# Biostructures.jl and md trajectory files

**URL:** <https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789>\
**Category:** Biology, Health, and Medicine\
**Created:** [November 26, 2020, 1:42am UTC](https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789 "2020-11-26T01:42:38Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![bharland](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bharland/32/22762_2.png) [@bharland](https://discourse.julialang.org/u/bharland)\
**Post date:** [November 26, 2020, 1:42am UTC](https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789/1 "2020-11-26T01:42:38Z")

</div>

I’m wondering how horrendous it would be to include parsing of popular trajectory files, so I had a look at how MDTraj did it with (e.g.) the xtc format. A layer of python, then cython and then a set of c files adapted from gromacs.

Would the approach be similar in julia?

---

<div class="post-metadata">

**Author:** ![lmiq](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lmiq/32/18314_2.png) [@lmiq](https://discourse.julialang.org/u/lmiq)\
**Post date:** [November 26, 2020, 2:27am UTC](https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789/2 "2020-11-26T02:27:13Z")

</div>

Check the Chemfiles package:

[https://github.com/chemfiles/Chemfiles.jl](https://github.com/chemfiles/Chemfiles.jl)

---

<div class="post-metadata">

**Author:** ![jgreener64](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jgreener64/32/2483_2.png) [@jgreener64](https://discourse.julialang.org/u/jgreener64)\
**Post date:** [November 26, 2020, 11:01am UTC](https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789/3 "2020-11-26T11:01:03Z")

</div>

Yes I think Chemfiles.jl is the way to do this in Julia at the minute. It wraps the chemfiles C++ library.

It should be possible to write pure Julia parsers as well, and they should be able to achieve similar speeds to C++. Personally I have no plans to add such parsers to BioStructures.jl due to time constraints.

---

<div class="post-metadata">

**Author:** ![bharland](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bharland/32/22762_2.png) [@bharland](https://discourse.julialang.org/u/bharland)\
**Post date:** [November 26, 2020, 11:59am UTC](https://discourse.julialang.org/t/biostructures-jl-and-md-trajectory-files/50789/4 "2020-11-26T11:59:01Z")

</div>

Many thanks! I’ll have a closer look.