hng / biomolecularstructures.jl Goto Github PK

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The PdbTool.jl Julia package was already providing a way to deal with PDB files.
It seems to me that efforts could be made to have all PDB-related functionality in a single package if possible.

cc: @christophfeinauer

Running package tests as discussed in JuliaLang/julia#18276 (comment) gave me this error

ERROR: LoadError: LoadError: LoadError: PyError (:PyImport_ImportModule) <type 'exceptions.ImportError'>
ImportError('No module named Bio.PDB',)

Reporting here in case something needs to be done. I am using a mac.

Try this:

P = [-1. 0. 0.; 0. 2. 0.; 0. 1. 0.; 0. 1. 1]
Q = [0. -1. -1.; 0. -1. 0; 0. 0. 0.; -1. 0. 0.]

BiomolecularStructures.Kabsch.kabsch_rmsd(P,Q)

It returns

1.058767176431898

But the correct least RMSD is

0.695

unfortunately.

See: http://julia.readthedocs.org/en/latest/manual/packages/#guidelines-for-naming-a-package

As described in https://discourse.julialang.org/t/ann-plans-for-removing-packages-that-do-not-yet-support-1-0-from-the-general-registry/ we are planning on removing packages that do not support 1.0 from the General registry. This package has been detected to not support 1.0 and is thus slated to be removed. The removal of packages from the registry will happen approximately a month after this issue is open.

To transition to the new Pkg system using Project.toml, see https://github.com/JuliaRegistries/Registrator.jl#transitioning-from-require-to-projecttoml.
To then tag a new version of the package, see https://github.com/JuliaRegistries/Registrator.jl#via-the-github-app.

If you believe this package has erroneously been detected as not supporting 1.0 or have any other questions, don't hesitate to discuss it here or in the thread linked at the top of this post.

Drop the .jl pls

The way the matrices are used is probably less than ideal as multidimensional arrays in Julia are stored in column-major order.

http://julia.readthedocs.org/en/latest/manual/performance-tips/

... braucht etwas mehr an Parametern:
http://www.ebi.ac.uk/Tools/webservices/services/sss/wu_blast_rest