hildebrandtlab / biochemicalalgorithms.jl Goto Github PK

When loading pdb files, I would assume to be able to iterate over the residues of a chain or a molecule (given that it is a protein).

FragmentTuple and NucleotideTuple name the exact same (named tuple) type as they have identical field names and types in the exact same order.

julia> NucleotideTuple === FragmentTuple
true

Our current implementation of load_pubchem_json takes a lot of initial compilation time, which is about to get worse with future Julia versions.

• 1.9.4

julia> @time load_pubchem_json("test/data/aspirin_pug.json")
 23.307613 seconds (32.02 M allocations: 1.461 GiB, 2.31% gc time, 99.99% compilation time)
System with 21 atoms

• 1.10.4

julia> @time load_pubchem_json("test/data/aspirin_pug.json")
 23.326633 seconds (31.65 M allocations: 1.421 GiB, 0.98% gc time, 99.97% compilation time)
System with 21 atoms

• 1.11.0-beta1

julia> @time load_pubchem_json("test/data/aspirin_pug.json")
 71.187262 seconds (78.62 M allocations: 3.180 GiB, 1.37% gc time, 100.00% compilation time)
System with 21 atoms

• 1.12.0-DEV.741 (b0b7a859ed5)

julia> @time load_pubchem_json("test/data/aspirin_pug.json")
 66.493225 seconds (64.33 M allocations: 2.760 GiB, 0.86% gc time, 100.00% compilation time: 100% of which was recompilation)
System with 21 atoms

is causing LoadError: ArgumentError: Symbol e0 could not be found in unit modules Module[UnitfulAtomic] in test_AmberFF

Find a consistent solution for PDB_atom.jl, pdb_molecule.jl and PDB.jl.

atom_properties is defined here: const AtomProperties = Dict{String, Any}

Although it is possible to put a dataframe row as a value to the dictionary (only in case we have alternative locations for an atom), it might not be optimal with regard to large PDB files.

PDB and Pubchem files often contain alternative location for atom coordinates (or entire conformation). Mechanisms to switch between these alternative conformations are needed e.g., to generate an alternative atoms data frame.
Particularly, interested with regard to the multiple variants present in the Fragment database.

fails with message:
"type DataType has no field Unknown"

Bond has no member Unknown.

May I suggest we change the naming of molecules when the import with load_pubchem_json takes place.
Currently, the CID is added to the name regardlessly of weither the CID is already contained in the name and weither there is a file ending such as .json or .mol2. An example of what would work can be seen the following commit: b439177

Chain.jl provides accession functions for internal DataFrames members of the different structs representing a specific chain type.

hey all!

a long time go, i wrote a (private sadly) wrapper around PubChem and had some simple code for taking https://pubchem.ncbi.nlm.nih.gov/docs/pathways, using Groebner.jl to then balance the chemical reactions robustly.
i might be allowed to rewrite in open source soon though

Then I would lower this to https://github.com/SciML/Catalyst.jl/ so that I could simulate the chemical reactions in the DiffEq ecosystem.

I see that you guys have a nice wrapper around the PubChem API and was wondering what the directions for this project are.

One of my huge gripes about the models I work with from https://www.ebi.ac.uk/biomodels/ is they rarely have canonical IDs for species. My naive, highschool biology educated self thought that simulating glycolysis would be easy 😅 , luckily @Denis-Titov is making https://github.com/DenisTitovLab/Glycolysis.jl.

anyways, a big thanks are in order, I plan to shift all of my pubchem related code like https://github.com/anandijain/ChemicalOfTheDay.jl to BA.jl.

One other question I had is if you would consider splitting the API part of the package and the algorithms part.

also if you guys want to come to juliacon, we're doing a symposium on systems biology and I think standardizing on species database will be an important need for reproducible modeling in the future.

if you guys want to give a short 5 minute talk, id be happy to try to work you in

tested with Julia 1.7.3 and StaticArrays version 1.4.7