diff --git a/docs/src/assets/ComplexMixtures.py b/docs/src/assets/ComplexMixtures.py index 22c46b77..6af5b7e1 100644 --- a/docs/src/assets/ComplexMixtures.py +++ b/docs/src/assets/ComplexMixtures.py @@ -1,7 +1,7 @@ # # ComplexMixtures.py # -# A Python module to provide an inferface for the Julia ComplexMixtures.jl package. +# A Python module to provide an interface for the Julia ComplexMixtures.jl package. # # See: https://m3g.github.com/ComplexMixtures.jl # diff --git a/docs/src/assets/scripts/python/script3.py b/docs/src/assets/scripts/python/script3.py index 65c2e7bc..ba1db8e6 100644 --- a/docs/src/assets/scripts/python/script3.py +++ b/docs/src/assets/scripts/python/script3.py @@ -7,7 +7,7 @@ protein = cm.select(atoms, "protein") glyc = cm.select(atoms, "resname GLYC") -# load previusly computed MDDF results +# load previously computed MDDF results results = cm.load("./glyc50.json") # Select atoms by name diff --git a/docs/src/python.md b/docs/src/python.md index 96a17636..d3cc912b 100644 --- a/docs/src/python.md +++ b/docs/src/python.md @@ -57,13 +57,13 @@ The files required to run this example are: - [system.pdb](https://raw.githubusercontent.com/m3g/ComplexMixturesExamples/main/Protein_in_Glycerol/Data/system.pdb): The PDB file of the complete system. - [glyc50_sample.dcd](https://www.dropbox.com/scl/fi/n3gtyotavo00jtz8bajti/glyc50_sample.dcd?rlkey=5ax8t4w7e0dr5w0n5g797p02j&dl=0): A 30Mb sample trajectory file. The [full trajectory](https://www.dropbox.com/scl/fi/zfq4o21dkttobg2pqd41m/glyc50_traj.dcd?rlkey=el3k6t0fx6w5yiqktyx96gzg6&dl=0) can also be used, but it is a 1GB file. -To start, create a directory and copy the [`ComplexMixtures.py`](./assets/ComplexMixtures.py) file to it. Navigate into this directory, and, to start, set the number of threads that Julia will use, to run the calculations in parallel. Typicall, in `bash`, this means defining teh following environment variable: +To start, create a directory and copy the [`ComplexMixtures.py`](./assets/ComplexMixtures.py) file to it. Navigate into this directory, and, to start, set the number of threads that Julia will use, to run the calculations in parallel. Typically, in `bash`, this means defining teh following environment variable: ```bash export JULIA_NUM_THREADS=8 ``` where `8` is the number of CPU cores available in your computer. For further information about Julia multi-threading, and on setting this environment variable in other systems, please read [this section](https://docs.julialang.org/en/v1/manual/multi-threading/#Starting-Julia-with-multiple-threads) of the Julia manual. -Finall, each script can be executed with, for example: +Finally, each script can be executed with, for example: ```bash python3 script.py ``` @@ -123,7 +123,7 @@ $(read("./assets/scripts/python/script2.py", String)) ![](./assets/scripts/python/mddf_kb.png) In the top plot, we see that glycerol and water display clear solvation shells around the protein, -with glycerol having a gerater peak. This accumulation leads to a greater (less negative) KB integral for glycerol than water, as shown in the second plot. This indicates that the proteni is preferentially solvated by glycerol in this system (assuming that sampling is adequate in this small +with glycerol having a greater peak. This accumulation leads to a greater (less negative) KB integral for glycerol than water, as shown in the second plot. This indicates that the protein is preferentially solvated by glycerol in this system (assuming that sampling is adequate in this small trajectory). ### [Atomic contributions to the MDDF](@id python-plotting2) diff --git a/docs/src/updating_scripts.md b/docs/src/updating_scripts.md index 722e0ba9..721d56bc 100644 --- a/docs/src/updating_scripts.md +++ b/docs/src/updating_scripts.md @@ -17,7 +17,7 @@ water = AtomSelection(water; natomspermol=3) ## Group contributions syntax -The syntax to computing group contributions is improved. Previusly, the `contrib` or +The syntax to computing group contributions is improved. Previously, the `contrib` or `contributions` functions required three somewhat redundant parameters. - Before: The call to `contributions` required 3 parameters: the `Selection` structure,