BioStructures.jl
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BioJulia
A Julia package to read, write and manipulate macromolecular structures (particularly proteins)
This pull request changes the compat entry for the `BioSequences` package from `2` to `2, 3`. This keeps the compat entries for earlier versions. Note: I have not tested your...
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I just was trying to use BioStructures to solve a problem which required making copies of chains, rename them, alter atom serial numbers and other modifications to structural elements. In...
Hello. In my project, I am using secondary structures. Without going into detail, I need to sample CA atoms from different secondary structures for my algorithm. This can easily be...
This is a great library and I'm already using it lots. I would like to evaluate positions of a protein's atoms with the full expression of symmetry in the complete...
I think it would be good to support the BinaryCIF format. This might perhaps make for a good GSoC project. "BinaryCIF is a data format for storing text based CIF...
When looking at an atom record I discovered that the whitespaces do not get stripped from the atom/element names when they are parsed. An example: `Dict{String, AbstractAtom}(" CA " =>...
When trying to read this file (and other similar ones), I get: ```julia julia> read("vmd.pdb", BioStructures.PDB) ERROR: Two copies of the same atom have the same alternative location ID. Existing...
This package has utilities like `collectresidues` and `collectatoms`. Because this allocates storage, it might be of interest to implement an alternative. I see two main options: - an iterator interface,...
Most of the `struct`s in this package are now quite efficient, but I see one more potential opportunity: `Atom`'s `coords` field is a `Vector{Float64}`. Assuming this will always be a...
I'm getting an error while `read`ing basically any file generated by [OpenBabel](https://openbabel.org/). ```log ERROR: Two copies of the same atom have the same alternative location ID. ``` The same error...
