5 files as a system file and trajectory respectively

Checklist

- Does this pull request address an open issue? If so, which one?

No

- Have you applied a formatter to your code (e.g. flake8 or black for python, clang-format for C++)?

Yes

agrossfield and others added 29 commits June 21, 2023 17:09
@agrossfield
added highfive as dependency
ef39963
@agrossfield
add test prog to build list
ee7f6b9
@agrossfield
totally non-functional
378fcf9
@agrossfield
going to give up on HighFive, storing
204fc0e
@agrossfield
build broken
19d6cd9
@tromo
Builds under ubuntu...
eb56bbd
@agrossfield
link against boost::json
557ab99
@agrossfield
find_package boost json
e1ec914
@agrossfield
parsing works, converting to string sorta
753e03b
@agrossfield
successfully read the topology
2b00a77
@agrossfield
successfully reads topology!
76f1936
@agrossfield
removed comments
5900ea9
@agrossfield
preliminary reading box dimensions
46a90c1
@agrossfield
can read box size for arbitrary frame
338068c
@agrossfield
can read individual coordinate frames
0a9abc8
@agrossfield
preliminary setup for MDTraj class
59c67ae
@agrossfield
added mdtraj.* to build dependencies
e95804d
@agrossfield
compiles, so it must be right, all pieces present
9dbd30e
@agrossfield
add a missing exception
86725fd
@agrossfield
mdtraj.i breaks swig, temporarily removed
fd0148c
@agrossfield
builds, get H5::FileIException on read
4db58af
@agrossfield
success reading topology and bonds
4e8a767
@agrossfield
compiles, so it must be right
f261f85
@agrossfield
interim commit, reading crashes
85a04e5
@agrossfield
trajectory reading works
bba703c
@agrossfield
MDTraj reads first coords on read
db9062e
@agrossfield
updated createTrajectory
199a4e4
@agrossfield
check if system is periodic
78e8d1f
@agrossfield
fixed logic to recognize end of file
91853f7
@agrossfield agrossfield requested a review from tromo June 30, 2023 19:18
@agrossfield
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There are a couple of test programs in Packages/User that will need to be removed before the final merge. I'm leaving them for now in case more testing is needed

@agrossfield
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One other thing that will need to be done is adding hdf5 as a dependency in the conda-forge recipe.

@tromo
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tromo commented Jul 20, 2023

Looks good for small values of looking...

tromo
tromo approved these changes Jul 20, 2023
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Looks good.

@agrossfield agrossfield merged commit 50d8603 into main Jul 21, 2023
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@tromo tromo tromo approved these changes

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@agrossfield @tromo